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= 002017
(981 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 256 bits (653), Expect = 6e-68, Method: Compositional matrix adjust.
Identities = 151/403 (37%), Positives = 234/403 (58%), Gaps = 19/403 (4%)
Query: 561 FMNFIIMFMASPKYIRNPYLRSKMVEVLNCW-MPRRSGSSSATATLFEGHQMSLEYLVRN 619
F+ F M + P+ + NP+L+ K+V++L+ MP S +FE ++ + L+
Sbjct: 579 FVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFMMDIFEHDELVNKNLLYA 638
Query: 620 LLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLW-QVPSHRNA--WRQIAKEEEKGVYL 676
LL YV +E TGS +QFYDKFN R++I+ +LE L+ ++PS++N W+ + ++
Sbjct: 639 LLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQS---QNNADFFV 695
Query: 677 NFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAEWE--RRPAQERQERTRLFHSQENI 734
F+ ++ND +LLDE L+ + E+ I+ E+ N A R ++++ +TRL S
Sbjct: 696 RFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRL-ASASRQ 754
Query: 735 IRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVASMLNYFLLQLVGPQRKSLTLKDPE 794
+ LA++ + + S+ I A F+ PE++ R+ASMLNY L LVGP+ L +KDP+
Sbjct: 755 AKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQ 814
Query: 795 KYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSDGRSYNEQLFSAAADVLWKIGEDGR 854
Y F PK LLK + +Y++L+ Q+ F +A++ D RS+N LF A D+L + + G
Sbjct: 815 SYSFNPKDLLKALTTVYINLSE---QSEFISAVAKDERSFNRNLFVRAVDILGR--KTGL 869
Query: 855 IIQEFIE----LGXXXXXXXXXXXXXXXXLGDIPDEFLDPIQYTLMKDPVILPSSRITVD 910
EFIE GD+PDEFLDP+ YT+MKDPVILP+S++ +D
Sbjct: 870 ASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNID 929
Query: 911 RPVIQRHLLSDATDPFNRSHLTADMLIPNTELKAKIEEFIKSQ 953
R I+ HLLSD+TDPFNR L + + PN EL+ KI F K +
Sbjct: 930 RSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQK 972
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 333 DTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDK 392
++R +++ Y A + N+N R +S+G N++ +++R PFLD + K DK
Sbjct: 298 NSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDK 357
Query: 393 IDPKYVFYSSR-LDLRSLTALHASSEEVSEWINKGNPAKADGSKHF 437
ID Y S +DL T L++ +E + +K N AD +F
Sbjct: 358 IDANYFNNPSLFIDLSGETRLNSDFKEADAFYDK-NRKTADSKPNF 402
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 8 RSPEEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVD 67
RS IEDI+ + TTD Y L +E + +G L D ++ +L+
Sbjct: 20 RSMTAIEDIL----------QITTDPSDTRGY-SLLKSEEVPQGS--TLGVDFIDTLLLY 66
Query: 68 RLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIH 127
+L+ N + PF YL +C+RR + K+I K+K L + ++ ++++ Y +
Sbjct: 67 QLTEN-EKLDKPFEYLNDCFRRNQQQ-KRI--TKNKPNAESLHSTFQEIDRLVIGYGVVA 122
Query: 128 LANPDF 133
L +F
Sbjct: 123 LQIENF 128
>pdb|3M62|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
pdb|3M63|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 968
Score = 255 bits (652), Expect = 8e-68, Method: Compositional matrix adjust.
Identities = 151/403 (37%), Positives = 234/403 (58%), Gaps = 19/403 (4%)
Query: 561 FMNFIIMFMASPKYIRNPYLRSKMVEVLNCW-MPRRSGSSSATATLFEGHQMSLEYLVRN 619
F+ F M + P+ + NP+L+ K+V++L+ MP S +FE ++ + L+
Sbjct: 565 FVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFMMDIFEHDELVNKNLLYA 624
Query: 620 LLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLW-QVPSHRNA--WRQIAKEEEKGVYL 676
LL YV +E TGS +QFYDKFN R++I+ +LE L+ ++PS++N W+ + ++
Sbjct: 625 LLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQS---QNNADFFV 681
Query: 677 NFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAEWE--RRPAQERQERTRLFHSQENI 734
F+ ++ND +LLDE L+ + E+ I+ E+ N A R ++++ +TRL S
Sbjct: 682 RFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRL-ASASRQ 740
Query: 735 IRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVASMLNYFLLQLVGPQRKSLTLKDPE 794
+ LA++ + + S+ I A F+ PE++ R+ASMLNY L LVGP+ L +KDP+
Sbjct: 741 AKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQ 800
Query: 795 KYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSDGRSYNEQLFSAAADVLWKIGEDGR 854
Y F PK LLK + +Y++L+ Q+ F +A++ D RS+N LF A D+L + + G
Sbjct: 801 SYSFNPKDLLKALTTVYINLSE---QSEFISAVAKDERSFNRNLFVRAVDILGR--KTGL 855
Query: 855 IIQEFIE----LGXXXXXXXXXXXXXXXXLGDIPDEFLDPIQYTLMKDPVILPSSRITVD 910
EFIE GD+PDEFLDP+ YT+MKDPVILP+S++ +D
Sbjct: 856 ASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNID 915
Query: 911 RPVIQRHLLSDATDPFNRSHLTADMLIPNTELKAKIEEFIKSQ 953
R I+ HLLSD+TDPFNR L + + PN EL+ KI F K +
Sbjct: 916 RSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQK 958
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 333 DTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDK 392
++R +++ Y A + N+N R +S+G N++ +++R PFLD + K DK
Sbjct: 284 NSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDK 343
Query: 393 IDPKYVFYSSR-LDLRSLTALHASSEEVSEWINKGNPAKADGSKHF 437
ID Y S +DL T L++ +E + +K N AD +F
Sbjct: 344 IDANYFNNPSLFIDLSGETRLNSDFKEADAFYDK-NRKTADSKPNF 388
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 8 RSPEEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVD 67
RS IEDI+ + TTD Y L +E + +G L D ++ +L+
Sbjct: 6 RSMTAIEDIL----------QITTDPSDTRGY-SLLKSEEVPQGS--TLGVDFIDTLLLY 52
Query: 68 RLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIH 127
+L+ N + PF YL +C+RR + K+I K+K L + ++ ++++ Y +
Sbjct: 53 QLTEN-EKLDKPFEYLNDCFRRNQQQ-KRI--TKNKPNAESLHSTFQEIDRLVIGYGVVA 108
Query: 128 LANPDF 133
L +F
Sbjct: 109 LQIENF 114
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 244 bits (622), Expect = 2e-64, Method: Compositional matrix adjust.
Identities = 147/403 (36%), Positives = 227/403 (56%), Gaps = 19/403 (4%)
Query: 561 FMNFIIMFMASPKYIRNPYLRSKMVEVLNCW-MPRRSGSSSATATLFEGHQMSLEYLVRN 619
F+ F + P+ + NP+L+ K+V++L+ P S +FE ++ + L+
Sbjct: 579 FVEFTTXVLRCPELVSNPHLKGKLVQLLSVGAXPLTDNSPGFXXDIFEHDELVNKNLLYA 638
Query: 620 LLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLW-QVPSHRNA--WRQIAKEEEKGVYL 676
LL YV +E TGS +QFYDKFN R++I+ +LE L+ ++PS++N W+ + ++
Sbjct: 639 LLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQS---QNNADFFV 695
Query: 677 NFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAEWE--RRPAQERQERTRLFHSQENI 734
F+ +ND +LLDE L+ + E+ I+ E+ N A R ++++ +TRL S
Sbjct: 696 RFVARXLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRL-ASASRQ 754
Query: 735 IRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVASMLNYFLLQLVGPQRKSLTLKDPE 794
+ LA++ + S+ I A F+ PE++ R+AS LNY L LVGP+ L +KDP+
Sbjct: 755 AKSSCGLADKSXKLFEIYSKDIPAAFVTPEIVYRLASXLNYNLESLVGPKCGELKVKDPQ 814
Query: 795 KYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSDGRSYNEQLFSAAADVLWKIGEDGR 854
Y F PK LLK + +Y++L+ Q+ F +A++ D RS+N LF A D+L + + G
Sbjct: 815 SYSFNPKDLLKALTTVYINLSE---QSEFISAVAKDERSFNRNLFVRAVDILGR--KTGL 869
Query: 855 IIQEFIE----LGXXXXXXXXXXXXXXXXLGDIPDEFLDPIQYTLMKDPVILPSSRITVD 910
EFIE GD+PDEFLDP+ YT+ KDPVILP+S+ +D
Sbjct: 870 ASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLXYTIXKDPVILPASKXNID 929
Query: 911 RPVIQRHLLSDATDPFNRSHLTADMLIPNTELKAKIEEFIKSQ 953
R I+ HLLSD+TDPFNR L + + PN EL+ KI F K +
Sbjct: 930 RSTIKAHLLSDSTDPFNRXPLKLEDVTPNEELRQKILCFKKQK 972
Score = 46.2 bits (108), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 2/106 (1%)
Query: 333 DTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDK 392
++R + + Y A + N+N R +S+G N++ +++R PFLD + K DK
Sbjct: 298 NSRTDXISYFAHIANKNHLRRADHPPFKELSSNGFXSNITLLLVRFSQPFLDISYKKIDK 357
Query: 393 IDPKYVFYSSR-LDLRSLTALHASSEEVSEWINKGNPAKADGSKHF 437
ID Y S +DL T L++ +E + +K N AD +F
Sbjct: 358 IDANYFNNPSLFIDLSGETRLNSDFKEADAFYDK-NRKTADSKPNF 402
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 8 RSPEEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVD 67
RS IEDI+ + TTD Y L +E + +G L D ++ +L+
Sbjct: 20 RSXTAIEDIL----------QITTDPSDTRGY-SLLKSEEVPQGS--TLGVDFIDTLLLY 66
Query: 68 RLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIH 127
+L+ N + PF YL +C+RR + K+I K+K L + ++ ++++ Y +
Sbjct: 67 QLTEN-EKLDKPFEYLNDCFRRNQQQ-KRI--TKNKPNAESLHSTFQEIDRLVIGYGVVA 122
Query: 128 LANPDF 133
L +F
Sbjct: 123 LQIENF 128
>pdb|1WGM|A Chain A, Solution Structure Of The U-Box In Human Ubiquitin
Conjugation Factor E4a
Length = 98
Score = 101 bits (251), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 48/70 (68%), Positives = 54/70 (77%)
Query: 881 GDIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDATDPFNRSHLTADMLIPNT 940
D DEFLDPI TLM DPV+LPSSR+TVDR I RHLLSD TDPFNRS LT D + PNT
Sbjct: 17 ADACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNT 76
Query: 941 ELKAKIEEFI 950
ELK KI+ ++
Sbjct: 77 ELKEKIQRWL 86
>pdb|2KRE|A Chain A, Solution Structure Of E4bUFD2A U-Box Domain
pdb|3L1X|A Chain A, Crystal Structure Of U-Box Domain Of Human E4b Ubiquitin
Ligase
pdb|3L1Z|B Chain B, Crystal Structure Of The U-Box Domain Of Human E4b
Ubiquitin Ligase In Complex With Ubch5c E2 Ubiquitin
Conjugating Enzyme
Length = 100
Score = 75.1 bits (183), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 40/78 (51%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 881 GDIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDATDPFNRSHLTADMLIPNT 940
D PDEF DP+ TLM DPV LPS I +DR +I RHLL+ TDPFNR LT ML P
Sbjct: 24 SDAPDEFRDPLMDTLMTDPVRLPSGTI-MDRSIILRHLLNSPTDPFNRQTLTESMLEPVP 82
Query: 941 ELKAKIEEFIKSQGLKRH 958
ELK +I+ +++ + H
Sbjct: 83 ELKEQIQAWMREKQNSDH 100
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 74.3 bits (181), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 39/78 (50%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 881 GDIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDATDPFNRSHLTADMLIPNT 940
D PDEF DP+ TLM DPV LPS + +DR +I RHLL+ TDPFNR LT ML P
Sbjct: 9 SDAPDEFRDPLMDTLMTDPVRLPSGTV-MDRSIILRHLLNSPTDPFNRQMLTESMLEPVP 67
Query: 941 ELKAKIEEFIKSQGLKRH 958
ELK +I+ +++ + H
Sbjct: 68 ELKEQIQAWMREKQSSDH 85
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 882 DIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDAT-DPFNRSHLTADMLIPNT 940
+IPD I + LM++P I PS IT DR I+ HL DP RS LT D LIPN
Sbjct: 102 EIPDYLCGKISFELMREPCITPSG-ITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNL 160
Query: 941 ELKAKIEEFIKSQG 954
+K I+ FI+ G
Sbjct: 161 AMKEVIDAFIQENG 174
>pdb|2C2L|A Chain A, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|B Chain B, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|C Chain C, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|D Chain D, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
Length = 281
Score = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 32/74 (43%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 882 DIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDAT-DPFNRSHLTADMLIPNT 940
DIPD I + LM++P I PS IT DR I+ HL +P RS LT + LIPN
Sbjct: 204 DIPDYLCGKISFELMREPCITPSG-ITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNL 262
Query: 941 ELKAKIEEFIKSQG 954
+K I+ FI G
Sbjct: 263 AMKEVIDAFISENG 276
>pdb|2C2V|S Chain S, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|T Chain T, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|U Chain U, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|V Chain V, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
Length = 78
Score = 53.1 bits (126), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 32/74 (43%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 882 DIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDAT-DPFNRSHLTADMLIPNT 940
DIPD I + LM++P I PS IT DR I+ HL +P RS LT + LIPN
Sbjct: 1 DIPDYLCGKISFELMREPCITPSG-ITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNL 59
Query: 941 ELKAKIEEFIKSQG 954
+K I+ FI G
Sbjct: 60 AMKEVIDAFISENG 73
>pdb|2OXQ|C Chain C, Structure Of The Ubch5 :chip U-Box Complex
pdb|2OXQ|D Chain D, Structure Of The Ubch5 :chip U-Box Complex
Length = 80
Score = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 882 DIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHLLSDAT-DPFNRSHLTADMLIPNT 940
+IPD I + LM +P I PS IT DR I+ HL DP RS LT D LIPN
Sbjct: 9 EIPDYLCGKISFELMAEPCITPSG-ITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNL 67
Query: 941 ELKAKIEEFIK 951
+K I+ FI+
Sbjct: 68 AMKEVIDAFIQ 78
>pdb|1T1H|A Chain A, Nmr Solution Structure Of The U Box Domain From Atpub14,
An Armadillo Repeat Containing Protein From Arabidopsis
Thaliana
Length = 78
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 882 DIPDEFLDPIQYTLMKDPVILPSSRITVDRPVIQRHL-LSDATDPFNRSHLTADMLIPNT 940
+ P+ F PI LMKDPVI+ S+ T +R IQ+ L T P ++ L L PN
Sbjct: 4 EFPEYFRCPISLELMKDPVIV-STGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY 62
Query: 941 ELKAKIEEFIKSQGLK 956
LK+ I + +S G++
Sbjct: 63 VLKSLIALWCESNGIE 78
>pdb|3FLE|A Chain A, Se_1780 Protein Of Unknown Function From Staphylococcus
Epidermidis.
pdb|3FLE|B Chain B, Se_1780 Protein Of Unknown Function From Staphylococcus
Epidermidis
Length = 249
Score = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 583 KMVEVLNCWMPRRSGSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGS---HTQFYDK 639
K +EVLN + GS S + SL+YL+R K Y + +F G+ H+Q ++
Sbjct: 178 KEIEVLNIYGDLEDGSHS-DGRVSNSSSQSLQYLLRGSTKSYQEXKFKGAKAQHSQLHEN 236
Query: 640 FNIRHNIAELLEYLWQ 655
++ + E++++LW+
Sbjct: 237 KDVAN---EIIQFLWE 249
>pdb|3HOA|A Chain A, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
pdb|3HOA|B Chain B, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
Length = 509
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 12/60 (20%)
Query: 34 DPRIA------YLELTAAELLSEGKDMRLSRDLMERVLVDRLSGNFPAAEPPFLYLINCY 87
+PR A +L+ T A + +EG R RVLV+R++G P+A P YL Y
Sbjct: 452 EPRFARGEFQPFLDWTRARIHAEGSRFR------PRVLVERVTGEAPSARPFLAYLEKKY 505
>pdb|1WGZ|A Chain A, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|B Chain B, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|C Chain C, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
Length = 510
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 12/60 (20%)
Query: 34 DPRIA------YLELTAAELLSEGKDMRLSRDLMERVLVDRLSGNFPAAEPPFLYLINCY 87
+PR A +L+ T A + +EG R RVLV+R++G P+A P YL Y
Sbjct: 452 EPRFARGEFQPFLDWTRARIHAEGSRFR------PRVLVERVTGEAPSARPFLAYLEKKY 505
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 30.4 bits (67), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 29/65 (44%)
Query: 202 LKGLYENLRGSVLNVSALGNFQQPLRALLYLVSFPVGVKSLVNHQWWIPKSVYLNGRVIE 261
++GL GS++ NF++ L L Y +S K L + S YL R+++
Sbjct: 743 MRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVD 802
Query: 262 MTSIL 266
+ L
Sbjct: 803 VAQDL 807
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 30.4 bits (67), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 29/65 (44%)
Query: 202 LKGLYENLRGSVLNVSALGNFQQPLRALLYLVSFPVGVKSLVNHQWWIPKSVYLNGRVIE 261
++GL GS++ NF++ L L Y +S K L + S YL R+++
Sbjct: 743 MRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVD 802
Query: 262 MTSIL 266
+ L
Sbjct: 803 VAQDL 807
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
0.320 0.136 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,859,949
Number of Sequences: 62578
Number of extensions: 1074339
Number of successful extensions: 2636
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2597
Number of HSP's gapped (non-prelim): 26
length of query: 981
length of database: 14,973,337
effective HSP length: 108
effective length of query: 873
effective length of database: 8,214,913
effective search space: 7171619049
effective search space used: 7171619049
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: 56 (26.2 bits)