RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5242
(217 letters)
>1rz4_A Eukaryotic translation initiation factor 3 subuni; heat analogous
motif, winged-helix, biosynthetic protein; 2.10A {Homo
sapiens} SCOP: a.4.5.53 a.118.1.18
Length = 226
Score = 268 bits (686), Expect = 4e-92
Identities = 122/216 (56%), Positives = 160/216 (74%), Gaps = 1/216 (0%)
Query: 1 MTQAELMKGSVDQLLVGIERYNPEHLSTLEKYVEVQCAENVYDLEANLAVLKLYQFH-QN 59
M E M+ +V +LL GI+RYNPE+L+TLE+YVE Q EN YDLEANLAVLKLYQF+
Sbjct: 1 MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAF 60
Query: 60 YNMKITSQILLKALTNFPHTDFILCKCLLSKDLCKEDPIDQIIYLADLLESCKFTQFWSR 119
+ +T+QILLKALTN PHTDF LCKC++ + +E PI QI+YL DLLE+C F FW
Sbjct: 61 FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA 120
Query: 120 MHTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWK 179
+ DL I GF DS+RKF+CHVVGIT+Q ID+ LL+E+L + DS L++W+ KYGW
Sbjct: 121 LDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWS 180
Query: 180 ELDNGYIFIANQDENIKTKNITEKIEFENAATIMTS 215
++G IFI +Q+E+IK KNI EKI+F++ ++IM S
Sbjct: 181 ADESGQIFICSQEESIKPKNIVEKIDFDSVSSIMAS 216
>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 = 44.5 bits (104), Expect = 2e-05
Identities = 33/225 (14%), Positives = 84/225 (37%), Gaps = 57/225 (25%)
Query: 24 EHLSTLEKYVEVQCAENVYDLEANLAVLKLYQFHQNY--------NMKITSQILLKALTN 75
+ L+T + + V C + +E++L VL+ ++ + + + I + +L +
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398
Query: 76 FPHTD--FILCKCLLSKDLCKEDPIDQIIYLADL-LESCKFTQFWSRMH-------TIPD 125
+D ++ K L ++ P + I + + LE + +H IP
Sbjct: 399 VIKSDVMVVVNKLH-KYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457
Query: 126 LFLNIEGFNDSIRKFVCHVVG-------------------ITFQTIDKKL---------L 157
F + + + ++ +G + F+ +++K+
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNAS 517
Query: 158 SELLDGVEDSTLRLWVKKY------GWKELDNGYI-FIANQDENI 195
+L+ ++ L+ + K Y ++ L N + F+ +EN+
Sbjct: 518 GSILNTLQQ--LKFY-KPYICDNDPKYERLVNAILDFLPKIEENL 559
Score = 37.1 bits (85), Expect = 0.003
Identities = 26/209 (12%), Positives = 65/209 (31%), Gaps = 52/209 (24%)
Query: 11 VDQLLVGIERYNPEHLSTLEKYVEVQCAENVYDL--EANLAVLKLYQFHQNYNMK----- 63
D+L + + ++S L+ Y++++ + + +L N+ + +
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLR--QALLELRPAKNVLI---------DGVLGSGKT 164
Query: 64 -ITSQILL--KALTNFPHTDFILCKCLLSKDLCKEDPIDQIIYLADLLESCKFTQFWSRM 120
+ + L K F L L E ++ + L ++ +T
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLN---LKNCNSPETVLEMLQKLLYQID-PNWTSRSDHS 220
Query: 121 HTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKE 180
I L I +R+ + + + LL +L V+++ W
Sbjct: 221 SNIK---LRIHSIQAELRRLLKS------KPYENCLL--VLLNVQNA----KA----WNA 261
Query: 181 LDNG--------YIFIANQDENIKTKNIT 201
+ + + + T +I+
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSAATTTHIS 290
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.063
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 4/54 (7%)
Query: 154 KKLLSELLDGVEDSTLRLWVKKYGWKELDNGYIFIANQDENIKTKN-ITEKIEF 206
+K L EL D + W +K K+L+ + Q E K N I +K F
Sbjct: 95 RKRLQEL-DAASKVMEQEWREK-AKKDLEEWNQRQSEQVEKNKINNRIADK-AF 145
>1t35_A Hypothetical protein YVDD, putative lysine decarboxylase;
structural genomics target, NYSGXRC, PSI, protein
structure initiative; 2.72A {Bacillus subtilis} SCOP:
c.129.1.1
Length = 191
Score = 28.7 bits (65), Expect = 0.92
Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 117 WSR--MHTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLS---------ELLDGVE 165
W++ +H P N+ G+ + + K V + + F ++ L EL++ ++
Sbjct: 120 WAQIGIHQKPIGLYNVNGYFEPMMKMVKYSIQEGF--SNESHLKLIHSSSRPDELIEQMQ 177
Query: 166 DSTLRLWVKKYGWKEL 181
+ + + KK W E+
Sbjct: 178 NYSYPILEKK--WTEI 191
>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 = 28.4 bits (62), Expect = 1.3
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 10/25 (40%)
Query: 30 EKYVEVQCAENVYDLEANLAVLKLY 54
EK + + L+A+L KLY
Sbjct: 18 EK-------QALKKLQASL---KLY 32
Score = 26.8 bits (58), Expect = 4.4
Identities = 6/29 (20%), Positives = 14/29 (48%), Gaps = 6/29 (20%)
Query: 8 KGSVDQLLVGIERYNPEH---L---STLE 30
K ++ +L ++ Y + L +T+E
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATME 47
>2kok_A Arsenate reductase; brucellosis, zoonotic, oxidoreductase, S
genomics, seattle structural genomics center for
infectious ssgcid; NMR {Brucella abortus}
Length = 120
Score = 27.2 bits (61), Expect = 2.4
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 146 GITFQTID-KKLLSELLDGVEDSTLRLWVKKYGWKELDN 183
GI + D KK +G++ TL ++K W++L N
Sbjct: 29 GIDYTFHDYKK------EGLDAETLDRFLKTVPWEQLLN 61
>1rw1_A Conserved hypothetical protein YFFB; thioredoxin fold, structure 2
function project, S2F, structu genomics, unknown
function; HET: MSE IPA; 1.02A {Pseudomonas aeruginosa}
SCOP: c.47.1.12
Length = 114
Score = 26.8 bits (60), Expect = 2.5
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 7/39 (17%)
Query: 146 GITFQTID-KKLLSELLDGVEDSTLRLWVKKYGWKELDN 183
+ + D K G++ LR W ++GW+ + N
Sbjct: 24 KVAYDFHDYKA------VGIDREHLRRWCAEHGWQTVLN 56
>3g36_A Protein DPY-30 homolog; X-type four-helix bundle, nucleus, nuclear
protein; 1.20A {Homo sapiens}
Length = 55
Score = 25.8 bits (57), Expect = 2.7
Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 16/51 (31%)
Query: 58 QNYNMKITSQILLKALTNFPHTDFILCKCLLSKDLCKEDPIDQIIYLADLL 108
+ Y + ILL+ + L KE P + I +LA L
Sbjct: 10 RAYLDQTVVPILLQGM----------------AVLAKERPPNPIEFLASYL 44
>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure,
structural genomics, protein structure initiative; NMR
{Corynebacterium glutamicum} SCOP: a.4.1.19
Length = 97
Score = 26.6 bits (59), Expect = 3.0
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 163 GVEDSTLRLWVKKYG 177
G+ TL+ W+ KYG
Sbjct: 34 GINRVTLKNWIIKYG 48
>3nje_A General secretion pathway protein J; type II secretion,
pseudopilin, minor pilin, pilin fold, SEC XCPU, XCPV,
XCPX, protein transport; 1.85A {Pseudomonas aeruginosa}
Length = 211
Score = 27.5 bits (60), Expect = 3.1
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 158 SELLDGVEDSTLRLWVKKYGWKE 180
++LDGV + R K++ W+
Sbjct: 113 QQVLDGVTALSWRFLDKEHNWQG 135
>2a33_A Hypothetical protein; structural genomics, protein structure
initiative, center for eukaryotic structural genomics,
CESG, AT2G37210; 1.95A {Arabidopsis thaliana} SCOP:
c.129.1.1 PDB: 2q4o_A
Length = 215
Score = 26.9 bits (60), Expect = 4.8
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 15/82 (18%)
Query: 117 WSR--MHTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLS---------ELLDGVE 165
W++ +H P LN++G+ +S+ F+ V F I EL+ +E
Sbjct: 132 WAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGF--ISPTAREIIVSAPTAKELVKKLE 189
Query: 166 DST--LRLWVKKYGWKELDNGY 185
+ K W+ GY
Sbjct: 190 EYAPCHERVATKLCWEMERIGY 211
>3sbx_A Putative uncharacterized protein; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid; HET: AMP; 2.50A {Mycobacterium marinum M}
Length = 189
Score = 26.8 bits (60), Expect = 4.9
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 117 WSR--MHTIPDLFLNIEGFNDSIRKFVCHVV 145
MH + L+ G D +R ++ +
Sbjct: 131 EGYLGMHDKSIVVLDPWGHFDGLRAWLSELA 161
>1ydh_A AT5G11950; structural genomics, protein structure initiative,
center for eukaryotic structural genomics, CESG; 2.15A
{Arabidopsis thaliana} SCOP: c.129.1.1 PDB: 2q4d_A
Length = 216
Score = 26.5 bits (59), Expect = 6.6
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 117 WSR--MHTIPDLFLNIEGFNDSIRKFVCHVV 145
WS+ +H LN++G+ +++ V
Sbjct: 128 WSQLGIHKKTVGLLNVDGYYNNLLALFDTGV 158
>3qua_A Putative uncharacterized protein; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid; 2.10A {Mycobacterium smegmatis str}
Length = 199
Score = 26.0 bits (58), Expect = 8.1
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 117 WSR--MHTIPDLFLNIEGFNDSIRKFVCHVV 145
MH P + L+ G D + ++ +V
Sbjct: 140 AGYLGMHDKPLILLDPFGHYDGLLTWLRGLV 170
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 0.406
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,289,315
Number of extensions: 190600
Number of successful extensions: 422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 419
Number of HSP's successfully gapped: 21
Length of query: 217
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 127
Effective length of database: 4,188,903
Effective search space: 531990681
Effective search space used: 531990681
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 (21.9 bits)
S2: 55 (24.9 bits)