RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10669
(337 letters)
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 297 bits (764), Expect = 3e-99
Identities = 118/350 (33%), Positives = 160/350 (45%), Gaps = 86/350 (24%)
Query: 10 TLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEGLPGKRYYG 69
+ + D L+ LI E+ RQ G+ELIASENF S V E +GS L NKY+EG PG RYYG
Sbjct: 3 STLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYG 62
Query: 70 GNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSG--------------------- 105
G + ID +E +A +R+ F G NVQP+SG
Sbjct: 63 GCEVIDRVESLAIERAKALF-------GAAWANVQPHSGSQANMAVYMALMEPGDTLMGM 115
Query: 106 -----------SPANFA-----VCEKALPTNNARFDF--------------LSSGTTCYS 135
S NF+ V + + D + +G + Y
Sbjct: 116 DLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYP 175
Query: 136 RCLDYARFRQICDETDSIMFADMSHISGLIAGVKG-----------VTKTGEKIL----- 179
R D+ FR+I DE + + DM+H +GL+A G VT T K L
Sbjct: 176 RFWDFKAFREIADEVGAYLVVDMAHFAGLVAA--GLHPNPLPYAHVVTSTTHKTLRGPRG 233
Query: 180 -------YDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFKSYQAQVKANASHL 232
+ ++I+ +FP +QGGP H I A A +A EFK Y V NA L
Sbjct: 234 GLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRL 293
Query: 233 SDEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIACNKNT 282
++E+ +RGY +VTGGTD HL L+DLR LTG + E L+ + I NKN
Sbjct: 294 AEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNA 343
>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 = 297 bits (762), Expect = 5e-99
Identities = 121/349 (34%), Positives = 175/349 (50%), Gaps = 85/349 (24%)
Query: 10 TLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEGLPGKRYYG 69
L Q DP++++ I++E+ RQ IELIASENF S AV+E GS L NKY+EG PG+RYYG
Sbjct: 3 YLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYG 62
Query: 70 GNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSG--------------------- 105
G +++D +E +A++R+ + F G NVQP+SG
Sbjct: 63 GCEYVDIVEELARERAKQLF-------GAEHANVQPHSGAQANMAVYFTVLEHGDTVLGM 115
Query: 106 -----------SPANFA-----VCEKALPTNNARFDF--------------LSSGTTCYS 135
SP NF+ + D+ + + Y
Sbjct: 116 NLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAAAAYP 175
Query: 136 RCLDYARFRQICDETDSIMFADMSHISGLIAGVKG-----------VTKTGEKIL----- 179
R +D+A+FR+I DE + + DM+HI+GL+A G VT T K L
Sbjct: 176 RIIDFAKFREIADEVGAYLMVDMAHIAGLVAA--GLHPNPVPYAHFVTTTTHKTLRGPRG 233
Query: 180 ------YDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFKSYQAQVKANASHLS 233
+ ++I+ A+FP +QGGP H I A A A +A D+FK+Y +V NA L+
Sbjct: 234 GMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLA 293
Query: 234 DEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIACNKNT 282
+ G+ +V+GGTD HL+L+DLR +LTG E VL+E+ I NKNT
Sbjct: 294 SALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNT 342
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 294 bits (756), Expect = 5e-98
Identities = 116/352 (32%), Positives = 164/352 (46%), Gaps = 91/352 (25%)
Query: 10 TLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEGLPGKRYYG 69
+L D E++ L KE RQ G+E+IASENFT V+E +GS L NKY+EG PGKRYYG
Sbjct: 5 SLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRYYG 64
Query: 70 GNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYS---------------------- 104
G +F+DEIE +A +R K F C NVQP S
Sbjct: 65 GCEFVDEIETLAIERCKKLF-------NCKFANVQPNSGSQANQGVYAALINPGDKILGM 117
Query: 105 ----------GSPANF---------------------AVCEKALPTNNARFDFLSSGTTC 133
G+ + V E A + + G +
Sbjct: 118 DLSHGGHLTHGAKVSSSGKMYESCFYGVELDGRIDYEKVREIAKKE---KPKLIVCGASA 174
Query: 134 YSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKG-----------VTKTGEKIL--- 179
Y+R +D+A+FR+I DE + +FAD++HI+GL+ G V+ T K L
Sbjct: 175 YARVIDFAKFREIADEIGAYLFADIAHIAGLVVA--GEHPSPFPYAHVVSSTTHKTLRGP 232
Query: 180 ---------YDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFKSYQAQVKANAS 230
+ +KIN+A+FP +QGGP H I A A SDE+K Y QV+ NA
Sbjct: 233 RGGIIMTNDEELAKKINSAIFPGIQGGPLMHVIAAKAVGFKFNLSDEWKVYAKQVRTNAQ 292
Query: 231 HLSDEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIACNKNT 282
L++ ++ R + +V+ GTD HL+L+ + +G +L L I NKNT
Sbjct: 293 VLANVLMDRKFKLVSDGTDNHLVLMSFLDREFSGKDADLALGNAGITANKNT 344
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 294 bits (756), Expect = 7e-98
Identities = 124/358 (34%), Positives = 169/358 (47%), Gaps = 86/358 (24%)
Query: 2 SSSTMLHGTLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEG 61
+++ +LA+ D + I KE RQ + +ELIASEN S AVL+ GS L NKY+EG
Sbjct: 4 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEG 63
Query: 62 LPGKRYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYS-------------- 104
PGKRYYGG +F DE+E +A +R + F NVQP+S
Sbjct: 64 YPGKRYYGGCEFADEVEALAIERVKRLF-------NAGHANVQPHSGAQANGAVMLALAK 116
Query: 105 ------------------GSPANFA-----VCEKALPTNNARFDF--------------L 127
G+ + + + + D+ +
Sbjct: 117 PGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLI 176
Query: 128 SSGTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKG-----------VTKTGE 176
+G + Y R LD+ARFR I D + + DM+HI+G+IA G VT T
Sbjct: 177 IAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAA--GRHANPVEHAHVVTSTTH 234
Query: 177 KIL------------YDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFKSYQAQ 224
K L + +KIN+AVFP LQGGP H I A A +A +D+FK+Y +
Sbjct: 235 KTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDR 294
Query: 225 VKANASHLSDEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIACNKNT 282
V ANA L D + G +VTGGTD HL+L+DLR L G++VE LE I CNKN
Sbjct: 295 VLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNG 352
>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 = 294 bits (756), Expect = 8e-98
Identities = 122/363 (33%), Positives = 168/363 (46%), Gaps = 96/363 (26%)
Query: 1 MSSSTMLHGTLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSE 60
M M +A D EL+ +++EK RQ IELIASEN+TS V++ GS L NKY+E
Sbjct: 4 MLKREM---NIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAE 60
Query: 61 GLPGKRYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYS------------- 104
G PGKRYYGG +++D +E +A R+ + F G NVQP+S
Sbjct: 61 GYPGKRYYGGCEYVDVVEQLAIDRAKELF-------GADYANVQPHSGSQANFAVYTALL 113
Query: 105 -------------------GSPANF---------------------AVCEKALPTNNARF 124
GSP NF + + A +
Sbjct: 114 QPGDTVLGMNLAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEH---KP 170
Query: 125 DFLSSGTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKG-----------VTK 173
+ G + YS +D+A+ R+I D + +F DM+H++GLIA G VT
Sbjct: 171 KMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAA--GVYPNPVPHAHVVTT 228
Query: 174 TGEKIL--------------YDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFK 219
T K L + +K+N+AVFPS QGGP H I A A+ +A EFK
Sbjct: 229 TTHKTLAGPRGGLILAKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFK 288
Query: 220 SYQAQVKANASHLSDEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIACN 279
YQ QV NA + + + RGY VV+GGT+ HL L+DL LTG + + L I N
Sbjct: 289 VYQQQVAKNAKAMVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVN 348
Query: 280 KNT 282
KN+
Sbjct: 349 KNS 351
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 289 bits (742), Expect = 2e-95
Identities = 116/362 (32%), Positives = 163/362 (45%), Gaps = 90/362 (24%)
Query: 2 SSSTMLHGTLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEG 61
+ LA+ DP++ L+ KE RQ + +E+IASENF AVL+ GS L NKY+EG
Sbjct: 17 QGPGSMSAPLAEVDPDIAELLAKELGRQRDTLEMIASENFVPRAVLQAQGSVLTNKYAEG 76
Query: 62 LPGKRYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSG------------- 105
LPG+RYYGG + +D +E +A+ R+ F G NVQP+SG
Sbjct: 77 LPGRRYYGGCEHVDVVENLARDRAKALF-------GAEFANVQPHSGAQANAAVLHALMS 129
Query: 106 -------------------SPANFA-----VCEKALPTNNARFDF--------------L 127
NF+ + D +
Sbjct: 130 PGERLLGLDLANGGHLTHGMRLNFSGKLYENGFYGVDPATHLIDMDAVRATALEFRPKVI 189
Query: 128 SSGTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKG-----------VTKTGE 176
+G + Y R LD+A FR I DE + + DM+H +GL+A G V+ T
Sbjct: 190 IAGWSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAA--GLHPSPVPHADVVSTTVH 247
Query: 177 KIL-----------YDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFKSYQAQV 225
K L Y + IN+AVFP QGGP H I A A+ A + EF Q +
Sbjct: 248 KTLGGGRSGLIVGKQQYAKAINSAVFPGQQGGPLMHVIAGKAVALKIAATPEFADRQRRT 307
Query: 226 KANASHLSDEMI-----KRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIACNK 280
+ A ++D ++ K G VV+GGTDVHL+L+DLR + L G E +L E+ I N+
Sbjct: 308 LSGARIIADRLMAPDVAKAGVSVVSGGTDVHLVLVDLRDSPLDGQAAEDLLHEVGITVNR 367
Query: 281 NT 282
N
Sbjct: 368 NA 369
>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 = 252 bits (645), Expect = 2e-80
Identities = 105/280 (37%), Positives = 139/280 (49%), Gaps = 76/280 (27%)
Query: 130 GTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAG---------------------- 167
GT+CYSR LDY R R+I DE + + ADM+HISGL+
Sbjct: 200 GTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLR 259
Query: 168 -------------VKGVTKTGEKILYDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQ 214
KTG++ILY+ E IN+AVFP LQGGPHNHAI +A A+ QA
Sbjct: 260 GCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAM 319
Query: 215 SDEFKSYQAQVKANASHLSDEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEI 274
+ EFK YQ QV AN LS +++ GY +VTGG+D HLIL+DLR G + E VLE
Sbjct: 320 TPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEAC 379
Query: 275 AIACNKNT---------------------------------------GISLAAEIQAISG 295
+IACNKNT GI L +IQ +G
Sbjct: 380 SIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTG 439
Query: 296 PK--LVDFQTCLHKNEDIVKKVAALKKEIEDYSNQFEMPG 333
P+ L +F+ L +E + V AL++E+E ++ F +PG
Sbjct: 440 PRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPG 479
Score = 216 bits (552), Expect = 1e-66
Identities = 71/111 (63%), Positives = 85/111 (76%)
Query: 2 SSSTMLHGTLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEG 61
S ML L +D E+Y +IKKE +RQ G+ELIASENF S AVLE LGSCL NKYS G
Sbjct: 16 SHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSLG 75
Query: 62 LPGKRYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAV 112
PG+RYYGG + IDE+E + Q+R+L+A+ LDP+ WG NVQPYSGSPANFAV
Sbjct: 76 YPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAV 126
>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 = 248 bits (635), Expect = 5e-79
Identities = 96/278 (34%), Positives = 145/278 (52%), Gaps = 75/278 (26%)
Query: 130 GTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAG---------------------- 167
GT+ Y+R +DYAR R++CDE + + ADM+HISGL+A
Sbjct: 210 GTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLR 269
Query: 168 -------------VKGVTKTGEKILYDYEEKINNAVFPSLQGGPHNHAIGAIATAMLQAQ 214
KTG +I Y +E++IN AVFPSLQGGPHNHAI A+A A+ QA
Sbjct: 270 GARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQAC 329
Query: 215 SDEFKSYQAQVKANASHLSDEMIKRGYHVVTGGTDVHLILIDLRKNKLTGSKVELVLEEI 274
+ F+ Y QV NA ++D +++RGY +V+GGTD HL+L+DLR L G++ E VLE +
Sbjct: 330 TPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELV 389
Query: 275 AIACNKNT---------------------------------------GISLAAEIQAISG 295
+I NKNT G+++ E+++ +
Sbjct: 390 SITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTA 449
Query: 296 PKLVDFQTCLHKNEDIVKKVAALKKEIEDYSNQFEMPG 333
KL DF++ L K+ + +++A L++ +E ++ F MPG
Sbjct: 450 -KLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPG 486
Score = 212 bits (542), Expect = 4e-65
Identities = 69/103 (66%), Positives = 86/103 (83%)
Query: 10 TLAQTDPELYSLIKKEKHRQINGIELIASENFTSLAVLECLGSCLQNKYSEGLPGKRYYG 69
+L+ +DPE++ L+++EK RQ G+ELIASENF S A LE LGSCL NKYSEG PGKRYYG
Sbjct: 34 SLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYG 93
Query: 70 GNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAV 112
G + +DEIE++ Q+R+L+AF+LDP QWG NVQPYSGSPAN AV
Sbjct: 94 GAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAV 136
>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 = 8e-05
Identities = 63/360 (17%), Positives = 112/360 (31%), Gaps = 119/360 (33%)
Query: 6 MLHGTLAQTDPELYSLIKKEKH--RQINGIE-----LIASENF-TSLAVLECLGSCLQNK 57
ML L Q DP S + +I+ I+ L+ S+ + L VL
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL---------- 250
Query: 58 YSEGLPGKRYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVCEKAL 117
V ++ AFNL C K L
Sbjct: 251 -----------------LN---VQNAKAWNAFNL-----SC----------------KIL 269
Query: 118 PTNNARFDFLSSGTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKGVTKT-GE 176
T T RF+Q+ TD + A +HIS L +T +
Sbjct: 270 LT-----------T----------RFKQV---TDFLSAATTTHIS-LDHHSMTLTPDEVK 304
Query: 177 KILYDYEEKINNAVF--PS--LQGGPHNHAIGAIATAMLQ---AQSDEFKSYQAQ----- 224
+L Y ++ P L P + IA ++ A D +K
Sbjct: 305 SLLLKY---LDCRPQDLPREVLTTNP--RRLSIIA-ESIRDGLATWDNWKHVNCDKLTTI 358
Query: 225 VKANASHLSDEMIKRGYH---VVTGGTDVHLILIDLRKNKLTGSKVELVLEEIAIAC--- 278
++++ + L ++ + V + IL+ L + S V +V+ ++
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418
Query: 279 --NKNTGISLAAEIQAISGPKLVDFQTCLHKNEDIVKKVAALKKEIEDYSNQFEMPGQAD 336
K + IS+ + + ++ + LH++ IV K + + +P D
Sbjct: 419 KQPKESTISIPSIYLELKVK--LENEYALHRS--IVDHYNIPKT----FDSDDLIPPYLD 470
>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 = 40.4 bits (94), Expect = 7e-04
Identities = 35/256 (13%), Positives = 68/256 (26%), Gaps = 79/256 (30%)
Query: 54 LQNKYSEGLPGKRYYGG--NQFIDEI-----EIVAQQRSLKAF---NLDPEQW--GCNVQ 101
L++ Y Y I E++ + L+ +W +
Sbjct: 173 LRDLYQT-------YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT 225
Query: 102 PYSGSPANFAVCEKALPTNNARFDFLSSGTTCYSRCLDYARFRQICDETDSIMFADMSHI 161
P + P + Y ++ T + + +
Sbjct: 226 P---DKDYLLSIPISCPLI-----GVIQ-------LAHYVVTAKLLGFTPGELRSYLKGA 270
Query: 162 SGLIAGVKGVT-------KTGEKILYDYEEKINNAV-------------FPSLQGGPH-- 199
+G G+ VT + E + + A+ +P+ P
Sbjct: 271 TGHSQGL--VTAVAIAETDSWE----SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSIL 324
Query: 200 ----NHAIGAIATAMLQAQSDEFKSYQAQVKANASHLSDEMIKRGY---------HVVTG 246
+ G + ML + + Q V SHL K+ VV+G
Sbjct: 325 EDSLENNEGV-PSPMLSISNLTQEQVQDYVNKTNSHLPAG--KQVEISLVNGAKNLVVSG 381
Query: 247 GT-DVHLILIDLRKNK 261
++ + + LRK K
Sbjct: 382 PPQSLYGLNLTLRKAK 397
Score = 40.0 bits (93), Expect = 0.001
Identities = 51/294 (17%), Positives = 93/294 (31%), Gaps = 108/294 (36%)
Query: 103 YSGSPANFAVCEKA--------------LPTNN-ARFDFLSSGTTCYSRCLDYARFRQIC 147
Y S A V +A + NN G + ++I
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGG----------EKGKRIR 1685
Query: 148 DETDSIMFADMSHISGLIAGVKGVTKTGEKILYDYEEKINNAVFPS----L------QGG 197
+ +++F + V G KT EKI + E + F S L Q
Sbjct: 1686 ENYSAMIFETI---------VDGKLKT-EKIFKEINEHSTSYTFRSEKGLLSATQFTQ-- 1733
Query: 198 PHNHAIGAIATAMLQAQSDEFK----------S---YQAQVKANASHLS-DEMIK----R 239
P A+ + A + + S Y A + A +S + +++ R
Sbjct: 1734 P---ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALA-SLADVMSIESLVEVVFYR 1789
Query: 240 G---YHVV----TGGTDVHLILID------------LRK-----NKLTGSKVELVLEEIA 275
G V G ++ +I I+ L+ K TG VE+V
Sbjct: 1790 GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIV----- 1844
Query: 276 IACNKNT-G--ISLAAEIQAISGPKLVDFQTCLH-KNEDIVK-KVAALKKEIED 324
N N A +++A+ + + + + DI++ + + +E+E
Sbjct: 1845 ---NYNVENQQYVAAGDLRALD--TVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 33.5 bits (76), Expect = 0.12
Identities = 32/184 (17%), Positives = 57/184 (30%), Gaps = 70/184 (38%)
Query: 190 VFPSLQGGPHNHAIG---AIATAMLQAQSDEFKS-YQAQVKA------------------ 227
+ L+G A G + TA+ A++D ++S + + KA
Sbjct: 263 LRSYLKG-----ATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 228 --NASHLSDE----------MIKRGYHVVTGGTDVHLI-LIDLRKNKLTGSKVELVLEEI 274
S L D M+ ++ T + ++ + L K +
Sbjct: 318 SLPPSILEDSLENNEGVPSPML-----SISNLTQEQVQDYVNKTNSHLPAGKQ------V 366
Query: 275 AIACNKNTGISLAAEIQAISGP--KLVDFQTCLHKNEDIVKKVAALK-------KEIEDY 325
I+ N +L +SGP L L K K + L + +
Sbjct: 367 EIS-LVNGAKNL-----VVSGPPQSLYGLNLTLRK----AKAPSGLDQSRIPFSERKLKF 416
Query: 326 SNQF 329
SN+F
Sbjct: 417 SNRF 420
Score = 32.3 bits (73), Expect = 0.24
Identities = 42/266 (15%), Positives = 78/266 (29%), Gaps = 103/266 (38%)
Query: 44 LAVLECLGSCLQ------NKYSEGLP-GKRYY-----GGNQFIDEIEIVA-QQRSLKAFN 90
L++ +Q N + LP GK+ G + V+ +SL N
Sbjct: 339 LSISNLTQEQVQDYVNKTNSH---LPAGKQVEISLVNGAKNLV-----VSGPPQSLYGLN 390
Query: 91 L---------DPEQWGCNVQPYSGSPANFAVCEKALPTNNARFDFLSSGTTCYSRCLDYA 141
L +Q + P+S F+ + LP + F +S L A
Sbjct: 391 LTLRKAKAPSGLDQ--SRI-PFSERKLKFSN--RFLPVA-SPF---------HSHLLVPA 435
Query: 142 RFRQICDETDSIMFADMSHISGLIAG------VKGVTKTGEKILYDYEEKINNAVFPSLQ 195
+D I D+ + V T G D ++ ++ +
Sbjct: 436 --------SDLIN-KDLVKNNVSFNAKDIQIPVYD-TFDGS----DLRV-LSGSISERI- 479
Query: 196 GGPHNHAIGAIATAMLQAQSDEFKSYQAQVKANASHLSD----------EMIKR-----G 240
+ I ++ ++ + A+H+ D + R G
Sbjct: 480 -------VDCIIRLPVK--------WETTTQFKATHILDFGPGGASGLGVLTHRNKDGTG 524
Query: 241 YHVVTGGTDVHLILIDLRKNKLTGSK 266
V+ GT +D+ + G K
Sbjct: 525 VRVIVAGT------LDINPDDDYGFK 544
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 32.5 bits (74), Expect = 0.21
Identities = 28/183 (15%), Positives = 47/183 (25%), Gaps = 68/183 (37%)
Query: 92 DPEQWGCN------VQPYSGSPANFAVCEKALPTNNARFDFLSSGTTCYSRCLDYARFRQ 145
+ + +G + V P F + + F++SG
Sbjct: 995 NAKTYGISDDIISQVDPI----TLFVLV--S-----VVEAFIASG--------------- 1028
Query: 146 ICDETDSIMFADMSHISGLIAGVKGVTKTGEKILYDYEEK------------INNA---V 190
I D + + +S + G + D + IN V
Sbjct: 1029 ITDPYEMYKYVHVSEVGNCSGSGMGGVSALRGMFKDRFKDEPVQNDILQESFINTMSAWV 1088
Query: 191 FPSLQG--GPHNHAIGAIATAMLQAQSDEFKSYQAQVKANASHLSDEMIKRGYH--VVTG 246
L GP +GA AT+ + + E I G + G
Sbjct: 1089 NMLLISSSGPIKTPVGACATS-----------------VESVDIGVETILSGKARICIVG 1131
Query: 247 GTD 249
G D
Sbjct: 1132 GYD 1134
>3l8q_A Cellulosomal scaffoldin adaptor protein B; dockerin-binding module,
protein-protein interactions, linke segment; HET: EDO;
1.57A {Acetivibrio cellulolyticus} PDB: 3fnk_A
Length = 350
Score = 30.2 bits (67), Expect = 0.94
Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 125 DFLSSGTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKGVTKTGEKILYDYE- 183
+ +S + + L F+ + + +++F D + I G G +I Y
Sbjct: 270 VYRASESPEETGTLAVVGFKVLQKKATTVVFEDSETMPNGITGTTLFNWYGNRIQSGYFV 329
Query: 184 ---EKINNAVFPSLQGGPHNH 201
+IN+A +L+ H+H
Sbjct: 330 IQPGEINSAPIATLEHHHHHH 350
>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport
element (CTE), RNA recogni motif (RRM); HET: GTP CCC;
2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A
1fo1_A
Length = 267
Score = 28.8 bits (64), Expect = 2.5
Identities = 11/90 (12%), Positives = 30/90 (33%), Gaps = 2/90 (2%)
Query: 82 QQRSLKAFNLDPEQWGCNVQPYSGSPANFAVCEKALPTNNARFDFLSSGTTCYSRCLDYA 141
+ + K + + + ++ S +P + + E +S + LD
Sbjct: 78 KAVNYKILDRENRRI--SIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLK 135
Query: 142 RFRQICDETDSIMFADMSHISGLIAGVKGV 171
R D + ++ S + A ++ +
Sbjct: 136 GLRSDPDLVAQNIDVVLNRRSCMAATLRII 165
>3m2p_A UDP-N-acetylglucosamine 4-epimerase; SGXNY, 11155J, isomerase,
structural genomics, PSI-2, protein structure
initiative; HET: UDP; 2.95A {Bacillus cereus}
Length = 311
Score = 28.3 bits (64), Expect = 3.3
Identities = 5/41 (12%), Positives = 11/41 (26%), Gaps = 8/41 (19%)
Query: 230 SHLSDEMIKRGYHVV-----TGG---TDVHLILIDLRKNKL 262
++ + + G + G D + D L
Sbjct: 16 QYVVESIKNDGNTPIILTRSIGNKAINDYEYRVSDYTLEDL 56
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 28.2 bits (63), Expect = 3.7
Identities = 34/265 (12%), Positives = 75/265 (28%), Gaps = 39/265 (14%)
Query: 91 LDPEQWGCNVQPYSGSPANFAVCEKALPTNNARFDFLSSGTTCYSRCLDYARFRQICDET 150
++ P + V L + + L+ Y + + +
Sbjct: 123 IETH-----QSPLTNHYN--KVNLSRLNNDGHKLVVLTYPN-YYGETFNVEEVIKSLHQL 174
Query: 151 DSIMFADMSHI----------SGLIAGVKGVTKTGEKIL--------------YDYEEKI 186
+ + D +H S L V ++ K L Y E I
Sbjct: 175 NIPVLIDEAHGAHFGLQGFPDSTLNYQADYVVQSFHKTLPALTMGSVLYIHKNAPYRENI 234
Query: 187 NNAVFPSLQGGPHNHAIGAIATAMLQAQSDEFKSYQAQVKANASHLSDEMIKRGYHVVTG 246
+ P + ++ +A ++ + + A+ L + +G+ ++
Sbjct: 235 IEYLSYFQTSSPSYLIMASLESAAQFYKTYDSTLFFAKRAQLIECLEN----KGFEML-- 288
Query: 247 GTDVHLILIDLRKNKLTGSKVELVLEEIAIACNKNTGISLAAEIQAISGPKLVDFQTCLH 306
D L L+ ++ TG ++ I A + F + L
Sbjct: 289 QVDDPLKLL-IKYEGFTGHDIQNWFMNAHIYLELADDYQALAILPLWHHDDTYLFDSLLR 347
Query: 307 KNEDIVKKVAALKKEIEDYSNQFEM 331
K ED++ ++ K + E
Sbjct: 348 KIEDMILPKKSVSKVKQTQLLTTEG 372
>3ko8_A NAD-dependent epimerase/dehydratase; isomerase, UDP-galactose
4-epimerase; HET: NAD; 1.80A {Pyrobaculum calidifontis}
PDB: 3icp_A* 3aw9_A*
Length = 312
Score = 27.5 bits (62), Expect = 6.5
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 12/54 (22%)
Query: 230 SHLSDEMIKRGYHVV------TG-----GTDVHLILIDLR-KNKLTGSKVELVL 271
SHL D++++ GY VV +G L + DL+ + G K ++V
Sbjct: 14 SHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSWGAGIKGDVVF 67
>1o70_A Fasciclin I, FAS I, FCN; cell adhesion, AXON guidance,
extracellular module, genetic disorder, corneal
dystrophy; HET: NAG; 2.6A {Drosophila melanogaster}
SCOP: b.118.1.1 b.118.1.1
Length = 324
Score = 27.2 bits (60), Expect = 8.1
Identities = 7/89 (7%), Positives = 21/89 (23%), Gaps = 9/89 (10%)
Query: 198 PHNHAIGAIATAMLQAQSDEFKSYQAQVKANASHLSDEMIKRGYHVVTGGTDVHLILIDL 257
P + A F + H + H+ + + +
Sbjct: 199 PRDKGWQKTELDYPSAHKKLFM------ADFSYHSKSIL---ERHLAISDKEYTMKDLVK 249
Query: 258 RKNKLTGSKVELVLEEIAIACNKNTGISL 286
+ + + ++I + G +
Sbjct: 250 FSQESGSVILPTFRDSLSIRVEEEAGRYV 278
>3bwz_A Cellulosomal scaffoldin adaptor protein B; cohesins II,
cellulosome, structural protein; 1.20A {Acetivibrio
cellulolyticus} PDB: 3f2l_A 1qzn_A 1zv9_A*
Length = 181
Score = 26.6 bits (58), Expect = 8.2
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 125 DFLSSGTTCYSRCLDYARFRQICDETDSIMFADMSHISGLIAGVKGVTKTGEKILYDYE- 183
D+ ++ + + +F+ + +ET SI F D + + I G G++I Y
Sbjct: 100 DYRTAAAPEQTGTVAVVKFKVLKEETSSISFEDTTSVPNAIDGTVLFDWNGDRIQSGYSV 159
Query: 184 ---EKINNAVFPSLQGGPHNH 201
IN + + H+H
Sbjct: 160 IQPAVINLDMIKASLEHHHHH 180
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
0.316 0.133 0.381
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,182,649
Number of extensions: 314039
Number of successful extensions: 935
Number of sequences better than 10.0: 1
Number of HSP's gapped: 921
Number of HSP's successfully gapped: 42
Length of query: 337
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 243
Effective length of database: 4,077,219
Effective search space: 990764217
Effective search space used: 990764217
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 (21.6 bits)
S2: 57 (25.6 bits)