RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16520
(353 letters)
>2bfd_A 2-oxoisovalerate dehydrogenase alpha subunit; oxidoreductase,
multi-enzyme complex, acylation, oxidative
decarboxylation, maple syrup urine disease; HET: TDP;
1.39A {Homo sapiens} SCOP: c.36.1.11 PDB: 1v16_A*
2bfc_A* 1v1r_A* 1olu_A* 2bfb_A* 1v1m_A* 2bew_A* 1dtw_A*
1olx_A* 1ols_A* 1wci_A* 1x80_A* 2beu_A* 1u5b_A* 2bev_A*
1v11_A* 1x7x_A* 1x7y_A* 1x7w_A* 1x7z_A* ...
Length = 400
Score = 225 bits (575), Expect = 7e-71
Identities = 92/146 (63%), Positives = 114/146 (78%)
Query: 31 NVDNETNIRMYKTMVTLNEMDKVMYESQRQGRISFYMTSSGEEGSHVGSAAALDPEDLVY 90
++ E +++YK+M LN MD+++YESQRQGRISFYMT+ GEEG+HVGSAAALD DLV+
Sbjct: 51 HLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVF 110
Query: 91 AQYRETGVLMWRGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQHHFVTISSPLATQLPQ 150
Q RE GVLM+R + +E + Q YGNI KG+QMPVHYG ++ HFVTISSPLATQ+PQ
Sbjct: 111 GQAREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQ 170
Query: 151 AVGSAYAYKLKKNEKVVIVYFGEGAA 176
AVG+AYA K +VVI YFGEGAA
Sbjct: 171 AVGAAYAAKRANANRVVICYFGEGAA 196
Score = 120 bits (304), Expect = 3e-31
Identities = 36/89 (40%), Positives = 58/89 (65%)
Query: 265 IGHHSTSDDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEKQDEQLKKESKQLVLN 324
IGH STSDDS+A+RS EV ++ ++PI R + L + W E+Q++ +K+S++ V+
Sbjct: 288 IGHASTSDDSSAFRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVME 347
Query: 325 SIRISEKKLKPSWKEMFEDVYHEMPPHIR 353
+ +E+K KP+ +F DVY EMP +R
Sbjct: 348 AFEQAERKPKPNPNLLFSDVYQEMPAQLR 376
>1qs0_A 2-oxoisovalerate dehydrogenase alpha-subunit; heterotetramer, THDP
cofactor, oxidoreductase; HET: TDP; 2.40A {Pseudomonas
putida} SCOP: c.36.1.11 PDB: 2bp7_A
Length = 407
Score = 221 bits (565), Expect = 3e-69
Identities = 56/146 (38%), Positives = 81/146 (55%)
Query: 31 NVDNETNIRMYKTMVTLNEMDKVMYESQRQGRISFYMTSSGEEGSHVGSAAALDPEDLVY 90
++D + + + M+ D M +QRQ ++SFYM S GEE G A AL+ D+ +
Sbjct: 70 DIDPQILRQGMRAMLKTRIFDSRMVVAQRQKKMSFYMQSLGEEAIGSGQALALNRTDMCF 129
Query: 91 AQYRETGVLMWRGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQHHFVTISSPLATQLPQ 150
YR+ +LM R S+ +MI QL N KG+Q+P+ Y R+ F TIS LATQ Q
Sbjct: 130 PTYRQQSILMARDVSLVEMICQLLSNERDPLKGRQLPIMYSVREAGFFTISGNLATQFVQ 189
Query: 151 AVGSAYAYKLKKNEKVVIVYFGEGAA 176
AVG A A +K + K+ + G+GA
Sbjct: 190 AVGWAMASAIKGDTKIASAWIGDGAT 215
Score = 109 bits (275), Expect = 3e-27
Identities = 34/95 (35%), Positives = 48/95 (50%), Gaps = 7/95 (7%)
Query: 265 IGHHSTSDDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEKQDEQLKKESKQLVLN 324
G HSTSDD + YR + + +PI R K L K WSE++ + E + V+
Sbjct: 308 AGPHSTSDDPSKYRPADDWSHFP-LGDPIARLKQHLIKIGHWSEEEHQATTAEFEAAVIA 366
Query: 325 SIRISEKKLK------PSWKEMFEDVYHEMPPHIR 353
+ + +E+ PS MFEDVY EMP H+R
Sbjct: 367 AQKEAEQYGTLANGHIPSAASMFEDVYKEMPDHLR 401
>1umd_A E1-alpha, 2-OXO acid dehydrogenase alpha subunit; alpha(2)beta(2)
tetramer, structural genomics; HET: TDP; 1.90A {Thermus
thermophilus} SCOP: c.36.1.11 PDB: 1um9_A* 1umc_A*
1umb_A*
Length = 367
Score = 215 bits (551), Expect = 1e-67
Identities = 46/147 (31%), Positives = 84/147 (57%), Gaps = 1/147 (0%)
Query: 31 NVDNETNIRMYKTMVTLNEMDKVMYESQRQGRISFYMTSSGEEGSHVGSAAALDPE-DLV 89
+++ E R+Y+ M+ +D+ R G+ SF ++G E + V A A+ P D V
Sbjct: 32 DLEGEKLRRLYRDMLAARMLDERYTILIRTGKTSFIAPAAGHEAAQVAIAHAIRPGFDWV 91
Query: 90 YAQYRETGVLMWRGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQHHFVTISSPLATQLP 149
+ YR+ G+ + G +++++ Q+ +KG+QMP H GS+ +F T++SP+A+ +P
Sbjct: 92 FPYYRDHGLALALGIPLKELLGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVP 151
Query: 150 QAVGSAYAYKLKKNEKVVIVYFGEGAA 176
A G+A + KL + +V + FG+GA
Sbjct: 152 PAAGAAISMKLLRTGQVAVCTFGDGAT 178
Score = 114 bits (287), Expect = 4e-29
Identities = 29/89 (32%), Positives = 51/89 (57%), Gaps = 1/89 (1%)
Query: 265 IGHHSTSDDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEKQDEQLKKESKQLVLN 324
G HS++DD + YR K EV + +PI RF+ L + LW+E+ +E +++E + +
Sbjct: 270 YGPHSSADDDSRYRPKEEVAFWR-KKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELER 328
Query: 325 SIRISEKKLKPSWKEMFEDVYHEMPPHIR 353
++ +E+ + MFEDV+ E P H+
Sbjct: 329 GLKEAEEAGPVPPEWMFEDVFAEKPWHLL 357
>1w85_A Pyruvate dehydrogenase E1 component, alpha subunit; dehydrogenase,
multienzyme complex, oxidoreductase; HET: TDP; 2.0A
{Geobacillus stearothermophilus} SCOP: c.36.1.11 PDB:
3duf_A* 3dv0_A* 3dva_A* 1w88_A*
Length = 368
Score = 201 bits (513), Expect = 5e-62
Identities = 39/156 (25%), Positives = 66/156 (42%), Gaps = 9/156 (5%)
Query: 21 GSNGQSSHLSNVDNETNIRMYKTMVTLNEMDKVMYESQRQGRISFYMTSSGEEGSHVGSA 80
G + + +E + + MV +D+ RQGR+ FY ++G+E S + S
Sbjct: 30 GEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASH 89
Query: 81 AALDPEDLVYAQYRETGVLMWRGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQHHFVTI 140
AL+ ED + YR+ ++W G + Q G+ G Q+P + +
Sbjct: 90 FALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGH----FHGNQIPEG-----VNVLPP 140
Query: 141 SSPLATQLPQAVGSAYAYKLKKNEKVVIVYFGEGAA 176
+ Q QA G A K++ + V I Y G+G
Sbjct: 141 QIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGT 176
Score = 110 bits (276), Expect = 2e-27
Identities = 25/90 (27%), Positives = 53/90 (58%), Gaps = 2/90 (2%)
Query: 265 IGHHSTS-DDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEKQDEQLKKESKQLVL 323
G H+ S DD T YRSK E+ +P++RF+ L K LWSE+++ + +++K+ +
Sbjct: 268 YGPHTMSGDDPTRYRSKELENEWA-KKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIK 326
Query: 324 NSIRISEKKLKPSWKEMFEDVYHEMPPHIR 353
+I+ +++ K ++ ++ E+P +++
Sbjct: 327 EAIKKADETPKQKVTDLISIMFEELPFNLK 356
>2ozl_A PDHE1-A type I, pyruvate dehydrogenase E1 component alpha subunit,
somatic form; pyruvate_dehydrogenase_complex, human,
multienzyme_complex_component; HET: TPP; 1.90A {Homo
sapiens} SCOP: c.36.1.11 PDB: 1ni4_A* 3exe_A* 3exi_A
3exh_A* 3exg_A 3exf_A*
Length = 365
Score = 89.7 bits (223), Expect = 3e-20
Identities = 41/152 (26%), Positives = 68/152 (44%), Gaps = 11/152 (7%)
Query: 30 SNVDNETNIRMYKTMVTLNEMDKVMYESQRQGRIS-FYMTSSGEEGSHVGSAAALDPEDL 88
+ + E ++ Y+ M T+ M+ + +Q I F G+E VG A ++P D
Sbjct: 29 TVLTREDGLKYYRMMQTVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDH 88
Query: 89 VYAQYRETGVLMWRGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQ----HHFVTISSPL 144
+ YR G RG SV +++ +L G G KGK +H ++ + V
Sbjct: 89 LITAYRAHGFTFTRGLSVREILAELTGRKGGCAKGKGGSMHMYAKNFYGGNGIV------ 142
Query: 145 ATQLPQAVGSAYAYKLKKNEKVVIVYFGEGAA 176
Q+P G A A K ++V + +G+GAA
Sbjct: 143 GAQVPLGAGIALACKYNGKDEVCLTLYGDGAA 174
Score = 71.2 bits (175), Expect = 6e-14
Identities = 19/83 (22%), Positives = 43/83 (51%)
Query: 268 HSTSDDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEKQDEQLKKESKQLVLNSIR 327
H SD +YR++ E+QE ++PI+ K + L S ++ +++ E ++ + ++ +
Sbjct: 267 HEMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQ 326
Query: 328 ISEKKLKPSWKEMFEDVYHEMPP 350
+ +P +E+ +Y PP
Sbjct: 327 FATADPEPPLEELGYHIYSSDPP 349
Score = 52.3 bits (126), Expect = 9e-08
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 219 HSTSDDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEEQDEQI 265
H SD +YR++ E+QE ++PI+ K + L S E+ ++I
Sbjct: 267 HEMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEI 313
>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 = 52.9 bits (126), Expect = 9e-08
Identities = 38/354 (10%), Positives = 98/354 (27%), Gaps = 91/354 (25%)
Query: 40 MYKTMVTLNEMDKVMYESQRQGRISFYMT---SSGEEGSHVGSAAALDPE-DLVYAQYRE 95
M K++++ E+D ++ S EE L + + +
Sbjct: 41 MPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT 100
Query: 96 TGV---LMWRGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQHHFVTISSPLATQLPQAV 152
+M R + + D+LY + K V SR ++ + L
Sbjct: 101 EQRQPSMMTRMY--IEQRDRLYNDNQVFAK---YNV---SRLQPYLKLRQAL-------- 144
Query: 153 GSAYAYKLKKNEKVVIVY--FGEG----AAIVTMATPFQPQRRNSMEEMGSRPEGLAWVF 206
+L+ + V+ + G G A V ++ Q + + W+
Sbjct: 145 -----LELRPAKNVL-IDGVLGSGKTWVALDVCLSYKVQCKM----------DFKIFWL- 187
Query: 207 QPLELTETTIGHHSTSDD------STAYR-SKSEVQEYEINNNPILRFKTL-LFKKKLWS 258
+ + ++ + Y+ + + ++N LR ++ ++L
Sbjct: 188 --------NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239
Query: 259 EEQDEQIGHHSTS----DDSTAYRSKSEVQEYEIN--------NNPILRFKTLLFKKKLW 306
+ + + ++ + ++ + F + +
Sbjct: 240 SKP------YENCLLVLLN---VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHIS 290
Query: 307 SEKQDEQL-KKESKQLVLNSIRISEKKLKPSWKE-------MFEDVYHEMPPHI 352
+ L E K L+L + + L + + +
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 43.6 bits (102), Expect = 3e-05
Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 28/94 (29%)
Query: 253 KKKLWSEEQDEQIGHHSTSDDSTAYRSKSEVQEYEINNNPILRFKTLLFKKKL--WSEKQ 310
+ W EEQ +++ D+ + + E +E KK L W+++Q
Sbjct: 86 SIRKWREEQRKRL----QELDAASKVMEQEWRE--------------KAKKDLEEWNQRQ 127
Query: 311 DEQLKKESKQLVLNSIRISEKKLKPSWKEMFEDV 344
EQ++K N RI++K ++ D+
Sbjct: 128 SEQVEKNKIN---N--RIADKAFY---QQPDADI 153
Score = 32.4 bits (73), Expect = 0.15
Identities = 8/56 (14%), Positives = 19/56 (33%), Gaps = 13/56 (23%)
Query: 302 KKKLWSEKQDEQLKKESKQLVLNSIRISEKKLKPSWKEMF----EDVYHEMPPHIR 353
+ W E+Q ++L++ K ++ W+E E+ +
Sbjct: 86 SIRKWREEQRKRLQELDAA---------SKVMEQEWREKAKKDLEEWNQRQSEQVE 132
>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 = 30.4 bits (68), Expect = 1.3
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 69 SSGEEGSHVGSAAALDPEDLVYAQYRETGVLMWRGFSVEQMIDQLYGNIGSSDKG 123
S GE + A + E LV V+ +RG +++ + + +G S+ G
Sbjct: 1763 SLGEYAALASLADVMSIESLVE-------VVFYRGMTMQVAVPR--DELGRSNYG 1808
Score = 29.6 bits (66), Expect = 2.2
Identities = 20/128 (15%), Positives = 41/128 (32%), Gaps = 38/128 (29%)
Query: 118 GSSDKGKQMPVH-YGSRQHHFVTISSPLATQL-PQA---VGSAYAYKL----KKNEKVVI 168
GS ++G M + Y + S A + +A Y + + N +
Sbjct: 1625 GSQEQG--MGMDLYKT---------SKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLT 1673
Query: 169 VYFG--EGAAIVTMATPFQPQRRNSMEEMGSRPEGLAWVFQPL--ELTETTIGHHSTSD- 223
++FG +G I R N + + + E+ E + + S+
Sbjct: 1674 IHFGGEKGKRI----------RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK 1723
Query: 224 ---DSTAY 228
+T +
Sbjct: 1724 GLLSATQF 1731
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial
ribosome, large ribosomal subunit, ribosomal R ribosome;
12.10A {Bos taurus}
Length = 211
Score = 28.2 bits (64), Expect = 3.5
Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 8/31 (25%)
Query: 115 GNIGSSD-----KGKQMPVHYGSRQHHFVTI 140
G + + D G +MP G+ T
Sbjct: 146 GAVATGDIGRVWPGTKMPGKMGNIY---RTE 173
>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 = 27.6 bits (60), Expect = 4.6
Identities = 9/28 (32%), Positives = 10/28 (35%), Gaps = 14/28 (50%)
Query: 308 EKQDEQLKKESKQLVLNSIRISEKKLKP 335
EKQ LKK L + LK
Sbjct: 18 EKQ--ALKK------L------QASLKL 31
>3nyy_A Putative glycyl-glycine endopeptidase LYTM; structural genomics,
joint center for structural genomics, J protein
structure initiative; HET: MSE 2PE SO4; 1.60A
{Ruminococcus gnavus}
Length = 252
Score = 27.6 bits (61), Expect = 6.3
Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 3/69 (4%)
Query: 90 YAQYRETGVLMW---RGFSVEQMIDQLYGNIGSSDKGKQMPVHYGSRQHHFVTISSPLAT 146
+ Y ++ +W + F + Q +D I D + G R H I + T
Sbjct: 77 WDAYVQSCRAIWNDVKYFPIPQSLDDTEDKISYVDSWMFERNYGGKRGHEGTDIMAEKNT 136
Query: 147 QLPQAVGSA 155
V S
Sbjct: 137 PGYYPVVSM 145
>1flg_A Protein (quinoprotein ethanol dehydrogenase); superbarrel,
oxidoreductase; HET: PQQ; 2.60A {Pseudomonas aeruginosa}
SCOP: b.70.1.1
Length = 582
Score = 27.6 bits (61), Expect = 7.2
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 61 GRISFYMTSSGEEGSHVGSAAALDPEDLVYAQYRETGVLMWRGFSVEQMIDQLYG 115
G++ SSG+E VG A DP+ TG +W VE + +L G
Sbjct: 167 GKVLLIHGSSGDEFGVVGRLFARDPD---------TGEEIWMRPFVEGHMGRLNG 212
>1u6g_C TIP120 protein, CAND1; cullin repeat, heat repeat, ring finger,
ligase; 3.10A {Homo sapiens} SCOP: a.118.1.2 PDB: 4a0c_A
Length = 1230
Score = 27.8 bits (60), Expect = 7.3
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 5/73 (6%)
Query: 276 AYRSKSEVQEYEINNNPILRFKTLLFKKKLWSEKQDEQLKKESKQLVLNSI----RISEK 331
+ S V + LR T K K S KQ+ + + E K+ + ++ I E
Sbjct: 1131 STLCPSAVLQRLDRLVEPLR-ATCTTKVKANSVKQEFEKQDELKRSAMRAVAALLTIPEA 1189
Query: 332 KLKPSWKEMFEDV 344
+ P E +
Sbjct: 1190 EKSPLMSEFQSQI 1202
>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur
binding, oxidoreductase; HET: HCN; 1.39A {Clostridium
pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB:
1c4c_A* 1c4a_A* 1feh_A*
Length = 574
Score = 27.4 bits (61), Expect = 8.0
Identities = 5/18 (27%), Positives = 9/18 (50%)
Query: 335 PSWKEMFEDVYHEMPPHI 352
P W E+ Y E+ ++
Sbjct: 301 PGWVRQAENYYPELLNNL 318
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
0.313 0.129 0.371
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,248,778
Number of extensions: 297104
Number of successful extensions: 546
Number of sequences better than 10.0: 1
Number of HSP's gapped: 526
Number of HSP's successfully gapped: 33
Length of query: 353
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 258
Effective length of database: 4,049,298
Effective search space: 1044718884
Effective search space used: 1044718884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.4 bits)