Query psy18031
Match_columns 136
No_of_seqs 110 out of 209
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 20:42:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18031.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18031hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02271 UCR_14kD: Ubiquinol-c 100.0 3.9E-48 8.4E-53 285.4 10.6 99 33-131 6-105 (105)
2 KOG3440|consensus 100.0 4.1E-47 9E-52 286.2 9.0 106 30-135 8-114 (122)
3 TIGR03761 ICE_PFL4669 integrat 76.9 2.8 6.1E-05 34.6 3.2 57 25-81 142-201 (216)
4 KOG1673|consensus 72.3 3.8 8.2E-05 33.8 2.9 40 35-74 105-150 (205)
5 COG0568 RpoD DNA-directed RNA 65.7 3.9 8.4E-05 36.0 1.8 39 35-79 112-151 (342)
6 PF08900 DUF1845: Domain of un 61.0 6.9 0.00015 31.9 2.3 52 25-76 144-195 (217)
7 PF05965 FYRC: F/Y rich C-term 44.9 29 0.00062 23.7 3.0 52 22-80 15-76 (86)
8 PRK07122 RNA polymerase sigma 27.7 31 0.00067 28.2 1.1 47 51-98 60-112 (264)
9 PF09803 DUF2346: Uncharacteri 27.7 1.1E+02 0.0023 21.8 3.7 61 34-94 12-76 (80)
10 PF08134 cIII: cIII protein fa 26.6 72 0.0016 20.7 2.4 18 76-93 18-35 (44)
11 PF02197 RIIa: Regulatory subu 25.9 25 0.00055 21.4 0.2 20 11-30 11-30 (38)
12 PF08707 PriCT_2: Primase C te 23.2 61 0.0013 21.8 1.7 24 67-90 1-24 (78)
13 TIGR02393 RpoD_Cterm RNA polym 21.4 57 0.0012 25.8 1.5 48 51-99 20-73 (238)
14 PRK05658 RNA polymerase sigma 20.5 88 0.0019 28.9 2.7 57 35-98 390-452 (619)
15 PRK05901 RNA polymerase sigma 20.0 67 0.0015 29.7 1.8 47 50-97 290-342 (509)
No 1
>PF02271 UCR_14kD: Ubiquinol-cytochrome C reductase complex 14kD subunit; InterPro: IPR003197 The cytochrome bd type terminal oxidases catalyse quinol dependent, Na+ independent oxygen uptake []. Members of this family are integral membrane proteins and contain a protoheame IX centre B558. Cytochrome bd may play an important role in microaerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae, where it is expressed under all conditions that permit diazotrophy []. The 14 kDa (or VI) subunit of the complex is not directly involved in electron transfer, but has a role in assembly of the complex [].; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006122 mitochondrial electron transport, ubiquinol to cytochrome c; PDB: 3L74_F 3H1K_F 3L72_F 3H1L_S 3L71_S 3L70_S 3L73_F 3L75_F 1P84_G 3CXH_G ....
Probab=100.00 E-value=3.9e-48 Score=285.36 Aligned_cols=99 Identities=55% Similarity=0.900 Sum_probs=83.6
Q ss_pred hHHHHHHHHHHHHHHhccccccCcccccCCCC-ChHHHHHHhcCCHHHHHHHHHHHHHHHhhhhcCcCCCcccCcCcccC
Q psy18031 33 IFVYISGALQKWAWEYSGFRKYGLYYDDLANE-TPVVEEALRRLPEKLKNERHFRQLRAVQLNIQKSILPKDQWTKYEDE 111 (136)
Q Consensus 33 ~~~~~~~p~a~wy~n~sgyrk~GL~yDDLl~E-~p~VqeALrRLP~~e~~~R~fRi~RA~qlSl~h~~LPkeqWtk~EeD 111 (136)
+..+|+.|+++||+|++|||||||+||||++| ||+|+|||+|||+++.++|+|||+||+|||++|++||||||||+|+|
T Consensus 6 ~~~~~~~~~~~w~~n~~gyrk~GL~~DDl~~e~~~~v~eAl~RLp~~~~~~R~~Ri~RA~~ls~~~~~LPke~wtk~e~d 85 (105)
T PF02271_consen 6 WLSKFFKPLAKWYYNASGYRKYGLRYDDLLNEEDPDVQEALRRLPPDEQYDRNFRIKRAMQLSLKHQYLPKEQWTKPEED 85 (105)
T ss_dssp HHHHHHHHHHHHHHHHHGGGGGT--GGGGS---SHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHT----GGGS--GGGS
T ss_pred HHHHHHHHHHHHHHHhcchhhhcccHHhccCCCCHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhcccCCHHHccCcccc
Confidence 35689999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred ccChHHHHHHHHHHHHHHHH
Q psy18031 112 TRYLKPYIEQVEKEFKEKEE 131 (136)
Q Consensus 112 ~~YL~PyI~EVe~E~~ER~~ 131 (136)
++||+|||+||++|.+||++
T Consensus 86 ~~YL~p~i~ev~~E~~Er~e 105 (105)
T PF02271_consen 86 VPYLQPYIEEVEKERKEREE 105 (105)
T ss_dssp --SSHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999986
No 2
>KOG3440|consensus
Probab=100.00 E-value=4.1e-47 Score=286.22 Aligned_cols=106 Identities=49% Similarity=0.865 Sum_probs=102.5
Q ss_pred chhhHHHHHHHHHHHHHHhccccccCcccccCCCC-ChHHHHHHhcCCHHHHHHHHHHHHHHHhhhhcCcCCCcccCcCc
Q psy18031 30 THLIFVYISGALQKWAWEYSGFRKYGLYYDDLANE-TPVVEEALRRLPEKLKNERHFRQLRAVQLNIQKSILPKDQWTKY 108 (136)
Q Consensus 30 ~~~~~~~~~~p~a~wy~n~sgyrk~GL~yDDLl~E-~p~VqeALrRLP~~e~~~R~fRi~RA~qlSl~h~~LPkeqWtk~ 108 (136)
.+...++++.|+++|++|++|||||||+||||+.| ||+|+|||+|||.+++++|++||+||+|||++|++|||+||||+
T Consensus 8 ~~~~~~k~~~~~~~~~~nl~g~rkyGL~~DDl~~e~n~dvkeAlrRLPr~~~d~R~~Ri~RA~~Lsm~h~~LPk~ewtk~ 87 (122)
T KOG3440|consen 8 KSPVLGKLFLPLRKWAYNLSGFRKYGLRYDDLYYEENEDVKEALRRLPRELYDARNYRIKRAMDLSMTHEILPKEEWTKY 87 (122)
T ss_pred HcccchHHHHHHHHHHHHHhhhhhhCccccccccccCHHHHHHHHHCcHHHHHHHHHHHHHHHHHhhhcccCCHHHhhcc
Confidence 34566899999999999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred ccCccChHHHHHHHHHHHHHHHHhccc
Q psy18031 109 EDETRYLKPYIEQVEKEFKEKEEWGKL 135 (136)
Q Consensus 109 EeD~~YL~PyI~EVe~E~~ER~~~d~~ 135 (136)
+||++||+|||.||++|++||++|++.
T Consensus 88 eed~~YL~pyL~ev~~ErkERee~~~l 114 (122)
T KOG3440|consen 88 EEDVKYLEPYLAEVEAERKEREELDAL 114 (122)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHhhCC
Confidence 999999999999999999999999975
No 3
>TIGR03761 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=76.87 E-value=2.8 Score=34.62 Aligned_cols=57 Identities=16% Similarity=0.201 Sum_probs=42.7
Q ss_pred hccccchhhHHHHHHHHHHHHHHhccccccCcccccCCCCChHHHHHHhc---CCHHHHH
Q psy18031 25 FESSKTHLIFVYISGALQKWAWEYSGFRKYGLYYDDLANETPVVEEALRR---LPEKLKN 81 (136)
Q Consensus 25 ~~s~~~~~~~~~~~~p~a~wy~n~sgyrk~GL~yDDLl~E~p~VqeALrR---LP~~e~~ 81 (136)
.+.+.+..+.......+.+=|.-+..||-.|+-.+|....|+..++|+.+ ||+++..
T Consensus 142 isr~~~~~~l~~g~~~vR~vf~~~~~yr~~gvtR~D~~~~n~~a~~Aie~~G~lp~dIL~ 201 (216)
T TIGR03761 142 ISRQDLEDWLDKGAHLIRRLFGLAQRYRHSGVTRDDFAANNARARKAIERFGELPQDILE 201 (216)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCHHHHHhCCHHHHHHHHHcCCCCHHHHc
Confidence 34445555555555666677777789999999999999779999999988 4666543
No 4
>KOG1673|consensus
Probab=72.34 E-value=3.8 Score=33.83 Aligned_cols=40 Identities=23% Similarity=0.453 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHhccccc------cCcccccCCCCChHHHHHHhc
Q psy18031 35 VYISGALQKWAWEYSGFRK------YGLYYDDLANETPVVEEALRR 74 (136)
Q Consensus 35 ~~~~~p~a~wy~n~sgyrk------~GL~yDDLl~E~p~VqeALrR 74 (136)
+--+..+..||..|-|+|| .|-+||+++.=.|+.|+-+.|
T Consensus 105 r~TLnSi~~WY~QAr~~NktAiPilvGTKyD~fi~lp~e~Q~~I~~ 150 (205)
T KOG1673|consen 105 RSTLNSIKEWYRQARGLNKTAIPILVGTKYDLFIDLPPELQETISR 150 (205)
T ss_pred hHHHHHHHHHHHHHhccCCccceEEeccchHhhhcCCHHHHHHHHH
Confidence 5668899999999999998 599999998878888888765
No 5
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=65.74 E-value=3.9 Score=36.04 Aligned_cols=39 Identities=18% Similarity=0.257 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhccccccCcccccCCCC-ChHHHHHHhcCCHHH
Q psy18031 35 VYISGALQKWAWEYSGFRKYGLYYDDLANE-TPVVEEALRRLPEKL 79 (136)
Q Consensus 35 ~~~~~p~a~wy~n~sgyrk~GL~yDDLl~E-~p~VqeALrRLP~~e 79 (136)
-+++..||+ +|..+||-+-||+.| |.-+.+|+.+..|+-
T Consensus 112 LRlVvsIAk------~Y~~rGL~~~DLIQEGniGLmkAVekFdp~r 151 (342)
T COG0568 112 LRLVVSIAK------KYTGRGLPFLDLIQEGNIGLMKAVEKFDPEK 151 (342)
T ss_pred HHHHHHHHH------HhhcCCCcHHHHHhcccHHHHHHHHhcCccc
Confidence 444555555 889999999999999 999999999988764
No 6
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=60.98 E-value=6.9 Score=31.86 Aligned_cols=52 Identities=15% Similarity=0.153 Sum_probs=38.8
Q ss_pred hccccchhhHHHHHHHHHHHHHHhccccccCcccccCCCCChHHHHHHhcCC
Q psy18031 25 FESSKTHLIFVYISGALQKWAWEYSGFRKYGLYYDDLANETPVVEEALRRLP 76 (136)
Q Consensus 25 ~~s~~~~~~~~~~~~p~a~wy~n~sgyrk~GL~yDDLl~E~p~VqeALrRLP 76 (136)
++++...-+.......+.+-|.-+-+|+-.|+..+|+...|+..++|+.++.
T Consensus 144 is~~~~~~~l~~~~~~iR~v~~~~~~yr~~gvtR~D~~~~n~~~~~A~~~~G 195 (217)
T PF08900_consen 144 ISRQEREDWLRRGGRAIRRVFGLAQRYRHSGVTRDDFAANNARAQAAIERFG 195 (217)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHhcCHHHHHHHHHcC
Confidence 3444455555555556666666677899999999999977999999988753
No 7
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=44.92 E-value=29 Score=23.75 Aligned_cols=52 Identities=25% Similarity=0.279 Sum_probs=35.1
Q ss_pred hhhhccccchhhHHHHHHHHHHH----------HHHhccccccCcccccCCCCChHHHHHHhcCCHHHH
Q psy18031 22 VHDFESSKTHLIFVYISGALQKW----------AWEYSGFRKYGLYYDDLANETPVVEEALRRLPEKLK 80 (136)
Q Consensus 22 ~~~~~s~~~~~~~~~~~~p~a~w----------y~n~sgyrk~GL~yDDLl~E~p~VqeALrRLP~~e~ 80 (136)
-..|+++-...--..++..|.+. -...+|..-+||- +|.|+.+|.-||....
T Consensus 15 ~~~~~g~s~~~~W~~i~~~v~~~r~~~~~~~~~~~~isG~~~FGls-------~p~V~~lie~Lp~a~~ 76 (86)
T PF05965_consen 15 GEVFEGSSPTEAWSEILERVNEARKQSGLLKLPPNSISGPEMFGLS-------NPAVQRLIESLPGADK 76 (86)
T ss_dssp GG-EEESSHHHHHHHHHHHHHHHHT-------TT----HHHHHSTT-------SHHHHHHHTTSTTGGG
T ss_pred CCEEEeCCHHHHHHHHHHHHHHHHhhccccccCCCCCCHhHhcCCC-------CHHHHHHHHhCCCcch
Confidence 34566666665556777777664 2345799999998 8999999999997553
No 8
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=27.72 E-value=31 Score=28.24 Aligned_cols=47 Identities=17% Similarity=0.123 Sum_probs=36.9
Q ss_pred ccccCcccccCCCC-ChHHHHHHhcCCHHH-----HHHHHHHHHHHHhhhhcCc
Q psy18031 51 FRKYGLYYDDLANE-TPVVEEALRRLPEKL-----KNERHFRQLRAVQLNIQKS 98 (136)
Q Consensus 51 yrk~GL~yDDLl~E-~p~VqeALrRLP~~e-----~~~R~fRi~RA~qlSl~h~ 98 (136)
|...|+-+|||+.+ +--+-+|+.+..+.- .| =.++|+-|+.-.+.+.
T Consensus 60 y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTY-A~~~Irg~I~~~lr~~ 112 (264)
T PRK07122 60 FDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSF-AVPTIMGEVRRHFRDN 112 (264)
T ss_pred HHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHH-HHHHHHHHHHHHHHHc
Confidence 34459999999999 888999999998752 44 3568888888777654
No 9
>PF09803 DUF2346: Uncharacterized conserved protein (DUF2346); InterPro: IPR018625 Members of this family of proteins have no known function.
Probab=27.65 E-value=1.1e+02 Score=21.75 Aligned_cols=61 Identities=20% Similarity=0.261 Sum_probs=39.1
Q ss_pred HHHHHHHHHH-HHHHhc-ccccc-CcccccCCCC-ChHHHHHHhcCCHHHHHHHHHHHHHHHhhh
Q psy18031 34 FVYISGALQK-WAWEYS-GFRKY-GLYYDDLANE-TPVVEEALRRLPEKLKNERHFRQLRAVQLN 94 (136)
Q Consensus 34 ~~~~~~p~a~-wy~n~s-gyrk~-GL~yDDLl~E-~p~VqeALrRLP~~e~~~R~fRi~RA~qlS 94 (136)
+..++-||+- |+||.. -|.++ +-...-+++. ++...++|.++=.+....|..||.++++-.
T Consensus 12 g~Yv~fPI~~~~~fN~pe~f~~~v~~~~~~~~ppe~~~~~~ele~~~~~~~~k~~~rl~~~~e~~ 76 (80)
T PF09803_consen 12 GMYVFFPIGMFYYFNQPEWFEKWVIKRKRELYPPENEEIREELEEFKEELRKKREERLLREMEEE 76 (80)
T ss_pred HHHHHHHHHHHHhcCCcHHHHHHhHHHhcccCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556667752 333322 23332 3334445544 778888888888888999999999988743
No 10
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=26.58 E-value=72 Score=20.70 Aligned_cols=18 Identities=28% Similarity=0.239 Sum_probs=13.9
Q ss_pred CHHHHHHHHHHHHHHHhh
Q psy18031 76 PEKLKNERHFRQLRAVQL 93 (136)
Q Consensus 76 P~~e~~~R~fRi~RA~ql 93 (136)
++.|.-.|++|++||...
T Consensus 18 ~ESELskr~rrLIRaa~k 35 (44)
T PF08134_consen 18 TESELSKRIRRLIRAARK 35 (44)
T ss_pred cHHHHHHHHHHHHHHHHH
Confidence 356777899999999753
No 11
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=25.92 E-value=25 Score=21.36 Aligned_cols=20 Identities=30% Similarity=0.386 Sum_probs=13.5
Q ss_pred HHHhhhccccchhhhccccc
Q psy18031 11 TYEVLTHTSADVHDFESSKT 30 (136)
Q Consensus 11 ~~~~~~~~~~~~~~~~s~~~ 30 (136)
+-+|+.+...|++.||++-+
T Consensus 11 ~~~vl~~qP~Di~~F~a~yF 30 (38)
T PF02197_consen 11 TREVLREQPDDILQFAADYF 30 (38)
T ss_dssp HHHHHHH--S-HHHHHHHHH
T ss_pred HHHHHHHCCCcHHHHHHHHH
Confidence 34899999999999998643
No 12
>PF08707 PriCT_2: Primase C terminal 2 (PriCT-2) ; InterPro: IPR014819 This alpha helical domain is found at the C-terminal of primases. ; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=23.19 E-value=61 Score=21.82 Aligned_cols=24 Identities=17% Similarity=0.217 Sum_probs=17.2
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHH
Q psy18031 67 VVEEALRRLPEKLKNERHFRQLRA 90 (136)
Q Consensus 67 ~VqeALrRLP~~e~~~R~fRi~RA 90 (136)
+|++||+-||++...+|.-=++.+
T Consensus 1 ~~~~~L~~i~~~~~~~y~~W~~vg 24 (78)
T PF08707_consen 1 DIREALDHIPPDIADDYDDWIRVG 24 (78)
T ss_pred CHHHHHhcCCcccccCHHHHHHHH
Confidence 478999999998655555555444
No 13
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=21.39 E-value=57 Score=25.85 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=35.2
Q ss_pred ccccCcccccCCCC-ChHHHHHHhcCCHHH-----HHHHHHHHHHHHhhhhcCcC
Q psy18031 51 FRKYGLYYDDLANE-TPVVEEALRRLPEKL-----KNERHFRQLRAVQLNIQKSI 99 (136)
Q Consensus 51 yrk~GL~yDDLl~E-~p~VqeALrRLP~~e-----~~~R~fRi~RA~qlSl~h~~ 99 (136)
|...|+-.+||+.| +--+-+|+.+..++- .|+ .++|+.|+.-.+..+.
T Consensus 20 ~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA-~~~Ir~~I~~~l~~~~ 73 (238)
T TIGR02393 20 YTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYA-TWWIRQAITRAIADQA 73 (238)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHh-HHHHHHHHHHHHHHcC
Confidence 34458999999999 888999999997642 333 4788888766665543
No 14
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=20.52 E-value=88 Score=28.92 Aligned_cols=57 Identities=16% Similarity=0.205 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHhccccccCcccccCCCC-ChHHHHHHhcCCHHH-----HHHHHHHHHHHHhhhhcCc
Q psy18031 35 VYISGALQKWAWEYSGFRKYGLYYDDLANE-TPVVEEALRRLPEKL-----KNERHFRQLRAVQLNIQKS 98 (136)
Q Consensus 35 ~~~~~p~a~wy~n~sgyrk~GL~yDDLl~E-~p~VqeALrRLP~~e-----~~~R~fRi~RA~qlSl~h~ 98 (136)
-.++..|++- |+..|+-++||+.| |--+-+|+.+..+.- .|+ .++|+.|+.-++..+
T Consensus 390 lrlV~~iA~k------y~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA-~~wIr~aI~~~i~~~ 452 (619)
T PRK05658 390 LRLVISIAKK------YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA-TWWIRQAITRSIADQ 452 (619)
T ss_pred HHHHHHHHHH------HhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHh-HHHHHHHHHHHHHHc
Confidence 3444555554 45569999999999 998999999987532 343 467777777666554
No 15
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=20.00 E-value=67 Score=29.70 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=34.5
Q ss_pred cccccCcccccCCCC-ChHHHHHHhcCCHHH-----HHHHHHHHHHHHhhhhcC
Q psy18031 50 GFRKYGLYYDDLANE-TPVVEEALRRLPEKL-----KNERHFRQLRAVQLNIQK 97 (136)
Q Consensus 50 gyrk~GL~yDDLl~E-~p~VqeALrRLP~~e-----~~~R~fRi~RA~qlSl~h 97 (136)
.|...|+-++||+.| +--+-+|+.|..+.- .| =.++|+.|+.-.+..
T Consensus 290 rY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTY-A~wWIRqaI~raI~d 342 (509)
T PRK05901 290 RYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTY-ATWWIRQAITRAMAD 342 (509)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhh-hHHHHHHHHHHHHHH
Confidence 345569999999999 998999999998643 33 356777777655543
Done!