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|15646089|ref|NP_208271.1| seryl-tRNA synthetase
(serS) [Helicobacter pylori 26695]
(415 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1SES|A Chain A, Seryl-Trna Synthetase (E.C.6.1.1.11) (S... 235 6e-63
pdb|1B8A|A Chain A, Aspartyl-Trna Synthetase >gi|4388837|pd... 33 0.045
pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyos... 33 0.077
pdb|1QF6|A Chain A, Structure Of E. Coli Threonyl-Trna Synt... 28 1.5
pdb|1KOG|A Chain A, Crystal Structure Of E. Coli Threonyl-T... 28 1.5
pdb|1BUI|A Chain A, Structure Of The Ternary Microplasmin-S... 26 7.2
pdb|1DDJ|A Chain A, Crystal Structure Of Human Plasminogen ... 26 7.2
pdb|1QRZ|A Chain A, Catalytic Domain Of Plasminogen >gi|643... 26 7.2
pdb|1BML|A Chain A, Complex Of The Catalytic Domain Of Huma... 26 7.2
>pdb|1SES|A Chain A, Seryl-Trna Synthetase (E.C.6.1.1.11) (Serine-Trna Ligase)
Complexed With Seryl-Hydroxamate-Amp
pdb|1SES|B Chain B, Seryl-Trna Synthetase (E.C.6.1.1.11) (Serine-Trna Ligase)
Complexed With Seryl-Hydroxamate-Amp
pdb|1SET|A Chain A, Seryl-Trna Synthetase (E.C.6.1.1.11) (Serine-Trna Ligase)
Complexed With 5'-O-[n-(L-Seryl)-Sulphamoyl]adenosine
pdb|1SET|B Chain B, Seryl-Trna Synthetase (E.C.6.1.1.11) (Serine-Trna Ligase)
Complexed With 5'-O-[n-(L-Seryl)-Sulphamoyl]adenosine
pdb|1SRY|A Chain A, Seryl-Trna Synthetase (E.C.6.1.1.11)
pdb|1SRY|B Chain B, Seryl-Trna Synthetase (E.C.6.1.1.11)
pdb|1SER|B Chain B, Seryl-Trna Synthetase (E.C.6.1.1.11) Complexed With
Trna-Ser 2 (Gga Anticodon)
pdb|1SER|A Chain A, Seryl-Trna Synthetase (E.C.6.1.1.11) Complexed With
Trna-Ser 2 (Gga Anticodon)
Length = 421
Score = 235 bits (600), Expect = 6e-63
Identities = 148/419 (35%), Positives = 237/419 (56%), Gaps = 11/419 (2%)
Query: 1 MIDRKLLLQDFDKVALSLKKRNNAMDDE-LERLREVITHYKKRLIELEGLQAFQNKVSKE 59
M+D K L Q+ + +++++ A+D E L L + KKRL E+ Q +N+V+K
Sbjct: 1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEV---QTERNQVAKR 57
Query: 60 FGIKMAQKVDTSDLKKELENNKIKLNELSKSVGELEQQIDLKLSIIPNLVDEKTPLGTNE 119
++ + + + + K L +++ E E +++ L +P P+G E
Sbjct: 58 VPKAPPEEKEALIARGKALGEEAK--RLEEALREKEARLEALLLQVPLPPWPGAPVG-GE 114
Query: 120 EDNIEIKKILTPRVFTFKPKEHFELAQQNGWIDFESGVKLAKSRFSVIRGFGAKIYRALI 179
E N EIK++ P F+F P +H L ++NGW + +++ SR ++G A AL+
Sbjct: 115 EANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRIS-QVSGSRSYALKGDLALYELALL 173
Query: 180 HLMLDFNEKNGFEIIYTPALVNEKMLFGTGQLPKFKEDVFKIENENLYLIPTAEVTLTNL 239
+DF + GF + P+ EK GTG P +++ V+ I +LYL TAEV L L
Sbjct: 174 RFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNAL 233
Query: 240 YNDTIISVENLPIKMTAHTPCFRSEAGSAGKDTRGMIRQHQFDKVELVAITHP--KESDV 297
++ I+ E LP++ + P FRSEAGS GKD RG++R HQF KVE +T + SD
Sbjct: 234 HSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDR 293
Query: 298 MQEHMLESASEILKALELPHRFVQLCSGDLGFSASNTIDIEVWLPGQNCYREISSVSNTR 357
+ +LE+A EIL+ LELP+R V++ +GD+G +DIEV+LP + YRE S S
Sbjct: 294 AFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALL 353
Query: 358 DFQARRAKIRFKENQ-KNQLAHTLNGSSLAVGRTMVALMENHQQADGSIHIPKALEKYL 415
D+QARRA +R+++ + + + A+TLN ++LA R + L+ENHQ DG + +P+AL Y+
Sbjct: 354 DWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYM 412
>pdb|1B8A|A Chain A, Aspartyl-Trna Synthetase
pdb|1B8A|B Chain B, Aspartyl-Trna Synthetase
Length = 438
Score = 33.5 bits (75), Expect = 0.045
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 173 KIYRALIHLMLDFNEKNGFEIIYTPALVNEKMLFGTGQLPK--FKEDVFKIENENLY 227
KI ++ + DF +NGF I+TP ++ GT P F+ED F E+ LY
Sbjct: 138 KIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAESPQLY 194
>pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment.
pdb|1I84|V Chain V, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment
Length = 1184
Score = 32.7 bits (73), Expect = 0.077
Identities = 22/110 (20%), Positives = 58/110 (52%), Gaps = 8/110 (7%)
Query: 9 QDFDKVALSLKKRNNAMDDELERLREVITHYKKRLIELE-----GLQAFQNKVS-KEFGI 62
Q+ +K+ L+ ++ + +++ L+ I K +L + E L +++ S K +
Sbjct: 1056 QELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNAL 1115
Query: 63 KMAQKVDT--SDLKKELENNKIKLNELSKSVGELEQQIDLKLSIIPNLVD 110
K +++++ SDL+++LE+ K N+ K +L ++++ + + + +D
Sbjct: 1116 KKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTELEDTLD 1165
>pdb|1QF6|A Chain A, Structure Of E. Coli Threonyl-Trna Synthetase Complexed
With Its Cognate Trna
Length = 642
Score = 28.5 bits (62), Expect = 1.5
Identities = 25/113 (22%), Positives = 50/113 (44%), Gaps = 5/113 (4%)
Query: 171 GAKIYRALIHLMLDFNEKNGFEIIYTPALVNEKMLFGTGQLPKFKEDVFKIENENL-YLI 229
G I+R L + ++ ++ + P +++ + TG +K+ +F +EN Y I
Sbjct: 270 GWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSSENREYCI 329
Query: 230 -PTAEVTLTNLYNDTIISVENLPIKMTAHTPCFRSEAGSAGKDTRGMIRQHQF 281
P ++N + S +LP++M C R+E + G++R F
Sbjct: 330 KPMNCPGHVQIFNQGLKSYRDLPLRMAEFGSCHRNEPSGS---LHGLMRVRGF 379
>pdb|1KOG|A Chain A, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|B Chain B, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|C Chain C, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|D Chain D, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|E Chain E, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|F Chain F, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|G Chain G, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|H Chain H, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1EVK|A Chain A, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With The Ligand Threonine
pdb|1EVK|B Chain B, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With The Ligand Threonine
pdb|1EVL|B Chain B, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1EVL|C Chain C, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1FYF|B Chain B, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase Complexed With A Seryl Adenylate Analog
pdb|1EVL|A Chain A, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1FYF|A Chain A, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase Complexed With A Seryl Adenylate Analog
pdb|1EVL|D Chain D, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
Length = 401
Score = 28.5 bits (62), Expect = 1.5
Identities = 25/113 (22%), Positives = 50/113 (44%), Gaps = 5/113 (4%)
Query: 171 GAKIYRALIHLMLDFNEKNGFEIIYTPALVNEKMLFGTGQLPKFKEDVFKIENENL-YLI 229
G I+R L + ++ ++ + P +++ + TG +K+ +F +EN Y I
Sbjct: 29 GWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSSENREYCI 88
Query: 230 -PTAEVTLTNLYNDTIISVENLPIKMTAHTPCFRSEAGSAGKDTRGMIRQHQF 281
P ++N + S +LP++M C R+E + G++R F
Sbjct: 89 KPMNCPGHVQIFNQGLKSYRDLPLRMAEFGSCHRNEPSGS---LHGLMRVRGF 138
>pdb|1BUI|A Chain A, Structure Of The Ternary Microplasmin-Staphylokinase-
Microplasmin Complex: A Proteinase-Cofactor-Substrate
Complex In Action.
pdb|1BUI|B Chain B, Structure Of The Ternary Microplasmin-Staphylokinase-
Microplasmin Complex: A Proteinase-Cofactor-Substrate
Complex In Action
Length = 250
Score = 26.2 bits (56), Expect = 7.2
Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 9/99 (9%)
Query: 196 TPALVNEKMLFGTGQLPKFKEDVFKIENENLYLIPT-AEVTLTNLYNDTIISVENLPIKM 254
+P + K++ G Q + V +IE L+L PT ++ L L + +I+ + +P +
Sbjct: 67 SPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACL 126
Query: 255 TA-------HTPCFRSEAG-SAGKDTRGMIRQHQFDKVE 285
+ T CF + G + G G++++ Q +E
Sbjct: 127 PSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIE 165
>pdb|1DDJ|A Chain A, Crystal Structure Of Human Plasminogen Catalytic Domain
pdb|1DDJ|B Chain B, Crystal Structure Of Human Plasminogen Catalytic Domain
pdb|1DDJ|C Chain C, Crystal Structure Of Human Plasminogen Catalytic Domain
pdb|1DDJ|D Chain D, Crystal Structure Of Human Plasminogen Catalytic Domain
Length = 247
Score = 26.2 bits (56), Expect = 7.2
Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 9/99 (9%)
Query: 196 TPALVNEKMLFGTGQLPKFKEDVFKIENENLYLIPT-AEVTLTNLYNDTIISVENLPIKM 254
+P + K++ G Q + V +IE L+L PT ++ L L + +I+ + +P +
Sbjct: 64 SPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACL 123
Query: 255 TA-------HTPCFRSEAG-SAGKDTRGMIRQHQFDKVE 285
+ T CF + G + G G++++ Q +E
Sbjct: 124 PSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIE 162
>pdb|1QRZ|A Chain A, Catalytic Domain Of Plasminogen
pdb|1QRZ|B Chain B, Catalytic Domain Of Plasminogen
pdb|1QRZ|C Chain C, Catalytic Domain Of Plasminogen
pdb|1QRZ|D Chain D, Catalytic Domain Of Plasminogen
Length = 246
Score = 26.2 bits (56), Expect = 7.2
Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 9/99 (9%)
Query: 196 TPALVNEKMLFGTGQLPKFKEDVFKIENENLYLIPT-AEVTLTNLYNDTIISVENLPIKM 254
+P + K++ G Q + V +IE L+L PT ++ L L + +I+ + +P +
Sbjct: 63 SPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACL 122
Query: 255 TA-------HTPCFRSEAG-SAGKDTRGMIRQHQFDKVE 285
+ T CF + G + G G++++ Q +E
Sbjct: 123 PSPNYMVADRTECFITGWGETQGTFGAGLLKEAQLPVIE 161
>pdb|1BML|A Chain A, Complex Of The Catalytic Domain Of Human Plasmin And
Streptokinase
pdb|1BML|B Chain B, Complex Of The Catalytic Domain Of Human Plasmin And
Streptokinase
Length = 250
Score = 26.2 bits (56), Expect = 7.2
Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 9/99 (9%)
Query: 196 TPALVNEKMLFGTGQLPKFKEDVFKIENENLYLIPT-AEVTLTNLYNDTIISVENLPIKM 254
+P + K++ G Q + V +IE L+L PT ++ L L + +I+ + +P +
Sbjct: 67 SPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACL 126
Query: 255 TA-------HTPCFRSEAG-SAGKDTRGMIRQHQFDKVE 285
+ T CF + G + G G++++ Q +E
Sbjct: 127 PSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIE 165
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.317 0.135 0.374
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,252,021
Number of Sequences: 13198
Number of extensions: 90764
Number of successful extensions: 189
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 184
Number of HSP's gapped (non-prelim): 10
length of query: 415
length of database: 2,899,336
effective HSP length: 91
effective length of query: 324
effective length of database: 1,698,318
effective search space: 550255032
effective search space used: 550255032
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: 55 (25.8 bits)