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= 003374
(825 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4IOY|X Chain X, Structure Of The Spt16 Middle Domain Reveals Functional
Features Of The Histone Chaperone Fact
Length = 285
Score = 206 bits (523), Expect = 6e-53, Method: Compositional matrix adjust.
Identities = 116/275 (42%), Positives = 164/275 (59%), Gaps = 9/275 (3%)
Query: 438 KLHDLWIRPVFGGRGRKIPGTLEAHLNGFRFATS-RPEERVDIMFGNIKHAFFQPAEKEM 496
+L +++RP +++P T+ H NG RF + R + R+DI+F NIK+ FQ + E+
Sbjct: 13 RLDQIFVRP--NPDTKRVPSTVFIHENGIRFQSPLRTDSRIDILFSNIKNLIFQSCKGEL 70
Query: 497 ITLVHFHLHNHIMVGNKKTKDVQFYVEVMDVVQTLGGGKRSAYDPDEIEEEQRERARKNK 556
I ++H HL N I++G KK +DVQFY E D+ G R D DE+E+EQ ER ++
Sbjct: 71 IVVIHIHLKNPILMGKKKIQDVQFYREASDMSVDETGRFRRYGDEDELEQEQEERRKRAA 130
Query: 557 INMDFQSFVNRVNDLWGQPKFNGLDLEFDQPLRDLGFHGVPHKASAFIVPTSSCLVELIE 616
++ +F+ F + + + NGL L + RDLGF GVP++++ F +PT+ CLV+LIE
Sbjct: 131 LDKEFKYFADAIAE-----ASNGL-LTVENTFRDLGFQGVPNRSAVFCMPTTDCLVQLIE 184
Query: 617 TPFLVVTLGEIEIVNLERVGLGQKNFDMTIVFKDFKKDVLRXXXXXXXXXXXXKEWLDTT 676
PFLV+ L E+EI LERV G KNFDM V+KDF K V K+WL
Sbjct: 185 PPFLVINLEEVEICILERVQFGLKNFDMVFVYKDFNKPVTHINTVPIESLDFLKQWLTDM 244
Query: 677 DIKYYESRLNLNWRQILKTITDDPQSFIDDGGWEF 711
DI Y S +NLNW I+K++ DDP F DGGW F
Sbjct: 245 DIPYTVSTINLNWATIMKSLQDDPYQFFLDGGWNF 279
>pdb|3CB6|A Chain A, Crystal Structure Of The S. Pombe Peptidase Homology
Domain Of Fact Complex Subunit Spt16 (Form B)
Length = 444
Score = 82.4 bits (202), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 60/205 (29%), Positives = 100/205 (48%), Gaps = 16/205 (7%)
Query: 16 GGANAYSINLENFSTRLKALYSHWNKHKSD---YWGSADVLAIATPPASEDLRYLKSSAL 72
G Y I+ F RL L + W K++ D + D + + + Y KS+AL
Sbjct: 1 GAMAEYEIDEITFHKRLGILLTSW-KNEEDGKTLFQDCDSILVTVGAHDDTNPYQKSTAL 59
Query: 73 NIWLLGYEFPETVMVFMKKQIQFLCSQKKASLLGMVKRSAKDAVGADVVIHVKAK-TDDG 131
+ WLLGYEFP T+++ K +I L S KA++L K + ADV I + K ++
Sbjct: 60 HTWLLGYEFPSTLILLEKHRITILTSVNKANML--TKLAETKGAAADVNILKRTKDAEEN 117
Query: 132 VELMDAIFNAVRSQSNVDSGDGPIVGSIARETPEGRLLETWADRLQ--NSGFQLSDVTNG 189
+L + I +R+ + VG ++ +G+ + W + S F L D + G
Sbjct: 118 KKLFEKIIEYIRATNKK-------VGVFPKDKTQGKFINEWDSIFEPVKSEFNLVDASLG 170
Query: 190 LSELFAVKDQEEIMNVKKAAVKDVA 214
L++ A+KD++E+ N+K A+ VA
Sbjct: 171 LAKCLAIKDEQELANIKGASRVSVA 195
>pdb|3CB5|A Chain A, Crystal Structure Of The S. Pombe Peptidase Homology
Domain Of Fact Complex Subunit Spt16 (form A)
pdb|3CB5|B Chain B, Crystal Structure Of The S. Pombe Peptidase Homology
Domain Of Fact Complex Subunit Spt16 (form A)
Length = 444
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 60/205 (29%), Positives = 99/205 (48%), Gaps = 16/205 (7%)
Query: 16 GGANAYSINLENFSTRLKALYSHWNKHKSD---YWGSADVLAIATPPASEDLRYLKSSAL 72
G Y I+ F RL L + W K++ D + D + + + Y KS+AL
Sbjct: 1 GAXAEYEIDEITFHKRLGILLTSW-KNEEDGKTLFQDCDSILVTVGAHDDTNPYQKSTAL 59
Query: 73 NIWLLGYEFPETVMVFMKKQIQFLCSQKKASLLGMVKRSAKDAVGADVVIHVKAK-TDDG 131
+ WLLGYEFP T+++ K +I L S KA+ L K + ADV I + K ++
Sbjct: 60 HTWLLGYEFPSTLILLEKHRITILTSVNKANXL--TKLAETKGAAADVNILKRTKDAEEN 117
Query: 132 VELMDAIFNAVRSQSNVDSGDGPIVGSIARETPEGRLLETWADRLQ--NSGFQLSDVTNG 189
+L + I +R+ + VG ++ +G+ + W + S F L D + G
Sbjct: 118 KKLFEKIIEYIRATNKK-------VGVFPKDKTQGKFINEWDSIFEPVKSEFNLVDASLG 170
Query: 190 LSELFAVKDQEEIMNVKKAAVKDVA 214
L++ A+KD++E+ N+K A+ VA
Sbjct: 171 LAKCLAIKDEQELANIKGASRVSVA 195
>pdb|3BIP|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIP|B Chain B, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIQ|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
Length = 467
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 92/190 (48%), Gaps = 12/190 (6%)
Query: 16 GGANAYSINLENFSTRLKALYSHWNKHKSDYWGSADVLAIATPPASEDLRYLKSSALNIW 75
G +I+ + F R++ LYS +N ++ GS + L ++ + Y K++ L+ W
Sbjct: 1 GHMEELNIDFDVFKKRIELLYSKYN----EFEGSPNSLLFVLGSSNAENPYQKTTILHNW 56
Query: 76 LLGYEFPETVMVFMKKQIQFLCSQKKASLLGMVKRSAKDAVGADVVIHVKAKTDDGVELM 135
LL YEFP T++ + ++ + S KA L KD + + + + + + EL
Sbjct: 57 LLSYEFPATLIALVPGKVIIITSSAKAKHLQKAIDLFKDP-ESKITLELWQRNNKEPELN 115
Query: 136 DAIFNAVRSQSNVDSGDGPIVGSIARETPEGRLLE----TWADRLQNSGFQLSDVTNGLS 191
+F+ V + N G VG +++ +G+ + W ++ + F + D++ GLS
Sbjct: 116 KKLFDDVIALIN---SAGKTVGIPEKDSYQGKFMTEWNPVWEAAVKENEFNVIDISLGLS 172
Query: 192 ELFAVKDQEE 201
+++ VKD E
Sbjct: 173 KVWEVKDVNE 182
>pdb|3BIT|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIT|B Chain B, Crystal Structure Of Yeast Spt16 N-Terminal Domain
Length = 453
Score = 60.1 bits (144), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 91/190 (47%), Gaps = 12/190 (6%)
Query: 16 GGANAYSINLENFSTRLKALYSHWNKHKSDYWGSADVLAIATPPASEDLRYLKSSALNIW 75
G +I+ + F R++ LYS +N ++ GS + L ++ + Y K++ L+ W
Sbjct: 1 GHXEELNIDFDVFKKRIELLYSKYN----EFEGSPNSLLFVLGSSNAENPYQKTTILHNW 56
Query: 76 LLGYEFPETVMVFMKKQIQFLCSQKKASLLGMVKRSAKDAVGADVVIHVKAKTDDGVELM 135
LL YEFP T++ + ++ + S KA L KD + + + + + + EL
Sbjct: 57 LLSYEFPATLIALVPGKVIIITSSAKAKHLQKAIDLFKDP-ESKITLELWQRNNKEPELN 115
Query: 136 DAIFNAVRSQSNVDSGDGPIVGSIARETPEGRLLE----TWADRLQNSGFQLSDVTNGLS 191
+F+ V + N G VG +++ +G+ W ++ + F + D++ GLS
Sbjct: 116 KKLFDDVIALIN---SAGKTVGIPEKDSYQGKFXTEWNPVWEAAVKENEFNVIDISLGLS 172
Query: 192 ELFAVKDQEE 201
+++ VKD E
Sbjct: 173 KVWEVKDVNE 182
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
0.317 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,254,548
Number of Sequences: 62578
Number of extensions: 876583
Number of successful extensions: 1930
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1918
Number of HSP's gapped (non-prelim): 6
length of query: 825
length of database: 14,973,337
effective HSP length: 107
effective length of query: 718
effective length of database: 8,277,491
effective search space: 5943238538
effective search space used: 5943238538
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)