RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1882
(233 letters)
>1vaj_A Hypothetical protein PH0010; alpha + beta fold, structural
genomics, unknown function; 1.82A {Pyrococcus
horikoshii} SCOP: d.309.1.1
Length = 214
Score = 153 bits (389), Expect = 6e-47
Identities = 44/185 (23%), Positives = 71/185 (38%), Gaps = 19/185 (10%)
Query: 49 FDVLYCHLHSLEPPNPPSGIS---NDAFPLFVTWK---IGKDQRLRGCIGTFNAI-NLHG 101
+ +L + + PP + +FVT + LRGCIG I L
Sbjct: 18 RRAIEEYLKTGKEIEPPKDTPPELWEKMGVFVTLNRYNVPPQTALRGCIGFPTPIYPLVE 77
Query: 102 GLREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFE-----DGNDYTDWKIGVHGIRI 156
+ A+ SA D RF P+ ++E L V VS+L E K+G G+ +
Sbjct: 78 ATIKAAIYSAVDDPRFPPVKLEEMDNLVVEVSVLTPPELIEGPPEERPRKIKVGRDGLIV 137
Query: 157 EFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIRCNIKLTRYQSEL 216
+ LP+V E GWD+ + + K G D + K+ ++ +E+
Sbjct: 138 -----EKGIYSGLLLPQVPVEWGWDEEEFLAETCWKAGLPPDCWLDE--DTKVYKFTAEI 190
Query: 217 VSVSY 221
Y
Sbjct: 191 FEEEY 195
>1zq7_A Hypothetical protein MM0484; X-RAY, NESG, MAR9, Q8PZK8, structural
genomics, PSI, protein structure initiative; 2.11A
{Methanosarcina mazei} SCOP: d.309.1.1
Length = 207
Score = 150 bits (381), Expect = 6e-46
Identities = 42/200 (21%), Positives = 72/200 (36%), Gaps = 29/200 (14%)
Query: 50 DVLYCHLHSLEPPNPPSGIS------NDAFPLFVTWKIGKDQRLRGCIGTFNAI-NLHGG 102
+ L + P P + + +FVT + LRGCIG L
Sbjct: 16 KTIEIFLSKGKSPRPDASGVELSPVFEEYRGVFVTLT--EGGLLRGCIGHPYPDSTLKEA 73
Query: 103 LREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFE-----DGNDYTDWKIGVHGIRIE 157
+ + A+++A +D RF + DE + V V+IL E +IG HG+ ++
Sbjct: 74 ILDSAISAATRDPRFPTVEQDEMKNILVEVTILTQPEKINASPKELPDKVEIGKHGLIVK 133
Query: 158 FHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIRCNIKLTRYQSELV 217
LP+VAPE D I + K G ++ ++ ++
Sbjct: 134 Q-----GYCQGLLLPQVAPENDMDSIDFLSHTCMKAGLSPDAWVK---GAEVYCFEGQIF 185
Query: 218 S-------VSYQDYLNHWKN 230
V + +L H +
Sbjct: 186 KEKEPDGEVIEEKFLEHHHH 205
>1wsc_A Hypothetical protein ST0229; structural genomics, function unknown
protein, unknown function; 2.45A {Sulfolobus tokodaii}
SCOP: d.309.1.1
Length = 230
Score = 151 bits (382), Expect = 9e-46
Identities = 41/174 (23%), Positives = 72/174 (41%), Gaps = 15/174 (8%)
Query: 60 EPPNPPSGISNDAFPLFVTWKI--GKDQRLRGCIGTFNAI-NLHGGLREYAVTSAFKDSR 116
+ I N FVT + G LRGCIG A+ L + + A+ +AF D R
Sbjct: 42 YLSSLNDPILNKKGLAFVTLETYYGNSTSLRGCIGYVEAVAPLKEIVSKAAIAAAFSDPR 101
Query: 117 FNPITVDEFSKLHVSVSILRHFEDGNDYTDW------KIGVHGIRIEFHNERGNKRTATY 170
F P++ EF + + V++L ++ + W K+G G+ +E+ G +
Sbjct: 102 FPPLSKGEFDNIIIEVTVLTKPQEIDVENRWELPKKIKVGEDGLIVEY----GILYSGLL 157
Query: 171 LPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIRCNIKLTRYQSELVSVSYQDY 224
LP+V E WD+ + K G + + +K+ ++Q +
Sbjct: 158 LPQVPMEYCWDEETFLAETCIKAGLEPDCWLNN--KVKIKKFQGIIFREEKPKS 209
>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 = 35.0 bits (80), Expect = 0.021
Identities = 40/186 (21%), Positives = 57/186 (30%), Gaps = 58/186 (31%)
Query: 26 LTNGHG-PSS--SVDKIAQPEMCFFCFDVLYCHLHSLEPPNPPSGIS--N--DAFPLFVT 78
L N G PS S+ + Q ++ + + HL P IS N V+
Sbjct: 328 LENNEGVPSPMLSISNLTQEQVQDYV-NKTNSHL----PAGKQVEISLVNGAKNL--VVS 380
Query: 79 WKIGKDQRLRGCIGTFNAINLHGGLREYAVTSAFKDSR-------------FNPITVDEF 125
G Q L G +NL LR+ S SR F P+
Sbjct: 381 ---GPPQSLYG-------LNLT--LRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH 428
Query: 126 SKLHVSVS--ILRHFEDGN---DYTDWKIGVHGIRIEFHNERG-NKRT--ATYLPEVAPE 177
S L V S I + N + D +I V + G + R + +
Sbjct: 429 SHLLVPASDLINKDLVKNNVSFNAKDIQIPV------YDTFDGSDLRVLSGSISERIV-- 480
Query: 178 QGWDQI 183
D I
Sbjct: 481 ---DCI 483
Score = 26.9 bits (59), Expect = 7.3
Identities = 10/60 (16%), Positives = 17/60 (28%), Gaps = 15/60 (25%)
Query: 101 GG----------LRE-YAVTSAFKDSRFNPI--TVDEFSKLHVSVSILRHFEDGNDYTDW 147
GG LR+ Y T+ E + + + F G + +W
Sbjct: 161 GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAE--KVFTQGLNILEW 218
>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 = 32.5 bits (73), Expect = 0.13
Identities = 25/142 (17%), Positives = 44/142 (30%), Gaps = 25/142 (17%)
Query: 95 NAINLHGGLRE-YAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFEDGNDYTDWKIGVHG 153
N LH + + Y + F P +D++ H I H ++ +
Sbjct: 441 NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH----IGHHLKNIEHPERMTL---- 492
Query: 154 IRIEFHNER--GNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIR------C 205
R+ F + R K A + +Q L+ +K I +
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQ----LKF--YKPYICDNDPKYERLVN 546
Query: 206 NIK--LTRYQSELVSVSYQDYL 225
I L + + L+ Y D L
Sbjct: 547 AILDFLPKIEENLICSKYTDLL 568
Score = 29.8 bits (66), Expect = 0.97
Identities = 25/229 (10%), Positives = 52/229 (22%), Gaps = 84/229 (36%)
Query: 11 QKLNNSTGVVCNGHGLTNGHGPSSSVDKIAQPE--MCFFCFDVLYCHLHSLEPPNPPSGI 68
+L + V+ G+ G G + + C F +
Sbjct: 145 LELRPAKNVLI--DGVL-GSGKTWVALDVCLSYKVQCKMDFKI----------------- 184
Query: 69 SNDAFPLFVTW-KIGKDQRLRGCIGTFNAINLHGGLREYAVTSAFKDSRFNPITVDEFSK 127
F W + + + I + S+
Sbjct: 185 -------F--WLNLKNCNSPETVLEMLQKLLYQ-------------------IDPNWTSR 216
Query: 128 LHVSVSILRHFEDGNDYTDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTID 187
S +I +R + + L V + + +
Sbjct: 217 SDHSSNIKLRIHSIQAE---------LRRLLK-SKPYENCLLVLLNV-----QNA-KAWN 260
Query: 188 SLLRKGGFKGPITPDIRCNIKL-TRYQS---ELVSVSYQDY-LNHWKNG 231
+ F ++ C I L TR++ L + + L+H
Sbjct: 261 A------F------NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
>3ghy_A Ketopantoate reductase protein; oxidoreductase, NAD-binding domain,
PSI-2, NYSGXRC, structur genomics, protein structure
initiative; 2.00A {Ralstonia solanacearum}
Length = 335
Score = 29.2 bits (66), Expect = 1.2
Identities = 7/31 (22%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 181 DQIQTIDSLLRKGGFKGPITPDIRCNI--KL 209
++ +I +L + G + + I+ +I KL
Sbjct: 177 PRLASIAALFGRAGLQAECSEAIQRDIWFKL 207
>3p4t_A Putative acyl-COA dehydrogenase; ssgcid, structural genomics,
seattle structural genomics CEN infectious disease,
oxidoreductase; HET: FAO; 1.70A {Mycobacterium
smegmatis} PDB: 3oib_A*
Length = 403
Score = 29.0 bits (66), Expect = 1.3
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 96 AINLHGG---LREYAVTSAFKDSRFNPI 120
A+ L GG + E V ++D R I
Sbjct: 356 AVQLFGGMGYMAESEVERQYRDMRILGI 383
>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 = 28.4 bits (62), Expect = 1.3
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 15/41 (36%)
Query: 95 NAIN-LHGGLREYAVTSAFKDSRFNPITVDEFSKLHVSVSI 134
A+ L L+ YA SA P L + ++
Sbjct: 20 QALKKLQASLKLYADDSA-------P-------ALAIKATM 46
>2pg0_A Acyl-COA dehydrogenase; GK1316, geobacillus kaustophilus HTA
structural genomics, PSI, protein structure initiative;
HET: FAD; 1.80A {Geobacillus kaustophilus}
Length = 385
Score = 28.6 bits (65), Expect = 1.5
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 96 AINLHGG---LREYAVTSAFKDSRFNPI 120
A+ LHGG + EY + ++D + I
Sbjct: 340 AMQLHGGYGYMEEYEIARRYRDIPVSAI 367
>3r7k_A Probable acyl COA dehydrogenase; ssgcid, structural genomics,
seattle structural genomics CEN infectious disease,
oxidoreductase; HET: FDA; 2.50A {Mycobacterium
abscessus}
Length = 403
Score = 28.7 bits (65), Expect = 1.6
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 96 AINLHGG---LREYAVTSAFKDSRFNPI 120
A+ + GG +RE + ++D R I
Sbjct: 358 AVQIFGGMGYMRESEIERHYRDCRILGI 385
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 27.9 bits (63), Expect = 2.9
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 156 IEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGF 195
I+ N +GN++ + +LPE E+ W I ++ K G+
Sbjct: 157 IDLKNWKGNQKNSGFLPE---EREW-----IGKVIHKLGW 188
>3i83_A 2-dehydropantoate 2-reductase; structural genomics, oxidoreductase,
NADP, pantothenate BIOS PSI-2, protein structure
initiative; 1.90A {Methylococcus capsulatus}
Length = 320
Score = 27.6 bits (62), Expect = 3.4
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 181 DQIQTIDSLLRKGGFKGPITPDIR 204
++++T+ + + G G T +I
Sbjct: 159 ERVKTLAAAFEEAGIDGIATENIT 182
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair,
endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens}
SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A
Length = 318
Score = 27.3 bits (61), Expect = 3.9
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 156 IEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGF 195
I+ N +GNK+ A + P+ E+ LL+
Sbjct: 218 IDLRNPKGNKKNAGFTPQ---ERQG-----FGELLQAVPL 249
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A
{Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A*
2o3c_A
Length = 285
Score = 27.2 bits (61), Expect = 4.0
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 156 IEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGF 195
I+ N +GNK+ A + P+ E+ LL+
Sbjct: 185 IDLRNPKGNKKNAGFTPQ---ERQG-----FGELLQAVPL 216
>2qyt_A 2-dehydropantoate 2-reductase; APC81190, porphyromonas gingi W83,
structural genomics, PSI-2; HET: MSE; 2.15A
{Porphyromonas gingivalis}
Length = 317
Score = 27.2 bits (61), Expect = 4.6
Identities = 6/24 (25%), Positives = 8/24 (33%)
Query: 181 DQIQTIDSLLRKGGFKGPITPDIR 204
D + LL G + DI
Sbjct: 172 DDEVRLAELLTAAGIRAYNPTDID 195
>3hn2_A 2-dehydropantoate 2-reductase; PSI-2, NYSGXRC, structural GE
protein structure initiative; 2.50A {Geobacter
metallireducens}
Length = 312
Score = 27.2 bits (61), Expect = 5.0
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 181 DQIQTIDSLLRKGGFKGPITPDIR 204
+I+ + ++ R+ G T D++
Sbjct: 157 GRIEELAAMFRQAGVDCRTTDDLK 180
>3e0g_A Leukemia inhibitory factor receptor; IG domain, cytokine binding
homology region (CHR), cell MEMB disease mutation,
glycoprotein, membrane; HET: NAG MAN FUC; 3.10A {Homo
sapiens}
Length = 483
Score = 27.1 bits (59), Expect = 5.2
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 5/54 (9%)
Query: 45 CFFCFDVLYCH--LHSLEPPNPPSGIS---NDAFPLFVTWKIGKDQRLRGCIGT 93
F + + + PP+ P ++ +D + +W G+ L G T
Sbjct: 263 VVFTTEDNIFGTVIFAGYPPDTPQQLNCETHDLKEIICSWNPGRVTALVGPRAT 316
>3hwr_A 2-dehydropantoate 2-reductase; YP_299159.1, PANE/APBA family
ketopantoate reductase, struct genomics, joint center
for structural genomics; HET: NDP BCN; 2.15A {Ralstonia
eutropha}
Length = 318
Score = 26.8 bits (60), Expect = 6.1
Identities = 2/27 (7%), Positives = 9/27 (33%)
Query: 178 QGWDQIQTIDSLLRKGGFKGPITPDIR 204
+ + ++ G + ++R
Sbjct: 165 EPTSHGANLAAIFAAAGVPVETSDNVR 191
>1tdj_A Biosynthetic threonine deaminase; allostery, cooperative, tetramer,
regulation, pyridoxal PHOS isoleucine biosynthesis; HET:
PLP; 2.80A {Escherichia coli} SCOP: c.79.1.1 d.58.18.2
d.58.18.2
Length = 514
Score = 26.8 bits (60), Expect = 6.2
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 149 IGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFK 196
+G + EF+ + + A V +G ++ + I +L GG+
Sbjct: 359 LGGRSV-TEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYS 405
>2y4o_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: DLL; 1.90A {Burkholderia cenocepacia}
Length = 443
Score = 26.9 bits (60), Expect = 6.3
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 168 ATYLPEVAPEQGWDQIQTIDSLLRKGGFKG-PITPDIRCNI 207
L + QG D +S L+ G F P T +R +
Sbjct: 195 MLNLIDEMVRQGMD---PAESSLKIGIFGAEPWTQALRNEV 232
>3h9m_A P-aminobenzoate synthetase, component I; para-aminobenzoate
synthetase, cytophaga hutchinsonii,YP_678417.1,
CHU_1808; HET: PGE; 1.57A {Cytophaga hutchinsonii atcc
33406}
Length = 436
Score = 26.5 bits (59), Expect = 7.6
Identities = 5/28 (17%), Positives = 9/28 (32%)
Query: 30 HGPSSSVDKIAQPEMCFFCFDVLYCHLH 57
+S IA FF + ++
Sbjct: 96 QLHTSKEAGIAFAAATFFIPEHVWEIQP 123
>2y27_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: MSE PG4 ATP; 1.60A {Burkholderia
cenocepacia} PDB: 2y4n_A*
Length = 437
Score = 26.5 bits (59), Expect = 8.3
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 168 ATYLPEVAPEQGWDQIQTIDSLLRKGGFKG-PITPDIRCNI 207
+ + QG D + S LR G F P T D+R I
Sbjct: 193 MLSIADEIERQGLD---PVQSSLRIGIFGAEPWTNDMRVAI 230
>3qov_A Phenylacetate-coenzyme A ligase; acetyl-COA synthetase-like,
structural genomics, joint cente structural genomics,
JCSG; HET: MSE ADP COA; 2.20A {Bacteroides
thetaiotaomicron} PDB: 3s89_A*
Length = 436
Score = 26.5 bits (59), Expect = 8.3
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 168 ATYLPEVAPEQGWDQIQTIDSLLRKGGFKG-PITPDIRCNI 207
A L EV E+G D ++ L+ P T + R I
Sbjct: 189 AIRLAEVFQEEGID---PRETTLKTLVIGAEPHTDEQRRKI 226
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 0.445
Gapped
Lambda K H
0.267 0.0816 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,709,442
Number of extensions: 215643
Number of successful extensions: 428
Number of sequences better than 10.0: 1
Number of HSP's gapped: 412
Number of HSP's successfully gapped: 26
Length of query: 233
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 143
Effective length of database: 4,188,903
Effective search space: 599013129
Effective search space used: 599013129
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 (25.2 bits)