RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9408
(219 letters)
>1efv_B Electron transfer flavoprotein; electron transport, glutaric
acidemia type II; HET: FAD AMP; 2.10A {Homo sapiens}
SCOP: c.26.2.3 PDB: 1t9g_S* 2a1u_B* 2a1t_S*
Length = 255
Score = 280 bits (718), Expect = 3e-96
Identities = 104/222 (46%), Positives = 152/222 (68%), Gaps = 6/222 (2%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
S+NPF EIA+E A+RL+E +KE+IA+SCG +C+E ++ A+AMG DR I +E
Sbjct: 36 HSMNPFCEIAVEEAVRLKEK-KLVKEVIAVSCGPAQCQETIRTALAMGADRGIHVEVPPA 94
Query: 61 ----LQSLSVAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIV 116
L L VA++L + +KE LV+LGKQ+ID D NQTGQM A L+WPQ TFAS++
Sbjct: 95 EAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDCNQTGQMTAGFLDWPQGTFASQVT 154
Query: 117 LKKNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFKIDE 176
L+ +K+ V +EI+ G ET+ L LPA++T DLR+NEPRY TL NI+KA+KK I + K +
Sbjct: 155 LE-GDKLKVEREIDGGLETLRLKLPAVVTADLRLNEPRYATLPNIMKAKKKKIEVIKPGD 213
Query: 177 LNVNINTGLNIIKVKESHKNNLGIKVKNVIELIDKLKNEAKI 218
L V++ + L++I V++ + G+KV+ +L+ KLK +I
Sbjct: 214 LGVDLTSKLSVISVEDPPQRTAGVKVETTEDLVAKLKEIGRI 255
>1efp_B ETF, protein (electron transfer flavoprotein); electron transport,
glutaric acidemia type II; HET: FAD AMP; 2.60A
{Paracoccus denitrificans} SCOP: c.26.2.3
Length = 252
Score = 273 bits (700), Expect = 1e-93
Identities = 108/223 (48%), Positives = 154/223 (69%), Gaps = 7/223 (3%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
MS+NPFDEIA+E AIRL+E + +EIIA+S G K+ E L+ A+AMG DRAIL+
Sbjct: 33 MSMNPFDEIAVEEAIRLKEK-GQAEEIIAVSIGVKQAAETLRTALAMGADRAILVVAADD 91
Query: 61 ----LQSLSVAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIV 116
++ L+VAK+L + + E +L+I GKQ+ID+D N TGQMLAA+L W QATFASK+
Sbjct: 92 VQQDIEPLAVAKILAAVARAEGTELIIAGKQAIDNDMNATGQMLAAILGWAQATFASKVE 151
Query: 117 LKKNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFKIDE 176
++ K VT+E++ G +TI +SLPA++T DLR+NEPRY +L NI+KA+KK ++ +
Sbjct: 152 IE-GAKAKVTREVDGGLQTIAVSLPAVVTADLRLNEPRYASLPNIMKAKKKPLDEKTAAD 210
Query: 177 LNVNINTGLNIIKVKESHKNNLGIKVKNVIELIDKLKNEAKII 219
V++ L ++ V+E GIKV +V EL+ KLK EA +I
Sbjct: 211 YGVDVAPRLEVVSVREPEGRKAGIKVGSVDELVGKLK-EAGVI 252
>1o97_C Electron transferring flavoprotein beta-subunit; FAD binding; HET:
AMP FAD; 1.6A {Methylophilus methylotrophus} SCOP:
c.26.2.3 PDB: 1o95_C* 1o96_A* 1o94_C* 3clr_C* 3cls_C*
3clt_C* 3clu_C*
Length = 264
Score = 268 bits (687), Expect = 2e-91
Identities = 62/231 (26%), Positives = 118/231 (51%), Gaps = 13/231 (5%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
+N +D+ ++E A++++ESS+ E++ +S G + E L+ +A G DRA+ + D
Sbjct: 33 YDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRVDESLRKCLAKGADRAVRVWDDAA 92
Query: 61 --LQSLSVAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLK 118
++ V ++L ++KKE P +V G QS D TG +A+ LNWP A + + K
Sbjct: 93 EGSDAIVVGRILTEVIKKEAPDMVFAGVQSSDQAYASTGISVASYLNWPHAAVVADLQYK 152
Query: 119 K-NNKILVTQEIEDGK-ETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFKIDE 176
+NK ++ +E+E G + + ++ PA++T L +N+PRY +L I +A K I + +
Sbjct: 153 PGDNKAVIRRELEGGMLQEVEINCPAVLTIQLGINKPRYASLRGIKQAATKPIEEVSLAD 212
Query: 177 LNVNI------NTGLNIIKVKESHKNNLGIKVKNVIELIDKLK---NEAKI 218
+ ++ + + ++ K + + E K+ NE K
Sbjct: 213 IGLSANDVGAAQSMSRVRRMYIPEKGRATMIEGTISEQAAKIIQIINEFKG 263
>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 = 40.8 bits (95), Expect = 2e-04
Identities = 24/152 (15%), Positives = 51/152 (33%), Gaps = 55/152 (36%)
Query: 9 IAIESAIRL---R-----------ESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAIL 54
++IES + + R E +IAI+ G +A + L
Sbjct: 1777 MSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPG----------RVAASFSQEAL 1826
Query: 55 IETDTILQSLSVA--KLLQVIV--KKENPQLVILG-KQSIDSDNNQTGQMLAALLNWPQA 109
+++ + L++ IV EN Q V G +++D + +LN
Sbjct: 1827 ---QYVVERVGKRTGWLVE-IVNYNVENQQYVAAGDLRALD--------TVTNVLN---- 1870
Query: 110 TFASKIVLKKNN----KILVTQEIEDGKETIL 137
+K ++ + +E+ + +
Sbjct: 1871 ------FIKLQKIDIIELQKSLSLEEVEGHLF 1896
>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 = 37.1 bits (85), Expect = 0.003
Identities = 43/306 (14%), Positives = 98/306 (32%), Gaps = 124/306 (40%)
Query: 5 PFDEIAIESAIRLRESSNKI--------KEIIAIS-CGNKKCKEILQIAMAMGV------ 49
P+ ++ ++ + LR + N + K +A+ C + K +Q M +
Sbjct: 136 PYLKL-RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK----VQCKMDFKIFWLNLK 190
Query: 50 ----DRAILIETDTILQSLSV------------------------AKLLQVIVKKENPQ- 80
+L +LQ L A+L +++ K
Sbjct: 191 NCNSPETVLE----MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 81 LVIL----GKQSIDSDNNQTGQML-----AALLNWPQATFASKIVLKKNNKILVTQEIED 131
L++L ++ ++ N ++L + ++ A + I L ++ L E++
Sbjct: 247 LLVLLNVQNAKAWNAFNLSC-KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 132 GKETILLS---------LP-----------AIITTDLRMNEP------RYVTLMNIIKAR 165
LL LP +II +R + ++V +
Sbjct: 306 -----LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR-DGLATWDNWKHVNCDKLTTII 359
Query: 166 KKNINIFKIDEL------------NVNINTGLNIIKVKESHKNNLGI----KVKNVIELI 209
+ ++N+ + E + +I T L L + +K+ + ++
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL------------LSLIWFDVIKSDVMVV 407
Query: 210 -DKLKN 214
+KL
Sbjct: 408 VNKLHK 413
Score = 33.7 bits (76), Expect = 0.043
Identities = 31/200 (15%), Positives = 70/200 (35%), Gaps = 42/200 (21%)
Query: 55 IETDTILQSLSVAKLLQVIVKK----------ENPQLVILGKQSID------SDNNQTGQ 98
++ +T +L V ++ IL K+ ID + T +
Sbjct: 7 MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 99 MLAALLNWPQATFASKI--VLKKNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYV 156
+ LL+ + + VL+ N K L++ + ++ +++ I D N+ +
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 157 TLMNIIKARKKNINIFK--IDELNVNINTGLN----------IIKVKESHK----NNLGI 200
N+ +R + + + EL N ++ + V S+K + I
Sbjct: 127 AKYNV--SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184
Query: 201 ---KVKNVI---ELIDKLKN 214
+KN +++ L+
Sbjct: 185 FWLNLKNCNSPETVLEMLQK 204
Score = 31.4 bits (70), Expect = 0.25
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 23 KIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTILQ 62
KI+E + S K ++L+IA+ M D AI E +Q
Sbjct: 554 KIEENLICS----KYTDLLRIAL-MAEDEAIFEEAHKQVQ 588
>1xp4_A D-alanyl-D-alanine carboxypeptidase; five-stranded antiparallel
beta-sheet, omega-like loop, hydrolase; 2.80A
{Streptococcus pneumoniae R6} SCOP: b.105.1.1 e.3.1.1
Length = 379
Score = 28.1 bits (63), Expect = 2.3
Identities = 13/74 (17%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 82 VILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLKKNNKILVTQ-EIEDGKETILLSL 140
V+L D++ ++L+++ +TF + ++++ + ++ ++DGKE ++
Sbjct: 249 VVLNADHQDNNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKED---TV 305
Query: 141 PAIITTDLRMNEPR 154
A+ D+ + E
Sbjct: 306 IAVAPEDIYLIERV 319
>3a3j_A PBP5; penicillin binding protein 5, DACA, hydrolase; 2.15A
{Haemophilus influenzae}
Length = 344
Score = 28.0 bits (63), Expect = 2.4
Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 8/73 (10%)
Query: 82 VILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLKKNNKILVTQEIEDGKETILLSLP 141
V++G + ++ LL W A F + L+ K + Q + G + S+
Sbjct: 228 VVMGVPTYKGREVES----KKLLQWGFANFETFKTLEA-GKEISEQRVYYGDKN---SVK 279
Query: 142 AIITTDLRMNEPR 154
D + P+
Sbjct: 280 LGAFMDHFITIPK 292
>3p54_A Envelope glycoprotein; viral envelope proteins, structural
genomics, fusion peptide antibody epitopes, flavivirus;
2.10A {Japanese encephalitis virus} PDB: 2i69_A* 3i50_E
3ixx_A 2of6_A 3iyw_A* 2hg0_A* 1pjw_A 1s6n_A 2p5p_A
1ztx_E
Length = 406
Score = 26.9 bits (59), Expect = 5.5
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 86 KQSIDSDNNQTGQMLAALLNWPQATFASKIVLK 118
KQS+ + +Q G + AL ++S ++L
Sbjct: 249 KQSVVALGSQEGGLHQALAGAIVVEYSSSVMLT 281
>3ita_A D-alanyl-D-alanine carboxypeptidase DACC; ppenicillin-binding
protein, BP6, DD-carboxypeptidase, peptidoglycan,
ampicillin, acyl-enzyme complex; HET: AIX AIC; 1.80A
{Escherichia coli} PDB: 3it9_A* 3itb_A*
Length = 352
Score = 26.8 bits (60), Expect = 5.8
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 8/73 (10%)
Query: 82 VILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLKKNNKILVTQEIEDGKETILLSLP 141
V+LG ++ N++ LL W F + +K + VTQ + G ++ +
Sbjct: 234 VVLGAKTDRIRFNES----EKLLTWGFRFFETVTPIKP-DATFVTQRVWFGDKS---EVN 285
Query: 142 AIITTDLRMNEPR 154
+ PR
Sbjct: 286 LGAGEAGSVTIPR 298
>3mzf_A D-alanyl-D-alanine carboxypeptidase DACA; beta-lactam antibiotic,
penicillin-binding protein, DD- carboxypeptidase,
hydrolase; HET: IM2; 1.50A {Escherichia coli} PDB:
1nzu_A 1nzo_A* 3beb_A* 3bec_A* 3mzd_A* 3mze_A* 1z6f_A*
1nj4_A 1hd8_A 1sdn_A 4drt_A
Length = 363
Score = 26.8 bits (60), Expect = 6.4
Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 8/73 (10%)
Query: 82 VILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLKKNNKILVTQEIEDGKETILLSLP 141
++G ++ ++ LL W F + LK K ++ + G
Sbjct: 238 AVMGGRTFKGREAES----KKLLTWGFRFFETVNPLKV-GKEFASEPVWFGDSD---RAS 289
Query: 142 AIITTDLRMNEPR 154
+ D+ + PR
Sbjct: 290 LGVDKDVYLTIPR 302
>3qbx_A Anhydro-N-acetylmuramic acid kinase; acetate and sugar kinases,
HSP70, actin superfamily, anhydro-N-actetylmuramic acid
binding; HET: AH0; 2.10A {Pseudomonas aeruginosa} PDB:
3qbw_A*
Length = 371
Score = 26.8 bits (60), Expect = 6.5
Identities = 4/24 (16%), Positives = 7/24 (29%)
Query: 157 TLMNIIKARKKNINIFKIDELNVN 180
LM + + DE +
Sbjct: 298 ALMKRLAMLMPEARVASTDEYGIP 321
>2gzx_A Putative TATD related DNAse; deoxyribonuclease, NESG, ZR237,
structural GENO PSI, protein structure initiative; 2.20A
{Staphylococcus aureus subsp}
Length = 265
Score = 26.7 bits (60), Expect = 6.5
Identities = 8/24 (33%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 35 KKCKEILQIAMAMGVDRAILIETD 58
K K+ ++A + ++R +L+ETD
Sbjct: 182 KNAKQPKEVAKHVSMER-LLVETD 204
>1j6o_A TATD-related deoxyribonuclease; structural genomics, TM0667, JCSG,
PSI, protein structure initiative, joint center for
structural genomics; 1.80A {Thermotoga maritima} SCOP:
c.1.9.12
Length = 268
Score = 26.3 bits (59), Expect = 6.9
Identities = 6/24 (25%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 35 KKCKEILQIAMAMGVDRAILIETD 58
K + + ++ +G++ I++ETD
Sbjct: 192 PKNEALREVVKRVGLEY-IVLETD 214
>1tvf_A PBP4, penicillin binding protein 4; structural genomics, nysgxrc
target, SAV0642, PSI, protein structure initiative;
2.00A {Staphylococcus aureus} SCOP: b.105.1.2 e.3.1.1
Length = 369
Score = 26.3 bits (58), Expect = 8.8
Identities = 10/69 (14%), Positives = 23/69 (33%), Gaps = 3/69 (4%)
Query: 82 VILGKQSIDSDNNQTG--QMLAALLNWPQATFASKIVLKKNNKILVTQEIEDGKETILLS 139
VI+G + + M AL+ + +L K + + + + +
Sbjct: 270 VIMGAGDYKNLGGEKQRNMMGNALMERSFDQYKYVKILSK-GEQRINGKKYYVENDLYDV 328
Query: 140 LPAIITTDL 148
LP+ +
Sbjct: 329 LPSDFSKKD 337
>3cqy_A Anhydro-N-acetylmuramic acid kinase; APC7501, SO_1313, structural
genomics, PSI-2, shewanella one MR-1, protein structure
initiative; 2.30A {Shewanella oneidensis}
Length = 370
Score = 26.4 bits (59), Expect = 9.3
Identities = 6/24 (25%), Positives = 8/24 (33%)
Query: 157 TLMNIIKARKKNINIFKIDELNVN 180
LM + A I L V+
Sbjct: 304 ELMQRLAALLPGYRIDTTSALGVD 327
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 0.134 0.351
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,161,838
Number of extensions: 188198
Number of successful extensions: 496
Number of sequences better than 10.0: 1
Number of HSP's gapped: 487
Number of HSP's successfully gapped: 29
Length of query: 219
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 129
Effective length of database: 4,188,903
Effective search space: 540368487
Effective search space used: 540368487
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: 55 (25.0 bits)