RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9900
(191 letters)
>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain.
Length = 66
Score = 65.7 bits (161), Expect = 8e-15
Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 4/70 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+ G VK++++K+GFGFIT D +D+FVH S+I F+SL G+ V+F+I G K
Sbjct: 1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTK 56
Query: 69 DIEAINVTGP 78
+A NVT
Sbjct: 57 GPQAANVTLL 66
Score = 65.7 bits (161), Expect = 8e-15
Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 4/70 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
+ G VK++++K+GFGFIT D +D+FVH S+I F+SL G+ V+F+I G K
Sbjct: 1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTK 56
Query: 170 DIEAINVTGP 179
+A NVT
Sbjct: 57 GPQAANVTLL 66
>gnl|CDD|239905 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like
cold-shock domain (CSD) that is found in eukaryotes,
prokaryotes, and archaea. CSP's include the major
cold-shock proteins CspA and CspB in bacteria and the
eukaryotic gene regulatory factor Y-box protein. CSP
expression is up-regulated by an abrupt drop in growth
temperature. CSP's are also expressed under normal
condition at lower level. The function of cold-shock
proteins is not fully understood. They preferentially
bind poly-pyrimidine region of single-stranded RNA and
DNA. CSP's are thought to bind mRNA and regulate
ribosomal translation, mRNA degradation, and the rate
of transcription termination. The human Y-box protein,
which contains a CSD, regulates transcription and
translation of genes that contain the Y-box sequence in
their promoters. This specific ssDNA-binding properties
of CSD are required for the binding of Y-box protein to
the promoter's Y-box sequence, thereby regulating
transcription.
Length = 65
Score = 65.3 bits (160), Expect = 9e-15
Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
V G VK++D ++GFGFIT D ED+FVH S++ F+SL G+ V+F + G K
Sbjct: 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDK 56
Query: 69 DIEAINVTG 77
+A+NV
Sbjct: 57 GPQAVNVRL 65
Score = 65.3 bits (160), Expect = 9e-15
Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
V G VK++D ++GFGFIT D ED+FVH S++ F+SL G+ V+F + G K
Sbjct: 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDK 56
Query: 170 DIEAINVTG 178
+A+NV
Sbjct: 57 GPQAVNVRL 65
>gnl|CDD|224197 COG1278, CspC, Cold shock proteins [Transcription].
Length = 67
Score = 53.7 bits (130), Expect = 3e-10
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
G VK++++ +GFGFIT D +D+FVH S+I + F++L G+ V+F + G+K
Sbjct: 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKG 58
Query: 70 IEAINVT 76
A NV
Sbjct: 59 PSAANVR 65
Score = 53.7 bits (130), Expect = 3e-10
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
G VK++++ +GFGFIT D +D+FVH S+I + F++L G+ V+F + G+K
Sbjct: 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKG 58
Query: 171 IEAINVT 177
A NV
Sbjct: 59 PSAANVR 65
>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional.
Length = 69
Score = 47.8 bits (113), Expect = 5e-08
Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G+K
Sbjct: 4 IKGQVKWFNESKGFGFITPADGSKDVFVHFSAI----QGNGFKTLAEGQNVEFEIQDGQK 59
Query: 69 DIEAINVT 76
A+NVT
Sbjct: 60 GPAAVNVT 67
Score = 47.8 bits (113), Expect = 5e-08
Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G+K
Sbjct: 4 IKGQVKWFNESKGFGFITPADGSKDVFVHFSAI----QGNGFKTLAEGQNVEFEIQDGQK 59
Query: 170 DIEAINVT 177
A+NVT
Sbjct: 60 GPAAVNVT 67
>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed.
Length = 69
Score = 47.0 bits (111), Expect = 9e-08
Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G K
Sbjct: 4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 59
Query: 69 DIEAINVT 76
A NV
Sbjct: 60 GPSAANVI 67
Score = 47.0 bits (111), Expect = 9e-08
Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G K
Sbjct: 4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 59
Query: 170 DIEAINVT 177
A NV
Sbjct: 60 GPSAANVI 67
>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional.
Length = 70
Score = 46.9 bits (111), Expect = 1e-07
Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
GIVK++++ +GFGFIT D +D+FVH S+I ++SL G+ V F I G K
Sbjct: 7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGP 62
Query: 71 EAINVT 76
A NVT
Sbjct: 63 AAGNVT 68
Score = 46.9 bits (111), Expect = 1e-07
Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
GIVK++++ +GFGFIT D +D+FVH S+I ++SL G+ V F I G K
Sbjct: 7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGP 62
Query: 172 EAINVT 177
A NVT
Sbjct: 63 AAGNVT 68
>gnl|CDD|214633 smart00357, CSP, Cold shock protein domain. RNA-binding domain
that functions as a RNA-chaperone in bacteria and is
involved in regulating translation in eukaryotes.
Contains sub-family of RNA-binding domains in the Rho
transcription termination factor.
Length = 64
Score = 45.7 bits (109), Expect = 2e-07
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 9/71 (12%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGK 67
G+VK+++ +GFGFI D +D+FVH S I + +SL G+ V+F + G
Sbjct: 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI-----QGGLKSLREGDEVEFKVVSPEGG 53
Query: 68 KDIEAINVTGP 78
+ EA NV
Sbjct: 54 EKPEAENVVKL 64
Score = 45.7 bits (109), Expect = 2e-07
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 9/71 (12%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGK 168
G+VK+++ +GFGFI D +D+FVH S I + +SL G+ V+F + G
Sbjct: 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI-----QGGLKSLREGDEVEFKVVSPEGG 53
Query: 169 KDIEAINVTGP 179
+ EA NV
Sbjct: 54 EKPEAENVVKL 64
>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional.
Length = 70
Score = 42.4 bits (99), Expect = 5e-06
Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 4/65 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
G+VK++++ +GFGFIT D +D+FVH ++I F++L + V+F+I G++
Sbjct: 7 GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGP 62
Query: 71 EAINV 75
A NV
Sbjct: 63 AAANV 67
Score = 42.4 bits (99), Expect = 5e-06
Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 4/65 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
G+VK++++ +GFGFIT D +D+FVH ++I F++L + V+F+I G++
Sbjct: 7 GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGP 62
Query: 172 EAINV 176
A NV
Sbjct: 63 AAANV 67
>gnl|CDD|131434 TIGR02381, cspD, cold shock domain protein CspD. This model
represents what appears to be a phylogenetically
distinct clade, containing E. coli CspD (SP|P24245) and
related proteobacterial proteins within the larger
family of cold shock domain proteins described by Pfam
model pfam00313. The gene symbol cspD may have been
used idependently for other subfamilies of cold shock
domain proteins, such as for B. subtilis CspD. These
proteins typically are shorter than 70 amino acids. In
E. coli, CspD is a stress response protein induced in
stationary phase. This homodimer binds single-stranded
DNA and appears to inhibit DNA replication [DNA
metabolism, DNA replication, recombination, and repair,
Cellular processes, Adaptations to atypical
conditions].
Length = 68
Score = 41.4 bits (97), Expect = 1e-05
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
GIVK++++ +GFGFI DIF H S+I +M+ +++L G+ V F + G K
Sbjct: 4 GIVKWFNNAKGFGFICPEGVDGDIFAHYSTI-QMDG---YRTLKAGQKVQFEVVQGPKGA 59
Query: 71 EAINV 75
A ++
Sbjct: 60 HATHI 64
Score = 41.4 bits (97), Expect = 1e-05
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
GIVK++++ +GFGFI DIF H S+I +M+ +++L G+ V F + G K
Sbjct: 4 GIVKWFNNAKGFGFICPEGVDGDIFAHYSTI-QMDG---YRTLKAGQKVQFEVVQGPKGA 59
Query: 172 EAINV 176
A ++
Sbjct: 60 HATHI 64
>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional.
Length = 73
Score = 38.5 bits (89), Expect = 1e-04
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
G VK++++ +GFGFI EDIF H S+I +M+ +++L G+ V F++ G K
Sbjct: 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVRFDVHQGPK 57
Score = 38.5 bits (89), Expect = 1e-04
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
G VK++++ +GFGFI EDIF H S+I +M+ +++L G+ V F++ G K
Sbjct: 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVRFDVHQGPK 57
>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible
regulatory protein CspD; Provisional.
Length = 74
Score = 37.8 bits (87), Expect = 3e-04
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+G VK++++ +GFGFI EDIF H S+I +M+ +++L G+ V F++ G K
Sbjct: 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVQFDVHQGPK 57
Score = 37.8 bits (87), Expect = 3e-04
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
+G VK++++ +GFGFI EDIF H S+I +M+ +++L G+ V F++ G K
Sbjct: 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTI-QMDG---YRTLKAGQSVQFDVHQGPK 57
>gnl|CDD|185360 PRK15463, PRK15463, cold shock-like protein CspF; Provisional.
Length = 70
Score = 36.0 bits (83), Expect = 0.001
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSI 41
GIVK +D K G G IT D ++D+ VH S++
Sbjct: 7 GIVKTFDGKSGKGLITPSDGRKDVQVHISAL 37
Score = 36.0 bits (83), Expect = 0.001
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSI 142
GIVK +D K G G IT D ++D+ VH S++
Sbjct: 7 GIVKTFDGKSGKGLITPSDGRKDVQVHISAL 37
>gnl|CDD|185361 PRK15464, PRK15464, cold shock-like protein CspH; Provisional.
Length = 70
Score = 28.9 bits (64), Expect = 0.36
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSS 40
GIVK +D K G GFI D ++++ VH S+
Sbjct: 7 GIVKTFDRKSGKGFIIPSDGRKEVQVHISA 36
Score = 28.9 bits (64), Expect = 0.36
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSS 141
GIVK +D K G GFI D ++++ VH S+
Sbjct: 7 GIVKTFDRKSGKGFIIPSDGRKEVQVHISA 36
>gnl|CDD|203875 pfam08206, OB_RNB, Ribonuclease B OB domain. This family
includes the N-terminal OB domain found in ribonuclease
B proteins in one or two copies.
Length = 58
Score = 28.2 bits (64), Expect = 0.45
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKS 39
G V+ K+GFGF+ D ++DIF+
Sbjct: 1 GTVRG--HKKGFGFLIPDDEEDDIFIPPE 27
Score = 28.2 bits (64), Expect = 0.45
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKS 140
G V+ K+GFGF+ D ++DIF+
Sbjct: 1 GTVRG--HKKGFGFLIPDDEEDDIFIPPE 27
>gnl|CDD|233305 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA.
This model describes the cyt c biogenesis protein
encoded by ccmA in bacteria. An exception is, an
arabidopsis protein. Quite likely this is encoded by an
organelle. Bacterial c-type cytocromes are located on
the periplasmic side of the cytoplasmic membrane.
Several gene products encoded in a locus designated as
'ccm' are implicated in the transport and assembly of
the functional cytochrome C. This cluster includes
genes: ccmA;B;C;D;E;F;G and H. The posttranslational
pathway includes the transport of heme moiety, the
secretion of the apoprotein and the covalent attachment
of the heme with the apoprotein. The proteins ccmA and
B represent an ABC transporter; ccmC and D participate
in heme transfer to ccmE, which function as a
periplasmic heme chaperone. The presence of ccmF, G and
H is suggested to be obligatory for the final
functional assembly of cytochrome c [Protein fate,
Protein and peptide secretion and trafficking,
Transport and binding proteins, Other].
Length = 198
Score = 28.5 bits (64), Expect = 1.7
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 4/23 (17%)
Query: 59 VDFNIGVGKKDIEAINVTGPNGI 81
+ F + G EA+ VTGPNGI
Sbjct: 19 LSFTLNAG----EALQVTGPNGI 37
Score = 28.5 bits (64), Expect = 1.7
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 4/23 (17%)
Query: 160 VDFNIGVGKKDIEAINVTGPNGI 182
+ F + G EA+ VTGPNGI
Sbjct: 19 LSFTLNAG----EALQVTGPNGI 37
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 28.4 bits (64), Expect = 2.7
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 1/43 (2%)
Query: 99 RNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKE-DIFVHKS 140
R + + GFGF+ D+ E DIF+
Sbjct: 56 RRGLYALPESLKLVKGTVIAHRDGFGFLRPEDDDEDDIFIPPR 98
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 28.0 bits (62), Expect = 3.0
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 28 LDNKEDI-FVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGPNGIPVQGA 86
L KE + F+ S++ N +K FQ++ L EI ++I + KK + A +G+P QG
Sbjct: 143 LAEKEGLSFLETSALEATNVEKAFQTI-LLEI--YHI-ISKKALAAQEAAANSGLPGQGT 198
Query: 87 PKSSSETVSGTYR 99
+ ++T R
Sbjct: 199 TINVADTSGNNKR 211
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 26.4 bits (59), Expect = 3.2
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 4 FEIHTVRGIVKFYDSKRGFGFITRLDNKE 32
++ +VR KF S RGF F+ + +E
Sbjct: 25 GQVKSVRLPKKFDGSHRGFAFVEFVTKQE 53
Score = 25.7 bits (57), Expect = 6.0
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 107 VHTVRGIVKFYDSKRGFGFITRLDNKE 133
V +VR KF S RGF F+ + +E
Sbjct: 27 VKSVRLPKKFDGSHRGFAFVEFVTKQE 53
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 25.6 bits (57), Expect = 4.8
Identities = 11/56 (19%), Positives = 18/56 (32%), Gaps = 3/56 (5%)
Query: 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 63
V G V G L N + + S + K + L +G+ V +
Sbjct: 5 VVEGTVT---EITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKV 57
Score = 25.6 bits (57), Expect = 4.8
Identities = 11/56 (19%), Positives = 18/56 (32%), Gaps = 3/56 (5%)
Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
V G V G L N + + S + K + L +G+ V +
Sbjct: 5 VVEGTVT---EITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKV 57
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 26.7 bits (60), Expect = 9.4
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI-GVG 66
V G V + G L++ + + S + + + + L +G+ V+ + +
Sbjct: 463 IVTGTVT---EVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519
Query: 67 KK 68
+K
Sbjct: 520 RK 521
Score = 26.7 bits (60), Expect = 9.4
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI-GVG 167
V G V + G L++ + + S + + + + L +G+ V+ + +
Sbjct: 463 IVTGTVT---EVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519
Query: 168 KK 169
+K
Sbjct: 520 RK 521
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 0.141 0.411
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,846,502
Number of extensions: 922901
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 813
Number of HSP's successfully gapped: 54
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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 (21.7 bits)
S2: 56 (25.3 bits)