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|15644682|ref|NP_206852.1| cytosine specific DNA
methyltransferase (DDEM) [Helicobacter pylori 26695]
(355 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_223153.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 230 4e-62
ref|NP_222766.1| putative TYPE II DNA MODIFICATION ENZYME (... 129 1e-31
ref|NP_223767.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 81 5e-17
ref|NP_223449.1| TRIGGER FACTOR [Helicobacter pylori J99] 28 0.47
ref|NP_223288.1| putative 2,3,4,5-TETRAHYDROPYRIDINE-2-CARB... 27 0.61
ref|NP_223778.1| ATP synthase F1, subunit gamma [Helicobact... 27 0.80
ref|NP_223017.1| putative [Helicobacter pylori J99] 27 0.80
ref|NP_222912.1| putative [Helicobacter pylori J99] 27 1.0
ref|NP_223956.1| 50S RIBOSOMAL PROTEIN L4 [Helicobacter pyl... 26 1.4
ref|NP_223886.1| putative [Helicobacter pylori J99] 26 1.4
ref|NP_224079.1| BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE... 25 3.0
ref|NP_223737.1| UDP-GLUCOSE 4-EPIMERASE [Helicobacter pylo... 25 4.0
ref|NP_223913.1| FLAGELLAR FUNCTIONAL PROTEIN [Helicobacter... 24 5.2
ref|NP_222768.1| putative TYPE II restriction enzyme [Helic... 24 5.2
ref|NP_223661.1| putative [Helicobacter pylori J99] 24 6.8
ref|NP_223414.1| putative [Helicobacter pylori J99] 24 6.8
ref|NP_223274.1| putative vacuolating cytotoxin (VacA) para... 24 6.8
ref|NP_223185.1| putative [Helicobacter pylori J99] 24 6.8
ref|NP_223357.1| putative [Helicobacter pylori J99] 23 8.9
>ref|NP_223153.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 351
Score = 230 bits (587), Expect = 4e-62
Identities = 131/354 (37%), Positives = 199/354 (56%), Gaps = 10/354 (2%)
Query: 3 YKILDLFCGAGGFSAGLECLEEFDALIGLDCDKQALITFENNHKNAIGVCGDITQTEIKE 62
YK+ D+FCGAGG S G F+ + D DK A+++++ NHK + DI Q
Sbjct: 2 YKVADIFCGAGGLSYGFSTHPYFELIWANDIDKDAILSYQANHKETQTILCDIAQLHCHN 61
Query: 63 KVIKLAKKLEINMIIGGPPCQGFSNKGKNLGLKDPRNFLFLEYIEIVKAIKPEIFIIENV 122
++ I++++GGPPCQ +S GK D + LF EY+ I+ +KP+IF+ ENV
Sbjct: 62 -----LPRVPIDILLGGPPCQSYSTLGKRK--MDEKANLFKEYLRILDLVKPKIFVFENV 114
Query: 123 KNLISCAKGYFLEEIKERLNALGYQLSYQILNAKDYGVPQNRERAFIVGASR-FSFDFNL 181
L+S KG + I GY L + ILNA DYGVPQ RER +VGA + F F
Sbjct: 115 VGLMSMQKGQLFQRICNAFKERGYILEHAILNALDYGVPQVRERVILVGALKSFKQKFYF 174
Query: 182 LEPSQS-VNVQDAISDLAYLCSNEGAFESDYLNPIQSSYQALMRKDSPKLYNHQATNHSQ 240
+P ++ +++DA+ DL + S E YL + + +R +S +L H + +++
Sbjct: 175 PKPIKTHFSLKDALGDLPPIQSGENGDALGYLKNADNVFLEFVR-NSKELSEHSSPKNNE 233
Query: 241 AALEKLKLINKEQGKECLPKNLHGKQQFKSTWGRLNWNKISPTIDTRFDTPSNGTNSHPE 300
++ ++ + Q K+ LP++L K + +T+ ++ W K +PTI F TPS+ HP
Sbjct: 234 KLIKIMQTLKDGQSKDDLPESLRPKSGYINTYAKMWWEKPAPTITRNFSTPSSSRCIHPR 293
Query: 301 LHRSITPREAARIQSFSDNYIFYGNKTSVCKQIGNAVPPLLALALGKAILKSLR 354
R+++ RE AR+QSF DNY FYG+ + QIGNAVPPLL+ AL A+ LR
Sbjct: 294 DSRALSIREGARLQSFPDNYKFYGSANAKRLQIGNAVPPLLSAALAHAVFDFLR 347
>ref|NP_222766.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 185
Score = 129 bits (324), Expect = 1e-31
Identities = 63/65 (96%), Positives = 64/65 (97%)
Query: 290 TPSNGTNSHPELHRSITPREAARIQSFSDNYIFYGNKTSVCKQIGNAVPPLLALALGKAI 349
TPSNGTNSHPELHRSITPREAARIQSFSD+YIFYGNKTSVCKQIGNAVPPLLALALGKAI
Sbjct: 114 TPSNGTNSHPELHRSITPREAARIQSFSDDYIFYGNKTSVCKQIGNAVPPLLALALGKAI 173
Query: 350 LKSLR 354
LKS R
Sbjct: 174 LKSAR 178
>ref|NP_223767.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 321
Score = 80.9 bits (198), Expect = 5e-17
Identities = 63/214 (29%), Positives = 99/214 (45%), Gaps = 15/214 (7%)
Query: 6 LDLFCGAGGFSAGLECLEEFDALIGLDCDKQALITFENNHKNAIGVCGDITQTEIKEKVI 65
+D G GG GLE + + + +A+ T+E K+ GD+ + +
Sbjct: 7 MDFCSGIGGGRLGLERCH-LKCVGHAEINHEAIRTYELFFKDTHNF-GDLMRINPNDLP- 63
Query: 66 KLAKKLEINMIIGGPPCQGFSNKGKNLGLKDPRNFLFLEYIEIVKAIKPEIFIIENVKNL 125
++++ G PCQ FS GK GL+D R + I I+K +P+ F++ENVK L
Sbjct: 64 ------NFDVLVSGFPCQAFSINGKRKGLEDERGTIIYGLIRILKVKQPKCFLLENVKGL 117
Query: 126 ISCAKGYFLEEIKERLNALGYQLSYQILNAKDYGVPQNRERAFIVGASR-----FSFDFN 180
I + + I + L GY YQILN+ D+ + Q RER +IVG + F+F
Sbjct: 118 IHHKQQETFKTIIKALQEAGYTTHYQILNSADFQLAQKRERLYIVGFRKDLKRPFNFPLG 177
Query: 181 LLEPSQSVNVQDAISDLAYLCSNEGAFESDYLNP 214
L + DA ++ YL + F+ NP
Sbjct: 178 LANDYCFKDFLDADNE-CYLDVSNATFQRYLRNP 210
>ref|NP_223449.1| TRIGGER FACTOR [Helicobacter pylori J99]
Length = 451
Score = 27.7 bits (60), Expect = 0.47
Identities = 57/258 (22%), Positives = 108/258 (41%), Gaps = 29/258 (11%)
Query: 20 ECLEEFD-ALIGLDC--DKQALITFENNHKNAIGVCGDITQTEIKEKVIKLAKKLEINMI 76
+ LE+F+ AL+G+ +K+ +TF + + +A + G ++K + I++ + LEIN
Sbjct: 197 QMLEDFEKALLGMQASEEKEFPLTFPSGY-HAEHLAGKEALFKVKLRQIQVREALEINDE 255
Query: 77 IGGPPCQGFSNKGKNLGLKDPRNFLFLEYIEIVKAIKPEIFIIENV--KNLISCAKGYFL 134
+ N L + + LFLE + + + +IEN+ K L K
Sbjct: 256 LAKIVLANEENATLELLKERVKGQLFLENKARLYNEELKEKLIENLDEKILFDLPKTIIE 315
Query: 135 EEIKERL-NALGYQLSYQILNAKDYGVPQNRERAFI----VGASRFSFDFNLLEPSQSVN 189
+E+ NAL + ++ + +D +R + + +F + L + +
Sbjct: 316 QEMDLLFRNALYSMQAEEVKSLQDSQEKAKEKRESFRNDATKSVKITFVIDALAKEEKIG 375
Query: 190 VQDAISDLAYLCSNEGAFESDYLNPIQSSYQALMRKDSPKLYNHQATNHSQAALEKLKLI 249
V D NE F++ Y Y+A+M +P+ Q ++ A K+ +I
Sbjct: 376 VHD----------NE-VFQTLY-------YEAMMTGQNPENLIEQYRKNNMLAAVKMAMI 417
Query: 250 NKEQGKECLPKNLHGKQQ 267
L KNL +QQ
Sbjct: 418 EDRVLAYLLDKNLPKEQQ 435
>ref|NP_223288.1| putative 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE
N-SUCCINYLTRANSFERASE [Helicobacter pylori J99]
Length = 401
Score = 27.3 bits (59), Expect = 0.61
Identities = 13/24 (54%), Positives = 18/24 (74%)
Query: 330 CKQIGNAVPPLLALALGKAILKSL 353
C+ + +A LLAL+LGKA L+SL
Sbjct: 144 CESVESAYMKLLALSLGKAPLRSL 167
>ref|NP_223778.1| ATP synthase F1, subunit gamma [Helicobacter pylori J99]
Length = 301
Score = 26.9 bits (58), Expect = 0.80
Identities = 19/71 (26%), Positives = 35/71 (48%), Gaps = 13/71 (18%)
Query: 87 NKGKNLGLKDPRNFLFLEYIEIVKAIKPEIFII------------ENVKNLISCAKGYFL 134
+K KN G++D ++ F E +E ++ K +I I +K +++C Y
Sbjct: 58 SKMKNQGIEDIQSKYFRE-LERLEIKKVDIIFITADKGLCGGFNTNTIKKVLACTNEYKE 116
Query: 135 EEIKERLNALG 145
++IK RL +G
Sbjct: 117 KDIKVRLRGIG 127
>ref|NP_223017.1| putative [Helicobacter pylori J99]
Length = 321
Score = 26.9 bits (58), Expect = 0.80
Identities = 22/79 (27%), Positives = 33/79 (40%), Gaps = 2/79 (2%)
Query: 199 YLCSNEGAFESDYLNPIQSSYQALMRKDSPKLYNHQATNHSQAALEKLKLINKEQGKECL 258
+L S + +F S+YLN I AL+ + + Q Q EK+ +N G C
Sbjct: 12 FLGSGKTSFLSEYLNQIDHQGVALIINEIGQAALDQRILSVQYCGEKMLYLN--AGCVCC 69
Query: 259 PKNLHGKQQFKSTWGRLNW 277
K L + K+T W
Sbjct: 70 NKRLDLVESLKATLNNYEW 88
>ref|NP_222912.1| putative [Helicobacter pylori J99]
Length = 916
Score = 26.6 bits (57), Expect = 1.0
Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 17/93 (18%)
Query: 183 EPSQSVNVQDAISDLAYLCSNEGAFESDYLNPIQSSYQALM----RKDSPKLYNHQATNH 238
EP +N D + ++ +C N ES +N + +++M K L N + +
Sbjct: 259 EPEYKIN--DLLKNIQQICKNY--IESHAVNDVSKDIKSMMCQFYLKQIDLLVNSEIVRY 314
Query: 239 SQAAL---------EKLKLINKEQGKECLPKNL 262
+ L E +K+++ E G PKN+
Sbjct: 315 RYSNLFEPIQRSLWESIKILDNESGIYLFPKNI 347
>ref|NP_223956.1| 50S RIBOSOMAL PROTEIN L4 [Helicobacter pylori J99]
Length = 215
Score = 26.2 bits (56), Expect = 1.4
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 75 MIIGGPPCQGFSNKGK-NLGLKDPRNFLFLEYIEIVKAIKPEIFIIENVKNLISCAKGYF 133
+ +GG G +NK NL + + L LEY KA ++F++E + KG
Sbjct: 80 VFVGGGVSHGATNKRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKI-----AIKGVV 134
Query: 134 LEEIKERLNALGYQLSYQILNAKD 157
+ ++ L Q+ +Q L +D
Sbjct: 135 EDNKRKHLTKEANQM-FQALEQRD 157
>ref|NP_223886.1| putative [Helicobacter pylori J99]
Length = 340
Score = 26.2 bits (56), Expect = 1.4
Identities = 20/72 (27%), Positives = 30/72 (40%), Gaps = 11/72 (15%)
Query: 134 LEEIKERLNALGYQLSYQILNAKDYGVPQNRERAFIVGASRFSFDFNLLEPSQSVNVQDA 193
L+ ++ER N L +S +LNA F + S FN L+ +N
Sbjct: 157 LKFLQERANFLHLDISGHLLNA-----------LFEINNEDLSVSFNDLDKLAVLNAPIT 205
Query: 194 ISDLAYLCSNEG 205
+ D+ L SN G
Sbjct: 206 LEDIQELSSNAG 217
>ref|NP_224079.1| BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE [Helicobacter pylori
J99]
Length = 340
Score = 25.0 bits (53), Expect = 3.0
Identities = 13/45 (28%), Positives = 24/45 (52%)
Query: 237 NHSQAALEKLKLINKEQGKECLPKNLHGKQQFKSTWGRLNWNKIS 281
++ QA E LK ++GK L + L ++ +++ RL K+S
Sbjct: 53 HYGQACFEGLKAYRSQKGKALLFRPLENAKRLQTSCERLLMPKVS 97
>ref|NP_223737.1| UDP-GLUCOSE 4-EPIMERASE [Helicobacter pylori J99]
Length = 344
Score = 24.6 bits (52), Expect = 4.0
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 201 CSNEGAFESDYLNPIQSSYQALMRKDSPKLYN--HQATNHSQAALEKLKLI-NKEQGKEC 257
C + D N +SY L+ K+ ++YN + + + +EK+K I NK+ E
Sbjct: 236 CIRDYIHVDDLANAHLASYHTLLEKNKSEIYNVGYNQGHSVKEVIEKVKEISNKDFLVEI 295
Query: 258 LPK 260
L K
Sbjct: 296 LDK 298
>ref|NP_223913.1| FLAGELLAR FUNCTIONAL PROTEIN [Helicobacter pylori J99]
Length = 803
Score = 24.3 bits (51), Expect = 5.2
Identities = 11/19 (57%), Positives = 13/19 (67%)
Query: 238 HSQAALEKLKLINKEQGKE 256
HS+ ALE LKL+ K Q E
Sbjct: 382 HSELALELLKLLKKNQMNE 400
>ref|NP_222768.1| putative TYPE II restriction enzyme [Helicobacter pylori J99]
Length = 260
Score = 24.3 bits (51), Expect = 5.2
Identities = 21/78 (26%), Positives = 34/78 (42%), Gaps = 3/78 (3%)
Query: 34 DKQALITFENNHKNAIGVCGDITQTEIKEKVIKLAKKLEINMIIGGPPCQGFSNKGKNLG 93
DK AL E N + +CG + + + + K ++ E N IG +NK +
Sbjct: 78 DKSAL---ERNPRTINRICGRLYEMGLNKIFEKCSEPKETNRQIGPMFKDWINNKSLGVE 134
Query: 94 LKDPRNFLFLEYIEIVKA 111
D +F+ E I+KA
Sbjct: 135 PVDLNDFIANENDAILKA 152
>ref|NP_223661.1| putative [Helicobacter pylori J99]
Length = 255
Score = 23.9 bits (50), Expect = 6.8
Identities = 24/94 (25%), Positives = 39/94 (40%), Gaps = 6/94 (6%)
Query: 229 KLYNHQATNHSQAALEKLKLINKEQGKECL-PKNLHGKQQFKSTWGRLNWNKISPTIDTR 287
+ YNH ++ EKLK+ KE KE L P N + KQ + L N+I
Sbjct: 68 RTYNHSLGIFNENIAEKLKIPKKE--KEILQPLNANEKQVLNTA---LENNEIDARTFKP 122
Query: 288 FDTPSNGTNSHPELHRSITPREAARIQSFSDNYI 321
+D S + + +++ F++N I
Sbjct: 123 WDLGSKEASKENASMSEELTQNNSKLSHFNENSI 156
>ref|NP_223414.1| putative [Helicobacter pylori J99]
Length = 417
Score = 23.9 bits (50), Expect = 6.8
Identities = 13/44 (29%), Positives = 23/44 (51%), Gaps = 4/44 (9%)
Query: 94 LKDPRNFLFLEYIEIVKAIKPEIFIIENVKNLISCAKGYFLEEI 137
L+DP L +Y+E++ P IF+ KN++ A F + +
Sbjct: 94 LQDPSRQLTQDYLEVLVIALPSIFL----KNVLVSALASFSDTL 133
>ref|NP_223274.1| putative vacuolating cytotoxin (VacA) paralog [Helicobacter pylori
J99]
Length = 3194
Score = 23.9 bits (50), Expect = 6.8
Identities = 10/28 (35%), Positives = 15/28 (52%)
Query: 141 LNALGYQLSYQILNAKDYGVPQNRERAF 168
L++L +YQ+LNAK G N +
Sbjct: 805 LSSLSVGTTYQLLNAKSVGYKDNNNALY 832
>ref|NP_223185.1| putative [Helicobacter pylori J99]
Length = 330
Score = 23.9 bits (50), Expect = 6.8
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 157 DYGVPQNRERAFIVGASRFSFDFNLLEPSQSVNVQDAISDLAYLCSNEG--AFESDYLNP 214
D+G QN++ F+ S+ S +F +E + + S A + S +G E D P
Sbjct: 60 DFGYYQNKQFLFVADKSKPSLEFYEIENNMLKKIN---SSKALVGSKKGDKTLEGDLATP 116
Query: 215 I 215
I
Sbjct: 117 I 117
>ref|NP_223357.1| putative [Helicobacter pylori J99]
Length = 342
Score = 23.5 bits (49), Expect = 8.9
Identities = 40/195 (20%), Positives = 75/195 (37%), Gaps = 25/195 (12%)
Query: 76 IIGGP-PCQGFSN---KGKNLGLKDPRNFLFLEYIEIVKAIKPEIFIIENVKNLISCAKG 131
IIG P C+GF K L DP+N +++ K +K ++ ++ +S
Sbjct: 54 IIGVPFKCEGFFKIACVSKELRFLDPQNSPIMDF----KNLKIKLHSLDKSSLTLSIHSQ 109
Query: 132 YFLEEIKERLNALGYQLSYQILNAKDYGVPQNRERAFIVGASRFSFDFNLLEPSQSVNVQ 191
+++ + Q+ + LNA + + + + + D L + ++
Sbjct: 110 IQSPILEQSIQQKISQIPLKNLNAL---LEKFKPTRLNCSLTFNALDEKTLNDNLKCDLT 166
Query: 192 DAISDLAYLCSNEGAFESDYLNPIQSSYQALMRKD--------------SPKLYNHQATN 237
+A + LAY EG E+ +++ ++ L KD +PKL
Sbjct: 167 NAENILAYTFFQEGLMEAQENLSLKNIFKTLSSKDAKAIEELQDKLRFLAPKLSVSIQAR 226
Query: 238 HSQAALEKLKLINKE 252
H + LE NKE
Sbjct: 227 HFKNVLESFYQQNKE 241
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
0.318 0.137 0.400
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 394,023
Number of Sequences: 1491
Number of extensions: 18966
Number of successful extensions: 56
Number of sequences better than 10.0: 19
Number of HSP's better than 10.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 42
Number of HSP's gapped (non-prelim): 21
length of query: 355
length of database: 494,079
effective HSP length: 79
effective length of query: 276
effective length of database: 376,290
effective search space: 103856040
effective search space used: 103856040
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)