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= psy3836
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LCK|A Chain A, Structure Of The Mitochondrial Uncoupling Protein 2
Determined By Nmr Molecular Fragment Replacement
Length = 303
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 59/194 (30%), Positives = 87/194 (44%), Gaps = 9/194 (4%)
Query: 16 EHLLAGVTGGVTSTLILHPLDLLKIRFAVSDGRSPNPSYNNLSNAVHTIFRQEGFKGLYK 75
LLAG T G + + P D++K+RF Y + A TI R+EG +GL+K
Sbjct: 106 SRLLAGSTTGALAVAVAQPTDVVKVRFQAQARAGGGRRYQSTVEAYKTIAREEGIRGLWK 165
Query: 76 GVTPNIWGSGSAWGFYFLFYNTIKTWIQQGNTTKPIGPTMNMVAAAEAGILTLVMTNPVW 135
G +PN+ + + Y+ IK + + N P + +A AG T V+ +PV
Sbjct: 166 GTSPNVARNAIVNCAELVTYDLIKDTLLKANLMTDDLPC-HFTSAFGAGFCTTVIASPVD 224
Query: 136 VVKTRLCLQYANDKVPTSKRYSGMIDALHKIYSVEGIRGLYKGFVPGMFGV-SHGAVQFM 194
VVKTR Y N + +Y + EG R YKGF+P + S V F+
Sbjct: 225 VVKTR----YMNSAL---GQYHSAGHCALTMLRKEGPRAFYKGFMPSFLRLGSWNVVMFV 277
Query: 195 VYEEMKSHYTQYYD 208
YE++K Y
Sbjct: 278 TYEQLKRALMAAYQ 291
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 4/96 (4%)
Query: 114 TMNMVAAAEAGILTLVMTNPVWVVKTRLCLQYAND---KVPTSKRYSGMIDALHKIYSVE 170
T+ + A A + ++T P+ K RL +Q + + S +Y G++ + + E
Sbjct: 2 TVKFLGAGTAACIADLITFPLDTAKVRLQIQGESQGLVRTAASAQYRGVLGTILTMVRTE 61
Query: 171 GIRGLYKGFVPGM-FGVSHGAVQFMVYEEMKSHYTQ 205
G R LY G V G+ +S +V+ +Y+ +K YT+
Sbjct: 62 GPRSLYNGLVAGLQRQMSFASVRIGLYDSVKQFYTK 97
>pdb|1OKC|A Chain A, Structure Of Mitochondrial AdpATP CARRIER IN COMPLEX WITH
Carboxyatractyloside
pdb|2C3E|A Chain A, The Bovine Mitochondrial Adp-Atp Carrier
Length = 297
Score = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 49/185 (26%), Positives = 83/185 (44%), Gaps = 6/185 (3%)
Query: 17 HLLAGVTGGVTSTLILHPLDLLKIRFAVSDGR-SPNPSYNNLSNAVHTIFRQEGFKGLYK 75
+L +G G TS ++PLD + R A G+ + + L N + IF+ +G +GLY+
Sbjct: 115 NLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFTGLGNCITKIFKSDGLRGLYQ 174
Query: 76 GVTPNIWGSGSAWGFYFLFYNTIKTWIQQGNTTKPIGPTMNMVAAAEAGILTLVMTNPVW 135
G ++ G YF Y+T K + I M+A + LV + P
Sbjct: 175 GFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHII--VSWMIAQTVTAVAGLV-SYPFD 231
Query: 136 VVKTRLCLQYANDKVPTSKRYSGMIDALHKIYSVEGIRGLYKGFVPGMFGVSHGAVQFMV 195
V+ R+ +Q + + Y+G +D KI EG + +KG + GA ++
Sbjct: 232 TVRRRMMMQ--SGRKGADIMYTGTVDCWRKIAKDEGPKAFFKGAWSNVLRGMGGAFVLVL 289
Query: 196 YEEMK 200
Y+E+K
Sbjct: 290 YDEIK 294
Score = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 33/63 (52%)
Query: 116 NMVAAAEAGILTLVMTNPVWVVKTRLCLQYANDKVPTSKRYSGMIDALHKIYSVEGIRGL 175
+ +A A ++ P+ VK L +Q+A+ ++ K+Y G+ID + +I +G
Sbjct: 10 DFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSF 69
Query: 176 YKG 178
++G
Sbjct: 70 WRG 72
>pdb|1YQA|A Chain A, Engineering The Structural Stability And Functional
Properties Of The Gi Domain Into The Intrinsically
Unfolded Gii Domain Of The Yeast Linker Histone Hho1p
Length = 87
Score = 30.8 bits (68), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 85 GSAWGFYFLFYNTIKTWIQQGNTTKPIGPT 114
GSA F +LF + IK ++ G +P GP+
Sbjct: 44 GSASNFDYLFNSAIKKCVENGELVQPKGPS 73
>pdb|3RH9|A Chain A, The Crystal Structure Of Oxidoreductase From Marinobacter
Aquaeolei
pdb|3RH9|B Chain B, The Crystal Structure Of Oxidoreductase From Marinobacter
Aquaeolei
Length = 506
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 110 PIGPTMNMVAAAEAGILTLVMTNPVWVVKTR 140
P P ++VAA EAG L +TNP W ++TR
Sbjct: 44 PSXPEEDVVAAVEAGQSALRLTNP-WPIETR 73
>pdb|2W27|A Chain A, Crystal Structure Of The Bacillus Subtilis Ykui Protein,
With An Eal Domain, In Complex With Substrate C-Di-Gmp
And Calcium
pdb|2W27|B Chain B, Crystal Structure Of The Bacillus Subtilis Ykui Protein,
With An Eal Domain, In Complex With Substrate C-Di-Gmp
And Calcium
Length = 431
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 23 TGGVTSTLILHPLDLLKIRFAVSDGRSPNPSYNNLSNAVHTIFRQEGFKGLYKGVTPNI- 81
+ + +L P DLLKI P+PSY ++ ++ + R+ G LY+ + N
Sbjct: 182 SSNLDRIALLSP-DLLKIDLQALKVSQPSPSYEHVLYSISLLARKIGAALLYEDIEANFQ 240
Query: 82 ----WGSGSAW--GFYFL 93
W +G + G+Y +
Sbjct: 241 LQYAWRNGGRYFQGYYLV 258
>pdb|2BAS|A Chain A, Crystal Structure Of The Bacillus Subtilis Ykui Protein,
With An Eal Domain.
pdb|2BAS|B Chain B, Crystal Structure Of The Bacillus Subtilis Ykui Protein,
With An Eal Domain
Length = 431
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 23 TGGVTSTLILHPLDLLKIRFAVSDGRSPNPSYNNLSNAVHTIFRQEGFKGLYKGVTPNI- 81
+ + +L P DLLKI P+PSY ++ ++ + R+ G LY+ + N
Sbjct: 182 SSNLDRIALLSP-DLLKIDLQALKVSQPSPSYEHVLYSISLLARKIGAALLYEDIEANFQ 240
Query: 82 ----WGSGSAW--GFYFL 93
W +G + G+Y +
Sbjct: 241 LQYAWRNGGRYFQGYYLV 258
>pdb|2OEB|A Chain A, The Crystal Structure Of Gene Product Af1862 From
Archaeoglobus Fulgidus
Length = 155
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 74 YKGVTPNIWGSGSAWGFYFLFYNTIKTWIQQGN 106
YK + P +G+ + FL Y + TW+ +GN
Sbjct: 71 YKSINPESFGNAENIAYAFL-YKHLSTWLAEGN 102
>pdb|2EF0|A Chain A, Crystal Structure Of Ornithine Carbamoyltransferase From
Thermus Thermophilus
Length = 301
Score = 27.3 bits (59), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 26 VTSTLILHPLDLLKIRFAVSDGRSPNPSYNNLSNAVHTIFRQEGFKGLYKGVTPNIWGS 84
+ S L + PL LK+R A G P+P +NA T +E G + T ++W S
Sbjct: 167 LNSLLEVAPLAGLKVRVATPKGYEPDPGLLKRANAFFTHDPKEAALGAHALYT-DVWTS 224
>pdb|3S7V|A Chain A, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|B Chain B, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|C Chain C, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|D Chain D, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|E Chain E, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|F Chain F, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|G Chain G, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|H Chain H, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|I Chain I, Unassembled Ki Polyomavirus Vp1 Pentamer
pdb|3S7V|J Chain J, Unassembled Ki Polyomavirus Vp1 Pentamer
Length = 277
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 43 AVSDGRSPNPSYNNLSNAVH 62
A DGR P P Y ++S+A+H
Sbjct: 36 AAQDGREPTPHYWSISSAIH 55
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
0.320 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,140,909
Number of Sequences: 62578
Number of extensions: 302113
Number of successful extensions: 499
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 483
Number of HSP's gapped (non-prelim): 13
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)