RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 018231
(359 letters)
>1rv3_A Serine hydroxymethyltransferase, cytosolic; one-carbon metabolism;
HET: GLY PLP; 2.40A {Oryctolagus cuniculus} SCOP:
c.67.1.4 PDB: 1rv4_A* 1rvu_A* 1rvy_A* 1ls3_A* 1cj0_A*
1bj4_A* 1eji_A*
Length = 483
Score = 605 bits (1563), Expect = 0.0
Identities = 196/319 (61%), Positives = 242/319 (75%), Gaps = 4/319 (1%)
Query: 7 EAVYEKEKNGVTWP---KQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVM 63
AV ++ W + L PL+ D E+ DII+ E RQ GLELI SENF S +V+
Sbjct: 2 TAVNGAPRDAALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVL 61
Query: 64 QAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSP 123
+A+GS + NKYS GYPG RYYGG E+ID E+LCQKRAL+A+ LDP+ WGVNVQ SGSP
Sbjct: 62 EALGSCLNNKYSLGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSP 121
Query: 124 SNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGYID 183
+NF VYTAL++PH RIM LDLP GGHL+HG+ TD KKISA SIFFE+M Y++N TGYID
Sbjct: 122 ANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYID 181
Query: 184 YDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIP 243
YD+LE++A LF PKLI+AG S Y+R DY R+RK+ ++ A ++ADMAHISGLV AGV+P
Sbjct: 182 YDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVP 241
Query: 244 SPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEIN-KQGKEVFYDYEEKINQAVFPGLQG 302
SPFE+ VVTTTTHK+LRG R MIF+R+GV+ ++ K GKE+ Y+ E IN AVFPGLQG
Sbjct: 242 SPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQG 301
Query: 303 GPHNHTITGLAVALKQVCT 321
GPHNH I G+AVALKQ T
Sbjct: 302 GPHNHAIAGVAVALKQAMT 320
>2a7v_A Serine hydroxymethyltransferase; structural genomics, structural
genomics consortium, SGC; 2.04A {Homo sapiens} SCOP:
c.67.1.4 PDB: 3ou5_A
Length = 490
Score = 599 bits (1546), Expect = 0.0
Identities = 199/321 (61%), Positives = 246/321 (76%), Gaps = 3/321 (0%)
Query: 2 SSLPNEAVYEKEKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVS 61
+ N A + + W L DPE+ ++++ EK RQ +GLELI SENF S +
Sbjct: 12 AQHSNAAQTQTGEANRGWTG--QESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRA 69
Query: 62 VMQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSG 121
++A+GS + NKYSEGYPG RYYGG E +D E LCQ+RALEAF LDP +WGVNVQ SG
Sbjct: 70 ALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSG 129
Query: 122 SPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRLNESTGY 181
SP+N VYTALL+PHDRIM LDLP GGHL+HGY +D K+ISA SIFFE+MPY+LN TG
Sbjct: 130 SPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGL 189
Query: 182 IDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGV 241
IDY+QL +A LFRP+LI+AG SAYARL DY R+R+VC++ KA +LADMAHISGLVAA V
Sbjct: 190 IDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKV 249
Query: 242 IPSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEIN-KQGKEVFYDYEEKINQAVFPGL 300
IPSPF++AD+VTTTTHK+LRG R +IF+RKGVK ++ K G+E+ Y +E++IN AVFP L
Sbjct: 250 IPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSL 309
Query: 301 QGGPHNHTITGLAVALKQVCT 321
QGGPHNH I +AVALKQ CT
Sbjct: 310 QGGPHNHAIAAVAVALKQACT 330
>2vi8_A Serine hydroxymethyltransferase; SHMT, E53Q, FTHF, enzyme memory,
pyridoxal phosphate, one-carbon metabolism,
PLP-dependent enzymes; HET: PLP; 1.67A {Bacillus
stearothermophilus} PDB: 2vi9_A* 2via_A* 2vib_A* 1kkj_A*
1kkp_A* 1kl1_A* 1kl2_A* 1yjs_A* 2w7f_A* 2w7d_A* 2w7e_A*
2w7g_A* 2w7h_A* 1yjz_A* 1yjy_A* 2vgu_A* 2vgs_A* 2vgt_A*
2vgv_A* 2vgw_A* ...
Length = 405
Score = 382 bits (984), Expect = e-132
Identities = 130/294 (44%), Positives = 183/294 (62%), Gaps = 29/294 (9%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
L DP++ IE E+ RQ +ELI SENF S +VM+A GSV+TNKY+EGYPG RYYGG
Sbjct: 4 LPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGG 63
Query: 87 NEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPH 146
EY+D+ E L ++RA + F + NVQ SG+ +N VY +L+ D ++ ++L H
Sbjct: 64 CEYVDIVEELARERAKQLFGAE----HANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSH 119
Query: 147 GGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA 203
GGHL+HG S V+ + + Y ++ T IDYD + + A L RPKLIVA A
Sbjct: 120 GGHLTHG--------SPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAA 171
Query: 204 SAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGP 263
+AY R+ D+ + R++ ++ A ++ DMAHI+GLVAAG+ P+P YA VTTTTHK+LRGP
Sbjct: 172 AAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGP 231
Query: 264 RGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
RG MI ++ + ++I++A+FPG+QGGP H I AVA
Sbjct: 232 RGGMILCQE--------------QFAKQIDKAIFPGIQGGPLMHVIAAKAVAFG 271
>3gbx_A Serine hydroxymethyltransferase; structural genomics, IDP01011,
serine hydroxymethyltransfera salmonella typhimurium.;
HET: MSE; 1.80A {Salmonella typhimurium} PDB: 1dfo_A*
3g8m_A* 1eqb_A*
Length = 420
Score = 381 bits (982), Expect = e-132
Identities = 138/297 (46%), Positives = 186/297 (62%), Gaps = 27/297 (9%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
+ D E+ +E EK RQ + +ELI SEN+TS VMQA GS +TNKY+EGYPG RY
Sbjct: 8 EMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRY 67
Query: 84 YGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALD 143
YGG EY+D+ E L RA E F D NVQ SGS +NF VYTALL+P D ++ ++
Sbjct: 68 YGGCEYVDVVEQLAIDRAKELFGAD----YANVQPHSGSQANFAVYTALLQPGDTVLGMN 123
Query: 144 LPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIV 200
L GGHL+HG S V+ + +PY ++E +G IDYD++ K A +PK+I+
Sbjct: 124 LAQGGHLTHG--------SPVNFSGKLYNIVPYGIDE-SGKIDYDEMAKLAKEHKPKMII 174
Query: 201 AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSL 260
G SAY+ + D+ ++R++ + A + DMAH++GL+AAGV P+P +A VVTTTTHK+L
Sbjct: 175 GGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTL 234
Query: 261 RGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
GPRG +I + G +E+ K K+N AVFP QGGP H I G AVALK
Sbjct: 235 AGPRGGLILAKGGDEELYK-----------KLNSAVFPSAQGGPLMHVIAGKAVALK 280
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 380 bits (979), Expect = e-131
Identities = 132/315 (41%), Positives = 184/315 (58%), Gaps = 29/315 (9%)
Query: 6 NEAVYEKEKNGVTWPKQLNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQA 65
+ + P ++APL VDP+IA+++ E RQ LE+I SENF +V+QA
Sbjct: 5 HHHHMGTLEAQTQGPGSMSAPLAEVDPDIAELLAKELGRQRDTLEMIASENFVPRAVLQA 64
Query: 66 VGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSN 125
GSV+TNKY+EG PG RYYGG E++D+ E+L + RA F + NVQ SG+ +N
Sbjct: 65 QGSVLTNKYAEGLPGRRYYGGCEHVDVVENLARDRAKALFGAE----FANVQPHSGAQAN 120
Query: 126 FQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYI 182
V AL+ P +R++ LDL +GGHL+HG ++ +E Y ++ +T I
Sbjct: 121 AAVLHALMSPGERLLGLDLANGGHLTHG--------MRLNFSGKLYENGFYGVDPATHLI 172
Query: 183 DYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVI 242
D D + +A FRPK+I+AG SAY R+ D+ R + ++ A +L DMAH +GLVAAG+
Sbjct: 173 DMDAVRATALEFRPKVIIAGWSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLH 232
Query: 243 PSPFEYADVVTTTTHKSLRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQG 302
PSP +ADVV+TT HK+L G R +I ++ Y + IN AVFPG QG
Sbjct: 233 PSPVPHADVVSTTVHKTLGGGRSGLIVGKQ--------------QYAKAINSAVFPGQQG 278
Query: 303 GPHNHTITGLAVALK 317
GP H I G AVALK
Sbjct: 279 GPLMHVIAGKAVALK 293
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 378 bits (973), Expect = e-130
Identities = 131/294 (44%), Positives = 178/294 (60%), Gaps = 28/294 (9%)
Query: 27 LEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGG 86
D + ++I E+ RQ +GLELI SENF S V +AVGSV+TNKY+EGYPGARYYGG
Sbjct: 4 TLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGG 63
Query: 87 NEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPH 146
E ID ESL +RA F NVQ SGS +N VY AL++P D +M +DL
Sbjct: 64 CEVIDRVESLAIERAKALFGAA----WANVQPHSGSQANMAVYMALMEPGDTLMGMDLAA 119
Query: 147 GGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA 203
GGHL+HG S V+ ++ + Y + T ID +++ + A RPK+IVAGA
Sbjct: 120 GGHLTHG--------SRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGA 171
Query: 204 SAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGP 263
SAY R +D++ R++ ++ A ++ DMAH +GLVAAG+ P+P YA VVT+TTHK+LRGP
Sbjct: 172 SAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGP 231
Query: 264 RGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
RG +I + ++I++ +FPG+QGGP H I G AVA
Sbjct: 232 RGGLILSNDP-------------ELGKRIDKLIFPGIQGGPLEHVIAGKAVAFF 272
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 378 bits (974), Expect = e-130
Identities = 124/298 (41%), Positives = 165/298 (55%), Gaps = 28/298 (9%)
Query: 23 LNAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGAR 82
+ L D + I E RQ +ELI SEN S +V+ A GSV+TNKY+EGYPG R
Sbjct: 9 FSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKR 68
Query: 83 YYGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMAL 142
YYGG E+ D E+L +R F NVQ SG+ +N V AL KP D ++ +
Sbjct: 69 YYGGCEFADEVEALAIERVKRLFNAG----HANVQPHSGAQANGAVMLALAKPGDTVLGM 124
Query: 143 DLPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLI 199
L GGHL+HG + ++ +F + Y ++ T IDYDQ+E A +P LI
Sbjct: 125 SLDAGGHLTHG--------AKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLI 176
Query: 200 VAGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKS 259
+AG SAY R D+ R R + + A ++ DMAHI+G++AAG +P E+A VVT+TTHK+
Sbjct: 177 IAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKT 236
Query: 260 LRGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
LRGPRG + + +KIN AVFPGLQGGP H I G AVA
Sbjct: 237 LRGPRGGFVLTNDE-------------EIAKKINSAVFPGLQGGPLMHVIAGKAVAFG 281
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 374 bits (962), Expect = e-128
Identities = 134/297 (45%), Positives = 181/297 (60%), Gaps = 29/297 (9%)
Query: 24 NAPLEVVDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARY 83
LE+ D EI D+ E RQ +GLE+I SENFT VM+ +GS++TNKY+EGYPG RY
Sbjct: 3 AMSLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRY 62
Query: 84 YGGNEYIDMAESLCQKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALD 143
YGG E++D E+L +R + F NVQ SGS +N VY AL+ P D+I+ +D
Sbjct: 63 YGGCEFVDEIETLAIERCKKLFNCK----FANVQPNSGSQANQGVYAALINPGDKILGMD 118
Query: 144 LPHGGHLSHGYQTDTKKISAVSI---FFETMPYRLNESTGYIDYDQLEKSATLFRPKLIV 200
L HGGHL+HG + VS +E+ Y + G IDY+++ + A +PKLIV
Sbjct: 119 LSHGGHLTHG--------AKVSSSGKMYESCFYGVEL-DGRIDYEKVREIAKKEKPKLIV 169
Query: 201 AGASAYARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSL 260
GASAYAR+ D+ + R++ ++ A + AD+AHI+GLV AG PSPF YA VV++TTHK+L
Sbjct: 170 CGASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTL 229
Query: 261 RGPRGAMIFFRKGVKEINKQGKEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
RGPRG +I + +KIN A+FPG+QGGP H I AV K
Sbjct: 230 RGPRGGIIMTNDE-------------ELAKKINSAIFPGIQGGPLMHVIAAKAVGFK 273
>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 = 48.9 bits (116), Expect = 2e-06
Identities = 29/214 (13%), Positives = 58/214 (27%), Gaps = 81/214 (37%)
Query: 174 RLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNK----QKAIMLAD 229
R+ E+ + ++ + I + ++ Y + + + + Q A+ L +
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEK--IFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 230 MA-------------------H----ISGLVA-AGVIPSPFEYADVVTTTTHKSLRG--- 262
A H + L + A V+ E +V RG
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM--SIE--SLVEVV---FYRGMTM 1793
Query: 263 ----PRG-------AMI--------------FFRKGVKEINKQGKEVFYDYEEKINQAV- 296
PR MI + V+ + K+ + + V
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLV--------EIVN 1845
Query: 297 --FPGLQGGPHNHTITGLAVALKQVCTLITFSHI 328
Q + G AL V ++ F +
Sbjct: 1846 YNVENQQ-----YVAAGDLRALDTVTNVLNFIKL 1874
Score = 43.1 bits (101), Expect = 1e-04
Identities = 52/342 (15%), Positives = 99/342 (28%), Gaps = 105/342 (30%)
Query: 34 IADIIEHEKARQWKGLELI------------PSENFTSVSVMQAVGSVMTNKYSEGYPGA 81
A +++ K ELI P + ++ ++ +AV EG A
Sbjct: 105 AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAV--------GEG--NA 154
Query: 82 RYY---GG----NEYIDMAESLCQKRAL-EAFR--LDP--EKWGVNVQSLSGSPSN---- 125
+ GG ++Y + E L R L + + + + + L + +
Sbjct: 155 QLVAIFGGQGNTDDYFE--E-L---RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKV 208
Query: 126 ----FQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKISAVS---IF------FETMP 172
+ L P + P +L +S I +
Sbjct: 209 FTQGLNILEWLENPSNT------PDKDYLLS---------IPISCPLIGVIQLAHYVVTA 253
Query: 173 YRLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYD--YERIRKVCNKQKAIMLADM 230
L + G + L K AT L+ A A A ++ + + +KAI + +
Sbjct: 254 KLLGFTPGEL-RSYL-KGATGHSQGLVTAVAIAETDSWESFFV------SVRKAITV--L 303
Query: 231 AHISGLVAAGVIP----SPFEYADVV----TTTTHK-SLRGPRGAMIFFRKGVKEINKQG 281
I G+ P P D + + S+ + V + N
Sbjct: 304 FFI-GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ--DYVNKTNSHL 360
Query: 282 KEVFYDYEEKINQAVFPGLQGGPHNHTITGLAVALKQVCTLI 323
+ V L G N ++G +L + +
Sbjct: 361 PA---------GKQVEISLVNGAKNLVVSGPPQSLYGLNLTL 393
>2ez2_A Beta-tyrosinase, tyrosine phenol-lyase; PLP-dependent enzyme,
pyridoxal-5'-phosphate, domain lyase; 1.85A {Citrobacter
freundii} PDB: 2ez1_A 2vlf_A* 2vlh_A* 2yct_A* 1tpl_A
2tpl_A* 2ycn_A* 2yhk_A* 2ycp_A* 1c7g_A*
Length = 456
Score = 42.0 bits (98), Expect = 2e-04
Identities = 33/261 (12%), Positives = 68/261 (26%), Gaps = 50/261 (19%)
Query: 42 KARQWKGLELIPSENFTSVSVMQAVGSVMTNKYSEGYPGARYYGGNEYIDMAESLCQKRA 101
+ + L + + + ++ +++ G Y G+E E
Sbjct: 29 QEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMMGDEAYAGSENFYHLE------- 81
Query: 102 LEAFRLDPEKWGVN--VQSLSGSPSNFQVYTALLKPHDRIMA---LDLPHGGHLSHGYQT 156
+ E +G V + G + + +KP + +G
Sbjct: 82 -RTVQ---ELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRYHQEKNG--- 134
Query: 157 DTKKISAVSIFFETM--PYRLNESTGYIDYDQLEKSATLFRPKLI----------VAGAS 204
V I + G ID +L+K + I +AG
Sbjct: 135 ----AVFVDIVRDEAHDAGLNIAFKGDIDLKKLQKLIDEKGAENIAYICLAVTVNLAGGQ 190
Query: 205 AYARLYDYERIRKVCNKQKAIMLADMAHISG--------------LVAAGVIPSPFEYAD 250
+ + + +R++ + D A ++ F YAD
Sbjct: 191 PVS-MANMRAVRELTEAHGIKVFYDATRCVENAYFIKEQEQGFENKSIAEIVHEMFSYAD 249
Query: 251 VVTTTTHKSLRGPRGAMIFFR 271
T + K G +
Sbjct: 250 GCTMSGKKDCLVNIGGFLCMN 270
>1ax4_A Tryptophanase; tryptophan biosynthesis, tryptophan indole-lyase,
pyridoxal 5'-phosphate, monovalent cation binding site;
HET: LLP; 2.10A {Proteus vulgaris} SCOP: c.67.1.2
Length = 467
Score = 39.4 bits (91), Expect = 0.001
Identities = 26/181 (14%), Positives = 54/181 (29%), Gaps = 29/181 (16%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPHGGHLSHGYQTDTKKI----SAVSIFFETM--PY 173
G + ++ LLK + P H T A++I E
Sbjct: 99 QGRGAENILFPVLLKYKQKEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSE 158
Query: 174 RLNESTGYIDYDQLE---KSATLFRPKLIVAGASAYAR------LYDYERIRKVCNKQKA 224
++ G D +L+ IV+ + + + + + + ++ +
Sbjct: 159 TYDDWKGDFDIKKLKENIAQHGADNIVAIVSTVTCNSAGGQPVSMSNLKEVYEIAKQHGI 218
Query: 225 IMLADMAHI--------------SGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFF 270
++ D A VI ++YAD +T + K G ++
Sbjct: 219 FVVMDSARFCENAYFIKARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVAI 278
Query: 271 R 271
R
Sbjct: 279 R 279
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 37.5 bits (87), Expect = 0.006
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 206 YARLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEY-ADVVTTTTHKSLRGPR 264
Y ++ E + K ++ +L D AH + G S Y AD V + HK+L
Sbjct: 158 YGETFNVEEVIKSLHQLNIPVLIDEAHGAHFGLQGFPDSTLNYQADYVVQSFHKTLPALT 217
Query: 265 -GAMIFFRKG 273
G++++ K
Sbjct: 218 MGSVLYIHKN 227
>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate,
PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A
{Escherichia coli}
Length = 755
Score = 37.4 bits (86), Expect = 0.007
Identities = 41/221 (18%), Positives = 62/221 (28%), Gaps = 40/221 (18%)
Query: 98 QKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLS--HG-Y 154
+K A F D V S SN + A + +D ++ + H S G
Sbjct: 211 EKYAARVFGADRSWSVVV----GTSGSNRTIMQACMTDNDVVV---VDRNCHKSIEQGLM 263
Query: 155 QTDTK------KISAVSIFFETMPYRLNEST--GYIDYDQLEKSATLFRPKLIVAGASAY 206
T K + I P + T I L K +P V Y
Sbjct: 264 LTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTNCTY 323
Query: 207 ARL-YDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPS----------PFEYADVVTTT 255
+ Y+ + + + K + D A + T +
Sbjct: 324 DGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTVFATHS 383
Query: 256 THKSLRGPR-GAMIFFRKGVKEINKQGKEVFYDYEEKINQA 295
THK L + I R+G IN + NQA
Sbjct: 384 THKLLNALSQASYIHVREGRGAIN----------FSRFNQA 414
>2fnu_A Aminotransferase; protein-product complex, structural genomics,
montreal-kings bacterial structural genomics initiative,
BSGI; HET: PMP UD1; 1.50A {Helicobacter pylori} SCOP:
c.67.1.4 PDB: 2fni_A* 2fn6_A*
Length = 375
Score = 36.0 bits (84), Expect = 0.015
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 177 ESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMAH 232
++ G ID LEK R K IV AG S + E ++K+C K L+D +H
Sbjct: 104 KNDGNIDELALEKLIN-ERTKAIVSVDYAGKSV-----EVESVQKLCKKHSLSFLSDSSH 157
>3f0h_A Aminotransferase; RER070207000802, structural genomics, JOIN for
structural genomics, JCSG; HET: MSE LLP; 1.70A
{Eubacterium rectale}
Length = 376
Score = 33.7 bits (78), Expect = 0.082
Identities = 25/124 (20%), Positives = 40/124 (32%), Gaps = 26/124 (20%)
Query: 209 LYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFE--YADVVTTTTHKSLRGPRG- 265
LYD I + C K + D +S P ADV+ T + K L P G
Sbjct: 160 LYDTMMIGEFCKKNNMFFVCDC--VSAF---LADPFNMNECGADVMITGSQKVLACPPGI 214
Query: 266 AMIFFRKGVKEINKQGKEV-----FYDYEEKINQAVFPGLQGGPHNHT-----ITGLAVA 315
++I E ++ K D + + P T + +
Sbjct: 215 SVIVLAPRGVERVEKSKVRTMYFDLKDALKNQERGQTP--------FTPAVGILLQINER 266
Query: 316 LKQV 319
LK++
Sbjct: 267 LKEI 270
>1mdo_A ARNB aminotransferase; type 1 aminotransferase fold; HET: MSE PMP;
1.70A {Salmonella typhimurium} SCOP: c.67.1.4 PDB:
1mdx_A* 1mdz_A*
Length = 393
Score = 33.3 bits (77), Expect = 0.11
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 176 NESTGYIDYDQLEKSATLFRPKLIV----AGASAYARLYDYERIRKVCNKQKAIMLADMA 231
+ T + + +E + T + K I+ AGA A D + I + + ++ D A
Sbjct: 109 DRDTLMVTPEHIEAAIT-PQTKAIIPVHYAGAPA-----DLDAIYALGERYGIPVIEDAA 162
Query: 232 H 232
H
Sbjct: 163 H 163
>1c4k_A Protein (ornithine decarboxylase); lyase; HET: PLP GTP; 2.70A
{Lactobacillus SP} SCOP: c.23.1.4 c.67.1.5 d.125.1.1
PDB: 1ord_A*
Length = 730
Score = 33.1 bits (75), Expect = 0.13
Identities = 15/126 (11%), Positives = 35/126 (27%), Gaps = 17/126 (13%)
Query: 182 IDYDQLEKSATLFRPKLIVAGASAYARL-YDYERIRKVCNKQKAIMLADMAHISGLVAAG 240
E++ +L V Y Y+ + K + D A +
Sbjct: 268 AAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIP 327
Query: 241 VIPSPF----------EYADVVTTTTHKSLRGPR-GAMIFFRKGVKEINKQGKEVFYDYE 289
++ + + +V + HK G + I + + ++ Y
Sbjct: 328 MMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKD-----SHIKGQLRYCDH 382
Query: 290 EKINQA 295
+ N +
Sbjct: 383 KHFNNS 388
>2z67_A O-phosphoseryl-tRNA(SEC) selenium transferase; selenocysteine
biosynthesis, seven-stranded BETE-strand, PYR
5'-phosphate; HET: PLP; 2.50A {Methanococcus
maripaludis} SCOP: c.67.1.9
Length = 456
Score = 32.3 bits (73), Expect = 0.22
Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 4/92 (4%)
Query: 185 DQLEKSATLFRPKLIVAGASAYA-RLYD-YERIRKVCNKQKAIMLADMAH-ISGLVAAGV 241
+ ++K L +++ + + R D I K+C + + A+ I
Sbjct: 221 NAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEK 280
Query: 242 IPSPF-EYADVVTTTTHKSLRGPRGAMIFFRK 272
+ F D V +++ K+L P G + +
Sbjct: 281 LKKAFKYRVDAVVSSSDKNLLTPIGGGLVYST 312
>3n75_A LDC, lysine decarboxylase, inducible; pyridoxal-5'-phosphate
dependent decarboxylase, acid stress stringent response;
HET: LLP G4P P6G; 2.00A {Escherichia coli} PDB: 3q16_A*
Length = 715
Score = 32.3 bits (73), Expect = 0.24
Identities = 33/200 (16%), Positives = 58/200 (29%), Gaps = 35/200 (17%)
Query: 98 QKRALEAFRLDPEKWGVNVQSLSGSPSNFQVYTALLKPHDRIMALDLPHGGHLS--HG-Y 154
++ F D N S +N V I+ + H S H
Sbjct: 201 EQYIARVFNADRSYMVTN----GTSTANKIVGMYSAPAGSTIL---IDRNCHKSLTHLMM 253
Query: 155 QTDTKKISAVSIFFET--------MPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAY 206
+D I+F +E +++++ P V S Y
Sbjct: 254 MSD-----VTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTY 308
Query: 207 ARL-YDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPS--------PFEYADVVTTTTH 257
L Y+ + I+K + + + D A + + + T +TH
Sbjct: 309 DGLLYNTDFIKKTLDVKS--IHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTH 366
Query: 258 KSLRGPR-GAMIFFRKGVKE 276
K L +MI + V E
Sbjct: 367 KLLAAFSQASMIHVKGDVNE 386
>1qz9_A Kynureninase; kynurenine, tryptophan, PLP, vitamin B6,
pyridoxal-5'-phosph hydrolase; HET: PLP P3G; 1.85A
{Pseudomonas fluorescens} SCOP: c.67.1.3
Length = 416
Score = 31.6 bits (72), Expect = 0.39
Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 208 RLYDYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAM 267
++D + + + ++ A+ + D+AH +G V + + AD T+K L G G+
Sbjct: 180 YMHDMQALTALSHECGALAIWDLAHSAGAVPVDLHQAG---ADYAIGCTYKYLNGGPGSQ 236
Query: 268 IFF 270
F
Sbjct: 237 AFV 239
>3e9k_A Kynureninase; kynurenine-L-hydrolase, kynurenine hydrolase,
pyridoxal-5'-phosphate, inhibitor complex, 3-hydroxy
hippur hydroxyhippuric acid, PLP; HET: PLP 3XH; 1.70A
{Homo sapiens} PDB: 2hzp_A*
Length = 465
Score = 31.1 bits (70), Expect = 0.56
Identities = 21/152 (13%), Positives = 46/152 (30%), Gaps = 10/152 (6%)
Query: 126 FQVYTALLKPHDRIMALDLPHGGHLSHGY----QTDTKKISAVSIFFETMPYRLNESTGY 181
+ + KP + + L S Y Q ++ P E+
Sbjct: 142 HLLMLSFFKPTPKRYKILLEAKAFPSDHYAIESQLQLHGLNIEESMRMIKPREGEETLRI 201
Query: 182 IDYDQLEKSATLFRPKLIVAGASAYA--RLYDYERIRKVCNKQKAIMLADMAHISGLVAA 239
D ++ + +I+ + + ++ I K + + D+AH G V
Sbjct: 202 EDILEVIEKEGD-SIAVILFSGVHFYTGQHFNIPAITKAGQAKGCYVGFDLAHAVGNVEL 260
Query: 240 GVIPSPFEYADVVTTTTHKSLRGPRGAMIFFR 271
+ ++A ++K L G +
Sbjct: 261 YLHDWGVDFA---CWCSYKYLNAGAGGIAGAF 289
>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 = 29.5 bits (65), Expect = 0.96
Identities = 7/23 (30%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 13 EKNGVTWPKQLNAPLEVVDPEIA 35
EK + K+L A L++ + A
Sbjct: 18 EKQAL---KKLQASLKLYADDSA 37
>3kki_A CAI-1 autoinducer synthase; quorum sensing, CQSA, P virulence,
acyltransferase, aminotransferase, pyridoxal PHO
transferase; HET: PLP; 1.80A {Vibrio cholerae} PDB:
3hqt_A* 2wk9_A* 2wk8_A* 2wka_A* 2wk7_A
Length = 409
Score = 29.1 bits (66), Expect = 2.5
Identities = 24/170 (14%), Positives = 45/170 (26%), Gaps = 52/170 (30%)
Query: 120 SGSPSNFQVYTALLKPHDRIMALDLPH-----GGHLSHGYQTDTKKISAVSIFFETMPYR 174
SG +N + + +P+ + H G ++ + P+
Sbjct: 127 SGWNANVGLLQTICQPNTNVYIDFFAHMSLWEGARYANA---------------QAHPFM 171
Query: 175 LNESTGYIDYDQLEKSATLFRPKLIVA-------GASAYARLYDYERIRKVCNKQKAIML 227
N + D L P +IV G A + + + +L
Sbjct: 172 HN------NCDHLRMLIQRHGPGIIVVDSIYSTLGTIA-----PLAELVNISKEFGCALL 220
Query: 228 ADMAHISGLV---------AAGVIPSPFEYADVVTTTTHKSLRGPRGAMI 268
D +H G G+ +T + K+ R I
Sbjct: 221 VDESHSLGTHGPNGAGLLAELGLTREV----HFMTASLAKTF-AYRAGAI 265
>2e7j_A SEP-tRNA:Cys-tRNA synthase; seven-stranded BETE-strand, lyase,
structural genomics; HET: PLP; 2.40A {Archaeoglobus
fulgidus} SCOP: c.67.1.9 PDB: 2e7i_A*
Length = 371
Score = 28.5 bits (64), Expect = 3.2
Identities = 27/151 (17%), Positives = 53/151 (35%), Gaps = 23/151 (15%)
Query: 177 ESTGYIDYDQLEK---SATLFRPKLIVA---GASAYARLYDYERIRKVCNKQKAIMLADM 230
I + + ++ Y L D ++I KVC++ +L +
Sbjct: 125 YPDYAITPENFAQTIEETKKRGEVVLALITYPDGNYGNLPDVKKIAKVCSEYDVPLLVNG 184
Query: 231 AHISGLVAAGVIPSPFEY--ADVVTTTTHKSLRGPRG--AMIFFRKGVKEINKQGKEVFY 286
A+ A G +P + AD + + HKS+ G ++ ++ EI + E +
Sbjct: 185 AY-----AIGRMPVSLKEIGADFIVGSGHKSM-AASGPIGVMGMKEEWAEIVLRRSEKYK 238
Query: 287 DYEEKINQAVFPGLQGGPHNHTITGLAVALK 317
+ E ++ L TI L +
Sbjct: 239 NKEVEL-------LGCTARGATIITLMASFP 262
>1omo_A Alanine dehydrogenase; two-domain, beta-sandwich-dimer,
rossmann-fold NAD domain, human MU crystallin homolog;
HET: NAD; 2.32A {Archaeoglobus fulgidus} SCOP: c.2.1.13
PDB: 1vll_A
Length = 322
Score = 28.4 bits (64), Expect = 3.4
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 205 AYARLYDYERIRKVC--NKQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTT 256
A R++D ++ ++ A G+ A+ DV+ TTT
Sbjct: 143 ALRRVFDIGEVK-AYDVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTT 195
>3b8x_A WBDK, pyridoxamine 5-phosphate-dependent dehydrase; aspartate
aminotransferase, colitose, perosamine, O-antigen,
pyridoxal phosphate,; HET: G4M; 1.70A {Escherichia coli}
PDB: 2gms_A* 2gmu_A* 2r0t_A* 3gr9_A*
Length = 390
Score = 28.3 bits (64), Expect = 4.2
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 176 NESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYERIRKVCNKQKAIMLADMAH 232
+ +T ID + L+++ T K I+ + +++ I K+ + I+L D
Sbjct: 110 DINTLNIDIESLKEAVTD-STKAILT-VNLLGNPNNFDEINKIIGGRDIILLEDNCE 164
>3hdj_A Probable ornithine cyclodeaminase; APC62486, bordetella pertussis
TOH structural genomics, PSI-2, protein structure
initiative; 1.70A {Bordetella pertussis}
Length = 313
Score = 28.0 bits (63), Expect = 5.5
Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 205 AYARLYDYERIRKVCNKQKAI-MLADMAHISGLVAAGVIPSPFEY---ADVVTTTT 256
+ + E I V + + +L + G+ A + +P + AD+V T T
Sbjct: 139 QLSARFALEAIL-VHDPYASPEILERIGRRCGVPA--RMAAPADIAAQADIVVTAT 191
>2vty_A Protein F1, F1L; BCL-2, apoptosis; 2.10A {Vaccinia virus}
Length = 182
Score = 27.1 bits (59), Expect = 7.2
Identities = 24/110 (21%), Positives = 38/110 (34%), Gaps = 8/110 (7%)
Query: 169 ETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGA---SAYARLYDYER-----IRKVCN 220
E M YR ++ST +DY E+ + + ++ Y +L R I C+
Sbjct: 35 ENMVYRFDKSTNILDYLSTERDHVMMAVRYYMSKQRLDDLYRQLPTKTRSYIDIINIYCD 94
Query: 221 KQKAIMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMIFF 270
K DM + + + +V T G R A I F
Sbjct: 95 KVSNDYNRDMNIMYDMASTKSFTVYDINNEVNTIMLDNKGLGVRLATISF 144
>1eix_A Orotidine 5'-monophosphate decarboxylase; alpha-beta-barrel,
protein-inhibitor complex, homodimer, lyase; HET: BMQ;
2.50A {Escherichia coli} SCOP: c.1.2.3 PDB: 1jjk_A*
1l2u_A
Length = 245
Score = 27.2 bits (61), Expect = 7.6
Identities = 5/17 (29%), Positives = 12/17 (70%)
Query: 271 RKGVKEINKQGKEVFYD 287
+ V+E+ ++G ++F D
Sbjct: 55 PQFVRELQQRGFDIFLD 71
>1x7d_A Ornithine cyclodeaminase; binds NAD+, binds L-ornithine, binds
L-proline, 2 bundle, beta barrel, rossmann fold, lyase;
HET: NAD ORN MES; 1.60A {Pseudomonas putida} SCOP:
c.2.1.13 PDB: 1u7h_A*
Length = 350
Score = 27.3 bits (61), Expect = 7.8
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 10/77 (12%)
Query: 205 AYARLYDYERIRKVCN--KQKAIMLA-DMAHISGL--VAAGVIPSPFEYADVVTTTTHKS 259
A+ + E I + L ++ SGL A + + D++TT T
Sbjct: 147 AFHKHLGIEEIV-AYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADK 205
Query: 260 LRGP--RGAMIFFRKGV 274
M+ G+
Sbjct: 206 AYATIITPDML--EPGM 220
>2aeu_A Hypothetical protein MJ0158; selenocysteine synthase, PLP,
pyridoxal phosphate, HOMO- oligomerization, unknown
function; 1.70A {Methanocaldococcus jannaschii} SCOP:
c.67.1.8 PDB: 2aev_A*
Length = 374
Score = 27.5 bits (61), Expect = 7.9
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 211 DYERIRKVCNKQKAIMLADMAHISGLVAAGVIPSPFEY-ADVVTTTTHKSLRGPRGAMIF 269
+++++ ++AI+ D A + + P + AD+V T+T K + GPRG ++
Sbjct: 160 NFKKVINTAKNKEAIVFVDDASGARVRLLFNQPPALKLGADLVVTSTDKLMEGPRGGLLA 219
Query: 270 FRK 272
+K
Sbjct: 220 GKK 222
>1o69_A Aminotransferase; structural genomics, unknown function; HET: X04;
1.84A {Campylobacter jejuni} SCOP: c.67.1.4 PDB: 1o62_A
1o61_A*
Length = 394
Score = 27.2 bits (61), Expect = 8.7
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 11/62 (17%)
Query: 177 ESTGYIDYDQLEKSATLF--RPKLIVA----GASAYARLYDYERIRKVCNKQKAIMLADM 230
+ T ID D L+ + +PK ++ G +A + I ++C + +++ D
Sbjct: 102 DETYNIDVDLLKLAIKECEKKPKALILTHLYGNAA-----KMDEIVEICKENDIVLIEDA 156
Query: 231 AH 232
A
Sbjct: 157 AE 158
>3ldv_A Orotidine 5'-phosphate decarboxylase; structural genomics,
infectious diseases; 1.77A {Vibrio cholerae o1 biovar el
tor} PDB: 3uwq_A*
Length = 255
Score = 27.2 bits (61), Expect = 9.1
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 271 RKGVKEINKQGKEVFYD 287
V+E++K+G VF D
Sbjct: 68 PDFVRELHKRGFSVFLD 84
>3tfx_A Orotidine 5'-phosphate decarboxylase; PSI-biology, nysgrc, 000529,
structural genomics, NEW YORK S genomics research
consortium; 2.19A {Lactobacillus acidophilus}
Length = 259
Score = 26.8 bits (60), Expect = 9.4
Identities = 5/17 (29%), Positives = 11/17 (64%)
Query: 271 RKGVKEINKQGKEVFYD 287
+K++ +QG ++F D
Sbjct: 46 IDVIKKLTQQGYKIFLD 62
>1dbt_A Orotidine 5'-phosphate decarboxylase; UMP, TIM barrel, lyase; HET:
U5P; 2.40A {Bacillus subtilis} SCOP: c.1.2.3
Length = 239
Score = 26.8 bits (60), Expect = 9.9
Identities = 5/17 (29%), Positives = 10/17 (58%)
Query: 271 RKGVKEINKQGKEVFYD 287
VK++ ++ E+F D
Sbjct: 44 PSIVKQLKERNCELFLD 60
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
0.317 0.134 0.395
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,663,977
Number of extensions: 343162
Number of successful extensions: 771
Number of sequences better than 10.0: 1
Number of HSP's gapped: 743
Number of HSP's successfully gapped: 43
Length of query: 359
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 264
Effective length of database: 4,049,298
Effective search space: 1069014672
Effective search space used: 1069014672
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: 58 (26.0 bits)