RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8736
(290 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 = 49.3 bits (117), Expect = 8e-07
Identities = 53/290 (18%), Positives = 94/290 (32%), Gaps = 93/290 (32%)
Query: 15 ILDY-KTLLQLYRSY---IRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLA--LGAFKS 68
DY + L LY++Y + + +++ S ++L + V QG+ + L +
Sbjct: 166 TDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDA-EKVFTQGLNILEWLENPSN 224
Query: 69 SPIKSILSEAGEP---PLSSRREI-LT--CNYLLNTLR----DPRHLHFNL----IKNDN 114
+P K L P PL I + +Y++ T + P L L +
Sbjct: 225 TPDKDYLLSI--PISCPL-----IGVIQLAHYVV-TAKLLGFTPGELRSYLKGATGHSQG 276
Query: 115 V-----------------NLHQEIQIGFF---ELAQKFPNYK---QIFTDASKNEHSVSS 151
+ ++ + I + FF + +PN I D+ +N V S
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS 336
Query: 152 AFCCEETKFSVK------LDPRISICNAEL-ISIQYAISFIISTTPLQVPTPKFVL--YS 202
S+ + ++ N+ L Q IS + V+
Sbjct: 337 PM------LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK-------NLVVSGPP 383
Query: 203 DSLSAL--------------QSREQVSLTRLRIGHTNLT-----HVHLMK 233
SL L QSR S +L+ + L H HL+
Sbjct: 384 QSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLV 433
Score = 46.6 bits (110), Expect = 7e-06
Identities = 52/295 (17%), Positives = 95/295 (32%), Gaps = 101/295 (34%)
Query: 55 HHQGVRLALGAFKSSPI-KSILSEAGEPPLS----SRREILTCNYLLNTLRDPRHL--HF 107
QG+ + L +K+S + + + A S +I+ N P +L HF
Sbjct: 1627 QEQGMGMDL--YKTSKAAQDVWNRADNHFKDTYGFSILDIVINN--------PVNLTIHF 1676
Query: 108 NLIKNDNVNLHQEIQIGF----FE-LAQKFPNYKQIFTDASKNEHSVSSAFCCEE----- 157
K + I+ + FE + ++IF + NEHS S F E+
Sbjct: 1677 GGEKG------KRIRENYSAMIFETIVDGKLKTEKIFKEI--NEHSTSYTFRSEKGLLSA 1728
Query: 158 TKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSD------SL---SAL 208
T+F+ Q A+ ++ + K ++ +D SL +AL
Sbjct: 1729 TQFT-----------------QPAL-TLMEKAAFEDLKSKGLIPADATFAGHSLGEYAAL 1770
Query: 209 QSR-------EQVSLTRLR---------IGHTNLTHVHLMKREPPPECDTCN---CRLTV 249
S V + R ++ ++ P + + + V
Sbjct: 1771 ASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVV 1830
Query: 250 KHLLKYCNKY-----HNIRSPNDLYAC---------LSNDENSVLEFLKKSKIKL 290
+ + K +N N Y ++N VL F+K KI +
Sbjct: 1831 ERVGKRTGWLVEIVNYN--VENQQYVAAGDLRALDTVTN----VLNFIKLQKIDI 1879
>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 = 48.3 bits (114), Expect = 2e-06
Identities = 43/269 (15%), Positives = 85/269 (31%), Gaps = 79/269 (29%)
Query: 13 KRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAF-KSSPI 71
+ I D ++ KL ++ +SSL VL+ ++ + L F S+ I
Sbjct: 335 ESIRDGLATWDNWKHVNCDKL-------TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 72 KSILSEA--GEPPLSSRREILT--CNYLLNTLRDPR-------HLHFNL-IKNDN-VNLH 118
+IL + S ++ Y L + P+ ++ L +K +N LH
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSL-VEKQPKESTISIPSIYLELKVKLENEYALH 446
Query: 119 QEI--------------------------QIGF----FELAQKFPNYKQIFTD----ASK 144
+ I IG E ++ ++ +F D K
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK 506
Query: 145 NEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS 204
H S+A+ + + + Y +I P Y
Sbjct: 507 IRHD-STAWNASGSILNTLQQLKF-----------YK-PYICDNDP---------KYERL 544
Query: 205 LSALQS-REQVSLTRLRIGHTNLTHVHLM 232
++A+ ++ + +T+L + LM
Sbjct: 545 VNAILDFLPKIEENLICSKYTDLLRIALM 573
Score = 39.8 bits (92), Expect = 8e-04
Identities = 60/332 (18%), Positives = 104/332 (31%), Gaps = 100/332 (30%)
Query: 16 LDYKTLLQLYRSYIRSKLDYASI------VYSSAS-DSSLKVLDTVHHQGVRLALGAFKS 68
YK +L ++ D + + S D + D V G S
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV--SGTLRLFWTLLS 73
Query: 69 SPIKSILSEAGEPPLSSRREILTCNY--LLNTL----RDP----------RHLHFN---L 109
+ ++ + E E+L NY L++ + R P R +N +
Sbjct: 74 KQ-EEMVQKFVE-------EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 110 IKNDNVN---LHQEIQIGFFELAQKFPNYKQIFTD----ASKNEHSVSSAFCCEETKFSV 162
NV+ + +++ EL + N + D + K + + C K
Sbjct: 126 FAKYNVSRLQPYLKLRQALLEL-RPAKN---VLIDGVLGSGK---TWVALDVCLSYKVQC 178
Query: 163 KLDPRI---SI--CN--AELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVS 215
K+D +I ++ CN ++ + + + I P + SD S ++ R
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQI--------DPNWTSRSDHSSNIKLRIHSI 230
Query: 216 LTRLRIGHTNLTHVHLMKREPPPEC-----DTCN----------CR--LT-----VKHLL 253
LR L+K +P C + N C+ LT V L
Sbjct: 231 QAELR---------RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281
Query: 254 KYCNKYHNIRSPNDLYACLSNDENSVLEFLKK 285
H S + L+ DE V L K
Sbjct: 282 SAATTTH--ISLDHHSMTLTPDE--VKSLLLK 309
Score = 32.1 bits (72), Expect = 0.27
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 28/85 (32%)
Query: 8 AWSKVKRILDYKTLLQL--YRSYI-RSKLDYASIVYSSASDSSLKVLDTVHHQG------ 58
AW+ IL+ TL QL Y+ YI + Y +V + +LD +
Sbjct: 513 AWNASGSILN--TLQQLKFYKPYICDNDPKYERLVNA--------ILDFLPKIEENLICS 562
Query: 59 -----VRLALGAFKSSPIKSILSEA 78
+R+AL + ++I EA
Sbjct: 563 KYTDLLRIAL----MAEDEAIFEEA 583
>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase,
transferase; HET: T5A; 1.98A {Escherichia coli} SCOP:
c.37.1.1 PDB: 5tmp_A*
Length = 213
Score = 30.6 bits (70), Expect = 0.42
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 110 IKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSA 152
I+ ++ + + + ELA + + I DA++ +V A
Sbjct: 159 IEQESFDFFNRTRARYLELAAQDKSIHTI--DATQPLEAVMDA 199
>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide
biosynthesis, TMP-binding, A binding, structural
genomics, NPPSFA; 1.96A {Aquifex aeolicus}
Length = 195
Score = 30.2 bits (69), Expect = 0.51
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 113 DNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSS 151
+N ++++ GF ELA++ N I DAS E V
Sbjct: 147 ENKEFLEKVRKGFLELAKEEENVVVI--DASGEEEEVFK 183
>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases,
center for structural genomics of infectious DISE
ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1
biovar eltor} PDB: 3n2i_A*
Length = 236
Score = 29.9 bits (68), Expect = 0.75
Identities = 8/43 (18%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 110 IKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSA 152
I+ +++ + + + ELA + I DA+++ V++
Sbjct: 181 IEKMDISFFERARERYLELANSDDSVVMI--DAAQSIEQVTAD 221
>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH;
2'O-methyltransferase, knot, montreal- kingston
bacterial structural genomics initiative, BSGI; 2.5A
{Escherichia coli} SCOP: c.116.1.1 d.79.3.3
Length = 253
Score = 29.5 bits (67), Expect = 0.97
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 12/80 (15%)
Query: 29 IRSKLDYASIVYSSASDSSL-KVLDTVHHQGVRLALGAFKSSPIKSILS--EAGEPPLSS 85
+ L+ +V A+ L + D HQG+ + + + + + P
Sbjct: 49 LIHALESQGVVIQLANRQYLDEKSDGAVHQGIIARVKPGRQYQENDLPDLIASLDQPF-- 106
Query: 86 RREILTCNYLLNTLRDPRHL 105
+L +L+ + DP +L
Sbjct: 107 ---LL----ILDGVTDPHNL 119
>2bhu_A Maltooligosyltrehalose trehalohydrolase; alpha-amylase,
protein-carbohydrate complex, desiccation resistance;
HET: TRS PGE; 1.1A {Deinococcus radiodurans} SCOP:
b.1.18.2 b.71.1.1 c.1.8.1 PDB: 2bhy_A* 2bhz_A* 2bxy_A*
2bxz_A* 2by0_A* 2by1_A* 2by2_A* 2by3_A*
Length = 602
Score = 29.6 bits (67), Expect = 1.4
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 6/81 (7%)
Query: 13 KRILD-YKTLLQLYRSYIR-SKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSP 70
R L Y+ LL+L R ++ ++ D + + TV G R+ L
Sbjct: 508 ARTLRLYRDLLRLRREDPVLHNRQRENL--TTGHDGDVLWVRTVTGAGERVLLWNL--GQ 563
Query: 71 IKSILSEAGEPPLSSRREILT 91
++E P RR +L
Sbjct: 564 DTRAVAEVKLPFTVPRRLLLH 584
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A
{Streptomyces viridochromogenes} PDB: 1x7p_A*
Length = 287
Score = 29.2 bits (66), Expect = 1.6
Identities = 7/51 (13%), Positives = 13/51 (25%), Gaps = 12/51 (23%)
Query: 52 DTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDP 102
V +A+ + + I E L + L + P
Sbjct: 99 KNEAPPEV-VAVVEMPADDLDRIP--VREDFL-----GV----LFDRPTSP 137
>2ccj_A DTMP kinase, thymidylate kinase; transferase, nucleotide
biosynthesis, TMP-binding, ATP-binding; HET: TMP; 1.7A
{Staphylococcus aureus} PDB: 2cck_A 2ccg_A*
Length = 205
Score = 28.7 bits (65), Expect = 1.9
Identities = 7/46 (15%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 108 NLIKNDNVNLHQEIQIGFFELAQKFPN-YKQIFTDASKNEHSVSSA 152
N + +++ H+++ G+ E+ +K + +A + +V
Sbjct: 150 NRLDQEDLKFHEKVIEGYQEIIHNESQRFKSV--NADQPLENVVED 193
>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, MTBI,
transferase; HET: ATM; 1.85A {Staphylococcus aureus
subsp} PDB: 4dwj_A* 4f4i_A
Length = 229
Score = 28.8 bits (65), Expect = 1.9
Identities = 7/46 (15%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 108 NLIKNDNVNLHQEIQIGFFELAQKFPN-YKQIFTDASKNEHSVSSA 152
N + +++ H+++ G+ E+ +K + +A + +V
Sbjct: 174 NRLDQEDLKFHEKVIEGYQEIIHNESQRFKSV--NADQPLENVVED 217
>2z0h_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide
biosynthesis, nucleotide-binding, transferase,
structural genomics, NPPSFA; HET: ADP TYD; 2.10A
{Thermotoga maritima} PDB: 3hjn_A*
Length = 197
Score = 27.9 bits (63), Expect = 3.3
Identities = 5/41 (12%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 113 DNVNLHQEIQIGFFELAQKFPN-YKQIFTDASKNEHSVSSA 152
+ + ++ G+ LA++ P + D ++ +
Sbjct: 146 EKREFLERVREGYLVLAREHPERIVVL--DGKRSIEEIHRD 184
>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ehrlich chaffeensis; 2.15A
{Ehrlichia chaffeensis}
Length = 223
Score = 27.6 bits (62), Expect = 3.7
Identities = 6/42 (14%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 110 IKNDNVNLHQEIQIGFFELAQKFPN-YKQIFTDASKNEHSVS 150
+ ++ + ++ GF+++A+K P+ I + +
Sbjct: 168 YEFADMEFYYRVRDGFYDIAKKNPHRCHVI--TDKSETYDID 207
>3oky_B Putative uncharacterized protein; transmembrane, ligand,
SEMA-domain, cell-CELL signalling, SI protein; HET: NAG;
2.19A {Mus musculus} PDB: 3okw_A* 3afc_A* 3al8_A*
Length = 565
Score = 28.2 bits (61), Expect = 4.3
Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 236 PPPECDTCNCRLTVKHLLKYCNKYHNI---RSPNDLYACLSNDENSVLEFLKKSKIKL 290
+ D CR+ KH C+ + + ++ + L+ C +N N + ++
Sbjct: 83 KSRQADVDTCRMKGKHK-DECHNFIKVLLKKNDDTLFVCGTNAFNPSCRNYRVDTLET 139
>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology;
HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB:
4e5u_A* 4esh_A* 3uwk_A* 3uwo_A* 3uxm_A*
Length = 213
Score = 27.5 bits (62), Expect = 4.4
Identities = 6/42 (14%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 112 NDNVNLHQEIQIGFFELAQKFPN-YKQIFTDASKNEHSVSSA 152
++ + ++ + + A + P Y+ + DA V +
Sbjct: 160 QEDRRFFEAVRQTYLQRAAQAPERYQVL--DAGLPLAEVQAG 199
>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle
structural genomics center for infectious transferase;
1.90A {Burkholderia thailandensis}
Length = 227
Score = 27.2 bits (61), Expect = 5.3
Identities = 5/42 (11%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 112 NDNVNLHQEIQIGFFELAQKFPN-YKQIFTDASKNEHSVSSA 152
+++ + + AQ+ P+ + + D+S+ +
Sbjct: 180 SESDAFFARTRAEYLRRAQEAPHRFVIV--DSSEPIAQIRKQ 219
>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 = 26.5 bits (57), Expect = 7.2
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 9/32 (28%)
Query: 47 SLKVLDTVHHQGVRLALGAFKSSP---IKSIL 75
+LK L L L A S+P IK+ +
Sbjct: 21 ALKKLQA------SLKLYADDSAPALAIKATM 46
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
0.319 0.133 0.386
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,101,190
Number of extensions: 225103
Number of successful extensions: 534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 24
Length of query: 290
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 197
Effective length of database: 4,105,140
Effective search space: 808712580
Effective search space used: 808712580
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 (25.6 bits)