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= 006483
(643 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BZE|A Chain A, Nmr Structure Of Human Rtf1 Plus3 Domain
Length = 153
Score = 69.7 bits (169), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 38/129 (29%), Positives = 68/129 (52%), Gaps = 4/129 (3%)
Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
+++ + + R KL +W PFF + + GCFVR+GIG + P+YR+ + V E +
Sbjct: 26 EELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VETAKV 83
Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
Y+L T K L + GN+ R + VS+ E EF +W + ++P+ ++
Sbjct: 84 YQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 141
Query: 381 LEKKESIQK 389
+K+ SI++
Sbjct: 142 NKKELSIKE 150
>pdb|2DB9|A Chain A, Solution Structure Of The Plus-3 Domain Of Human Kiaa0252
Protein
Length = 149
Score = 68.9 bits (167), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 38/129 (29%), Positives = 68/129 (52%), Gaps = 4/129 (3%)
Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
+++ + + R KL +W PFF + + GCFVR+GIG + P+YR+ + V E +
Sbjct: 18 EELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VETAKV 75
Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
Y+L T K L + GN+ R + VS+ E EF +W + ++P+ ++
Sbjct: 76 YQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEI 133
Query: 381 LEKKESIQK 389
+K+ SI++
Sbjct: 134 NKKELSIKE 142
>pdb|3U1U|A Chain A, Crystal Structure Of Rna Polymerase-Associated Protein
Rtf1 Homolog Plus-3 Domain
pdb|3U1U|B Chain B, Crystal Structure Of Rna Polymerase-Associated Protein
Rtf1 Homolog Plus-3 Domain
Length = 137
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 38/129 (29%), Positives = 67/129 (51%), Gaps = 4/129 (3%)
Query: 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRS 320
+++ + + R KL +W PFF + + GCFVR+GIG + P+YR+ + V E +
Sbjct: 12 EELNRVRLSRHKLERWCHXPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGV--VETAKV 69
Query: 321 YKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDV 380
Y+L T K L + GN+ R + VS+ E EF +W ++P+ ++
Sbjct: 70 YQLGGTRTNKGLQLRHGNDQRVFR--LEFVSNQEFTESEFXKWKEAXFSAGXQLPTLDEI 127
Query: 381 LEKKESIQK 389
+K+ SI++
Sbjct: 128 NKKELSIKE 136
>pdb|2Z87|A Chain A, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With Udp-
Galnac And Udp
pdb|2Z87|B Chain B, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With Udp-
Galnac And Udp
Length = 624
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 474 RVENFKNASELKRVNTSLKAGEAGYDPFSRRW 505
R+E+FKN L+ NT + G F+++W
Sbjct: 255 RIEHFKNTDNLRLCNTPFRFFSGGNVAFAKKW 286
>pdb|2Z86|A Chain A, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
pdb|2Z86|B Chain B, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
pdb|2Z86|C Chain C, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
pdb|2Z86|D Chain D, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
Length = 625
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 474 RVENFKNASELKRVNTSLKAGEAGYDPFSRRW 505
R+E+FKN L+ NT + G F+++W
Sbjct: 256 RIEHFKNTDNLRLCNTPFRFFSGGNVAFAKKW 287
>pdb|1REQ|B Chain B, Methylmalonyl-Coa Mutase
pdb|1REQ|D Chain D, Methylmalonyl-Coa Mutase
pdb|2REQ|B Chain B, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|D Chain D, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|B Chain B, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|B Chain B, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|D Chain D, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|B Chain B, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|D Chain D, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|B Chain B, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|D Chain D, Methylmalonyl-Coa Mutase Substrate Complex
pdb|5REQ|B Chain B, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|D Chain D, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|1E1C|B Chain B, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|D Chain D, Methylmalonyl-Coa Mutase H244a Mutant
Length = 637
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 347 MAMVSDSPPLEEEFKQWLREVER--NSGRMPSKQDVLEKKESIQKINTFVYSAATVKQML 404
+++ D P EE QW REVE+ N GR P KQ L E ++++ + M
Sbjct: 20 LSLAGDFPKATEE--QWEREVEKVLNRGRPPEKQ--LTFAECLKRLTVHTVDGIDIVPMY 75
Query: 405 QEKKS 409
+ K +
Sbjct: 76 RPKDA 80
>pdb|2DFS|A Chain A, 3-D Structure Of Myosin-V Inhibited State
pdb|2DFS|M Chain M, 3-D Structure Of Myosin-V Inhibited State
Length = 1080
Score = 28.9 bits (63), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 35/155 (22%), Positives = 63/155 (40%), Gaps = 34/155 (21%)
Query: 288 GCFVRVGIGRSKNGPIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGNESSAARWQM 347
G RV R+ +Y C R + A + K+E R+ +Y + G
Sbjct: 876 GWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIG---------- 925
Query: 348 AMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAAT-------- 399
LE + Q R+++ + S +LEK +++ YS T
Sbjct: 926 --------LENKIMQLQRKIDEQNKEYKS---LLEKMNNLE----ITYSTETEKLRSDVE 970
Query: 400 -VKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQS 433
++ +E K+A++R L++ E +LR+EL Q+
Sbjct: 971 RLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQT 1005
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
0.314 0.130 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,208,762
Number of Sequences: 62578
Number of extensions: 471453
Number of successful extensions: 871
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: 863
Number of HSP's gapped (non-prelim): 15
length of query: 643
length of database: 14,973,337
effective HSP length: 105
effective length of query: 538
effective length of database: 8,402,647
effective search space: 4520624086
effective search space used: 4520624086
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)