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|15646055|ref|NP_208237.1| biopolymer transport
protein (exbD) [Helicobacter pylori 26695]
(133 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_224057.1| BIOPOLYMER TRANSPORT PROTEIN [Helicobacter... 256 1e-70
ref|NP_223977.1| BIOPOLYMER TRANSPORT EXBD PROTEIN [Helicob... 79 4e-17
ref|NP_223774.1| BIOPOLYMER TRANSPORT PROTEIN [Helicobacter... 48 1e-07
ref|NP_223150.1| putative [Helicobacter pylori J99] 27 0.25
ref|NP_223308.1| LYTIC MUREIN TRANSGLYCOSYLASE [Helicobacte... 25 0.56
ref|NP_223574.1| putative vacuolating cytotoxin (VacA) para... 25 0.96
ref|NP_222834.1| THREONYL-TRNA SYNTHETASE [Helicobacter pyl... 24 1.3
ref|NP_224042.1| putative [Helicobacter pylori J99] 24 1.6
ref|NP_223699.1| 30S RIBOSOMAL PROTEIN S1 [Helicobacter pyl... 24 1.6
ref|NP_223847.1| abc transporter, ATP-binding protein [Heli... 23 2.1
ref|NP_222964.1| EXODEOXYRIBONUCLEASE LARGE SUBUNIT [Helico... 23 3.6
ref|NP_223880.1| ALANYL-TRNA SYNTHETASE [Helicobacter pylor... 22 4.8
ref|NP_223787.1| putative [Helicobacter pylori J99] 22 4.8
ref|NP_223696.1| PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN [H... 22 4.8
ref|NP_223373.1| DNA POLYMERASE III SUBUNITS GAMMA AND TAU ... 22 4.8
ref|NP_222993.1| putative [Helicobacter pylori J99] 22 4.8
ref|NP_224121.1| DIHYDRONEOPTERIN ALDOLASE [Helicobacter py... 22 6.2
ref|NP_224012.1| PREPHENATE DEHYDROGENASE [Helicobacter pyl... 22 6.2
ref|NP_223892.1| TRYPTOPHANYL-TRNA SYNTHETASE [Helicobacter... 22 6.2
ref|NP_223859.1| putative ABC transporter, ATP-binding prot... 22 6.2
ref|NP_223655.1| putative [Helicobacter pylori J99] 22 6.2
ref|NP_223361.1| putative TRANSCRIPTIONAL REGULATOR [Helico... 22 6.2
ref|NP_224119.1| putative ferredoxin-like protein [Helicoba... 22 8.1
ref|NP_223838.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT ... 22 8.1
ref|NP_223415.1| putative [Helicobacter pylori J99] 22 8.1
ref|NP_223102.1| FLAGELLAR BIOSYNTHESIS PROTEIN [Helicobact... 22 8.1
ref|NP_222843.1| PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLAS... 22 8.1
>ref|NP_224057.1| BIOPOLYMER TRANSPORT PROTEIN [Helicobacter pylori J99]
Length = 133
Score = 256 bits (655), Expect = 1e-70
Identities = 133/133 (100%), Positives = 133/133 (100%)
Query: 1 MKKVESMNVVPFIDIMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTI 60
MKKVESMNVVPFIDIMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTI
Sbjct: 1 MKKVESMNVVPFIDIMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTI 60
Query: 61 AISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQTNNLKQ 120
AISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQTNNLKQ
Sbjct: 61 AISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQTNNLKQ 120
Query: 121 LYILVEDKKNQKN 133
LYILVEDKKNQKN
Sbjct: 121 LYILVEDKKNQKN 133
>ref|NP_223977.1| BIOPOLYMER TRANSPORT EXBD PROTEIN [Helicobacter pylori J99]
Length = 129
Score = 79.0 bits (193), Expect = 4e-17
Identities = 41/117 (35%), Positives = 69/117 (58%), Gaps = 2/117 (1%)
Query: 1 MKKVESMNVVPFIDIMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTI 60
+++ + +NVVPFIDIMLVLL IVL+ ++F+ K+ +S+P + + + D+K V I
Sbjct: 4 IRRGDGLNVVPFIDIMLVLLAIVLSISTFIAQGKIKVSLP--NAKNAEKSQPNDQKVVVI 61
Query: 61 AISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQTNN 117
++ + + DDK + E L V T I L+ DK S + FI ++D+L+ +N
Sbjct: 62 SVDEHDNIFVDDKPTNLEALSAVVKQTDPKTLIDLKSDKSSRFETFISIMDILKEHN 118
>ref|NP_223774.1| BIOPOLYMER TRANSPORT PROTEIN [Helicobacter pylori J99]
Length = 133
Score = 47.8 bits (112), Expect = 1e-07
Identities = 32/113 (28%), Positives = 57/113 (50%), Gaps = 12/113 (10%)
Query: 7 MNVVPFIDIMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTIAISNKG 66
+N+ P +D+MLVLL I++ T + T K I++P K + ++D K + I +
Sbjct: 14 LNITPLVDVMLVLLAILMVTTPTL-TYKEEIALPSGSKTARATQD----KVIEIRMDKDA 68
Query: 67 SFYFDDKEISFENLKHKVSTLA----KDTPIVLQGDKKSNLDNFIKVVDLLQT 115
Y D + + + + L+ KDT + ++ DK+ D KV+ LL+T
Sbjct: 69 KIYIDSQTYEYNSFPDTFNLLSKKYDKDTRVSIRADKRLTYD---KVIYLLKT 118
>ref|NP_223150.1| putative [Helicobacter pylori J99]
Length = 599
Score = 26.6 bits (57), Expect = 0.25
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 1 MKKVESMNVVPFIDIMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTI 60
MK + ++ V+ +D LV L + S + + +VD+ DS D+ ++ +TI
Sbjct: 1 MKNIRNIAVIAHVDHGKTTLVDGLLSQSGTFSER-----EKVDERVMDSNDLEKERGITI 55
Query: 61 AISNKGSFYFDDK 73
N +Y D K
Sbjct: 56 LSKNTAIYYKDTK 68
>ref|NP_223308.1| LYTIC MUREIN TRANSGLYCOSYLASE [Helicobacter pylori J99]
Length = 560
Score = 25.4 bits (54), Expect = 0.56
Identities = 14/49 (28%), Positives = 26/49 (52%), Gaps = 1/49 (2%)
Query: 70 FDDKEISFENLKHKVSTLAKDTPIVLQ-GDKKSNLDNFIKVVDLLQTNN 117
F E+ ++L+ K + + +D + DKK++L+N K +L Q N
Sbjct: 16 FSQTELDLKDLEKKPAGIVRDYYLWRYISDKKTSLENAKKAYELTQNKN 64
>ref|NP_223574.1| putative vacuolating cytotoxin (VacA) paralog [Helicobacter pylori
J99]
Length = 2399
Score = 24.6 bits (52), Expect = 0.96
Identities = 12/43 (27%), Positives = 25/43 (57%)
Query: 72 DKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQ 114
+K S ENLK + L++++ + + + + LDN + ++LQ
Sbjct: 1222 NKGFSSENLKTLLGILSQNSATLKEMIESNQLDNITNINEVLQ 1264
>ref|NP_222834.1| THREONYL-TRNA SYNTHETASE [Helicobacter pylori J99]
Length = 612
Score = 24.3 bits (51), Expect = 1.3
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 48 DSKDVLDKKQVTIAISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKK 100
+S VL A+ YFDD ++ E ++H + L + L D K
Sbjct: 18 ESAKVLGLSDGIKALKGTEPIYFDDSPLALEVIRHSCAHLLAQSLKALYPDAK 70
>ref|NP_224042.1| putative [Helicobacter pylori J99]
Length = 329
Score = 23.9 bits (50), Expect = 1.6
Identities = 10/13 (76%), Positives = 11/13 (83%)
Query: 106 FIKVVDLLQTNNL 118
F+KV DLLQT NL
Sbjct: 203 FVKVKDLLQTTNL 215
>ref|NP_223699.1| 30S RIBOSOMAL PROTEIN S1 [Helicobacter pylori J99]
Length = 552
Score = 23.9 bits (50), Expect = 1.6
Identities = 11/23 (47%), Positives = 13/23 (55%)
Query: 69 YFDDKEISFENLKHKVSTLAKDT 91
YF+D+E F L K TL K T
Sbjct: 9 YFNDEEEDFAKLLEKEETLEKGT 31
>ref|NP_223847.1| abc transporter, ATP-binding protein [Helicobacter pylori J99]
Length = 578
Score = 23.5 bits (49), Expect = 2.1
Identities = 12/41 (29%), Positives = 23/41 (55%)
Query: 15 IMLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDK 55
++ LLV++ +SFV+ L + +P + S S+ + DK
Sbjct: 31 MIFFLLVLMAVFSSFVEVMSLTLLMPFITLASDPSRALDDK 71
>ref|NP_222964.1| EXODEOXYRIBONUCLEASE LARGE SUBUNIT [Helicobacter pylori J99]
Length = 420
Score = 22.7 bits (47), Expect = 3.6
Identities = 17/76 (22%), Positives = 39/76 (50%), Gaps = 5/76 (6%)
Query: 35 LPISIPQVDKDSTDSKDVLDKKQVTIAISNKGSFYFDDKEISFENLKHKVSTLAKDTPIV 94
L S+ ++ ++ + L +++TIA+ NK + K + L K+ST +P +
Sbjct: 298 LAASLKRLSFENKHHLNALKLEKLTIALDNKTLEFLRLK----KTLLEKISTQLSTSPFL 353
Query: 95 -LQGDKKSNLDNFIKV 109
+ ++ + L+N +K+
Sbjct: 354 QTKTERLNRLENALKL 369
>ref|NP_223880.1| ALANYL-TRNA SYNTHETASE [Helicobacter pylori J99]
Length = 847
Score = 22.3 bits (46), Expect = 4.8
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 66 GSFYFDDKEISFENLKHKVSTLAKDTPIVLQ-----GDKKSNLDNFIKVVDLLQTNNLKQ 120
G F D KEI+ N +V L + TP + GD+ + + + +L T N
Sbjct: 462 GFFDSDFKEITEANPNQEVWVLLEKTPFYAEGGGAIGDRGTLFKDNEEAALVLDTKNFFG 521
Query: 121 L-YILVEDKKNQK 132
L + L+E KK K
Sbjct: 522 LNFSLLEIKKALK 534
>ref|NP_223787.1| putative [Helicobacter pylori J99]
Length = 759
Score = 22.3 bits (46), Expect = 4.8
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 54 DKKQVTIA-----ISNKGSFYFDDKEISFENLK 81
DK+Q ++ IS K FD+ SFENLK
Sbjct: 10 DKQQQNVSSGISQISLKKVATFDENGASFENLK 42
>ref|NP_223696.1| PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN [Helicobacter pylori J99]
Length = 764
Score = 22.3 bits (46), Expect = 4.8
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 62 ISNKGSFYFDDKEISFENLKHK 83
+S+K S D FENLKHK
Sbjct: 461 VSSKNSNPHYDTHRFFENLKHK 482
>ref|NP_223373.1| DNA POLYMERASE III SUBUNITS GAMMA AND TAU [Helicobacter pylori J99]
Length = 582
Score = 22.3 bits (46), Expect = 4.8
Identities = 15/67 (22%), Positives = 29/67 (42%)
Query: 21 VIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQVTIAISNKGSFYFDDKEISFENL 80
++ L F Q+ + + P+ + ST+ + +K + I + K+ F NL
Sbjct: 344 IVELEQTPFNQSPSISYNAPKQEPKSTERIEGREKLEKRERIETPQTPMLSAKDRIFHNL 403
Query: 81 KHKVSTL 87
+V TL
Sbjct: 404 FKQVQTL 410
>ref|NP_222993.1| putative [Helicobacter pylori J99]
Length = 172
Score = 22.3 bits (46), Expect = 4.8
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 80 LKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDL 112
L HK + + Q D +S +DNF K V L
Sbjct: 62 LAHKSLAFKRLQLFLFQKDPQSYMDNFYKEVGL 94
>ref|NP_224121.1| DIHYDRONEOPTERIN ALDOLASE [Helicobacter pylori J99]
Length = 117
Score = 21.9 bits (45), Expect = 6.2
Identities = 13/53 (24%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 75 ISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQTNNLKQLYILVED 127
+ FE LK + ++ D + K+ LD ++++ +++Q ++ Y+L+ED
Sbjct: 21 LEFERLKPQKISVDLDL-FYTELPNKAYLD-YMEIQEIIQNTMREKQYLLIED 71
>ref|NP_224012.1| PREPHENATE DEHYDROGENASE [Helicobacter pylori J99]
Length = 275
Score = 21.9 bits (45), Expect = 6.2
Identities = 8/28 (28%), Positives = 18/28 (63%)
Query: 84 VSTLAKDTPIVLQGDKKSNLDNFIKVVD 111
+S L+K +P++ + K N DN ++ ++
Sbjct: 213 MSRLSKSSPLMWKDIFKQNRDNVLEAIE 240
>ref|NP_223892.1| TRYPTOPHANYL-TRNA SYNTHETASE [Helicobacter pylori J99]
Length = 326
Score = 21.9 bits (45), Expect = 6.2
Identities = 13/45 (28%), Positives = 20/45 (43%)
Query: 48 DSKDVLDKKQVTIAISNKGSFYFDDKEISFENLKHKVSTLAKDTP 92
D DV+ KK A + G FD+ NL + L+ ++P
Sbjct: 211 DEPDVIVKKIKKAATDSMGVIAFDETREGVFNLLNIYMLLSDESP 255
>ref|NP_223859.1| putative ABC transporter, ATP-binding protein [Helicobacter pylori
J99]
Length = 228
Score = 21.9 bits (45), Expect = 6.2
Identities = 10/39 (25%), Positives = 20/39 (50%)
Query: 38 SIPQVDKDSTDSKDVLDKKQVTIAISNKGSFYFDDKEIS 76
S+P + SK + +K Q+ + +S S Y D+ ++
Sbjct: 116 SVPLKREFKALSKGMREKLQLILTLSRNASLYLFDEPVA 154
>ref|NP_223655.1| putative [Helicobacter pylori J99]
Length = 416
Score = 21.9 bits (45), Expect = 6.2
Identities = 9/16 (56%), Positives = 12/16 (74%)
Query: 100 KSNLDNFIKVVDLLQT 115
K LD F+K +D+LQT
Sbjct: 240 KDKLDPFLKRLDVLQT 255
>ref|NP_223361.1| putative TRANSCRIPTIONAL REGULATOR [Helicobacter pylori J99]
Length = 381
Score = 21.9 bits (45), Expect = 6.2
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 63 SNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKS 101
+NKG+ + D+ L+ K+ + ++ I GD KS
Sbjct: 227 ANKGTIFLDEIAEMPLQLQSKLLRVVQEKEITRLGDNKS 265
>ref|NP_224119.1| putative ferredoxin-like protein [Helicobacter pylori J99]
Length = 458
Score = 21.6 bits (44), Expect = 8.1
Identities = 7/23 (30%), Positives = 16/23 (69%)
Query: 5 ESMNVVPFIDIMLVLLVIVLTTA 27
E + ++PF+ I+L + + +TT+
Sbjct: 60 EELQILPFMVILLFIGIFFITTS 82
>ref|NP_223838.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT [Helicobacter pylori J99]
Length = 2890
Score = 21.6 bits (44), Expect = 8.1
Identities = 10/28 (35%), Positives = 13/28 (45%)
Query: 67 SFYFDDKEISFENLKHKVSTLAKDTPIV 94
S + +KE+ LKH V D P V
Sbjct: 840 STHIYEKEVDARELKHGVEEFTADIPDV 867
>ref|NP_223415.1| putative [Helicobacter pylori J99]
Length = 529
Score = 21.6 bits (44), Expect = 8.1
Identities = 15/58 (25%), Positives = 29/58 (49%), Gaps = 1/58 (1%)
Query: 69 YFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVVDLLQTNNLKQLYILVE 126
+FD KE ++L+ + +D L+ +KK L+ ++++ + N KQ I E
Sbjct: 85 HFDKKEAHLKHLEAQHKEFVRDEKRYLEKEKK-ELEKERQILEQERENFKKQRAICKE 141
>ref|NP_223102.1| FLAGELLAR BIOSYNTHESIS PROTEIN [Helicobacter pylori J99]
Length = 733
Score = 21.6 bits (44), Expect = 8.1
Identities = 9/26 (34%), Positives = 16/26 (60%)
Query: 75 ISFENLKHKVSTLAKDTPIVLQGDKK 100
I+ + +K + LAKD P +++ KK
Sbjct: 539 ITKDEVKSLLERLAKDYPTIVEESKK 564
>ref|NP_222843.1| PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE [Helicobacter pylori
J99]
Length = 449
Score = 21.6 bits (44), Expect = 8.1
Identities = 11/43 (25%), Positives = 24/43 (55%)
Query: 16 MLVLLVIVLTTASFVQTSKLPISIPQVDKDSTDSKDVLDKKQV 58
+++ + IVLT A + K+ Q K +++ ++LD ++V
Sbjct: 88 VMMQMAIVLTFAGSIPIVKVGRIAGQFAKPRSNATEILDDEEV 130
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
0.315 0.134 0.348
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 140,734
Number of Sequences: 1491
Number of extensions: 6400
Number of successful extensions: 38
Number of sequences better than 10.0: 27
Number of HSP's better than 10.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 12
Number of HSP's gapped (non-prelim): 28
length of query: 133
length of database: 494,079
effective HSP length: 69
effective length of query: 64
effective length of database: 391,200
effective search space: 25036800
effective search space used: 25036800
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 44 (21.6 bits)