RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3897
(240 letters)
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET:
U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5
Length = 189
Score = 187 bits (476), Expect = 3e-60
Identities = 52/168 (30%), Positives = 83/168 (49%), Gaps = 13/168 (7%)
Query: 75 PNGYGVYALDTEMVYTVHGLE--VARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISA 132
V A+D EMV E +AR ++VNV G ++Y+ ++P+ EI DY T+ SG++
Sbjct: 2 AGSREVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTP 61
Query: 133 KDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIH--SNIIDTSV----LF 186
+ + +++ + K ++VGH L++D +ALK I DTS
Sbjct: 62 QHM--VGATPFAVARLEILQLL-KGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWR 118
Query: 187 PHSFGLPYRRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDLILWKL 232
R SL+ + +LLH+SIQ+ H S EDARA ++L
Sbjct: 119 EAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQ 166
>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 = 43.1 bits (101), Expect = 5e-05
Identities = 42/224 (18%), Positives = 67/224 (29%), Gaps = 70/224 (31%)
Query: 6 RSDEKRLKAKSLTS--MSVWERKSLFRKLPPRTGFNPVCT-SGLRI---SALDHVGGING 59
RS++ L A T +++ E K+ F L + T +G + +AL + +
Sbjct: 1720 RSEKGLLSATQFTQPALTLME-KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM- 1777
Query: 60 PLEGYVKT-----------KPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNV---D 105
+E V+ PR + YG+ A++ V E + V V
Sbjct: 1778 SIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRT 1837
Query: 106 GRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIV-GH- 163
G L EI++YN Q + G
Sbjct: 1838 GWL---------VEIVNYNV--EN----------------QQ-----------YVAAGDL 1859
Query: 164 -GLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLL 206
L+ L I ID L S SL+ + L
Sbjct: 1860 RALDTVTNVLNFIKLQKIDIIEL-QKSL------SLEEVEGHLF 1896
Score = 42.0 bits (98), Expect = 1e-04
Identities = 46/249 (18%), Positives = 73/249 (29%), Gaps = 104/249 (41%)
Query: 48 ISALDHVGGINGPLEGYVKTKPRKSPPP--------NGYGVYALDTEMVYTVHGLEVA-- 97
I+ L +G + Y + P S PP N GV + M+ ++ L
Sbjct: 300 ITVLFFIG-----VRCY-EAYPNTSLPPSILEDSLENNEGV---PSPML-SISNLTQEQV 349
Query: 98 --RVTVVNV---DGRLIYNTLV-KPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151
V N G+ + +LV ++ SG P ++L
Sbjct: 350 QDYVNKTNSHLPAGKQVEISLVNGAKNLVV------SG---------PPQSL-------- 386
Query: 152 GFVSKDSIIVGHGLENDLRALK----LIHSNI------IDTSVLF-----P-HSFGLPY- 194
+GL LR K L S I + S F P HS
Sbjct: 387 -----------YGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHS---HLL 432
Query: 195 RRSLKSIVSQLLHQSIQ-SG---------THDSFEDARAC--------IDLIL-----WK 231
+ I L+ ++ + T D D R +D I+ W+
Sbjct: 433 VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG-SDLRVLSGSISERIVDCIIRLPVKWE 491
Query: 232 LLSDFRYNH 240
+ F+ H
Sbjct: 492 TTTQFKATH 500
Score = 40.0 bits (93), Expect = 5e-04
Identities = 38/209 (18%), Positives = 61/209 (29%), Gaps = 87/209 (41%)
Query: 1 MKRRRRSDEKRLKAKSLTSMSVWER--KSLFRKLPPRTGFNPVCTSGLRISALDHVGGIN 58
M + S A+ VW R GF S LD V IN
Sbjct: 1633 MDLYKTSKA----AQD-----VWNRADNHFKDTY----GF----------SILDIV--IN 1667
Query: 59 GPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDC 118
P+ + G + + M++ VDG+L + K
Sbjct: 1668 NPVNLTIH-----FGGEKGKRIRENYSAMIFET-----------IVDGKLKTEKIFK--- 1708
Query: 119 EIIDYNTKYSGISAKDFIRNPYKTLKDVQN--------------DL--MGFVSKDSIIVG 162
EI +++T Y+ F R+ L Q DL G + D+ G
Sbjct: 1709 EINEHSTSYT------F-RSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG 1761
Query: 163 H--G-------------LENDLRALKLIH 176
H G +E+ ++++
Sbjct: 1762 HSLGEYAALASLADVMSIES---LVEVVF 1787
Score = 27.7 bits (61), Expect = 4.6
Identities = 40/186 (21%), Positives = 59/186 (31%), Gaps = 71/186 (38%)
Query: 14 AKSLTSMSVWERKS-----------LF--RKLPPRTGFNPVCT---SGLRISALDHVGGI 57
+SL +++ RK+ F RKL F PV + S L + A D I
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL---I 439
Query: 58 NGPLEGY---VKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLV 114
N L K + P VY T G ++ RV ++ R++ +
Sbjct: 440 NKDLVKNNVSFNAKDIQIP------VYD-------TFDGSDL-RVLSGSISERIVDCIIR 485
Query: 115 KP-DCE---------IIDY--------------NTKYSG---ISAKDFIRNPYKTLKDVQ 147
P E I+D+ N +G I A NP
Sbjct: 486 LPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINP-------- 537
Query: 148 NDLMGF 153
+D GF
Sbjct: 538 DDDYGF 543
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics,
exonuclease, PSI-2, protein structure initiative; HET:
DNA; 2.50A {Thermotoga maritima MSB8}
Length = 186
Score = 40.2 bits (95), Expect = 2e-04
Identities = 39/162 (24%), Positives = 70/162 (43%), Gaps = 36/162 (22%)
Query: 95 EVARVTVVNVDGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152
E+ V + G+++ Y+TL+KP EI +++ +GI+ + ++++V + +G
Sbjct: 33 EIGAVKIQG--GQIVDEYHTLIKPSREISRKSSEITGITQEMLENKR--SIEEVLPEFLG 88
Query: 153 FVSKDSIIVGHGLEN---DLRALKL---------IHSNIIDT----SVLFPHSFGLPYRR 196
F+ +DSIIV H N D R L+L IDT L
Sbjct: 89 FL-EDSIIVAH---NANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLKLR-----SY 139
Query: 197 SLKSIVSQLLHQSIQ-SGTHDSFEDARACIDLILWKLLSDFR 237
SL S+V +L + H + +DAR + + + +
Sbjct: 140 SLDSVVEKL---GLGPFRHHRALDDARVTAQV-FLRFVEMMK 177
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline
type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus
musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A*
3b6p_A* 2o4i_A 2oa8_A
Length = 242
Score = 39.2 bits (91), Expect = 6e-04
Identities = 19/156 (12%), Positives = 42/156 (26%), Gaps = 36/156 (23%)
Query: 110 YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLK-DVQNDLMGFVS---KDSIIVGH-- 163
+ + P ++ +G+S + + ++ L F+ + +V H
Sbjct: 67 LSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNG 126
Query: 164 ---------------GLENDLRALKLIHSNIIDTSVLF--------PHSFGLPYRRSLKS 200
+ L +D+ P G SL S
Sbjct: 127 DRYDFPLLQTELARLSTPSPLDGTFC-----VDSIAALKALEQASSPSGNGSRKSYSLGS 181
Query: 201 IVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDF 236
I ++ L+ + +H + D + I
Sbjct: 182 IYTR-LYWQAPTDSHTAEGDDLTLLS-ICQWKPQAL 215
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 39.1 bits (91), Expect = 6e-04
Identities = 18/152 (11%), Positives = 39/152 (25%), Gaps = 26/152 (17%)
Query: 110 YNTLVKPDCEIIDYNTKYSGISAKDFIRNP----YKTLKDVQNDLMGFVSKDSIIVGH-- 163
+ P+ ++ +G+S++ R + + + +V H
Sbjct: 62 LTLCMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNG 121
Query: 164 -----G-LENDLRALKLIHSN---IIDTSVLF---------PHSFGLPYRRSLKSIVSQL 205
L +LR L +DT SL S+ +
Sbjct: 122 FDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRY 181
Query: 206 LHQSIQSGTHDSFEDARACIDLILWKLLSDFR 237
+ H + D + I ++
Sbjct: 182 FRAEPSA-AHSAEGDVHTLLL-IFLHRAAELL 211
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form,
hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A
2fbv_A 2fbx_A 2fbt_A 2fc0_A*
Length = 208
Score = 37.8 bits (88), Expect = 0.001
Identities = 10/62 (16%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 153 FVSKDSIIVGHGLENDLRALKLIH----SNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQ 208
+K G G+E D L + ++ + + SL +V +L +
Sbjct: 92 LENKSIKKAGVGIEGDQWKLLRDFDVKLESFVELTDVANEKLKCAETWSLNGLVKHVLGK 151
Query: 209 SI 210
+
Sbjct: 152 QL 153
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease,
homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus
musculus} PDB: 3u6f_B*
Length = 314
Score = 36.7 bits (84), Expect = 0.004
Identities = 19/156 (12%), Positives = 41/156 (26%), Gaps = 36/156 (23%)
Query: 110 YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLK-DVQNDLMGFVS---KDSIIVGH-- 163
+ + P ++ +G+S + + ++ L F+ + +V H
Sbjct: 67 LSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNG 126
Query: 164 ---------------GLENDLRALKLIHSNIIDTSVLF--------PHSFGLPYRRSLKS 200
+ L +D+ P G SL S
Sbjct: 127 DRYDFPLLQTELARLSTPSPLDGTFC-----VDSIAALKALEQASSPSGNGSRKSYSLGS 181
Query: 201 IVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDF 236
I ++L Q+ +H + + I
Sbjct: 182 IYTRLYWQAPTD-SHTAEGHVLTLLS-ICQWKPQAL 215
>2znl_A Polymerase acidic protein; PA, PB1, subunit interaction,
phosphoprotein, nucleotide-binding,
nucleotidyltransferase; 2.30A {Influenza a virus} PDB:
3cm8_A
Length = 478
Score = 31.4 bits (70), Expect = 0.26
Identities = 25/157 (15%), Positives = 53/157 (33%), Gaps = 9/157 (5%)
Query: 57 INGPLEGYVKTKPRK-----SPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYN 111
+N +E ++KT PR PP + + L + ++ + D
Sbjct: 15 VNARIEPFLKTTPRPLRLPNGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMR 74
Query: 112 TLVK-PDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGH---GLEN 167
T + ++ + K + + L+D++N+ +K+ L
Sbjct: 75 TFFGWKEPNVVKPHEKGINPNYLLSWKQVLAELQDIENEEKIPKTKNMKKTSQLKWALGE 134
Query: 168 DLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQ 204
++ K+ + D L + P RSL S +
Sbjct: 135 NMAPEKVDFDDCKDVGDLKQYDSDEPELRSLASWIQN 171
>1z70_X C-alpha-formyglycine-generating enzyme; formylglycine, multiple
sulfatase deficiency, cysteine sulfe oxidoreductase;
HET: OCS NAG CXS; 1.15A {Homo sapiens} SCOP: d.169.1.7
PDB: 1y1f_X* 1y1e_X* 1y1h_X* 1y1i_X* 1y1g_X* 1y1j_X*
2aii_X* 2aij_X* 2aft_X* 2aik_X* 2hi8_X* 2hib_X* 2afy_X*
Length = 311
Score = 28.7 bits (64), Expect = 1.5
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 58 NGPLEGYVKTKPRKSPPPNGYGVY 81
N +G+ T P + PPNGYG+Y
Sbjct: 197 NTGEDGFQGTAPVDAFPPNGYGLY 220
>2e9q_A 11S globulin subunit beta; cucubitin, pumpkin SEED storage
globulin, plant protein; 2.20A {Cucurbita maxima} PDB:
2evx_A
Length = 459
Score = 28.7 bits (63), Expect = 1.7
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 85 TEMVYTVHGLEVARVTVVNVDGRLIYNTLVKP 116
++Y G ARV VV+ G+ +++ V+
Sbjct: 344 HSVMYATRG--NARVQVVDNFGQSVFDGEVRE 373
>2q17_A Formylglycine generating enzyme; FGE, sulfatase, unknown function;
2.10A {Streptomyces coelicolor}
Length = 346
Score = 28.8 bits (64), Expect = 1.8
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 58 NGPLEGYVKTKPRKSPPPNGYGVY 81
N +G++ T P KS PNG+G++
Sbjct: 236 NTAEDGHLSTAPVKSYRPNGHGLW 259
>2vqa_A SLL1358 protein, MNCA; periplasmic binding protein, metal-binding
protein, cupin, BI-cupin, oxalate decarboxylase; 2.95A
{Synechocystis SP}
Length = 361
Score = 28.6 bits (63), Expect = 2.0
Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 85 TEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEII 121
E Y + G +TV +G+ + L + D +
Sbjct: 256 DEWQYVLDG--EMDLTVFASEGKASVSRLQQGDVGYV 290
Score = 26.7 bits (58), Expect = 7.1
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 85 TEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEII 121
E Y + G R+T+ + +G++ + K
Sbjct: 74 AEWAYVMEG--RTRITLTSPEGKVEIADVDKGGLWYF 108
>1y4j_A Sulfatase modifying factor 2; formylglycine, sulfatases, multiple
sulfatase deficiency, HO DUF323, sugar binding protein;
HET: NAG FUC; 1.86A {Homo sapiens} SCOP: d.169.1.7
Length = 284
Score = 28.3 bits (63), Expect = 2.2
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 58 NGPLEGYVKTKPRKS-PPPNGYGVY 81
+ +G+ P + P N YG+Y
Sbjct: 178 DKAEDGFHGVSPVNAFPAQNNYGLY 202
>3ksc_A LEGA class, prolegumin; PEA prolegumin, 11S SEED storage protein,
pisum sativum L., SEED storage protein, storage protein,
plant protein; 2.61A {Pisum sativum}
Length = 496
Score = 28.0 bits (61), Expect = 3.2
Identities = 8/32 (25%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 85 TEMVYTVHGLEVARVTVVNVDGRLIYNTLVKP 116
++Y + G AR+ VVN +G +++ ++
Sbjct: 380 NSIIYALKG--RARLQVVNCNGNTVFDGELEA 409
>3t4e_A Quinate/shikimate dehydrogenase; structural genomics, center for
structural genomics of infec diseases, csgid; HET: NAD;
1.95A {Salmonella enterica subsp} PDB: 1npd_A* 1o9b_A*
1vi2_A*
Length = 312
Score = 27.6 bits (62), Expect = 3.3
Identities = 9/14 (64%), Positives = 10/14 (71%), Gaps = 1/14 (7%)
Query: 100 TVVNVDGRLI-YNT 112
T+VN DG L YNT
Sbjct: 117 TIVNDDGYLRGYNT 130
>3kgl_A Cruciferin; 11S SEED globulin, rapeseed, SEED storage protein,
storage protein, plant protein; 2.98A {Brassica napus}
Length = 466
Score = 28.0 bits (61), Expect = 3.7
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 85 TEMVYTVHGLEVARVTVVNVDGRLIYNTLVKP 116
++Y G A V VVN +G +++ V
Sbjct: 345 NAVLYVTDG--EAHVQVVNDNGDRVFDGQVSQ 374
>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 = 27.9 bits (61), Expect = 3.8
Identities = 8/65 (12%), Positives = 25/65 (38%), Gaps = 15/65 (23%)
Query: 126 KYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVL 185
Y K +I + + + N ++ F+ +E +L K +++++ +++
Sbjct: 529 FY-----KPYICDNDPKYERLVNAILDFL--------PKIEENLICSK--YTDLLRIALM 573
Query: 186 FPHSF 190
Sbjct: 574 AEDEA 578
>1npy_A Hypothetical shikimate 5-dehydrogenase-like protein HI0607;
structural genomics, PSI, protein structure initiative;
1.75A {Haemophilus influenzae} SCOP: c.2.1.7 c.58.1.5
Length = 271
Score = 27.5 bits (62), Expect = 4.0
Identities = 8/14 (57%), Positives = 10/14 (71%), Gaps = 1/14 (7%)
Query: 100 TVVNVDGRLI-YNT 112
T+VN +G L YNT
Sbjct: 89 TIVNDNGFLRAYNT 102
>3tnl_A Shikimate dehydrogenase; structural genomics, center for structural
genomics of infec diseases, csgid; HET: NAD SKM; 1.45A
{Listeria monocytogenes} PDB: 3toz_A*
Length = 315
Score = 27.6 bits (62), Expect = 4.3
Identities = 8/14 (57%), Positives = 9/14 (64%), Gaps = 1/14 (7%)
Query: 100 TVVNVDGRLI-YNT 112
TVVN DG L + T
Sbjct: 123 TVVNDDGVLTGHIT 136
Score = 26.4 bits (59), Expect = 8.7
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 12/54 (22%)
Query: 111 NTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHG 164
NT+V D + + T +G ++R LK+ +D++G K I G G
Sbjct: 122 NTVVNDDGVLTGHITDGTG-----YMRA----LKEAGHDIIG---KKMTICGAG 163
>3qac_A 11S globulin SEED storage protein; 11S SEED storage protein
(globulins) family, SEED storage PR plant protein; 2.27A
{Amaranthus hypochondriacus}
Length = 465
Score = 27.2 bits (59), Expect = 5.1
Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 85 TEMVYTVHGLEVARVTVVNVDGRLIYNTLVKP 116
++Y V G R+ +VN G+ +++ +
Sbjct: 345 HNIMYCVRG--RGRIQIVNDQGQSVFDEELSR 374
>1ji6_A Pesticidial crystal protein CRY3BB; toxin; 2.40A {Bacillus
thuringiensis} SCOP: b.18.1.3 b.77.2.1 f.1.3.1
Length = 589
Score = 27.1 bits (59), Expect = 5.8
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 99 VTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDF 135
V ++ DG+ +Y T+ D Y G++ DF
Sbjct: 327 VQKLSFDGQKVYRTIANTDVAAWPNGKVYLGVTKVDF 363
>2edd_A Netrin receptor DCC; tumor suppressor protein DCC, colorectal
cancer suppressor, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 123
Score = 26.0 bits (57), Expect = 5.9
Identities = 10/57 (17%), Positives = 15/57 (26%), Gaps = 6/57 (10%)
Query: 55 GGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLE-----VARVTVVNVDG 106
+ Y + R S + T + YT GL+ V V
Sbjct: 47 NQKTSEVRLYT-VRWRTSFSASAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRR 102
>1nvt_A Shikimate 5'-dehydrogenase; structural genomics, PSI, protein
structure initiative; HET: NAP; 2.35A
{Methanocaldococcus jannaschii} SCOP: c.2.1.7 c.58.1.5
Length = 287
Score = 26.8 bits (60), Expect = 6.2
Identities = 7/14 (50%), Positives = 9/14 (64%), Gaps = 1/14 (7%)
Query: 100 TVVNVDGRLI-YNT 112
T+ DG+ I YNT
Sbjct: 97 TIKIEDGKAIGYNT 110
Score = 26.8 bits (60), Expect = 7.3
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 12/54 (22%)
Query: 111 NTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHG 164
NT+ D + I YNT G L++ + K+ +I G G
Sbjct: 96 NTIKIEDGKAIGYNTDGIG-----ARMA----LEEEIGRVKD---KNIVIYGAG 137
>2egg_A AROE, shikimate 5-dehydrogenase; dimer, X-RAY diffraction,
structural genomics, NPPSFA; 2.25A {Geobacillus
kaustophilus}
Length = 297
Score = 26.8 bits (60), Expect = 6.2
Identities = 9/14 (64%), Positives = 12/14 (85%), Gaps = 1/14 (7%)
Query: 100 TVVNVDGRLI-YNT 112
T++N DGRL+ YNT
Sbjct: 109 TIINNDGRLVGYNT 122
>2y3c_A Treponema denticola variable protein 1; unknown function,
periodontal disease; HET: CME; 1.40A {Treponema
denticola}
Length = 294
Score = 26.7 bits (59), Expect = 6.4
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 63 GYVKTKPRKSPPPNGYGVY 81
KT K PN YG+Y
Sbjct: 201 SGSKTHEVKKKKPNWYGLY 219
>1j58_A YVRK protein; cupin, decarboxyklase, oxalate, manganese, formate,
metal BI protein; 1.75A {Bacillus subtilis} SCOP:
b.82.1.2 PDB: 1l3j_A 1uw8_A 2uyb_A 2uy9_A 2uy8_A 2v09_A
2uya_A 3s0m_A
Length = 385
Score = 26.7 bits (58), Expect = 7.0
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 75 PNGYGV--YALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEII 121
P + + E Y ++G ARVT+V+ GR + + + D
Sbjct: 88 PGAIRELHWHKEAEWAYMIYG--SARVTIVDEKGRSFIDDVGEGDLWYF 134
>2hk9_A Shikimate dehydrogenase; shikimate pathway, drug design,
oxidoreductase; HET: ATR SKM NAP; 2.20A {Aquifex
aeolicus} PDB: 2hk8_A 2hk7_A
Length = 275
Score = 26.7 bits (60), Expect = 7.1
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 12/54 (22%)
Query: 111 NTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHG 164
NT+ + + YNT + G F+++ LK + ++ K +++G G
Sbjct: 97 NTVKFENGKAYGYNTDWIG-----FLKS----LKSLIPEVKE---KSILVLGAG 138
>3fcg_A F1 capsule-anchoring protein; beta barrel, beta strand swapping,
cell membrane, cell outer membrane, cell projection,
fimbrium, membrane; 2.85A {Yersinia pestis}
Length = 90
Score = 25.4 bits (56), Expect = 7.2
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 97 ARVTVVNVDGRLIYNTLVKP-DCEIID-YNTKYSG 129
ARV V DG + N LV E+ + SG
Sbjct: 27 ARVEV-LRDGYTVSNELVPSGPFELANLPLGGGSG 60
>1dcq_A PYK2-associated protein beta; zinc-binding module, ankyrin repeats,
metal binding protein; 2.10A {Mus musculus} SCOP:
d.211.1.1 g.45.1.1
Length = 278
Score = 26.5 bits (58), Expect = 8.1
Identities = 19/116 (16%), Positives = 39/116 (33%), Gaps = 8/116 (6%)
Query: 103 NVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVG 162
N I + P + + N I+ KD+I Y + + +K +
Sbjct: 78 NAGFNEIMECCL-PSEDPVKPNPGSDMIARKDYITAKYMERRYARKKHADTAAKLHSLCE 136
Query: 163 HGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSF 218
D+ L +++ +D + P + G + LH +++S S
Sbjct: 137 AVKTRDIFGLLQAYADGVDLTEKIPLANGHEPDET-------ALHLAVRSVDRTSL 185
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
0.320 0.138 0.411
Gapped
Lambda K H
0.267 0.0498 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,705,789
Number of extensions: 214677
Number of successful extensions: 531
Number of sequences better than 10.0: 1
Number of HSP's gapped: 524
Number of HSP's successfully gapped: 49
Length of query: 240
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,160,982
Effective search space: 619986318
Effective search space used: 619986318
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.9 bits)