RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16152
(295 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 = 257 bits (658), Expect = 2e-86
Identities = 71/229 (31%), Positives = 118/229 (51%), Gaps = 10/229 (4%)
Query: 25 VPKHIAFIMDGNRRYAKRSNAKTIE-GHSKGFDKLAETLQWCLDLGVREVTVYAFSIENF 83
+P+HIA + DGNRR+A+ + + G+ G K+AE L+WC + G+ TVY S EN
Sbjct: 2 LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENL 61
Query: 84 KRTEEEVNGLMDLARAKFKRLIEEKDKLNEKGIRIRIIGNIELLPSDLIASFKEAMHITK 143
+R +E+ L+++ + + +R +G++ L+ + + A+ T
Sbjct: 62 QRDPDELAALIEIITDVVEEICAPA-----NHWSVRTVGDLGLIGEEPARRLRGAVESTP 116
Query: 144 DNTEGFLNVAFSYTSRDEMVETSRILI----DGLRTNKITNEDVTMDLFDKCLYTGTSPE 199
+ +NVA Y R E+V+ R L+ T + + VT++ + LYT P+
Sbjct: 117 EVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPD 176
Query: 200 PDLIIRTSGETRLSDFMLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQ 248
PDL+IRTSGE RLS F+L QS S ++F WP F + + A+ +
Sbjct: 177 PDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYS 225
>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 = 2e-85
Identities = 79/229 (34%), Positives = 130/229 (56%), Gaps = 3/229 (1%)
Query: 20 LKKGHVPKHIAFIMDGNRRYAKRSNAKTIEGHSKGFDKLAETLQWCLDLGVREVTVYAFS 79
+ +PKHIA IMDGN R+AK+ I+GH +G + + ++ DLGV+ +T+YAFS
Sbjct: 15 INAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFS 74
Query: 80 IENFKRTEEEVNGLMDLARAKFKRLIEEKDKLNEKGIRIRIIGNIELLPSDLIASFKEAM 139
EN+ R ++EVN LM L +L EK +++ IG I+ LP + EA
Sbjct: 75 TENWSRPKDEVNYLMKLPGDFLNT---FLPELIEKNVKVETIGFIDDLPDHTKKAVLEAK 131
Query: 140 HITKDNTEGFLNVAFSYTSRDEMVETSRILIDGLRTNKITNEDVTMDLFDKCLYTGTSPE 199
TK NT L A +Y R E++ +++ + ++ +I+ ++++ F++ L+T P+
Sbjct: 132 EKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPD 191
Query: 200 PDLIIRTSGETRLSDFMLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQ 248
P+L+IRTSGE RLS+F++ Q S F + WP+F +L + +Q
Sbjct: 192 PELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQ 240
>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 = 252 bits (647), Expect = 7e-84
Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 3/229 (1%)
Query: 20 LKKGHVPKHIAFIMDGNRRYAKRSNAKTIEGHSKGFDKLAETLQWCLDLGVREVTVYAFS 79
+ +P H+A +MDGN R+A + EGH G + + ++LG++ +++YAFS
Sbjct: 50 IPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFS 109
Query: 80 IENFKRTEEEVNGLMDLARAKFKRLIEEKDKLNEKGIRIRIIGNIELLPSDLIASFKEAM 139
EN+KR+ EEV LM R +R +D L + G+RIR +G+ L +I A
Sbjct: 110 TENWKRSPEEVRFLMGFNRDVVRR---RRDTLKKLGVRIRWVGSRPRLWRSVINELAVAE 166
Query: 140 HITKDNTEGFLNVAFSYTSRDEMVETSRILIDGLRTNKITNEDVTMDLFDKCLYTGTSPE 199
+TK N +N +Y R E+ E +R + + ++ E +T + L P+
Sbjct: 167 EMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRPDIPD 226
Query: 200 PDLIIRTSGETRLSDFMLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQ 248
DL +RTSGE R S+FML Q+ + F KLWP++ +L A +
Sbjct: 227 VDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYA 275
>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 = 248 bits (635), Expect = 2e-82
Identities = 72/227 (31%), Positives = 119/227 (52%), Gaps = 5/227 (2%)
Query: 23 GHVPKHIAFIMDGNRRYAKRSNAKTIEGHSKGFDKLAETLQWCLDLGVREVTVYAFSIEN 82
H +H+A IMDGN R+AK+ GH G + + + + G+ +T+YAFS EN
Sbjct: 15 AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSEN 74
Query: 83 FKRTEEEVNGLMDLARAKFKR-LIEEKDKLNEKGIRIRIIGNIELLPSDLIASFKEAMHI 141
+ R +EV+ LM+L F L E L+ +R+RIIG+ S L +++ +
Sbjct: 75 WNRPAQEVSALMEL----FVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEAL 130
Query: 142 TKDNTEGFLNVAFSYTSRDEMVETSRILIDGLRTNKITNEDVTMDLFDKCLYTGTSPEPD 201
T NT LN+A +Y R ++V+ R L + ++ + + + ++ ++ + D
Sbjct: 131 TAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVD 190
Query: 202 LIIRTSGETRLSDFMLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQ 248
L+IRT GE R+S+F+L Q + LYF LWP+F + A+ AF
Sbjct: 191 LVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFA 237
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 240 bits (614), Expect = 2e-79
Identities = 77/230 (33%), Positives = 121/230 (52%), Gaps = 6/230 (2%)
Query: 20 LKKGHVPKHIAFIMDGNRRYAKRSNAKTIEGHSKGFDKLAETLQWCLDLGVREVTVYAFS 79
K KH+A IMDGN R+AK N GH KG L + WC + + +T+YAFS
Sbjct: 10 EKLDSTLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAFS 69
Query: 80 IENFKRTEEEVNGLMDLARAKFKR-LIEEKDKLNEKGIRIRIIGNIELLPSDLIASFKEA 138
EN+KR + EV+ LM + K+ L +E+ + IR R IG++E +L + +
Sbjct: 70 TENWKRPKSEVDFLMKM----LKKYLKDERSTYLDNNIRFRAIGDLEGFSKELRDTILQL 125
Query: 139 MHITKDNTEGFLNVAFSYTSRDEMVETSRILIDGLRTNKITNEDVTMDLFDKCLYTGTSP 198
+ T+ + +A +Y S++E+ + L++ + I+ + + L T P
Sbjct: 126 ENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPP-SNISLLESLENEISNRLDTRNLP 184
Query: 199 EPDLIIRTSGETRLSDFMLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQ 248
E DL++RT GE RLS+F+L QS + L+F LWP+FT +L N + F
Sbjct: 185 EVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFY 234
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural
genomics, center for structural GEN infectious diseases;
HET: FFT; 2.46A {Campylobacter jejuni}
Length = 225
Score = 229 bits (587), Expect = 1e-75
Identities = 58/225 (25%), Positives = 112/225 (49%), Gaps = 14/225 (6%)
Query: 25 VPKHIAFIMDGNRRYAKRSNAKTIEGHSKGFDKLAETLQWCLDLGVREVTVYAFSIENFK 84
KH+A +MDGNRR+A+ G+S+G + + ++ C++ + ++++AFS EN+K
Sbjct: 6 ELKHLAVVMDGNRRWARAKGFLAKLGYSQGVKTMQKLMEVCMEENISNLSLFAFSTENWK 65
Query: 85 RTEEEVNGLMDLARAKFKR-LIEEKDKLNEKGIRIRIIGNIELLPSDLIASFKEAMHITK 143
R ++E++ + +L R L E +K + +R+R IG++ L + TK
Sbjct: 66 RPKDEIDFIFEL----LDRCLDEALEKFEKNNVRLRAIGDLSRLEDKVREKITLVEEKTK 121
Query: 144 DNTEGFLNVAFSYTSRDEMVETSRILIDGLRTNKITNEDVTMDLFDKCLYTGTSPEPDLI 203
+N+A SY +RDE++ ++ +I+ ++ + + L + DL+
Sbjct: 122 HCDALCVNLAISYGARDEIIRAAKRVIEK-------KLELNEENLTQNLD--LPLDVDLM 172
Query: 204 IRTSGETRLSDFMLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQ 248
+R RLS+F+L Q + +YF L+P T + F+
Sbjct: 173 LRVGNAKRLSNFLLWQCSYAEIYFSETLFPSLTKREFKRIIKEFR 217
>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 = 49.5 bits (117), Expect = 8e-07
Identities = 48/300 (16%), Positives = 94/300 (31%), Gaps = 74/300 (24%)
Query: 14 YAIIKLLKKGHVPKHIAFIMDGNRRYA----KRSNAKTIEGHSKGFDK--LAETLQWCLD 67
Y ++ K +V + ++ R A + + I+G G K +A L CL
Sbjct: 120 YNDNQVFAKYNVSRLQPYL---KLRQALLELRPAKNVLIDG-VLGSGKTWVA--LDVCLS 173
Query: 68 LGVREV---TVYAFSIENFKRTEEEVNGLMDLARAKFKRLIEEKDKLNEKGIRIRIIGNI 124
V+ ++ +++N E + L L D + I++RI +I
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD--HSSNIKLRI-HSI 230
Query: 125 ELLPSDLIAS--FKEAMHITKD-NTEGFLNVAFSY------TSRDEMVETSRILIDGLRT 175
+ L+ S ++ + + + N AF+ T+R + V + T
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWN-AFNLSCKILLTTRFKQVTDF---LSAATT 286
Query: 176 NKITNEDV--------TMDLFDKCLYTGTSPEPDLIIRTSGETRLSDFMLVQSKSSFLYF 227
I+ + L K L P ++ T+
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN-------------------- 326
Query: 228 CHKLWPEFTAWNLINAVFA--FQYDFYTNEMWRADKSKSLTSAGEAFVNELYSK--RDEY 283
P ++ A + T + W+ LT+ E+ +N L R +
Sbjct: 327 -----P------RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF 375
Score = 27.5 bits (60), Expect = 7.5
Identities = 19/149 (12%), Positives = 46/149 (30%), Gaps = 29/149 (19%)
Query: 156 YTSRDEMVETSRILIDGLRTNKITNEDVTMDLFDKCLYTGTSPEPDLIIRTSGETRLSDF 215
Y +D + +D + +D+ + + E D II +
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDV--QDMPKSIL-------SKEEIDHIIMSKDA------ 60
Query: 216 MLVQSKSSFLYFCHKLWPEFTAWNLINAVFAFQYDFYTNEMWRADKSKSLTSAGEAFV-- 273
S + L++ E + V Y F + + + S+ + ++
Sbjct: 61 ---VSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMT--RMYIEQ 115
Query: 274 -------NELYSKRDEYIANPQCNLQHGI 295
N++++K + P L+ +
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144
>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 = 46.6 bits (110), Expect = 7e-06
Identities = 43/212 (20%), Positives = 68/212 (32%), Gaps = 93/212 (43%)
Query: 14 YAIIKLLK-KGHVPKHIAFIMDGNRRYAKRSNAKTIEGHSKGFDKLAETLQWCLDLGVRE 72
A + LK KG +P F A GHS LG E
Sbjct: 1741 KAAFEDLKSKGLIPADATF-------------A----GHS---------------LG--E 1766
Query: 73 VTVY--------AFSIENFKRTEEEVNGLMDL--ARAKFKRLIEEKDKLNEKGIRIRIIG 122
Y SIE+ L+++ R ++ +D+L +
Sbjct: 1767 ---YAALASLADVMSIES----------LVEVVFYRGMTMQVAVPRDELGRSNYGM---- 1809
Query: 123 NIELLPSDLIASF-KEAMH-----ITK----------DNTEGFLNVAFSYTSRDEMVET- 165
I + P + ASF +EA+ + K N E VA + R ++T
Sbjct: 1810 -IAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVA-AGDLRA--LDTV 1865
Query: 166 SRILIDGLRTNKITN---------EDVTMDLF 188
+ +L + ++ KI E+V LF
Sbjct: 1866 TNVL-NFIKLQKIDIIELQKSLSLEEVEGHLF 1896
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.5 bits (68), Expect = 0.50
Identities = 12/83 (14%), Positives = 24/83 (28%), Gaps = 16/83 (19%)
Query: 84 KRTEEEVNGLMDLARAKFKRLIEEKDKLNEKGI-RIRIIGNIELLPSDLIASFKEAMHIT 142
E E + R + ++ ++E D ++ R +L + E +
Sbjct: 80 LTQEPES---IRKWREEQRKRLQELDAASKVMEQEWREKAKKDL--EEWNQRQSEQVEKN 134
Query: 143 KDNT----EGFLNVAFSYTSRDE 161
K N + F D
Sbjct: 135 KINNRIADKAFYQ------QPDA 151
>3p6l_A Sugar phosphate isomerase/epimerase; TIM barrel, structural
genomics, joint center for structural genomics, JCSG;
HET: CIT; 1.85A {Parabacteroides distasonis}
Length = 262
Score = 30.2 bits (68), Expect = 0.65
Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 6/82 (7%)
Query: 58 LAETLQWCLDLGVREVTVYAFSIENFKRTEEEVNGLMDLARAKFKRLIEEKDKLNEKGIR 117
L E L +LG++ + +Y K ++ + +D K E K+ KGI+
Sbjct: 24 LTEALDKTQELGLKYIEIYPGHKLGGKWGDKVFDFNLDAQTQK-----EIKELAASKGIK 78
Query: 118 IRIIG-NIELLPSDLIASFKEA 138
I G + SD FK A
Sbjct: 79 IVGTGVYVAEKSSDWEKMFKFA 100
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
DNA-binding, DNA- directed RNA polymerase, isopeptide
bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Length = 345
Score = 27.6 bits (60), Expect = 5.2
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 69 GVREVTVY-AFSIENFKRTEEEVNGLMDLA----RAKFKRLIEEKDKLNEKGIRIRIIGN 123
+ V++Y + T +V + + ++ +K L E +DKL + + + +
Sbjct: 276 TIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVS 335
Query: 124 IELLPS 129
++ LP
Sbjct: 336 LDNLPG 341
>1vp4_A Aminotransferase, putative; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI; HET: MSE PLP; 1.82A {Thermotoga maritima} SCOP:
c.67.1.1
Length = 425
Score = 27.6 bits (62), Expect = 5.7
Identities = 2/39 (5%), Positives = 11/39 (28%), Gaps = 5/39 (12%)
Query: 7 STLNWFQYAIIKLLKKGHVPKHIAFIMDGNRRYAKRSNA 45
+ + L++ + + + Y ++
Sbjct: 293 PAIT--HRLAARYLERYDLLEQLKPT---IELYRRKRTV 326
>3aow_A Putative uncharacterized protein PH0207; protein-PLP-AKG triple
complex, schiff-base linkage, kynuren aminotransferase;
HET: PLP AKG; 1.56A {Pyrococcus horikoshii} PDB: 3aov_A*
3ath_A* 3av7_A* 1x0m_A 1wst_A*
Length = 448
Score = 27.2 bits (61), Expect = 6.6
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 5/39 (12%)
Query: 7 STLNWFQYAIIKLLKKGHVPKHIAFIMDGNRRYAKRSNA 45
+ Q + + G++ KHI I + Y R +A
Sbjct: 322 NVFG--QVVAWRYVDGGYLEKHIPEI---RKFYKPRRDA 355
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 0.135 0.403
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: 4,510,766
Number of extensions: 267296
Number of successful extensions: 665
Number of sequences better than 10.0: 1
Number of HSP's gapped: 648
Number of HSP's successfully gapped: 25
Length of query: 295
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 202
Effective length of database: 4,105,140
Effective search space: 829238280
Effective search space used: 829238280
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 (21.8 bits)
S2: 57 (26.2 bits)