RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8853
(242 letters)
>4f3q_A Transcriptional regulatory protein CBU_1566; YEBC family; 2.15A
{Coxiella burnetii}
Length = 247
Score = 279 bits (717), Expect = 7e-96
Identities = 97/243 (39%), Positives = 149/243 (61%), Gaps = 3/243 (1%)
Query: 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINFGN-NPDTNIKLRLAIEKALDAN 59
MAGHSKWANIK K DAKRGK+ T+++RE+ VA G + D+N +LR ++KA AN
Sbjct: 4 MAGHSKWANIKHAKARQDAKRGKVFTKLIREITVAARLGGEDIDSNPRLRAVVDKAFAAN 63
Query: 60 IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFN 119
+PK+ I RAI++ N +EVRYEGY +G A++VDC+T+N+ RTV+ +R+ F+
Sbjct: 64 MPKDTITRAIKR--GAGSGAGDNLVEVRYEGYGPSGVAVMVDCLTDNKNRTVAEVRHAFS 121
Query: 120 KNGGNLSKEGSVLFMFKHCGQLLFLPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPS 179
K GNL EGSV ++FK G + F PN+ + ++++ALE GAED + D I + T P
Sbjct: 122 KCDGNLGTEGSVAYLFKQRGLITFPPNSDEEKIMEIALEVGAEDVTTNDDGSIDVTTLPE 181
Query: 180 KFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNAL 239
F +I+N+++ + + + T + A ++ +L L+ L DV+ VY+NA
Sbjct: 182 DFEKIRNAMKAADLNPSHAEVTVLASTEVGLDKDSAEQMLRLTEMLEDLDDVQNVYSNAD 241
Query: 240 IFD 242
+
Sbjct: 242 YPE 244
>1kon_A Protein YEBC, YEBC; alpha/beta, two-domains, montreal-kingston
bacterial structural genomics initiative, BSGI,
structural genomics; 2.20A {Escherichia coli} SCOP:
e.39.1.1
Length = 249
Score = 276 bits (708), Expect = 2e-94
Identities = 96/243 (39%), Positives = 150/243 (61%), Gaps = 4/243 (1%)
Query: 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINFGN-NPDTNIKLRLAIEKALDAN 59
MAGHSKWAN + +K DAKRGKI T+I+REL A G +PD N +LR A++KAL N
Sbjct: 4 MAGHSKWANTRHRKAAQDAKRGKIFTKIIRELVTAAKLGGGDPDANPRLRAAVDKALSNN 63
Query: 60 IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFN 119
+ ++ + RAI + +++ N + YEGY G AI+++C+++NR RTV+ +R+ F+
Sbjct: 64 MTRDTLNRAIARGVGG--DDDANMETIIYEGYGPGGTAIMIECLSDNRNRTVAEVRHAFS 121
Query: 120 KNGGNLSKEGSVLFMFKHCGQLLFLPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPS 179
K GGNL +GSV ++F G + F ++T+++ ALE GAED + D I + T+
Sbjct: 122 KCGGNLGTDGSVAYLFSKKGVISF-EKGDEDTIMEAALEAGAEDVVTYDDGAIDVYTAWE 180
Query: 180 KFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNAL 239
+ +++++LE G KA+S+ + M P T A KL +L++ L+ DV++VY N
Sbjct: 181 EMGKVRDALEAAGLKADSAEVSMIPSTKADMDAETAPKLMRLIDMLEDCDDVQEVYHNGE 240
Query: 240 IFD 242
I D
Sbjct: 241 ISD 243
>1lfp_A Hypothetical protein AQ_1575; NEW fold, thermostability, structural
genomics, BSGC structure funded by NIH, protein
structure initiative, PSI; 1.72A {Aquifex aeolicus}
SCOP: e.39.1.1
Length = 249
Score = 271 bits (696), Expect = 1e-92
Identities = 101/245 (41%), Positives = 144/245 (58%), Gaps = 6/245 (2%)
Query: 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINFGN-NPDTNIKLRLAIEKALDAN 59
MAGHS WA IK KK VDA+RGK+ ++++RE+ VA G NP+ N +LR AIE+A AN
Sbjct: 1 MAGHSHWAQIKHKKAKVDAQRGKLFSKLIREIIVATRLGGPNPEFNPRLRTAIEQAKKAN 60
Query: 60 IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFN 119
+P NI RAI+K + E + EV YEGY+ G A++V T+NR RT S +R++F
Sbjct: 61 MPWENIERAIKK--GAGELEGEQFEEVIYEGYAPGGVAVMVLATTDNRNRTTSEVRHVFT 118
Query: 120 KNGGNLSKEGSVLFMFKHCGQLLF-LPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSP 178
K+GGNL G V ++F+ G + + LL+ A+E GAED + I T P
Sbjct: 119 KHGGNLGASGCVSYLFERKGYIEVPAKEVSEEELLEKAIEVGAEDV-QPGEEVHIIYTVP 177
Query: 179 SKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGE-AIKLQKLLNELKKLHDVKKVYTN 237
+ E+K +LE G E + I +P + + D E A K+ KLLN L++L DV++V N
Sbjct: 178 EELYEVKENLEKLGVPIEKAQITWKPISTVQINDEETAQKVIKLLNALEELDDVQQVIAN 237
Query: 238 ALIFD 242
I +
Sbjct: 238 FEIPE 242
>1mw7_A Hypothetical protein HP0162; structural genomics, PSI, protein
structure initiative, northeast structural genomics
consortium, NESG; 2.00A {Helicobacter pylori} SCOP:
e.39.1.1
Length = 240
Score = 236 bits (604), Expect = 8e-79
Identities = 67/241 (27%), Positives = 113/241 (46%), Gaps = 13/241 (5%)
Query: 6 KWANIKRKKLIVDAKRGKICTRIMRELRVAINFGN-NPDTNIKLRLAIEKALDANIPKNN 64
+ + K K K+ ++ + + +A G PDTN KLR AI A N+PK+N
Sbjct: 4 AFEYRRAAKEKRWDKMSKVFPKLAKAITLAAKDGGSEPDTNAKLRTAILNAKAQNMPKDN 63
Query: 65 IFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNK-NGG 123
I AI++ + ++ N E+ YEG + G II++C+T+N RT++N+++ FNK G
Sbjct: 64 IDAAIKRAS----SKEGNLSEITYEGKANFGVLIIMECMTDNPTRTIANLKSYFNKTQGA 119
Query: 124 NLSKEGSVLFMFKHCGQLLFLPNTKKN------TLLDLALEKGAEDFLIDKDNKITIITS 177
++ GS+ FMF L N +N L ++ G E+ + ++KI I
Sbjct: 120 SIVPNGSLEFMFNRKSVFECLKNEVENLKLSLEDLEFALIDYGLEEL-EEVEDKIIIRGD 178
Query: 178 PSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTN 237
+ F + E + + T I D + +KLL+ ++ DV +YTN
Sbjct: 179 YNSFKLLNEGFESLKLPILKASLQRIATTPIELNDEQMELTEKLLDRIEDDDDVVALYTN 238
Query: 238 A 238
Sbjct: 239 I 239
>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 = 42.9 bits (100), Expect = 6e-05
Identities = 35/243 (14%), Positives = 79/243 (32%), Gaps = 78/243 (32%)
Query: 7 WANIK------------RKKLIVDAKRGKICTRIMRELRVAINFGNNPDTNIKLRLAIEK 54
W ++ + L+ K+ K E ++I P ++L++ +E
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSLV--EKQPK-------ESTISI-----PSIYLELKVKLEN 441
Query: 55 ALDAN---IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTV 111
+ + NI + ++ I Y + G+ + +
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDL-IPPYLDQYF-YSHIGHHLKNI---------EHPERM 490
Query: 112 SNIRNIFNKNGGNLSKEGSVLFM---FKHCGQLLFLPNTKKNTLLDLALEKGAEDFLIDK 168
+ R +F + F+ +H + NTL L K + ++ D
Sbjct: 491 TLFRMVFL----DFR------FLEQKIRHDSTAWNASGSILNTLQQL---KFYKPYICDN 537
Query: 169 DNKIT-IITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIV----FKDGEAI------K 217
D K ++ + F+ K E + ++ YT+++ + EAI +
Sbjct: 538 DPKYERLVNAILDFL----------PKIEEN-LICSKYTDLLRIALMAEDEAIFEEAHKQ 586
Query: 218 LQK 220
+Q+
Sbjct: 587 VQR 589
Score = 32.9 bits (74), Expect = 0.11
Identities = 19/110 (17%), Positives = 34/110 (30%), Gaps = 16/110 (14%)
Query: 136 KHCGQLLFLPNTKKNT--LLDLALEKGAE---DFLIDKDNK-ITIITSPSKFIEIKNSLE 189
+ ++ + T L L K E F+ + + SP K + + S+
Sbjct: 49 EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMM 108
Query: 190 MTGF-----KAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKV 234
+ + + V Y N+ KL L +L K V
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKY-NVSRLQ----PYLKLRQALLELRPAKNV 153
>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 = 34.6 bits (79), Expect = 0.028
Identities = 28/142 (19%), Positives = 44/142 (30%), Gaps = 48/142 (33%)
Query: 1 MAGHS--------KWANIKRKKL-IVDA-----KRGKICTRIM-RELRVAINFG---NNP 42
AGHS A++ + I RG + R+ N+G NP
Sbjct: 1759 FAGHSLGEYAALASLADV----MSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 43 DTNIKLRLAIEKALDANIPKNNIFRAIQKNNSN---IKNENINYIEVRYEG--YSVNGAA 97
+ + E AL + + K I N N+ E Y G
Sbjct: 1815 GR-VAASFSQE-ALQY------VVERVGKRTGWLVEIVNYNV-------ENQQYVAAGDL 1859
Query: 98 IIVDCITN--NRMRTVSNIRNI 117
+D +TN N + ++ I
Sbjct: 1860 RALDTVTNVLNFI----KLQKI 1877
Score = 32.3 bits (73), Expect = 0.17
Identities = 21/111 (18%), Positives = 36/111 (32%), Gaps = 27/111 (24%)
Query: 152 LLDLALEKGAEDFLIDKDNKI-----TIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYT 206
+L+L L + +L D I ++ + L A + RP+
Sbjct: 83 VLNLCLTEFENCYLEGND--IHALAAKLLQENDTTLVKTKELIKNYITARI--MAKRPFD 138
Query: 207 N----IVFK---DGEAIKL------Q----KLLNELKKLHDVKKVYTNALI 240
+F+ +G A +L Q EL+ L+ V LI
Sbjct: 139 KKSNSALFRAVGEGNA-QLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLI 188
Score = 30.4 bits (68), Expect = 0.56
Identities = 41/266 (15%), Positives = 77/266 (28%), Gaps = 96/266 (36%)
Query: 9 NIKRKKLIVDAKRGKICTRIMRELRVAINFGNNPDTNIKLRLAIEKALDANI-------P 61
N + ++GK RI RE A+ F D +K I K ++ +
Sbjct: 1668 NPVNLTIHFGGEKGK---RI-RENYSAMIFETIVDGKLKTE-KIFKEINEHSTSYTFRSE 1722
Query: 62 KN------N-----------IFRAIQKNNSNIKNENINYIEVRYEGYSVNG-----AAI- 98
K F + K+ I + + G+S+ G A++
Sbjct: 1723 KGLLSATQFTQPALTLMEKAAFEDL-KSKGLIPADAT------FAGHSL-GEYAALASLA 1774
Query: 99 ----IVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQLLFLPNTKKNTLLD 154
I + V R + + + G + G + P +
Sbjct: 1775 DVMSIESLV-----EVVF-YRGMTMQVAVPRDELGR-----SNYGMIAINPGRVAASFSQ 1823
Query: 155 LALEKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTGFKAES-----SGIVMRPYTNIV 209
AL+ E + +EI N + E+ +G
Sbjct: 1824 EALQYVVER----------VGKRTGWLVEIVN------YNVENQQYVAAG---------- 1857
Query: 210 FKDGEAI-KLQKLLNELKKLHDVKKV 234
D A+ + +LN +K ++K+
Sbjct: 1858 --DLRALDTVTNVLNFIK----LQKI 1877
>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 = 31.1 bits (69), Expect = 0.16
Identities = 8/31 (25%), Positives = 11/31 (35%), Gaps = 11/31 (35%)
Query: 219 QKLLNELKKLHDVKKVYT---------NALI 240
+K LKKL K+Y A +
Sbjct: 18 EK--QALKKLQASLKLYADDSAPALAIKATM 46
>3ne5_A Cation efflux system protein CUSA; transmembrane helix, metal
transport; 2.90A {Escherichia coli} PDB: 3k07_A 3k0i_A
3kso_A 3kss_A
Length = 1054
Score = 29.5 bits (67), Expect = 1.0
Identities = 11/73 (15%), Positives = 26/73 (35%), Gaps = 15/73 (20%)
Query: 53 EKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVS 112
++ I + A+ +N + IE+ Y V + + +T+
Sbjct: 201 QRLAQYGISLAEVKSALDASNQEA---GGSSIELAEAEYMVRASGYL---------QTLD 248
Query: 113 NIRNI---FNKNG 122
+ +I ++NG
Sbjct: 249 DFNHIVLKASENG 261
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.8 bits (61), Expect = 2.7
Identities = 11/64 (17%), Positives = 19/64 (29%), Gaps = 22/64 (34%)
Query: 158 EKGAEDFLIDKDNKITIITSPSKFIEIKNSLEMTG----------FKAESSGIVMRPYTN 207
+ E+ + D P I I + LE++ E P+ N
Sbjct: 126 SEVKENSVDSDDKAKVP---P--LIRIVSGLELSDTKQKGKKFLVIAYE-------PFEN 173
Query: 208 IVFK 211
I +
Sbjct: 174 IAIE 177
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 0.136 0.382
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,666,921
Number of extensions: 220693
Number of successful extensions: 591
Number of sequences better than 10.0: 1
Number of HSP's gapped: 575
Number of HSP's successfully gapped: 23
Length of query: 242
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 151
Effective length of database: 4,160,982
Effective search space: 628308282
Effective search space used: 628308282
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 (21.7 bits)
S2: 56 (25.2 bits)