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= 040073
(407 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 = 78.2 bits (191), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 40/82 (48%), Positives = 53/82 (64%), Gaps = 7/82 (8%)
Query: 5 EVPAHFLCPISLQLMRDPVTVSTGITYDRVNIERWLFTCKNNTCPVTKQVLQETDLTSTT 64
E P +F CPISL+LM+DPV VSTG TY+R +I++WL + TCP +++ L L T
Sbjct: 4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWL-DAGHKTCPKSQETLLHAGL---T 59
Query: 65 PNHTLRRLIQAWCTINACHGIE 86
PN+ L+ LI WC N GIE
Sbjct: 60 PNYVLKSLIALWCESN---GIE 78
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 5 EVPAHFLCPISLQLMRDPVTVSTGITYDRVNIERWLFTCKNNTCPVTKQVLQETDLTSTT 64
E+P + IS +LMR+P +GITYDR +IE L + PVT+ L + L
Sbjct: 102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRV-GHFDPVTRSPLTQDQL---I 157
Query: 65 PNHTLRRLIQAWCTINA 81
PN ++ +I A+ N
Sbjct: 158 PNLAMKEVIDAFIQENG 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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 5 EVPAHFLCPISLQLMRDPVTVSTGITYDRVNIERWLFTCKNNTCPVTKQVLQETDLTSTT 64
++P + IS +LMR+P +GITYDR +IE L + PVT+ L + L
Sbjct: 204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRV-GHFNPVTRSPLTQEQL---I 259
Query: 65 PNHTLRRLIQAWCTINA 81
PN ++ +I A+ + N
Sbjct: 260 PNLAMKEVIDAFISENG 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 = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 5 EVPAHFLCPISLQLMRDPVTVSTGITYDRVNIERWLFTCKNNTCPVTKQVLQETDLTSTT 64
++P + IS +LMR+P +GITYDR +IE L + PVT+ L + L
Sbjct: 1 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN-PVTRSPLTQEQL---I 56
Query: 65 PNHTLRRLIQAWCTINA 81
PN ++ +I A+ + N
Sbjct: 57 PNLAMKEVIDAFISENG 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 = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 5 EVPAHFLCPISLQLMRDPVTVSTGITYDRVNIERWLFTCKNNTCPVTKQVLQETDLTSTT 64
E+P + IS +LM +P +GITYDR +IE L + PVT+ L + L
Sbjct: 9 EIPDYLCGKISFELMAEPCITPSGITYDRKDIEEHLQRVGHFD-PVTRSPLTQDQL---I 64
Query: 65 PNHTLRRLIQAWCTIN 80
PN ++ +I A+ N
Sbjct: 65 PNLAMKEVIDAFIQEN 80
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 1 MEEIEVPAHFLCPISLQLMRDPVTV-STGITYDRVNIERWLFTCKNNTCPVTKQVLQETD 59
+E +VP FL P+ +M+DPV + ++ + DR I+ L + ++T P + L+
Sbjct: 897 LEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLS--DSTDPFNRMPLK--- 951
Query: 60 LTSTTPNHTLRRLI 73
L TPN LR+ I
Sbjct: 952 LEDVTPNEELRQKI 965
>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 = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 1 MEEIEVPAHFLCPISLQLMRDPVTV-STGITYDRVNIERWLFTCKNNTCPVTKQVLQETD 59
+E +VP FL P+ +M+DPV + ++ + DR I+ L + ++T P + L+
Sbjct: 883 LEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLS--DSTDPFNRMPLK--- 937
Query: 60 LTSTTPNHTLRRLI 73
L TPN LR+ I
Sbjct: 938 LEDVTPNEELRQKI 951
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 1 MEEIEVPAHFLCPISLQLMRDPVTV-STGITYDRVNIERWLFTCKNNTCPVTKQVLQETD 59
+E +VP FL P+ + +DPV + ++ DR I+ L + ++T P + L+
Sbjct: 897 LEYGDVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLS--DSTDPFNRXPLK--- 951
Query: 60 LTSTTPNHTLRRLI 73
L TPN LR+ I
Sbjct: 952 LEDVTPNEELRQKI 965
>pdb|1V0D|A Chain A, Crystal Structure Of Caspase-Activated Dnase (Cad)
Length = 329
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 335 VRILCSVCKFSATARVLQEMLQVGVV--------SKLCL 365
+R L S CKF AR QE+L+ G V S+LCL
Sbjct: 13 LRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCL 51
>pdb|1C9F|A Chain A, Nmr Structure Of The Cad Domain Of Caspase-Activated Dnase
Length = 90
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 335 VRILCSVCKFSATARVLQEMLQVGVV--------SKLCL 365
+R L S CKF AR QE+L+ G V S+LCL
Sbjct: 16 LRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCL 54
>pdb|1F2R|C Chain C, Nmr Structure Of The Heterodimeric Complex Between Cad
Domains Of Cad And Icad
Length = 87
Score = 29.3 bits (64), Expect = 4.2, Method: Composition-based stats.
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 335 VRILCSVCKFSATARVLQEMLQVGVV--------SKLCL 365
+R L S CKF AR QE+L+ G V S+LCL
Sbjct: 13 LRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCL 51
>pdb|1RV3|A Chain A, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
pdb|1RV4|A Chain A, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RV4|B Chain B, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RV3|B Chain B, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
Length = 483
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 42 TCKNNTCPVTKQVLQETDLTSTTPNHTLRRLIQ 74
C NTCP K L+ + L TP T R L++
Sbjct: 382 ACNKNTCPGDKSALRPSGLRLGTPALTSRGLLE 414
>pdb|1LS3|B Chain B, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|D Chain D, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|A Chain A, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|C Chain C, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
Length = 483
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 42 TCKNNTCPVTKQVLQETDLTSTTPNHTLRRLIQ 74
C NTCP K L+ + L TP T R L++
Sbjct: 382 ACNKNTCPGDKSALRPSGLRLGTPALTSRGLLE 414
>pdb|1RVU|A Chain A, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RVU|B Chain B, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RVY|A Chain A, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
pdb|1RVY|B Chain B, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
Length = 483
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 42 TCKNNTCPVTKQVLQETDLTSTTPNHTLRRLIQ 74
C NTCP K L+ + L TP T R L++
Sbjct: 382 ACNKNTCPGDKSALRPSGLRLGTPALTSRGLLE 414
>pdb|1CJ0|A Chain A, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
pdb|1CJ0|B Chain B, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
Length = 470
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 42 TCKNNTCPVTKQVLQETDLTSTTPNHTLRRLIQ 74
C NTCP K L+ + L TP T R L++
Sbjct: 369 ACNKNTCPGDKSALRPSGLRLGTPALTSRGLLE 401
>pdb|1EJI|A Chain A, Recombinant Serine Hydroxymethyltransferase (Mouse)
pdb|1EJI|B Chain B, Recombinant Serine Hydroxymethyltransferase (Mouse)
pdb|1EJI|C Chain C, Recombinant Serine Hydroxymethyltransferase (Mouse)
pdb|1EJI|D Chain D, Recombinant Serine Hydroxymethyltransferase (Mouse)
Length = 478
Score = 28.5 bits (62), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 43 CKNNTCPVTKQVLQETDLTSTTPNHTLRRLIQ 74
C NTCP K L+ + L TP T R L++
Sbjct: 378 CNKNTCPGDKSALRPSGLRLGTPALTSRGLLE 409
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
0.322 0.133 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,864,430
Number of Sequences: 62578
Number of extensions: 328811
Number of successful extensions: 787
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 775
Number of HSP's gapped (non-prelim): 18
length of query: 407
length of database: 14,973,337
effective HSP length: 101
effective length of query: 306
effective length of database: 8,652,959
effective search space: 2647805454
effective search space used: 2647805454
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: 53 (25.0 bits)