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= psy16255
(156 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZWF|A Chain A, Crystal Structure Of Human Trnase Z, Short Form (Elac1).
pdb|3ZWF|B Chain B, Crystal Structure Of Human Trnase Z, Short Form (Elac1)
Length = 368
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 51/98 (52%), Gaps = 12/98 (12%)
Query: 32 VNLQVLGSGA------RGAPKSLYLFTDQSRYLFNCGEGTQRLAHEHKMKLAKLDSVFIT 85
+++ LG+GA RGA ++ L + +LF+CGEGTQ + ++K ++ +FIT
Sbjct: 1 MDVTFLGTGAAYPSPTRGA-SAVVLRCEGECWLFDCGEGTQTQLMKSQLKAGRITKIFIT 59
Query: 86 QPVWENLGGLLGLALTI-----QDVGVPEINLHGPEGL 118
++ GL GL TI V I ++GP GL
Sbjct: 60 HLHGDHFFGLPGLLCTISLQSGSMVSKQPIEIYGPVGL 97
>pdb|2CBN|A Chain A, Crystal Structure Of Zipd From Escherichia Coli
Length = 306
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 52 TDQSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQPVWENLGGLLGLALTIQDVGVPE-I 110
T +LF+CGEGTQ KLD +FI+ ++L GL GL + G+ + +
Sbjct: 31 TQSGLWLFDCGEGTQHQLLHTAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMSGIIQPL 90
Query: 111 NLHGPEGL 118
++GP+G+
Sbjct: 91 TIYGPQGI 98
>pdb|2FK6|A Chain A, Crystal Structure Of Rnase ZTRNA(THR) COMPLEX
Length = 320
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 54 QSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQPVWENLGGLLGL--ALTIQDVGVPEIN 111
+S +LF+CGE TQ +K K++ +FIT +++ GL GL + + Q G E+
Sbjct: 31 RSVWLFDCGEATQHQMLHTTIKPRKIEKIFITHMAGDHVYGLPGLLGSRSFQG-GEDELT 89
Query: 112 LHGPEGL 118
++GP+G+
Sbjct: 90 VYGPKGI 96
>pdb|1Y44|A Chain A, Crystal Structure Of Rnase Z
pdb|1Y44|B Chain B, Crystal Structure Of Rnase Z
Length = 320
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 54 QSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQPVWENLGGLLGL--ALTIQDVGVPEIN 111
+S +LF+CGE TQ +K K++ +FIT +++ GL GL + + Q G E+
Sbjct: 31 RSVWLFDCGEATQHQXLHTTIKPRKIEKIFITHXHGDHVYGLPGLLGSRSFQG-GEDELT 89
Query: 112 LHGPEGL 118
++GP+G+
Sbjct: 90 VYGPKGI 96
>pdb|4GCW|A Chain A, Crystal Structure Of Rnase Z In Complex With Precursor
Trna(Thr)
Length = 320
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 54 QSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQPVWENLGGLLGL--ALTIQDVGVPEIN 111
+S +LF+CGE TQ +K K++ +FIT +++ GL GL + + Q G E+
Sbjct: 31 RSVWLFDCGEATQHQMLHTTIKPRKIEKIFITHMHGDHVYGLPGLLGSRSFQG-GEDELT 89
Query: 112 LHGPEGL 118
++GP+G+
Sbjct: 90 VYGPKGI 96
>pdb|1J3N|A Chain A, Crystal Structure Of 3-Oxoacyl-(Acyl-Carrier Protein)
Synthase Ii From Thermus Thermophilus Hb8
pdb|1J3N|B Chain B, Crystal Structure Of 3-Oxoacyl-(Acyl-Carrier Protein)
Synthase Ii From Thermus Thermophilus Hb8
Length = 408
Score = 29.3 bits (64), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 37/80 (46%), Gaps = 20/80 (25%)
Query: 55 SRYLFNCGEGTQRL---AHEHKMK-----LAKL-------DSVFITQPVWENLGGLLGLA 99
SR F GEG L A+EH K A+L D+ IT+P E G L +A
Sbjct: 223 SRDGFVMGEGAGVLVLEAYEHAKKRGARIYAELVGFGRSADAHHITEPHPEGKGAALAMA 282
Query: 100 LTIQDVGV-PE----INLHG 114
++D G+ PE IN HG
Sbjct: 283 RALKDAGIAPEQVGYINAHG 302
>pdb|2YEW|C Chain C, Modeling Barmah Forest Virus Structural Proteins
pdb|2YEW|F Chain F, Modeling Barmah Forest Virus Structural Proteins
pdb|2YEW|I Chain I, Modeling Barmah Forest Virus Structural Proteins
pdb|2YEW|L Chain L, Modeling Barmah Forest Virus Structural Proteins
Length = 421
Score = 29.3 bits (64), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 39/173 (22%), Positives = 64/173 (36%), Gaps = 21/173 (12%)
Query: 2 SGNKVMQHAQNLKFQRVKMREKSMKYVPGIVNLQVLGSGARGAPKSLYLFTDQSRYLFNC 61
+G+K + Q RE+ +VP V +Q L S G SL T +Y C
Sbjct: 142 TGHKTRIPCKTYSHQTDLTREEITMHVPPDVPIQGLVSNT-GKSYSLDPKTKTIKYKCTC 200
Query: 62 GEGTQRLAHEHKMKLAKLDSV------FITQPVWE------------NLGGLLGLALTIQ 103
GE + +K+ L D+ + VW+ + G + + +
Sbjct: 201 GETVKEGTATNKITLFNCDTAPKCITYAVDNTVWQYNSQYVPRSEVTEVKGKIHVPFPLT 260
Query: 104 DVGVPEINLHGPEGLVSENMGLASNSISPSDPALIQARTLMKIPLRPRLPLDT 156
D +++ PE V+ +G P P L R+L K P + +DT
Sbjct: 261 DSTC-AVSV-APEPQVTYRLGEVEFHFHPMYPTLFSIRSLGKDPSHSQEWIDT 311
>pdb|3CX5|C Chain C, Structure Of Complex Iii With Bound Cytochrome C In
Reduced State And Definition Of A Minimal Core Interface
For Electron Transfer.
pdb|3CX5|N Chain N, Structure Of Complex Iii With Bound Cytochrome C In
Reduced State And Definition Of A Minimal Core Interface
For Electron Transfer.
pdb|3CXH|C Chain C, Structure Of Yeast Complex Iii With Isoform-2 Cytochrome C
Bound And Definition Of A Minimal Core Interface For
Electron Transfer.
pdb|3CXH|N Chain N, Structure Of Yeast Complex Iii With Isoform-2 Cytochrome C
Bound And Definition Of A Minimal Core Interface For
Electron Transfer
Length = 385
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 11/64 (17%)
Query: 73 KMKLAKLDSVFITQP------VWENLGGLLGLALTIQDVGVPEINLHGPEGLVSENMGLA 126
+ L+ ++S I P W N+G LLGL L IQ V + +H S N+ LA
Sbjct: 7 NVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMH-----YSSNIELA 61
Query: 127 SNSI 130
+S+
Sbjct: 62 FSSV 65
>pdb|1EZV|C Chain C, Structure Of The Yeast Cytochrome Bc1 Complex Co-
Crystallized With An Antibody Fv-Fragment
pdb|1KYO|C Chain C, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
pdb|1KYO|N Chain N, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
pdb|1KB9|C Chain C, Yeast Cytochrome Bc1 Complex
pdb|1P84|C Chain C, Hdbt Inhibited Yeast Cytochrome Bc1 Complex
pdb|2IBZ|C Chain C, Yeast Cytochrome Bc1 Complex With Stigmatellin
Length = 385
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 11/64 (17%)
Query: 73 KMKLAKLDSVFITQP------VWENLGGLLGLALTIQDVGVPEINLHGPEGLVSENMGLA 126
+ L+ ++S I P W N+G LLGL L IQ V + +H S N+ LA
Sbjct: 7 NVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMH-----YSSNIELA 61
Query: 127 SNSI 130
+S+
Sbjct: 62 FSSV 65
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 27.3 bits (59), Expect = 3.3, Method: Composition-based stats.
Identities = 31/95 (32%), Positives = 40/95 (42%), Gaps = 24/95 (25%)
Query: 4 NKVMQH--AQNLKFQRVKMREKSMKYVPGIVNLQVLGSGARGAPKSLYLFTDQSRYLFNC 61
N +M+H Q LK R+K K + +P I+ L G GA K
Sbjct: 155 NNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTA-SPGVGGATK--------------- 198
Query: 62 GEGTQRLAHEHKMKL-AKLDSVFITQPVWENLGGL 95
Q A EH +KL A LD+ F + V ENL L
Sbjct: 199 ----QAKAEEHILKLCANLDA-FTIKTVKENLDQL 228
>pdb|2BDD|A Chain A, Crystal Structure Of Holo-Acp-Synthase From Plasmodium
Yoelii
Length = 182
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 30/134 (22%), Positives = 56/134 (41%), Gaps = 23/134 (17%)
Query: 19 KMREKSMKYVPGIVNLQVLGSGARGAPKSLYLFTDQSRYL---FNCGEGTQRLAHEHKMK 75
K+ EK++ ++ ++N P L F Q + L N ++LA K
Sbjct: 39 KILEKNINFIKKVLN-----------PFELAEFETQKKKLNEKINKSNELKKLAIYVSKK 87
Query: 76 LAKLDSVFITQPVWENLGGLLGLALTIQDV-------GVPEINLHGPEGLVSENMGLASN 128
A ++ I + + L + L++ D+ G P + L+G V+ MG+
Sbjct: 88 FAAKEA--ILKSMGRGLSSISKYGLSMNDIEIKNDKYGKPHVYLYGKAKKVAYEMGIVKI 145
Query: 129 SISPSDPALIQART 142
+S SD +I ++T
Sbjct: 146 FLSISDEKIINSQT 159
>pdb|2QG8|A Chain A, Plasmodium Yoelii Acyl Carrier Protein Synthase Py06285
With Adp Bound
Length = 163
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 29/134 (21%), Positives = 56/134 (41%), Gaps = 23/134 (17%)
Query: 19 KMREKSMKYVPGIVNLQVLGSGARGAPKSLYLFTDQSRYL---FNCGEGTQRLAHEHKMK 75
K+ EK++ ++ ++N P L F Q + L N ++LA K
Sbjct: 20 KILEKNINFIKKVLN-----------PFELAEFETQKKKLNEKINKSNELKKLAIYVSKK 68
Query: 76 LAKLDSVFITQPVWENLGGLLGLALTIQDV-------GVPEINLHGPEGLVSENMGLASN 128
A +++ + + L + L++ D+ G P + L+G V+ MG+
Sbjct: 69 FAAKEAIL--KSMGRGLSSISKYGLSMNDIEIKNDKYGKPHVYLYGKAKKVAYEMGIVKI 126
Query: 129 SISPSDPALIQART 142
+S SD +I ++T
Sbjct: 127 FLSISDEKIINSQT 140
>pdb|2W3Y|A Chain A, Structure Of The Evf Virulence Factor
pdb|2W3Y|B Chain B, Structure Of The Evf Virulence Factor
Length = 283
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 102 IQDVGVPEINLHGPEGLVSEN 122
IQDV + N+HGPEG ++ N
Sbjct: 7 IQDVDLYFQNIHGPEGRLASN 27
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
0.318 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: 4,464,756
Number of Sequences: 62578
Number of extensions: 171875
Number of successful extensions: 386
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 380
Number of HSP's gapped (non-prelim): 13
length of query: 156
length of database: 14,973,337
effective HSP length: 91
effective length of query: 65
effective length of database: 9,278,739
effective search space: 603118035
effective search space used: 603118035
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)