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= psy2946
(455 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NPI|A Chain A, Clp1-Atp-Pcf11 Complex
pdb|2NPI|B Chain B, Clp1-Atp-Pcf11 Complex
Length = 460
Score = 115 bits (288), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 109/429 (25%), Positives = 185/429 (43%), Gaps = 38/429 (8%)
Query: 16 DQELRFEVENAQIEIEVTSGLAEIFGVELVKSKKYLFPIGAKGAVYTWHGCSITMK--NA 73
D ++ + E I ++V SG+ EIFG EL +Y F K +Y + K +
Sbjct: 48 DWQIDLKAEGKLI-VKVNSGIVEIFGTELAVDDEYTFQ-NWKFPIYAVEETELLWKCPDL 105
Query: 74 RKNMTYVSKETPMNYYMNVHIILEKQRSEAEQQSKRGPITMIVGPQDVGKSTLCHILLNY 133
N V Y N+H LEK R + GP +IVG GK++L L +Y
Sbjct: 106 TTNTITVKPNHTXKYIYNLHFXLEKIRX----SNFEGPRVVIVGGSQTGKTSLSRTLCSY 161
Query: 134 AVRMPGLNRKPIFVDLDVGQGHVSVPGTIGALVI------ERPA---TIEDGFSQL---A 181
A++ +P++++LD Q +VPG I A I + P ++ G + L
Sbjct: 162 ALKFNAY--QPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQ 219
Query: 182 PIVYNYGHLTPNANLELYQHCVERLWKSVDERMNKDSKTNSSGMIINTCGWIKGD-GFKC 240
P V N+G N N +LY C+ +L + V +R++ D + SG I++T + D
Sbjct: 220 PXVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAE 279
Query: 241 LMACAKSLRVDNILVLDQERLYNELIRELPKSY-------DVVLLPKSGGVVDRSRQFRA 293
L + L V+ LVL E + L ++ K++ ++ +PK GV ++
Sbjct: 280 LHHIIEKLNVNIXLVLCSET--DPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKR 337
Query: 294 EARDKRIKEYFYGSRLKPFNPHSFDIKFGEVQIYKIGAPVLPDSCMPLGVTATEFLTKVV 353
+ I+EYFYGS +P++ + + ++ I+K P + V E +
Sbjct: 338 SLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWK------PSNVFDNEVGRVELFPVTI 391
Query: 354 LVQPGPXXXXXXXXXXXXXXESEILEQNIVGFVCVTHVDMLRQSLSVLCLQARPLPCSKL 413
++ +++ I+GF +T V+ R+ L VL LP
Sbjct: 392 TPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAX 451
Query: 414 ILTDIQYMD 422
ILT +Y++
Sbjct: 452 ILTSYRYLE 460
>pdb|1F3U|B Chain B, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
pdb|1F3U|D Chain D, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
pdb|1F3U|F Chain F, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
pdb|1F3U|H Chain H, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
Length = 171
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 241 LMACAKSLRVDNILVLDQERLYNELIRELPKSYDVVLLPKSGGVVDRSRQFRAEARDKRI 300
+MA + +V N +Q RL +L + K Y +P+SG + +R+ R EAR K+
Sbjct: 27 IMAFNAADKV-NFATWNQARLERDLSNK--KIYQEEEMPESGAGSEFNRKLREEARRKK- 82
Query: 301 KEYFYGSRLKPFNPH 315
YG LK F P
Sbjct: 83 ----YGIVLKEFRPE 93
>pdb|2QEN|A Chain A, The Walker-type Atpase Paby2304 Of Pyrococcus Abyssi
Length = 350
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 11/72 (15%)
Query: 97 EKQRSEAEQQSKRGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVD---LDVGQ 153
E++ + E+ + P+T+++G + VGKS+L LN R I +D L +
Sbjct: 18 EEESRKLEESLENYPLTLLLGIRRVGKSSLLRAFLN--------ERPGILIDCRELYAER 69
Query: 154 GHVSVPGTIGAL 165
GH++ I L
Sbjct: 70 GHITREELIKEL 81
>pdb|1GAJ|A Chain A, Crystal Structure Of A Nucleotide-Free Atp-Binding
Cassette From An Abc Transporter
Length = 257
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNY 133
+G +T+I+GP GKSTL +++ +
Sbjct: 32 KGDVTLIIGPNGSGKSTLINVITGF 56
>pdb|1G6H|A Chain A, Crystal Structure Of The Adp Conformation Of Mj1267, An
Atp- Binding Cassette Of An Abc Transporter
Length = 257
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNY 133
+G +T+I+GP GKSTL +++ +
Sbjct: 32 KGDVTLIIGPNGSGKSTLINVITGF 56
>pdb|1G9X|A Chain A, Characterization Of The Twinning Structure Of Mj1267, An
Atp-Binding Cassette Of An Abc Transporter
pdb|1G9X|B Chain B, Characterization Of The Twinning Structure Of Mj1267, An
Atp-Binding Cassette Of An Abc Transporter
pdb|1G9X|C Chain C, Characterization Of The Twinning Structure Of Mj1267, An
Atp-Binding Cassette Of An Abc Transporter
Length = 257
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNY 133
+G +T+I+GP GKSTL +++ +
Sbjct: 32 KGDVTLIIGPNGSGKSTLINVITGF 56
>pdb|2DBS|A Chain A, Crystal Structure Of A Hypothetical Protein Tthc002 From
Thermus Thermophilus Hb8
pdb|2DBS|B Chain B, Crystal Structure Of A Hypothetical Protein Tthc002 From
Thermus Thermophilus Hb8
Length = 90
Score = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 255 VLDQERLYNELIRELPKSYDVVLLP 279
VL Q L +L+RELP +Y +VLLP
Sbjct: 14 VLXQYLLEADLLRELPPTYRLVLLP 38
>pdb|1MKY|A Chain A, Structural Analysis Of The Domain Interactions In Der, A
Switch Protein Containing Two Gtpase Domains
Length = 439
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 42/92 (45%), Gaps = 16/92 (17%)
Query: 80 VSKETPMNYYMNVHIILEKQRSEAEQQSKRGPIT-----MIVGPQDVGKSTLCHILLNYA 134
VS E +N + I++K + + IT IVG +VGKSTL + +LN
Sbjct: 145 VSAEHNINLDTXLETIIKKLEEKGLDLESKPEITDAIKVAIVGRPNVGKSTLFNAILNKE 204
Query: 135 VRM----PGLNRKP----IFVDLDVGQGHVSV 158
+ PG R P +F+D G+ +V V
Sbjct: 205 RALVSPIPGTTRDPVDDEVFID---GRKYVFV 233
>pdb|1XZP|A Chain A, Structure Of The Gtp-Binding Protein Trme From Thermotoga
Maritima
pdb|1XZQ|A Chain A, Structure Of The Gtp-binding Protein Trme From Thermotoga
Maritima Complexed With 5-formyl-thf
Length = 482
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 97 EKQRSEAEQQSKRGPITMIVGPQDVGKSTLCHILLN----YAVRMPGLNRKPI 145
E ++++A RG +IVG +VGKSTL + LLN +PG R I
Sbjct: 230 ELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVI 282
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 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,189,293
Number of Sequences: 62578
Number of extensions: 533742
Number of successful extensions: 1451
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1438
Number of HSP's gapped (non-prelim): 11
length of query: 455
length of database: 14,973,337
effective HSP length: 102
effective length of query: 353
effective length of database: 8,590,381
effective search space: 3032404493
effective search space used: 3032404493
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: 53 (25.0 bits)