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|15645980|ref|NP_208160.1| type IIS restriction enzyme
M2 protein (mod) [Helicobacter pylori 26695]
(287 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_222969.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 102 9e-24
ref|NP_223989.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 77 4e-16
ref|NP_223347.1| putative TYPE II DNA MODIFICATION ENZYME (... 67 5e-13
ref|NP_223474.1| putative TYPE II DNA MODIFICATION ENZYME (... 60 7e-11
ref|NP_222765.1| putative TYPE II DNA MODIFICATION ENZYME (... 52 1e-08
ref|NP_222806.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 52 2e-08
ref|NP_224002.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 45 2e-06
ref|NP_224014.1| putative TYPE III DNA MODIFICATION ENZYME ... 43 1e-05
ref|NP_222767.1| putative TYPE II DNA MODIFICATION ENZYME (... 42 1e-05
ref|NP_223194.1| cag island protein [Helicobacter pylori J99] 28 0.21
ref|NP_223610.1| putative [Helicobacter pylori J99] 28 0.28
ref|NP_224129.1| TYPE III DNA MODIFICATION ENZYME (METHYLTR... 28 0.36
ref|NP_222965.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 25 2.3
ref|NP_222737.1| DNA transfer protein [Helicobacter pylori ... 25 3.0
ref|NP_223748.1| putative lipopolysaccharide biosynthesis p... 23 6.8
ref|NP_223395.1| D-ALANYL-D-ALANINE-ADDING ENZYME [Helicoba... 23 6.8
ref|NP_223213.1| cag island protein, CYTOTOXICITY ASSOCIATE... 23 8.9
>ref|NP_222969.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 252
Score = 102 bits (255), Expect = 9e-24
Identities = 82/275 (29%), Positives = 131/275 (46%), Gaps = 44/275 (16%)
Query: 8 YHSSTNMNEVPDNSV-DLIITSPPYFNIKDYAKNGTQDLQHSAQHVEDLGALEKYEDYLL 66
YH ++ E + DL +TSPPY +Y G+ D + Y+DYL
Sbjct: 13 YHGDASVLETFEKGFYDLCVTSPPYNLSIEY--QGSNDFR-------------AYDDYL- 56
Query: 67 GLLKVWLE-CYRALKPNGKLCINVPLMPMLKKVLNTHYNRHIFDLHADIQHSILHDLNNM 125
K WL+ CY K +LC+NVPL D + + S+ D+ +
Sbjct: 57 NWCKNWLKNCYFWGKEQARLCLNVPL-----------------DTNKHGKQSLGADITIV 99
Query: 126 LKNKPKMFLLDVYIWKRANPTKRLMFGSYPYPRNFYAQNTIEFIGVFVKDGKPKQPTEEQ 185
K + + IW +N ++R +GS+ YA +E I VF K+ + +
Sbjct: 100 AKECGWKYQ-NTIIWNESNISRRTAWGSWLQASAPYAIAPVELIVVFYKN-----EYKRK 153
Query: 186 KEQSQLTQEEWVEFTKQIWEIPIPNKNDIAFGKHAALMPAELARRLIRLYSCVGDVVLDP 245
K+ S +++EE++ +T +W +K + KH A P EL RR I+L+S + D + DP
Sbjct: 154 KQTSTMSREEFLLYTNGLWNFSGESKKRL---KHPAPFPRELPRRCIQLFSFLEDTIFDP 210
Query: 246 FSGSGTTLREAKLLKRNFIGYELYENYKPLIEQKL 280
FSGSGTT+ EA L R +G E+ + Y L ++++
Sbjct: 211 FSGSGTTILEANALGRFSVGLEIEKEYCELSKKRI 245
>ref|NP_223989.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 359
Score = 77.4 bits (189), Expect = 4e-16
Identities = 73/264 (27%), Positives = 114/264 (42%), Gaps = 54/264 (20%)
Query: 14 MNEVPDNSVDLIITSPPYF-----NIKDYAKNGTQDLQHSAQHVEDLGALEKYEDYLLGL 68
+ + P+ SVD I PPYF +K + GT+ Q H + G+ E+Y+ + LG
Sbjct: 20 LKDFPNKSVDFIFADPPYFMQTEGELKRF--EGTK-FQGVEDHWDKFGSFEEYDTFCLGW 76
Query: 69 LKVWLECYRALKPNGKLCINVPLMPMLKKVLNTHYNRHIFDLHADIQHSILHDLNNMLKN 128
LK EC R LK NG +C V+ + N H L N+
Sbjct: 77 LK---ECQRILKDNGSIC-----------VIGSFQNIFRIGFH----------LQNL--- 109
Query: 129 KPKMFLLDVYIWKRANPTKRLMFGSYPYPRNFYAQNTIEFIGVFVKDGKPKQPTEEQKEQ 188
++L+ +W ++NP ++ R A T+ ++ K + T K
Sbjct: 110 --GFWILNDIVWHKSNPVP-----NFAGKRLCNAHETL----IWCAKHKNSKVTFNYKTM 158
Query: 189 SQLTQEEWVEFTKQIWEIPIPNKN----DIAFGK-HAALMPAELARRLIRLYSCVGDVVL 243
L ++ K +W+IPI N D+ K H+ P L +++I + D++L
Sbjct: 159 KYLNNDKQ---EKSVWQIPICMGNERLKDVQGKKVHSTQKPEALLKKIILSATKPKDIIL 215
Query: 244 DPFSGSGTTLREAKLLKRNFIGYE 267
DPF G+GTT AK + R FIG E
Sbjct: 216 DPFFGTGTTGAVAKSMDRYFIGIE 239
>ref|NP_223347.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 404
Score = 67.0 bits (162), Expect = 5e-13
Identities = 65/265 (24%), Positives = 109/265 (40%), Gaps = 47/265 (17%)
Query: 10 SSTNMNEVPDNSVDLIITSPPYFNIKDYAKNGTQDLQHSAQHVEDLGALEKYEDYLLGLL 69
++ +N++ +SV+LI TSPPY+N + Y+ + Y+DYL +
Sbjct: 151 NAQTLNKIAPSSVNLIFTSPPYYNARIYSD------------------YKNYKDYLSAMS 192
Query: 70 KVWLECYRALKPNGKLCINVPLMPMLKKVLNTHYNRHIFDLHADIQHSILHDLNNMLKNK 129
+ C+R L+ + INV P++ K + + +H D H IL D
Sbjct: 193 QSLKACFRVLEEGRFIIINVS--PIITKRAGREFESVRYPIHFDF-HQILIDNG------ 243
Query: 130 PKMFLLDVYIWKRANPTKRLMFGSY-------PYPRNFYAQNTIEFI--GVFVKDGKPKQ 180
+ +D +W + + + G Y Y N +++ + + F+ D K
Sbjct: 244 --FYFVDEILWIKPDFSVPNRIGGYLQNKKPLGYKPNCVSESLLVYRKKAPFLLDKNIKI 301
Query: 181 PTEEQKEQSQ----LTQEEWVEFTKQIWEIPIPNKNDIAFGKHAALMPAELARRLIRLYS 236
+ K Q ++E T W I + D H A+ P L R++ YS
Sbjct: 302 AEKRLKPIKQNHTLFGKKELPIETTNCWYITPKSSKD-----HPAVFPESLCERVLNYYS 356
Query: 237 CVGDVVLDPFSGSGTTLREAKLLKR 261
+VV DPF+GSGT AK + R
Sbjct: 357 FENEVVCDPFAGSGTFGMVAKSMGR 381
>ref|NP_223474.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 272
Score = 60.1 bits (144), Expect = 7e-11
Identities = 72/302 (23%), Positives = 121/302 (39%), Gaps = 76/302 (25%)
Query: 3 INKVFYHSSTNM--NEVPDNSVDLIITSPPYFNIKDYAKNGTQDLQHSAQHVEDLGALEK 60
+N + S N +++ + S+D+I+TSPPY N+++Y
Sbjct: 13 LNNFYVDSCVNFMQHKLQNESIDMILTSPPYDNLRNY----------------------- 49
Query: 61 YEDYLLGLLKVWLECYRALKPNGKLCINVPLMPMLKKVLNTHYNRHIFDLHADIQHSILH 120
+ Y + E +R +K G V + + K+ N + + F Q +
Sbjct: 50 -QGYTFAFENIANEIFRVIKKGG-----VVVWIVGDKIKNGNKSLTSFRQALYFQQIGFN 103
Query: 121 DLNNMLKNKPKMFLLDVYIWKRANPTKRLMFGSYPYPRNFYAQNTIEFIGVFVKDGKPK- 179
+ DV I+ + N P+ R+ N E++ V K GKPK
Sbjct: 104 -------------MHDVMIYAKKNT---------PFMRSNAYTNAYEYMFVLSK-GKPKT 140
Query: 180 -----QPTEEQ------------KEQSQLTQEEWVEFTKQ-IWEIPIP---NKNDIAFGK 218
+PT + +++ +E E TK IW + + ND
Sbjct: 141 FNPLKEPTARNGMEMLVTNKGADAKNNKILKELKKEKTKNNIWHYAVGLGGSTNDKIAFN 200
Query: 219 HAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYELYENYKPLIEQ 278
H A+ P +LA I +S D+V DP GSGTT + A L RNFIG ++ + Y + ++
Sbjct: 201 HPAIFPEQLALDHILSWSNERDIVFDPMCGSGTTCKMAFLHNRNFIGVDISKEYIQIAQK 260
Query: 279 KL 280
+L
Sbjct: 261 RL 262
>ref|NP_222765.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 230
Score = 52.4 bits (124), Expect = 1e-08
Identities = 75/267 (28%), Positives = 104/267 (38%), Gaps = 68/267 (25%)
Query: 22 VDLIITSPPYFNIKDYAKNGTQDLQHSAQHVEDLGALEKYEDYLLGLLKVWLECYRAL-K 80
VD IIT PPY NI KN L+ + + D G +K L W+ Y +L
Sbjct: 23 VDAIITDPPY-NIS--VKNNFSTLKSAKRQGIDFGEWDKNFKLL-----EWIARYASLIN 74
Query: 81 PNGKLCINVPLMPMLKKVLNTHYNRHIFDLHADIQHSILHDLNNMLKNKPKMFLLDVYIW 140
PNG + I + + +I D L + ++K D W
Sbjct: 75 PNGCMVI----------FCSYRFISYIADF--------LEENGFVVK--------DFIQW 108
Query: 141 KRANPTKRLMFGSYPYPRNF---YAQNTIEFIGVFVKDGKPKQPTEEQKEQSQLTQEEWV 197
+ NP PRN Y Q+T EF VK K K + K + L
Sbjct: 109 VKNNPM----------PRNIHRRYVQDT-EFALWAVKK-KAKWVFNKPKNEKYLR----- 151
Query: 198 EFTKQIWEIPIPNKNDIAFG----KHAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTL 253
P+ K+ + G KH L ++I ++ D VLDPF GSGTT
Sbjct: 152 ---------PLILKSPVVSGIERVKHPTQKSLTLMEKIISTHTNPNDTVLDPFMGSGTTG 202
Query: 254 REAKLLKRNFIGYELYENYKPLIEQKL 280
K LKRNFIG E + Y + +++L
Sbjct: 203 LACKNLKRNFIGIESEKEYFQIAQKRL 229
>ref|NP_222806.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 277
Score = 52.0 bits (123), Expect = 2e-08
Identities = 71/281 (25%), Positives = 107/281 (37%), Gaps = 71/281 (25%)
Query: 4 NKVFYHSSTNMNEVP---DNSVDLIITSPPYFNIKD----------YAKNGTQDLQHSAQ 50
+K+F + NEV +N+ DLI PPYF D G D ++
Sbjct: 18 DKLFTLYQGDCNEVLPQFENAFDLIFADPPYFLSNDGLSIQSGKIVSVNKGDWDKENGIN 77
Query: 51 HVEDLGALEKYEDYLLGLLKVWLE-CYRALKPNGKLCINVPLMPMLKKVLNTHYNRHIFD 109
+++ Y+ W+ +ALK G L I+ T++N
Sbjct: 78 DIDEFN----YQ---------WINNAKKALKNTGSLLIS-----------GTYHN----- 108
Query: 110 LHADIQHSILHDLNNMLKNKPKMFLLDVYIWKRANPTKRLMFGSYPYPRNF---YAQNTI 166
L L +L+ K +L++ W++ NP P NF Y ++
Sbjct: 109 ---------LFSLGRILQ-KLDFKILNLITWQKTNP-----------PPNFSCRYLTHSA 147
Query: 167 EFIGVFVKDGKPKQPTEEQKEQSQLTQEEWVEFTKQIWEIPIPNKNDIAFGKHAALMPAE 226
E I K K K + + ++ + +W P + A GKH P
Sbjct: 148 EQIIWARKSYKHKHVFNYEILKKINNNKQM----RDVWNFPAIAPWEKANGKHPTQKPLA 203
Query: 227 LARRLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYE 267
L RL+ + S ++ DPFSGS TT A LLKR FIG E
Sbjct: 204 LLVRLLLMASDDNSLIGDPFSGSSTTGIAANLLKREFIGIE 244
>ref|NP_224002.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 649
Score = 45.1 bits (105), Expect = 2e-06
Identities = 26/72 (36%), Positives = 38/72 (52%)
Query: 209 PNKNDIAFGKHAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYEL 268
P K D P +L R+I+ S +V D F+GSGTT A LKR +IG E+
Sbjct: 461 PKKADERLQGTLTQKPEKLLERIIKASSNENSIVCDFFAGSGTTCAVAHKLKRKYIGVEM 520
Query: 269 YENYKPLIEQKL 280
E+++ +I +L
Sbjct: 521 GEHFESVILPRL 532
>ref|NP_224014.1| putative TYPE III DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 620
Score = 42.7 bits (99), Expect = 1e-05
Identities = 21/64 (32%), Positives = 38/64 (58%)
Query: 224 PAELARRLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYELYENYKPLIEQKLGNL 283
P L +R++ + + D+VLD F+GSGTT A +KR +IG E + + + +++L +
Sbjct: 441 PEALLQRILEISTNENDLVLDFFAGSGTTCAVAHKMKRRYIGIEQMDYIETITKERLKKV 500
Query: 284 FDFE 287
+ E
Sbjct: 501 IEGE 504
>ref|NP_222767.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 343
Score = 42.4 bits (98), Expect = 1e-05
Identities = 31/111 (27%), Positives = 50/111 (44%), Gaps = 5/111 (4%)
Query: 157 PRNFYAQNTIEFIGVFVKDGKPKQPTEEQKEQSQLTQEEWVEFTKQIWEIPIPNKNDIAF 216
P+ + + I + + K+G + + E+ + + IWE P
Sbjct: 206 PKGRHWRTDIATLERWDKEGLIEYSNNNNPRKKIYALEQVGKRVQDIWEFKDPQYPSYPT 265
Query: 217 GKHAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYE 267
K+A L+ +I+ S +VLD F GSGTTL+ A LL+R FIG +
Sbjct: 266 EKNAQLLDL-----IIKTSSNKDSIVLDCFCGSGTTLKSAFLLQRKFIGID 311
>ref|NP_223194.1| cag island protein [Helicobacter pylori J99]
Length = 1819
Score = 28.5 bits (62), Expect = 0.21
Identities = 14/37 (37%), Positives = 20/37 (53%)
Query: 177 KPKQPTEEQKEQSQLTQEEWVEFTKQIWEIPIPNKND 213
K K+PT E K +S ++ E K I EI + NK +
Sbjct: 1506 KGKKPTAETKAESNKIDKDVAETAKNISEIALKNKKE 1542
>ref|NP_223610.1| putative [Helicobacter pylori J99]
Length = 267
Score = 28.1 bits (61), Expect = 0.28
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 158 RNFYAQNTIEFIGVFVKDGKPKQPTEEQKEQSQLTQEEWV 197
R YA++T E K+ +PK+ EE +E+SQ +E V
Sbjct: 228 RILYAESTHESNAQPPKESQPKESQEESQEESQEESQESV 267
>ref|NP_224129.1| TYPE III DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 641
Score = 27.7 bits (60), Expect = 0.36
Identities = 23/75 (30%), Positives = 37/75 (48%), Gaps = 11/75 (14%)
Query: 181 PTEEQKEQSQLTQEEWVEFTKQIWEIPIPNKNDIAFGKHAALMPAELARRLIRLYSC--- 237
PT E ++ + E +K+++++ N F K P L + LI + S
Sbjct: 358 PTNEISKKDNVGTNETA--SKELFKL-FDNNKIFNFNK-----PVSLIKYLISICSNNTN 409
Query: 238 VGDVVLDPFSGSGTT 252
GD++LD F+GSGTT
Sbjct: 410 EGDIILDFFAGSGTT 424
>ref|NP_222965.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 390
Score = 25.0 bits (53), Expect = 2.3
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 224 PAELARRLIRLYSCVGDVVLDPFSGSGTTLREA-KLLKRNFIGYELYENYKPLIEQKLGN 282
P L + L+ + ++LD F+GSGTT + ++ K ++ + Y K E+K+ N
Sbjct: 290 PVALIKYLLLCSTPKDSIILDFFAGSGTTAQAVIEVNKDYYLNWSFYLCQK---EEKIKN 346
>ref|NP_222737.1| DNA transfer protein [Helicobacter pylori J99]
Length = 787
Score = 24.6 bits (52), Expect = 3.0
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 95 LKKVLNTHYNRHIFDLHADIQHSILHDLNNMLKNKPKMFLLDVYIWKRANPTKRLMFGSY 154
L+ +LN N+ +++ + H L+ +L++K K F+ AN SY
Sbjct: 109 LQAILNQFENKEVYENQYFLVLESTHSLHGVLEHKKKSFM-------HANRENFKDILSY 161
Query: 155 PYPRNFYAQNTIEFIGVFVKDGKPK 179
+ + Q T++ + + +K+ PK
Sbjct: 162 ---KAHFLQETLKSLEIQLKNYAPK 183
>ref|NP_223748.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 393
Score = 23.5 bits (49), Expect = 6.8
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 7/50 (14%)
Query: 84 KLCINVPLMPMLKKVLNTHYNRHIFDLHADIQHSILHDLNNMLKNKPKMF 133
K CI++PL + K L LHA ++ IL L + KN+ + F
Sbjct: 351 KYCISIPLKSFISKTLK------FLKLHALVK-KILIQLKLLKKNQSQNF 393
>ref|NP_223395.1| D-ALANYL-D-ALANINE-ADDING ENZYME [Helicobacter pylori J99]
Length = 493
Score = 23.5 bits (49), Expect = 6.8
Identities = 9/42 (21%), Positives = 22/42 (51%)
Query: 95 LKKVLNTHYNRHIFDLHADIQHSILHDLNNMLKNKPKMFLLD 136
L ++L T +N H + I +D+N L ++ ++++ +
Sbjct: 186 LHQILQTQFNAHASPKSVNTLLGIANDINQNLDDRSEIYIAE 227
>ref|NP_223213.1| cag island protein, CYTOTOXICITY ASSOCIATED IMMUNODOMINANT ANTIGEN
[Helicobacter pylori J99]
Length = 1167
Score = 23.1 bits (48), Expect = 8.9
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 234 LYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYELYENYKPLIEQKLGN 282
LY V + V G+G + EA L +NF + K + KLGN
Sbjct: 840 LYQSVKNGVNGTLVGNGLSKAEATTLSKNF------SDIKKELNAKLGN 882
Database: NC_000921.faa
Posted date: Dec 10, 2001 4:36 PM
Number of letters in database: 494,079
Number of sequences in database: 1491
Lambda K H
0.320 0.139 0.421
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 335,003
Number of Sequences: 1491
Number of extensions: 16032
Number of successful extensions: 81
Number of sequences better than 10.0: 17
Number of HSP's better than 10.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 54
Number of HSP's gapped (non-prelim): 20
length of query: 287
length of database: 494,079
effective HSP length: 77
effective length of query: 210
effective length of database: 379,272
effective search space: 79647120
effective search space used: 79647120
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: 48 (23.1 bits)