RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032838
(132 letters)
>gnl|CDD|216422 pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has
been shown to bind preferentially to dsRNA. The domain
is found in SUA5 as well as HypF and YrdC. It has also
been shown to be required for telomere recombniation in
yeast.
Length = 178
Score = 51.7 bits (125), Expect = 3e-09
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 99 ELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRR 132
E L++G + PTDT+Y + CD + A+ERLR
Sbjct: 1 EALRQGGIVAYPTDTVYGLGCDATNEEAVERLRE 34
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 51.5 bits (124), Expect = 7e-09
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 84 ADPSGADSWKLEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRR 132
P +E VE L++G V PTDT+Y + D + A+ERL
Sbjct: 6 IHPENPQPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYE 54
>gnl|CDD|232802 TIGR00057, TIGR00057, tRNA threonylcarbamoyl adenosine modification
protein, Sua5/YciO/YrdC/YwlC family. Has paralogs, but
YrdC called a tRNA modification protein. Ref 2 authors
say probably heteromultimeric complex. Paralogs may mean
its does the final binding to the tRNA [Protein
synthesis, tRNA and rRNA base modification].
Length = 201
Score = 43.9 bits (104), Expect = 3e-06
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 94 LEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRR 132
+E V++L++G + V PTDT+Y I D A+ RL R
Sbjct: 11 IEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYR 49
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 39.1 bits (91), Expect = 2e-04
Identities = 15/35 (42%), Positives = 26/35 (74%)
Query: 98 VELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRR 132
VE++++G V V PTD+ YA+ C ++ +A+ER+ R
Sbjct: 21 VEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICR 55
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine
modification protein; Provisional.
Length = 190
Score = 30.1 bits (68), Expect = 0.21
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 94 LEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERL 130
+ V++L E V PT+ ++ + CD S +A+ RL
Sbjct: 10 IAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRL 46
>gnl|CDD|185017 PRK15057, PRK15057, UDP-glucose 6-dehydrogenase; Provisional.
Length = 388
Score = 29.6 bits (66), Expect = 0.46
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 56 AMTVKRSPKRLKYSAPQFTKEGGLMYVEADPS----GADSWKLEPVVELLKEGAVGV-IP 110
AM K + + +S P+F +EG +Y PS G S + E LL+EGA+ IP
Sbjct: 126 AMHKKYRTENIIFS-PEFLREGKALYDNLHPSRIVIGERSERAERFAALLQEGAIKQNIP 184
Query: 111 T 111
T
Sbjct: 185 T 185
>gnl|CDD|176923 cd09030, DUF1425, Putative periplasmic lipoprotein. This
bacterial family of proteins contains members described
as putative lipoproteins, some are also known as YcfL.
The function of this family is unknown. Family members
have also been annotated as predicted periplasmic
lipoproteins (COG5633), and appear to contain an
N-terminal membrane lipoprotein lipid attachment side
(pfam08139), which is not included in this alignment
model.
Length = 101
Score = 26.1 bits (58), Expect = 3.1
Identities = 5/16 (31%), Positives = 11/16 (68%)
Query: 39 RVSSVSPNPKPSRYRI 54
+ +V+PNP+ +R+
Sbjct: 83 TLQAVAPNPEAKDFRL 98
>gnl|CDD|182196 PRK10017, PRK10017, colanic acid biosynthesis protein; Provisional.
Length = 426
Score = 27.0 bits (60), Expect = 3.5
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 15/48 (31%)
Query: 8 GGDTAFLLRSH------SHSHSHFLEAATRRA---------APFPGRV 40
G DTA+L+ H S++ H+L+ A ++ APF R+
Sbjct: 204 GVDTAWLVDHHTEDFTASYAVQHWLDVAAQQKTVAITLRELAPFDKRL 251
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 27.0 bits (60), Expect = 3.9
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 44 SPNPKPSRYRILAMTVKRSPKRLKY--SAPQFTKEGGLMYVEADPSGADSWKLEPVVELL 101
SP SRY + +R+ + SAPQ + + EA+ +G D ++ VV+ L
Sbjct: 628 SPLADRSRYSGHLIDFNVRAERMGWLPSAPQLNRNPLDIADEAEAAGLDP--VDYVVQQL 685
Query: 102 KEGAV 106
K G +
Sbjct: 686 KSGKL 690
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and
archaea also match the model The seed members used to
make the model include Nitrate reductases from
Pseudomonas fluorescens (GP:11344601), E.coli and
B.subtilis. All seed members are experimentally
characterized. Some unpublished nitrate reductases, that
are shorter sequences, and probably fragments fall in
between the noise and trusted cutoffs. Pfam models
pfam00384 (Molybdopterin oxidoreductase) and
pfam01568(Molydopterin dinucleotide binding domain) will
also match the nitrate reductase, alpha subunit [Energy
metabolism, Anaerobic].
Length = 1235
Score = 26.1 bits (57), Expect = 8.6
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 43 VSPNPKPSRYRILAMTVKRSPKRLKY--SAPQFTKEGGLMYVEADPSGADSWKLEPVVEL 100
+SP SRY + +R+ + SAPQ + EA+ +G + ++ VV+
Sbjct: 629 LSPMADKSRYTGHLIDYNVRAERMGWLPSAPQLNTNPLTIAGEAEKAGMNP--VDYVVKS 686
Query: 101 LKEGAV 106
L+EG++
Sbjct: 687 LQEGSL 692
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 25.2 bits (56), Expect = 9.5
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 113 TLYAIVCDLKSHSAIERLRR 132
+L AI+ L + S I RL++
Sbjct: 93 SLMAIISGL-NSSPISRLKK 111
>gnl|CDD|184499 PRK14090, PRK14090, phosphoribosylformylglycinamidine synthase II;
Provisional.
Length = 601
Score = 25.6 bits (56), Expect = 9.6
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 103 EGAVGVIPTDTLYAIVCDLKSH---SAIE 128
EG GV+ D Y+I ++SH SAIE
Sbjct: 49 EGNAGVVNLDDYYSIAFKIESHNHPSAIE 77
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.132 0.393
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,829,062
Number of extensions: 602176
Number of successful extensions: 579
Number of sequences better than 10.0: 1
Number of HSP's gapped: 576
Number of HSP's successfully gapped: 27
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)