RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031347
(161 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 = 60.2 bits (147), Expect = 6e-12
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 99 ELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKNVEPSK 140
E L++G + PTDT+Y + CD + A+ERLR IK K
Sbjct: 1 EALRQGGIVAYPTDTVYGLGCDATNEEAVERLREIKGRPRDK 42
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 56.9 bits (138), Expect = 1e-10
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 84 ADPSGADSWKLEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKNVEPSK 140
P +E VE L++G V PTDT+Y + D + A+ERL IK K
Sbjct: 6 IHPENPQPRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDK 62
>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 = 48.9 bits (117), Expect = 1e-07
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 94 LEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKNVEPSK 140
+E V++L++G + V PTDT+Y I D A+ RL RIK +K
Sbjct: 11 IEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNK 57
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 42.6 bits (100), Expect = 2e-05
Identities = 16/40 (40%), Positives = 29/40 (72%)
Query: 98 VELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKNVE 137
VE++++G V V PTD+ YA+ C ++ +A+ER+ RI+ +
Sbjct: 21 VEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLP 60
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine
modification protein; Provisional.
Length = 190
Score = 32.0 bits (73), Expect = 0.070
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 94 LEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKN 135
+ V++L E V PT+ ++ + CD S +A+ RL +K
Sbjct: 10 IAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQ 51
>gnl|CDD|185017 PRK15057, PRK15057, UDP-glucose 6-dehydrogenase; Provisional.
Length = 388
Score = 29.2 bits (65), Expect = 0.89
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|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 27.8 bits (62), Expect = 3.0
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 98 VELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKN 135
+LLK+G + I + + CD ++ +ERLR KN
Sbjct: 169 AKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKN 206
>gnl|CDD|227669 COG5378, COG5378, Predicted nucleotide-binding protein [General
function prediction only].
Length = 175
Score = 27.2 bits (60), Expect = 3.4
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 5/40 (12%)
Query: 114 LYA---IVCDLKSHSAIERLRRIKNVEPSKVRKIASHIFS 150
LYA I+ +LK H IE+ + NV+ SK KIA+ I S
Sbjct: 48 LYAPQLILDELKEH--IEKKCKKANVDESKFIKIANLILS 85
>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases. Small GTP-binding proteins of the Ras
superfamily function as molecular switches in
fundamental events such as signal transduction,
cytoskeleton dynamics and intracellular trafficking.
Guanine-nucleotide-exchange factors (GEFs) positively
regulate these GTP-binding proteins in response to a
variety of signals. GEFs catalyze the dissociation of
GDP from the inactive GTP-binding proteins. GTP can then
bind and induce structural changes that allow
interaction with effectors.
Length = 237
Score = 26.8 bits (60), Expect = 4.4
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 113 TLYAIVCDLKSHSAIERLRRIKNVEPSKVRKI 144
+L AIV L S S I RL++ V SK++K+
Sbjct: 96 SLMAIVSAL-SSSPISRLKKTWEVLSSKLKKL 126
>gnl|CDD|216448 pfam01347, Vitellogenin_N, Lipoprotein amino terminal region. This
family contains regions from: Vitellogenin, Microsomal
triglyceride transfer protein and apolipoprotein B-100.
These proteins are all involved in lipid transport. This
family contains the LV1n chain from lipovitellin, that
contains two structural domains.
Length = 579
Score = 27.3 bits (61), Expect = 4.6
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 126 AIERLRRIKNVEPSKVRKIASHIF 149
A+ LR + P KV+ + I+
Sbjct: 505 AVLALRNLAKKCPRKVQSVLLQIY 528
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 27.0 bits (60), Expect = 5.2
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|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 26.4 bits (59), Expect = 5.5
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 113 TLYAIVCDLKSHSAIERLRRIKNVEPSKVRKI 144
+L AI+ L + S I RL++ + K +K+
Sbjct: 93 SLMAIISGL-NSSPISRLKKTWELVSKKYKKL 123
>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 = 25.7 bits (57), Expect = 5.7
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 = 26.7 bits (59), Expect = 5.9
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|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 26.6 bits (59), Expect = 8.1
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 94 LEPVVELLKEGAVGVIPTDTLYAIVCDLKSHSAIERLRRIKN 135
+ +LLK G + I + + CD ++ A+ +LR+ KN
Sbjct: 200 IRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKN 241
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
0.320 0.133 0.397
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,376,543
Number of extensions: 763295
Number of successful extensions: 767
Number of sequences better than 10.0: 1
Number of HSP's gapped: 764
Number of HSP's successfully gapped: 32
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (25.0 bits)