RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy198
(245 letters)
>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY
crystallography, putative translation factor, PSI,
protein structure initiative; 1.40A {Escherichia coli}
SCOP: d.115.1.1 PDB: 1kk9_A
Length = 206
Score = 159 bits (406), Expect = 3e-49
Identities = 42/202 (20%), Positives = 91/202 (45%), Gaps = 11/202 (5%)
Query: 25 MCSIVKV--TDPKAALL--AAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRD 80
M + +P+ L+ A + ++KG V+ PTD+ Y L C + A+ + I++
Sbjct: 1 MSQFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLP 60
Query: 81 VNKPLAICVSEITDIPKWADTHTVSFELLAELLPGPVTIVFNRSEHL-NLELNPNVTKVA 139
+ +++++ ++ V+F L+ PG T + ++ + L +
Sbjct: 61 DGHNFTLMCRDLSELSTYSFVDNVAFRLMKNNTPGNYTFILKGTKEVPRRLLQEKRKTIG 120
Query: 140 VRIPDHKFLRQLLKLMDSPLALTSANESNEPSTLCINE--FQKLWSQLSVVIDGGIISNP 197
+R+P + + LL+ + P+ TS T E +L Q+ ++I GG +
Sbjct: 121 MRVPSNPIAQALLEALGEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLGQK 180
Query: 198 ERFGSTIVDLSEENVYSIVRKG 219
+T++DL+++ +VR+G
Sbjct: 181 P---TTVIDLTDD-TPVVVREG 198
>1jcu_A Conserved protein MTH1692; mixed alpha-beta structure, structural
genomics; NMR {Methanothermobacterthermautotrophicus}
SCOP: d.115.1.1
Length = 208
Score = 153 bits (388), Expect = 1e-46
Identities = 58/202 (28%), Positives = 103/202 (50%), Gaps = 21/202 (10%)
Query: 28 IVKVT----DPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNK 83
I K+T P A ++ G +V PTDT+YGL +A + A+ L+ +K R +K
Sbjct: 3 IRKITRKNPSPDVLEEAISVMEGGGIVIYPTDTIYGLGVNALDEDAVRRLFRVKGRSPHK 62
Query: 84 PLAICVSEITDIPKWADTHTVSFELLAELLPGPVTIVFNRSEHLNLELNPNVTKVAVRIP 143
P++ICVS + +IP+++ + EL+ +LPGP T+V R+E + + ++V +R+P
Sbjct: 63 PVSICVSCVDEIPRFSRPSGDAMELMERILPGPYTVVLERNELIPDVITGGSSRVGIRVP 122
Query: 144 DHKFLRQLLKLMDSPLALTSANESNEPS----TLCINEFQKLWSQLSVVIDGGIISNPER 199
D + R++ P+ TSAN S +P + + + +V+D G
Sbjct: 123 DDEICRRIAA--RFPVTATSANISGKPPSPRLEEIVRDLDA----VDLVLDAG----DCL 172
Query: 200 FG--STIVDLSEENVYSIVRKG 219
ST++DL+ ++R+G
Sbjct: 173 DMEPSTVIDLTVNPP-RVLRRG 193
>1hru_A YRDC gene product; protein folding, structural genomics, RNA, SUA5,
PSI, protein structure initiative, midwest center for
structural genomics; 2.00A {Escherichia coli} SCOP:
d.115.1.1
Length = 188
Score = 136 bits (345), Expect = 2e-40
Identities = 50/188 (26%), Positives = 77/188 (40%), Gaps = 15/188 (7%)
Query: 33 DPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEI 92
A A L + V+A PT+ ++G+ CD + A+ L E+K+R V+K L + +
Sbjct: 6 QRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANY 65
Query: 93 TDIPKWADTHTVS---FELLAELLPGPVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLR 149
+ + D ++ E + PGPVT VF L +AVR+ DH +
Sbjct: 66 EQLKPYIDDTMLTDVQRETIFSRWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVV 125
Query: 150 QLLKLMDSPLALTSANESNEPSTLCINEFQKLWSQLS---VVIDGGI--ISNPERFGSTI 204
L + PL TSAN S P ++ +Q V+ G NP S I
Sbjct: 126 ALCQAYGKPLVSTSANLSGLPP---CRTVDEVRAQFGAAFPVVPGETGGRLNP----SEI 178
Query: 205 VDLSEENV 212
D +
Sbjct: 179 RDALTGEL 186
>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5
domain, structural genomics, NPPSFA; HET: AMP; 1.80A
{Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A*
Length = 352
Score = 131 bits (333), Expect = 6e-37
Identities = 61/207 (29%), Positives = 104/207 (50%), Gaps = 21/207 (10%)
Query: 25 MCSIVKVT----DPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRD 80
M I+K+ + +AA ++ G VA PT+T+YGL +A + A +++ K R
Sbjct: 1 MTQIIKIDPLNPEIDKIKIAADVIRNGGTVAFPTETVYGLGANAFDGNACLKIFQAKNRP 60
Query: 81 VNKPLAICVSEITDIPKWADTHTVSFELLAELL-PGPVTIVFNRSEHLNLELNPNVT--- 136
V+ PL + +++ + + A +A+++ PGP+T V ++E + VT
Sbjct: 61 VDNPLIVHIADFNQLFEVAKDIPDKVLEIAQIVWPGPLTFVLKKTER----VPKEVTAGL 116
Query: 137 -KVAVRIPDHKFLRQLLKLMDSPLALTSANESNEPS-TLCINEFQKLWSQLSVVIDGGII 194
VAVR+P H QL++ P+A SAN + PS T + L ++ V+IDGG
Sbjct: 117 DTVAVRMPAHPIALQLIRESGVPIAAPSANLATRPSPTKAEDVIVDLNGRVDVIIDGG-- 174
Query: 195 SNPERFG--STIVDLSEENVYSIVRKG 219
FG STI++++ E ++R G
Sbjct: 175 --HTFFGVESTIINVTVEPP-VLLRPG 198
>3vth_A Hydrogenase maturation factor; carbamoyltransfer, maturation of
[NIFE]-hydrogenase, carbamoylphosphate, iron, HYPE; HET:
APC AP2; 2.00A {Thermoanaerobacter tengcongensis} PDB:
3vti_A
Length = 761
Score = 121 bits (306), Expect = 1e-31
Identities = 44/213 (20%), Positives = 91/213 (42%), Gaps = 15/213 (7%)
Query: 40 AAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICVSEITDIPKWA 99
A+ LK+G +VA+ + LA +A + +A+ L KKR KP A+ + ++ ++ K+
Sbjct: 208 VAKALKEGKIVAIKGIGGFHLAVNALDDEAVATLRRRKKRY-GKPFAVMMRDVEEVKKYC 266
Query: 100 DTHTVSFELLAELLPGPVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLRQLLKLMDSPL 159
LL P+ ++ + E L + ++ + V +P L++ +D P+
Sbjct: 267 IVSPEEERLLLSQ-RRPIVLLKKKGEKLAKGIADDLDTLGVMLPYAPIHYLLMEEIDFPI 325
Query: 160 ALTSANESNEPSTLCINEFQKLWSQLSVVIDGGIISNPE---RFGSTIVDLSEENVYSIV 216
+TS N S EP + ++ +L + D +++N + R ++ + I
Sbjct: 326 VMTSGNVSEEPI---CKDNEEALEKLKDIADVFLLNNRDIVNRIDDSVTSFNAGAERIIR 382
Query: 217 RKGVCYDKILKILHKYHLV-------EKNTFPI 242
R + + + + KNTF +
Sbjct: 383 RARGYAPQPILLKKEVKASILAVGGFYKNTFCM 415
>3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A
{Streptococcus mutans}
Length = 295
Score = 108 bits (271), Expect = 1e-28
Identities = 34/249 (13%), Positives = 78/249 (31%), Gaps = 45/249 (18%)
Query: 24 KMCSIVKVTDPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNK 83
M + + +G V+ PT Y + ++ K + +E KKR+ NK
Sbjct: 34 SMTKHIHWDGNLSQEGFEIVKGEGGVIVCPTKVGYIIM--TSDKKGLERKFEAKKRNRNK 91
Query: 84 PLAICVSEITDIPKWADTHTVSFELLAELLPGPVTIVF---NRSEHLNLELNPNVTK--- 137
P + + ++ A + + + ++E +
Sbjct: 92 PGVVLCGSMEELRALAQLTPEIDAFYQKHWDEDILLGCILPWKAEAYEKLKAYGDGREEL 151
Query: 138 -----------VAVRIPDHKFLRQLLKLMDSPLALTSANESNEPSTLCINE-FQKLWSQL 185
+ + + +++ + + +SAN S + + + +++ S +
Sbjct: 152 MTDIRGTSCFVIKFGVAGEQIAKEMWEKEGRMVYASSANPSGKGNRGKVEGIGERIESMV 211
Query: 186 SVVIDGGIISNPERFGSTIVDLSEENVYS-------------------------IVRKGV 220
+VI+ + TI E+ V ++RKG+
Sbjct: 212 DLVIEADDYVASIQPDKTIETRYEQGVMVSMVDKDGKLIPQQGADSRSVEPCPVVIRKGL 271
Query: 221 CYDKILKIL 229
DKI+ L
Sbjct: 272 DIDKIMMHL 280
>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide
binding, hydrogenase maturation factor transferase; HET:
ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A*
3ttf_A* 3ttd_A 3tsq_A
Length = 657
Score = 104 bits (262), Expect = 6e-26
Identities = 45/162 (27%), Positives = 68/162 (41%), Gaps = 10/162 (6%)
Query: 30 KVTDPKAALLAAQCLKKGCVVALPTDTLYGLACDATNSKAINILYEIKKRDVNKPLAICV 89
A A LK G +VA+ + LACDA NS A+ L K R KPLA+ +
Sbjct: 107 HAEQEAALQAAIAQLKMGNIVAIKGIGGFHLACDARNSNAVATLRARKHRP-AKPLAVML 165
Query: 90 SEITDIPKWADTHTVSFELLAELLPGPVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLR 149
+P A +LL V + L ++ P + +V V +P +
Sbjct: 166 PVADGLPDAAR------QLLTTPAAPIVLVDKKYVPELCDDIAPGLNEVGVMLPANPLQH 219
Query: 150 QLLKLMDSPLALTSANESNEPSTLCINEFQKLWSQLSVVIDG 191
LL+ + PL +TS N S +P I+ ++ L + DG
Sbjct: 220 LLLQELQCPLVMTSGNLSGKPP--AISN-EQALEDLQGIADG 258
>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 = 41.8 bits (97), Expect = 1e-04
Identities = 35/168 (20%), Positives = 63/168 (37%), Gaps = 50/168 (29%)
Query: 85 LAICVS-EITDIPKWA-DTHTVSFELLAELL-PGPVTIVFNRSEHLNLELNPNVTKVAVR 141
L + D+P+ T+ ++AE + G T ++ +H+N +
Sbjct: 307 LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT--WDNWKHVNCD----------- 353
Query: 142 IPDHKFLRQLLKLMDSPLALTSANESNEPSTLCINEFQKLWSQLSVVIDGGIISNPERFG 201
+L +++S L EP E++K++ +LSV I P
Sbjct: 354 --------KLTTIIESSL------NVLEP-----AEYRKMFDRLSVFPPSAHI--PT--- 389
Query: 202 STIVDLSEENVYSIVRKGVCYDKILKILHKYHLVEKN----TFPIPVL 245
+ + + + S V ++ LHKY LVEK T IP +
Sbjct: 390 ILLSLIWFDVIKSDVMV------VVNKLHKYSLVEKQPKESTISIPSI 431
>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 = 34.3 bits (78), Expect = 0.038
Identities = 44/248 (17%), Positives = 67/248 (27%), Gaps = 109/248 (43%)
Query: 17 NAIALPSKMCSIVKVTDPKAALLAAQC-------------LKKG---CVVALPTDTLYGL 60
N +PS M SI +T + + L G VV+ P +LYGL
Sbjct: 330 NNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGL 389
Query: 61 ACDATNSKAIN------ILYEIKKRDVNKPLAICVSEITDIPKWADTHTVSFELLAELLP 114
+KA + I + +R K S L
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFS--ER---KL------------------KFSNRFL----- 421
Query: 115 GPVTIVFNRSEHL--------------NLELNPNVTKVAVRIP-----DHKFLRQLLKLM 155
PV F+ S L N+ N ++IP D LR L +
Sbjct: 422 -PVASPFH-SHLLVPASDLINKDLVKNNVSFNAK----DIQIPVYDTFDGSDLRVLSGSI 475
Query: 156 DSPLA--LTSANESNEPSTLCINEFQKLWSQLSV-----VIDGGIISNPERFG----STI 204
+ + L + W + ++D FG S +
Sbjct: 476 SERIVDCII---------RLPVK-----WETTTQFKATHILD---------FGPGGASGL 512
Query: 205 VDLSEENV 212
L+ N
Sbjct: 513 GVLTHRNK 520
Score = 32.3 bits (73), Expect = 0.18
Identities = 45/270 (16%), Positives = 83/270 (30%), Gaps = 76/270 (28%)
Query: 9 FTLGLFYHNAIALPSKMCSI-VKVTDPKAALLAAQCLKKGCVVALPTDTLYGLACDATNS 67
TL H ++ + V P A+ A L++ LP T G A D +
Sbjct: 9 LTLS---HGSLE-----HVLLV----PTASFFIASQLQEQFNKILPEPTE-GFAADDEPT 55
Query: 68 KAINIL-----YEIKKRDVNKP------LAICVSEI-TDIPKWADTHTVSFELLAELLPG 115
++ Y + +K L +C++E + D H L A+LL
Sbjct: 56 TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHA----LAAKLLQE 111
Query: 116 PVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLRQLLKLMDSPLALTSANESNEP----- 170
T + E + + RI R K +S L + E N
Sbjct: 112 NDTTLVKTKELIK-------NYITARIMAK---RPFDKKSNSAL-FRAVGEGNAQLVAIF 160
Query: 171 -----STLCINEFQKLWSQLSVVIDGGIISNPERFGSTIVDLSEENVYSIVRKGVCYDKI 225
+ E + L+ + ++ S E + ++R + +K+
Sbjct: 161 GGQGNTDDYFEELRDLYQ----------TYHV--LVGDLIKFSAETLSELIRTTLDAEKV 208
Query: 226 LKILHKYHLVE----KNTFP-------IPV 244
+++E + P IP+
Sbjct: 209 FT--QGLNILEWLENPSNTPDKDYLLSIPI 236
>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 = 31.5 bits (70), Expect = 0.13
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 149 RQLLKLMDSPLALTSANESNEPSTLCIN 176
+Q LK + + L L A++S P+ L I
Sbjct: 19 KQALKKLQASLKLY-ADDS-APA-LAIK 43
>1e8g_A Vanillyl-alcohol oxidase; oxidoreductase, flavoenzyme, specificity;
HET: FAD FCR; 2.1A {Penicillium simplicissimum} SCOP:
d.58.32.1 d.145.1.1 PDB: 1e8f_A* 1e8h_A* 1qlt_A* 1qlu_A*
1vao_A* 1ahv_A* 1ahz_A* 1ahu_A* 2vao_A* 1w1j_A* 1dzn_A*
1w1l_A* 1e0y_A* 1w1k_A* 1w1m_A*
Length = 560
Score = 31.4 bits (71), Expect = 0.30
Identities = 11/58 (18%), Positives = 28/58 (48%)
Query: 186 SVVIDGGIISNPERFGSTIVDLSEENVYSIVRKGVCYDKILKILHKYHLVEKNTFPIP 243
+ + G ++ + + + +++++ E Y +V GV Y + L +L +K +P
Sbjct: 112 APRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVP 169
>2rk3_A Protein DJ-1; parkinson'S disease, THIJ, PFPI, chaperone,
cytoplasm, disease mutation, nucleus, oncogene,
oxidation, parkinson disease; 1.05A {Homo sapiens} PDB:
1pdv_A 1pdw_A 3cy6_A 1pe0_A 3cza_A 3cyf_A 2rk4_A 3cz9_A*
3ezg_A 3f71_A 3sf8_A 1p5f_A 1ps4_A 1q2u_A 1soa_A 1ucf_A
2or3_A 3bwe_A 3b38_A 3b36_A ...
Length = 197
Score = 28.3 bits (64), Expect = 1.8
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 182 WSQLSVVIDGGIIS--NP---ERFGSTIVD-LSEENVYSIVRKGVCYDKILKILHKYH 233
+S+ V DG I++ P F IV+ L+ + V + V+ + + H +H
Sbjct: 141 YSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKDLEHH-HHHH 197
>2we8_A Xanthine dehydrogenase; oxidoreductase; 2.30A {Mycobacterium
smegmatis} PDB: 2we7_A
Length = 386
Score = 28.3 bits (63), Expect = 2.8
Identities = 9/46 (19%), Positives = 11/46 (23%)
Query: 109 LAELLPGPVTIVFNRSEHLNLELNPNVTKVAVRIPDHKFLRQLLKL 154
L VT+ R P +V V P Q
Sbjct: 222 QGAFLGYRVTVCDARPVFATTARFPTADEVVVDWPHRYLAAQAEAG 267
>1ho8_A Vacuolar ATP synthase subunit H; heat repeat, hydrolase; 2.95A
{Saccharomyces cerevisiae} SCOP: a.118.1.9
Length = 480
Score = 27.8 bits (61), Expect = 3.3
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 144 DHKFLRQLLKLMDSPLALTSANESNEPSTLCI 175
++K RQL++L+ + + N E + +
Sbjct: 393 NYKIFRQLIELLQAKVRNGDVNAKQEKIIIQV 424
>4e08_A DJ-1 beta; flavodoxin-like fold, stress response, motor protein;
2.00A {Drosophila melanogaster}
Length = 190
Score = 26.7 bits (60), Expect = 5.8
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 182 WSQLSVVIDGGIIS--NP---ERFGSTIVD-LSEENVYSIVRKGVCYD 223
+VV DG +I+ P F I + L+ + V KG+
Sbjct: 141 VDDKTVVKDGNLITSRGPGTAYEFALKIAEELAGKEKVQEVAKGLLVA 188
>4gdh_A DJ-1, uncharacterized protein C22E12.03C; unknown function,
cysteine oxidation; 1.05A {Schizosaccharomyces pombe}
PDB: 4ge3_A 4ge0_A
Length = 194
Score = 26.0 bits (58), Expect = 9.5
Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 182 WSQLSVVIDGGIIS--NP---ERFGSTIVD-LSEENVYSIVRKGVCY 222
+ VV++ +I+ P FG +++ ++ ++ Y+ V K +
Sbjct: 147 YLDQPVVLEENLITSQGPGTAMLFGLKLLEQVASKDKYNAVYKSLSM 193
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
0.321 0.137 0.406
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,678,748
Number of extensions: 212020
Number of successful extensions: 477
Number of sequences better than 10.0: 1
Number of HSP's gapped: 464
Number of HSP's successfully gapped: 26
Length of query: 245
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,160,982
Effective search space: 640791228
Effective search space used: 640791228
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 (21.9 bits)
S2: 56 (25.2 bits)