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= 042084
(1124 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HG6|A Chain A, Structure Of A Cellulose Synthase - Cellulose
Translocation Intermediate
Length = 802
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 52/108 (48%), Gaps = 4/108 (3%)
Query: 817 GWIYGSVTEDVVTGYRMHNRGWHSVYCVTKRDAFRGSAPINLTDRLHQVLRWATGSVEIF 876
G+ ++TED T +H+RGW S+Y R G P + Q RWATG +++
Sbjct: 334 GFAGETITEDAETALEIHSRGWKSLYI--DRAMIAGLQPETFASFIQQRGRWATGMMQML 391
Query: 877 FSRNNAFLASRKLKLLQRLAYLNVGIYPFTSLFLIVYCFLPALSLISG 924
+N F R L + QRL YLN + F L +++ P + L G
Sbjct: 392 LLKNPLF--RRGLGIAQRLCYLNSMSFWFFPLVRMMFLVAPLIYLFFG 437
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 42/153 (27%), Positives = 60/153 (39%), Gaps = 19/153 (12%)
Query: 563 SPDPLMGSADDDKLIDFTDVDIRLPLFVYMSREKRPGYEHNKKAGAMNALVRASAILSNG 622
SPDP + ++ + + L + VY +RE+ EH K AL R G
Sbjct: 189 SPDPELAQKAQERRRELQQLCRELGV-VYSTRERN---EHAKAGNMSAALERL-----KG 239
Query: 623 PFILNLDCDHYIYNCKAIREGMCFMMDKGGEDICYIQFPQRFEGIDP-------SDRYAN 675
++ D DH R F+ D D+ +Q P F DP DR
Sbjct: 240 ELVVVFDADHVPSRDFLARTVGYFVEDP---DLFLVQTPHFFINPDPIQRNLALGDRCPP 296
Query: 676 NNTVFFDGNMRALDGLQGPFYVGTGTMFRRFAL 708
N +F+ R LD G F+ G+ + RR AL
Sbjct: 297 ENEMFYGKIHRGLDRWGGAFFCGSAAVLRRRAL 329
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 42.7 bits (99), Expect = 0.001, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 150 DIIPCECRFKICRDCYMDAQKD-TGLCPGCKEPY 182
+ PC C ++ICR C+ + D GLCP C++PY
Sbjct: 16 NFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 42.4 bits (98), Expect = 0.002, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 150 DIIPCECRFKICRDCYMDAQKD-TGLCPGCKEPY 182
+ PC C ++ICR C+ + D GLCP C++PY
Sbjct: 27 NFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 60
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 40.0 bits (92), Expect = 0.007, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 114 KVIESQVNHPQMAGAKGSSCGMPAC-DGKAMKDERGNDIIPCECRFKICRDCYMDAQKDT 172
K I + HP G+ SC P C DG + + G I+ EC C C D+ K+
Sbjct: 56 KKINHKRYHPIYIGSGTVSC--PICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA 113
Query: 173 GLCPGCKE 180
CP C++
Sbjct: 114 NTCPTCRK 121
Score = 36.6 bits (83), Expect = 0.092, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 127 GAKGS-SCGMPAC-DGKAMKDERGNDIIPCECRFKICRDCYMDAQKDTGLCPGCKE 180
GA GS + P C DG + + G I+ EC C C D+ K+ CP C++
Sbjct: 1 GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 56
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 35.0 bits (79), Expect = 0.21, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 130 GSSCGMPAC-DGKAMKDERGNDIIPCECRFKICRDCYMDAQKDTGLCPGCKE 180
G+ P C DG + + G I+ EC C C D+ K+ CP C++
Sbjct: 1 GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 52
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 34.3 bits (77), Expect = 0.38, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 132 SCGMPAC-DGKAMKDERGNDIIPCECRFKICRDCYMDAQKDTGLCPGCKE 180
SC P C DG + + G I+ EC C C D+ K+ CP C++
Sbjct: 12 SC--PICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 59
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 34.3 bits (77), Expect = 0.38, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 132 SCGMPAC-DGKAMKDERGNDIIPCECRFKICRDCYMDAQKDTGLCPGCKE 180
SC P C DG + + G I+ EC C C D+ K+ CP C++
Sbjct: 17 SC--PICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 64
>pdb|1WEO|A Chain A, Solution Structure Of Ring-Finger In The Catalytic Subunit
(Irx3) Of Cellulose Synthase
Length = 93
Score = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 148 GNDIIPC-ECRFKICRDCY-MDAQKDTGLCPGCKEPYK 183
G+ + C EC F CR CY + ++ T CP CK YK
Sbjct: 32 GDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK 69
>pdb|1FWR|A Chain A, Crystal Structure Of Kdpg Aldolase Double Mutant
K133qT161K
pdb|1FWR|B Chain B, Crystal Structure Of Kdpg Aldolase Double Mutant
K133qT161K
pdb|1FWR|C Chain C, Crystal Structure Of Kdpg Aldolase Double Mutant
K133qT161K
Length = 213
Score = 31.6 bits (70), Expect = 2.4, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 370 PGIDMYVSTADPEKEPPLTTANTILS--ILAVDYPVEKLACYVSDDGGALLTFEAMAEAA 427
PG+ + A E PL + +S +L +DY +++ + ++ G + +A+A
Sbjct: 94 PGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFQFFPAEANGGVKALQAIAGPF 153
Query: 428 SFADLWVPFCRKHNIEPRNPDSYFSLK 454
S V FC K I P N Y +LK
Sbjct: 154 S----QVRFCPKGGISPANYRDYLALK 176
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 359 SPSNPTGRSDLPGIDMYVSTADPEKEPPLTTANTILSILAVDYPVEKLACYVSDDGGALL 418
+ + GRS L G+ V +EPPL A+ + I + Y E L YVS G +L
Sbjct: 965 AETRERGRSGLVGLFAEV------EEPPLVEASPLDEITMLRYEKEALGIYVS--GHPVL 1016
Query: 419 TFEAMAEAAS 428
+ + E AS
Sbjct: 1017 RYPGLREVAS 1026
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
Length = 1220
Score = 30.4 bits (67), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 359 SPSNPTGRSDLPGIDMYVSTADPEKEPPLTTANTILSILAVDYPVEKLACYVSDDGGALL 418
+ + GRS L G+ V +EPPL A+ + I + Y E L YVS G +L
Sbjct: 965 AETRERGRSGLVGLFAEV------EEPPLVEASPLDEITMLRYEKEALGIYVS--GHPVL 1016
Query: 419 TFEAMAEAAS 428
+ + E AS
Sbjct: 1017 RYPGLREVAS 1026
>pdb|3TOT|A Chain A, Crystal Structure Of Glutathione Transferase (Target
Efi-501058) From Ralstonia Solanacearum Gmi1000
pdb|3TOT|B Chain B, Crystal Structure Of Glutathione Transferase (Target
Efi-501058) From Ralstonia Solanacearum Gmi1000
pdb|3TOU|A Chain A, Crystal Structure Of Glutathione Transferase (Target
Efi-501058) From Ralstonia Solanacearum Gmi1000 With Gsh
Bound
pdb|3TOU|B Chain B, Crystal Structure Of Glutathione Transferase (Target
Efi-501058) From Ralstonia Solanacearum Gmi1000 With Gsh
Bound
Length = 226
Score = 30.0 bits (66), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 402 PVEKLACYVSDDGGALLTFEAMAEAASFADLWVPFCR 438
P+ K+ C V DDGGAL +AE +AD P R
Sbjct: 47 PLGKVPCLVMDDGGALFDSRVIAE---YADTLSPVAR 80
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
0.321 0.137 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 36,136,979
Number of Sequences: 62578
Number of extensions: 1622708
Number of successful extensions: 2567
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2550
Number of HSP's gapped (non-prelim): 23
length of query: 1124
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1015
effective length of database: 8,152,335
effective search space: 8274620025
effective search space used: 8274620025
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: 57 (26.6 bits)