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= 007421
(604 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
Length = 398
Score = 174 bits (440), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 118/370 (31%), Positives = 176/370 (47%), Gaps = 37/370 (10%)
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 VANTHVNVHQELKDVKLWQVHTLLKGLEKIAASA------------DIPMLVCGDFNSVP 467
VAN H++ E DVKL Q + ++ I A IP+++C D NS+P
Sbjct: 199 VANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLP 258
Query: 468 GSAPHALLAMGKVEPVHPDLAVDPLTILRPHTKLTHQLPLVSAYSSFARIGVGLGMEHQR 527
S L+ G V H D LR + L + SS RI G ++
Sbjct: 259 DSGVVEYLSNGGVADNHKDFKE-----LRYNECLMNFSCNGKNGSSEGRITHGFQLKSAY 313
Query: 528 RRMDPTTNEPLFTHCTRDFIGTLDYIFYTAXXXXXXXXXXXXXXXXXRKD--TALPSPEW 585
N +T+ T DF G +DYIFY+ ++ T P P
Sbjct: 314 E-----NNLMPYTNYTFDFKGVIDYIFYSKTHMNVEGVLGPLDPQWLVENNITGCPHPHI 368
Query: 586 SSDHIALLAE 595
SDH +LL +
Sbjct: 369 PSDHFSLLTQ 378
>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 = 174 bits (440), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 118/370 (31%), Positives = 176/370 (47%), Gaps = 37/370 (10%)
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 VANTHVNVHQELKDVKLWQVHTLLKGLEKIAASA------------DIPMLVCGDFNSVP 467
VAN H++ E DVKL Q + ++ I A IP+++C D NS+P
Sbjct: 199 VANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLP 258
Query: 468 GSAPHALLAMGKVEPVHPDLAVDPLTILRPHTKLTHQLPLVSAYSSFARIGVGLGMEHQR 527
S L+ G V H D LR + L + SS RI G ++
Sbjct: 259 DSGVVEYLSNGGVADNHKDFKE-----LRYNECLMNFSCNGKNGSSEGRITHGFQLKSAY 313
Query: 528 RRMDPTTNEPLFTHCTRDFIGTLDYIFYTAXXXXXXXXXXXXXXXXXRKD--TALPSPEW 585
N +T+ T DF G +DYIFY+ ++ T P P
Sbjct: 314 E-----NNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHI 368
Query: 586 SSDHIALLAE 595
SDH +LL +
Sbjct: 369 PSDHFSLLTQ 378
>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 = 169 bits (427), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 115/358 (32%), Positives = 173/358 (48%), Gaps = 48/358 (13%)
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+ P + V TH++
Sbjct: 514 KHKKF----QRTEDYLNRAMNKDNVALFLKLQ--------HIPSGDTIWAVT-THLHWDP 560
Query: 430 ELKDVKLWQVHTLLKGLEKIAAS-------ADI---PMLVCGDFNSVPGSAPHALLAMGK 479
+ DVK +QV LL LE + DI P+L+CGDFNS SA + L+ G+
Sbjct: 561 KFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGR 620
Query: 480 VEPVHPDLAVDPLTILRPHTKLTHQLPLVSAYSSFARIGVGLGMEHQRRRMDPTTNEPLF 539
V+ +H + + +H L L S+Y+ + F
Sbjct: 621 VQ-IHQEGNGRDFGYMS-EKNFSHNLALKSSYNCIGELP--------------------F 658
Query: 540 THCTRDFIGTLDYIFYTAXXXXXXXXXXXXXXXXXRKDTALPSPEWSSDHIALLAEFR 597
T+ T F +DYI+++ K P+ ++ SDHI LLA F
Sbjct: 659 TNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFE 716
>pdb|3G6S|A Chain A, Crystal Structure Of The
EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM
Bacteroides Vulgatus. Northeast Structural Genomics
Consortium Target Bvr56d
Length = 267
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 45/201 (22%), Positives = 79/201 (39%), Gaps = 35/201 (17%)
Query: 281 SWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFA--PELDKHGYQALYKRKTNEVYNG 338
+W YR+ + + I + DIV QEV ++ F++ A PE D G + E
Sbjct: 22 NWQYRKDRVCQFIKDHELDIVGXQEVLHNQFQDLRAGLPEYDGIGVGRDDGKTAGEY--- 78
Query: 339 NPHTIDGCATFFRRDRFSHVKKYEVEFNKAAQSLTDAILPSAQKKNALNRLVKDNVALIV 398
F+R+D KYEV L A+ +++ D V + +
Sbjct: 79 -------APLFYRKD------KYEV--------LDSNTFWLAENPDSVGXXGWDAVCVRI 117
Query: 399 VLEAKFSNQGADTPGKRQLLCVANTHVNVHQELKDVKLWQVHTLLKGLEKIAASADIPML 458
AKF ++ GK + NTH + E + + +++ +++I P +
Sbjct: 118 ATWAKFKDKAT---GK--IFXAVNTHFDHVGE--EARRQSALLIIRKIKEIVGER--PAV 168
Query: 459 VCGDFNSVPGSAPHALLAMGK 479
V GDFN S + + +
Sbjct: 169 VTGDFNVTDASDAYETITTNE 189
>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 = 30.0 bits (66), Expect = 4.3, 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 = 29.6 bits (65), Expect = 5.3, 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|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 = 5.4, 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
>pdb|1BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase
Bifunctional Enzyme Complexed With Atp-G-S And Phosphate
Length = 469
Score = 29.6 bits (65), Expect = 5.6, 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
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 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,409,388
Number of Sequences: 62578
Number of extensions: 694415
Number of successful extensions: 1640
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: 1622
Number of HSP's gapped (non-prelim): 31
length of query: 604
length of database: 14,973,337
effective HSP length: 104
effective length of query: 500
effective length of database: 8,465,225
effective search space: 4232612500
effective search space used: 4232612500
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: 54 (25.4 bits)