RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5332
(287 letters)
>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 = 174 bits (440), Expect = 9e-53
Identities = 89/226 (39%), Positives = 137/226 (60%), Gaps = 10/226 (4%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
+AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV TL
Sbjct: 44 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 102
Query: 61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
+ T +V + DL + RN + + E + +LI KLRKGQEL+L
Sbjct: 103 AFGESESTTNVYSKDLVIVS----NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 158
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELD-ETQHEAP 175
AKKG KEHAKW P A + FEYDP N ++HT + EWP+S+ E + P
Sbjct: 159 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 218
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
++++A+ + ++ NVES G++ + +V+ G+ L++K++++ L
Sbjct: 219 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQ 264
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 297
Score = 166 bits (421), Expect = 3e-50
Identities = 84/231 (36%), Positives = 134/231 (58%), Gaps = 16/231 (6%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRIL----YSRDCTCVDFCSECSVE 56
+AID V++ N++V+ DEF+A R+G+IPL S + + Y+R+C C +C +CSVE
Sbjct: 43 VAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVE 102
Query: 57 FTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELR 116
L+ KC + T + DL + + ++ LI KLRK QE+
Sbjct: 103 LFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADP-------KSRGPLICKLRKEQEIS 155
Query: 117 LRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDETQH 172
LR AKKG KEHAKW+PT+ V FEYDP N ++HT + EWPKS+ ++ +E
Sbjct: 156 LRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSKNADWEEPPR 215
Query: 173 E-APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222
E P+N++ +P +++ +VES G++ P I++ G+ +L++KL+ L L +
Sbjct: 216 EGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDEE 266
>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 = 159 bits (402), Expect = 1e-47
Identities = 61/239 (25%), Positives = 103/239 (43%), Gaps = 33/239 (13%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTL 59
MA+D V N++ L DE +A R+ LIP S+E +D + +C C + C +C + +
Sbjct: 39 MAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYI 98
Query: 60 DVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRA 119
+ + ++ R + + D+KS D VVP++ DI IV L Q++ L A
Sbjct: 99 EAEA-PNEPRMIYSKDIKSEDPSVVPIS--------------GDIPIVLLGTNQKISLEA 143
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDET--------- 170
+ G+GKEHAK+ P + Y P + + P+ + D
Sbjct: 144 RLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSC 203
Query: 171 --------QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
+KY +ES G+LKPE I++ + +K+ L+ +L
Sbjct: 204 TLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVE 262
>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 = 59.9 bits (144), Expect = 3e-10
Identities = 47/297 (15%), Positives = 89/297 (29%), Gaps = 83/297 (27%)
Query: 5 WVQLEANSTVLSDEFIASRIGLIPLTSDEVVD---RILYSRD-CTCV----DFCSECSVE 56
Q++ N T SD I L + R+L S+ C+ + + +
Sbjct: 206 LYQIDPNWTSRSDHSSN-----IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260
Query: 57 FTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYG----ETDDILIVKLR-K 111
++ C + +TT + TD + T+ + D + E +L+ L +
Sbjct: 261 -AFNLSC---KIL-LTTRFKQVTDF-LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 112 GQELRLRA-----YAKKGFG---KEH-AKWNP-----------TAGVCFEY-DPDNSMRH 150
Q+L ++ A W+ +P R
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAE-YRK 373
Query: 151 -----TLFPK----PDE-----WPKSEYSELDETQHEAPYNWEAKPNKYFFNVES--AGA 194
++FP P W S++ ++ + S
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK-------------LHKYSLVEKQ 420
Query: 195 LKPENIVIMGVTV-LKQKLSNLQTQLAHDRV--FYVINEAPYNWEAKPN---KYFFN 245
K I I + + LK KL N H + Y I + + + P +YF++
Sbjct: 421 PKESTISIPSIYLELKVKLENEYA--LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYS 475
Score = 41.4 bits (96), Expect = 3e-04
Identities = 42/252 (16%), Positives = 72/252 (28%), Gaps = 69/252 (27%)
Query: 28 PLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQT----RHVTTADLKSTDARV 83
+ S E +D I+ S+D + Q + V + +
Sbjct: 44 SILSKEEIDHIIMSKD-------AVSGTLRLFWTLL-SKQEEMVQKFVEEVLRINYKFLM 95
Query: 84 VPVTSRNRDADMN--EYGETDDIL-----------------IVKLRKG-QELR----LRA 119
P+ + R M Y E D L +KLR+ ELR +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEW--------PKSEYSELDETQ 171
G G K VC Y M +F W P++ L +
Sbjct: 156 DGVLGSG----KTWVALDVCLSYKVQCKMDFKIF-----WLNLKNCNSPETVLEMLQKLL 206
Query: 172 HEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEA 231
++ NW ++ + NI + + ++ +L L ++ V+
Sbjct: 207 YQIDPNWTSRSD------------HSSNI-KLRIHSIQAELRRLLKSKPYENCLLVLLNV 253
Query: 232 PYNWEAKPNKYF 243
AK F
Sbjct: 254 ---QNAKAWNAF 262
Score = 37.5 bits (86), Expect = 0.005
Identities = 38/243 (15%), Positives = 64/243 (26%), Gaps = 81/243 (33%)
Query: 59 LDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLR 118
D K V D + + + + E D I++ K LRL
Sbjct: 33 FDCKDVQDMPKSILSKE------------------------EIDHIIMSKDAVSGTLRL- 67
Query: 119 AYAKKGFGKEHAKWNPTAGVCFE--YDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPY 176
F +K E + + P Q + Y
Sbjct: 68 ------FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY-IEQRDRLY 120
Query: 177 NWEAKPNKYFFNV----------ESAGALKPENIVI---M---GVTVL-KQKLSNLQTQL 219
N KY NV ++ L+P V+ + G T + + + Q
Sbjct: 121 NDNQVFAKY--NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178
Query: 220 AHD-RVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 278
D ++F+ +N N PE ++ M L L Q+
Sbjct: 179 KMDFKIFW-LNLKNCN------------------SPETVLEM--------LQKLLYQIDP 211
Query: 279 ELS 281
+
Sbjct: 212 NWT 214
>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 = 35.8 bits (82), Expect = 0.016
Identities = 44/292 (15%), Positives = 81/292 (27%), Gaps = 100/292 (34%)
Query: 13 TVLSDEFIASRIGLIPLTSDEVV--DRI-----LYSRDCTCVDFCSECSVEFTLDVKCVD 65
+ L ++F +P ++ D L + F L
Sbjct: 31 SQLQEQFNKI----LPEPTEGFAADDEPTTPAELVGK--------------F-LG----- 66
Query: 66 DQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDI--LIVKLRKGQELR------- 116
+V++ S + V + N Y E +DI L KL + +
Sbjct: 67 ----YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 117 LRAY--AKKGFGKEHAKWNPTAGVCFEYDPDNSMR-HTLFP---KPDEWPKSEYSELDET 170
++ Y A+ + K + +A F + + + +F D++ + EL +
Sbjct: 123 IKNYITARIMAKRPFDKKSNSA--LFRAVGEGNAQLVAIFGGQGNTDDY----FEELRDL 176
Query: 171 QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINE 230
Y Y V + + LS L +
Sbjct: 177 -----YQ------TYHVLVGDL------------IKFSAETLSELIRTTLDAEKVFTQGL 213
Query: 231 APYNW----EAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 278
W P+K + S P + ++GV QLAH
Sbjct: 214 NILEWLENPSNTPDKDYLL--SI----PISCPLIGVI-----------QLAH 248
Score = 33.1 bits (75), Expect = 0.12
Identities = 44/235 (18%), Positives = 68/235 (28%), Gaps = 118/235 (50%)
Query: 75 DL--KSTDARVVPVTSRNRDAD---MNEYGETDDIL-IVK-----------LRKGQELRL 117
DL S A+ V NR AD + YG + IL IV KG+ +R
Sbjct: 1634 DLYKTSKAAQDV----WNR-ADNHFKDTYGFS--ILDIVINNPVNLTIHFGGEKGKRIRE 1686
Query: 118 RAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHT-LFPKPDEWPKSEYSELDETQHEAPY 176
Y+ + FE D ++ +F E++E H Y
Sbjct: 1687 N-YSA---------------MIFETIVDGKLKTEKIFK-----------EINE--HSTSY 1717
Query: 177 NWEAKPNKYFFNVESAGAL-KPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNW 235
+ + G L + TQ A + ++ +A +
Sbjct: 1718 TFRS----------EKGLLSATQF-----------------TQPA---LT-LMEKAA--F 1744
Query: 236 EAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH---ELSHDALAC 287
E ++S G L P + G H E + ALA
Sbjct: 1745 ED--------LKSKG-LIPADATFAG----------------HSLGEYA--ALAS 1772
>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 = 32.6 bits (73), Expect = 0.069
Identities = 9/24 (37%), Positives = 10/24 (41%), Gaps = 4/24 (16%)
Query: 209 KQKLSNLQTQLAHDRVFYVINEAP 232
KQ L LQ L Y + AP
Sbjct: 19 KQALKKLQASLK----LYADDSAP 38
Score = 29.9 bits (66), Expect = 0.59
Identities = 11/24 (45%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 266 KQKLSNLQTQL---AHELSHDALA 286
KQ L LQ L A + S ALA
Sbjct: 19 KQALKKLQASLKLYADD-SAPALA 41
>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium,
protein STRU initiative, PSI, structural genomics, DNA
synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum}
SCOP: c.37.1.24 g.39.1.14
Length = 191
Score = 28.7 bits (65), Expect = 1.4
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 12/75 (16%)
Query: 16 SDEFIASRIGL----IPLTS-DEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCVDDQ 67
S E + S +G + + + E++ + +D F + VE V + +
Sbjct: 51 SKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEIVEI---VNKIAES 107
Query: 68 TRHVTTADLKSTDAR 82
R V A L D R
Sbjct: 108 GRRVICAGLD-MDFR 121
>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis,
nucleotide-B transferase; HET: MSE; 2.01A
{Staphylococcus aureus}
Length = 219
Score = 27.7 bits (62), Expect = 4.2
Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 12/75 (16%)
Query: 16 SDEFIASRIGL----IPLTS-DEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCVDDQ 67
E + S G I ++ E++ L + D +D F + V V+ +
Sbjct: 71 HKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVIGIDEVQFFDDEIVSI---VEKLSAD 127
Query: 68 TRHVTTADLKSTDAR 82
V A L D R
Sbjct: 128 GHRVIVAGLD-MDFR 141
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas;
INPP5BA,phosphoinositide 5-phosphatase, inositol
signalling, phosphatase, magnesium; HET: PIF; 2.40A
{Homo sapiens} PDB: 3n9v_A
Length = 313
Score = 27.1 bits (60), Expect = 7.6
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 11/46 (23%)
Query: 36 DRILY-SRDCTCVDFCSECSV----------EFTLDVKCVDDQTRH 70
DRIL+ ++ T + + S ++ F + V+ V H
Sbjct: 267 DRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVAHHHHH 312
>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling
protein; 2.85A {Arabidopsis thaliana}
Length = 338
Score = 26.9 bits (59), Expect = 8.0
Identities = 12/87 (13%), Positives = 25/87 (28%), Gaps = 5/87 (5%)
Query: 103 DILIVKLRKGQELRLRAYAKKGFGKEHAKWN----PTAGVCFEYDPDNSMRHTLFPKPDE 158
I + ++ G+ + + +GKE P A + +E + +
Sbjct: 110 AIGVASMKSGERALVHVGWELAYGKEGNFSFPNVPPMADLLYEVEVIGFDETKEGKARSD 169
Query: 159 WPKSEYSELDETQHEAPYNWEAKPNKY 185
E + + N K K
Sbjct: 170 MTVEERIGAADRRKMDG-NSLFKEEKL 195
>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding,
deoxyribonucleoside kinase, DNA synthesis, phosphate
accept nucleotide-binding; HET: THM; 2.7A {Bacillus
anthracis} PDB: 2ja1_A*
Length = 214
Score = 26.5 bits (59), Expect = 9.3
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 16 SDEFIASRIGL----IPLTS-DEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCVDDQ 67
S+E + S GL +P+++ ++ I D +D F VE V+ + ++
Sbjct: 71 SEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAIDEVQFFDGDIVEV---VQVLANR 127
Query: 68 TRHVTTADLKSTDAR 82
V A L D R
Sbjct: 128 GYRVIVAGLD-QDFR 141
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
0.317 0.132 0.398
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,385,003
Number of extensions: 255206
Number of successful extensions: 675
Number of sequences better than 10.0: 1
Number of HSP's gapped: 661
Number of HSP's successfully gapped: 23
Length of query: 287
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 194
Effective length of database: 4,105,140
Effective search space: 796397160
Effective search space used: 796397160
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: 57 (25.9 bits)