RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 038167
(292 letters)
>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 = 212 bits (542), Expect = 7e-69
Identities = 61/248 (24%), Positives = 111/248 (44%), Gaps = 23/248 (9%)
Query: 33 IPNHIAFILDGNRRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAELSVKYVSIYAFSIDNF 92
+P HIA + DGNRR+A+ G+R G + +L++C E ++ ++Y S +N
Sbjct: 2 LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENL 61
Query: 93 KRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGVRVCFIGNLGLVSEPIRVTAEKVMRATS 152
+R +E+ L++++ + +E + V +G+LGL+ E + +T
Sbjct: 62 QRDPDELAALIEIITDVVEEICAP-----ANHWSVRTVGDLGLIGEEPARRLRGAVESTP 116
Query: 153 KNTRIVILICLAYSSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKNKEQN 212
+ + + + Y EIV V + K + VT +
Sbjct: 117 EVASFHVNVAVGYGGRREIVDAVRA---LLSKELANGATAEELVDAVTVE---------- 163
Query: 213 TIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSPAALWPEIGLRHLI 272
+ +++Y P+PD++IRTSGE RLS FLLWQS+ ++ A WP +
Sbjct: 164 -----GISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFL 218
Query: 273 WAILNFQR 280
A+ ++
Sbjct: 219 RALRDYSA 226
>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 = 205 bits (524), Expect = 8e-66
Identities = 71/248 (28%), Positives = 120/248 (48%), Gaps = 26/248 (10%)
Query: 33 IPNHIAFILDGNRRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAELSVKYVSIYAFSIDNF 92
IP HIA I+DGN R+AK+ + GH G T+ + +Y ++L VKY+++YAFS +N+
Sbjct: 20 IPKHIAIIMDGNGRWAKQKKMPRI-KGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENW 78
Query: 93 KRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGVRVCFIGNLGLVSEPIRVTAEKVMRATS 152
R ++E+ YLM L +FL L + V+V IG + + + + + T
Sbjct: 79 SRPKDEVNYLMKLP---GDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTK 135
Query: 153 KNTRIVILICLAYSSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKNKEQN 212
NT + ++ L Y +EI+ V+ + ++ + ++++E
Sbjct: 136 HNTGLTLVFALNYGGRKEIISAVQL---IAERYKSGEISL----DEISET---------- 178
Query: 213 TIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSPAALWPEIGLRHLI 272
++++ P+P++LIRTSGE RLSNFL+WQ S WP+ L
Sbjct: 179 -----HFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLA 233
Query: 273 WAILNFQR 280
I +Q
Sbjct: 234 QCISIYQN 241
>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 = 203 bits (519), Expect = 1e-64
Identities = 69/248 (27%), Positives = 112/248 (45%), Gaps = 26/248 (10%)
Query: 33 IPNHIAFILDGNRRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAELSVKYVSIYAFSIDNF 92
+PNH+A ++DGN R+A + LA GH+ G ++ + EL +K++S+YAFS +N+
Sbjct: 55 LPNHVAIVMDGNGRWATQRGLART-EGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENW 113
Query: 93 KRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGVRVCFIGNLGLVSEPIRVTAEKVMRATS 152
KR+ E+R+LM + + R L K GVR+ ++G+ + + T
Sbjct: 114 KRSPEEVRFLMGFN---RDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTK 170
Query: 153 KNTRIVILICLAYSSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKNKEQN 212
N I I C+ Y EI E + ++ P +TE
Sbjct: 171 SNDVITINYCVNYGGRTEITEATRE---IAREVAAGRLNP----ERITES---------- 213
Query: 213 TIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSPAALWPEIGLRHLI 272
+ +H+ P+ D+ +RTSGE R SNF+LWQ++ LWP+ R L
Sbjct: 214 -----TIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLW 268
Query: 273 WAILNFQR 280
A +
Sbjct: 269 AACEEYAS 276
>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 = 201 bits (513), Expect = 4e-64
Identities = 69/248 (27%), Positives = 115/248 (46%), Gaps = 26/248 (10%)
Query: 33 IPNHIAFILDGNRRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAELSVKYVSIYAFSIDNF 92
H+A I+DGN R+AKK GH+AG ++ + + A ++ +++YAFS +N+
Sbjct: 17 GCRHVAIIMDGNGRWAKKQGKIR-AFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENW 75
Query: 93 KRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGVRVCFIGNLGLVSEPIRVTAEKVMRATS 152
R E+ LM+L + L E L ++ VR+ IG+ + ++ K T+
Sbjct: 76 NRPAQEVSALMELF---VWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTA 132
Query: 153 KNTRIVILICLAYSSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKNKEQN 212
NT + + I Y +IV V + + +K Q +P + + E+
Sbjct: 133 GNTGLTLNIAANYGGRWDIVQGVRQ---LAEKVQQGNLQP----DQIDEEM--------- 176
Query: 213 TIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSPAALWPEIGLRHLI 272
L +H+ M D++IRT GE+R+SNFLLWQ + LY LWP+ +
Sbjct: 177 ------LNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFE 230
Query: 273 WAILNFQR 280
A+ F
Sbjct: 231 GALNAFAN 238
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 200 bits (510), Expect = 8e-64
Identities = 71/248 (28%), Positives = 116/248 (46%), Gaps = 27/248 (10%)
Query: 33 IPNHIAFILDGNRRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAELSVKYVSIYAFSIDNF 92
H+A I+DGN R+AK N A GH+ G TL + +CA ++ +++YAFS +N+
Sbjct: 15 TLKHLAIIMDGNGRWAKLKNKARA-YGHKKGVKTLKDITIWCANHKLECLTLYAFSTENW 73
Query: 93 KRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGVRVCFIGNLGLVSEPIRVTAEKVMRATS 152
KR ++E+ +LM ++ ++L E +R IG+L S+ +R T ++ T
Sbjct: 74 KRPKSEVDFLMKML---KKYLKDERSTYLDNNIRFRAIGDLEGFSKELRDTILQLENDTR 130
Query: 153 KNTRIVILICLAYSSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKNKEQN 212
++ L Y S E+ +AFK + E + + ++
Sbjct: 131 HFKDFTQVLALNYGSKNELS---------------RAFK------SLLESPPSNISLLES 169
Query: 213 TIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSPAALWPEIGLRHLI 272
+ + P D+L+RT GE RLSNFLLWQSS L+ LWP+ + L
Sbjct: 170 LENE--ISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLE 227
Query: 273 WAILNFQR 280
I +F +
Sbjct: 228 NIISDFYK 235
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural
genomics, center for structural GEN infectious diseases;
HET: FFT; 2.46A {Campylobacter jejuni}
Length = 225
Score = 197 bits (503), Expect = 5e-63
Identities = 59/248 (23%), Positives = 114/248 (45%), Gaps = 35/248 (14%)
Query: 33 IPNHIAFILDGNRRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAELSVKYVSIYAFSIDNF 92
H+A ++DGNRR+A+ + G+ G T+ L++ C E ++ +S++AFS +N+
Sbjct: 6 ELKHLAVVMDGNRRWARAKGFLAK-LGYSQGVKTMQKLMEVCMEENISNLSLFAFSTENW 64
Query: 93 KRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGVRVCFIGNLGLVSEPIRVTAEKVMRATS 152
KR ++EI ++ +L+ L K VR+ IG+L + + +R V T
Sbjct: 65 KRPKDEIDFIFELL---DRCLDEALEKFEKNNVRLRAIGDLSRLEDKVREKITLVEEKTK 121
Query: 153 KNTRIVILICLAYSSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKNKEQN 212
+ + + ++Y + +EI+ + ++ KK ++ E+
Sbjct: 122 HCDALCVNLAISYGARDEIIRAAKR--VIEKK------------LELNEE---------- 157
Query: 213 TIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSPAALWPEIGLRHLI 272
+L +++ + + D+++R RLSNFLLWQ S +Y L+P + R
Sbjct: 158 -----NLTQNLDL--PLDVDLMLRVGNAKRLSNFLLWQCSYAEIYFSETLFPSLTKREFK 210
Query: 273 WAILNFQR 280
I F+
Sbjct: 211 RIIKEFRN 218
>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 = 35.0 bits (80), Expect = 0.035
Identities = 16/109 (14%), Positives = 38/109 (34%), Gaps = 26/109 (23%)
Query: 11 KLCRKLGVFMRKCV----FGILSVGVI---PNHIAFILDGN------RRFAKK------- 50
++ G+ M+ V G + G+I P +A R K+
Sbjct: 1784 EVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEI 1843
Query: 51 --HNLAGE---GAGHRAGFLTLMSLLKYCAELSVKYVSI-YAFSIDNFK 93
+N+ + AG T+ ++L + + + + + S++ +
Sbjct: 1844 VNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVE 1892
>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 = 31.0 bits (69), Expect = 0.54
Identities = 26/213 (12%), Positives = 57/213 (26%), Gaps = 56/213 (26%)
Query: 85 YAFSIDNFKRTQNEIRYLMDLMLEKMEFLLREDGFLSKYGV-RVCFIGNLGLVSEPIRVT 143
Y F + K Q + + + +E+ + L ++ +KY V R+ +P
Sbjct: 91 YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL----------QPYLKL 140
Query: 144 AEKVMRATSKNTRIVILICLAYSSTEEIVHTVE---ETCLVTKKTQPQAFKPRNPQN--- 197
+ ++ ++ + V +T + + +
Sbjct: 141 RQALLELRP-AKNVL-------------IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186
Query: 198 -DVTEDADEHKNKEQNTIKLVDLEKHMYMGVYPNPDILIRT-----SGENRLSNFLLWQS 251
++ E L L + D S + L L +
Sbjct: 187 LNLKNCNSP----ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 252 -SNCMLYSPAALWPEIGLRHL----IWAILNFQ 279
NC+L + L ++ W N
Sbjct: 243 YENCLL---------V-LLNVQNAKAWNAFNLS 265
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 29.8 bits (67), Expect = 0.88
Identities = 9/43 (20%), Positives = 18/43 (41%)
Query: 166 SSTEEIVHTVEETCLVTKKTQPQAFKPRNPQNDVTEDADEHKN 208
S + + +E + + + + R Q +V + A E KN
Sbjct: 8 SDSGTMGSDSDEENVAARASPEPELQLRPYQMEVAQPALEGKN 50
>3arc_Z Photosystem II reaction center protein Z; PSII, membrane-protein
complex, transmembrane alpha-helix, E transport,
photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT
HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus}
PDB: 1s5l_Z* 3a0b_Z* 3a0h_Z* 2axt_Z* 3bz1_Z* 3bz2_Z*
3kzi_Z* 3prq_Z* 3prr_Z*
Length = 62
Score = 27.1 bits (60), Expect = 1.5
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 249 WQSSNCMLYSPAALWPEIGLRHLIWAILNF 278
W S +++ + LW I L ++ +LNF
Sbjct: 33 WDRSKQLIFLGSGLW--IALVLVVG-VLNF 59
>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 = 28.4 bits (62), Expect = 1.7
Identities = 9/64 (14%), Positives = 18/64 (28%), Gaps = 36/64 (56%)
Query: 210 EQNTIKLVDLEKHMYMGVYPNPDILIRTSGENRLSNFLLWQSSNCMLYSP-AALWPEIGL 268
E+ +K K L + L LY+ +A P + +
Sbjct: 18 EKQALK-----K------------L-----QASLK-----------LYADDSA--PALAI 42
Query: 269 RHLI 272
+ +
Sbjct: 43 KATM 46
>1onw_A Isoaspartyl dipeptidase; amidohydrolase, hydrolase,
metalloprotease; HET: KCX; 1.65A {Escherichia coli}
SCOP: b.92.1.7 c.1.9.13 PDB: 1onx_A* 1po9_A* 1poj_A*
1pok_B* 2aqo_A* 1ybq_A* 2aqv_A*
Length = 390
Score = 28.6 bits (64), Expect = 2.6
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 6/49 (12%)
Query: 31 GVIPNHIAFILDGN---RRFAKKHNLAGEGAGHRAGFLTLMSLLKYCAE 76
G+ + DGN F + NL G GF TL+ ++ +
Sbjct: 274 GIPLARVTLSSDGNGSQPFFDDEGNLTHIGVA---GFETLLETVQVLVK 319
>3dsm_A Uncharacterized protein bacuni_02894; seven_blated beta propeller,
structural genomics, PSI-2, Pro structure initiative;
1.90A {Bacteroides uniformis}
Length = 328
Score = 27.7 bits (61), Expect = 5.3
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 28 LSVGVIPNHIAFILDGNRRF 47
VG+IP + L+ +
Sbjct: 308 FYVGIIPGAFCWKLEHHHHH 327
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 0.408
Gapped
Lambda K H
0.267 0.0859 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,368,826
Number of extensions: 255046
Number of successful extensions: 550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 527
Number of HSP's successfully gapped: 15
Length of query: 292
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 199
Effective length of database: 4,105,140
Effective search space: 816922860
Effective search space used: 816922860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.5 bits)