RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4197
(124 letters)
>3c0t_A Mediator of RNA polymerase II transcription subunit 18; beta
barrel, channel, protein-protein complex, activator,
nucleus; 2.40A {Schizosaccharomyces pombe}
Length = 207
Score = 84.8 bits (209), Expect = 9e-22
Identities = 16/118 (13%), Positives = 40/118 (33%), Gaps = 7/118 (5%)
Query: 3 VGDKARPTIVRSSIDVACSCTVVEFLTEMGCRMDFEYISRGYMFRKGRMKILVSKIFKMS 62
+ + I + + +V EF+ +MG EYI +G + + + + S
Sbjct: 88 PKREDKCGIRPVNRAKLTNGSVTEFVEKMGYEFSHEYIIQGLEYFFFDTTVRIYQTLIPS 147
Query: 63 QGKPSDSGVEPI--SQSYLVELSILAPGGQDVIG-----EDMKAFAEQLKPLVQLEKI 113
Q + P+ Q +++ + + + ++ L L+ +
Sbjct: 148 QQRSIKPPFHPMNEEQPWILHVYTHVADASNQVAMAKAEANLTKVKTLLSAFCDLKNV 205
>2hzm_B RNA polymerase II mediator complex subunit 18; beta barrel,
channel, transcription; 2.40A {Saccharomyces cerevisiae}
PDB: 2hzs_B 3rj1_E
Length = 317
Score = 71.4 bits (174), Expect = 4e-16
Identities = 21/116 (18%), Positives = 47/116 (40%), Gaps = 10/116 (8%)
Query: 10 TIVRSSIDVAC--SCTVVEFLTEMGCRMDFEYISRGYMFRKGRMKILVSKIFKMSQGKPS 67
TI + I + + +V + +G +F+Y++ G F L+ ++ K+ Q
Sbjct: 183 TIAETIILSSAGKNSSVSSLMNGLGYVFEFQYLTIGVKFFMKH--GLILELQKIWQ-IEE 239
Query: 68 DSGVEPISQSYLVELSILAPGG--QDVIG---EDMKAFAEQLKPLVQLEKIDYKRL 118
+ S +L++ I G D I + ++L+ ++L D + +
Sbjct: 240 AGNSQITSGGFLLKAYINVSRGTDIDRINYTETVLMNLKKELQGYIELSVPDRQSM 295
>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 = 43.1 bits (101), Expect = 6e-06
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 13/61 (21%)
Query: 71 VEPISQS--YLVELSILA----PGGQDVIGEDMKA---FAEQLKPLVQLEKIDYKRLPLS 121
VE + + +LVE+ Q V D++A L ++L+KID L S
Sbjct: 1830 VERVGKRTGWLVEI---VNYNVENQQYVAAGDLRALDTVTNVLN-FIKLQKIDIIELQKS 1885
Query: 122 M 122
+
Sbjct: 1886 L 1886
Score = 25.4 bits (55), Expect = 6.8
Identities = 10/56 (17%), Positives = 20/56 (35%), Gaps = 8/56 (14%)
Query: 59 FKMSQGKPSDSGV---EPISQSYLVE--LSILAPGGQDVIGEDMKAFAEQLKPLVQ 109
F +P++ EP + + LV L ++ V + F + L +
Sbjct: 37 FNKILPEPTEGFAADDEPTTPAELVGKFLGYVS---SLVEPSKVGQFDQVLNLCLT 89
>2o3l_A Hypothetical protein; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, unknown function; HET: MSE; 2.05A {Bacillus
cereus} SCOP: a.69.4.1
Length = 85
Score = 27.4 bits (61), Expect = 0.59
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 90 QDVIGEDMKAFAEQL 104
D+ GED+ +FA++L
Sbjct: 61 LDITGEDVASFADEL 75
>2o4t_A BH3976 protein; LEFT-handed superhelix fold, structural genomics,
joint CENT structural genomics, JCSG, protein structure
initiative; 1.95A {Bacillus halodurans} SCOP: a.69.4.1
Length = 100
Score = 27.5 bits (61), Expect = 0.62
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 90 QDVIGEDMKAFAEQL 104
DV G D+ AF + L
Sbjct: 58 LDVTGTDVAAFCDAL 72
>2hh6_A BH3980 protein; 10176605, structural genomics, joint center for
STRU genomics, JCSG, protein structure initiative, PSI,
unknown; 2.04A {Bacillus halodurans} SCOP: a.69.4.1
Length = 113
Score = 27.1 bits (60), Expect = 0.82
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 90 QDVIGEDMKAFAEQL 104
D+ GED+ AF ++L
Sbjct: 77 TDLTGEDVAAFCDEL 91
>3nap_A Capsid protein; insect cripavirus, icosahedral virus; 2.50A
{Triatoma virus}
Length = 271
Score = 27.7 bits (60), Expect = 1.2
Identities = 13/88 (14%), Positives = 25/88 (28%), Gaps = 3/88 (3%)
Query: 37 FEYISRGYMFRKGRMKILVSKIFKMSQGKPSDSGVEPISQSYLVELSILAPGGQDVIGED 96
I Y F +G +++ KI +P + I A
Sbjct: 103 LTSIGAMYAFYRGGIRL---KIVPGVADQPKPLVEVALFTMQDQGYIIKANDYSTDFCSS 159
Query: 97 MKAFAEQLKPLVQLEKIDYKRLPLSMAP 124
K + +++ Y R+ S+
Sbjct: 160 NIYENFVTKGIAEVQTPYYSRVNTSVVS 187
>1o5h_A Formiminotetrahydrofolate cyclodeaminase; TM1560, structural
genomics, JCSG, PSI, protein structure initiative, joint
CE structural genomics; 2.80A {Thermotoga maritima}
SCOP: a.191.1.1
Length = 214
Score = 26.3 bits (57), Expect = 2.7
Identities = 10/49 (20%), Positives = 20/49 (40%)
Query: 54 LVSKIFKMSQGKPSDSGVEPISQSYLVELSILAPGGQDVIGEDMKAFAE 102
L + ++ K VEP + + + D+ +DM+AF +
Sbjct: 50 LAEMVANFTRKKKGYEDVEPEMERIVEAMEEARLKLFDLAKKDMEAFEK 98
>1tt9_A Formimidoyltransferase-cyclodeaminase (formiminotransferase-
cyclodeaminase) (FTCD)...; hepatitis autoantigen,
intermediate channeling; 3.42A {Rattus norvegicus} PDB:
2pfd_A
Length = 541
Score = 25.9 bits (56), Expect = 4.3
Identities = 8/49 (16%), Positives = 20/49 (40%)
Query: 54 LVSKIFKMSQGKPSDSGVEPISQSYLVELSILAPGGQDVIGEDMKAFAE 102
L S + +M+ G+ ++ + + + ++ D +AFA
Sbjct: 370 LASMVGQMTYGRRQFDHLDSTMRRLIPPFHAASAQLTSLVDADARAFAA 418
>2a8x_A Dihydrolipoyl dehydrogenase, E3 component of alpha; lipoamide
dehydrogenase, pyruvate dehydrogenase, alpha keto acid
dehydrogenase; HET: FAD; 2.40A {Mycobacterium
tuberculosis} PDB: 3ii4_A*
Length = 464
Score = 25.6 bits (57), Expect = 5.3
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 23 TVVEFLTEMGCRMDFEYISRGYM--FRKGRMKILVSKIFKMSQGKPSDSGVE 72
T+VEFL D + +S+ F+K + IL + K+ S V
Sbjct: 198 TIVEFLPRALPNEDAD-VSKEIEKQFKKLGVTILTAT--KVESIADGGSQVT 246
>1jqk_A CODH, carbon monoxide dehydrogenase; rossmann fold, oxidoreductase;
2.80A {Rhodospirillum rubrum} SCOP: e.26.1.2
Length = 639
Score = 25.3 bits (55), Expect = 7.3
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 78 YLVELSILAPGGQDVIGEDMKAFAEQLKPLVQLEKIDYKRLPL 120
+ E + GG ++ D K+ ++L I +R L
Sbjct: 600 LVTETAKDLVGGYFIVDTDPKSAGDKL-----YAAIQERRAGL 637
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 0.138 0.393
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,854,405
Number of extensions: 99729
Number of successful extensions: 229
Number of sequences better than 10.0: 1
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 15
Length of query: 124
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,412,271
Effective search space: 185315382
Effective search space used: 185315382
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: 51 (23.3 bits)