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= 039015
(685 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 88.2 bits (217), Expect = 1e-17, Method: Composition-based stats.
Identities = 40/72 (55%), Positives = 49/72 (68%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
P+ F CPISLE+MKDPV +STG TY+R+SI KW AG+ TCPK+ E L L N VLK
Sbjct: 6 PEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLK 65
Query: 338 RIIQDWSVDNGV 349
+I W NG+
Sbjct: 66 SLIALWCESNGI 77
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
PD IS E+M++P +G TYDR I + + P T L ++L+ NL +K
Sbjct: 206 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMK 265
Query: 338 RIIQDWSVDNG 348
+I + +NG
Sbjct: 266 EVIDAFISENG 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 = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 36/71 (50%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
PD IS E+M++P +G TYDR I + + P T L ++L+ NL +K
Sbjct: 3 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMK 62
Query: 338 RIIQDWSVDNG 348
+I + +NG
Sbjct: 63 EVIDAFISENG 73
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 275 GLTPDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFR------AGNSTCPKTG-----E 323
G ++ TCPI LE++ +P++L GH+ RA I + G S+CP G E
Sbjct: 7 GNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE 66
Query: 324 RLQSKELLVNLV 335
LQ+ + L N+V
Sbjct: 67 HLQANQHLANIV 78
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 35/71 (49%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
PD IS E+M++P +G TYDR I + + P T L +L+ NL +K
Sbjct: 104 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMK 163
Query: 338 RIIQDWSVDNG 348
+I + +NG
Sbjct: 164 EVIDAFIQENG 174
>pdb|4HXT|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or329
Length = 252
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 50/167 (29%), Positives = 83/167 (49%), Gaps = 24/167 (14%)
Query: 458 VVESGGLDFIVDMVKKGLKVEARQHAAATLFYIASIEEYRKLIGENP-EAIPALVD---- 512
+V++GG++ +V ++ E ++ AA L IAS P EAI A+VD
Sbjct: 40 IVDAGGVEVLVKLLTS-TDSEVQKEAARALANIAS----------GPDEAIKAIVDAGGV 88
Query: 513 --MVR--DGTDRS-KKNALVAIFGLLMHSGNHWRFLA-AGAVPLLLNLLTSSDSEELITD 566
+V+ TD +K A A+ + + + AG V +L+ LLTS+DS E+ +
Sbjct: 89 EVLVKLLTSTDSEVQKEAARALANIASGPDEAIKAIVDAGGVEVLVKLLTSTDS-EVQKE 147
Query: 567 SLAVLATLAEKLDGTI-AILHHGALDMIMKILDSCTSRAGKEYCVSL 612
+ LA +A D I AI+ G +++++K+L S S KE +L
Sbjct: 148 AARALANIASGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARAL 194
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 43/158 (27%), Positives = 71/158 (44%), Gaps = 23/158 (14%)
Query: 416 CLVEVGCIPXXXXXXXXXXXXTQENAIAALLNL-SKHCKSKSMVVESGGLDFIVDMVKKG 474
+V+ G + Q+ A AL N+ S ++ +V++GG++ +V ++
Sbjct: 81 AIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPDEAIKAIVDAGGVEVLVKLLTS- 139
Query: 475 LKVEARQHAAATLFYIASIEEYRKLIGENP-EAIPALVD------MVR--DGTDRS-KKN 524
E ++ AA L IAS P EAI A+VD +V+ TD +K
Sbjct: 140 TDSEVQKEAARALANIAS----------GPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKE 189
Query: 525 ALVAIFGLLMHSGNHWRFLA-AGAVPLLLNLLTSSDSE 561
A A+ + + + + AG V +L LLTS+DSE
Sbjct: 190 AARALANIASGPTSAIKAIVDAGGVEVLQKLLTSTDSE 227
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 33/70 (47%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
PD IS E+M +P +G TYDR I + + P T L +L+ NL +K
Sbjct: 11 PDYLCGKISFELMAEPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMK 70
Query: 338 RIIQDWSVDN 347
+I + +N
Sbjct: 71 EVIDAFIQEN 80
>pdb|2YU4|A Chain A, Solution Structure Of The Sp-Ring Domain In Non-Smc
Element 2 Homolog (Mms21, S. Cerevisiae)
Length = 94
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 9/71 (12%)
Query: 281 FTCPISLEIMKDPVTLST-GHTYDRASILKWF-----RAGNSTCPKTG---ERLQSKELL 331
FTCPI+ E MK PV GHTY+ +I++ R + CP+ G ++ +L+
Sbjct: 8 FTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLI 67
Query: 332 VNLVLKRIIQD 342
+ L+R I++
Sbjct: 68 QDEALRRAIEN 78
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 28/60 (46%)
Query: 281 FTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLKRII 340
+ CPI L +++ V GH + +A I+K R CP E L +L + KR I
Sbjct: 26 YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI 85
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 276 LTPDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRA-----GNSTCP 319
+ ++ TCPI LE++K+PV+ H++ RA I + + G CP
Sbjct: 15 MIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCP 63
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 37.0 bits (84), Expect = 0.034, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 28/60 (46%)
Query: 281 FTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLKRII 340
+ CPI L +++ V GH + +A I+K R CP E L +L + KR I
Sbjct: 19 YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI 78
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1
Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
Length = 118
Score = 37.0 bits (84), Expect = 0.039, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 28/60 (46%)
Query: 281 FTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLKRII 340
+ CPI L +++ V GH + +A I+K R CP E L +L + KR I
Sbjct: 19 YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI 78
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 36.2 bits (82), Expect = 0.058, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 283 CPISLEIMKDPVTLSTGHTYDRASILKWF--RAGNSTCPK-----TGERLQSKELLVNLV 335
CPI LE++K+PV+ H + + +LK + G S CP T LQ LV
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLV 83
Query: 336 --LKRIIQDWSVDNGVSIA 352
L +II + +D G+ A
Sbjct: 84 EELLKIICAFQLDTGLEYA 102
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 35.8 bits (81), Expect = 0.088, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 24/51 (47%)
Query: 281 FTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELL 331
+ CPI L +++ V GH + +A I+K R CP E L +L
Sbjct: 7 YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLF 57
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 279 DDFTCPISLEIMKDPVTLSTGHTYDRASIL-----KWFRAGNSTCP 319
++ TCPI LE++ P++L GH++ +A + G S+CP
Sbjct: 18 EEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCP 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 282 TCPISLEIMKDPVTLSTGHTYDRASILKWF 311
+C + LE +K+PV + GH + +A I +W+
Sbjct: 17 SCSVCLEYLKEPVIIECGHNFCKACITRWW 46
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
PD+F P+ +M DPV L +G DR+ IL+ + T P + L L LK
Sbjct: 12 PDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHL-LNSPTDPFNRQMLTESMLEPVPELK 70
Query: 338 RIIQDW 343
IQ W
Sbjct: 71 EQIQAW 76
>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 = 33.9 bits (76), Expect = 0.35, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 278 PDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
PD+F P+ +M DPV L +G DR+ IL+ + T P + L L LK
Sbjct: 27 PDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHL-LNSPTDPFNRQTLTESMLEPVPELK 85
Query: 338 RIIQDW 343
IQ W
Sbjct: 86 EQIQAW 91
>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 = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%)
Query: 258 NEASQQVSKKCCNNMLGGLTPDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNST 317
N+A +Q ++ G PD+F P+ IMKDPV L S +K +ST
Sbjct: 869 NKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDST 928
Query: 318 CPKTGERLQSKELLVNLVLKRII 340
P L+ +++ N L++ I
Sbjct: 929 DPFNRMPLKLEDVTPNEELRQKI 951
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%)
Query: 258 NEASQQVSKKCCNNMLGGLTPDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNST 317
N+A +Q ++ G PD+F P+ IMKDPV L S +K +ST
Sbjct: 883 NKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDST 942
Query: 318 CPKTGERLQSKELLVNLVLKRII 340
P L+ +++ N L++ I
Sbjct: 943 DPFNRMPLKLEDVTPNEELRQKI 965
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 32.7 bits (73), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 280 DFTCPISLEIMKDPVTLSTG-HTYDRASILKWFRAGNSTCPKTGERLQSKELL 331
+ CPI L+++K+ +T H + I+ R+GN CP ++L SK L
Sbjct: 34 ELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 86
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 32.3 bits (72), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 280 DFTCPISLEIMKDPVTLSTG-HTYDRASILKWFRAGNSTCPKTGERLQSKELL 331
+ CPI L+++K+ +T H + I+ R+GN CP ++L SK L
Sbjct: 54 ELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 106
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 37/83 (44%)
Query: 258 NEASQQVSKKCCNNMLGGLTPDDFTCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNST 317
N+A +Q ++ G PD+F P+ I KDPV L S +K +ST
Sbjct: 883 NKAEEQRKADEEEDLEYGDVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLSDST 942
Query: 318 CPKTGERLQSKELLVNLVLKRII 340
P L+ +++ N L++ I
Sbjct: 943 DPFNRXPLKLEDVTPNEELRQKI 965
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 282 TCPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCP 319
+C I I+ DPV S H + R IL+ + S CP
Sbjct: 25 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCP 62
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 280 DFTCPISLEIMKDPVTLSTG-HTYDRASILKWFRAGNSTCPKTGERLQSKELL 331
+ CPI L+++K+ +T H + I+ R+GN CP ++L SK L
Sbjct: 53 ELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 105
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 279 DDFTCPISLEIMKDPVTLSTGHTY 302
++ CPI L+I++ PVT+ GH +
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNF 42
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 279 DDFTCPISLEIMKDPVTLSTGHTY 302
++ CPI L+I++ PVT+ GH +
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNF 42
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 283 CPISLEIMKDPVTLSTGHTYDRASILKWFRAGNSTCPKTGERLQS-------KELLVNLV 335
C I +EI+ +PVTL HT + + CP R+ S + LVN+
Sbjct: 18 CGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHTRRNSLVNVE 77
Query: 336 LKRIIQ 341
L IIQ
Sbjct: 78 LWTIIQ 83
>pdb|1WGM|A Chain A, Solution Structure Of The U-Box In Human Ubiquitin
Conjugation Factor E4a
Length = 98
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 2/79 (2%)
Query: 279 DDFTCPISLEIMKDPVTLSTGH-TYDRASILKWFRAGNSTCPKTGERLQSKELLVNLVLK 337
D+F PI +M DPV L + T DR++I + + + T P L ++ N LK
Sbjct: 21 DEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMDQIRPNTELK 79
Query: 338 RIIQDWSVDNGVSIAEESG 356
IQ W + SG
Sbjct: 80 EKIQRWLAERKQQSGPSSG 98
>pdb|3UPD|A Chain A, 2.9 Angstrom Crystal Structure Of Ornithine
Carbamoyltransferase (Argf) From Vibrio Vulnificus
pdb|4H31|A Chain A, Crystal Structure Of Anabolic Ornithine
Carbamoyltransferase From Vibrio Vulnificus In Complex
With Carbamoyl Phosphate And L-Norvaline
pdb|4H31|B Chain B, Crystal Structure Of Anabolic Ornithine
Carbamoyltransferase From Vibrio Vulnificus In Complex
With Carbamoyl Phosphate And L-Norvaline
pdb|4H31|C Chain C, Crystal Structure Of Anabolic Ornithine
Carbamoyltransferase From Vibrio Vulnificus In Complex
With Carbamoyl Phosphate And L-Norvaline
Length = 358
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 171 DKRVLNDVIRILGRFEDGIRP---DKSEVKRVLDYLGITKWSQCNQEVKFLDSEITIEYL 227
DK + D R+LGR DGI+ ++ V+ + + G+ W+ E F ++I ++L
Sbjct: 111 DKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDE--FHPTQILADFL 168
Query: 228 NVDKRSELALLSSL 241
+ + S+ L+ +
Sbjct: 169 TMLEHSQGKALADI 182
>pdb|2I0Z|A Chain A, Crystal Structure Of A Fad Binding Protein From Bacillus
Cereus, A Putative Nad(Fad)-Utilizing Dehydrogenases
Length = 447
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 320 KTGERLQSKELLVNLVLKRIIQDWSVDNGVSIAEESGHKNRDITRTVLAGSLAAEGAMKL 379
+TGE L++ +++ + K + Q S +G + AE++GH ++ T + +
Sbjct: 173 QTGEVLETNHVVIAVGGKSVPQTGSTGDGYAWAEKAGHTITELFPT----------EVPI 222
Query: 380 LAN--FISDRLLEG 391
L+N FI DR L+G
Sbjct: 223 LSNEPFIRDRSLQG 236
>pdb|4B8J|A Chain A, Rimp_alpha1a
Length = 528
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 3/100 (3%)
Query: 505 EAIPALVDMVRDGTDRSKKNALVAIFGLLM--HSGNHWRFLAAGAVPLLLNLLTSSDSEE 562
E++PA++ V + + A LL S + +G VP + LT D +
Sbjct: 74 ESLPAMIGGVYSDDNNLQLEATTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTREDFPQ 133
Query: 563 LITDSLAVLATLAEKL-DGTIAILHHGALDMIMKILDSCT 601
L ++ L +A + T ++ HGA+ + +K+L S +
Sbjct: 134 LQFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLGSSS 173
>pdb|4AMU|A Chain A, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4AMU|B Chain B, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4AMU|C Chain C, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4AMU|D Chain D, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4ANF|A Chain A, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
pdb|4ANF|B Chain B, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
pdb|4ANF|C Chain C, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
pdb|4ANF|D Chain D, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
Length = 365
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 172 KRVLNDVIRILGRFEDGIR---PDKSEVKRVLDYLGITKWS 209
K + D ++LGRF DGI +S+V ++ Y G+ W+
Sbjct: 113 KESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWN 153
>pdb|1PKY|A Chain A, Pyruvate Kinase From E. Coli In The T-State
pdb|1PKY|B Chain B, Pyruvate Kinase From E. Coli In The T-State
pdb|1PKY|C Chain C, Pyruvate Kinase From E. Coli In The T-State
pdb|1PKY|D Chain D, Pyruvate Kinase From E. Coli In The T-State
Length = 470
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 539 HWRFLAAGAVPLLLNLLTSSDSEELITDSLAVLATLAEKLDGTIAILHHGAL 590
H L+ G VP L+ +TS+D + LA+ + LA K G + ++ GAL
Sbjct: 407 HQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHK--GDVVVMVSGAL 456
>pdb|1E0T|A Chain A, R292d Mutant Of E. Coli Pyruvate Kinase
pdb|1E0T|B Chain B, R292d Mutant Of E. Coli Pyruvate Kinase
pdb|1E0T|C Chain C, R292d Mutant Of E. Coli Pyruvate Kinase
pdb|1E0T|D Chain D, R292d Mutant Of E. Coli Pyruvate Kinase
Length = 470
Score = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 539 HWRFLAAGAVPLLLNLLTSSDSEELITDSLAVLATLAEKLDGTIAILHHGAL 590
H L+ G VP L+ +TS+D + LA+ + LA K G + ++ GAL
Sbjct: 407 HQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHK--GDVVVMVSGAL 456
>pdb|1PKF|A Chain A, Crystal Structure Of Epothilone D-Bound Cytochrome
P450epok
Length = 419
Score = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 51/189 (26%), Positives = 84/189 (44%), Gaps = 16/189 (8%)
Query: 441 AIAALLNLSKHCKSK-----SMVVESGGLDFI--VDMVKKGLKVEARQHAAATLFYIASI 493
AI+ALL + C K S + G+ + VD K L V + A L + +
Sbjct: 157 AISALLKVPAECDEKFRRFGSATARALGVGLVPRVDEETKTL-VASVTEGLALLHGV--L 213
Query: 494 EEYRKLIGENPEAIPALVDMVRDGTDRSKKNALVAIFGLLMHSGNHWR-FLAAGAVPLLL 552
+E R+ EN + + L+ DG+ S K LVA+ G ++ +G +L A AV L
Sbjct: 214 DERRRNPLEN-DVLTMLLQAEADGSRLSTKE-LVALVGAIIAAGTDTTIYLIAFAV---L 268
Query: 553 NLLTSSDSEELITDSLAVLATLAEKLDGTIAILHHGALDMIMKILDSCTSRAGKEYCVSL 612
NLL S ++ EL+ ++ +++ IL G + + L+ C + K V L
Sbjct: 269 NLLRSPEALELVKAEPGLMRNALDEVLRFENILRIGTVRFARQDLEYCGASIKKGEMVFL 328
Query: 613 LLALCINGG 621
L+ + G
Sbjct: 329 LIPSALRDG 337
>pdb|1Q5D|A Chain A, Epothilone B-Bound Cytochrome P450epok
pdb|1Q5E|A Chain A, Substrate-Free Cytochrome P450epok
Length = 419
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 51/189 (26%), Positives = 84/189 (44%), Gaps = 16/189 (8%)
Query: 441 AIAALLNLSKHCKSK-----SMVVESGGLDFI--VDMVKKGLKVEARQHAAATLFYIASI 493
AI+ALL + C K S + G+ + VD K L V + A L + +
Sbjct: 157 AISALLKVPAECDEKFRRFGSATARALGVGLVPRVDEETKTL-VASVTEGLALLHGV--L 213
Query: 494 EEYRKLIGENPEAIPALVDMVRDGTDRSKKNALVAIFGLLMHSGNHWR-FLAAGAVPLLL 552
+E R+ EN + + L+ DG+ S K LVA+ G ++ +G +L A AV L
Sbjct: 214 DERRRNPLEN-DVLTMLLQAEADGSRLSTKE-LVALVGAIIAAGTDTTIYLIAFAV---L 268
Query: 553 NLLTSSDSEELITDSLAVLATLAEKLDGTIAILHHGALDMIMKILDSCTSRAGKEYCVSL 612
NLL S ++ EL+ ++ +++ IL G + + L+ C + K V L
Sbjct: 269 NLLRSPEALELVKAEPGLMRNALDEVLRFDNILRIGTVRFARQDLEYCGASIKKGEMVFL 328
Query: 613 LLALCINGG 621
L+ + G
Sbjct: 329 LIPSALRDG 337
>pdb|1E0U|A Chain A, Structure R271l Mutant Of E. Coli Pyruvate Kinase
pdb|1E0U|B Chain B, Structure R271l Mutant Of E. Coli Pyruvate Kinase
pdb|1E0U|C Chain C, Structure R271l Mutant Of E. Coli Pyruvate Kinase
pdb|1E0U|D Chain D, Structure R271l Mutant Of E. Coli Pyruvate Kinase
Length = 470
Score = 28.9 bits (63), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 539 HWRFLAAGAVPLLLNLLTSSDSEELITDSLAVLATLAEKLDGTIAILHHGAL 590
H L+ G VP L+ +TS+D + LA+ + LA K G + ++ GAL
Sbjct: 407 HQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHK--GDVVVMVSGAL 456
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 0.135 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,090,771
Number of Sequences: 62578
Number of extensions: 624893
Number of successful extensions: 1879
Number of sequences better than 100.0: 58
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 1822
Number of HSP's gapped (non-prelim): 89
length of query: 685
length of database: 14,973,337
effective HSP length: 105
effective length of query: 580
effective length of database: 8,402,647
effective search space: 4873535260
effective search space used: 4873535260
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)