Query 537021.9.peg.423_1
Match_columns 37
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Tue May 24 20:51:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_423.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02954 Sig70_famx3 RNA poly 43.2 12 0.00031 18.2 1.3 10 25-34 75-84 (173)
2 pfam06407 BDV_P40 Borna diseas 24.2 43 0.0011 15.4 1.5 11 26-36 137-147 (370)
3 PRK00573 lspA signal peptidase 24.1 62 0.0016 14.6 2.4 14 17-30 91-104 (184)
4 TIGR02061 aprA adenylylsulfate 20.3 36 0.00093 15.8 0.5 13 20-32 44-56 (651)
5 KOG1060 consensus 15.2 59 0.0015 14.8 0.6 17 14-30 90-114 (968)
6 KOG3574 consensus 14.4 67 0.0017 14.5 0.7 11 13-23 35-45 (510)
7 COG1008 NuoM NADH:ubiquinone o 12.3 1.2E+02 0.0031 13.1 3.2 23 3-25 132-154 (497)
8 pfam12606 RELT Tumour necrosis 12.1 1.3E+02 0.0032 13.1 1.6 20 12-31 4-23 (50)
9 TIGR01972 NDH_I_M proton-trans 11.8 1.3E+02 0.0033 13.0 3.3 21 3-23 142-162 (532)
10 pfam08710 nsp9 nsp9 replicase. 10.7 17 0.00042 17.5 -3.3 12 16-27 85-96 (111)
No 1
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This entry is found in certain Bacillus and Clostridium species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=43.20 E-value=12 Score=18.20 Aligned_cols=10 Identities=70% Similarity=1.056 Sum_probs=8.0
Q ss_pred HHHHHHHHHH
Q ss_conf 6989999998
Q 537021.9.peg.4 25 SINTCIDLLI 34 (37)
Q Consensus 25 sintcidlli 34 (37)
-||+||++|-
T Consensus 75 LIn~ci~lL~ 84 (173)
T TIGR02954 75 LINECIDLLK 84 (173)
T ss_pred HHHHHHHHHH
T ss_conf 9999999984
No 2
>pfam06407 BDV_P40 Borna disease virus P40 protein. This family consists of several Borna disease virus P40 proteins. Borna disease (BD) is a persistent viral infection of the central nervous system caused by the single-negative-strand, nonsegmented RNA Borna disease virus (BDV). P40 is known to be a nucleoprotein.
Probab=24.23 E-value=43 Score=15.43 Aligned_cols=11 Identities=45% Similarity=1.035 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q ss_conf 98999999841
Q 537021.9.peg.4 26 INTCIDLLIGI 36 (37)
Q Consensus 26 intcidlligi 36 (37)
.+.|-|||||+
T Consensus 137 ~~HCCdLLIGv 147 (370)
T pfam06407 137 FSHCCSLLIGV 147 (370)
T ss_pred HHHHHHHHHHH
T ss_conf 99989988877
No 3
>PRK00573 lspA signal peptidase II; Provisional
Probab=24.08 E-value=62 Score=14.63 Aligned_cols=14 Identities=43% Similarity=0.814 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999998698999
Q 537021.9.peg.4 17 LYFVQGLLSINTCI 30 (37)
Q Consensus 17 lyfvqgllsintci 30 (37)
.||+||++|+-.-+
T Consensus 91 vYflQ~~ls~i~lf 104 (184)
T PRK00573 91 VYFLQGFLSFIALF 104 (184)
T ss_pred CHHHHHHHHHHHHH
T ss_conf 03998889999999
No 4
>TIGR02061 aprA adenylylsulfate reductase, alpha subunit; InterPro: IPR011803 During dissimilatory sulphate reduction or sulphur oxidation, adenylylsulphate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulphite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. This entry describes the alpha subunit of APS reductase, which shares a common evolutionary origin with fumarate reductase/succinate dehydrogenase flavoproteins..
Probab=20.28 E-value=36 Score=15.80 Aligned_cols=13 Identities=54% Similarity=0.746 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999869899999
Q 537021.9.peg.4 20 VQGLLSINTCIDL 32 (37)
Q Consensus 20 vqgllsintcidl 32 (37)
-|||-.|||-||+
T Consensus 44 AQGLsAINtY~g~ 56 (651)
T TIGR02061 44 AQGLSAINTYLGL 56 (651)
T ss_pred HHHHHHHHHHCCC
T ss_conf 7667898865167
No 5
>KOG1060 consensus
Probab=15.22 E-value=59 Score=14.75 Aligned_cols=17 Identities=47% Similarity=0.890 Sum_probs=12.4
Q ss_pred HHHHHHHH--------HHHHHHHHH
Q ss_conf 99999999--------998698999
Q 537021.9.peg.4 14 LIFLYFVQ--------GLLSINTCI 30 (37)
Q Consensus 14 liflyfvq--------gllsintci 30 (37)
|+++|.+| .||||||--
T Consensus 90 LVyvYLlrYAEeqpdLALLSIntfQ 114 (968)
T KOG1060 90 LVYVYLLRYAEEQPDLALLSINTFQ 114 (968)
T ss_pred HHHHHHHHHHHCCCCCEEEEHHHHH
T ss_conf 8999988775308881355678888
No 6
>KOG3574 consensus
Probab=14.36 E-value=67 Score=14.47 Aligned_cols=11 Identities=55% Similarity=1.310 Sum_probs=7.7
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999999
Q 537021.9.peg.4 13 VLIFLYFVQGL 23 (37)
Q Consensus 13 vliflyfvqgl 23 (37)
.|+|||.+||+
T Consensus 35 lLl~LYllQGi 45 (510)
T KOG3574 35 LLLFLYLLQGI 45 (510)
T ss_pred HHHHHHHHCCC
T ss_conf 99999998378
No 7
>COG1008 NuoM NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion]
Probab=12.31 E-value=1.2e+02 Score=13.12 Aligned_cols=23 Identities=39% Similarity=0.938 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999986
Q 537021.9.peg.4 3 LFLFLFFFDFVLIFLYFVQGLLS 25 (37)
Q Consensus 3 lflflfffdfvliflyfvqglls 25 (37)
+++|-.||+..||=.||.-|.-.
T Consensus 132 llLFyvFwE~~LIPmy~iIgiwG 154 (497)
T COG1008 132 LLLFYVFWELMLIPMYFLIGIWG 154 (497)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999999999999999754206
No 8
>pfam12606 RELT Tumour necrosis factor receptor superfamily member 19. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 49 and 288 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important. The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1.
Probab=12.13 E-value=1.3e+02 Score=13.09 Aligned_cols=20 Identities=40% Similarity=0.825 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999986989999
Q 537021.9.peg.4 12 FVLIFLYFVQGLLSINTCID 31 (37)
Q Consensus 12 fvliflyfvqgllsintcid 31 (37)
|.++...|+-|++.+--|--
T Consensus 4 ~llV~vf~v~gllg~~Ic~~ 23 (50)
T pfam12606 4 FLLVPVFFVMGLLGLLICTL 23 (50)
T ss_pred EEEHHHHHHHHHHHHHHHHH
T ss_conf 43049999999999999999
No 9
>TIGR01972 NDH_I_M proton-translocating NADH-quinone oxidoreductase, chain M; InterPro: IPR010227 This entry describes the 13th (based on Escherichia coli) structural gene, M, of bacterial NADH dehydrogenase I, as well as chain 4 of the corresponding mitochondrial complex I and of the chloroplast NAD(P)H dehydrogenase complex.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=11.77 E-value=1.3e+02 Score=13.03 Aligned_cols=21 Identities=38% Similarity=0.869 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999999
Q 537021.9.peg.4 3 LFLFLFFFDFVLIFLYFVQGL 23 (37)
Q Consensus 3 lflflfffdfvliflyfvqgl 23 (37)
++||-.||+..||=+|+.=|.
T Consensus 142 ~~LFY~FwE~~LiPmyllIg~ 162 (532)
T TIGR01972 142 LLLFYVFWEAMLIPMYLLIGV 162 (532)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999889999864
No 10
>pfam08710 nsp9 nsp9 replicase. nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis. Its structure comprises of a single beta barrel.
Probab=10.69 E-value=17 Score=17.51 Aligned_cols=12 Identities=42% Similarity=0.949 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999998698
Q 537021.9.peg.4 16 FLYFVQGLLSIN 27 (37)
Q Consensus 16 flyfvqgllsin 27 (37)
+||||+++-+++
T Consensus 85 YLYFVKnln~L~ 96 (111)
T pfam08710 85 YLYFVKNLNNLR 96 (111)
T ss_pred EEEEECCCCHHH
T ss_conf 999861643010
Done!