RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6303
(270 letters)
>2gak_A Beta-1,6-N-acetylglucosaminyltransferase; glycoprotein,
CIS-peptide, dimer; HET: NAG; 2.00A {Mus musculus} PDB:
2gam_A* 3otk_A*
Length = 391
Score = 105 bits (263), Expect = 1e-26
Identities = 30/179 (16%), Positives = 71/179 (39%), Gaps = 9/179 (5%)
Query: 48 RQDYLFRELLSLELR-LPNVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNL 106
+ + F + NV ++ + ++ ++ + V L+ M+ L W +++NL
Sbjct: 120 KAEESFLAAVQGIASCFDNVFVASQLESVVYASWTRVKADLNCMKDLYRMNANWKYLINL 179
Query: 107 SESDYPVKTNRALVDFLSANRDKNFVKSHGRQVHRFISKQGLDKSFVECEARMWRVGDRT 166
D+P+KTN +V L + +N +++ ++ ++ K + + ++ G
Sbjct: 180 CGMDFPIKTNLEIVRKLKCSTGENNLETEKMPPNK---EERWKKRYAVVDGKLTNTGIVK 236
Query: 167 LPQGIVMDGGSGTGWL-LSPIFVSYVASPEKDELVRGLLNPIQSTPLLPAELLMEQLAN 224
P + SG+ + ++ +V YV E + + P E L +
Sbjct: 237 APPPLKTPLFSGSAYFVVTREYVGYVLENENIQKLMEWAQDT----YSPDEFLWATIQR 291
Score = 36.3 bits (83), Expect = 0.008
Identities = 11/95 (11%), Positives = 35/95 (36%), Gaps = 5/95 (5%)
Query: 23 RTNRALVDFLSANRDKNFVKSHG-----RQRQDYLFRELLSLELRLPNVRLSRRRQATIW 77
+TN +V L + +N +++ +R + + V+ + ++
Sbjct: 187 KTNLEIVRKLKCSTGENNLETEKMPPNKEERWKKRYAVVDGKLTNTGIVKAPPPLKTPLF 246
Query: 78 GGASLVTILLDSMQQLLESGWRWDFIVNLSESDYP 112
G++ + + + +LE+ + ++ P
Sbjct: 247 SGSAYFVVTREYVGYVLENENIQKLMEWAQDTYSP 281
>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 = 55.2 bits (132), Expect = 7e-09
Identities = 48/299 (16%), Positives = 92/299 (30%), Gaps = 94/299 (31%)
Query: 10 HRRELVKKQEDLKRTNRALVDFLSANRDKNFVKSHG-RQRQDYLFRELLSLE-----LRL 63
H + + + + + D LS D FV + + QD + +LS E +
Sbjct: 3 HHHHMDFETGEHQYQYK---DILSVFEDA-FVDNFDCKDVQDMP-KSILSKEEIDHIIMS 57
Query: 64 PNVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNLSESDYPVKTNRALVDFL 123
+ R L LL +++++ F+ + +Y FL
Sbjct: 58 KDAVSGTLR---------LFWTLLSKQEEMVQ-----KFVEEVLRINYK---------FL 94
Query: 124 SANRDKNFVKSHGRQVHRFISKQGLDKSFVECEARMWRVGDRTLP--------------- 168
+ +K+ RQ + + ++E R++
Sbjct: 95 MSP-----IKTEQRQ------PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA 143
Query: 169 -------QGIVMDGGSGTG--WLLSPIFVSYVASPEKDELVRGLLNPI-------QSTPL 212
+ +++DG G+G W+ V K + + I ++P
Sbjct: 144 LLELRPAKNVLIDGVLGSGKTWV-----ALDVCLSYK--VQCKMDFKIFWLNLKNCNSP- 195
Query: 213 LPAELLMEQLANAGIVMDGGSDWLVLSRSFVSYVASPE--KDELVRGLLTLFKY--TLL 267
E ++E L +D +W S + + EL R LL Y LL
Sbjct: 196 ---ETVLEMLQKLLYQID--PNWTSRSDHSSNIKLRIHSIQAEL-RRLLKSKPYENCLL 248
Score = 43.7 bits (102), Expect = 5e-05
Identities = 30/175 (17%), Positives = 61/175 (34%), Gaps = 58/175 (33%)
Query: 5 IVDTVHRRELVKKQ-------------------EDLKRTNRALVDF-----------LSA 34
+V+ +H+ LV+KQ E+ +R++VD L
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 35 NRDKNFVKSH--------GRQRQDYLFRELLSLELRLPNVRLSRRRQATIWGGASLVTIL 86
+ SH + LFR + L+ R ++ R +T W + +
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVF-LDFRFLEQKI--RHDSTAWNASGS---I 520
Query: 87 LDSMQQLLESGWRWDFIVNLSESDYPVKTNRALVDFLSANRDKNFVKSHGRQVHR 141
L+++QQL ++ +I + ++ Y R + L +F+ +
Sbjct: 521 LNTLQQL--KFYK-PYICD-NDPKY----ERLVNAIL------DFLPKIEENLIC 561
Score = 33.7 bits (76), Expect = 0.060
Identities = 28/186 (15%), Positives = 58/186 (31%), Gaps = 44/186 (23%)
Query: 5 IVDTVHRRELVKKQEDLK-RT-----NRALVDFLSANRDKNFVKSHGRQRQDYLFRELLS 58
++ V + +L + + + DFLSA + H E+ S
Sbjct: 249 VLLNVQNAKAWNAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDH--HSMTLTPDEVKS 305
Query: 59 LELRLPNVRLSR-RRQATIWGGASL-VTILLDSMQQLLESGWRWDFIVNLSESDYPVKTN 116
L L+ + R R+ ++I+ +S++ L WD +++ K
Sbjct: 306 LLLKYLDCRPQDLPREVL--TTNPRRLSIIAESIRDGLA---TWDNWKHVNCD----KLT 356
Query: 117 RAL---VDFLSANRDKN-------FVKSHGRQVHRFISKQGLDKSFVECEARMWRVGDRT 166
+ ++ L + F S H I L + +W ++
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVFPPS----AH--IPTILL--------SLIWFDVIKS 402
Query: 167 LPQGIV 172
+V
Sbjct: 403 DVMVVV 408
>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 = 36.2 bits (83), Expect = 0.011
Identities = 41/256 (16%), Positives = 71/256 (27%), Gaps = 98/256 (38%)
Query: 12 RELVKKQEDLKRTNRALVDFLSANRDKN-----FVKSHGRQ--RQDYLFRELLSLELRLP 64
R + K+ D K++N AL F + F G Q DY F EL
Sbjct: 130 RIMAKRPFD-KKSNSAL--FRAVGEGNAQLVAIF----GGQGNTDDY-FEEL-------- 173
Query: 65 NVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNLSESDYPVKTNRALVDFLS 124
R T LV L+ + L +
Sbjct: 174 -----RDLYQT---YHVLVGDLIKFSAETLSE-------------------------LIR 200
Query: 125 ANRDKNFVKSHGRQVHRFISKQGL--DKSF--------------------VECEARMWRV 162
D V + G + ++ DK + V + +
Sbjct: 201 TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
Query: 163 GD-RTLPQGIVMDGGSGTGWLLSPIFVSYVASPEKDELVRGLLNPI-----------QST 210
G+ R+ +G G G L++ + ++ + + + I ++
Sbjct: 261 GELRSYLKGAT---GHSQG-LVTAVAIA--ETDSWESFFVSVRKAITVLFFIGVRCYEAY 314
Query: 211 PL--LPAELLMEQLAN 224
P LP +L + L N
Sbjct: 315 PNTSLPPSILEDSLEN 330
Score = 35.0 bits (80), Expect = 0.030
Identities = 38/180 (21%), Positives = 58/180 (32%), Gaps = 80/180 (44%)
Query: 114 KTNR----------ALVDFLSANRDKNFV-----KS-HG--RQVHRFISKQGLDKSFVEC 155
KTN +LV N KN V +S +G + + + GLD+S +
Sbjct: 355 KTNSHLPAGKQVEISLV-----NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF 409
Query: 156 EARMWRVGDRTLPQGIVMDGGSGTGWLLSPIFVSYVASPEKDELVRGLLNPIQSTPLL-P 214
R + +R LP VASP + LL P
Sbjct: 410 SERKLKFSNRFLP----------------------VASPFH-------------SHLLVP 434
Query: 215 A-ELLMEQLANAGIVMDG------------GSDWLVLSRSFVSYVASPEKDELVRGLLTL 261
A +L+ + L + + GSD VLS S + +V ++ L
Sbjct: 435 ASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS--------ERIVDCIIRL 486
Score = 33.9 bits (77), Expect = 0.058
Identities = 28/130 (21%), Positives = 48/130 (36%), Gaps = 32/130 (24%)
Query: 118 ALV---DFLSANRDKNF------VKSHGRQVHRFISKQGLDKSFVECEA----RMWRVGD 164
AL D +S V G + + + L +S A R+
Sbjct: 1769 ALASLADVMS------IESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFS 1822
Query: 165 RTLPQGIVMDGGSGTGWLLSPI-F-VS---YVASPEK---DELVRGLLNP--IQSTPL-- 212
+ Q +V G TGWL+ + + V YVA+ + D + +LN +Q +
Sbjct: 1823 QEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTN-VLNFIKLQKIDIIE 1881
Query: 213 LPAELLMEQL 222
L L +E++
Sbjct: 1882 LQKSLSLEEV 1891
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 29.2 bits (65), Expect = 1.1
Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 9/22 (40%)
Query: 226 GIVM-----DGGSDWLVLSRSF 242
G+V+ D S+W R+F
Sbjct: 49 GLVLSDKLVDTRSEW----RTF 66
>1x0t_A Ribonuclease P protein component 4; pyrococcus horikoshii OT3,
hydrolase; 1.60A {Pyrococcus horikoshii} PDB: 2zae_B
Length = 120
Score = 28.1 bits (62), Expect = 1.4
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 35 NRDKNFVKSHGRQRQDYLFRELLSLELRLPNVRLSRR 71
+ +K K +R D LF L+ + + L++R
Sbjct: 9 DWEKKEKKKIAIERIDTLFT--LAERVARYSPDLAKR 43
>1v4v_A UDP-N-acetylglucosamine 2-epimerase; UDP-GLCNAC, two domains,
homodimer, riken structural genomics/proteomics
initiative, RSGI; HET: MSE; 1.80A {Thermus thermophilus}
SCOP: c.87.1.3
Length = 376
Score = 28.6 bits (65), Expect = 2.4
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 2 GPHIVDTVHRRELVKKQEDLKRTNRALVDFLSANRDKNFV 41
GP++ T+HRRE L +AL A FV
Sbjct: 198 GPYVTVTMHRRE---NWPLLSDLAQALKRVAEAFPHLTFV 234
>3gek_A Putative thioesterase YHDA; structure genomics, NESG, KR113,
Q9CHK5_lacla, lactococcus L YHDA, structural genomics,
PSI-2; 2.24A {Lactococcus lactis subsp}
Length = 146
Score = 27.0 bits (59), Expect = 4.1
Identities = 16/114 (14%), Positives = 34/114 (29%), Gaps = 14/114 (12%)
Query: 28 LVDFLSANRDKNFVKSHGRQRQDYLFRELLSLELRLPNVRLSRRRQATIWGGASLVTILL 87
++D L+ + F + D ++ ++ + Q + GGASL
Sbjct: 3 MIDQLNITDFQVFTDENS----DKFVSKIYKFSSKMILSDFHAQPQGFLNGGASLA---- 54
Query: 88 DSMQQLLESGWRWDFIVNLSESDYPVKTNRALVDFLSANRDKNFVKSHGRQVHR 141
L + Y + L+ + + FV + G +
Sbjct: 55 ------LAEITAGMASNAIGSGQYFAFGQSINANHLNPKKCEGFVNARGLLLKN 102
>2k3r_A Ribonuclease P protein component 4; PFU RPP21, RNAse P,
hydrolase, tRNA processing; NMR {Pyrococcus furiosus}
PDB: 2ki7_B
Length = 123
Score = 26.5 bits (58), Expect = 5.7
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 36 RDKNFVKSHGRQRQDYLFRELLSLELRLPNVRLSRR 71
+K K ++R D LF L+ + + L++R
Sbjct: 5 NEKKEKKRIAKERIDILFS--LAERVFPYSPELAKR 38
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 27.2 bits (59), Expect = 6.3
Identities = 12/49 (24%), Positives = 21/49 (42%)
Query: 63 LPNVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNLSESDY 111
LP+ R R+ G + + LD++ QL GW + + + Y
Sbjct: 36 LPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGY 84
>1j1i_A META cleavage compound hydrolase; carbazole degradation, META
cleavage product hydrolase, histidine tagged protein,
alpha/beta-hydrolase; 1.86A {Janthinobacterium} SCOP:
c.69.1.10
Length = 296
Score = 26.9 bits (60), Expect = 7.6
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 19 EDLKRTNRALVDFLSANRDKNFVKSHGRQRQ 49
E + A + FLS D +H
Sbjct: 266 EHPEDFANATLSFLSLRVDITPAAAHHHHHH 296
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 26.9 bits (58), Expect = 8.9
Identities = 12/49 (24%), Positives = 21/49 (42%)
Query: 63 LPNVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNLSESDY 111
LP+ R R+ G + + LD++ QL GW + + + Y
Sbjct: 36 LPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGY 84
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 0.137 0.407
Gapped
Lambda K H
0.267 0.0443 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,100,383
Number of extensions: 237721
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 20
Length of query: 270
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 178
Effective length of database: 4,133,061
Effective search space: 735684858
Effective search space used: 735684858
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: 56 (26.1 bits)