RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7415
(396 letters)
>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 = 51.6 bits (123), Expect = 3e-07
Identities = 47/337 (13%), Positives = 90/337 (26%), Gaps = 147/337 (43%)
Query: 23 TDPD--PEFDRYLSSSSDHIVSTPTPNKPDPPPLIVVPEDEVTQ-------PKSIALNP- 72
+P P+ D YL S +S P LI V Q K + P
Sbjct: 220 ENPSNTPDKD-YLLSIP---ISCP---------LIGV-----IQLAHYVVTAKLLGFTPG 261
Query: 73 DVKNL------DIQHVITSLV--------EFLSSKHN------------QVLWPYEDITA 106
++++ Q ++T++ F S +P +
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 107 KVW--TIRSGE-----QLDI------FLRHVLRLFRESLPHALISERWAQTALQLGLSCG 153
+ ++ + E L I ++ + LP A +++ L G
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLP--------AGKQVEISLVNG 373
Query: 154 SRHY--AG--RSLQIF-RALR------------------------------VPINSRMLT 178
+++ +G +SL LR P +S +L
Sbjct: 374 AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLV 433
Query: 179 DILSRLVETVA------------------ETGEDMQGYVTELLLTLESAVDALESDFRPL 220
+ + + G D++ + + VD + P+
Sbjct: 434 PASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERI---VDCIIRL--PV 488
Query: 221 DHMKEL-FKST------P-------NLNNKEAGGAGA 243
FK+T P L ++ G G
Sbjct: 489 KWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGV 525
Score = 43.5 bits (102), Expect = 1e-04
Identities = 69/376 (18%), Positives = 114/376 (30%), Gaps = 105/376 (27%)
Query: 33 LSSSS-DHIVSTPTP------------NKPDPPPLIVVPEDEVTQPKSIALNPDVKNLDI 79
LS S +H++ PT NK P P D+ +P + A
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADD--EPTTPA---------- 58
Query: 80 QHVITSLV-EFLSSKHNQVLWPYEDITAKVWTIRSGEQLDIFLRHVLRLFRES-LP---- 133
LV +FL Y +++ V + G+ + L L F L
Sbjct: 59 -----ELVGKFLG---------Y--VSSLVEPSKVGQFDQV-LNLCLTEFENCYLEGNDI 101
Query: 134 HALIS-----ERWAQTALQLGLSCGSRHYAGRSLQIFRALRVPINSRMLTDILSRLVETV 188
HAL + + + + R + R NS + + + V
Sbjct: 102 HALAAKLLQENDTTLVKTKELIKN---YITARIM-AKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 189 AETGEDMQG----YVTELLLTLESAVDALESDFRPLDHMKELFK-STPNLNNKEAGGAGA 243
A G QG Y EL L + L + +L K S L+ A
Sbjct: 158 AIFGG--QGNTDDYFEELR--------DLYQTYHVL--VGDLIKFSAETLSELIRTTLDA 205
Query: 244 SGKRSPGLNVPGGMMGLCSHMSGVHARSTSYSISYCTRKAANC-------AANMDSKAAE 296
+ GLN+ + + S + Y +C A+
Sbjct: 206 EKVFTQGLNI----------LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHY-----V 250
Query: 297 LRARGVGISPGDLEARCGGTASPSAKYSPSLARSRSAMSG-WYPPCFKSLSQTKL-VYFL 354
+ A+ +G +PG+L + G S ++A A + W F + + V F
Sbjct: 251 VTAKLLGFTPGELRSYLKGATGHSQGLVTAVA---IAETDSW--ESFFVSVRKAITVLFF 305
Query: 355 I--EVPQLYRPSWSTP 368
I + Y + P
Sbjct: 306 IGVRCYEAYPNTSLPP 321
Score = 28.1 bits (62), Expect = 6.0
Identities = 56/325 (17%), Positives = 86/325 (26%), Gaps = 113/325 (34%)
Query: 110 TIRSGEQLDIFLRHVLRLFRESLPHALISERWAQTALQLGLSCGSRHYAGRSLQ-IFRA- 167
T+ G L HVL +P A + LQ F
Sbjct: 10 TLSHGS-----LEHVL-----LVPTAS-------------------FFIASQLQEQFNKI 40
Query: 168 LRVPINSRMLTDILSRLVETVAETGEDMQGYVTELLLT---------LESAVDALESDFR 218
L P D + E V + GYV+ L+ L + E+ +
Sbjct: 41 LPEPTEGFAADDEPTTPAELVGK----FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCY- 95
Query: 219 PLDHMKELFKSTPNLNNKEAGGAGASGKRSPGLNVPGGMMGLCSHMSGVHARS----TSY 274
L + A L ++ +Y
Sbjct: 96 --------------LEGNDIHALAAK---------------LLQENDTTLVKTKELIKNY 126
Query: 275 SISYCTRKAANCAANMDSKAAELRARGVGISPGDLEARCGGTASPSAKYSPSLARSRSAM 334
R A + S +A RA G G + L A GG + Y L R
Sbjct: 127 ---ITARIMAKRPFDKKSNSALFRAVGEGNAQ--LVAIFGGQGNTDD-YFEEL-RDLYQT 179
Query: 335 SGWYPP----CFKSLSQT--KLVYFLIEVPQLYRP-----SW-STPCSKSPSQTKLVYSQ 382
Y K ++T +L+ ++ +++ W P S +P + L+
Sbjct: 180 ---YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP-SNTPDKDYLLSIP 235
Query: 383 IKVP-----QL-------NQAGLLP 395
I P QL G P
Sbjct: 236 ISCPLIGVIQLAHYVVTAKLLGFTP 260
>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 = 47.5 bits (112), Expect = 6e-06
Identities = 39/218 (17%), Positives = 68/218 (31%), Gaps = 66/218 (30%)
Query: 29 FDRYLSSSSDHIVSTPTP-------------NKPDPPPLIVVPEDEVTQPKSI-ALNPDV 74
D +S SDH + +KP L+V+ V K+ A N
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL--LNVQNAKAWNAFNLSC 266
Query: 75 KNLDIQHVIT---SLVEFLSSKHNQVLWPYEDITAKVWTIRSGEQLDIFLRHVLRLFRES 131
K L + T + +FLS+ + + + T+ E + L+ L +
Sbjct: 267 KIL----LTTRFKQVTDFLSAATTTHI-SLDHHS---MTLTPDEVKSLLLK-YLDCRPQD 317
Query: 132 LPHALISERWAQTALQLGLSCGSRHYAGRSLQIFRALRVPINSRMLTDILSRLVETVAET 191
LP T LS I + D L+ +
Sbjct: 318 LPRE------VLTTNPRRLS------------IIAE--------SIRDGLATW-DNWKHV 350
Query: 192 GEDMQGYVTELLLTLESAVDALESDFRPLDHMKELFKS 229
D +L +ES+++ LE P + +++F
Sbjct: 351 NCD------KLTTIIESSLNVLE----PAE-YRKMFDR 377
Score = 39.1 bits (90), Expect = 0.002
Identities = 32/168 (19%), Positives = 50/168 (29%), Gaps = 35/168 (20%)
Query: 74 VKNLDIQHVITSLVEFLSSKHNQVLWPYEDITAK----------VWTIRS--GEQLDIFL 121
V N D + V LS + + I WT+ S E + F+
Sbjct: 30 VDNFDCKDVQDMPKSILSKEE------IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFV 83
Query: 122 RHVLRLFRESLPHALISERWAQTALQLGL--SCGSRHYAGRSLQIFRALRVPINSRM--L 177
VLR+ + L I Q ++ + R Y Q+F V L
Sbjct: 84 EEVLRINYKFLMSP-IKTEQRQPSMMTRMYIEQRDRLY--NDNQVFAKYNVSRLQPYLKL 140
Query: 178 TDILSRL--VETVAETGEDMQGYVTELLLTLESAVDALESDFRPLDHM 223
L L + V G + G + A+D ++ M
Sbjct: 141 RQALLELRPAKNVLIDG--VLGSGKTWV-----ALDVC-LSYKVQCKM 180
Score = 29.4 bits (65), Expect = 2.5
Identities = 37/318 (11%), Positives = 81/318 (25%), Gaps = 115/318 (36%)
Query: 16 HVTQHNFT-DPD----PEFDRYLSSSS--DHIVSTPTP---------------------- 46
V + F + D + + + S DHI+ +
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF 82
Query: 47 -----------------NKPDPPPLI----------------VVPEDEVTQPKSI-ALNP 72
+ P ++ V + V++ + L
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ 142
Query: 73 DVKNL-DIQHVI---------TSLV-------EFLSSKHNQVLWPYEDITAKVWTIRSGE 115
+ L ++V+ T + + ++ W + K
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW----LNLKNCN-SPET 197
Query: 116 QLDIF--LRHVLRLFRESLPHALISER----WAQTALQLGLSCGSRHYAGRSL------- 162
L++ L + + S + + Q L+ L S+ Y L
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK--SKPYE-NCLLVLLNVQ 254
Query: 163 --QIFRAL----RVPINSR--MLTDILSRLVETVAETGEDMQGYVTELLLTL-ESAVDAL 213
+ + A ++ + +R +TD LS T + + +L +D
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 214 ESDFRPLDHMKELFKSTP 231
D E+ + P
Sbjct: 315 PQDLPR-----EVLTTNP 327
Score = 29.4 bits (65), Expect = 2.6
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 22 FTDPDPEFDRYLSSSSDHIVSTPTPNKPDPPPLIVVPEDEVTQPKSIALNPD 73
D DP+++R +++ D + P LI ++ + IAL +
Sbjct: 534 ICDNDPKYERLVNAILDFL---PKIE----ENLICSKYTDLLR---IALMAE 575
>2uvp_A HOBA; hypothetical protein, unknown function, DNAA, SIS fold, DNA
replication; 1.7A {Helicobacter pylori} PDB: 2uvp_B
2wp0_A
Length = 186
Score = 33.5 bits (76), Expect = 0.068
Identities = 24/128 (18%), Positives = 41/128 (32%), Gaps = 15/128 (11%)
Query: 23 TDPDPE-FDRYLSSSSDHIVSTPTPNKPDPPPLIVVPEDEVTQPKSIALNPDVKNLDIQ- 80
D F Y+ S ++ +P +I L+ + Q
Sbjct: 60 ADSSRHWFLNYILS---NLNPKDLKERP-LLSVIDFNASSFYPKNDANLSLATIEMTYQN 115
Query: 81 ----HVITS----LVEFLSSKHNQVLWPYEDITAKVWTIRS-GEQLDIFLRHVLRLFRES 131
HV L L SK LW +E++ ++ LD L + +LF +
Sbjct: 116 PMFWHVGKIENEGLKTILLSKIPSFLWLFEELKEDCLLLKEHDSLLDYKLLQLFKLFENA 175
Query: 132 LPHALISE 139
L L ++
Sbjct: 176 LFSVLYNK 183
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript
evidence; PUF repeats, RNA binding protein-RNA complex;
HET: EPE; 2.90A {Caenorhabditis elegans}
Length = 382
Score = 30.4 bits (68), Expect = 1.0
Identities = 22/193 (11%), Positives = 47/193 (24%), Gaps = 28/193 (14%)
Query: 56 VVPEDEVTQPKSIALNPDVKNLDIQ----HVITSLVEFLSSKHNQVLWPYEDITAKVWTI 111
V Q D+ + HVI +V+ L + + +
Sbjct: 118 KFDHSNVFQLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAV 177
Query: 112 RSGEQ--------------------LDIFLRHVLRLFRESLPHA--LISERWAQTALQLG 149
+ ++ + L + + L S +A +Q
Sbjct: 178 CQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYV 237
Query: 150 LSCGSRHYAGRSLQIFRALRVPINSRMLTDILSRLVETVAETG--EDMQGYVTELLLTLE 207
+ R I + L + S S ++E + + E+
Sbjct: 238 IKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYV 297
Query: 208 SAVDALESDFRPL 220
V++ L
Sbjct: 298 KDVESNRDALDIL 310
>3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2, lyase; 1.65A {Shewanella amazonensis}
Length = 240
Score = 29.6 bits (67), Expect = 1.5
Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 3/47 (6%)
Query: 108 VWTIRSGEQLDIFLRHVLRLFRESLPHAL---ISERWAQTALQLGLS 151
+ SGE L+ + V + L S R A + GL
Sbjct: 175 TIVVTSGEVLENLINLVPKDSFAWLRDCHIIVPSARVETQARKKGLR 221
>3tqs_A Ribosomal RNA small subunit methyltransferase A; protein synthesis;
1.98A {Coxiella burnetii}
Length = 255
Score = 28.6 bits (65), Expect = 3.5
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 9/67 (13%)
Query: 177 LTD--ILSRLVETVAETGEDM-------QGYVTELLLTLESAVDALESDFRPLDHMKELF 227
L D +L ++V + D +G +T+ LLT + +E D + +++ +
Sbjct: 12 LHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKY 71
Query: 228 KSTPNLN 234
N+
Sbjct: 72 NQQKNIT 78
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 4.6
Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 9/39 (23%)
Query: 13 PPTHVTQHNFTDPDPEFDRYLSSSSDHIVSTPTPNKPDP 51
P N + D +++ ++++ K D
Sbjct: 1407 PGNR----NADNVDKILEQF-----EYVLYPSKTLKTDG 1436
>3re1_A Uroporphyrinogen-III synthetase; HEMD-like family, uroporphyrinogen
III synthase, HMB, lyase; 2.50A {Pseudomonas syringae
PV}
Length = 269
Score = 27.7 bits (62), Expect = 6.8
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 10/50 (20%)
Query: 108 VWTIRSGEQLDIFLRHVLRLFRE------SLPHALISERWAQTALQLGLS 151
+ SG+ H+L+L + LP + S R A A G
Sbjct: 196 GLVVSSGQGF----EHLLQLAGDSWPDLAGLPLFVPSPRVASLAQAAGAR 241
>3l6t_A TRAI, mobilization protein TRAI; TRWC superfamily of relaxase
enzymes, conjugative relaxase, relaxase, conjugal
nickase, hydrolase; HET: CIT; 1.93A {Escherichia coli}
PDB: 3l57_A*
Length = 302
Score = 27.4 bits (60), Expect = 7.8
Identities = 14/92 (15%), Positives = 26/92 (28%), Gaps = 2/92 (2%)
Query: 68 IALNPDVKNLDIQHVITSLVEFLSSKHNQVLWPYEDITAKVWTIRSGEQLDIFLRHVLRL 127
+ N D+ H + S + Q+ + + R
Sbjct: 213 LRYNSKNNTFDMAHFSDEQIRAFSRRSEQIE-KGLAAMGLTRETADAQTKSR-VSMATRE 270
Query: 128 FRESLPHALISERWAQTALQLGLSCGSRHYAG 159
+ I + WA A LG+ +R + G
Sbjct: 271 KKTEHSREEIHQEWASRAKTLGIDFDNREWQG 302
>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold,
hydro; HET: ADP; 2.91A {Escherichia coli}
Length = 500
Score = 27.4 bits (61), Expect = 8.8
Identities = 8/30 (26%), Positives = 10/30 (33%)
Query: 115 EQLDIFLRHVLRLFRESLPHALISERWAQT 144
E+L+ R LF E I W
Sbjct: 453 EELESDWRKQHALFSEQQKCLFIPGDWLGR 482
>2qkf_A 3-deoxy-D-manno-octulosonic acid 8- phosphate SYN;
manno-octulosonate, synthase, lipopolysaccharide, KDOP,
KDO8 KDO8PS; 1.75A {Neisseria meningitidis serogroup B}
PDB: 3stf_A 3qpy_A 3ste_A 3qpz_A 3qq0_A 3fyo_A* 3qq1_A
3fyp_A* 3stc_A 3stg_A 1phw_A 1g7v_A* 1gg0_A 1phq_A*
1d9e_A 1pl9_A* 1q3n_A* 1x6u_A* 1x8f_A 1g7u_A*
Length = 280
Score = 27.1 bits (61), Expect = 9.8
Identities = 23/121 (19%), Positives = 37/121 (30%), Gaps = 50/121 (41%)
Query: 160 RSLQIFRALRVPINSRMLTDI---------------------LSR---LVETVAETG--- 192
L+IF ++ ++TD+ L+R LV +A+TG
Sbjct: 73 EGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVV 132
Query: 193 ----------EDMQGYVT--------ELLLTLESAV----DALESDFRPLDHMKELFKST 230
M+ V +L+L E D L D MK+ +
Sbjct: 133 NIKKPQFLSPSQMKNIVEKFHEAGNGKLILC-ERGSSFGYDNLVVDMLGFGVMKQTCGNL 191
Query: 231 P 231
P
Sbjct: 192 P 192
>2w3s_A Xanthine dehydrogenase; XO, XDH, GOUT, iron, 2Fe-2S, iron-sulfur,
oxidoreductase, purine metabolism, molybdenum cofactor,
hypoxanthine; HET: MPN FAD XAN; 2.60A {Rhodobacter
capsulatus} PDB: 2w3r_A* 2w54_A* 2w55_A* 1jro_A* 1jrp_A*
Length = 462
Score = 27.5 bits (61), Expect = 9.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 205 TLESAVDALESDFRPLDHM 223
T+ +A+ L DF PL M
Sbjct: 410 TIAAALPLLAQDFTPLSDM 428
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 0.395
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,943,240
Number of extensions: 350734
Number of successful extensions: 1074
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1069
Number of HSP's successfully gapped: 25
Length of query: 396
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 300
Effective length of database: 4,021,377
Effective search space: 1206413100
Effective search space used: 1206413100
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 (21.6 bits)
S2: 58 (26.0 bits)