RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 016805
(382 letters)
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding
motif, platform for RNA polymer assembly, transferase;
1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D
2waq_D 2wb1_D 2y0s_D
Length = 265
Score = 203 bits (518), Expect = 9e-64
Identities = 85/311 (27%), Positives = 126/311 (40%), Gaps = 56/311 (18%)
Query: 77 RVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHR 136
+ ++ ++ G NA RR + +P MA++ V N S + DE+LAHR
Sbjct: 2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61
Query: 137 LGLIPIIVDPRLFEY-----MSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPN 191
L LIP + + L Y E + EK + + + ++K
Sbjct: 62 LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAPNEP--RMIYSKDIKSEDP 119
Query: 192 GSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEA 251
S PI DI I LG Q+I LEA
Sbjct: 120 ----------------------------------SVVPISG--DIPIVLLGTNQKISLEA 143
Query: 252 HAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311
G GK HAK+ PV+ + R P++ +L + EK V CP VF+++D
Sbjct: 144 RLRLGYGKEHAKFIPVSLSVVRYYPKVEILAN-----CEKAVNVCPEGVFELKD-----G 193
Query: 312 RATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILE 371
+ +V +CTLC ECLR + I V+D +I IES G+L PE + EA K +
Sbjct: 194 KLSVKNELSCTLCEECLR---YCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSII 250
Query: 372 DKCERVITELS 382
K E + +L
Sbjct: 251 RKIEELEKKLV 261
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 297
Score = 193 bits (492), Expect = 1e-59
Identities = 69/317 (21%), Positives = 117/317 (36%), Gaps = 63/317 (19%)
Query: 74 NNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVL 133
+ + + ++K+ ++F L A+AN+ RR+++AE+PT+AI+ V I NTSV+ DE L
Sbjct: 3 SETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFL 62
Query: 134 AHRLGLIPIIVDPRLFEYMS--------ENDTSNEKNTIVFKLHVLCERGGPRLTVKTNE 185
AHRLG+IP+ + D K ++ L+ C G + +
Sbjct: 63 AHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTM-EIYARD 121
Query: 186 LKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQ 245
L N L +P I +L Q
Sbjct: 122 LVVSSNS---------------------------SLGHPILADPKSR--GPLICKLRKEQ 152
Query: 246 EIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIED 305
EI L A KGI K HAKWSP + + P L + + + D E+
Sbjct: 153 EISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSKNADWEE 212
Query: 306 IGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTE 365
+ + + F +ES G++ P + +
Sbjct: 213 P-------------------------PREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQ 247
Query: 366 AVKILEDKCERVITELS 382
++IL++K ++ +L
Sbjct: 248 GLRILQEKLAVLVRDLD 264
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1
d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C
1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C*
1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C
1y77_C* ...
Length = 318
Score = 185 bits (470), Expect = 5e-56
Identities = 67/311 (21%), Positives = 119/311 (38%), Gaps = 55/311 (17%)
Query: 75 NFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLA 134
+V++ +KD+++F L +D A+AN+ RR++IAE+PT+AI+ V + NT+V+ DE +A
Sbjct: 5 GPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIA 64
Query: 135 HRLGLIPII---VDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPN 191
HRLGLIP+ ++ + + +K ++V L E V + +L + N
Sbjct: 65 HRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTT-NVYSKDLVIVSN 123
Query: 192 GSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEA 251
+ + + I +L GQE++L
Sbjct: 124 LMGRNIGHPIIQDKEGN--------------------------GVLICKLRKGQELKLTC 157
Query: 252 HAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311
A KGI K HAKW P A + P L + + + + E
Sbjct: 158 VAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYE------- 210
Query: 312 RATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILE 371
+ D F +ES G++ + + + L+
Sbjct: 211 ------------------DPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQ 252
Query: 372 DKCERVITELS 382
K ++ L+
Sbjct: 253 KKVASILLALT 263
>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 = 47.2 bits (111), Expect = 8e-06
Identities = 44/320 (13%), Positives = 93/320 (29%), Gaps = 83/320 (25%)
Query: 88 MEFDLIGIDAA---IANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIV 144
M+F+ I + F + ++ + S++ E + H II+
Sbjct: 7 MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMP----KSILSKEEIDH------IIM 56
Query: 145 DPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNEL-----KWLPNGSELPLET 199
+ + + L + + E+ K+L + P++T
Sbjct: 57 SK------------DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMS----PIKT 100
Query: 200 KPDSNPSSKPRTYTS-----FSSSQDLLPEFSNNPIRPMLDITIA--RLGPGQEIELEAH 252
+ PS R Y ++ +Q + +P L + A L P + + +
Sbjct: 101 EQRQ-PSMMTRMYIEQRDRLYNDNQVFAKYNVSRL-QPYLKLRQALLELRPAKNVLI--D 156
Query: 253 AVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKR 312
V G GKT + DV K+ +F + ++ +
Sbjct: 157 GVLGSGKT------------------WVALDVCLS--YKVQCKMDFKIFWL-NLKNCNSP 195
Query: 313 ATVAQPRACTLCRECLRCGEEWEKRVSI-RRVKDHFIFTIESTGALSPETLFTEAVKILE 371
TV + L + + W R +K L + + +L
Sbjct: 196 ETVLEM----LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251
Query: 372 D------------KCERVIT 379
+ C+ ++T
Sbjct: 252 NVQNAKAWNAFNLSCKILLT 271
Score = 37.1 bits (85), Expect = 0.009
Identities = 70/460 (15%), Positives = 121/460 (26%), Gaps = 136/460 (29%)
Query: 8 EKKKEAESFSI-W----------DLPDVPQKLPPHIE---FQRTRVQCNLDAPIHTENVM 53
K + F I W + ++ QKL I+ R+ N+ IH+
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 54 YSGAYASMGVDNSLQ-LDHFCN-------NFRVEVIRLTKDDMEFDLIGIDAAIANAFRR 105
S +N L L + N N +++ T+ D + A
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA----ATTTHI 289
Query: 106 ILIAELPTMAIEKV--LIANNTSV-IQD---EVLAH---RLGLIP--IIVDPRLFEYMSE 154
L T+ ++V L+ QD EVL RL +I I ++
Sbjct: 290 SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH 349
Query: 155 NDTSNEKNTI--------------------VFKLHVLCERGGPRLTVKTNELKWLPNGSE 194
+ I VF + L W
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA-------HIPTILLSLIWFDVIKS 402
Query: 195 LP------LETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPI--RPMLD-ITIARLGPGQ 245
L K T + S +L + N R ++D I +
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 246 EIELE----------AHAVKGIGKTHAKWSPVATAWYRMLPEIVL----LEDVEDEDAEK 291
++ H +K I + + + + L LE +K
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPE-RMT--------LFRMVFLDFRFLE-------QK 506
Query: 292 LVKT-----CPVNVFD-IEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKD 345
+ ++ + ++ + K P ++E R V
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDNDP--------------KYE-----RLVNA 547
Query: 346 --HFIFTIESTGALSPET------LFTEAVKILEDKCERV 377
F+ IE S T L E I E+ ++V
Sbjct: 548 ILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
>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 = 43.5 bits (102), Expect = 1e-04
Identities = 71/413 (17%), Positives = 129/413 (31%), Gaps = 129/413 (31%)
Query: 18 IWDLPDVPQKLPPHIEFQRTRVQCN----LDAPIHTENVMY-SGAYASM---GVDNSLQL 69
+ +L F + N L+ P +T + Y S GV +QL
Sbjct: 195 LSELIRTTLDAEKV--FTQG---LNILEWLENPSNTPDKDYLLSIPISCPLIGV---IQL 246
Query: 70 DHFCNNFRVEVIRLTKDDMEFD----LIGIDAAIANAFRRILIAELPTMAIEKVLIANNT 125
H+ ++ + T ++ G + A + IAE + + +
Sbjct: 247 AHYVVTAKL--LGFTPGEL-RSYLKGATGHSQGLVTA---VAIAETDS---WESFFVSVR 297
Query: 126 SVIQDEVLAHRLGL-----IPII-VDPRLFEYMSENDTSNEKN-TIVFKLHVLCERGGPR 178
I VL +G+ P + P + E EN NE + +L +
Sbjct: 298 KAI--TVLFF-IGVRCYEAYPNTSLPPSILEDSLEN---NEGVPS-----PMLSISNLTQ 346
Query: 179 LTV-----KTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPM 233
V KTN LP G ++ S L+ N + +
Sbjct: 347 EQVQDYVNKTN--SHLPAGKQV------------------EIS----LV----NGA-KNL 377
Query: 234 LDITIARLGP-----GQEIELE-AHAVKGIGKTHAKWS---PVATAWYRMLPEI------ 278
+ ++ GP G + L A A G+ ++ +S + R LP +
Sbjct: 378 V-VS----GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFS--NRFLP-VASPFHS 429
Query: 279 --------VLLEDVEDEDAEKLVKTCPVNVFDIEDIGSG--KKRATVAQPRAC-TLCREC 327
++ +D+ + K + V+D D GS +++ R + R
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFD-GSDLRVLSGSIS-ERIVDCIIRLP 487
Query: 328 LRCGEEWEKRVSIRRVKDHFI-FTIESTGALSPETLFTEAVKILEDKCERVIT 379
++ WE + H + F G S + T + + RVI
Sbjct: 488 VK----WETTTQFK--ATHILDF---GPGGASGLGVLTH--RNKDGTGVRVIV 529
>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A
{Desulfovibrio gigas}
Length = 166
Score = 32.1 bits (72), Expect = 0.18
Identities = 8/35 (22%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCREC 327
+ CP ++ ++ + +A +P AC C C
Sbjct: 21 MYICPNDLMILDP---EEMKAFNQEPEACWECYSC 52
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 32.9 bits (75), Expect = 0.19
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 268 ATAWYRMLPEIVLLEDVE-----DEDAEKLVKTCPVNVFDIEDIG-------SGKKRATV 315
M+ E+++ ED+E E AE+ V DI +I K AT+
Sbjct: 916 NPEKKEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKV-DIFEIPETGEYSVKLLKGATL 974
Query: 316 AQPRA 320
P+A
Sbjct: 975 YIPKA 979
>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A
{Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB:
1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B*
Length = 150
Score = 31.6 bits (71), Expect = 0.22
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329
CP ++ ++ K +A +P C C C++
Sbjct: 22 EYICPNDLMTLDK---EKMKAYNREPDMCWECYSCVK 55
>1jb0_C Photosystem I iron-sulfur center; membrane protein,
multiprotein-pigment complex, photosynthes; HET: CL1 PQN
BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP:
d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C*
3lw5_C* 2o01_C*
Length = 80
Score = 29.0 bits (65), Expect = 0.56
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 293 VKTCPVNVFDI--EDIGSGKKRATVAQPRACTLCREC 327
V+ CP +V ++ D + A+ + C C+ C
Sbjct: 17 VRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRC 53
>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A
{Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A
Length = 103
Score = 29.1 bits (65), Expect = 0.70
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 293 VKTCPVNVF---DIEDIGSGKKRATVAQPRACTLCREC 327
+ CPVNVF D + +K+A +AC C C
Sbjct: 52 INACPVNVFQWYDTPGHPASEKKADPVNEQACIFCMAC 89
>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 = 29.5 bits (65), Expect = 1.1
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 182 KTNELKWLPNGSELPLETKPDSNPS 206
+ LK L + L L DS P+
Sbjct: 18 EKQALKKLQ--ASLKL-YADDSAPA 39
>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix
motif, interacting with DNAA-BOX, DNAA-box; HET: DNA;
2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A*
Length = 101
Score = 26.1 bits (58), Expect = 7.7
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 303 IEDIGSGKKRATVAQPR--ACTLCRE 326
+E++ K +AQ R A LCRE
Sbjct: 22 VEELRGPGKTRALAQSRQIAMYLCRE 47
>3aqp_A Probable secdf protein-export membrane protein; translocon, cell
membrane, MEM protein transport, translocation,
transmembrane, transport; 3.30A {Thermus thermophilus}
PDB: 2rrn_A
Length = 741
Score = 27.4 bits (61), Expect = 8.8
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 95 IDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLI 140
++ +I R ++ L T+ L+ SV++D LA +G+
Sbjct: 661 VNRSINQTLSRTVMTSLTTLLPILALLFLGGSVLRDFALAIFVGIF 706
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
0.318 0.134 0.397
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,933,089
Number of extensions: 365777
Number of successful extensions: 859
Number of sequences better than 10.0: 1
Number of HSP's gapped: 849
Number of HSP's successfully gapped: 25
Length of query: 382
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 287
Effective length of database: 4,049,298
Effective search space: 1162148526
Effective search space used: 1162148526
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 (21.7 bits)
S2: 58 (26.0 bits)