RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10920
(271 letters)
>gnl|CDD|215026 smart01104, CTD, Spt5 C-terminal nonapeptide repeat binding Spt4.
The C-terminal domain of the transcription elongation
factor protein Spt5 is necessary for binding to Spt4 to
form the functional complex that regulates early
transcription elongation by RNA polymerase II. The
complex may be involved in pre-mRNA processing through
its association with mRNA capping enzymes. This CTD
domain carries a regular nonapeptide repeat that can be
present in up to 18 copies, as in S. pombe. The repeat
has a characteristic TPA motif.
Length = 121
Score = 36.0 bits (83), Expect = 0.005
Identities = 22/72 (30%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 96 GGKECAWDSTGGKECAWDGRGGKECAWDSRGGKECAWDGRGGKECAWDSRGGKECAWDGR 155
GG+ AW ++G K AW R A + A G G + AW G + AW G
Sbjct: 1 GGRTPAWGASGSKTPAWGSRTPGTAAGGAPT----ARGGSGSRTPAWGGAGSRTPAWGGA 56
Query: 156 GGKECAWDSRGG 167
G + GG
Sbjct: 57 GPTGSRTPAWGG 68
Score = 34.8 bits (80), Expect = 0.011
Identities = 22/72 (30%), Positives = 28/72 (38%), Gaps = 4/72 (5%)
Query: 176 GGKECAWDSRGGKECAWDGRGGKECAWDSRGGKECAWDGRGGKECAWDSRGGKECAWDGR 235
GG+ AW + G K AW R A + A G G + AW G + AW G
Sbjct: 1 GGRTPAWGASGSKTPAWGSRTPGTAAGGAPT----ARGGSGSRTPAWGGAGSRTPAWGGA 56
Query: 236 GGKECAWDSRGG 247
G + GG
Sbjct: 57 GPTGSRTPAWGG 68
Score = 33.6 bits (77), Expect = 0.033
Identities = 20/67 (29%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 81 AWDGRGGKECAWDGRGGKECAWDSTGGKECAWDGRGGKECAWDSRGGKECAWDGRGGKEC 140
AW G K AW R A + A G G + AW G + AW G G
Sbjct: 6 AWGASGSKTPAWGSRTPGTAAGGAPT----ARGGSGSRTPAWGGAGSRTPAWGGAGPTGS 61
Query: 141 AWDSRGG 147
+ GG
Sbjct: 62 RTPAWGG 68
Score = 32.9 bits (75), Expect = 0.053
Identities = 22/72 (30%), Positives = 25/72 (34%), Gaps = 4/72 (5%)
Query: 146 GGKECAWDGRGGKECAWDSRGGKECAWDGRGGKECAWDSRGGKECAWDGRGGKECAWDSR 205
GG+ AW G K AW SR A A G + AW G G + AW
Sbjct: 1 GGRTPAWGASGSKTPAWGSRTPGTAAGGAPT----ARGGSGSRTPAWGGAGSRTPAWGGA 56
Query: 206 GGKECAWDGRGG 217
G GG
Sbjct: 57 GPTGSRTPAWGG 68
Score = 32.1 bits (73), Expect = 0.098
Identities = 21/72 (29%), Positives = 24/72 (33%), Gaps = 4/72 (5%)
Query: 86 GGKECAWDGRGGKECAWDSTGGKECAWDGRGGKECAWDSRGGKECAWDGRGGKECAWDSR 145
GG+ AW G K AW S A A G + AW G G + AW
Sbjct: 1 GGRTPAWGASGSKTPAWGSRTPGTAAGGAPT----ARGGSGSRTPAWGGAGSRTPAWGGA 56
Query: 146 GGKECAWDGRGG 157
G GG
Sbjct: 57 GPTGSRTPAWGG 68
>gnl|CDD|185273 PRK15375, PRK15375, pathogenicity island 1 effector protein StpP;
Provisional.
Length = 535
Score = 29.8 bits (66), Expect = 1.7
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 10 GMAEE-IKKFNVHGMAEEVKHVHGMAEEVKNVHGMAEEVK 48
G E + K + H + + VK +H +A+E+KNV E+++
Sbjct: 244 GEVERWVDKASTHELTQAVKKIHVIAKELKNVTAELEKIE 283
Score = 28.6 bits (63), Expect = 3.6
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 39 NVHGMAEEVKNVHGIAEEVKNVHGMAEEVK 68
+ H + + VK +H IA+E+KNV E+++
Sbjct: 254 STHELTQAVKKIHVIAKELKNVTAELEKIE 283
>gnl|CDD|226557 COG4071, COG4071, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 278
Score = 28.7 bits (64), Expect = 3.4
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 23 MAEEVKHVHGMAEEVKNVHGMAEEVKNVHGIAEEVKN 59
+AE VH + K V+ + EE N + I EE+
Sbjct: 230 IAEICDRVH---KTRKTVYDVLEEYSNPYVITEEILE 263
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the
C-terminus. The beta chain has catalytic activity,
while the alpha chain is a regulatory subunit. The
alpha-subunit contains a highly conserved
adenine-specific noncatalytic nucleotide-binding
domain. The conserved amino acid sequence is
Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase
F1, alpha subunit is homologous to proton translocating
ATP synthase archaeal/vacuolar(V1), B subunit [Energy
metabolism, ATP-proton motive force interconversion].
Length = 501
Score = 28.5 bits (64), Expect = 4.7
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 13 EEIKKFNVHGMAEEVKHVHGMAEEVKNVHG----MAEEV----KNVHGIA 54
+EIK FNV AEEV V + + + V+G M+ E+ V GIA
Sbjct: 13 QEIKNFNVDSEAEEVGTVVSVGDGIARVYGLENVMSGELIEFEGGVQGIA 62
>gnl|CDD|178778 PLN03240, PLN03240, putative Low-temperature-induced protein;
Provisional.
Length = 626
Score = 27.9 bits (61), Expect = 7.8
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 4 EVKNVHGMAEEIKKFNVHGMAEEVKHVHGMAEEVKNVHGMAEEVKNV---HGIAEEVKNV 60
+++ HG + + +H EE H G ++ +K V A+++KNV HG E
Sbjct: 6 QLQRPHGHHQAEEPIRIHHPEEEGHHEKGPSKVLKKVKEKAKKIKNVLTKHGHGHE---- 61
Query: 61 HGMAEEVKNVHGMAEE 76
H E + + H + +E
Sbjct: 62 HDRGEHIPDDHDLDQE 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
0.315 0.136 0.477
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,788,591
Number of extensions: 1261851
Number of successful extensions: 703
Number of sequences better than 10.0: 1
Number of HSP's gapped: 669
Number of HSP's successfully gapped: 39
Length of query: 271
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 176
Effective length of database: 6,723,972
Effective search space: 1183419072
Effective search space used: 1183419072
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: 42 (22.0 bits)
S2: 58 (26.3 bits)