Query gi|254780734|ref|YP_003065147.1| Flp/Fap pilin component [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 62
No_of_seqs 106 out of 228
Neff 4.3
Searched_HMMs 39220
Date Sun May 29 19:15:01 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780734.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3847 Flp Flp pilus assembly 99.8 1.8E-19 4.6E-24 120.1 7.3 58 2-59 1-58 (58)
2 pfam04964 Flp_Fap Flp/Fap pili 99.7 3E-18 7.6E-23 113.8 5.1 47 9-55 1-47 (47)
3 COG4961 TadG Flp pilus assembl 97.2 0.00043 1.1E-08 41.7 4.4 35 3-37 9-43 (185)
4 pfam04021 Class_IIIsignal Clas 83.3 1 2.6E-05 24.5 2.7 22 13-34 1-22 (28)
5 pfam05307 Bundlin Bundlin. Thi 74.0 3.4 8.6E-05 21.8 3.0 31 10-40 8-38 (97)
6 COG4537 ComGC Competence prote 73.1 6.4 0.00016 20.4 4.2 40 3-42 1-40 (107)
7 COG4966 PilW Tfp pilus assembl 57.9 11 0.00027 19.3 2.9 46 7-53 6-51 (318)
8 COG0342 SecD Preprotein transl 48.2 26 0.00067 17.3 5.3 42 12-53 335-376 (506)
9 pfam07811 TadE TadE-like prote 47.4 27 0.00068 17.2 3.6 23 15-37 1-23 (43)
10 TIGR01129 secD protein-export 43.4 31 0.0008 16.9 5.1 37 15-51 365-401 (522)
11 TIGR01960 ndhF3_CO2 NAD(P)H de 30.1 49 0.0013 15.9 2.7 22 25-46 282-303 (613)
12 TIGR00411 redox_disulf_1 redox 27.7 14 0.00035 18.7 -0.5 14 12-25 40-53 (82)
13 COG1681 FlaB Archaeal flagelli 26.0 63 0.0016 15.3 2.9 25 12-38 1-25 (209)
14 pfam12555 TPPK_C Thiamine pyro 23.4 71 0.0018 15.0 4.6 47 6-55 3-49 (53)
15 PRK13024 bifunctional preprote 23.3 72 0.0018 15.0 5.1 40 12-51 254-293 (741)
16 PRK10574 putative major pilin 23.3 72 0.0018 15.0 3.0 25 11-40 2-26 (146)
17 TIGR02885 spore_sigF RNA polym 20.7 33 0.00083 16.8 0.3 11 3-13 73-83 (231)
18 COG1991 Uncharacterized conser 20.5 14 0.00036 18.6 -1.6 34 3-36 2-35 (131)
No 1
>COG3847 Flp Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]
Probab=99.79 E-value=1.8e-19 Score=120.06 Aligned_cols=58 Identities=52% Similarity=0.771 Sum_probs=54.5
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 1599999961236831999999999999999999999744899999999963157777
Q gi|254780734|r 2 KMHIVKNFLQDESGATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAIDKAIVTTSP 59 (62)
Q Consensus 2 ~m~~i~~fl~De~GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~~~l~~a~~ 59 (62)
+.++++||+|||+||||||||||+++|++++|+.++++|+.+++.|++++++++++.+
T Consensus 1 m~~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~~l~~~l~~~ft~i~~al~~a~~ 58 (58)
T COG3847 1 MKKLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGSTLGTALKGAFTAIGAALTGAAA 58 (58)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 9178999977456518999999999999999999999989999999999998704689
No 2
>pfam04964 Flp_Fap Flp/Fap pilin component.
Probab=99.73 E-value=3e-18 Score=113.85 Aligned_cols=47 Identities=66% Similarity=0.940 Sum_probs=45.4
Q ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 96123683199999999999999999999974489999999996315
Q gi|254780734|r 9 FLQDESGATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAIDKAIV 55 (62)
Q Consensus 9 fl~De~GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~~~l~ 55 (62)
|+|||+|+||||||||++||+++||.+++.+|++++++|++++++++
T Consensus 1 F~kde~GaTAIEYgLIaalIav~iI~~~~~~g~~l~~~f~~i~~~l~ 47 (47)
T pfam04964 1 FLKDESGATAIEYGLIAALIAVVIIAYVTTLGTALKTKFTSIGTALT 47 (47)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 96565641599999999999999999999970129889999886239
No 3
>COG4961 TadG Flp pilus assembly protein TadG [Intracellular trafficking and secretion]
Probab=97.24 E-value=0.00043 Score=41.67 Aligned_cols=35 Identities=23% Similarity=0.512 Sum_probs=29.4
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 59999996123683199999999999999999999
Q gi|254780734|r 3 MHIVKNFLQDESGATAIEYGLLVSLIAVVIITSVT 37 (62)
Q Consensus 3 m~~i~~fl~De~GaTAIEYgLIaaLIav~ii~av~ 37 (62)
..+.+||++|++|+.|||.+||+-+..+++.+.+-
T Consensus 9 ~~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve 43 (185)
T COG4961 9 RGLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVE 43 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999887648768999999999999999999999
No 4
>pfam04021 Class_IIIsignal Class III signal peptide. This family of archaeal proteins contains. an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site. Two members of this family are cleaved by a type IV pilin-like signal peptidase.
Probab=83.34 E-value=1 Score=24.50 Aligned_cols=22 Identities=32% Similarity=0.522 Sum_probs=16.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 3683199999999999999999
Q gi|254780734|r 13 ESGATAIEYGLLVSLIAVVIIT 34 (62)
Q Consensus 13 e~GaTAIEYgLIaaLIav~ii~ 34 (62)
++|+.++||.++.+.+-++.+-
T Consensus 1 ~kGQ~SlE~~lLi~~vlv~~~i 22 (28)
T pfam04021 1 KKGQISLEFLLLILAVLVVAII 22 (28)
T ss_pred CCCEEEHHHHHHHHHHHHHHHH
T ss_conf 9865439999999999999977
No 5
>pfam05307 Bundlin Bundlin. This family consists of several bundlin proteins from E. coli. Bundlin is a type IV pilin protein that is the only known structural component of enteropathogenic Escherichia coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localized adherence to epithelial cells.
Probab=74.00 E-value=3.4 Score=21.80 Aligned_cols=31 Identities=23% Similarity=0.235 Sum_probs=26.3
Q ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6123683199999999999999999999974
Q gi|254780734|r 10 LQDESGATAIEYGLLVSLIAVVIITSVTTLG 40 (62)
Q Consensus 10 l~De~GaTAIEYgLIaaLIav~ii~av~~lG 40 (62)
-+.|+|-+-||-.+.+++++++|.+.+--+-
T Consensus 8 kK~~kGlsLiE~~mVLal~A~vIAGvf~YY~ 38 (97)
T pfam05307 8 KKYEKGLSLIESAMVLALAATVTAGVMFYYQ 38 (97)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHEEHH
T ss_conf 6675252199999999999999977510307
No 6
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=73.05 E-value=6.4 Score=20.38 Aligned_cols=40 Identities=23% Similarity=0.467 Sum_probs=32.2
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5999999612368319999999999999999999997448
Q gi|254780734|r 3 MHIVKNFLQDESGATAIEYGLLVSLIAVVIITSVTTLGGK 42 (62)
Q Consensus 3 m~~i~~fl~De~GaTAIEYgLIaaLIav~ii~av~~lG~~ 42 (62)
|+.++.|+++++|-|-||-=+....|++-++-.+-.+-.+
T Consensus 1 m~~~~k~~~~~kgFTLvEMLiVLlIISiLlLl~iPNltKq 40 (107)
T COG4537 1 MKKMKKFLKHKKGFTLVEMLIVLLIISILLLLFIPNLTKQ 40 (107)
T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 9167777776326259999999999999999974625443
No 7
>COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=57.86 E-value=11 Score=19.28 Aligned_cols=46 Identities=15% Similarity=0.312 Sum_probs=31.9
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99961236831999999999999999999999744899999999963
Q gi|254780734|r 7 KNFLQDESGATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAIDKA 53 (62)
Q Consensus 7 ~~fl~De~GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~~~ 53 (62)
+...+-.+|-+.||- ||+.+|+..++.++..+==.....|+...+.
T Consensus 6 ~~~~rrqrG~SLIEL-MIallIglivL~av~s~y~~sr~~y~~~~~~ 51 (318)
T COG4966 6 RARPRRQRGFSLIEL-MIALLIGLIVLLAVGSLYLSSRQLYTTLADR 51 (318)
T ss_pred CCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHEEEEHHHHHHHHHHH
T ss_conf 355455577439999-9999999999997763034356778877666
No 8
>COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion]
Probab=48.17 E-value=26 Score=17.28 Aligned_cols=42 Identities=26% Similarity=0.358 Sum_probs=31.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 236831999999999999999999999744899999999963
Q gi|254780734|r 12 DESGATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAIDKA 53 (62)
Q Consensus 12 De~GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~~~ 53 (62)
-+=|+.+++.|++|++++.+.+...-.+=-.+-+.+..++-.
T Consensus 335 psLG~~~i~~gi~Agl~g~~~V~vfm~~~Yr~~Gvia~ial~ 376 (506)
T COG0342 335 PTLGADSIKAGLIAGLIGLALVAVFMLLYYRLAGVIAAIALG 376 (506)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 454767899789999999999999999999875899999999
No 9
>pfam07811 TadE TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues.
Probab=47.41 E-value=27 Score=17.23 Aligned_cols=23 Identities=26% Similarity=0.631 Sum_probs=18.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 83199999999999999999999
Q gi|254780734|r 15 GATAIEYGLLVSLIAVVIITSVT 37 (62)
Q Consensus 15 GaTAIEYgLIaaLIav~ii~av~ 37 (62)
|+.+||..+++-++.+.+.+.+.
T Consensus 1 G~a~VEfalv~p~~l~l~~~~~~ 23 (43)
T pfam07811 1 GAAAVEFALVLPVLLLLLFGIVE 23 (43)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 91699999999999999999999
No 10
>TIGR01129 secD protein-export membrane protein SecD; InterPro: IPR005791 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains . Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. This entry describes the SecD family of transport proteins. Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed. SecD from Mycobacterium tuberculosis has a long Pro-rich insert. ; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=43.39 E-value=31 Score=16.87 Aligned_cols=37 Identities=30% Similarity=0.375 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8319999999999999999999997448999999999
Q gi|254780734|r 15 GATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAID 51 (62)
Q Consensus 15 GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~ 51 (62)
|+-+||=|++|++++.++|...-.+==.+-+.+..++
T Consensus 365 G~d~i~~G~~A~~~Gl~lV~~FM~~yY~~~G~~A~~a 401 (522)
T TIGR01129 365 GADSIEAGIKAGLIGLVLVLVFMIVYYRLFGLIAAIA 401 (522)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 3899999999999999999999999976788999999
No 11
>TIGR01960 ndhF3_CO2 NAD(P)H dehydrogenase, subunit NdhF3 family; InterPro: IPR010217 This family represents NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighbouring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=30.08 E-value=49 Score=15.87 Aligned_cols=22 Identities=36% Similarity=0.522 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999974489999
Q gi|254780734|r 25 VSLIAVVIITSVTTLGGKLKKA 46 (62)
Q Consensus 25 aaLIav~ii~av~~lG~~l~~~ 46 (62)
.|+.++.+||+||++|+++-..
T Consensus 282 vA~~~li~IG~VTAig~SLiaI 303 (613)
T TIGR01960 282 VALTVLIAIGSVTAIGASLIAI 303 (613)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8999998985578887889999
No 12
>TIGR00411 redox_disulf_1 redox-active disulfide protein 1; InterPro: IPR004502 This group of proteins includes thioredoxins, glutaredoxins, protein-disulphide isomerases, and others, some of which have several such domains. The sequence of proteins in this group at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although overall the sequence seems closer to thioredoxins. Proteins may be involved in a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis.
Probab=27.73 E-value=14 Score=18.72 Aligned_cols=14 Identities=36% Similarity=0.603 Sum_probs=11.2
Q ss_pred CCCCCCHHHHHHHH
Q ss_conf 23683199999999
Q gi|254780734|r 12 DESGATAIEYGLLV 25 (62)
Q Consensus 12 De~GaTAIEYgLIa 25 (62)
||.-.-|+|||+.+
T Consensus 40 ~e~~~kA~~yGi~a 53 (82)
T TIGR00411 40 MEDLKKALEYGIMA 53 (82)
T ss_pred CCCHHHHHHCCCCC
T ss_conf 54847887516352
No 13
>COG1681 FlaB Archaeal flagellins [Cell motility and secretion]
Probab=26.05 E-value=63 Score=15.32 Aligned_cols=25 Identities=36% Similarity=0.587 Sum_probs=16.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 236831999999999999999999999
Q gi|254780734|r 12 DESGATAIEYGLLVSLIAVVIITSVTT 38 (62)
Q Consensus 12 De~GaTAIEYgLIaaLIav~ii~av~~ 38 (62)
||+|++-||=..+ +|+.+++++|.+
T Consensus 1 ~rrG~~GIgtlIV--fIAmVlVAAVaA 25 (209)
T COG1681 1 DRRGATGIGTLIV--FIAMVLVAAVAA 25 (209)
T ss_pred CCCCCCCHHHHHH--HHHHHHHHHHHH
T ss_conf 9841104328999--999999999999
No 14
>pfam12555 TPPK_C Thiamine pyrophosphokinase C terminal. This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyses the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme.
Probab=23.39 E-value=71 Score=15.05 Aligned_cols=47 Identities=15% Similarity=0.219 Sum_probs=31.6
Q ss_pred HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99996123683199999999999999999999974489999999996315
Q gi|254780734|r 6 VKNFLQDESGATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAIDKAIV 55 (62)
Q Consensus 6 i~~fl~De~GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~~~l~ 55 (62)
+.++-|......++=--.+++|+++.++-.++..|+ ..|+.+.+.++
T Consensus 3 Vs~LYrsris~~~~~~lvla~Lva~~val~~s~~g~---~~~~~l~~~w~ 49 (53)
T pfam12555 3 VSRLYRSRISGGALLLLVLAALVALAVALLVSPAGQ---SFLDLLADRWN 49 (53)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHH---HHHHHHHHHHH
T ss_conf 888989227788999999999999999998084229---99999999987
No 15
>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=23.31 E-value=72 Score=15.04 Aligned_cols=40 Identities=23% Similarity=0.264 Sum_probs=28.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2368319999999999999999999997448999999999
Q gi|254780734|r 12 DESGATAIEYGLLVSLIAVVIITSVTTLGGKLKKAFEAID 51 (62)
Q Consensus 12 De~GaTAIEYgLIaaLIav~ii~av~~lG~~l~~~f~~v~ 51 (62)
-.-|+.+++.|++|++|+.+++...-.+-=.+-+....++
T Consensus 254 ptLG~~si~~g~~A~~ig~~lV~lfMi~~Yr~~G~iA~ia 293 (741)
T PRK13024 254 PTLGQDAINAGIIAGIIGFALIALFMLLFYGLPGLIANIA 293 (741)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 1310999999999999999999999999986769999999
No 16
>PRK10574 putative major pilin subunit; Provisional
Probab=23.26 E-value=72 Score=15.03 Aligned_cols=25 Identities=28% Similarity=0.549 Sum_probs=15.9
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 123683199999999999999999999974
Q gi|254780734|r 11 QDESGATAIEYGLLVSLIAVVIITSVTTLG 40 (62)
Q Consensus 11 ~De~GaTAIEYgLIaaLIav~ii~av~~lG 40 (62)
+.++|-|-||- +|.++||+.+.+++
T Consensus 2 ~~q~gftLiEl-----mivvaii~il~~ia 26 (146)
T PRK10574 2 TKQRGFTLIEL-----MVVIGIIAILSAIG 26 (146)
T ss_pred CCCCCCCHHHH-----HHHHHHHHHHHHHH
T ss_conf 75568165899-----99999999999999
No 17
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 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 , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=20.66 E-value=33 Score=16.78 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=6.9
Q ss_pred HHHHHHHHHCC
Q ss_conf 59999996123
Q gi|254780734|r 3 MHIVKNFLQDE 13 (62)
Q Consensus 3 m~~i~~fl~De 13 (62)
|==|+||+||+
T Consensus 73 ~GEIkRFLRDD 83 (231)
T TIGR02885 73 MGEIKRFLRDD 83 (231)
T ss_pred HHHHHHHHCCC
T ss_conf 21222310268
No 18
>COG1991 Uncharacterized conserved protein [Function unknown]
Probab=20.49 E-value=14 Score=18.65 Aligned_cols=34 Identities=15% Similarity=0.315 Sum_probs=26.3
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 5999999612368319999999999999999999
Q gi|254780734|r 3 MHIVKNFLQDESGATAIEYGLLVSLIAVVIITSV 36 (62)
Q Consensus 3 m~~i~~fl~De~GaTAIEYgLIaaLIav~ii~av 36 (62)
++++..|..+.+|+-..||.|....+-++.+.+.
T Consensus 2 ~~~i~~~~~~nkgQiSLEf~Ll~l~ivla~~i~~ 35 (131)
T COG1991 2 TTYITKIILSNKGQISLEFSLLLLAIVLAASIAG 35 (131)
T ss_pred CCEEEEEEECCCCCEEEEHHHHHHHHHHHHHHEE
T ss_conf 6166254224666256413899999999731211
Done!