RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 012855
(455 letters)
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 60.8 bits (147), Expect = 6e-10
Identities = 84/507 (16%), Positives = 148/507 (29%), Gaps = 156/507 (30%)
Query: 15 KNEFERDLKPATETISDSNEQN----LCVK-----CKANEPTPGAGEDG--KHCLDCFRS 63
+ +F + L TE + +E L K EP+ D CL F +
Sbjct: 34 QEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFEN 93
Query: 64 N-LFGK------FRLAVASNALITPADNVLVAF------SGGPSSRV---ALQFVHELQQ 107
L G +L ++ + ++ + + P + AL
Sbjct: 94 CYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL-------- 145
Query: 108 RAQKNFDASKDRSLPVF------GVGVVFVDE-----TAYYPVPSSEIDNAIQEIKLIVS 156
F A + + + G + +E Y+ + I + + + ++
Sbjct: 146 -----FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIR 200
Query: 157 NLSPPTKEL-HVIPIESIFCSNPCDGRERFKKLVDSVSDATGKEDLLLQ----LRMLSLQ 211
K + I + NP T +D LL ++ +
Sbjct: 201 TTLDAEKVFTQGLNILE-WLENP---------------SNTPDKDYLLSIPISCPLIGVI 244
Query: 212 KFASENGYNRLL--LGLCTSRIACHVITATVKGRGYSLPADIQYADARWE---------- 259
+ A Y LG + ++ AT +G I D+ WE
Sbjct: 245 QLAH---YVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDS-WESFFVSVRKAI 300
Query: 260 -----I--------PVV-LP---LRDCLAQELN----MLC-------QLDCLKTVELLNQ 291
I P LP L D L ML Q+ V N
Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ--DYVNKTNS 358
Query: 292 THSGINGLVS-SFVKILQEENPSRESTIMRTAG---KLTPF--HFNKI---PELNDSSVP 342
H V S V N ++ ++ +G L K L+ S +P
Sbjct: 359 -HLPAGKQVEISLV------N-GAKNLVV--SGPPQSLYGLNLTLRKAKAPSGLDQSRIP 408
Query: 343 LASQRR---QKRFNLKPNESISSESFCSLCYSPLNQSDLTSLSSHDNCKNSDIFVAACCS 399
S+R+ RF L P ++S F +S L + L + D +++ A
Sbjct: 409 F-SERKLKFSNRF-L-P---VAS-PF----HSHLLV-PASDLINKD-LVKNNVSFNA--K 453
Query: 400 SCRFQIF-PKDPSSMEKFYSLLPEPLV 425
+ ++ D S + + E +V
Sbjct: 454 DIQIPVYDTFDGSDLRVLSGSISERIV 480
Score = 37.0 bits (85), Expect = 0.014
Identities = 40/240 (16%), Positives = 83/240 (34%), Gaps = 89/240 (37%)
Query: 143 EIDNAIQE-----IKLIVSNLSPPTKELHVIPIE---------SIFCSNPCDGRERFKKL 188
DN ++ I IV N +P +H + ++ DG+ + +K+
Sbjct: 1648 RADNHFKDTYGFSILDIVIN-NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKI 1706
Query: 189 VDSVSDAT------GKEDLLL-----QLRMLS--------LQK---------FA--SENG 218
+++ + ++ LL Q + L+ FA S
Sbjct: 1707 FKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHS--- 1763
Query: 219 YNRLLLG----LCTSRIACHVIT-----ATVKGRG----YSLPADIQYADARWEIPVVLP 265
LG L + +A V++ V RG ++P D + + + + + P
Sbjct: 1764 -----LGEYAALAS--LA-DVMSIESLVEVVFYRGMTMQVAVPRD-ELGRSNYGMIAINP 1814
Query: 266 LRDC--LAQE-LNMLCQLDCLKT---VELLN------Q-----THSGINGLVS--SFVKI 306
R +QE L + + +T VE++N Q ++ + + +F+K+
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKL 1874
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 55.2 bits (132), Expect = 3e-08
Identities = 65/492 (13%), Positives = 127/492 (25%), Gaps = 147/492 (29%)
Query: 31 DSNEQNLCVK--CKANEPTPGAGEDGKHCLDCFRSNLFGK-FRLAVASNALITPADNVLV 87
++ E K E D K D +S L + + S ++ +
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 88 AFSGGPSSRVALQFVHELQQRAQKNFD--------ASKDRSL----------PVFGVGVV 129
V +FV E+ + N+ + S+ ++ V
Sbjct: 70 TLLSKQEEMVQ-KFVEEVLR---INYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 130 FVDETAYYPVPSSEIDNAIQEIKLIVSNLSPPTK-ELH--------VIPIES-------- 172
F Y V + +++ + L P + + ++
Sbjct: 126 FAK----YNVSRLQ---PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178
Query: 173 -----IF------CSNPCDGRERFKKL---VDSVSDATGKEDLLLQLRMLSLQ----KFA 214
IF C++P E +KL +D + ++LR+ S+Q +
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
Query: 215 SENGYNRLLLGL---CTSRIA------CHVITATVKGRGYSLPADIQYADARWEIPVVLP 265
Y LL L ++ C ++ T R + D A I +
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT---RFKQV-TDFLSAATTTHISLD-H 293
Query: 266 LRDCLAQELNMLCQLDCLKTVELLNQTHSGINGLVSSFVKILQEENPSRESTIMRTAGKL 325
L + + LL ++ ++ P T
Sbjct: 294 HSMTLTPD----------EVKSLL-----------LKYLDCRPQDLPREVLTTN------ 326
Query: 326 TPFHFNKIPELNDSSVPLASQRRQKRFNLKPNESISSESFCSLCYSPLNQSDLTSLSSHD 385
P + I E + K I S + L ++ +
Sbjct: 327 -PRRLSIIAES-IRDGLATWDNWKHVNCDKLTTIIES------SLNVLEPAEYRKM---- 374
Query: 386 NCKNSDIFVAACCSSCRFQIFPKDPSSMEKFYSLL--------PEPLVARAKHVRNGDSS 437
F +FP SL+ +V + S
Sbjct: 375 -------FDR-------LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH-----KYS 415
Query: 438 LLREQIQDFLLS 449
L+ +Q ++ +S
Sbjct: 416 LVEKQPKESTIS 427
>1wy5_A TILS, hypothetical UPF0072 protein AQ_1887; N-type ATP-ppase,
structural genomics, translation, NPPSFA; 2.42A {Aquifex
aeolicus} SCOP: c.26.2.5 d.229.1.1 PDB: 2e21_A* 2e89_A*
Length = 317
Score = 41.9 bits (99), Expect = 2e-04
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 63 SNLFGKFRLAVASNALITPADNVLVAFSGGPSSRVALQFVHELQQR 108
S + K + + VL+AFSGG S V + +L+
Sbjct: 5 SRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNY 50
>3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA
complex; 3.65A {Geobacillus kaustophilus}
Length = 464
Score = 41.2 bits (97), Expect = 6e-04
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 68 KFRLAVASNALITPADNVLVAFSGGPSSRVALQFVHELQQRAQKNFDA 115
K R + + L++ V+V SGGP S L L+ + A
Sbjct: 4 KVRAFIHRHQLLSEGAAVIVGVSGGPDSLALLHVFLSLRDEWKLQVIA 51
>1ni5_A Putative cell cycle protein MESJ; structural genomics, ATPase,
PP-type, putative cell cycle PR PSI, protein structure
initiative; 2.65A {Escherichia coli} SCOP: b.153.1.2
c.26.2.5 d.229.1.1
Length = 433
Score = 39.3 bits (92), Expect = 0.002
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 76 NALITPADNVLVAFSGGPSSRVALQFVHELQQR 108
N + + +LVAFSGG S V L + + +
Sbjct: 7 NRQLLTSRQILVAFSGGLDSTVLLHQLVQWRTE 39
>2e18_A NH(3)-dependent NAD(+) synthetase; ligase, structural genomics,
NPPSFA, national project on Pro structural and
functional analyses; 2.10A {Pyrococcus horikoshii}
Length = 257
Score = 30.6 bits (70), Expect = 0.86
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 164 ELHVIPIESIFCSNPCDGRERFKKLVDSVSDATGKEDLLLQLRMLSLQKFASENGYNRLL 223
VI I+ I + F + ++ D G +++ + RM+ L +A N R++
Sbjct: 77 GYKVINIKPIV--------DSFVENLELNLDRKGLGNIMSRTRMIML--YAHANSLGRIV 126
Query: 224 LG 225
LG
Sbjct: 127 LG 128
>2js3_A Uncharacterized protein; homodimer, protein structure,
spectroscopy, structural G PSI-2, protein structure
initiative; NMR {Rhodopseudomonas palustris}
Length = 96
Score = 29.0 bits (64), Expect = 0.94
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 22 LKPATETIS--DSNEQNLCVKCKANEPTPGAGEDGKHCLDC 60
LK A E +S D N C C A+ P G++ KH DC
Sbjct: 38 LKTAIEIVSEEDGGAHNQCKLCGASVPWLQTGDEIKHADDC 78
>3jq1_A SUSD superfamily protein; structural genomic center for structural
genomics, JCSG, protein structure INI PSI-2, RAGB; HET:
MSE; 1.55A {Bacteroides vulgatus atcc 8482}
Length = 481
Score = 30.4 bits (69), Expect = 1.2
Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 108 RAQKNFDASKDRSLPVFGVGVVFVDET-AYYPVPSSEIDN 146
++ D + G Y+P+P+ E+D
Sbjct: 432 LLEQTLKTCDDTRYKNYQTGKSDNINKFNYFPIPAKELDT 471
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 29.6 bits (66), Expect = 1.6
Identities = 11/46 (23%), Positives = 14/46 (30%), Gaps = 6/46 (13%)
Query: 19 ERDLKPATETISDSNEQNLCVKCKANEPT----PGAGEDGKHCLDC 60
E K A + N C +CK P G+ C C
Sbjct: 5 ESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGD--VVCALC 48
>3oix_A Putative dihydroorotate dehydrogenase; dihydrooro oxidase; TIM
barrel, oxidoreductase; HET: MLY FMN; 2.40A
{Streptococcus mutans}
Length = 345
Score = 29.8 bits (67), Expect = 1.7
Identities = 21/140 (15%), Positives = 37/140 (26%), Gaps = 15/140 (10%)
Query: 1 MACNSATGCQSGCYKNEFERDLKPATETISDSNEQNLCVKCKAN----EPTPGAGEDGKH 56
++C + G Y E + + + L +K A +
Sbjct: 163 LSCPNVPGXPQIAYDFETTDQI---LSEVFTYFTKPLGIKLPPYFDIVHFDQAAAIFNXY 219
Query: 57 CLDCFRSNLFGKFRLAVASNALITPADNVLVAFSGGPSSRVALQFVHELQQRAQKNFDAS 116
L L + ++ N G AL VH +R
Sbjct: 220 PLTFVNCINSIGNGLVIEDETVVIXPKNGFGGIGGDYVKPTALANVHAFYKRL------- 272
Query: 117 KDRSLPVFGVGVVFVDETAY 136
+ S+ + G G V A+
Sbjct: 273 -NPSIQIIGTGGVXTGRDAF 291
>1xng_A NH(3)-dependent NAD(+) synthetase; amidotransferase, ligase; HET:
DND ATP; 1.70A {Helicobacter pylori} SCOP: c.26.2.1 PDB:
1xnh_A
Length = 268
Score = 29.5 bits (67), Expect = 1.9
Identities = 10/62 (16%), Positives = 16/62 (25%), Gaps = 11/62 (17%)
Query: 164 ELHVIPIESIFCSNPCDGRERFKKLVDSVSDATGKEDLLLQLRMLSLQKFASENGYNRLL 223
I F S K + +LRM L + + L+
Sbjct: 81 PYTEYSIAPYD--------AIFSSHFKDASLTR-KGNFCARLRMAFL--YDYSLKSDSLV 129
Query: 224 LG 225
+G
Sbjct: 130 IG 131
>3p52_A NH(3)-dependent NAD(+) synthetase; structural genomics, center for
structural genomics of infec diseases, NADE, CSGI; 2.74A
{Campylobacter jejuni}
Length = 249
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 164 ELHVIPIESIFCSNPCDGRERFKKLVDSVSDATGKEDLLLQLRMLSLQKFASENGYNRLL 223
E +I I+SI + F K ++ + + + ++RM L + N L+
Sbjct: 82 EYKIIEIQSIL--------DAFIKQSENTTLVS-LGNFAARIRMSLL--YDYSALKNSLV 130
Query: 224 LG 225
+G
Sbjct: 131 IG 132
>3loq_A Universal stress protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus}
Length = 294
Score = 29.3 bits (66), Expect = 2.7
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 80 TPADNVLVAFSGGPSSRVALQFVHELQQR 108
+ D VLVA+ + AL++ + ++
Sbjct: 168 SLFDRVLVAYDFSKWADRALEYAKFVVKK 196
>3jzl_A Putative cystathionine beta-lyase involved in ALU resistance;
putative cystathionine beta-lyase involved in aluminum
resis structural genomics; HET: LLP; 1.91A {Listeria
monocytogenes str} PDB: 3fd0_A*
Length = 409
Score = 28.6 bits (64), Expect = 5.0
Identities = 28/166 (16%), Positives = 42/166 (25%), Gaps = 46/166 (27%)
Query: 120 SLPVFGVGVVFVDETAYYPVPSSEIDNAIQE-IKLIV---SNLSPPTKELHVIPIESI-- 173
SL F +G V V I + K+I S + I+ +
Sbjct: 128 SLKDFHIGYSSVPLLENGDVDFPRIAKKMTPKTKMIGIQRSRGYADRPSFTIEKIKEMIV 187
Query: 174 -----------FCSN----PCDGRERFKKLVDSV-----------SDATG-----KEDLL 202
F N + +E + D + TG KE L+
Sbjct: 188 FVKNINPEVIVFVDNCYGEFVEYQEPPEVGADIIAGSLIKNPGGGLAKTGGYIAGKEALV 247
Query: 203 LQLRMLSLQK-FASENG----YNRLLL-GLCTSRIACHVITATVKG 242
E G + G +A HV +KG
Sbjct: 248 DLCGYRLTTPGIGREAGASLYSLLEMYQGF---FLAPHVTAQAIKG 290
>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic
resolution, AMP complex, ribosome biogenesis,
thermophilic, hydrolase; HET: AMP; 1.20A {Thermus
thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A*
3mwl_A* 3nbf_A* 3nej_A
Length = 207
Score = 27.5 bits (62), Expect = 7.2
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 236 ITATVKGRGYSLPADIQYADARWEIPVVLPLRDCLAQ 272
I + GRG + P IQ A A +P+ L +D + Q
Sbjct: 12 ILEALHGRGLTTPTPIQ-AAA---LPLALEGKDLIGQ 44
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.133 0.393
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,543,420
Number of extensions: 379069
Number of successful extensions: 707
Number of sequences better than 10.0: 1
Number of HSP's gapped: 701
Number of HSP's successfully gapped: 19
Length of query: 455
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 358
Effective length of database: 3,993,456
Effective search space: 1429657248
Effective search space used: 1429657248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)