RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9210
(234 letters)
>3p9y_A CG14216, LD40846P; phosphatase, CIS proline, LMW PTP-like fold, RNA
polymerase hydrolase; HET: N7P SEP SET IMD PG4; 2.10A
{Drosophila melanogaster} PDB: 3fdf_A 3fmv_A 3omx_A
3omw_A
Length = 198
Score = 264 bits (677), Expect = 8e-91
Identities = 116/233 (49%), Positives = 158/233 (67%), Gaps = 41/233 (17%)
Query: 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELI 61
PS L VAVV SSNMNRSMEAH +L+KKG +V+S+GTG++
Sbjct: 7 PSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGER--------------------- 45
Query: 62 PLFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLL 121
V L G A DKPNVY+F T YEDIY+DL +KDK FYT+NGLL
Sbjct: 46 -------------VKL-----PGMAFDKPNVYEF-GTKYEDIYRDLESKDKEFYTQNGLL 86
Query: 122 HMLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDI 181
HML+RN+RIK PE+FQ++K++FDII+T EERVYD V+ H M S++N PVH++N+D+
Sbjct: 87 HMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHM-ESMESVDNRPVHVLNVDV 145
Query: 182 QDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEEKCSRPLLHTILFY 234
+N E+A +GAF+ +++++M K DLDN+IDE++QEFEE+ R +LH++LFY
Sbjct: 146 VNNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 198
>3o2q_B RNA polymerase II subunit A C-terminal domain PHO SSU72; heat
repeat, scaffold, phosphatase, polymerase II CTD, CIS-P
hydrolase; HET: SEP; 2.40A {Homo sapiens} PDB: 3o2s_B
Length = 214
Score = 263 bits (674), Expect = 4e-90
Identities = 120/233 (51%), Positives = 146/233 (62%), Gaps = 41/233 (17%)
Query: 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELI 61
S L+VAVV SSN NRSMEAH LSK+G V+SFGTG + V +
Sbjct: 23 SSPLRVAVVSSSNQNRSMEAHNILSKRGFSVRSFGTG--------THVK----------L 64
Query: 62 PLFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLL 121
P G A DKPNVYDF TTY+ +Y DL+ KDK YT+NG+L
Sbjct: 65 P---------------------GPAPDKPNVYDF-KTTYDQMYNDLLRKDKELYTQNGIL 102
Query: 122 HMLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDI 181
HML+RNKRIK +PE+FQ KD FD+I+TCEERVYDQV+E ++ PVH++N+DI
Sbjct: 103 HMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNS-REQETCQPVHVVNVDI 161
Query: 182 QDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEEKCSRPLLHTILFY 234
QDN EEATLGAFL EL ED++NEIDE++QEFEEK R LHT+ FY
Sbjct: 162 QDNHEEATLGAFLICELCQCIQHTEDMENEIDELLQEFEEKSGRTFLHTVCFY 214
>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase,
structural genomics, NPPSFA; 2.00A {Thermus
thermophilus}
Length = 94
Score = 31.0 bits (71), Expect = 0.085
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 6 KVAVVCSSNMNRSMEAHAYLSKKGVDVKS 34
+ +VC + S A YL +G + S
Sbjct: 55 PLLLVCEKGL-LSQVAALYLEAEGYEAMS 82
>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 = 32.9 bits (74), Expect = 0.095
Identities = 31/207 (14%), Positives = 62/207 (29%), Gaps = 60/207 (28%)
Query: 65 FHKVFVFQISVN--------LFFQSITGTAMD---------------KPNVYDFHTTTYE 101
F ++ VF S + ++F I M K +
Sbjct: 375 FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP----- 429
Query: 102 DIYQDLMNKDKAFYTRNGLLHMLERNKRIKLKPEKFQESKDKFDIIITCEER-VYDQVLE 160
IY +L K + Y LH + I + ++ D D+I ++ Y +
Sbjct: 430 SIYLELKVKLENEYA----LH-----RSI-VDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 161 HFDN----QMIS-----------LENTPVHLINIDIQDNQEEATLGAFLASELMSMFI-- 203
H N + ++ LE + + N + L + +I
Sbjct: 480 HLKNIEHPERMTLFRMVFLDFRFLEQK---IRHDSTAWNASGSILNTLQQLKFYKPYICD 536
Query: 204 KCEDLDNEIDEIMQEFEEKCSRPLLHT 230
+ ++ I+ +F K L+ +
Sbjct: 537 NDPKYERLVNAIL-DFLPKIEENLICS 562
Score = 26.7 bits (58), Expect = 9.7
Identities = 32/300 (10%), Positives = 79/300 (26%), Gaps = 128/300 (42%)
Query: 36 GTGDKKPQQWESVVIFHCCDFCSELIPLFFHKVF------------VFQISVNLFFQSIT 83
G+G K W V + C + ++ K+F V ++ L +Q
Sbjct: 160 GSG--K--TW--VALDVCLSY--KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ--- 208
Query: 84 GTAMDKP-NVYDFHTTTYEDIYQDLMNKDKAFYT----RNGLLHMLE--RNKRIKLKPEK 136
+D H++ + + + + N LL +L +N +
Sbjct: 209 ---IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL-VLLNVQNAKAW----- 259
Query: 137 FQESKDKFDI-----IITCEERVYDQVLEHFDNQMISLENTPVHL------------INI 179
+ F++ + T ++V D + ISL++ + L ++
Sbjct: 260 -----NAFNLSCKILLTTRFKQVTDFLSAATTTH-ISLDHHSMTLTPDEVKSLLLKYLDC 313
Query: 180 DIQDNQEEAT---------LGAFLA-----------------SELMSMFIKC-------- 205
QD E + + + ++ +
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
Query: 206 --EDL----------------------DNEIDEIMQEFEEKC--------SRPLLHTILF 233
+ L +++ ++ + + S + +I
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYL 433
>3eme_A Rhodanese-like domain protein; alpha-beta-alpha sandwich,
structural genomics; 2.00A {Staphylococcus aureus
subsp} PDB: 3iwh_A 3mzz_A
Length = 103
Score = 29.9 bits (68), Expect = 0.21
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDV 32
N +VC+ + RS + YL G+D
Sbjct: 54 NKNEIYYIVCAGGV-RSAKVVEYLEANGIDA 83
>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta
protein, structural genomics, PSI-2, protein structure
initiative; 2.40A {Thermoplasma volcanium GSS1}
Length = 108
Score = 29.9 bits (68), Expect = 0.23
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDVK 33
+ K AV+C+ RS A +LS+ G+++
Sbjct: 53 ERDKKYAVICAHGN-RSAAAVEFLSQLGLNIV 83
>3foj_A Uncharacterized protein; protein SSP1007, structural genomics,
PSI-2, protein structure initiative; 1.60A
{Staphylococcus saprophyticus subsp}
Length = 100
Score = 29.5 bits (67), Expect = 0.32
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 2 PSNLKVAVVCSSNMNRSMEAHAYLSKKGVDV 32
N ++C + RS + YL + GV+
Sbjct: 54 NDNETYYIICKAGG-RSAQVVQYLEQNGVNA 83
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 0.76
Identities = 8/73 (10%), Positives = 22/73 (30%), Gaps = 16/73 (21%)
Query: 125 ERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQDN 184
E+ KR++ + + + ++ ++ + Q+ E +N
Sbjct: 93 EQRKRLQELDAASKVMEQE---WREKAKKDLEEWNQRQSEQV---EKN--------KINN 138
Query: 185 QEEATLGAFLASE 197
+ AF
Sbjct: 139 RIADK--AFYQQP 149
>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 = 30.0 bits (67), Expect = 0.84
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 16/57 (28%)
Query: 122 HMLERNKRIK-LKPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLI 177
ML I L E+ Q+ +K + + ++V ISL N +L+
Sbjct: 337 PML----SISNLTQEQVQDYVNKTNSHLPAGKQVE-----------ISLVNGAKNLV 378
>2gjc_A Thiazole biosynthetic enzyme, mitochondrial; glutathione reductase
type II family, thiazole synthase, mitochondria DNA
repair; HET: AHZ; 1.82A {Saccharomyces cerevisiae} SCOP:
c.3.1.6 PDB: 3fpz_A*
Length = 326
Score = 28.6 bits (63), Expect = 1.9
Identities = 23/94 (24%), Positives = 35/94 (37%), Gaps = 11/94 (11%)
Query: 21 AHAYLSKKGVDVK--------SFGTGDKKPQQWESVVIFH--CCDFCSEL-IPLFFHKVF 69
A ++K D+K + G G Q S ++ F EL IP +
Sbjct: 80 AAYVIAKNRPDLKVCIIESSVAPGGGSWLGGQLFSAMVMRKPAHLFLQELEIPYEDEGDY 139
Query: 70 VFQISVNLFFQSITGTAMDKPNVYDFHTTTYEDI 103
V LF ++ + PNV F+ T ED+
Sbjct: 140 VVVKHAALFISTVLSKVLQLPNVKLFNATCVEDL 173
>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2,
protein STRU initiative, northeast structural genomics
consortium, NESG; 2.50A {Bacillus halodurans} PDB:
3o3w_A
Length = 144
Score = 27.8 bits (62), Expect = 2.0
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 2 PSNLKVAVVCSSNM-NRSMEAHAYLSKKGVDVKSF 35
+ C N + +A A ++ G VK
Sbjct: 70 SKEKVIITYCWGPACNGATKAAAKFAQLGFRVKEL 104
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory
protein, transcription; 3.00A {Escherichia coli}
Length = 228
Score = 28.1 bits (63), Expect = 2.2
Identities = 20/121 (16%), Positives = 44/121 (36%), Gaps = 21/121 (17%)
Query: 111 DKAFYTRNGLLHMLERNKRIKL--KPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMIS 168
D +TR+G+ E++KR + + Q KD + + E ++ ++ +
Sbjct: 101 DVQVFTRDGV----EKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVE 156
Query: 169 ---LENTPVH-LINIDIQDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEEKCS 224
L+ P + + + D +++ L E D E ++ E K
Sbjct: 157 AEKLDKLPRDRWLELGLTDEEKQNQLEQLA-----------EQYDELKHEFEKKLEAKRR 205
Query: 225 R 225
+
Sbjct: 206 K 206
>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp,
NSR437I, NESG, structural genomics, PSI-2, protein
structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A
Length = 106
Score = 26.4 bits (59), Expect = 4.0
Identities = 4/29 (13%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 1 MPSNLKVAVVCSSNMNRSMEAHAYLSKKG 29
+ + + V + + ++ +A L G
Sbjct: 49 LEKSRDIYVYGAGDE-QTSQAVNLLRSAG 76
>3hc1_A Uncharacterized HDOD domain protein; HDOD domain protein with
unknown function, STRU genomics, joint center for
structural genomics; 1.90A {Geobacter sulfurreducens}
Length = 305
Score = 27.4 bits (61), Expect = 4.1
Identities = 9/52 (17%), Positives = 20/52 (38%)
Query: 170 ENTPVHLINIDIQDNQEEATLGAFLASELMSMFIKCEDLDNEIDEIMQEFEE 221
+ PV + ++++ + L + +LD+ I EI +E
Sbjct: 250 GHKPVDSVRTLLENHPSWGVIRRSLGGSDFDEKLIVAELDSSIVEIRAAVDE 301
>2cwd_A Low molecular weight phosphotyrosine protein PHOS; tyrosine
phosphatase, structural genomics; 1.90A {Thermus
thermophilus}
Length = 161
Score = 26.7 bits (60), Expect = 4.7
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 1 MPSNLKVAVVCSSNMNRSMEAHA----YLSKKGVD----VKSFGTGD 39
M ++V VC N+ RS A L ++G++ V S GTG
Sbjct: 1 MDRPVRVLFVCLGNICRSPMAEGIFRKLLKERGLEDRFEVDSAGTGA 47
>1gxg_A Colicin E8 immunity protein; inhibitor, inhibitor protein of DNAse
colicin E8, bacteriocin immunity, plasmid,; NMR
{Escherichia coli} SCOP: a.28.2.1 PDB: 1gxh_A
Length = 85
Score = 25.9 bits (57), Expect = 5.1
Identities = 7/38 (18%), Positives = 18/38 (47%)
Query: 197 ELMSMFIKCEDLDNEIDEIMQEFEEKCSRPLLHTILFY 234
+++ I CE + + D+ ++ F P +++Y
Sbjct: 17 KIIEDIINCEGDEKKQDDNLEHFISVTEHPSGSDLIYY 54
>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine
rich repeat domain, type three effector, salmonella
virulence factor; 1.90A {Salmonella typhimurium}
Length = 622
Score = 26.8 bits (59), Expect = 6.7
Identities = 9/27 (33%), Positives = 11/27 (40%)
Query: 159 LEHFDNQMISLENTPVHLINIDIQDNQ 185
L F N + L P L + I NQ
Sbjct: 106 LSIFSNPLTHLPALPSGLCKLWIFGNQ 132
>3cc8_A Putative methyltransferase; structural genomics, joint center for
structural genomics, JCSG, protein structure initiative,
PS transferase; 1.64A {Bacillus cereus}
Length = 230
Score = 26.2 bits (58), Expect = 7.7
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 6/30 (20%)
Query: 135 EKFQESKDKFDIIITCEERVYDQVLEHFDN 164
+++FD +I + VLEH +
Sbjct: 85 MDMPYEEEQFDCVIFGD------VLEHLFD 108
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
0.323 0.137 0.406
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,567,331
Number of extensions: 207188
Number of successful extensions: 690
Number of sequences better than 10.0: 1
Number of HSP's gapped: 684
Number of HSP's successfully gapped: 32
Length of query: 234
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 143
Effective length of database: 4,160,982
Effective search space: 595020426
Effective search space used: 595020426
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 (22.0 bits)
S2: 56 (25.3 bits)