RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045140
(468 letters)
>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural
NPPSFA, national project on protein structural and
function analyses; 2.25A {Thermus thermophilus}
Length = 249
Score = 72.9 bits (180), Expect = 1e-14
Identities = 34/125 (27%), Positives = 55/125 (44%), Gaps = 17/125 (13%)
Query: 60 RKIAIFFAYCGVGYQGMQKNP-GAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118
R++ + Y G + G+Q+ G +T++G+LE AL G P+ + RT
Sbjct: 2 RRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIG-------ALPKAVA---AGRT 51
Query: 119 DKGVSAVGQVVSGRF----CIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRR 174
D GV A+ I + E LN LP +++ G + V F+A+K R
Sbjct: 52 DAGVHALAMPFH--VDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRA 109
Query: 175 YVYLL 179
Y Y +
Sbjct: 110 YRYRI 114
Score = 47.8 bits (115), Expect = 2e-06
Identities = 28/105 (26%), Positives = 42/105 (40%), Gaps = 7/105 (6%)
Query: 350 LKHYVGSHNFHNFT-TRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQI 408
L +G HNF F T+ + V E ++ G+SF+ Q+
Sbjct: 144 LSLLLGRHNFLGFAKEETRPGER--ELLEARL---QVAEGEAGLEVRLYFRGKSFLRGQV 198
Query: 409 RKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYLDE 452
R M+G + V P ++ L+ D + PTAP GLY E
Sbjct: 199 RGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVE 243
>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif,
RNA-modifying enzyme, lyase; 1.50A {Escherichia coli}
SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A
Length = 264
Score = 72.1 bits (178), Expect = 2e-14
Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 15/124 (12%)
Query: 60 RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTD 119
KIA+ Y G Y G Q+ ++++ LE+AL + RTD
Sbjct: 4 YKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFC---------AGRTD 54
Query: 120 KGVSAVGQVVSGRF----CIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRY 175
GV GQVV F +N+NLP I + K V F+A+ RRY
Sbjct: 55 AGVHGTGQVVH--FETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRY 112
Query: 176 VYLL 179
Y++
Sbjct: 113 RYII 116
Score = 45.2 bits (108), Expect = 2e-05
Identities = 25/116 (21%), Positives = 50/116 (43%), Gaps = 12/116 (10%)
Query: 350 LKHYVGSHNFHNF-TTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQI 408
+ +G ++F +F + ++ P R ++ V G ++ ++ +F+ H +
Sbjct: 146 AQCLLGENDFTSFRAVQCQSRTP--WRNVMHIN----VTRHG-PYVVVDIKANAFVHHMV 198
Query: 409 RKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYLDECIFASYNKKWK 463
R ++G + V + P+S I L KD + TA GLYL Y ++
Sbjct: 199 RNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVA---VDYPDRYD 251
>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 = 52.7 bits (126), Expect = 2e-07
Identities = 56/310 (18%), Positives = 97/310 (31%), Gaps = 106/310 (34%)
Query: 23 DPKRLKMSATSTSDDERDLIPAAAGADSTTKRQLCKRRKIAI---FFAYCGVGYQGMQKN 79
P L+ + + L+ A A A++ + + AI FF +G + +
Sbjct: 259 TPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF----IGVRCYEAY 314
Query: 80 PGAKTIEGDLEEALFHS-G------AVSERDRGNPRRYDWARSARTDKGVSAVGQ----- 127
P LE++L ++ G ++ + +T+ + A Q
Sbjct: 315 PNTSLPPSILEDSLENNEGVPSPMLSI----SNLTQEQVQDYVNKTNSHLPAGKQVEISL 370
Query: 128 -------VVSGRFCIDPPGLVERLNSNL-----PT---QIRIFGYKRVTASFNAKKFCDQ 172
VVSG PP + LN L P+ Q RI +R KF
Sbjct: 371 VNGAKNLVVSG-----PPQSLYGLNLTLRKAKAPSGLDQSRIPFSER------KLKF--S 417
Query: 173 RRYVYLLPVFA------LDSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRT 226
R+ LPV + L +S + + L N K
Sbjct: 418 NRF---LPVASPFHSHLLVPAS----DLINKDLVKNNVSFN---------------AK-- 453
Query: 227 YQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVN 286
+ +P V T +G ++L + + ISE +V+ V
Sbjct: 454 -DIQIP----------------VYDTFDG----SDLRVLSGS--ISER-IVDCIIRLPVK 489
Query: 287 -ETLVESRTS 295
ET + + +
Sbjct: 490 WETTTQFKAT 499
Score = 38.5 bits (89), Expect = 0.005
Identities = 56/319 (17%), Positives = 80/319 (25%), Gaps = 135/319 (42%)
Query: 26 RLKMSATSTSDDERDLIPAAAGADSTTKRQLCKRRKIAIF----------FAYCGVGYQG 75
+L +T ++LI A KR K+ A+F A G G QG
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFG-G-QG 164
Query: 76 MQKNPGAKTIEGDLEE-------------ALFHSGA---------VSERDRGNPRRYD-- 111
+ EE L A + ++ + +
Sbjct: 165 --------NTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 112 -WAR--SARTDKG------VS----AVGQVVS-GRFC----IDPPGLVERLNSNLPTQIR 153
W S DK +S V Q+ P L L
Sbjct: 217 EWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 154 IFGYKRVTA----------SF--NAKK-----F-----CDQRRYVYLLPVFALDSSSHRD 191
+ VTA SF + +K F C Y P +L S D
Sbjct: 277 L-----VTAVAIAETDSWESFFVSVRKAITVLFFIGVRC-YEAY----PNTSLPPSILED 326
Query: 192 RESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQL---GLPS-------NDENASL- 240
LE +E G + L L N N+ L
Sbjct: 327 ----------------SLENNE---------GVPSPMLSISNLTQEQVQDYVNKTNSHLP 361
Query: 241 -NSQVKVDTVVSTCNGDRH 258
QV +S NG ++
Sbjct: 362 AGKQV----EISLVNGAKN 376
Score = 35.4 bits (81), Expect = 0.051
Identities = 39/201 (19%), Positives = 65/201 (32%), Gaps = 76/201 (37%)
Query: 17 SPRQEPDPKRLKMSATS-TSDDERDLIPAAAGADSTTKRQLCKRRKIAIF---FAYCGVG 72
+ E K + +TS T E+ L+ +T Q A+ A
Sbjct: 1700 KLKTEKIFKEINEHSTSYTFRSEKGLL------SATQFTQ------PALTLMEKAA---- 1743
Query: 73 YQGMQKNPGAKTIEGDL-EEALF--HS-G------AVSE-----------RDRGN----- 106
++ ++ +G + +A F HS G ++++ RG
Sbjct: 1744 FEDLKS-------KGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVA 1796
Query: 107 -PRRYDWARSARTDKGVSAV--GQVVSG-----------RFCIDPPGLVERLNSNLP-TQ 151
PR R++ G+ A+ G+V + R LVE +N N+ Q
Sbjct: 1797 VPR----DELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQ 1852
Query: 152 IRIFGYKR----VTASFNAKK 168
G R VT N K
Sbjct: 1853 YVAAGDLRALDTVTNVLNFIK 1873
>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 = 51.0 bits (121), Expect = 7e-07
Identities = 68/436 (15%), Positives = 117/436 (26%), Gaps = 133/436 (30%)
Query: 70 GVGYQGMQKNPGA-KTIEGDL-EEALFHSGAVSERDRGNPRRYD----WARSARTDKGVS 123
V G+ G+ KT + + + D W
Sbjct: 152 NVLIDGV---LGSGKTW---VALDVC--------LSYKVQCKMDFKIFWLN--------- 188
Query: 124 AVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNA-----------KKFCDQ 172
+ C P ++E L L QI R S N ++
Sbjct: 189 -LKN------CNSPETVLEMLQ-KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240
Query: 173 RRYVYLLPVFALD---SSSH--------------RDRESVMASLGSGNE----------- 204
+ Y L V L ++ R + V L +
Sbjct: 241 KPYENCLLV--LLNVQNAKAWNAFNLSCKILLTTRFK-QVTDFLSAATTTHISLDHHSMT 297
Query: 205 ---------LVKCLECS-----ERGRK----VIGVMGKRTYQLGLPSNDENASLNSQVKV 246
L+K L+C + ++ + + GL + D +N K+
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES-IRDGLATWDNWKHVNCD-KL 355
Query: 247 DTVVSTCNGDRHNTNLESVESNKTISE-SVMVENAN-SESVNETL---VESRTSETVQNE 301
T++ + LE E K SV +A+ + + V V N+
Sbjct: 356 TTIIESSL-----NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK 410
Query: 302 NTDLSL-DLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFH 360
SL + K + S+ LK E E I+ HY F
Sbjct: 411 LHKYSLVEKQPKEST------ISIPSIYLELK----VKLENEYALHRSIVDHYNIPKTFD 460
Query: 361 NFTTRTKAEDPSARRYIISFGA---DSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVA 417
+ D +Y S ++ + E + + + F+ +IR A
Sbjct: 461 SDDLIPPYLD----QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRH-DSTAW- 514
Query: 418 VVRNCAPQSLIETALQ 433
A S++ T Q
Sbjct: 515 ----NASGSILNTLQQ 526
>2r52_A BMP-6, bone morphogenetic protein 6; TGF-beta ligand,
chondrogenesis, cleavage on PAIR of basic residues,
cytokine, developmental protein; 2.50A {Homo sapiens}
Length = 143
Score = 26.9 bits (59), Expect = 8.5
Identities = 8/51 (15%), Positives = 24/51 (47%)
Query: 16 LSPRQEPDPKRLKMSATSTSDDERDLIPAAAGADSTTKRQLCKRRKIAIFF 66
++P +R + ST + + +A+ +S+ + C++ ++ + F
Sbjct: 1 MAPTSASSRRRQQSRNRSTQSQDVARVSSASDYNSSELKTACRKHELYVSF 51
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
0.314 0.130 0.369
Gapped
Lambda K H
0.267 0.0541 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,665,398
Number of extensions: 391875
Number of successful extensions: 465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 15
Length of query: 468
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 371
Effective length of database: 3,993,456
Effective search space: 1481572176
Effective search space used: 1481572176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 59 (26.9 bits)