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= 004083
(775 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZXC|A Chain A, Seramidase Complexed With C2
pdb|2ZXC|B Chain B, Seramidase Complexed With C2
pdb|2ZWS|A Chain A, Crystal Structure Analysis Of Neutral Ceramidase From
Pseudomonas Aeruginosa
Length = 646
Score = 230 bits (586), Expect = 3e-60, Method: Compositional matrix adjust.
Identities = 161/447 (36%), Positives = 223/447 (49%), Gaps = 43/447 (9%)
Query: 331 KPQFVSAFCQSNCGDVSPNVLGAFCIDSGLPCDFNQSTCNGKNELCYGRGPGYPDEFEST 390
K FV+AF Q+N G++SPN+ L G GP + +EF++T
Sbjct: 234 KSGFVAAFAQTNAGNLSPNL-----------------------NLKPGSGP-FDNEFDNT 269
Query: 391 RIIGERQFRKAVELFNTATEQLTGKVGYKHAYVDFSNLEVGLPKRGGGTEVVKTCXXXXX 450
R IG RQF KA E+ A E++ G++ + +VDF+ L + P+ G
Sbjct: 270 REIGLRQFAKAYEIAGQAQEEVLGELDSRFRFVDFTRLPI-RPEFTDGQPRQLCTAAIGT 328
Query: 451 XXXXXXXXXXXXXXXFKQGDDKGNPFWKLVRNVLKA-PSKEQVKCQHPKPILLDTGEMKI 509
++G+ NPF + +L P +E V+CQ K IL DTG K
Sbjct: 329 SLAAGSTEDGPGPLGLEEGN---NPFLSALGGLLTGVPPQELVQCQAEKTILADTGNKK- 384
Query: 510 PYDWAPSILPVQILRIGQLVILNVPGEFTTMAGRRLRDAIKMALISGGGGQFNSNVHIVI 569
PY W P++LP+Q+ RIGQL +L P EFT MAG R+R A++ A + G H+V
Sbjct: 385 PYPWTPTVLPIQMFRIGQLELLGAPAEFTVMAGVRIRRAVQAASEAAG------IRHVVF 438
Query: 570 AGLTNTYSQYVTTFDEYQVQRYEGASTLYGPHTLSAYIQEFKKLAAALIIGQTVMPGPPP 629
G N Y+ YVTT +EY Q YEG STLYGP T +AY Q F +A AL V
Sbjct: 439 NGYANAYASYVTTREEYAAQEYEGGSTLYGPWTQAAYQQLFVDMAVALRERLPVETSAIA 498
Query: 630 PDLLDKQISLLPPVVVDATPLGVKFGDVKTDVPQNSTFKRGDMVAVTFWSACPRNDLMTE 689
PDL Q++ VV D +G FGDV P+ S ++ GD V V F + P+NDL TE
Sbjct: 499 PDLSCCQMNFQTGVVADDPYIGKSFGDVLQQ-PRES-YRIGDKVTVAFVTGHPKNDLRTE 556
Query: 690 GTFALVELL--QGQNAWVPAYDDDDFCLKFKWSRPAKLSPQSHATVEWKIPESAVSGVYR 747
TF V + G+ V D+D+ +++W R + S AT+ W IP G Y
Sbjct: 557 KTFLEVVNIGKDGKQTPVTVATDNDWDTQYRWERVGISA--SKATISWSIPPGTEPGHYY 614
Query: 748 IRHFGASKSL-VGSISHFIGSSSAFVV 773
IRH+G +K+ IS GS+ +F V
Sbjct: 615 IRHYGNAKNFWTQKISEIGGSTRSFEV 641
Score = 200 bits (508), Expect = 3e-51, Method: Compositional matrix adjust.
Identities = 103/226 (45%), Positives = 144/226 (63%), Gaps = 3/226 (1%)
Query: 30 YLIGLGSYDITGPAADVNMMGYASAEQIASGVHFRLRARTFIVAEP-QGNRVVFVNLDAC 88
Y GLG DITG AA+V MMGY+S EQ +G+H R AR F++ E G R+V+VN D
Sbjct: 5 YRFGLGKADITGEAAEVGMMGYSSLEQKTAGIHMRQWARAFVIEEAASGRRLVYVNTDLG 64
Query: 89 MASQLVTIKVLERLKARYGDLYTEQNVAISGIHTHAGPGGYLQYVVYIVTSLGFVRQSFD 148
M Q V +KVL RLKA+Y +Y E NV ++ HTH+GPGG+ Y +Y ++ LGF ++F+
Sbjct: 65 MIFQAVHLKVLARLKAKYPGVYDENNVMLAATHTHSGPGGFSHYAMYNLSVLGFQEKTFN 124
Query: 149 ALVDGIEKCIVQAHENLQPGSIYINKGELLDAGVNRSPSSYLNNPAAERSKYKYDVDKEM 208
A+VDGI + I +A LQPG ++ GEL +A NRS S+L NP + + Y+ +D +M
Sbjct: 125 AIVDGIVRSIERAQARLQPGRLFYGSGELRNASRNRSLLSHLKNP--DIAGYEDGIDPQM 182
Query: 209 TLIKFVNEEWGPIGSFNWFATHGTSMSRTNPLISGDNKGAAARFME 254
+++ FV+ G+ +WF H TSM+ N LIS DNKG A+ E
Sbjct: 183 SVLSFVDANGELAGAISWFPVHSTSMTNANHLISPDNKGYASYHWE 228
>pdb|3LR6|A Chain A, Self-Assembly Of Spider Silk Proteins Is Controlled By A
Ph- Relay
pdb|3LR6|B Chain B, Self-Assembly Of Spider Silk Proteins Is Controlled By A
Ph- Relay
Length = 137
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 57/139 (41%), Gaps = 25/139 (17%)
Query: 231 GTSMSRTNPLISGDNKGAAARFMEDWFEQRGSHNGFNSPYSNNPGT--DRVPRRISNLVH 288
G+ S T P N G A FM + + S GF + +N T + + I +L
Sbjct: 1 GSGNSHTTPWT---NPGLAENFMNSFMQGLSSMPGFTASQLDNMSTIAQSMVQSIQSLAA 57
Query: 289 NPLENGNELMKLAASF----------ERSEGRPATRSLSVASRVRNALKRA----DKP-- 332
+ N+L L +F E G +T++ S+AS + NA + ++P
Sbjct: 58 QGRTSPNKLQALNMAFASSMAEIAASEEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFI 117
Query: 333 ----QFVSAFCQSNCGDVS 347
Q VS F Q+ DVS
Sbjct: 118 NEITQLVSMFAQAGMNDVS 136
>pdb|3LRD|A Chain A, Self-Assembly Of Spider Silk Proteins Is Controlled By A
Ph- Relay
pdb|3LRD|B Chain B, Self-Assembly Of Spider Silk Proteins Is Controlled By A
Ph- Relay
Length = 137
Score = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 57/139 (41%), Gaps = 25/139 (17%)
Query: 231 GTSMSRTNPLISGDNKGAAARFMEDWFEQRGSHNGFNSPYSNNPGT--DRVPRRISNLVH 288
G+ S T P N G A FM + + S GF + +N T + + I +L
Sbjct: 1 GSGNSHTTPWT---NPGLAENFMNSFMQGLSSMPGFTASQLDNMSTIAQSMVQSIQSLAA 57
Query: 289 NPLENGNELMKLAASFERSE----------GRPATRSLSVASRVRNALKRA----DKP-- 332
+ N+L L +F S G +T++ S+AS + NA + ++P
Sbjct: 58 QGRTSPNKLQALNMAFASSMAEIAASQEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFI 117
Query: 333 ----QFVSAFCQSNCGDVS 347
Q VS F Q+ DVS
Sbjct: 118 NEITQLVSMFAQAGMNDVS 136
>pdb|2AJT|A Chain A, Crystal Structure Of L-Arabinose Isomerase From E.Coli
pdb|2AJT|B Chain B, Crystal Structure Of L-Arabinose Isomerase From E.Coli
pdb|2AJT|C Chain C, Crystal Structure Of L-Arabinose Isomerase From E.Coli
pdb|2HXG|A Chain A, Crystal Structure Of Mn2+ Bound Ecai
pdb|2HXG|B Chain B, Crystal Structure Of Mn2+ Bound Ecai
pdb|2HXG|C Chain C, Crystal Structure Of Mn2+ Bound Ecai
Length = 500
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 580 VTTFDEYQVQRYEGASTLYGPHTLSAYIQEFKKLAAAL 617
+T FD Y+V G+ LYGP TL Q + + AL
Sbjct: 1 MTIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNAL 38
>pdb|4F2D|A Chain A, Crystal Structure Of Escherichia Coli L-Arabinose
Isomerase (Ecai) Complexed With Ribitol
pdb|4F2D|B Chain B, Crystal Structure Of Escherichia Coli L-Arabinose
Isomerase (Ecai) Complexed With Ribitol
pdb|4F2D|C Chain C, Crystal Structure Of Escherichia Coli L-Arabinose
Isomerase (Ecai) Complexed With Ribitol
Length = 500
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 581 TTFDEYQVQRYEGASTLYGPHTLSAYIQEFKKLAAAL 617
T FD Y+V G+ LYGP TL Q + + AL
Sbjct: 2 TIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNAL 38
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
0.319 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,929,003
Number of Sequences: 62578
Number of extensions: 1049363
Number of successful extensions: 2275
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2260
Number of HSP's gapped (non-prelim): 14
length of query: 775
length of database: 14,973,337
effective HSP length: 106
effective length of query: 669
effective length of database: 8,340,069
effective search space: 5579506161
effective search space used: 5579506161
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)