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= 012457
(463 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QK9|A Chain A, Yeast Tim44 C-Terminal Domain Complexed With Cymal-3
pdb|3QK9|B Chain B, Yeast Tim44 C-Terminal Domain Complexed With Cymal-3
Length = 222
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/150 (30%), Positives = 78/150 (52%), Gaps = 7/150 (4%)
Query: 291 WETSDNPIV---HKIQDMNETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VL 346
W+ S+NP++ KI + F ET+++ + + DP+FS F ++E I P +L
Sbjct: 34 WDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEIL 93
Query: 347 SAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSS-- 404
AY+KGDV+ LKK+ S A+ ++ ++ D RIL + VE+ K++
Sbjct: 94 EAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDI 153
Query: 405 PIIIVAFQTQQIYCVRDKH-GTITEGGKVN 433
P+++V + Q+I R K G I G + N
Sbjct: 154 PVLVVGCRAQEINLYRKKKTGEIAAGDEAN 183
>pdb|2FXT|A Chain A, Crystal Structure Of Yeast Tim44
Length = 192
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 46/150 (30%), Positives = 78/150 (52%), Gaps = 7/150 (4%)
Query: 291 WETSDNPIV---HKIQDMNETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VL 346
W+ S+NP++ KI + F ET+++ + + DP+FS F ++E I P +L
Sbjct: 10 WDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEIL 69
Query: 347 SAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSS-- 404
AY+KGDV+ LKK+ S A+ ++ ++ D RIL + VE+ K++
Sbjct: 70 EAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDI 129
Query: 405 PIIIVAFQTQQIYCVRDKH-GTITEGGKVN 433
P+++V + Q+I R K G I G + N
Sbjct: 130 PVLVVGCRAQEINLYRKKKTGEIAAGDEAN 159
>pdb|2CW9|A Chain A, Crystal Structure Of Human Tim44 C-Terminal Domain
Length = 194
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 69/133 (51%), Gaps = 1/133 (0%)
Query: 298 IVHKIQDMNETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VLSAYMKGDVET 356
+ K+ D+ +F +T+ + + EI R DP+F F+ + + I P VL A + G+++
Sbjct: 21 LTDKVTDLLGGLFSKTEXSEVLTEILRVDPAFDKDRFLKQCENDIIPNVLEAXISGELDI 80
Query: 357 LKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQI 416
LK +C + ++ G+ F +RIL + V++ K + P++I+ FQ Q +
Sbjct: 81 LKDWCYEATYSQLAHPIQQAKALGLQFHSRILDIDNVDLAXGKXVEQGPVLIITFQAQLV 140
Query: 417 YCVRDKHGTITEG 429
VR+ G + EG
Sbjct: 141 XVVRNPKGEVVEG 153
>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
Length = 360
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 46/210 (21%), Positives = 89/210 (42%), Gaps = 38/210 (18%)
Query: 66 FKHSVKELKKKAEEIKGVKEELKERTKQTTEQ------LYKQVDGVW--MEAESTVKKVS 117
F VK + +E +EL+E+ ++ T+Q Y+ + +AE+ + +
Sbjct: 108 FGVGVKTANRWYQEGLRTLDELREQPQRLTQQQKAGLQYYQDLSTPVRRADAEALQQLIE 167
Query: 118 ASMKEKISAATEEVKGTFRTGSTDTSAKHDDDVRDGFKASSGEEKQK--------QTVSS 169
A++++ + AT + G FR G HD D F + EE Q+ + S
Sbjct: 168 AAVRQTLPGATVTLTGGFRRGKLQ---GHDVD----FLITHPEEGQEVGLLPKVMSCLQS 220
Query: 170 DTAETFYGKLKSSISSPKFTLAFQKLKEAKVVDLAKKGYDIVKDELSGSPSKRKHL---E 226
++ +S ++ L + + +D+ ++ + I+ G P ++
Sbjct: 221 QGLVLYHQYHRSHLADSAHNLR----QRSSTMDVFERSFCIL-----GLPQPQQAALAGA 271
Query: 227 YTPSPSWTGEKSTRTDLVVTPSKKSMWSKL 256
P P+W K+ R DLVVTPS + ++ L
Sbjct: 272 LPPCPTW---KAVRVDLVVTPSSQFPFALL 298
>pdb|2CFO|A Chain A, Non-discriminating Glutamyl-trna Synthetase From
Thermosynechococcus Elongatus In Complex With Glu
pdb|2CFO|B Chain B, Non-discriminating Glutamyl-trna Synthetase From
Thermosynechococcus Elongatus In Complex With Glu
Length = 492
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 360 YCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSPII 407
YC+PE +E +AE A + +DNR H++ E + G +P+I
Sbjct: 98 YCTPEELEALRAEQKA-KGQAPRYDNRHRHLTPEEQAAFEAAGRTPVI 144
>pdb|2ON7|A Chain A, Structure Of Nagst-1
pdb|2ON7|B Chain B, Structure Of Nagst-1
pdb|2ON7|C Chain C, Structure Of Nagst-1
pdb|2ON7|D Chain D, Structure Of Nagst-1
Length = 206
Score = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 4/89 (4%)
Query: 176 YGKLKSSISSPKFTLAFQKLKEAKVVDLAKKGYDIVKDELSGSPSKRKHLEYTPSPSWTG 235
Y + I S +T+ ++E V L K+ +D+ G +K L+ +PS G
Sbjct: 95 YSDYRVEIKSFFYTVI--GMREGDVEQLKKEVLLPARDKFFGFITK--FLKKSPSGFLVG 150
Query: 236 EKSTRTDLVVTPSKKSMWSKLKEKMQGYP 264
+ T DL+V+ +M + + E ++GYP
Sbjct: 151 DSLTWVDLLVSEHNATMLTFVPEFLEGYP 179
>pdb|2QE7|G Chain G, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
Length = 286
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 22/28 (78%), Gaps = 1/28 (3%)
Query: 259 KMQGYPVFKRITGISE-PVVTKGQEIAE 285
K +GYPV + +TGIS+ P +T+ Q+IA+
Sbjct: 127 KKRGYPVVEEVTGISDTPSLTEIQDIAQ 154
>pdb|1F1M|A Chain A, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|B Chain B, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|C Chain C, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|D Chain D, Crystal Structure Of Outer Surface Protein C (Ospc)
Length = 164
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 347 SAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDN 385
S +K ++E KK CS E + K EHT G+ DN
Sbjct: 80 SGELKAEIEKAKK-CSEEFTAKLKGEHTDLGKEGVTDDN 117
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
0.313 0.128 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,119,586
Number of Sequences: 62578
Number of extensions: 536883
Number of successful extensions: 1577
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1559
Number of HSP's gapped (non-prelim): 36
length of query: 463
length of database: 14,973,337
effective HSP length: 102
effective length of query: 361
effective length of database: 8,590,381
effective search space: 3101127541
effective search space used: 3101127541
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)