Query 031623
Match_columns 156
No_of_seqs 52 out of 54
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:06:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031623hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3262 H/ACA small nucleolar 20.7 43 0.00093 28.5 0.7 36 2-41 86-124 (215)
2 PF13684 Dak1_2: Dihydroxyacet 16.3 65 0.0014 28.1 0.8 10 106-115 297-306 (313)
3 PF11983 DUF3484: Domain of un 12.4 57 0.0012 23.1 -0.5 7 30-36 66-72 (73)
4 PF08765 Mor: Mor transcriptio 11.9 68 0.0015 23.5 -0.3 11 108-118 43-53 (108)
5 TIGR03599 YloV DAK2 domain fus 11.6 1.1E+02 0.0023 29.0 0.8 10 106-115 514-523 (530)
6 TIGR02593 CRISPR_cas5 CRISPR-a 8.6 64 0.0014 19.9 -1.2 11 34-44 24-34 (42)
7 KOG2199 Signal transducing ada 7.9 1.4E+02 0.0031 28.1 0.3 10 146-155 246-255 (462)
8 KOG2780 Ribosome biogenesis pr 7.2 1.5E+02 0.0032 26.6 0.0 18 31-48 216-233 (302)
9 PF15560 Imm8: Immunity protei 6.5 2.2E+02 0.0047 22.8 0.6 9 106-114 6-14 (133)
10 COG3350 Uncharacterized conser 6.4 1.4E+02 0.0031 20.3 -0.4 13 108-120 22-34 (53)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=20.67 E-value=43 Score=28.52 Aligned_cols=36 Identities=22% Similarity=0.396 Sum_probs=24.4
Q ss_pred CCCCccccCccccccccCCCCCC---CCCCccccccccCCCCc
Q 031623 2 DGKREMSSSFSFTTDLFGTKKSP---PPSSTGIFASILSPPST 41 (156)
Q Consensus 2 E~kK~~sSsss~~~~LFG~k~s~---sssssgiF~SIFppps~ 41 (156)
|+|+|+. -+|||||+-... --.+.+|-+|+|.|=.+
T Consensus 86 enk~qIG----KVDEIfG~i~d~~fsIK~~dgv~assfk~g~k 124 (215)
T KOG3262|consen 86 ENKEQIG----KVDEIFGPINDVHFSIKPSDGVQASSFKPGDK 124 (215)
T ss_pred cchhhhc----chhhhcccccccEEEEecCCCceeecccCCCe
Confidence 5666665 589999997543 22357888888876544
No 2
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=16.26 E-value=65 Score=28.11 Aligned_cols=10 Identities=50% Similarity=1.092 Sum_probs=8.3
Q ss_pred ceeecccccc
Q 031623 106 SLYYGGQDIY 115 (156)
Q Consensus 106 SIyYGGqD~Y 115 (156)
-+|||||.+|
T Consensus 297 e~~~GgQ~~y 306 (313)
T PF13684_consen 297 EVYDGGQPLY 306 (313)
T ss_pred EEEECCCcce
Confidence 4889999987
No 3
>PF11983 DUF3484: Domain of unknown function (DUF3484); InterPro: IPR021873 FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains []. This C-terminal domain is found in FtsA from Firmicutes (Gram-positive bacteria). It is typically between 65 to 81 amino acids in length.
Probab=12.35 E-value=57 Score=23.07 Aligned_cols=7 Identities=43% Similarity=1.037 Sum_probs=5.8
Q ss_pred ccccccc
Q 031623 30 GIFASIL 36 (156)
Q Consensus 30 giF~SIF 36 (156)
|||++||
T Consensus 66 ~~fgsmF 72 (73)
T PF11983_consen 66 GFFGSMF 72 (73)
T ss_pred HHHhhhc
Confidence 7888888
No 4
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=11.85 E-value=68 Score=23.50 Aligned_cols=11 Identities=55% Similarity=1.171 Sum_probs=3.7
Q ss_pred eeccccccCCC
Q 031623 108 YYGGQDIYSHS 118 (156)
Q Consensus 108 yYGGqD~Ys~~ 118 (156)
||||+.+|-|.
T Consensus 43 ~~gG~~iyiP~ 53 (108)
T PF08765_consen 43 YFGGQQIYIPK 53 (108)
T ss_dssp HH-SS------
T ss_pred HHCCEeEEeeC
Confidence 79999999874
No 5
>TIGR03599 YloV DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling.
Probab=11.56 E-value=1.1e+02 Score=29.04 Aligned_cols=10 Identities=50% Similarity=1.129 Sum_probs=6.6
Q ss_pred ceeecccccc
Q 031623 106 SLYYGGQDIY 115 (156)
Q Consensus 106 SIyYGGqD~Y 115 (156)
-+|||||.+|
T Consensus 514 e~~~GgQ~~y 523 (530)
T TIGR03599 514 EIYEGGQPLY 523 (530)
T ss_pred EEEECCCCce
Confidence 3677777766
No 6
>TIGR02593 CRISPR_cas5 CRISPR-associated protein Cas5, N-terminal domain. This model represents a shared N-terminal domain, about 43 amino acids in length, common to a number of related protein families each of which is associated with a distinct subtype of CRISPR/cas system, where CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeat and Cas is an abbreviation for CRISPR-associated. Members of this family are widely distributed enough that we designated the family Cas5. Homology appears remote, or absent, between the more C-terminal regions different subfamilies of these proteins, which typically are 210 to 265 amino acids in total length. Cas5 proteins of six different CRISPR/cas subtypes so far defined are described by respective full-length models TIGR01868, TIGR01876, TIGR01895, TIGR01874, TIGR02586, and TIGR02592. The best characterized protein in this family is DevS or Myxococcus xanthus, a Cas protein that appears to participate in a species-specific
Probab=8.56 E-value=64 Score=19.92 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=7.5
Q ss_pred cccCCCCccCC
Q 031623 34 SILSPPSTAMG 44 (156)
Q Consensus 34 SIFppps~v~G 44 (156)
--||||+++.|
T Consensus 24 y~~Pp~Stv~G 34 (42)
T TIGR02593 24 YPVPPPSALLG 34 (42)
T ss_pred CCCCCHHHHHH
Confidence 35778887665
No 7
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=7.92 E-value=1.4e+02 Score=28.11 Aligned_cols=10 Identities=50% Similarity=1.371 Sum_probs=7.3
Q ss_pred CCccCCCcCC
Q 031623 146 SRGNWWQGTQ 155 (156)
Q Consensus 146 SRGnWWqGSl 155 (156)
+--|||+|.+
T Consensus 246 s~~~WWKG~~ 255 (462)
T KOG2199|consen 246 SDPNWWKGEN 255 (462)
T ss_pred CCcchhcccc
Confidence 3359999974
No 8
>KOG2780 consensus Ribosome biogenesis protein RPF1, contains IMP4 domain [RNA processing and modification]
Probab=7.16 E-value=1.5e+02 Score=26.59 Aligned_cols=18 Identities=28% Similarity=0.462 Sum_probs=14.8
Q ss_pred ccccccCCCCccCCCCCc
Q 031623 31 IFASILSPPSTAMGRNSS 48 (156)
Q Consensus 31 iF~SIFppps~v~Gr~s~ 48 (156)
+|.||||+++.-.||..+
T Consensus 216 ~f~sLfp~~p~f~gRrvv 233 (302)
T KOG2780|consen 216 LFASLFPHDPQFTGRRVV 233 (302)
T ss_pred HHHHhCCCCccccceeEE
Confidence 689999999987777653
No 9
>PF15560 Imm8: Immunity protein 8
Probab=6.53 E-value=2.2e+02 Score=22.83 Aligned_cols=9 Identities=33% Similarity=0.379 Sum_probs=7.2
Q ss_pred ceeeccccc
Q 031623 106 SLYYGGQDI 114 (156)
Q Consensus 106 SIyYGGqD~ 114 (156)
+|+||||+.
T Consensus 6 n~ViGG~~~ 14 (133)
T PF15560_consen 6 NIVIGGQID 14 (133)
T ss_pred EEEEcCcch
Confidence 578999884
No 10
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=6.43 E-value=1.4e+02 Score=20.32 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=10.6
Q ss_pred eeccccccCCCCC
Q 031623 108 YYGGQDIYSHSLD 120 (156)
Q Consensus 108 yYGGqD~Ys~~~~ 120 (156)
-|+|+.+|.+++.
T Consensus 22 ~Y~GktYYFcse~ 34 (53)
T COG3350 22 SYGGKTYYFCSEE 34 (53)
T ss_pred EeCCEEEEEeCHH
Confidence 4999999998653
Done!