RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3927
(262 letters)
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 197 bits (504), Expect = 6e-64
Identities = 86/201 (42%), Positives = 111/201 (55%), Gaps = 24/201 (11%)
Query: 19 PNHIAQQLTHIELERLSFIGPEEFV-QAFAKENPHLETSFKDMKRTRNLENYVQWFNRLS 77
P +A+QLT IE E S I P E + A+ K KD K + N+E ++ FN+LS
Sbjct: 5 PLELARQLTLIESELFSAIDPRELLDSAWGK---------KDSKLSPNIEAFISRFNQLS 55
Query: 78 YLVATEVVKHVKKKQRVKVVEFWIEAARECFNIGNFNSLMAIIAGLNMSPISRLKKTWNK 137
VATE++ K+R KV++ +I+ A+ C + NFNSLMAII+GLN SPISRLKKTW
Sbjct: 56 RWVATEILSEEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLNSSPISRLKKTWEL 115
Query: 138 IQSG---KFSILEHQMDPSSNFSSYRSTLKAAMWRSAGATDERQRIVIPFFSLLVKDLYF 194
+ LE M PS NF +YR LK A IPF L +KDL F
Sbjct: 116 VSKKYKKLLEELEELMSPSKNFKNYREALKKA-----------NPPCIPFLGLYLKDLTF 164
Query: 195 LNEGCTNKLPNGHINFEKFWQ 215
+ EG + L NG INFEK +
Sbjct: 165 IEEGNPDFLDNGLINFEKRRK 185
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 187 bits (477), Expect = 4e-59
Identities = 80/241 (33%), Positives = 118/241 (48%), Gaps = 21/241 (8%)
Query: 19 PNHIAQQLTHIELERLSFIGPEEFVQAFAKENPHLETSFKDMKRTRNLENYVQWFNRLSY 78
P +A+QLT ++ E I P E + K NLE +++ FN +S
Sbjct: 6 PKELAEQLTLLDFELFRKIDPSELLG-SVWGKRS-----KKSPSPLNLEAFIRRFNEVSN 59
Query: 79 LVATEVVKHVKKKQRVKVVEFWIEAARECFNIGNFNSLMAIIAGLNMSPISRLKKTWNKI 138
VATE++K K R +++ +I+ A+ C + NFNSLMAI++ L+ SPISRLKKTW K+
Sbjct: 60 WVATEILKQTTPKDRAELLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKL 119
Query: 139 QSGK---FSILEHQMDPSSNFSSYRSTLKAAMWRSAGATDERQRIVIPFFSLLVKDLYFL 195
S F LE + P N+ +YR L + IPF +L+KDL F+
Sbjct: 120 PSKYKKLFEELEELLSPERNYKNYREALSS----------CNLPPCIPFLGVLLKDLTFI 169
Query: 196 NEGCTNKLPNGHINFEKFWQLAKQVTEFITWKQVTCPFGKVNKTI--MFLQSSPVLTEND 253
+EG + L NG +NFEK Q+A+ + E + I + Q L E +
Sbjct: 170 DEGNPDFLENGLVNFEKRRQIAEILREIRQLQSQPYNLRPNRSDIQSLLQQLLDHLDEEE 229
Query: 254 E 254
E
Sbjct: 230 E 230
>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 = 180 bits (459), Expect = 1e-56
Identities = 77/240 (32%), Positives = 124/240 (51%), Gaps = 18/240 (7%)
Query: 19 PNHIAQQLTHIELERLSFIGPEEFVQAFAKENPHLETSFKDMKRTRNLENYVQWFNRLSY 78
P +A+QLT ++ E I P E + + K++ + NLE +++ FN LS
Sbjct: 6 PKELAEQLTLLDFELFRKIEPFELLGSLWS------KKDKNIHLSPNLERFIERFNNLSN 59
Query: 79 LVATEVVKHVKKKQRVKVVEFWIEAARECFNIGNFNSLMAIIAGLNMSPISRLKKTWNKI 138
VA+E++ K+R +++ +I+ A+ C + NFNSLMAI++ L+ SPISRLKKTW +
Sbjct: 60 WVASEILLCTNPKKRARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVL 119
Query: 139 QSGK---FSILEHQMDPSSNFSSYRSTLKAAMWRSAGATDERQRIVIPFFSLLVKDLYFL 195
S F LE +DPS NF +YR LK+ +PF + +KDL FL
Sbjct: 120 SSKLKKLFEELEELVDPSRNFKNYRKLLKSV---------GPNPPCVPFLGVYLKDLTFL 170
Query: 196 NEGCTNKLPNGHINFEKFWQLAKQVTEFITWKQVTCPFGKVNKTIMFLQSSPVLTENDED 255
+EG + L +NFEK ++A+ + E + + + + FL L N+++
Sbjct: 171 HEGNPDFLEGNLVNFEKRRKIAEILREIRQLQSNSYELNRDEDILAFLWKLLELILNEDE 230
>gnl|CDD|215850 pfam00309, Sigma54_AID, Sigma-54 factor, Activator interacting
domain (AID). The sigma-54 holoenzyme is an enhancer
dependent form of the RNA polymerase. The AID is
necessary for activator interaction. In addition, the
AID also inhibits transcription initiation in the
sigma-54 holoenzyme prior to interaction with the
activator.
Length = 49
Score = 26.7 bits (60), Expect = 2.2
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 8/30 (26%)
Query: 25 QLTHIELERLSFIGPEEFVQAFAKENPHLE 54
QL+ +ELE E+++ +ENP LE
Sbjct: 25 QLSTLELE--------EYIEEELEENPLLE 46
>gnl|CDD|235648 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
Length = 455
Score = 29.0 bits (66), Expect = 2.5
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 8/30 (26%)
Query: 25 QLTHIELERLSFIGPEEFVQAFAKENPHLE 54
QL+ +EL+ + ++ +ENP LE
Sbjct: 27 QLSTLELQ--------QELEQALEENPLLE 48
>gnl|CDD|225209 COG2329, COG2329, Uncharacterized enzyme involved in biosynthesis
of extracellular polysaccharides [General function
prediction only].
Length = 105
Score = 27.3 bits (61), Expect = 3.9
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 40 EEFVQAFAKENPHLETS--FKDMKRTRNLE 67
EEF + FA LE F + R
Sbjct: 17 EEFEERFANRAGLLEEMPGFIGFELLRPKT 46
>gnl|CDD|233480 TIGR01579, MiaB-like-C, MiaB-like tRNA modifying enzyme. This
clade of sequences is closely related to MiaB, a
modifier of isopentenylated adenosine-37 of certain
eukaryotic and bacterial tRNAs (see TIGR01574). Sequence
alignments suggest that this equivalog performs the same
chemical transformation as MiaB, perhaps on a different
(or differently modified) tRNA base substrate. This
clade is a member of a subfamily (TIGR00089) and spans
low GC Gram positive bacteria, alpha and epsilon
proteobacteria, Campylobacter, Porphyromonas, Aquifex,
Thermotoga, Chlamydia, Treponema and Fusobacterium
[Protein synthesis, tRNA and rRNA base modification].
Length = 414
Score = 28.1 bits (63), Expect = 4.5
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 15/67 (22%)
Query: 25 QLTHIELERLSFIGP----EEFVQAFAKEN---PHLETS--------FKDMKRTRNLENY 69
Q+ I+ RLS I P EE ++A A E PHL S K M+R +++
Sbjct: 216 QIPGIKRIRLSSIDPEDIDEELLEAIASEKRLCPHLHLSLQSGSDRVLKRMRRKYTRDDF 275
Query: 70 VQWFNRL 76
++ N+L
Sbjct: 276 LKLVNKL 282
>gnl|CDD|224425 COG1508, RpoN, DNA-directed RNA polymerase specialized sigma
subunit, sigma54 homolog [Transcription].
Length = 444
Score = 27.7 bits (62), Expect = 6.2
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 25 QLTHIELERLSFIGPEEFVQAFAKENPHLETSFKDMKRTR 64
QL+ IELE + ++ ++NP LE D K
Sbjct: 27 QLSTIELE--------QEIEQELEDNPLLERKDTDDKEFS 58
>gnl|CDD|182513 PRK10519, PRK10519, hypothetical protein; Provisional.
Length = 151
Score = 26.9 bits (60), Expect = 7.4
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 90 KKQRVKVVEFWIEAARECFNIGNF----NSLMA--IIAGLNMS 126
+ + V + +I+ AR+ F I N LMA II LN++
Sbjct: 1 TQVKKNVTDIFIDGARKGFTIATTNLLPNVLMAFVIIQALNIT 43
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 0.405
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,334,142
Number of extensions: 1231311
Number of successful extensions: 973
Number of sequences better than 10.0: 1
Number of HSP's gapped: 964
Number of HSP's successfully gapped: 14
Length of query: 262
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 167
Effective length of database: 6,723,972
Effective search space: 1122903324
Effective search space used: 1122903324
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: 58 (26.1 bits)