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= 009761
(526 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 = 104 bits (260), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 72/255 (28%), Positives = 120/255 (47%), Gaps = 27/255 (10%)
Query: 91 PMVLVQIPMYNEK-EVYQLSIGAACGLSWPSDRITIQVLDD--------STDPTIKDLVE 141
P V + +P YNE ++ +++ AA + +P+ T+ + DD S DP + +
Sbjct: 140 PTVDILVPSYNEPADMLSVTLAAAKNMIYPARLRTVVLCDDGGTDQRCMSPDPELAQKAQ 199
Query: 142 ---LECQRWASKGINIKYEIRDSRNGYKAGALKEGMKHSYVKQCDYVAIFDADFEPEPDF 198
E Q+ + + + Y R+ KAG + ++ + + V +FDAD P DF
Sbjct: 200 ERRRELQQLC-RELGVVYSTRERNEHAKAGNMSAALER---LKGELVVVFDADHVPSRDF 255
Query: 199 LWRTIPFLVHNPDIALVQARWKFVNADECLMTRMQEMSLDYHFTVEQEV-------GSST 251
L RT+ + V +PD+ LVQ F+N D + ++L E E+ G
Sbjct: 256 LARTVGYFVEDPDLFLVQTPHFFINPDPI----QRNLALGDRCPPENEMFYGKIHRGLDR 311
Query: 252 YAFFGFNGTAGVWRISALNEAGGWKDRTTVEDMDLAVRASLKGWKFVYVGDLKVKNELPS 311
+ F G+A V R AL+EAGG+ T ED + A+ +GWK +Y+ + P
Sbjct: 312 WGGAFFCGSAAVLRRRALDEAGGFAGETITEDAETALEIHSRGWKSLYIDRAMIAGLQPE 371
Query: 312 TFKAYRYQQHRWSCG 326
TF ++ Q+ RW+ G
Sbjct: 372 TFASFIQQRGRWATG 386
>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 = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 11/123 (8%)
Query: 97 IPMYNEKEVYQLSIGAACGLSWPSDRITIQVLDDSTDPTIKDLVELECQRWASKGINIKY 156
IP YN ++ +++ C D I V DD + I+++V R +NIKY
Sbjct: 98 IPTYNRAKILAITLACLCNQKTIYDYEVI-VADDGSKENIEEIV-----REFESLLNIKY 151
Query: 157 EIRDSRNGYKAGALKE-GMKHSYVKQCDYVAIFDADFEPEPDFLWRTIPFLVHNPDIALV 215
+R GY+ A++ G++ + + +YVAI D D P P ++ + L + ++AL+
Sbjct: 152 -VRQKDYGYQLCAVRNLGLRAA---KYNYVAILDCDMAPNPLWVQSYMELLAVDDNVALI 207
Query: 216 QAR 218
R
Sbjct: 208 GPR 210
>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 = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 11/123 (8%)
Query: 97 IPMYNEKEVYQLSIGAACGLSWPSDRITIQVLDDSTDPTIKDLVELECQRWASKGINIKY 156
IP YN ++ +++ C D I V DD + I+++V R +NIKY
Sbjct: 99 IPTYNRAKILAITLACLCNQKTIYDYEVI-VADDGSKENIEEIV-----REFESLLNIKY 152
Query: 157 EIRDSRNGYKAGALKE-GMKHSYVKQCDYVAIFDADFEPEPDFLWRTIPFLVHNPDIALV 215
+R GY+ A++ G++ + + +YVAI D D P P ++ + L + ++AL+
Sbjct: 153 -VRQKDYGYQLCAVRNLGLRAA---KYNYVAILDCDMAPNPLWVQSYMELLAVDDNVALI 208
Query: 216 QAR 218
R
Sbjct: 209 GPR 211
>pdb|3IKO|B Chain B, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|E Chain E, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|H Chain H, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
Length = 442
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 131 STDPTIKDLVELECQRWASKGINIKYEI 158
S DP I+DL EL+ Q+W++ G +I I
Sbjct: 217 SNDPRIRDLAELQLQKWSTGGCSIDKNI 244
>pdb|3BG0|B Chain B, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|C Chain C, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|F Chain F, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|G Chain G, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|B Chain B, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|C Chain C, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|F Chain F, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|G Chain G, Architecture Of A Coat For The Nuclear Pore Membrane
Length = 442
Score = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 131 STDPTIKDLVELECQRWASKGINIKYEI 158
S DP I+DL EL+ Q+W++ G +I I
Sbjct: 217 SNDPRIRDLAELQLQKWSTGGCSIDKNI 244
>pdb|3JRO|A Chain A, Nup84-Nup145c-Sec13 Edge Element Of The Npc Lattice
Length = 753
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 131 STDPTIKDLVELECQRWASKGINIKYEI 158
S DP I+DL EL+ Q+W++ G +I I
Sbjct: 526 SNDPRIRDLAELQLQKWSTGGCSIDKNI 553
>pdb|2V71|A Chain A, Coiled-Coil Region Of Nudel
pdb|2V71|B Chain B, Coiled-Coil Region Of Nudel
Length = 189
Score = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 140 VELECQRWASKGINIKYEIRDSRNGYKAGALKEGMKHSYVKQCDYVAIFDADF 192
ELE Q ++ N + + R Y+ ALKE ++H Y + V++ + D
Sbjct: 45 AELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDL 97
>pdb|2BG9|E Chain E, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 28.9 bits (63), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 68 RKPEKRYKWEAIKDDVELGNSAYPMVLVQIPMYNEKEVYQLSIGAACGL 116
R +K Y W+ KDD++ + +++ + P++ Y ++I A C L
Sbjct: 181 RPAKKNYNWQLTKDDIDFQEIIFFLIIQRKPLF-----YIINIIAPCVL 224
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
0.325 0.140 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,368,900
Number of Sequences: 62578
Number of extensions: 628293
Number of successful extensions: 1504
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1498
Number of HSP's gapped (non-prelim): 9
length of query: 526
length of database: 14,973,337
effective HSP length: 103
effective length of query: 423
effective length of database: 8,527,803
effective search space: 3607260669
effective search space used: 3607260669
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)