BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14581
(124 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 94.0 bits (232), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 43/61 (70%), Positives = 52/61 (85%)
Query: 37 VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96
V + K VWEI+GAEFS++E HTADGISIRFPR T+IRDDKDWK+ATNLP+LK L++ S
Sbjct: 519 VPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLS 578
Query: 97 K 97
K
Sbjct: 579 K 579
Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 28/35 (80%), Positives = 30/35 (85%)
Query: 8 YSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKA 42
+SEIKYDGERVQVHK G+ F YFSRSLKPVL HK
Sbjct: 250 FSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKV 284
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To
5'-Adenylated, Nicked Dna
Length = 688
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 45 VWEISGAEFSQAEIHTAD--------GISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96
VWE+ A+ S + I+ A GIS+RFPR ++R+DK + AT ++ L++K
Sbjct: 610 VWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQ 669
Query: 97 KETSD 101
+ +
Sbjct: 670 SQIQN 674
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 10 EIKYDGERVQVHK-KGNEFKYFSRS 33
E KYDG+R Q+H +G E K FSR+
Sbjct: 335 EYKYDGQRAQIHALEGGEVKIFSRN 359
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
Length = 571
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/28 (64%), Positives = 21/28 (75%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
EIKYDG RVQVHK GN+ +SR L+ V
Sbjct: 259 EIKYDGARVQVHKNGNKVLIYSRRLENV 286
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 48/99 (48%), Gaps = 19/99 (19%)
Query: 7 CYSEIKYDGERVQVHKKGNEFK-----YFSRSLKPVL--------EHKAQPVWEISGAEF 53
Y +K G+ V V K G+ F F++ LKP++ E + + V E++ E
Sbjct: 465 AYDPVK--GDFVPVGKVGSGFTDEDLVEFTKMLKPLIKKEHGKEVELEPKVVIEVAYQEI 522
Query: 54 SQAEIHTADGISIRFPRVTKIRDDK---DWKTATNLPEL 89
++ + + G ++RFPR +R+DK D T L EL
Sbjct: 523 QKSPKYES-GFALRFPRYIALREDKGPEDADTVQRLAEL 560
>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The
Nucleotidyltransferase (Adenylation) Domain Of Human
Dna Ligase Iv
Length = 139
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/26 (61%), Positives = 21/26 (80%)
Query: 8 YSEIKYDGERVQVHKKGNEFKYFSRS 33
Y E K DGER+Q+HK G+ +KYFSR+
Sbjct: 2 YIETKLDGERMQMHKDGDVYKYFSRN 27
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus
pdb|2HIX|A Chain A, Atp Dependent Dna Ligase From S. Solfataricus Bound To Atp
Length = 621
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 10/64 (15%)
Query: 42 AQPVW--EISGAEFSQAEIHTA--------DGISIRFPRVTKIRDDKDWKTATNLPELKV 91
+PV+ EI G+E + + +HT G+SIRFPR + RDDK + AT E+
Sbjct: 543 VEPVYVAEIIGSEITISPLHTCCQDVVEKDAGLSIRFPRFIRWRDDKSPEDATTTDEILE 602
Query: 92 LFKK 95
++ K
Sbjct: 603 MYNK 606
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 12 KYDGERVQVHKKGNEFKYFSRSLKPV 37
KYDGER Q+HKK ++ FSR L+ +
Sbjct: 280 KYDGERAQIHKKEDKIFIFSRRLENI 305
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus
Length = 561
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/28 (60%), Positives = 21/28 (75%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
EIKYDG RVQVHK G++ +SR L+ V
Sbjct: 247 EIKYDGARVQVHKDGSKIIVYSRRLENV 274
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 49/93 (52%), Gaps = 14/93 (15%)
Query: 15 GERVQVHKKGNEFK-----YFSRSLKP-VLEHKAQPVW-------EISGAEFSQAEIHTA 61
GE ++V K G+ F F++ LKP +++ + + VW E++ E ++ + +
Sbjct: 459 GEFLEVGKVGSGFTDDDLVEFTKXLKPLIIKEEGKRVWLQPKVVIEVTYQEIQKSPKYRS 518
Query: 62 DGISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94
G ++RFPR +RDDK + A + + L++
Sbjct: 519 -GFALRFPRFVALRDDKGPEDADTIERIAQLYE 550
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
EIKYDG RVQVH+ G+ +SR L+ V
Sbjct: 258 EIKYDGARVQVHRDGDRVIIYSRRLENV 285
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 12/92 (13%)
Query: 15 GERVQVHKKGNEFK-----YFSRSLKPVLEHKAQPVWEISG---AEFSQAEIHTA----D 62
GE + V K G+ F F++ LKP++ + EI E + EI +
Sbjct: 470 GEFLPVGKVGSGFTDEDLVEFTKMLKPLILREEGKFVEIEPKVVIEVTYQEIQKSPKYRS 529
Query: 63 GISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94
G ++RFPR +R+DK + A + + L++
Sbjct: 530 GFALRFPRYVALREDKSPEEADTIERIAQLYE 561
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From
Archaeoglobus Fulgidus
Length = 558
Score = 32.3 bits (72), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 63 GISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94
G ++RFPR ++RDDKD A + ++ L+K
Sbjct: 519 GYALRFPRFVRLRDDKDVDEADTIERVENLYK 550
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEI 48
E K+DG RVQVH G+ +SR L+ V V EI
Sbjct: 250 EWKFDGSRVQVHWDGSRVTIYSRRLENVTNALPDIVEEI 288
>pdb|2V42|A Chain A, Crystal Structure Of Rseb: A Sensor For Periplasmic
Stress Response In E. Coli
pdb|2V42|B Chain B, Crystal Structure Of Rseb: A Sensor For Periplasmic
Stress Response In E. Coli
pdb|2V43|C Chain C, Crystal Structure Of Rseb: A Sensor For Periplasmic
Stress Response In E. Coli
pdb|2V43|A Chain A, Crystal Structure Of Rseb: A Sensor For Periplasmic
Stress Response In E. Coli
pdb|2V43|B Chain B, Crystal Structure Of Rseb: A Sensor For Periplasmic
Stress Response In E. Coli
Length = 303
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 11 IKYDGERVQVHKKGNEFKYFSRSLKP 36
++ DG R +V ++GNE YF L+P
Sbjct: 53 LQMDGPRREVVQRGNEISYFEPGLEP 78
>pdb|2P4B|A Chain A, Crystal Structure Of E.Coli Rseb
pdb|2P4B|B Chain B, Crystal Structure Of E.Coli Rseb
pdb|2P4B|C Chain C, Crystal Structure Of E.Coli Rseb
pdb|3M4W|A Chain A, Structural Basis For The Negative Regulation Of
Bacterial Stress Response By Rseb
pdb|3M4W|B Chain B, Structural Basis For The Negative Regulation Of
Bacterial Stress Response By Rseb
pdb|3M4W|C Chain C, Structural Basis For The Negative Regulation Of
Bacterial Stress Response By Rseb
pdb|3M4W|D Chain D, Structural Basis For The Negative Regulation Of
Bacterial Stress Response By Rseb
Length = 295
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 11 IKYDGERVQVHKKGNEFKYFSRSLKP 36
++ DG R +V ++GNE YF L+P
Sbjct: 51 LQMDGPRREVVQRGNEISYFEPGLEP 76
>pdb|1R6V|A Chain A, Crystal Structure Of Fervidolysin From Fervidobacterium
Pennivorans, A Keratinolytic Enzyme Related To
Subtilisin
Length = 671
Score = 28.9 bits (63), Expect = 0.75, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 47 EISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKP 106
E+ E+++ +I G + R V KI + K LP++KV+ S + + T+K
Sbjct: 23 ELRDGEYTEGKILV--GYNDR-SEVDKIVKAVNGKVVLELPQIKVV---SIKLNGMTVKQ 76
Query: 107 KYDRIKNLKLQKARCI 122
YD+IK L L+ R +
Sbjct: 77 AYDKIKALALKGIRYV 92
>pdb|1QU2|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
Structure With Trna(Ile) And Mupirocin
pdb|1QU3|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
Structure With Trna(Ile) And Mupirocin
pdb|1FFY|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
Structure With Trna(Ile) And Mupirocin
Length = 917
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 30 FSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRD---DKDWKTATNL 86
++ L P+L H A+ VW + + +H AD P+V ++ DK W+T NL
Sbjct: 752 MTKLLAPILVHTAEEVWSHT-PHVKEESVHLAD-----MPKVVEVDQALLDK-WRTFMNL 804
>pdb|4FYE|A Chain A, Crystal Structure Of A Legionella Phosphoinositide
Phosphatase, Sidf
pdb|4FYF|A Chain A, Structural Basis For Substrate Recognition By A Novel
Legionella Phosphoinositide Phosphatase
pdb|4FYG|A Chain A, Structural Basis For Substrate Recognition By A Novel
Legionella Phosphoinositide Phosphatase
Length = 761
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 7 CYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISI 66
CY+++ G+RV + +F+Y + + KA+ + S E+ TA G
Sbjct: 357 CYTQVVTAGQRVAAENQKEQFEYVRQMMDAFDGSKAKITIQTG----SNTEVETAVGYQA 412
Query: 67 RF 68
R
Sbjct: 413 RM 414
>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase
I At 1.5 Angstrom Resolution
pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase
I At 1.5 Angstrom Resolution
Length = 264
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 11 IKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPR 70
I+YDG + ++ NE + L+ L A + A + A +H G + F
Sbjct: 10 IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVH-GTGQVVHF-E 67
Query: 71 VTKIRDDKDWKTATN 85
T +R D W N
Sbjct: 68 TTALRKDAAWTLGVN 82
>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
Length = 270
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 11 IKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPR 70
I+YDG + ++ NE + L+ L A + A + A +H G + F
Sbjct: 16 IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVH-GTGQVVHF-E 73
Query: 71 VTKIRDDKDWKTATN 85
T +R D W N
Sbjct: 74 TTALRKDAAWTLGVN 88
>pdb|2E5A|A Chain A, Crystal Structure Of Bovine Lipoyltransferase In Complex
With Lipoyl-Amp
pdb|3A7U|A Chain A, Crystal Structure Of The Bovine Lipoyltransferase In Its
Unliganded Form
Length = 347
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 102 FTLKPKYDRIKNLKL 116
FT K KYDR++NLKL
Sbjct: 92 FTTKKKYDRMENLKL 106
>pdb|3MX3|A Chain A, Crystal Structure Of A Susd Homolog (Bf0972) From
Bacteroides Fragilis Nctc 9343 At 2.00 A Resolution
pdb|3MX3|B Chain B, Crystal Structure Of A Susd Homolog (Bf0972) From
Bacteroides Fragilis Nctc 9343 At 2.00 A Resolution
Length = 490
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 17/28 (60%)
Query: 80 WKTATNLPELKVLFKKSKETSDFTLKPK 107
WK AT +LKVL SK+ SD LK K
Sbjct: 174 WKKATTAFQLKVLXHLSKKESDADLKVK 201
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,693,134
Number of Sequences: 62578
Number of extensions: 133555
Number of successful extensions: 399
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 380
Number of HSP's gapped (non-prelim): 27
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)