RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 017611
(368 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 = 154 bits (392), Expect = 2e-45
Identities = 37/145 (25%), Positives = 73/145 (50%), Gaps = 6/145 (4%)
Query: 39 IPHHFAFIMDGNRRYAKKLNVEEGA-GHKEGFSSLISVLKYCYELGVKYVTIYAFSIDNF 97
+P H A + DGNRR+A+ ++ + G++ G + + +L++C+E G++ T+Y S +N
Sbjct: 2 LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENL 61
Query: 98 QRKPAEVQNLMDLLLEKINELLKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEVMMATA 157
QR P E+ L++++ + + E+ V +G+L + E + +T
Sbjct: 62 QRDPDELAALIEIITDVVEEICAP-----ANHWSVRTVGDLGLIGEEPARRLRGAVESTP 116
Query: 158 RNSKVVLLVCLAYTSADEIVHAVQE 182
+ + V + Y EIV AV+
Sbjct: 117 EVASFHVNVAVGYGGRREIVDAVRA 141
Score = 69.8 bits (172), Expect = 5e-14
Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 264 AQALRAGRIGNGVTEGFEEKQGNNPIINLVDVEKHMYMAVAPDPDILMRSSGETRLSNFL 323
A+R + + + + + + +++Y + PDPD+++R+SGE RLS FL
Sbjct: 136 VDAVR--ALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFL 193
Query: 324 LWQTSNCLLDSPA--------ALWPEIGLWHLVWAVLKFQR 356
LWQ+ A A WP + A+ +
Sbjct: 194 LWQS--------AYSEMWFTEAHWPAFRHVDFLRALRDYSA 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 = 143 bits (364), Expect = 4e-41
Identities = 53/149 (35%), Positives = 78/149 (52%), Gaps = 3/149 (2%)
Query: 34 LAVGPIPHHFAFIMDGNRRYAKKLNVEEGAGHKEGFSSLISVLKYCYELGVKYVTIYAFS 93
+ IP H A IMDGN R+AK+ + GH EG ++ + +Y +LGVKY+T+YAFS
Sbjct: 15 INAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFS 74
Query: 94 IDNFQRKPAEVQNLMDLLLEKINELLKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEVM 153
+N+ R EV LM L + +N L E + ++V IG + L + + A E
Sbjct: 75 TENWSRPKDEVNYLMKLPGDFLNTFLPE---LIEKNVKVETIGFIDDLPDHTKKAVLEAK 131
Query: 154 MATARNSKVVLLVCLAYTSADEIVHAVQE 182
T N+ + L+ L Y EI+ AVQ
Sbjct: 132 EKTKHNTGLTLVFALNYGGRKEIISAVQL 160
Score = 70.2 bits (173), Expect = 4e-14
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 18/76 (23%)
Query: 290 INLVDVEKHMYMAVAPDPDILMRSSGETRLSNFLLWQTSNCLLDSPAA---------LWP 340
I+ ++++ A PDP++L+R+SGE RLSNFL+WQ + WP
Sbjct: 175 ISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQ---------CSYSEFVFIDEFWP 225
Query: 341 EIGLWHLVWAVLKFQR 356
+ L + +Q
Sbjct: 226 DFNEESLAQCISIYQN 241
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural
genomics, center for structural GEN infectious diseases;
HET: FFT; 2.46A {Campylobacter jejuni}
Length = 225
Score = 139 bits (354), Expect = 7e-40
Identities = 37/155 (23%), Positives = 74/155 (47%), Gaps = 11/155 (7%)
Query: 39 IPHHFAFIMDGNRRYAKKLNVEEGAGHKEGFSSLISVLKYCYELGVKYVTIYAFSIDNFQ 98
H A +MDGNRR+A+ G+ +G ++ +++ C E + ++++AFS +N++
Sbjct: 6 ELKHLAVVMDGNRRWARAKGFLAKLGYSQGVKTMQKLMEVCMEENISNLSLFAFSTENWK 65
Query: 99 RKPAEVQNLMDLLLE----KINELLKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEVMM 154
R E+ + +LL + + K +R+ IG+L L + VR V
Sbjct: 66 RPKDEIDFIFELLDRCLDEALEKFEKN-------NVRLRAIGDLSRLEDKVREKITLVEE 118
Query: 155 ATARNSKVVLLVCLAYTSADEIVHAVQESFKNKSD 189
T + + + ++Y + DEI+ A + + K +
Sbjct: 119 KTKHCDALCVNLAISYGARDEIIRAAKRVIEKKLE 153
Score = 65.9 bits (162), Expect = 8e-13
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 20/76 (26%)
Query: 290 INLVDVEKHMYMAVAPDPDILMRSSGETRLSNFLLWQTSNCLLDSPAA---------LWP 340
+N ++ +++ + D D+++R RLSNFLLWQ + L+P
Sbjct: 154 LNEENLTQNLDLP--LDVDLMLRVGNAKRLSNFLLWQ---------CSYAEIYFSETLFP 202
Query: 341 EIGLWHLVWAVLKFQR 356
+ + +F+
Sbjct: 203 SLTKREFKRIIKEFRN 218
>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 = 139 bits (354), Expect = 1e-39
Identities = 41/150 (27%), Positives = 69/150 (46%), Gaps = 11/150 (7%)
Query: 37 GPIPHHFAFIMDGNRRYAKKLNVEEGAGHKEGFSSLISVLKYCYELGVKYVTIYAFSIDN 96
H A IMDGN R+AKK GHK G S+ + + G++ +T+YAFS +N
Sbjct: 15 AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSEN 74
Query: 97 FQRKPAEVQNLMDLLLE----KINELLKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEV 152
+ R EV LM+L + ++ L + +R+ IG+ + ++ +
Sbjct: 75 WNRPAQEVSALMELFVWALDSEVKSLHRH-------NVRLRIIGDTSRFNSRLQERIRKS 127
Query: 153 MMATARNSKVVLLVCLAYTSADEIVHAVQE 182
TA N+ + L + Y +IV V++
Sbjct: 128 EALTAGNTGLTLNIAANYGGRWDIVQGVRQ 157
Score = 71.0 bits (175), Expect = 3e-14
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 18/76 (23%)
Query: 290 INLVDVEKHMYMAVAPDPDILMRSSGETRLSNFLLWQTSNCLLDSPAA---------LWP 340
I+ + +H+ M D+++R+ GE R+SNFLLWQ A LWP
Sbjct: 172 IDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQ---------IAYAELYFTDVLWP 222
Query: 341 EIGLWHLVWAVLKFQR 356
+ A+ F
Sbjct: 223 DFDEQDFEGALNAFAN 238
>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 = 140 bits (354), Expect = 3e-39
Identities = 42/144 (29%), Positives = 72/144 (50%), Gaps = 3/144 (2%)
Query: 39 IPHHFAFIMDGNRRYAKKLNVEEGAGHKEGFSSLISVLKYCYELGVKYVTIYAFSIDNFQ 98
+P+H A +MDGN R+A + + GHK G + +I + ELG+K++++YAFS +N++
Sbjct: 55 LPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWK 114
Query: 99 RKPAEVQNLMDLLLEKINELLKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEVMMATAR 158
R P EV+ LM + + + G+R+ ++G+ L V T
Sbjct: 115 RSPEEVRFLMGFNRDVVRRRRDT---LKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKS 171
Query: 159 NSKVVLLVCLAYTSADEIVHAVQE 182
N + + C+ Y EI A +E
Sbjct: 172 NDVITINYCVNYGGRTEITEATRE 195
Score = 72.2 bits (178), Expect = 1e-14
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 18/76 (23%)
Query: 290 INLVDVEKHMYMAVAPDPDILMRSSGETRLSNFLLWQTSNCLLDSPAA---------LWP 340
I + +H+ PD D+ +R+SGE R SNF+LWQ AA LWP
Sbjct: 210 ITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQ---------AAYAEYIFQDKLWP 260
Query: 341 EIGLWHLVWAVLKFQR 356
+ L A ++
Sbjct: 261 DYDRRDLWAACEEYAS 276
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 138 bits (349), Expect = 7e-39
Identities = 43/148 (29%), Positives = 71/148 (47%), Gaps = 11/148 (7%)
Query: 39 IPHHFAFIMDGNRRYAKKLNVEEGAGHKEGFSSLISVLKYCYELGVKYVTIYAFSIDNFQ 98
H A IMDGN R+AK N GHK+G +L + +C ++ +T+YAFS +N++
Sbjct: 15 TLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWK 74
Query: 99 RKPAEVQNLMDLLLE----KINELLKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEVMM 154
R +EV LM +L + + + L IR IG+L+ S+ +R ++
Sbjct: 75 RPKSEVDFLMKMLKKYLKDERSTYLDN-------NIRFRAIGDLEGFSKELRDTILQLEN 127
Query: 155 ATARNSKVVLLVCLAYTSADEIVHAVQE 182
T ++ L Y S +E+ A +
Sbjct: 128 DTRHFKDFTQVLALNYGSKNELSRAFKS 155
Score = 71.0 bits (175), Expect = 2e-14
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 18/80 (22%)
Query: 286 NNPIINLVDVEKHMYMAVAPDPDILMRSSGETRLSNFLLWQTSNCLLDSPAA-------- 337
+ ++ + P+ D+L+R+ GE RLSNFLLWQ ++
Sbjct: 165 SLLESLENEISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQ---------SSYAELFFTP 215
Query: 338 -LWPEIGLWHLVWAVLKFQR 356
LWP+ L + F +
Sbjct: 216 ILWPDFTPKDLENIISDFYK 235
>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 = 38.5 bits (89), Expect = 0.003
Identities = 50/271 (18%), Positives = 80/271 (29%), Gaps = 97/271 (35%)
Query: 119 LKEQSIVNLYGIRVYFIGNLKFLSEPVRVAAEEVMMATARNSKVVLLVC-LAYTSADEIV 177
L+EQ F K L EP A + + L+ L Y S
Sbjct: 33 LQEQ-----------F---NKILPEPTEGFAAD----DEPTTPAELVGKFLGYVS----- 69
Query: 178 HAVQESFKNKSDESLAVNANQVSNGVINGAEKVEKIYSLTV--PSIEESCKEKASRVCNG 235
V+ S + D+ L + + N + G + I++L ++ K +
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGND----IHALAAKLLQENDTTLVKTKELIKN 125
Query: 236 AIERVKGTEDINGATVCTDGVSCDYKSEA--QALRAG--RI-----GNGVTEG-FEEKQG 285
I A + + A +A+ G ++ G G T+ FEE
Sbjct: 126 YIT----------ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEE--- 172
Query: 286 NNPIINLVDVEKHMYMAVAPDPDILMRSSGET--RLS--------------NFLLWQTSN 329
L D +Y L++ S ET L N L W
Sbjct: 173 ------LRD----LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW---- 218
Query: 330 CLLDSPAAL------------WPEIGLWHLV 348
L++P+ P IG+ L
Sbjct: 219 --LENPSNTPDKDYLLSIPISCPLIGVIQLA 247
Score = 34.6 bits (79), Expect = 0.058
Identities = 15/107 (14%), Positives = 35/107 (32%), Gaps = 36/107 (33%)
Query: 31 FRVLAVGPIPHHFAFIMDGNRRYAKKLNVEEG-----------------AGHKEGFSSLI 73
+ ++A+ P +F + + +++ G AG ++
Sbjct: 1807 YGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT 1866
Query: 74 SVLKYCYELGVKYVTIYAFSIDNFQRKPAEVQNLMD-LLLEKINELL 119
+VL + + ++ ID + L L LE++ L
Sbjct: 1867 NVLNF---IKLQ-------KID--------IIELQKSLSLEEVEGHL 1895
Score = 30.4 bits (68), Expect = 1.2
Identities = 26/120 (21%), Positives = 45/120 (37%), Gaps = 25/120 (20%)
Query: 153 M-MATARNSKVVLLVCLAYTSADEIVHAVQESFKNKSDESLA--VNANQVSNGVINGAEK 209
M M + SK A ++ + FK+ S+ V N V+ + G EK
Sbjct: 1631 MGMDLYKTSKA----------AQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEK 1680
Query: 210 VEKIYSLTVPSIEESCKEKASRVCNGAIERVKGTEDINGATVCTDGVSCDYKSEAQALRA 269
++I I E+ + G ++ K ++IN + S ++SE L A
Sbjct: 1681 GKRIRENYSAMIFETIVD-------GKLKTEKIFKEINEHS-----TSYTFRSEKGLLSA 1728
>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 = 30.3 bits (67), Expect = 0.51
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 3/24 (12%)
Query: 177 VHAVQESFKNKSDES---LAVNAN 197
+ +Q S K +D+S LA+ A
Sbjct: 22 LKKLQASLKLYADDSAPALAIKAT 45
>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 = 29.4 bits (65), Expect = 2.5
Identities = 32/237 (13%), Positives = 60/237 (25%), Gaps = 82/237 (34%)
Query: 15 PTQLL--------ESLGSFMRRCLFRVL------AVGPIPHHFAFIMDGNRRYAKKLNVE 60
LL ++ +F C ++L V + ++++
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSC--KILLTTRFKQV-------TDFLSAATT--THISLD 292
Query: 61 EGAGHKEGFS---SLISVLKYCYELGVKYVTIYAFSIDNFQRKPAEVQNLMDLLLEKINE 117
H + L +KY+ + P EV L I E
Sbjct: 293 H---HSMTLTPDEVK--------SLLLKYLDCRPQDL------PREVLTTNPRRLSIIAE 335
Query: 118 LLK---------------------EQSIVNL--YGIRVYFIGNLKFLSEPVRVAA----- 149
++ E S+ L R F L +
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD-RLSVFPPSAHIPTILLSL 394
Query: 150 -------EEVMMATARNSKVVLLVCLAYTSADEIVHAVQESFKNKSDESLAVNANQV 199
+VM+ + K L+ S I ++ K K + A++ + V
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI-PSIYLELKVKLENEYALHRSIV 450
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 0.389
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: 5,580,749
Number of extensions: 339340
Number of successful extensions: 832
Number of sequences better than 10.0: 1
Number of HSP's gapped: 813
Number of HSP's successfully gapped: 21
Length of query: 368
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 273
Effective length of database: 4,049,298
Effective search space: 1105458354
Effective search space used: 1105458354
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 (25.9 bits)