BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|15645763|ref|NP_207940.1| conserved hypothetical
protein [Helicobacter pylori 26695]
(184 letters)
Database: /home/scwang/download_20020708_db/nr
1,026,957 sequences; 324,149,939 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_207940.1| (NC_000915) conserved hypothetical protein... 361 2e-99
ref|NP_223793.1| (NC_000921) putative [Helicobacter pylori ... 342 2e-93
ref|NP_281884.1| (NC_002163) putative 16S rRNA processing p... 107 7e-23
ref|NP_371763.1| (NC_002758) probable 16S rRNA processing p... 54 9e-07
ref|NP_212831.1| (NC_001318) conserved hypothetical protein... 54 1e-06
ref|NP_471241.1| (NC_003212) similar to putative 16S rRNA p... 53 2e-06
ref|NP_657811.1| (NC_003995) RimM, RimM [Bacillus anthracis... 53 2e-06
ref|NP_465318.1| (NC_003210) similar to putative 16S rRNA p... 51 6e-06
ref|NP_389484.1| (NC_000964) similar to hypothetical protei... 48 6e-05
ref|NP_457145.1| (NC_003198) 16S rRNA processing protein [S... 46 2e-04
ref|NP_289161.1| (NC_002655) orf, hypothetical protein [Esc... 46 2e-04
ref|NP_358280.1| (NC_003098) 16S rRNA processing protein Ri... 46 2e-04
sp|P21504|RIMM_ECOLI 16S rRNA processing protein rimM (21K)... 46 2e-04
pir||S37174 hypothetical protein, 21K - Salmonella typhimur... 45 3e-04
ref|NP_345276.1| (NC_003028) 16S rRNA processing protein Ri... 45 4e-04
ref|NP_607058.1| (NC_003485) putative 16S rRNA processing p... 45 5e-04
ref|NP_243346.1| (NC_002570) 16S rRNA processing protein [B... 45 5e-04
ref|NP_660723.1| (NC_004061) 16S rRNA processing protein Ri... 44 9e-04
ref|NP_240212.1| (NC_002528) 16s rRNA processing protein ri... 44 0.001
ref|NP_230213.1| (NC_002505) 16S rRNA processing protein Ri... 43 0.002
sp|Q9KUF9|RIMM_VIBCH Probable 16S rRNA processing protein rimM 43 0.002
ref|NP_269055.1| (NC_002737) putative 16S rRNA processing p... 42 0.003
ref|NP_246234.1| (NC_002663) RimM [Pasteurella multocida] >... 42 0.004
ref|NP_562626.1| (NC_003366) probable 16S rRNA processing p... 42 0.004
ref|NP_623077.1| (NC_003869) RimM protein, required for 16S... 41 0.007
ref|NP_486852.1| (NC_003272) probable 16S rRNA processing p... 40 0.010
>ref|NP_207940.1| (NC_000915) conserved hypothetical protein [Helicobacter pylori
26695]
sp|O25767|RIMM_HELPY Probable 16S rRNA processing protein rimM
pir||E64663 conserved hypothetical protein HP1149 - Helicobacter pylori
(strain 26695)
gb|AAD08193.1| (AE000621) conserved hypothetical protein [Helicobacter pylori
26695]
Length = 184
Score = 361 bits (927), Expect = 2e-99
Identities = 184/184 (100%), Positives = 184/184 (100%)
Query: 1 MVSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSY 60
MVSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSY
Sbjct: 1 MVSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSY 60
Query: 61 EHAKNLLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEI 120
EHAKNLLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEI
Sbjct: 61 EHAKNLLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEI 120
Query: 121 LGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTL 180
LGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTL
Sbjct: 121 LGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTL 180
Query: 181 LENS 184
LENS
Sbjct: 181 LENS 184
>ref|NP_223793.1| (NC_000921) putative [Helicobacter pylori J99]
sp|Q9ZK65|RIMM_HELPJ Probable 16S rRNA processing protein rimM
pir||A71852 hypothetical protein jhp1076 - Helicobacter pylori (strain J99)
gb|AAD06656.1| (AE001535) putative [Helicobacter pylori J99]
Length = 181
Score = 342 bits (876), Expect = 2e-93
Identities = 170/181 (93%), Positives = 178/181 (97%)
Query: 4 MLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYEHA 63
MLLVGRIGKSVGLNGGL+LHLESDFPECLKKGVKVSVAP+NAFSC SSFK+Y+IHSYEHA
Sbjct: 1 MLLVGRIGKSVGLNGGLKLHLESDFPECLKKGVKVSVAPINAFSCASSFKDYVIHSYEHA 60
Query: 64 KNLLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEILGK 123
KNLLFLETI+TPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDL+GLSVVE NEILGK
Sbjct: 61 KNLLFLETIRTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLIGLSVVEGNEILGK 120
Query: 124 VIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTLLEN 183
VIEIQRISQTDYF+VETT +LVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTLLEN
Sbjct: 121 VIEIQRISQTDYFMVETTRSLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTLLEN 180
Query: 184 S 184
S
Sbjct: 181 S 181
>ref|NP_281884.1| (NC_002163) putative 16S rRNA processing protein [Campylobacter
jejuni]
sp|Q9PPJ5|RIMM_CAMJE Probable 16S rRNA processing protein rimM
pir||C81342 probable 16S rRNA processing protein Cj0712 [imported] -
Campylobacter jejuni (strain NCTC 11168)
emb|CAB72986.1| (AL139076) putative 16S rRNA processing protein [Campylobacter
jejuni]
Length = 179
Score = 107 bits (267), Expect = 7e-23
Identities = 68/180 (37%), Positives = 103/180 (56%), Gaps = 11/180 (6%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYI-IHSYEHAKN 65
V ++GK+VGL G ++LH SDF KK +A + + KE + I Y +
Sbjct: 9 VAKLGKTVGLKGYVKLHNLSDFSSQFKK---------DATFFIKNTKEMLKIKHYNANNS 59
Query: 66 LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEILGKVI 125
+ E + EKAKELTNL LF S +S++ C LK+ EFFY D++ V EE++ LGKV+
Sbjct: 60 TVLFENYEDIEKAKELTNLILFQSIEKSRQTCKLKKDEFFYFDILECEVFEEDKRLGKVV 119
Query: 126 EIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKI-TTHNAKTLLENS 184
+I + F +++ VEK KIF IPY D +++ I ++ ++I T +A +LENS
Sbjct: 120 DILETGASYLFEIQSDEKWVEKKYPKIFFIPYLDKFVKNIDIEKRQIFCTQDAFLILENS 179
>ref|NP_371763.1| (NC_002758) probable 16S rRNA processing protein [Staphylococcus
aureus subsp. aureus Mu50]
ref|NP_374355.1| (NC_002745) probable 16S rRNA processing protein [Staphylococcus
aureus subsp. aureus N315]
ref|NP_645939.1| (NC_003923) probable 16S rRNA processing protein [Staphylococcus
aureus subsp. aureus MW2]
sp|Q99UN1|RIMM_STAAM Probable 16S rRNA processing protein rimM
dbj|BAB42334.1| (AP003133) probable 16S rRNA processing protein [Staphylococcus
aureus subsp. aureus N315]
dbj|BAB57401.1| (AP003361) probable 16S rRNA processing protein [Staphylococcus
aureus subsp. aureus Mu50]
dbj|BAB94987.1| (AP004826) probable 16S rRNA processing protein [Staphylococcus
aureus subsp. aureus MW2]
Length = 167
Score = 53.9 bits (128), Expect = 9e-07
Identities = 45/177 (25%), Positives = 83/177 (46%), Gaps = 15/177 (8%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYEHAKNL 66
VG+I + G+ G +++ SDF + + +V N + K + +H H
Sbjct: 5 VGQIVNTHGIKGEIKVKSNSDFTDVRFQPGQVLTVVHNNNDLEYTVKSHRVHKGLHMLTF 64
Query: 67 LFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEI-LGKVI 125
+ I E K G + + + VL+E EF+Y D++G +V ++ E +G+VI
Sbjct: 65 EGINNINDIEHLK-----GSSIYQERDHEDIVLEENEFYYSDIIGCTVFDDQETPIGRVI 119
Query: 126 EIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTLLE 182
I D +++ KG +K +LIPY ++E+ +++KKI + LL+
Sbjct: 120 NIFETGANDVWVI--------KG-SKEYLIPYIADVVKEVDVENKKIIITPMEGLLD 167
>ref|NP_212831.1| (NC_001318) conserved hypothetical protein [Borrelia burgdorferi]
sp|O51640|RIMM_BORBU Probable 16S rRNA processing protein rimM
pir||H70186 conserved hypothetical protein BB0697 - Lyme disease spirochete
gb|AAC67046.1| (AE001170) conserved hypothetical protein [Borrelia burgdorferi]
Length = 166
Score = 53.5 bits (127), Expect = 1e-06
Identities = 50/173 (28%), Positives = 80/173 (45%), Gaps = 20/173 (11%)
Query: 4 MLLVGRIGKSVGLNGGLRLH-LESDFPECLK-KGVKVSVAPLNAFSCVSSFKEYIIHSYE 61
M + G I S G+NG R+ + ++F + + K KV + N SS E +
Sbjct: 1 MFIKGVILSSYGVNGYARVKSISNNFCDFINLKNNKVLLKKSN-----SSSVEVKVVDVN 55
Query: 62 HAKNLLFL--ETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENE 119
N LFL E I TPE + L L++ ++ + L KEGE++ L+G ++V N+
Sbjct: 56 IKGNSLFLKFEEIDTPEAVRPLIGFELWVDDSLASSL---KEGEYYLGKLIGYAIVNNNK 112
Query: 120 ILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKI 172
LG+V+ + + V + K F IP+ YI +I Q+K I
Sbjct: 113 KLGEVVAFFEYLNSVFLEVRVGI--------KFFFIPFLSIYIGDINTQEKTI 157
>ref|NP_471241.1| (NC_003212) similar to putative 16S rRNA processing protein RimM
[Listeria innocua]
sp|Q92AL5|RIMM_LISIN Probable 16S rRNA processing protein rimM
emb|CAC97137.1| (AL596170) similar to putative 16S rRNA processing protein RimM
[Listeria innocua]
Length = 172
Score = 52.8 bits (125), Expect = 2e-06
Identities = 57/187 (30%), Positives = 91/187 (48%), Gaps = 20/187 (10%)
Query: 1 MVSMLLVGRIGKSVGLNGGLRLHLESDFP-ECLKKGVKVSVAPLNAFSCVSSFKEYIIHS 59
M M VG+I + GL G +R+ +DFP E + G V + N+ ++ II S
Sbjct: 1 MEKMYNVGKIVNTHGLIGEIRVIATTDFPEERFQVGNTVYLFEKNS----KKPEKLIIRS 56
Query: 60 YEHAKN--LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-E 116
+ KN LL E + + + + L + EA+ L L+E EF++ +++G +VV
Sbjct: 57 HRKHKNFDLLMFEGLTGIHQVERMKEGVLKIKEAQ---LTDLEENEFYFHEIIGCTVVTT 113
Query: 117 ENEILGKVIEIQRISQTDYFLVETTLNLVEKGL-AKIFLIPYRDFYIQEILLQDKKITTH 175
+ E LG++ EI D ++V KG K LIPY +++I DKKIT
Sbjct: 114 DGEELGEITEILTPGANDVWVV--------KGADKKEKLIPYIADVVKDINTNDKKITIE 165
Query: 176 NAKTLLE 182
+ LL+
Sbjct: 166 VMEGLLD 172
>ref|NP_657811.1| (NC_003995) RimM, RimM [Bacillus anthracis A2012] [Bacillus
anthracis str. A2012]
Length = 171
Score = 52.8 bits (125), Expect = 2e-06
Identities = 44/183 (24%), Positives = 83/183 (45%), Gaps = 14/183 (7%)
Query: 1 MVSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSY 60
M VG+I + G+ G +R+ +DFPE + V S + + +
Sbjct: 1 MTKWFNVGKIVNTHGVKGEIRVVSRTDFPE-----ERYKVGNTLYISNEKGGEPFPVKXT 55
Query: 61 EHAKNLLF-LETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-EEN 118
H ++ F L T + E+ + + +L L EGE++Y +++G +VV EE
Sbjct: 56 SHRQHKTFDLLTFEGYGNVNEVEQFKGSLLKVPEDQLGELAEGEYYYHEIIGCNVVTEEG 115
Query: 119 EILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAK 178
E LG + E+ D + ++++ + LIPY D + ++ +++K +T H +
Sbjct: 116 EALGTIKEVLSPGANDVW-------VIKRPKGQDLLIPYIDDVVLQVNIENKLVTIHVTE 168
Query: 179 TLL 181
LL
Sbjct: 169 GLL 171
>ref|NP_465318.1| (NC_003210) similar to putative 16S rRNA processing protein RimM
[Listeria monocytogenes EGD-e]
sp|Q8Y6A2|RIMM_LISMO Probable 16S rRNA processing protein rimM
emb|CAC99871.1| (AL591981) similar to putative 16S rRNA processing protein RimM
[Listeria monocytogenes]
Length = 172
Score = 51.2 bits (121), Expect = 6e-06
Identities = 56/187 (29%), Positives = 90/187 (47%), Gaps = 20/187 (10%)
Query: 1 MVSMLLVGRIGKSVGLNGGLRLHLESDFP-ECLKKGVKVSVAPLNAFSCVSSFKEYIIHS 59
M M VG+I + GL G +R+ +DFP E + G V + N+ ++ II S
Sbjct: 1 MEKMYNVGKIVNTHGLIGEIRVIATTDFPEERFQVGNTVYLFEKNS----KKPEKLIIRS 56
Query: 60 YEHAKN--LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-E 116
+ KN LL E + + + L + E + L L+E EF++ +++G +VV
Sbjct: 57 HRKHKNFDLLMFEGFTGIHQVERMKEGVLKIKETQ---LTNLEENEFYFHEIIGCTVVTT 113
Query: 117 ENEILGKVIEIQRISQTDYFLVETTLNLVEKGL-AKIFLIPYRDFYIQEILLQDKKITTH 175
+ E LG++ EI D ++V KG K LIPY ++EI + D+KIT
Sbjct: 114 DGEELGEITEILTPGANDVWVV--------KGADKKEKLIPYIADVVKEINIDDQKITIE 165
Query: 176 NAKTLLE 182
+ LL+
Sbjct: 166 VMEGLLD 172
>ref|NP_389484.1| (NC_000964) similar to hypothetical proteins [Bacillus subtilis]
sp|O31740|RIMM_BACSU Probable 16S rRNA processing protein rimM
pir||E69880 conserved hypothetical protein ylqE - Bacillus subtilis
emb|CAB13475.1| (Z99112) similar to hypothetical proteins [Bacillus subtilis]
Length = 174
Score = 47.8 bits (112), Expect = 6e-05
Identities = 49/179 (27%), Positives = 86/179 (47%), Gaps = 16/179 (8%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFS--CVSSFKEYIIHSYEHAK 64
VG+I + G+ G +R+ ++DF E K ++ + + + +H H
Sbjct: 8 VGKIVNTHGIKGEVRVISKTDFAEERYKPGNTLYLFMDGRNEPVEVTVNTHRLHKQFH-- 65
Query: 65 NLLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSV-VEENEILGK 123
LL + Q + +EL N + + E E L L EGEF++ +++G V EE E++GK
Sbjct: 66 -LLQFKERQNLNEVEELKNAIIKVPEEE---LGELNEGEFYFHEIIGCEVFTEEGELIGK 121
Query: 124 VIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKTLLE 182
V EI D +++ KG K LIPY + ++ I +++KKI + L++
Sbjct: 122 VKEILTPGANDVWVIG------RKG-KKDALIPYIESVVKHIDVREKKIEIELMEGLID 173
>ref|NP_457145.1| (NC_003198) 16S rRNA processing protein [Salmonella enterica subsp.
enterica serovar Typhi]
ref|NP_461605.1| (NC_003197) 16S rRNA processing protein [Salmonella typhimurium
LT2]
sp|P36246|RIMM_SALTY 16S rRNA processing protein rimM
gb|AAL21564.1| (AE008821) 16S rRNA processing protein [Salmonella typhimurium LT2]
emb|CAD05854.1| (AL627276) 16S rRNA processing protein [Salmonella enterica subsp.
enterica serovar Typhi]
Length = 182
Score = 45.8 bits (107), Expect = 2e-04
Identities = 39/158 (24%), Positives = 77/158 (48%), Gaps = 14/158 (8%)
Query: 5 LLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYEHAK 64
+++G++G S G+ G LR+ ++ E + + + V + S++H
Sbjct: 14 VVLGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQ------LESWKHHN 67
Query: 65 N--LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-EENEIL 121
++ L+ + + A LTN + + +S +L L+EG++++ DL+G VV E L
Sbjct: 68 QDLIIKLKGVDDRDAANLLTNCEIVV---DSSQLPALEEGDYYWKDLMGCQVVTAEGYDL 124
Query: 122 GKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRD 159
GKVI++ D +++ NL + K L+P+ D
Sbjct: 125 GKVIDMMETGSNDVLVIKA--NLKDAFGIKERLVPFLD 160
>ref|NP_289161.1| (NC_002655) orf, hypothetical protein [Escherichia coli O157:H7
EDL933]
ref|NP_311498.1| (NC_002695) hypothetical protein [Escherichia coli O157:H7]
ref|NP_417099.1| (NC_000913) orf, hypothetical protein [Escherichia coli K12]
pir||C65039 hypothetical 21K protein (trmD-rpsP intergenic region) -
Escherichia coli
gb|AAC75657.1| (AE000346) orf, hypothetical protein [Escherichia coli K12]
dbj|BAA16493.1| (D90888) similar to [SwissProt Accession Number P21504]
[Escherichia coli]
gb|AAG57719.1|AE005490_14 (AE005490) orf, hypothetical protein [Escherichia coli O157:H7
EDL933]
dbj|BAB36894.1| (AP002562) hypothetical protein [Escherichia coli O157:H7]
Length = 185
Score = 45.8 bits (107), Expect = 2e-04
Identities = 39/161 (24%), Positives = 78/161 (48%), Gaps = 14/161 (8%)
Query: 2 VSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYE 61
V +++G++G S G+ G LR+ ++ E + + + V + S++
Sbjct: 14 VDPIVLGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQ------LESWK 67
Query: 62 HAKN--LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-EEN 118
H ++ L+ + + A LTN + + +S +L L+EG++++ DL+G VV E
Sbjct: 68 HHNQDMIIKLKGVDDRDAANLLTNCEIVV---DSSQLPQLEEGDYYWKDLMGCQVVTTEG 124
Query: 119 EILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRD 159
LGKV+++ D +++ NL + K L+P+ D
Sbjct: 125 YDLGKVVDMMETGSNDVLVIKA--NLKDAFGIKERLVPFLD 163
>ref|NP_358280.1| (NC_003098) 16S rRNA processing protein RimM [Streptococcus
pneumoniae R6]
gb|AAK99490.1| (AE008446) 16S rRNA processing protein RimM [Streptococcus
pneumoniae R6]
Length = 172
Score = 45.8 bits (107), Expect = 2e-04
Identities = 48/173 (27%), Positives = 85/173 (48%), Gaps = 25/173 (14%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPE-CLKKGVKVSVAPLNAFSCVSSFKEYI-IHSYEHAK 64
VG+I + GL G +R+ +DF E KKG ++++ F F + + I S+ K
Sbjct: 6 VGKIVNTQGLQGEMRVLSVTDFAEERFKKGAELAL-----FDEKDQFVQTVTIASHRKQK 60
Query: 65 NLLFLET-----IQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENE 119
N ++ I T EK K G + AE + L L +GEF+Y +++GL V E +
Sbjct: 61 NFDIIKFKDMYHINTIEKYK-----GYSLKVAE-EDLNDLDDGEFYYHEIIGLEVYEGDS 114
Query: 120 ILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKI 172
++G + EI + D ++V+ KG + L+PY + + + +K++
Sbjct: 115 LVGTIKEILQPGANDVWVVK------RKG-KRDLLLPYIPPVVLNVDIPNKRV 160
>sp|P21504|RIMM_ECOLI 16S rRNA processing protein rimM (21K)
pir||S07950 hypothetical protein, 21K (rpsP-trmD intergenic region) -
Escherichia coli
Length = 182
Score = 45.8 bits (107), Expect = 2e-04
Identities = 39/161 (24%), Positives = 78/161 (48%), Gaps = 14/161 (8%)
Query: 2 VSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYE 61
V +++G++G S G+ G LR+ ++ E + + + V + S++
Sbjct: 11 VDPIVLGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQ------LESWK 64
Query: 62 HAKN--LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-EEN 118
H ++ L+ + + A LTN + + +S +L L+EG++++ DL+G VV E
Sbjct: 65 HHNQDMIIKLKGVDDRDAANLLTNCEIVV---DSSQLPQLEEGDYYWKDLMGCQVVTTEG 121
Query: 119 EILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRD 159
LGKV+++ D +++ NL + K L+P+ D
Sbjct: 122 YDLGKVVDMMETGSNDVLVIKA--NLKDAFGIKERLVPFLD 160
>pir||S37174 hypothetical protein, 21K - Salmonella typhimurium
emb|CAA52886.1| (X74933) 21kD protein [Salmonella typhimurium]
Length = 183
Score = 45.4 bits (106), Expect = 3e-04
Identities = 41/159 (25%), Positives = 80/159 (49%), Gaps = 15/159 (9%)
Query: 5 LLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVS--SFKEYIIHSYEH 62
+++G++G S G+ G LR+ ++ E + + + V S+K++ H
Sbjct: 14 VVLGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQLESWKKH------H 67
Query: 63 AKNLLF-LETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV-EENEI 120
++L+ L+ + + A LTN + + +S +L L+EG++++ DL+G VV E
Sbjct: 68 NQDLIIKLKGVDDRDAANLLTNCEIVV---DSSQLPALEEGDYYWKDLMGCQVVTAEGYD 124
Query: 121 LGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRD 159
LGKVI++ D +++ NL + K L+P+ D
Sbjct: 125 LGKVIDMMETGSNDVLVIKA--NLKDAFGIKERLVPFLD 161
>ref|NP_345276.1| (NC_003028) 16S rRNA processing protein RimM [Streptococcus
pneumoniae TIGR4]
sp|Q97RM5|RIMM_STRPN Probable 16S rRNA processing protein rimM
gb|AAK74916.1| (AE007385) 16S rRNA processing protein RimM [Streptococcus
pneumoniae TIGR4]
Length = 172
Score = 45.1 bits (105), Expect = 4e-04
Identities = 50/173 (28%), Positives = 82/173 (46%), Gaps = 25/173 (14%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPE-CLKKGVKVSVAPLNAFSCVSSFKEYI-IHSYEHAK 64
VG+I + GL G +R+ +DF E KKG A L F F + + I S+ K
Sbjct: 6 VGKIVNTQGLQGEMRVLSVTDFAEERFKKG-----AELVLFDEKDQFVQTVTIASHRKQK 60
Query: 65 NLLFLET-----IQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENE 119
N ++ I T EK K G + AE + L L +GEF+Y +++GL V E +
Sbjct: 61 NFDIIKFKDMYHINTIEKYK-----GYSLKVAE-EDLNDLDDGEFYYHEIIGLEVYEGDS 114
Query: 120 ILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKI 172
++G + EI + D ++V+ KG + L+PY + + + K++
Sbjct: 115 LVGTIKEILQPGANDVWVVK------RKG-KRDLLLPYIPPVVLNVDIPSKRV 160
>ref|NP_607058.1| (NC_003485) putative 16S rRNA processing protein RIMM
[Streptococcus pyogenes MGAS8232]
gb|AAL97557.1| (AE010020) putative 16S rRNA processing protein RIMM [Streptococcus
pyogenes MGAS8232]
Length = 172
Score = 44.7 bits (104), Expect = 5e-04
Identities = 43/140 (30%), Positives = 72/140 (50%), Gaps = 18/140 (12%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPE-CLKKGVKVSVAPLNAFSCVSSF-KEYIIHSYEHAK 64
VG+I + GL G +R+ SDF E KKG ++++ F F +E I S+ K
Sbjct: 6 VGKIVNTQGLQGEMRVLSVSDFAEERFKKGSQLAL-----FDDKDQFVQEVTIVSHRKQK 60
Query: 65 NLLFLET-----IQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENE 119
+ ++ I EK K T L +S+A L +EGEF+Y ++G++V E++
Sbjct: 61 HFDIIKFKDMYHINAIEKYKGYT---LKVSKANQGDL---QEGEFYYHQIIGMAVYEKDR 114
Query: 120 ILGKVIEIQRISQTDYFLVE 139
++G V EI + D ++V+
Sbjct: 115 LIGYVKEILQPGANDVWVVK 134
>ref|NP_243346.1| (NC_002570) 16S rRNA processing protein [Bacillus halodurans]
sp|Q9KA14|RIMM_BACHD Probable 16S rRNA processing protein rimM
dbj|BAB06199.1| (AP001515) 16S rRNA processing protein [Bacillus halodurans]
Length = 173
Score = 44.7 bits (104), Expect = 5e-04
Identities = 31/85 (36%), Positives = 46/85 (53%), Gaps = 7/85 (8%)
Query: 99 LKEGEFFYCDLVGLSVVE-ENEILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPY 157
L EGEFFY +++G SVV E LGKV EI D ++V+ K LIPY
Sbjct: 95 LGEGEFFYHEIIGCSVVTIAGEELGKVKEILSPGANDVWVVQCRRG------GKDLLIPY 148
Query: 158 RDFYIQEILLQDKKITTHNAKTLLE 182
+ ++++ L+ ++IT + LLE
Sbjct: 149 IEQVVKQVDLEKQQITIEPMEGLLE 173
>ref|NP_660723.1| (NC_004061) 16S rRNA processing protein RimM [Buchnera aphidicola
str. Sg (Schizaphis graminum)]
gb|AAM67934.1| (AE014114) 16S rRNA processing protein RimM [Buchnera aphidicola
str. Sg (Schizaphis graminum)]
Length = 175
Score = 43.9 bits (102), Expect = 9e-04
Identities = 48/179 (26%), Positives = 80/179 (43%), Gaps = 28/179 (15%)
Query: 5 LLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSF----KEYIIHSY 60
+L+G+IGK+ G+ G ++ F E +K FS F K IIH
Sbjct: 12 ILIGKIGKAYGILGWVKFF---SFTENKEK----------IFSYFPWFILKKKWEIIHVD 58
Query: 61 EHAKN----LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV- 115
+ K+ ++ +E I + TNL +F+ + L +LKE E+++ D++ V
Sbjct: 59 KWKKHNNNFIIHIENILDRSTVSKFTNLEIFI---DKSILPILKEDEYYWNDVIDCKVFN 115
Query: 116 EENEILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKITT 174
E LGKVI + R D ++ N ++K K +IP+ I + + KI T
Sbjct: 116 SRKEYLGKVINLIRNQNNDVLIIR---NNLKKNNFKKIMIPFIHKKIVKYINVKHKIIT 171
>ref|NP_240212.1| (NC_002528) 16s rRNA processing protein rimm [Buchnera sp. APS]
sp|P57475|RIMM_BUCAI Probable 16S rRNA processing protein rimM
dbj|BAB13098.1| (AP001119) 16s rRNA processing protein rimm [Buchnera sp. APS]
Length = 176
Score = 43.5 bits (101), Expect = 0.001
Identities = 40/173 (23%), Positives = 81/173 (46%), Gaps = 16/173 (9%)
Query: 2 VSMLLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYE 61
+ LL+G++GKS G+ G + + ++ E + + P F ++ I +++
Sbjct: 10 IQPLLIGKVGKSYGILGWINIFSFTEEQEKI-----FNYLPWFFFK-EKNWTRIQIKNWK 63
Query: 62 HAKN--LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVE-EN 118
KN ++ ++ I + TN + +S+ L LK+ ++++ D++ V +
Sbjct: 64 KYKNNFIVHIKDISDRSVVSQFTNADIIISK---HTLPALKKNDYYWNDIINYKVFNIDQ 120
Query: 119 EILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKK 171
LG VI + R D +V+ L + +K + LIP+ D I + + DKK
Sbjct: 121 HYLGTVINLIRTRNNDILIVKNKLKIHQKNI----LIPFIDNKIIKNVNTDKK 169
>ref|NP_230213.1| (NC_002505) 16S rRNA processing protein RimM [Vibrio cholerae]
pir||B82307 16S rRNA processing protein RimM VC0562 [imported] - Vibrio
cholerae (group O1 strain N16961)
gb|AAF93730.1| (AE004142) 16S rRNA processing protein RimM [Vibrio cholerae]
Length = 184
Score = 42.7 bits (99), Expect = 0.002
Identities = 44/165 (26%), Positives = 78/165 (46%), Gaps = 14/165 (8%)
Query: 5 LLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYE-HA 63
L+VG++G S G+ G L++ +D PE + +P + EY + ++ H
Sbjct: 16 LVVGKLGSSYGIRGWLKVFSYTDNPESI-----FDYSPW-YIDQKGEWVEYKVEGWKRHN 69
Query: 64 KN-LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEI-L 121
K ++ L+ + E A LTN + + A L L E EF++ +L G+ VV N L
Sbjct: 70 KGWVVKLQGLDVREDAHLLTNFEIAIDPA---SLPELSEDEFYWRELFGMQVVTTNGYDL 126
Query: 122 GKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEIL 166
G V ++ D +V+ NL + K LIP+ + + +++
Sbjct: 127 GVVTDMMETGSNDVLVVKA--NLKDAFGQKERLIPFLEEQVIKVV 169
>sp|Q9KUF9|RIMM_VIBCH Probable 16S rRNA processing protein rimM
Length = 182
Score = 42.7 bits (99), Expect = 0.002
Identities = 44/165 (26%), Positives = 78/165 (46%), Gaps = 14/165 (8%)
Query: 5 LLVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYE-HA 63
L+VG++G S G+ G L++ +D PE + +P + EY + ++ H
Sbjct: 14 LVVGKLGSSYGIRGWLKVFSYTDNPESI-----FDYSPW-YIDQKGEWVEYKVEGWKRHN 67
Query: 64 KN-LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENEI-L 121
K ++ L+ + E A LTN + + A L L E EF++ +L G+ VV N L
Sbjct: 68 KGWVVKLQGLDVREDAHLLTNFEIAIDPA---SLPELSEDEFYWRELFGMQVVTTNGYDL 124
Query: 122 GKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEIL 166
G V ++ D +V+ NL + K LIP+ + + +++
Sbjct: 125 GVVTDMMETGSNDVLVVKA--NLKDAFGQKERLIPFLEEQVIKVV 167
>ref|NP_269055.1| (NC_002737) putative 16S rRNA processing protein [Streptococcus
pyogenes] [Streptococcus pyogenes M1 GAS]
sp|P58183|RIMM_STRPY Probable 16S rRNA processing protein rimM
gb|AAK33776.1| (AE006535) putative 16S rRNA processing protein [Streptococcus
pyogenes M1 GAS]
Length = 172
Score = 42.0 bits (97), Expect = 0.003
Identities = 42/140 (30%), Positives = 71/140 (50%), Gaps = 18/140 (12%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPE-CLKKGVKVSVAPLNAFSCVSSF-KEYIIHSYEHAK 64
VG+I + GL G +R+ SDF E KKG ++++ F F +E I S+ K
Sbjct: 6 VGKIVNTQGLQGEMRVLSVSDFAEERFKKGSQLAL-----FDDKDRFVQEVTIVSHRKQK 60
Query: 65 NLLFLET-----IQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVEENE 119
+ ++ I EK K T L +S+ L +EGEF+Y ++G++V E++
Sbjct: 61 HFDIIKFKDMYHINAIEKYKGYT---LKVSKDNQGDL---QEGEFYYHQIIGMAVYEKDV 114
Query: 120 ILGKVIEIQRISQTDYFLVE 139
++G V EI + D ++V+
Sbjct: 115 LIGHVKEILQPGANDVWIVK 134
>ref|NP_246234.1| (NC_002663) RimM [Pasteurella multocida]
sp|P57935|RIMM_PASMU 16S rRNA processing protein rimM
gb|AAK03380.1| (AE006168) RimM [Pasteurella multocida]
Length = 178
Score = 41.6 bits (96), Expect = 0.004
Identities = 32/136 (23%), Positives = 67/136 (48%), Gaps = 12/136 (8%)
Query: 6 LVGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYEHAKN 65
+VG++G + G+ G LR++ +++ E + P ++ + S+ + N
Sbjct: 11 VVGKLGSTYGIRGWLRIYSSTEYAESI-----FDYQPW-FLKIKGQWQPTELESWRYHNN 64
Query: 66 --LLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVE-ENEILG 122
++ L+ + E A+ L N+ + + A + L+EG++++ DL+G +VV EN +G
Sbjct: 65 DLIVKLKHVDDRETAQTLANIEIGVDLAVFPE---LEEGDYYWHDLIGCNVVNLENYAMG 121
Query: 123 KVIEIQRISQTDYFLV 138
V E+ D +V
Sbjct: 122 TVTEMMETGSNDVLVV 137
>ref|NP_562626.1| (NC_003366) probable 16S rRNA processing protein [Clostridium
perfringens]
sp|Q8XJP6|RIMM_CLOPE Probable 16S rRNA processing protein rimM
dbj|BAB81416.1| (AP003191) probable 16S rRNA processing protein [Clostridium
perfringens]
Length = 165
Score = 41.6 bits (96), Expect = 0.004
Identities = 51/181 (28%), Positives = 81/181 (44%), Gaps = 35/181 (19%)
Query: 1 MVSMLLVGRIGKSVGLNGGLR-LHLESDFPE------CLKKGVKVSVAPLNAFSCVSSFK 53
M +L+VG+I + GL G ++ + L D + KG KV V V FK
Sbjct: 1 MEDLLVVGQIINTHGLRGEMKVMPLTEDMRRFDYLEYVILKGKKVKVEG------VKYFK 54
Query: 54 EYIIHSYEHAKNLLFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLS 113
+ +I L LE I + E+A++L L E E + L+E E+F DLVG +
Sbjct: 55 DKVI---------LKLEGINSIEEAEKLKRTYL---EIEREDAIELEEDEYFIVDLVGCT 102
Query: 114 VVE-ENEILGKVIEIQRISQTDYFLVETTLNLVEKGLAKIFLIPYRDFYIQEILLQDKKI 172
VV+ E GK+ ++ + D + V+ K L+P + +I + +K I
Sbjct: 103 VVDTEGFEYGKIKDVIQTPSNDVYWVQG---------KKEVLVPVLKDIVLDINMDEKLI 153
Query: 173 T 173
T
Sbjct: 154 T 154
>ref|NP_623077.1| (NC_003869) RimM protein, required for 16S rRNA processing
[Thermoanaerobacter tengcongensis]
gb|AAM24681.1| (AE013104) RimM protein, required for 16S rRNA processing
[Thermoanaerobacter tengcongensis]
Length = 168
Score = 40.8 bits (94), Expect = 0.007
Identities = 34/134 (25%), Positives = 66/134 (48%), Gaps = 6/134 (4%)
Query: 7 VGRIGKSVGLNGGLRLHLESDFPECLKKGVKVSVAPLNAFSCVSSFKEYIIHSYEHAKNL 66
VG++ G+ G ++++ ++ PE + V C + I S L
Sbjct: 7 VGKVTSPHGIRGEIKVYPLTNVPERFYDIPYIWVFDEKDIPCKYEIENVKITS--KGMVL 64
Query: 67 LFLETIQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSV-VEENEILGKVI 125
L L+ I + A++L GLF+ + +++ L+E E+F DL+G+ V EE E++G +
Sbjct: 65 LKLKGIDSRNDAEKLK--GLFL-KVDAENALKLEEDEYFITDLIGMKVYTEEGELIGTLE 121
Query: 126 EIQRISQTDYFLVE 139
E+ + D ++V+
Sbjct: 122 EVLQTGANDVYVVK 135
>ref|NP_486852.1| (NC_003272) probable 16S rRNA processing protein [Nostoc sp. PCC
7120]
sp|Q8YTB1|RIMM_ANASP Probable 16S rRNA processing protein rimM
dbj|BAB74511.1| (AP003590) ORF_ID:alr2812~probable 16S rRNA processing protein
[Nostoc sp. PCC 7120]
Length = 246
Score = 40.4 bits (93), Expect = 0.010
Identities = 46/185 (24%), Positives = 85/185 (45%), Gaps = 16/185 (8%)
Query: 5 LLVGRIGKSVGLNGGLRLHLESDFPECLK-KGVKVSVAPLNAFSCVSSFKEYIIHSYEHA 63
L +G+I + GL+G +R++ +SDFPE + G + + P E + Y
Sbjct: 66 LQIGKIVSAQGLSGEVRVYPDSDFPERFEVPGTRWLLRP---GQTEPQPIELLHGRYLEN 122
Query: 64 KNLLFLET--IQTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVV--EENE 119
KNL L+ ++ +++EL LF+ ++ + L E E+ DL+G+ V +
Sbjct: 123 KNLYVLQLAGVENRSQSEELRGCMLFVPASDRPE---LGEDEYHVVDLIGMEVFLQASGD 179
Query: 120 ILGKVIEIQRISQTDYFLVETTLN--LVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNA 177
++G V+++ L+E +L+ + K LIP+ + LQ ++I
Sbjct: 180 LVGAVVDVIPAGND---LLEVSLHEPVTSDKKPKTVLIPFVKAIAPVVDLQTRRIEITPP 236
Query: 178 KTLLE 182
LLE
Sbjct: 237 PGLLE 241
Database: /home/scwang/download_20020708_db/nr
Posted date: Aug 7, 2002 12:55 PM
Number of letters in database: 324,149,939
Number of sequences in database: 1,026,957
Lambda K H
0.320 0.139 0.385
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 106,165,292
Number of Sequences: 1026957
Number of extensions: 4011106
Number of successful extensions: 14799
Number of sequences better than 1.0e-02: 26
Number of HSP's better than 0.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 14778
Number of HSP's gapped (non-prelim): 26
length of query: 184
length of database: 324,149,939
effective HSP length: 114
effective length of query: 70
effective length of database: 207,076,841
effective search space: 14495378870
effective search space used: 14495378870
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 93 (40.4 bits)