RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 044091
(275 letters)
>3qas_B Undecaprenyl pyrophosphate synthase; alpha-helix, isoprenoid
biosynthesis, transferase; 1.70A {Escherichia coli} PDB:
1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A*
2e9c_A* 2e9d_A* 1ueh_A 1x09_A* 1x08_A*
Length = 253
Score = 258 bits (663), Expect = 5e-87
Identities = 74/198 (37%), Positives = 111/198 (56%), Gaps = 3/198 (1%)
Query: 78 FTSDAPALAEELQRESMPRHVAVIMDGNRRWAHLRGLPVGSGYEAGVKSLKTLVELCCKW 137
S L+E+L RHVA+IMDGN RWA +G G++AG KS++ V
Sbjct: 2 MLSATQPLSEKLP-AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANN 60
Query: 138 GIRVLTVFAFSSDNWFRPEVEVEFLMSLLESGVKEEKESFIRERIRISVIGDTSKLPKCL 197
GI LT++AFSS+NW RP EV LM L + E +S R +R+ +IGDTS+ L
Sbjct: 61 GIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRL 120
Query: 198 EELVINVVETTKNNTRFQLIVAVSYSGQYDLVQACQRIAMKVKDGLIEPNDVSESLIEQE 257
+E + T NT L +A +Y G++D+VQ +++A KV+ G ++P+ + E ++ Q
Sbjct: 121 QERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQH 180
Query: 258 LETNCTEFPYPDLLIRTS 275
+ + E DL+IRT
Sbjct: 181 VCMH--ELAPVDLVIRTG 196
>1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW
fold for isoprenoid synthase, peptidoglycan synthesis,
transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1
Length = 249
Score = 255 bits (654), Expect = 8e-86
Identities = 63/199 (31%), Positives = 108/199 (54%), Gaps = 2/199 (1%)
Query: 77 KFTSDAPALAEELQRESMPRHVAVIMDGNRRWAHLRGLPVGSGYEAGVKSLKTLVELCCK 136
+ +P+H+A+IMDGN RWA + +P G+ G+++++ +
Sbjct: 3 PIKKRKAIKNNNINAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASD 62
Query: 137 WGIRVLTVFAFSSDNWFRPEVEVEFLMSLLESGVKEEKESFIRERIRISVIGDTSKLPKC 196
G++ LT++AFS++NW RP+ EV +LM L + I + +++ IG LP
Sbjct: 63 LGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDH 122
Query: 197 LEELVINVVETTKNNTRFQLIVAVSYSGQYDLVQACQRIAMKVKDGLIEPNDVSESLIEQ 256
++ V+ E TK+NT L+ A++Y G+ +++ A Q IA + K G I +++SE+ +
Sbjct: 123 TKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNE 182
Query: 257 ELETNCTEFPYPDLLIRTS 275
L T P P+LLIRTS
Sbjct: 183 YLFTA--NMPDPELLIRTS 199
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 247 bits (633), Expect = 4e-82
Identities = 60/194 (30%), Positives = 104/194 (53%), Gaps = 2/194 (1%)
Query: 82 APALAEELQRESMPRHVAVIMDGNRRWAHLRGLPVGSGYEAGVKSLKTLVELCCKWGIRV 141
+ A A + + +P HVA++MDGN RWA RGL G++ G + + + GI+
Sbjct: 43 SKAAAPRIPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKW 102
Query: 142 LTVFAFSSDNWFRPEVEVEFLMSLLESGVKEEKESFIRERIRISVIGDTSKLPKCLEELV 201
L+++AFS++NW R EV FLM V+ +++ + +RI +G +L + + +
Sbjct: 103 LSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINEL 162
Query: 202 INVVETTKNNTRFQLIVAVSYSGQYDLVQACQRIAMKVKDGLIEPNDVSESLIEQELETN 261
E TK+N + V+Y G+ ++ +A + IA +V G + P ++ES I + L+
Sbjct: 163 AVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRP 222
Query: 262 CTEFPYPDLLIRTS 275
+ P DL +RTS
Sbjct: 223 --DIPDVDLFLRTS 234
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 240 bits (615), Expect = 6e-80
Identities = 62/196 (31%), Positives = 107/196 (54%), Gaps = 5/196 (2%)
Query: 80 SDAPALAEELQRESMPRHVAVIMDGNRRWAHLRGLPVGSGYEAGVKSLKTLVELCCKWGI 139
S L+E+L +H+A+IMDGN RWA L+ G++ GVK+LK + C +
Sbjct: 3 SATQPLSEKLDS--TLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKL 60
Query: 140 RVLTVFAFSSDNWFRPEVEVEFLMSLLESGVKEEKESFIRERIRISVIGDTSKLPKCLEE 199
LT++AFS++NW RP+ EV+FLM +L+ +K+E+ +++ IR IGD K L +
Sbjct: 61 ECLTLYAFSTENWKRPKSEVDFLMKMLKKYLKDERSTYLDNNIRFRAIGDLEGFSKELRD 120
Query: 200 LVINVVETTKNNTRFQLIVAVSYSGQYDLVQACQRIAMKVKDGLIEPNDVSESLIEQELE 259
++ + T++ F ++A++Y + +L +A + + + + E+ I L+
Sbjct: 121 TILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPSNISLL-ESLENEISNRLD 179
Query: 260 TNCTEFPYPDLLIRTS 275
T P DLL+RT
Sbjct: 180 TR--NLPEVDLLLRTG 193
>2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan
synthesis, cell WALL biogenesis/degradation, secreted,
cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis}
PDB: 2vfw_A* 2vg1_A*
Length = 227
Score = 231 bits (592), Expect = 1e-76
Identities = 55/187 (29%), Positives = 88/187 (47%), Gaps = 9/187 (4%)
Query: 94 MPRHVAVIMDGNRRWAHLRGLP-VGSGYEAGVKSLKTLVELCCKWGIRVLTVFAFSSDNW 152
+PRH+AV+ DGNRRWA G V GY G + ++ C + GI + TV+ S++N
Sbjct: 2 LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENL 61
Query: 153 FRPEVEVEFLMSLLESGVKEEKESFIRERIRISVIGDTSKLPKCLEELVINVVETTKNNT 212
R E+ L+ ++ V+E + +GD + + + VE+T
Sbjct: 62 QRDPDELAALIEIITDVVEEICAP--ANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVA 119
Query: 213 RFQLIVAVSYSGQYDLVQACQRIAMKVKDGLIEP----NDVSESLIEQELETNCTEFPYP 268
F + VAV Y G+ ++V A + + K + V+ I + L T+ P P
Sbjct: 120 SFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTS--GQPDP 177
Query: 269 DLLIRTS 275
DL+IRTS
Sbjct: 178 DLVIRTS 184
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural
genomics, center for structural GEN infectious diseases;
HET: FFT; 2.46A {Campylobacter jejuni}
Length = 225
Score = 230 bits (590), Expect = 2e-76
Identities = 60/181 (33%), Positives = 104/181 (57%), Gaps = 11/181 (6%)
Query: 95 PRHVAVIMDGNRRWAHLRGLPVGSGYEAGVKSLKTLVELCCKWGIRVLTVFAFSSDNWFR 154
+H+AV+MDGNRRWA +G GY GVK+++ L+E+C + I L++FAFS++NW R
Sbjct: 7 LKHLAVVMDGNRRWARAKGFLAKLGYSQGVKTMQKLMEVCMEENISNLSLFAFSTENWKR 66
Query: 155 PEVEVEFLMSLLESGVKEEKESFIRERIRISVIGDTSKLPKCLEELVINVVETTKNNTRF 214
P+ E++F+ LL+ + E E F + +R+ IGD S+L + E + V E TK+
Sbjct: 67 PKDEIDFIFELLDRCLDEALEKFEKNNVRLRAIGDLSRLEDKVREKITLVEEKTKHCDAL 126
Query: 215 QLIVAVSYSGQYDLVQACQRIAMKVKDGLIEPNDVSESLIEQELETNCTEFPYPDLLIRT 274
+ +A+SY + ++++A +R+ K +++E + Q L+ DL++R
Sbjct: 127 CVNLAISYGARDEIIRAAKRVIEKKL-------ELNEENLTQNLDLP----LDVDLMLRV 175
Query: 275 S 275
Sbjct: 176 G 176
>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 = 48.9 bits (116), Expect = 1e-06
Identities = 39/222 (17%), Positives = 63/222 (28%), Gaps = 80/222 (36%)
Query: 6 SPQLLIKPNTATTLSPIPHVQ--NQRFKLASHVC---------------PSEL--LSIRK 46
SP L I T + +V N V P L L++
Sbjct: 336 SPMLSISNLTQEQV--QDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTL 393
Query: 47 RPGSACAATTQHR-----R------------------YLLFPAEE---EEEEEREVKFTS 80
R A + Q R R L+ PA + ++ + V F
Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLV-PASDLINKDLVKNNVSF-- 450
Query: 81 DAPALA---------EELQRES---MPRHVAVIMDGNRRWA--------HLRGLPVGSGY 120
+A + +L+ S R V I+ +W H+ L G G
Sbjct: 451 NAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHI--LDFGPGG 508
Query: 121 EAGVKSL-KTLVELCCKWGIRVLTVFAFSSDNWFRPEVEVEF 161
+G+ L + G+RV+ P+ + F
Sbjct: 509 ASGLGVLTHRNKDGT---GVRVIVAGTLDI----NPDDDYGF 543
Score = 45.4 bits (107), Expect = 1e-05
Identities = 48/266 (18%), Positives = 83/266 (31%), Gaps = 69/266 (25%)
Query: 25 VQNQRFKLASHVCPSELLSIRKRPGSACAATTQHRRYLLFPA-EEEEEEEREVKFTSDA- 82
V N L H + IR+ + T + +E E F S+
Sbjct: 1665 VINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG 1724
Query: 83 ---------PALA-------EELQRE-SMPRHVAVIMDGNRRWAHLRGLPVGSGYE---- 121
PAL E+L+ + +P A G +G E
Sbjct: 1725 LLSATQFTQPALTLMEKAAFEDLKSKGLIPADATF--------A---GHSLG---EYAAL 1770
Query: 122 ---AGVKSLKTLVELCCKWGIRVLTVFAFSSDNWFRPEVEVEFLMSLLESGVKEEKESFI 178
A V S+++LVE+ G+ A D + M + G
Sbjct: 1771 ASLADVMSIESLVEVVFYRGM--TMQVAVPRD----ELGRSNYGMIAINPG--------- 1815
Query: 179 RERIRISVIGDTSKLPKCLEELVIN---VVETTKNNTRFQLIVAVSYSGQYDLVQACQRI 235
R++ L +E + +VE N Q VA +G + +
Sbjct: 1816 ----RVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVA---AGDLRALDTVTNV 1868
Query: 236 --AMKVKDGLIEPNDVSESLIEQELE 259
+K++ I+ ++ +SL +E+E
Sbjct: 1869 LNFIKLQK--IDIIELQKSLSLEEVE 1892
Score = 40.0 bits (93), Expect = 7e-04
Identities = 35/217 (16%), Positives = 72/217 (33%), Gaps = 80/217 (36%)
Query: 98 VAVIMDGNRRWAHLRGLPVGSGYEAGVKSLKTLVELCCKW-GIRVLTVFAFSSDNWFRPE 156
AV + W + + K++ L + G+R + +S P
Sbjct: 279 TAVAIAETDSWESF--------FVSVRKAITVLF-----FIGVRCYEAYPNTS---LPPS 322
Query: 157 VEVEFL---------MSLLESGVKEEK-ESFIR---------ERIRISVI-GDT----SK 192
+ + L M L S + +E+ + ++ +++ IS++ G S
Sbjct: 323 ILEDSLENNEGVPSPM-LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSG 381
Query: 193 LPKCLEELVINV----VETTKNNTRFQLIVAVSYSGQYDLVQACQRIAMKVKDG------ 242
P+ L L + + + + +R + +S +R K+K
Sbjct: 382 PPQSLYGLNLTLRKAKAPSGLDQSR------IPFS---------ER---KLKFSNRFLPV 423
Query: 243 -------LIEPNDVSESLIEQELETNCTEFPYPDLLI 272
L+ P + LI ++L N F D+ I
Sbjct: 424 ASPFHSHLLVP---ASDLINKDLVKNNVSFNAKDIQI 457
>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 = 33.0 bits (74), Expect = 0.051
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 9/24 (37%)
Query: 72 EEREVK--------FTSD-APALA 86
E++ +K + D APALA
Sbjct: 18 EKQALKKLQASLKLYADDSAPALA 41
>2hqb_A Transcriptional activator of COMK gene; berkeley structure genomics
center target 1957B, structural genomics, PSI; 2.70A
{Bacillus halodurans}
Length = 296
Score = 28.8 bits (65), Expect = 2.1
Identities = 8/56 (14%), Positives = 14/56 (25%), Gaps = 12/56 (21%)
Query: 115 PVGSGYEAGVKSLKTLVELCCKWGIRVLTVFAFSSDNWFRPEVEVEFLMSLLESGV 170
P G+ G K + + W + +E L + V
Sbjct: 139 PEVEGFVDGAKYMN---------ESEAFVRYVGE---WTDADKALELFQELQKEQV 182
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 26.6 bits (58), Expect = 8.3
Identities = 7/43 (16%), Positives = 14/43 (32%), Gaps = 10/43 (23%)
Query: 59 RRYLLFPAE--E--------EEEEEREVKFTSDAPALAEELQR 91
+++L+ E E E E + +EL +
Sbjct: 161 KKFLVIAYEPFENIAIELPPNEILFSENNDMDNNNDGVDELNK 203
>2wbq_A L-arginine beta-hydroxylase; oxidoreductase, non-heme Fe(II)
hydroxylase, cbeta- hydroxylation, L-arginine oxygenase,
NRPS, viomycin; HET: ZZU; 1.10A {Streptomyces vinaceus}
PDB: 2wbp_A* 2wbo_A*
Length = 358
Score = 26.8 bits (58), Expect = 9.1
Identities = 18/84 (21%), Positives = 24/84 (28%), Gaps = 12/84 (14%)
Query: 48 PGSACAATTQHRRYLLFPAEEEEEEE------------REVKFTSDAPALAEELQRESMP 95
P S + L PAE +F DAP +A EL +
Sbjct: 14 PDSVATPVRPWSEFRLTPAEAAAAAALAARCAQRYDETDGPEFLLDAPVIAHELPKRLRT 73
Query: 96 RHVAVIMDGNRRWAHLRGLPVGSG 119
+D +RG PV
Sbjct: 74 FMARARLDAWPHALVVRGNPVDDA 97
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 0.133 0.384
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,140,130
Number of extensions: 245703
Number of successful extensions: 478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 470
Number of HSP's successfully gapped: 18
Length of query: 275
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 183
Effective length of database: 4,133,061
Effective search space: 756350163
Effective search space used: 756350163
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: 56 (25.9 bits)