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= 012812
(456 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NGN|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Amp
pdb|3NGO|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Poly(A) Dna
Length = 398
Score = 144 bits (363), Expect = 9e-35, Method: Compositional matrix adjust.
Identities = 76/204 (37%), Positives = 117/204 (57%), Gaps = 13/204 (6%)
Query: 247 RISSTGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEV 306
+I + +F+V+ YN+L D YAT + Y YCPSWAL+W YR++ ++ EI+ ADI+ LQEV
Sbjct: 25 QILPSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEV 84
Query: 307 QNDHFEEFFAPELDKHGYQALY--KRKTNEVYNGNPHTIDGCATFFRRDRFSHVKKYEVE 364
+ + + F P L + GY + K + + +DGCA FF+ ++F+ V+K+ VE
Sbjct: 85 ETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVE 144
Query: 365 FNKAAQSLTDAILPSAQKKNALNR-LVKDNVALIVVLEAKFSNQGADT----PGKRQLLC 419
FN+ A + +D + LNR + KDN+ + VVLE GA +QLL
Sbjct: 145 FNQVAMANSDG------SEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLI 198
Query: 420 VANTHVNVHQELKDVKLWQVLIIL 443
VAN H++ E DVKL Q ++ +
Sbjct: 199 VANAHMHWDPEYSDVKLIQTMMFV 222
>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
Length = 398
Score = 144 bits (363), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 76/204 (37%), Positives = 117/204 (57%), Gaps = 13/204 (6%)
Query: 247 RISSTGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEV 306
+I + +F+V+ YN+L D YAT + Y YCPSWAL+W YR++ ++ EI+ ADI+ LQEV
Sbjct: 25 QILPSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEV 84
Query: 307 QNDHFEEFFAPELDKHGYQALY--KRKTNEVYNGNPHTIDGCATFFRRDRFSHVKKYEVE 364
+ + + F P L + GY + K + + +DGCA FF+ ++F+ V+K+ VE
Sbjct: 85 ETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVE 144
Query: 365 FNKAAQSLTDAILPSAQKKNALNR-LVKDNVALIVVLEAKFSNQGADT----PGKRQLLC 419
FN+ A + +D + LNR + KDN+ + VVLE GA +QLL
Sbjct: 145 FNQVAMANSDG------SEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLI 198
Query: 420 VANTHVNVHQELKDVKLWQVLIIL 443
VAN H++ E DVKL Q ++ +
Sbjct: 199 VANAHMHWDPEYSDVKLIQTMMFV 222
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 132 bits (331), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 75/194 (38%), Positives = 113/194 (58%), Gaps = 16/194 (8%)
Query: 253 TFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFE 312
TF+VLSYN L YAT + Y Y PSWALSW YRR L +I+ Y +D++CLQEV++ FE
Sbjct: 394 TFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFE 453
Query: 313 EFFAPELDKHGYQALY--KRKTNEVYNGNPHTIDGCATFFRRDRFSHVKKYEVEFNKAAQ 370
E++ P LDKHGY ++ K + +++ + +DGC FF+RD+F + K ++F+ A
Sbjct: 454 EYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWM 513
Query: 371 SLTDAILPSAQKKNALNR-LVKDNVALIVVLEAKFSNQGADTPGKRQLLCVANTHVNVHQ 429
+ ++ LNR + KDNVAL + L+ S DT + TH++
Sbjct: 514 KHKKF----QRTEDYLNRAMNKDNVALFLKLQHIPS---GDT------IWAVTTHLHWDP 560
Query: 430 ELKDVKLWQVLIIL 443
+ DVK +QV ++L
Sbjct: 561 KFNDVKTFQVGVLL 574
>pdb|2BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase H256a
Mutant With F6p In Phosphatase Active Site
pdb|2BIF|B Chain B, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase H256a
Mutant With F6p In Phosphatase Active Site
Length = 469
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 51/112 (45%), Gaps = 10/112 (8%)
Query: 224 SPRRLFPVNG--SDMNMMGHIDSDGRISSTG-TFSVLSYNILSD-------VYATSESYS 273
+PR ++ S++N+ G I D +S G FS +SD V+ + +
Sbjct: 248 TPRSIYLCRAGESELNLKGRIGGDPGLSPRGREFSKHLAQFISDQNIKDLKVFTSQMKRT 307
Query: 274 YCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQ 325
+ ALS Y + +L EI + + +E+Q+ + EF + DK+ Y+
Sbjct: 308 IQTAEALSVPYEQFKVLNEIDAGVCEEMTYEEIQDHYPLEFALRDQDKYRYR 359
>pdb|3BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase Empty
6-Pf-2k Active Site
Length = 468
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 234 SDMNMMGHIDSDGRISSTG-TFSVLSYNILSD-------VYATSESYSYCPSWALSWAYR 285
S++N+ G I D +S G FS +SD V+ + + + ALS Y
Sbjct: 259 SELNLKGRIGGDPGLSPRGREFSKHLAQFISDQNIKDLKVFTSQMKRTIQTAEALSVPYE 318
Query: 286 RQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQ 325
+ +L EI + + +E+Q+ + EF + DK+ Y+
Sbjct: 319 QFKVLNEIDAGVCEEMTYEEIQDHYPLEFALRDQDKYRYR 358
>pdb|1BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase
Bifunctional Enzyme Complexed With Atp-G-S And Phosphate
Length = 469
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 234 SDMNMMGHIDSDGRISSTG-TFSVLSYNILSD-------VYATSESYSYCPSWALSWAYR 285
S++N+ G I D +S G FS +SD V+ + + + ALS Y
Sbjct: 260 SELNLKGRIGGDPGLSPRGREFSKHLAQFISDQNIKDLKVFTSQMKRTIQTAEALSVPYE 319
Query: 286 RQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQ 325
+ +L EI + + +E+Q+ + EF + DK+ Y+
Sbjct: 320 QFKVLNEIDAGVCEEMTYEEIQDHYPLEFALRDQDKYRYR 359
>pdb|3G6S|A Chain A, Crystal Structure Of The
EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM
Bacteroides Vulgatus. Northeast Structural Genomics
Consortium Target Bvr56d
Length = 267
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 14/73 (19%)
Query: 281 SWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFA--PELDKHG-----------YQAL 327
+W YR+ + + I + DIV QEV ++ F++ A PE D G Y L
Sbjct: 22 NWQYRKDRVCQFIKDHELDIVGXQEVLHNQFQDLRAGLPEYDGIGVGRDDGKTAGEYAPL 81
Query: 328 YKRKTN-EVYNGN 339
+ RK EV + N
Sbjct: 82 FYRKDKYEVLDSN 94
>pdb|2QQY|A Chain A, Crystal Structure Of Ferritin Like, Diiron-Carboxylate
Proteins From Bacillus Anthracis Str. Ames
Length = 149
Score = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 26/123 (21%), Positives = 43/123 (34%), Gaps = 18/123 (14%)
Query: 293 IIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALYKRKTNEVYNGNPHTID-------- 344
II Y + + + + FF E+ ALY + + G P TI
Sbjct: 26 IIXYNHNAATVSGIYRQVLKPFFESEISDEQGHALYLAEKIKTLGGTPTTIPLRVKQAED 85
Query: 345 --GCATFFRRDRFSHVKKYEVEFNKAAQ--------SLTDAILPSAQKKNALNRLVKDNV 394
+ R+ + +K+YE +AA L D I L+RL+ D
Sbjct: 86 VREXLEYARQSEYETIKRYEKRKEQAANLNXTELVVKLEDXIADETNHXEELDRLLNDKA 145
Query: 395 ALI 397
++
Sbjct: 146 XVL 148
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
0.321 0.135 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,127,083
Number of Sequences: 62578
Number of extensions: 520629
Number of successful extensions: 1202
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 1194
Number of HSP's gapped (non-prelim): 31
length of query: 456
length of database: 14,973,337
effective HSP length: 102
effective length of query: 354
effective length of database: 8,590,381
effective search space: 3040994874
effective search space used: 3040994874
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)