RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9039
(251 letters)
>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 = 43.7 bits (102), Expect = 4e-05
Identities = 36/233 (15%), Positives = 73/233 (31%), Gaps = 57/233 (24%)
Query: 31 MTRLCAEIRKVLPPSVPVGVQHGVIVENMHDVPYVLEAESGPEITA--NMTR--LCAEIR 86
M+ + E R+ PS+ + D Y + ++ A N++R ++R
Sbjct: 95 MSPIKTEQRQ---PSMMT-----RMYIEQRDRLY-----NDNQVFAKYNVSRLQPYLKLR 141
Query: 87 KVL---PPSVPVGVQILSGCNKAALATAQAAGLDFIRAESF-VF----GHM-ADEGLMN- 136
+ L P+ V + + G K +A F +F + + E ++
Sbjct: 142 QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEM 201
Query: 137 -----AQAGPLLRYRKQIGADNVLVFTDIKK------KHSSHA----ITADVDITETAKA 181
Q P R ++ L I+ K + + +V + A
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA 261
Query: 182 ASFFLSDG----LIITGNATGDPADVSQLMSVKNAVDLPI-LIGSGVTSDNVE 229
F + L+ T V+ +S + + +T D V+
Sbjct: 262 --F---NLSCKILLTTRF-----KQVTDFLSAATTTHISLDHHSMTLTPDEVK 304
Score = 35.2 bits (80), Expect = 0.020
Identities = 42/298 (14%), Positives = 78/298 (26%), Gaps = 103/298 (34%)
Query: 12 MHDVPYVLEAESGPEITANMTRLCAEIR-KVLPPSV----PVGVQHGVIVENMHDVP--- 63
+ L + + + R + LP V P + +I E++ D
Sbjct: 291 LDHHSMTLTPDEVKSLLLK----YLDCRPQDLPREVLTTNPRRL--SIIAESIRDGLATW 344
Query: 64 ----YVLEAESGPEITANMTRL-CAEIRK------VLPPSVPVGVQILS----------- 101
+V + I +++ L AE RK V PPS + +LS
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDV 404
Query: 102 -----GCNKAALATAQAAG---------LDFIRAESFVFGHMADEGLMNAQAGPLL-RYR 146
+K +L Q L+ + +E ++ ++ Y
Sbjct: 405 MVVVNKLHKYSLVEKQPKESTISIPSIYLELKV-------KLENEYALHRS---IVDHYN 454
Query: 147 KQIGADNVLVFTDIKKKHSS---------HAITADVDITETAKAASF--------FLSDG 189
D+ D+ + H + + F FL
Sbjct: 455 IPKTFDS----DDLIPPYLDQYFYSHIGHHLKNIE----HPERMTLFRMVFLDFRFLEQK 506
Query: 190 LIITGNATGDPADVSQLMSVKNAVDLPI---LIGSGVTSDNVEHY-MTADALIIGSHF 243
+ A + + L I DN Y +A++ F
Sbjct: 507 IRHDSTAWNASGSILNTLQ-----QLKFYKPYI-----CDNDPKYERLVNAIL---DF 551
>3nav_A Tryptophan synthase alpha chain; alpha subunit, structural
genomics, CSG center for structural genomics of
infectious diseases; 2.10A {Vibrio cholerae o1 biovar el
tor}
Length = 271
Score = 39.1 bits (92), Expect = 6e-04
Identities = 24/119 (20%), Positives = 41/119 (34%), Gaps = 26/119 (21%)
Query: 147 KQIGADNVLV----------FTDIKKKHSSHAI------TADVDITETAKAASFFL---- 186
++ G D+VL+ F +K I +D + A+ +
Sbjct: 122 QKAGVDSVLIADVPTNESQPFVAAAEKFGIQPIFIAPPTASDETLRAVAQLGKGYTYLLS 181
Query: 187 SDGLIITGNATGDPADVSQLMS-VKNAVDLPILIGSGV-TSDNVEHYMT--ADALIIGS 241
G +TG T V L+ ++ P L+G G+ V+ + A I GS
Sbjct: 182 RAG--VTGAETKANMPVHALLERLQQFDAPPALLGFGISEPAQVKQAIEAGAAGAISGS 238
>1geq_A Tryptophan synthase alpha-subunit; hyperthermophIle, pyrococ
furiosus, X-RAY analysis, stability, calorimetry, lyase;
2.00A {Pyrococcus furiosus} SCOP: c.1.2.4 PDB: 1wdw_A*
2dzu_A 2dzp_A 2e09_A 2dzw_A 2dzs_A 2dzv_A 2dzt_A 2dzx_A
Length = 248
Score = 37.9 bits (89), Expect = 0.001
Identities = 24/119 (20%), Positives = 42/119 (35%), Gaps = 26/119 (21%)
Query: 147 KQIGADNVLV----------FTDIKKKHSSHAI------TADVDITETAKAASFFL---- 186
K G D +LV FT+I ++ + T D + + F+
Sbjct: 105 KASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVS 164
Query: 187 SDGLIITGNATGDPADVSQLMS-VKNAVDLPILIGSGV-TSDNVEHYMT--ADALIIGS 241
G TG P L+ K + +G GV ++V + A+ +++GS
Sbjct: 165 LYG--TTGAREEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 221
>1qop_A Tryptophan synthase alpha chain; lyase, carbon-oxygen lyase,
tryptophan biosynthesis, pyridoxal phosphate; HET: IPL
PLP; 1.4A {Salmonella typhimurium} SCOP: c.1.2.4 PDB:
1k8x_A* 1wbj_A* 2clk_A* 2j9z_A* 3cep_A* 1k8y_A* 1a5s_A*
1a50_A* 1c29_A* 1c8v_A* 1c9d_A* 1bks_A* 1cx9_A* 1fuy_A*
1cw2_A* 1k7e_A* 1k7f_A* 1k7x_A* 1k3u_A* 1k8z_A* ...
Length = 268
Score = 37.9 bits (89), Expect = 0.001
Identities = 25/121 (20%), Positives = 41/121 (33%), Gaps = 26/121 (21%)
Query: 147 KQIGADNVLV----------FTDIKKKHSSHAI------TADVDITETAKAASFFL---- 186
+Q+G D+VLV F +H+ I D + + A +
Sbjct: 119 EQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLS 178
Query: 187 SDGLIITGNATGDPADVSQLMS-VKNAVDLPILIGSGV-TSDNVEHYMT--ADALIIGSH 242
G +TG + L+ +K P L G G+ + + V + A I GS
Sbjct: 179 RSG--VTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSA 236
Query: 243 F 243
Sbjct: 237 I 237
>1ujp_A Tryptophan synthase alpha chain; riken structural genomics/P
initiative, RSGI, structural genomics, lyase; HET: CIT;
1.34A {Thermus thermophilus} SCOP: c.1.2.4 PDB: 1wxj_A*
Length = 271
Score = 37.9 bits (89), Expect = 0.002
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 175 ITETAKAASFFL----SDGLIITGNATGDPADVSQLMS-VKNAVDLPILIGSGV-TSDNV 228
I + A+ F+ G +TG P +V L+ +K LP+ +G GV
Sbjct: 160 IATVVRHATGFVYAVSVTG--VTGMRERLPEEVKDLVRRIKARTALPVAVGFGVSGKATA 217
Query: 229 EHYMTADALIIGSHF 243
AD +++GS
Sbjct: 218 AQAAVADGVVVGSAL 232
>3tha_A Tryptophan synthase alpha chain; structural genomics, center for
structural genomics of infec diseases, csgid, lyase;
2.37A {Campylobacter jejuni}
Length = 252
Score = 36.8 bits (86), Expect = 0.003
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 175 ITETAKAASFFL----SDGLIITGNATGDPADVSQLMS-VKNAVDLPILIGSGVTSDNVE 229
+ + K A F+ S G ITG + + A + + +++ +LPI +G G+ N +
Sbjct: 157 VKKLVKHAKGFIYLLASIG--ITGTKSVEEAILQDKVKEIRSFTNLPIFVGFGIQ--NNQ 212
Query: 230 HYMT----ADALIIGSHF 243
AD +I+G+
Sbjct: 213 DVKRMRKVADGVIVGTSI 230
>1rd5_A Tryptophan synthase alpha chain, chloroplast; hydroxamic acid,
diboa, dimboa, indole, indole-glycerol-PHOS lyase; 2.02A
{Zea mays} SCOP: c.1.2.4 PDB: 1tjr_A
Length = 262
Score = 36.4 bits (85), Expect = 0.004
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 10/77 (12%)
Query: 175 ITETAKAASFFL----SDGLIITGNATGDPADVSQLMS-VKNAVDLPILIGSGV-TSDNV 228
+ E KA+ F+ +G +TG V L+ VK + P+ +G G+ ++V
Sbjct: 159 MKEITKASEGFVYLVSVNG--VTGPRANVNPRVESLIQEVKKVTNKPVAVGFGISKPEHV 216
Query: 229 EHY--MTADALIIGSHF 243
+ AD +IIGS
Sbjct: 217 KQIAQWGADGVIIGSAM 233
>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 = 36.6 bits (84), Expect = 0.007
Identities = 36/276 (13%), Positives = 76/276 (27%), Gaps = 100/276 (36%)
Query: 7 VIVENMHDVPYVLEAESGPEITANMTRLCAE--------IRKVLPPSVPVGVQHGVIVEN 58
+++ N ++ E G I N + + E K+ I E+
Sbjct: 1664 IVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE----------INEH 1713
Query: 59 MHDVPYVLEAESGPE----ITANMTRLCAEIRKVLPPSVPVGVQILSGCNKAALATAQAA 114
+ + T T Q AL + A
Sbjct: 1714 STSYTF-----RSEKGLLSATQF-T------------------QP-------ALTLMEKA 1742
Query: 115 GLDFIRAESF-----VF-GH--------MADEGLMN-AQAGPLLRYR----------KQI 149
+ ++++ F GH + +M+ ++ YR ++
Sbjct: 1743 AFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDEL 1802
Query: 150 GADNVLVF----TDIKKKHSSHAITADVDITETAKAASFFL------SDGL-IITGNATG 198
G N + + S A+ V+ K + + + + G
Sbjct: 1803 GRSNYGMIAINPGRVAASFSQEALQYVVE--RVGKRTGWLVEIVNYNVENQQYVAA---G 1857
Query: 199 DPADVSQLMSVKNA-----VDLPILIGSGVTSDNVE 229
D + + +V N +D+ L S ++ + VE
Sbjct: 1858 DLRALDTVTNVLNFIKLQKIDIIELQKS-LSLEEVE 1892
>1miw_A TRNA CCA-adding enzyme; tRNA nucleotidyltransferase, translation,
transferase; HET: ATP; 3.00A {Geobacillus
stearothermophilus} SCOP: a.173.1.1 d.218.1.4 PDB:
1miv_A* 1miy_A*
Length = 404
Score = 29.6 bits (67), Expect = 0.98
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 8/39 (20%)
Query: 37 EIRKVLPPSVPVGVQHGVIVENMHDVPYVLEAESGPEIT 75
++ + P ++ VG +HG +V Y E+T
Sbjct: 51 DVMAIFPKTIDVGSKHGTVVVVHKGKAY--------EVT 81
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 1.1
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 24/51 (47%)
Query: 147 KQIGADNVLVFTDIKKKHSSHAITADVDITETAKAASFFLSDGLIITGNAT 197
KQ +KK +S + AD ++A A L I AT
Sbjct: 19 KQ----------ALKKLQASLKLYAD----DSAPA--------LAI--KAT 45
>2ekc_A AQ_1548, tryptophan synthase alpha chain; structural genomics,
lyase, NPPSFA, national project on PROT structural and
functional analyses; 2.00A {Aquifex aeolicus}
Length = 262
Score = 28.7 bits (65), Expect = 1.5
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 14/79 (17%)
Query: 175 ITETAKAASFFL----SDGLIITGNATG-DPADVSQLMS-VKNAVDLPILIGSGVTSDNV 228
I +AA G TG + + + + D P+++G GV+
Sbjct: 163 IKLICEAADEMTYFVSVTG--TTGAREKLPYERIKKKVEEYRELCDKPVVVGFGVS--KK 218
Query: 229 EHYMT----ADALIIGSHF 243
EH AD +++GS
Sbjct: 219 EHAREIGSFADGVVVGSAL 237
>2agk_A 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]
imidazole-4-carboxamide...; TIM alpha/beta barrel; HET:
CIT; 1.30A {Saccharomyces cerevisiae}
Length = 260
Score = 28.6 bits (64), Expect = 1.7
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 1/44 (2%)
Query: 199 DPADVSQLMSVKNAVDLPILIGSGVTSDNVEHYMT-ADALIIGS 241
P + + +G G+ N ++ A +I+ S
Sbjct: 61 GPNNDDAAREALQESPQFLQVGGGINDTNCLEWLKWASKVIVTS 104
>3oa5_A CHI1; TIM barrel, hydrolase; HET: 2PE; 1.74A {Yersinia} PDB: 4a5q_A
Length = 574
Score = 28.7 bits (64), Expect = 2.1
Identities = 11/57 (19%), Positives = 17/57 (29%), Gaps = 10/57 (17%)
Query: 70 SGPEITANMTRLCAEIRKVLPPS-------VPVGVQILSGCNKAALATAQAAGLDFI 119
+ P+ AN L +I + + N AL AG+ I
Sbjct: 299 NSPDDGANFAILIQQITDAKISNLKGISIASSADPAKIDAANIPALM---DAGVTGI 352
>1jub_A Dihydroorotate dehydrogenase A; homodimer, alpha-beta barrel,
flavoprotein, mutant enzyme, oxidoreductase; HET: FMN;
1.40A {Lactococcus lactis} SCOP: c.1.4.1 PDB: 1ovd_A*
1jue_A* 1dor_A* 2bsl_A* 2bx7_A* 2dor_A* 1jqv_A* 1jrb_A*
1jrc_A* 1jqx_A*
Length = 311
Score = 27.9 bits (63), Expect = 3.2
Identities = 5/33 (15%), Positives = 11/33 (33%), Gaps = 2/33 (6%)
Query: 169 ITADVDITETAKAASFFLSDGL--IITGNATGD 199
+ D+ A L + + N+ G+
Sbjct: 165 LPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGN 197
>2f9h_A PTS system, IIA component; alpha-beta structure, beta-barrel,
dimer, structural genomic protein structure initiative;
1.57A {Enterococcus faecalis} SCOP: b.161.1.1
Length = 129
Score = 26.7 bits (59), Expect = 4.3
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 175 ITETAKAASFFLSDGLIIT--GNATGDPADVSQLMSVKNAVDLPILIGSGVTSDNVEHYM 232
+TE K A S+ +II AT + + S + + G + + + +
Sbjct: 12 VTEIGKHAIDD-SEKMIILFGETATDTLKQHAVIQSFPEKDQVTLAEGDHLKIGDTNYTI 70
Query: 233 TA 234
T
Sbjct: 71 TK 72
>3nrc_A Enoyl-[acyl-carrier-protein] reductase (NADH); rossmann fold, NADH
BI oxidoreductase; HET: NAD TCL; 2.10A {Francisella
tularensis subsp} PDB: 2jjy_A*
Length = 280
Score = 26.8 bits (60), Expect = 6.9
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 139 AGPLLRYRKQIGADNVLVFTDIKKKHSSHA-ITADVDITETAKAASFFLSD-GLIITG 194
AGP+ K + A + F + ++ + + +VDI E +F SD ITG
Sbjct: 209 AGPI----KTLAASGISNFKKMLDYNAMVSPLKKNVDIMEVGNTVAFLCSDMATGITG 262
>2y88_A Phosphoribosyl isomerase A; aromatic amino acid biosynthesis,
TIM-barrel, His biosynthesis, tryptophan biosynthesis;
HET: 2ER; 1.33A {Mycobacterium tuberculosis} PDB: 2y89_A
2y85_A*
Length = 244
Score = 26.4 bits (59), Expect = 8.1
Identities = 7/49 (14%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 196 ATGDPADVSQLMSVKNAVDLPILIGSGV-TSDNVEHYMT--ADALIIGS 241
A G ++ L V +D+ + + G+ +++ + + +G+
Sbjct: 56 AFGRGSNHELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGT 104
>1vzw_A Phosphoribosyl isomerase A; histidine biosynthesis, tryptophan
biosynthesis; 1.8A {Streptomyces coelicolor} SCOP:
c.1.2.1 PDB: 2vep_A 2x30_A
Length = 244
Score = 26.4 bits (59), Expect = 9.8
Identities = 8/49 (16%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 196 ATGDPADVSQLMSVKNAVDLPILIGSGV-TSDNVEHYMT--ADALIIGS 241
A G + + + V A+D+ + + G+ D + + + +G+
Sbjct: 57 AFGTGDNRALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGT 105
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 0.134 0.384
Gapped
Lambda K H
0.267 0.0823 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,909,176
Number of extensions: 242869
Number of successful extensions: 772
Number of sequences better than 10.0: 1
Number of HSP's gapped: 769
Number of HSP's successfully gapped: 46
Length of query: 251
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 160
Effective length of database: 4,160,982
Effective search space: 665757120
Effective search space used: 665757120
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: 56 (25.2 bits)