Query 031413
Match_columns 160
No_of_seqs 51 out of 53
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 13:45:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031413.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031413hhsearch_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 21.4 44 0.00096 28.6 0.9 34 2-39 86-124 (215)
2 PF13684 Dak1_2: Dihydroxyacet 12.4 95 0.0021 27.2 0.8 11 112-122 297-307 (313)
3 PF11983 DUF3484: Domain of un 11.7 59 0.0013 23.1 -0.6 8 27-34 65-72 (73)
4 PF08765 Mor: Mor transcriptio 11.1 72 0.0016 23.5 -0.3 10 114-123 43-52 (108)
5 TIGR03599 YloV DAK2 domain fus 8.7 1.5E+02 0.0033 28.1 0.8 11 112-122 514-524 (530)
6 KOG2199 Signal transducing ada 8.3 1.3E+02 0.0029 28.5 0.2 10 149-158 246-255 (462)
7 PF12206 DUF3599: Domain of un 7.7 1.2E+02 0.0026 24.0 -0.3 11 64-74 24-34 (117)
8 KOG2374 Uncharacterized conser 6.9 1.6E+02 0.0035 28.9 0.1 27 94-120 448-476 (661)
9 COG3350 Uncharacterized conser 6.1 1.5E+02 0.0033 20.4 -0.4 12 114-126 22-33 (53)
10 TIGR02593 CRISPR_cas5 CRISPR-a 6.0 1.2E+02 0.0026 18.8 -1.0 11 32-42 24-34 (42)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=21.45 E-value=44 Score=28.65 Aligned_cols=34 Identities=35% Similarity=0.632 Sum_probs=24.3
Q ss_pred CCCCCCCCCCcccccccCCCCC-----CCCCcccccccCCCcc
Q 031413 2 EGRKQTGSSSSLTNELFGSKES-----SSSSGIFGSIFSPPSK 39 (160)
Q Consensus 2 E~kKk~~sSsS~~~~LFG~k~s-----ssssgiF~SIFppps~ 39 (160)
|+|+|.+ -+|||||+-.. -.+.+|-.|+|.|=.+
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 5566655 38999999865 3567888888876544
No 2
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=12.45 E-value=95 Score=27.20 Aligned_cols=11 Identities=45% Similarity=1.014 Sum_probs=8.8
Q ss_pred ceeecCccccC
Q 031413 112 SIYYGGQDVYS 122 (160)
Q Consensus 112 SIyYGGqd~Ys 122 (160)
-+|||||.+|.
T Consensus 297 e~~~GgQ~~y~ 307 (313)
T PF13684_consen 297 EVYDGGQPLYP 307 (313)
T ss_pred EEEECCCcceE
Confidence 48899998874
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=11.73 E-value=59 Score=23.14 Aligned_cols=8 Identities=63% Similarity=1.360 Sum_probs=6.4
Q ss_pred Cccccccc
Q 031413 27 SGIFGSIF 34 (160)
Q Consensus 27 sgiF~SIF 34 (160)
-|||++||
T Consensus 65 R~~fgsmF 72 (73)
T PF11983_consen 65 RGFFGSMF 72 (73)
T ss_pred HHHHhhhc
Confidence 47888888
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=11.12 E-value=72 Score=23.47 Aligned_cols=10 Identities=60% Similarity=1.544 Sum_probs=3.7
Q ss_pred eecCccccCC
Q 031413 114 YYGGQDVYSP 123 (160)
Q Consensus 114 yYGGqd~Ys~ 123 (160)
||||+.+|-|
T Consensus 43 ~~gG~~iyiP 52 (108)
T PF08765_consen 43 YFGGQQIYIP 52 (108)
T ss_dssp HH-SS-----
T ss_pred HHCCEeEEee
Confidence 7999999985
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=8.73 E-value=1.5e+02 Score=28.10 Aligned_cols=11 Identities=55% Similarity=1.044 Sum_probs=7.2
Q ss_pred ceeecCccccC
Q 031413 112 SIYYGGQDVYS 122 (160)
Q Consensus 112 SIyYGGqd~Ys 122 (160)
-+|||||..|.
T Consensus 514 e~~~GgQ~~y~ 524 (530)
T TIGR03599 514 EIYEGGQPLYP 524 (530)
T ss_pred EEEECCCCcee
Confidence 46777777663
No 6
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=8.31 E-value=1.3e+02 Score=28.50 Aligned_cols=10 Identities=50% Similarity=1.258 Sum_probs=7.6
Q ss_pred CCCccCCccc
Q 031413 149 SRGNWWQGSL 158 (160)
Q Consensus 149 SRGnWWQGSl 158 (160)
+--|||+|.+
T Consensus 246 s~~~WWKG~~ 255 (462)
T KOG2199|consen 246 SDPNWWKGEN 255 (462)
T ss_pred CCcchhcccc
Confidence 3479999974
No 7
>PF12206 DUF3599: Domain of unknown function (DUF3599); InterPro: IPR024556 This family of bacterial proteins includes phage-like element PBSX protein xkdH from Bacillus subtilis. The function of the family is unknown.; PDB: 3F3B_A.
Probab=7.70 E-value=1.2e+02 Score=23.96 Aligned_cols=11 Identities=27% Similarity=0.054 Sum_probs=6.2
Q ss_pred CCCCCcccccC
Q 031413 64 TKPTTPVLLLS 74 (160)
Q Consensus 64 ~k~~~~~~~~~ 74 (160)
+|+|+|...++
T Consensus 24 gkfGip~e~~~ 34 (117)
T PF12206_consen 24 GKFGIPAEDLQ 34 (117)
T ss_dssp BTTTB---TTS
T ss_pred cccCCCHHHcC
Confidence 48999987775
No 8
>KOG2374 consensus Uncharacterized conserved protein [Function unknown]
Probab=6.88 E-value=1.6e+02 Score=28.93 Aligned_cols=27 Identities=15% Similarity=0.327 Sum_probs=21.0
Q ss_pred CCCccccCCCCCCC--ccccceeecCccc
Q 031413 94 DMSSMYQDQRVQPC--HLSSSIYYGGQDV 120 (160)
Q Consensus 94 d~~s~yq~e~~epc--~lSSSIyYGGqd~ 120 (160)
-.-+.|-+|+++.+ -|+=+++|+|++-
T Consensus 448 ~qa~~~~eer~~~ptVP~g~dLkywG~e~ 476 (661)
T KOG2374|consen 448 LQATVYREERTETPTVPCGADLKYWGLEQ 476 (661)
T ss_pred HHHHHHhhccccCCcCCcccchhhhhhhc
Confidence 34567788887766 6788999999984
No 9
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=6.11 E-value=1.5e+02 Score=20.35 Aligned_cols=12 Identities=33% Similarity=0.617 Sum_probs=9.6
Q ss_pred eecCccccCCCCC
Q 031413 114 YYGGQDVYSPRPP 126 (160)
Q Consensus 114 yYGGqd~Ys~~~~ 126 (160)
-|+|+.+|. +++
T Consensus 22 ~Y~GktYYF-cse 33 (53)
T COG3350 22 SYGGKTYYF-CSE 33 (53)
T ss_pred EeCCEEEEE-eCH
Confidence 499999999 554
No 10
>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=5.95 E-value=1.2e+02 Score=18.82 Aligned_cols=11 Identities=45% Similarity=0.770 Sum_probs=7.4
Q ss_pred cccCCCccccC
Q 031413 32 SIFSPPSKVLG 42 (160)
Q Consensus 32 SIFppps~v~g 42 (160)
--||||+++.|
T Consensus 24 y~~Pp~Stv~G 34 (42)
T TIGR02593 24 YPVPPPSALLG 34 (42)
T ss_pred CCCCCHHHHHH
Confidence 45777777665
Done!