Query 010450
Match_columns 510
No_of_seqs 149 out of 239
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 00:40:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03094 Mlo: Mlo family; Int 100.0 2E-185 5E-190 1449.5 39.2 443 6-472 1-445 (478)
2 PF06305 DUF1049: Protein of u 61.3 29 0.00063 27.5 6.0 47 16-62 18-64 (68)
3 PRK11677 hypothetical protein; 60.2 15 0.00033 34.4 4.7 44 15-62 2-45 (134)
4 COG1033 Predicted exporters of 60.2 18 0.0004 42.2 6.3 54 20-73 252-316 (727)
5 TIGR02976 phageshock_pspB phag 54.1 39 0.00085 28.7 5.8 44 15-60 3-56 (75)
6 PF07219 HemY_N: HemY protein 48.0 33 0.00072 30.1 4.7 46 12-57 13-65 (108)
7 TIGR03144 cytochr_II_ccsB cyto 41.0 1.1E+02 0.0023 30.7 7.5 29 50-78 142-170 (243)
8 TIGR01106 ATPase-IIC_X-K sodiu 37.5 1.3E+02 0.0028 36.4 8.7 43 358-400 809-853 (997)
9 PF09878 DUF2105: Predicted me 34.2 66 0.0014 32.3 4.7 47 285-336 158-207 (212)
10 TIGR03777 RPE4 Rickettsial pal 33.7 18 0.0004 26.3 0.6 10 353-362 23-32 (32)
11 PF01578 Cytochrom_C_asm: Cyto 32.4 1.3E+02 0.0028 29.0 6.4 30 50-79 116-145 (214)
12 PF15468 DUF4636: Domain of un 30.6 31 0.00066 35.0 1.8 37 276-317 25-61 (243)
13 PF12801 Fer4_5: 4Fe-4S bindin 26.2 1.2E+02 0.0026 22.6 4.0 24 15-38 2-25 (48)
14 TIGR00540 hemY_coli hemY prote 25.6 99 0.0021 32.8 4.7 38 12-49 38-82 (409)
15 TIGR00921 2A067 The (Largely A 24.5 2.5E+02 0.0054 31.9 7.9 57 17-73 620-686 (719)
16 COG3114 CcmD Heme exporter pro 23.9 2E+02 0.0043 24.3 5.1 39 306-345 9-57 (67)
17 PF01956 DUF106: Integral memb 23.7 61 0.0013 30.4 2.4 135 152-306 6-156 (168)
18 PRK10747 putative protoheme IX 23.6 1E+02 0.0023 32.6 4.4 37 12-48 38-81 (398)
19 PHA03105 EEV glycoprotein; Pro 23.3 96 0.0021 30.3 3.6 33 18-50 9-41 (188)
20 COG3105 Uncharacterized protei 22.7 1.6E+02 0.0034 28.0 4.8 61 14-78 6-75 (138)
21 PF06295 DUF1043: Protein of u 22.2 1.6E+02 0.0034 27.0 4.7 49 29-78 9-66 (128)
22 PF05568 ASFV_J13L: African sw 20.5 1.9E+02 0.0041 28.0 5.0 47 9-57 19-65 (189)
No 1
>PF03094 Mlo: Mlo family; InterPro: IPR004326 The Mlo-related proteins are a family of plant integral membrane proteins, first discovered in barley. Mutants lacking wild-type Mlo proteins show broad spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. Thus wild-type Mlo proteins are thought to be inhibitors of cell death whose deficiency lowers the threshold required to trigger the cascade of events that result in plant cell death. Mlo proteins are localized in the plasma membrane and possess seven transmembrane regions; thus the Mlo family is the only major higher plant family to possess 7 transmembrane domains. It has been suggested that Mlo proteins function as G-protein coupled receptors in plants []; however the molecular and biological functions of Mlo proteins is still unclear.; GO: 0008219 cell death, 0016021 integral to membrane
Probab=100.00 E-value=2.4e-185 Score=1449.51 Aligned_cols=443 Identities=57% Similarity=1.040 Sum_probs=421.2
Q ss_pred CCCcccCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccC
Q 010450 6 EGVTLEYTPTWVVAAVCTVIVAISLGAERLLHYLGRYLKNKKQKSLFEALQKVKEELMLLGFISLLLTVFQNTISKICVH 85 (510)
Q Consensus 6 ~~rsLe~TPTWaVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~kkaL~eALeKiK~ELMLLGFISLLLtv~q~~IskICIp 85 (510)
|+|+||+|||||||+||+|||++|+++||++|++||||+|++||+|+|||||||+|||||||||||||++|++|+|||||
T Consensus 1 e~rsLe~TptW~va~v~~v~v~is~~~E~~lh~l~~~l~~~~~k~L~~aLekik~ELMlLGfiSLlLt~~q~~IskICIp 80 (478)
T PF03094_consen 1 EGRSLEETPTWAVAVVCTVFVVISILLERGLHRLGKWLKKKKRKALYEALEKIKEELMLLGFISLLLTVFQNPISKICIP 80 (478)
T ss_pred CCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHeecC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccCCCCcccccCCCCCcccccccccccccccccchhhhhhhhhhccccCCccccCCccccccchhhhHHHHH
Q 010450 86 QDVLDNMLPCKRNKTAESEGQNSHVTTTSHFQTFFSSSISGTAKRLLAEEESAASERGYCAQKNKVPLLSTEALHHLHIF 165 (510)
Q Consensus 86 ~~~~~~~lPC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~RrlLa~~~~~~~~~~~C~~~GkvpliS~e~LHQLHIF 165 (510)
++++++|+||+..+..+. ..+ +..+||+|+.+++ +++++|++||||||+|.|||||||||
T Consensus 81 ~~~~~~~lPC~~~~~~~~--------~~~----------~~~~r~ll~~~~~--~~~~~C~~kGkvpliS~egLHQLHIF 140 (478)
T PF03094_consen 81 SSYASTMLPCKPPEESSK--------EGS----------SHNRRRLLASGAA--EGSDYCPKKGKVPLISAEGLHQLHIF 140 (478)
T ss_pred hhHHhcccCCCCcccccc--------ccc----------chhhhhhhhhhcc--cccCcccccCccccccchhHHHHHHH
Confidence 999999999986441111 000 1247999984332 25789998899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHhHhhHhhhccC--CccccccceEEEeeecchhhhhccCCCCCchhHHHHHHHH
Q 010450 166 IFVLAIVHVTFCVLTILFAGARIRQWKNWEDSIAKQDF--DPEQVLKTKVTHVHQHAFIKEHFLGYGKDSALLGWMLSFF 243 (510)
Q Consensus 166 IFvLAv~HV~ys~~Tm~Lg~~Kir~Wk~WE~e~~~~~~--~~~p~~~~r~r~~~qt~F~~~h~~~~~~~s~~l~Wi~cFf 243 (510)
||||||+||+|||+||+||++|||+||+||+|++++++ .+|| +|+|++||++|+|+|+ ++|++++++.|++|||
T Consensus 141 IFVLAV~HV~Ys~lTm~Lg~~KIr~Wk~WE~e~~~~~~~~~~d~---~r~~~~~qt~F~r~h~-~~w~~~~~~~wi~~Ff 216 (478)
T PF03094_consen 141 IFVLAVVHVLYSCLTMLLGRAKIRRWKKWEDEAQTDEYQFSNDP---RRFRLTRQTTFVRRHT-SFWSKSPVLSWIVCFF 216 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccCc---ceeeeecccHHHHhhc-CCcccChhHHhHHHHH
Confidence 99999999999999999999999999999999998766 4888 9999999999999997 8899999999999999
Q ss_pred HhhccCCchhhHHHHHHHHHhhhcCCCCCCchHHHHHHHhhhhcccccchhhHHHHHHHHHhhhccCcchhhHhhhhHHH
Q 010450 244 KQFYASITKADYVTLRLGFIMTHCRGSPKFNFHKYMIRALEDDFKRVVGISWYLWIFVVIFLLLNINEWHTYFWIAFIPF 323 (510)
Q Consensus 244 rQF~~SV~k~DYltLR~gFI~~H~~~~~~FdFhkYi~RsLE~DFk~VVGIS~~lW~~vviFlLlnv~Gw~~yfWlsfiPl 323 (510)
||||+||+|+||+|||+|||++|+.++++|||||||+||||||||+||||||+||++||+|+|+|++|||+|||+||||+
T Consensus 217 rQF~~SV~k~DYltLR~gFI~~H~~~~~~FDFh~Yi~RsLEdDFk~VVGIS~~lW~~vv~fll~nv~gw~~yfW~sfipl 296 (478)
T PF03094_consen 217 RQFYGSVTKSDYLTLRHGFITAHLLPNPKFDFHKYIKRSLEDDFKVVVGISWYLWAFVVLFLLLNVHGWHTYFWLSFIPL 296 (478)
T ss_pred HHhhccccHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHheeccccHhhhhheeeeecCCcceeEeehhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhHHHHHHHHHHHHHHhhcccccCcceecCCCCccccccchHHHHHHHHHHhhhhHHHHHHHHHHHHhCCcccc
Q 010450 324 ILLLAVGAKLEHVISQLAHEVAEKHIAIEGELVVQPSDQHFWFNRPQIVLFLIHFILFQNSFEIAFFFWILIQYGFDSCI 403 (510)
Q Consensus 324 illL~VGtKLq~IIt~lalei~e~~~~v~G~~~V~p~D~lFWF~rP~llL~LIhfiLFQNAFelAfF~W~~~~fG~~SC~ 403 (510)
+++|+||||||+||++||+|++|++++++|+|+|+|+|++|||+||+|||+||||+|||||||||||+|+||+||++|||
T Consensus 297 ~liL~VGtKLq~Ii~~ma~ei~~~~~~~~g~p~v~p~d~~FWF~rP~llL~lihfilFqnAFela~f~w~~~~~g~~sC~ 376 (478)
T PF03094_consen 297 ILILLVGTKLQHIITKMALEIAERHAVIKGTPLVKPSDDLFWFGRPRLLLHLIHFILFQNAFELAFFFWIWWQFGFDSCF 376 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCcccCcccccccccceecCCcHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCceeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccceeceeeeehhhhhhccccccchhhHhhhccccccccccchhHHHHHHhHHHHHhhhcCCCCCC
Q 010450 404 MGQVCYIVPRLIIGVFIQVLCSYSTLPLYAIVTQMGSSFKKAIFEENVQVGIVGWAEKVRRKKDPKAAK 472 (510)
Q Consensus 404 ~~~~~~ii~Rl~~Gv~vQ~lCSY~TLPLYALVTQMGS~~K~~if~e~v~~~l~~W~~~akkk~~~~~~~ 472 (510)
|++.+++++|+++||++|++|||+|||||||||||||+||++||+|+|+++|++||++||||++.++++
T Consensus 377 ~~~~~~~i~rl~~gv~vq~lcsy~tLPLYaLVTqMGS~~K~~if~e~v~~al~~W~~~ak~~~~~~~~~ 445 (478)
T PF03094_consen 377 MENTEYIIIRLVMGVVVQVLCSYVTLPLYALVTQMGSHMKKAIFNEQVSKALKKWHKKAKKKKKHKKSA 445 (478)
T ss_pred ecCccceeeehhhhhhhhhhcchhhhhHHHHHhccccccchhhhHHHHHHHHHHHHHHHHHhhccCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999887754
No 2
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=61.28 E-value=29 Score=27.51 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=35.4
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHH
Q 010450 16 WVVAAVCTVIVAISLGAERLLHYLGRYLKNKKQKSLFEALQKVKEEL 62 (510)
Q Consensus 16 WaVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~kkaL~eALeKiK~EL 62 (510)
+-++++.++..++++++=-.+.....+=.|++.+.+-..+++++.|+
T Consensus 18 ~pl~l~il~~f~~G~llg~l~~~~~~~~~r~~~~~~~k~l~~le~e~ 64 (68)
T PF06305_consen 18 LPLGLLILIAFLLGALLGWLLSLPSRLRLRRRIRRLRKELKKLEKEL 64 (68)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666666777777777777777666777788888999999886
No 3
>PRK11677 hypothetical protein; Provisional
Probab=60.22 E-value=15 Score=34.35 Aligned_cols=44 Identities=27% Similarity=0.298 Sum_probs=29.3
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHH
Q 010450 15 TWVVAAVCTVIVAISLGAERLLHYLGRYLKNKKQKSLFEALQKVKEEL 62 (510)
Q Consensus 15 TWaVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~kkaL~eALeKiK~EL 62 (510)
+|..|++++|+. +++=.++.+++..= .++++.|-+-||+.|.||
T Consensus 2 ~W~~a~i~livG---~iiG~~~~R~~~~~-~~~q~~le~eLe~~k~el 45 (134)
T PRK11677 2 TWEYALIGLVVG---IIIGAVAMRFGNRK-LRQQQALQYELEKNKAEL 45 (134)
T ss_pred cHHHHHHHHHHH---HHHHHHHHhhccch-hhHHHHHHHHHHHHHHHH
Confidence 488888766543 34444445544331 146789999999999998
No 4
>COG1033 Predicted exporters of the RND superfamily [General function prediction only]
Probab=60.19 E-value=18 Score=42.18 Aligned_cols=54 Identities=22% Similarity=0.485 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCc-----hHHHHHHHHHHHHHH------HHHHHHHHHH
Q 010450 20 AVCTVIVAISLGAERLLHYLGRYLKNKKQ-----KSLFEALQKVKEELM------LLGFISLLLT 73 (510)
Q Consensus 20 ~Vc~v~v~iSl~~Er~lH~lgk~lkkk~k-----kaL~eALeKiK~ELM------LLGFISLLLt 73 (510)
...++.++|++.+++++|...++.+.+++ .|+.+|+.+...=++ -+||+||+.+
T Consensus 252 s~~~~~llIgiGidy~vh~~nr~~ee~~~~~~~~eAv~~ai~~~g~avl~a~lTT~~GF~Sl~~s 316 (727)
T COG1033 252 TSAVPPLLIGIGIDYGVHFHNRYEEERRKGRTVEEAVVEAIKHTGPAVLIAALTTAAGFLSLLTS 316 (727)
T ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHc
Confidence 44566778899999999999999987776 377777777766554 4899999876
No 5
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=54.14 E-value=39 Score=28.73 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=30.4
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCc----------hHHHHHHHHHHH
Q 010450 15 TWVVAAVCTVIVAISLGAERLLHYLGRYLKNKKQ----------KSLFEALQKVKE 60 (510)
Q Consensus 15 TWaVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~k----------kaL~eALeKiK~ 60 (510)
.|.+++-.++|+++-..+.-.+||..|| +..+ ..|++-.+|+.+
T Consensus 3 ~~fl~~Pliif~ifVap~wl~lHY~~k~--~~~~~ls~~d~~~L~~L~~~a~rm~e 56 (75)
T TIGR02976 3 IFFLAIPLIIFVIFVAPLWLILHYRSKR--KTAASLSTDDQALLQELYAKADRLEE 56 (75)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 3566777777777778899999999997 4434 345555555544
No 6
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=47.99 E-value=33 Score=30.10 Aligned_cols=46 Identities=20% Similarity=0.353 Sum_probs=34.4
Q ss_pred CCCchhhhHHHHHHHHHHHHHHHHHHH-------HHHHHhhcCchHHHHHHHH
Q 010450 12 YTPTWVVAAVCTVIVAISLGAERLLHY-------LGRYLKNKKQKSLFEALQK 57 (510)
Q Consensus 12 ~TPTWaVA~Vc~v~v~iSl~~Er~lH~-------lgk~lkkk~kkaL~eALeK 57 (510)
||.-|...++..+++++-.++.+++-. +.+|+++++++.-.+||++
T Consensus 13 e~sl~~~~~~l~~~~~~l~ll~~ll~~~~~~p~~~~~~~~~rr~~ka~~al~~ 65 (108)
T PF07219_consen 13 ETSLWVALILLLLLFVVLYLLLRLLRRLLSLPSRVRRWRRRRRRRKAQRALSR 65 (108)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHH
Confidence 466677777777777777778887755 5778888888888887765
No 7
>TIGR03144 cytochr_II_ccsB cytochrome c-type biogenesis protein CcsB. Members of this protein family represent one of two essential proteins of system II for c-type cytochrome biogenesis. Additional proteins tend to be part of the system but can be replaced by chemical reductants such as dithiothreitol. This protein is designated CcsB in Bordetella pertussis and some other bacteria, resC in Bacillus (where there is additional N-terminal sequence), and CcsA in chloroplast. We use the CcsB designation here. Member sequences show regions of strong sequence conservation and variable-length, poorly conserved regions in between; sparsely filled columns were removed from the seed alignment prior to model construction.
Probab=41.03 E-value=1.1e+02 Score=30.72 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 010450 50 SLFEALQKVKEELMLLGFISLLLTVFQNT 78 (510)
Q Consensus 50 aL~eALeKiK~ELMLLGFISLLLtv~q~~ 78 (510)
+=.+.|||+--.....||+-|.+++..+.
T Consensus 142 p~L~~ld~l~~~~~~~Gf~~ltl~li~G~ 170 (243)
T TIGR03144 142 PLLETLDNLSYRTIAIGFPLLTIGIISGA 170 (243)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999988775
No 8
>TIGR01106 ATPase-IIC_X-K sodium or proton efflux -- potassium uptake antiporter, P-type ATPase, alpha subunit. Sequences from Blastocladiella emersonii (GP|6636502, GP|6636502 and PIR|T43025), C. elegans (GP|2315419, GP|6671808 and PIR|T31763) and Drosophila melanogaster (GP|7291424) score below trusted cutoff, apparently due to long branch length (excessive divergence from the last common ancestor) as evidenced by a phylogenetic tree. Experimental evidence is needed to determine whether these sequences represent ATPases with conserved function. Aside from fragments, other sequences between trusted and noise appear to be bacterial ATPases of unclear lineage, but most likely calcium pumps.
Probab=37.54 E-value=1.3e+02 Score=36.40 Aligned_cols=43 Identities=23% Similarity=0.222 Sum_probs=33.2
Q ss_pred cCCC--CccccccchHHHHHHHHHHhhhhHHHHHHHHHHHHhCCc
Q 010450 358 QPSD--QHFWFNRPQIVLFLIHFILFQNSFEIAFFFWILIQYGFD 400 (510)
Q Consensus 358 ~p~D--~lFWF~rP~llL~LIhfiLFQNAFelAfF~W~~~~fG~~ 400 (510)
+|++ +=..++++.++...+-..++|-.+.+++|+|.++.+|+.
T Consensus 809 ~P~~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~ 853 (997)
T TIGR01106 809 QPRNPKTDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFL 853 (997)
T ss_pred CCcCCccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 4554 346778877777777788899999999999988877753
No 9
>PF09878 DUF2105: Predicted membrane protein (DUF2105); InterPro: IPR019212 This entry represents a protein found in various hypothetical archaeal proteins, has no known function.
Probab=34.20 E-value=66 Score=32.29 Aligned_cols=47 Identities=34% Similarity=0.692 Sum_probs=30.3
Q ss_pred hhcccccchhhHHHHHHHHHhhhccCcchhhHhhhhHHH---HHHHHhhhHHHHH
Q 010450 285 DDFKRVVGISWYLWIFVVIFLLLNINEWHTYFWIAFIPF---ILLLAVGAKLEHV 336 (510)
Q Consensus 285 ~DFk~VVGIS~~lW~~vviFlLlnv~Gw~~yfWlsfiPl---illL~VGtKLq~I 336 (510)
|-...+-||.|-+|++.-+..++ .+-+|+.++=+ -+++=||+|+--|
T Consensus 158 egi~~~SGiaWalWi~gF~~Ff~-----~P~~Wl~~L~lAg~gl~iKV~sKlgLI 207 (212)
T PF09878_consen 158 EGIEGVSGIAWALWIAGFIGFFL-----FPQYWLLALMLAGCGLLIKVGSKLGLI 207 (212)
T ss_pred ehhhhhhhHHHHHHHHHHHHHHH-----hHHHHHHHHHHHhcchhhhhhhhhhhh
Confidence 44567889999999876555444 34567655433 3566778877543
No 10
>TIGR03777 RPE4 Rickettsial palindromic element RPE4 domain. This model describes protein translations of a family, RPE4, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else.
Probab=33.73 E-value=18 Score=26.27 Aligned_cols=10 Identities=40% Similarity=0.577 Sum_probs=7.3
Q ss_pred CcceecCCCC
Q 010450 353 GELVVQPSDQ 362 (510)
Q Consensus 353 G~~~V~p~D~ 362 (510)
=+|+||||||
T Consensus 23 LD~VvKPR~D 32 (32)
T TIGR03777 23 LDPVVKPRDD 32 (32)
T ss_pred cccccccCCC
Confidence 3678888876
No 11
>PF01578 Cytochrom_C_asm: Cytochrome C assembly protein; InterPro: IPR002541 This entry consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium leguminosarum [], CcmC from Escherichia coli and Paracoccus denitrificans [, ] and orf240 from Triticum aestivum (Wheat) mitochondria []. The members of this family are probably integral membrane proteins with six predicted transmembrane helices that may comprise the membrane component of an ABC (ATP binding cassette) transporter complex. This transporter may be necessary for transport of some component needed for cytochrome c assembly. One member, R. leguminosarum CycK, contains a putative haem-binding motif []. Wheat orf240 also contains a putative haem-binding motif and is a proposed ABC transporter with c-type haem as its proposed substrate []. However it seems unlikely that all members of this family transport haem or c-type apocytochromes because P. denitrificans CcmC transports neither [].; GO: 0006461 protein complex assembly, 0008535 respiratory chain complex IV assembly, 0016020 membrane
Probab=32.40 E-value=1.3e+02 Score=28.98 Aligned_cols=30 Identities=30% Similarity=0.595 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 010450 50 SLFEALQKVKEELMLLGFISLLLTVFQNTI 79 (510)
Q Consensus 50 aL~eALeKiK~ELMLLGFISLLLtv~q~~I 79 (510)
+-.+.||++-.-++..||+.|.++..-+.+
T Consensus 116 p~l~~le~~~~~~~~~gf~~lti~l~~G~~ 145 (214)
T PF01578_consen 116 PSLETLERLSYRLILIGFILLTIGLITGAI 145 (214)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence 445788999999999999999998777664
No 12
>PF15468 DUF4636: Domain of unknown function (DUF4636)
Probab=30.60 E-value=31 Score=35.04 Aligned_cols=37 Identities=35% Similarity=0.761 Sum_probs=25.8
Q ss_pred HHHHHHHhhhhcccccchhhHHHHHHHHHhhhccCcchhhHh
Q 010450 276 HKYMIRALEDDFKRVVGISWYLWIFVVIFLLLNINEWHTYFW 317 (510)
Q Consensus 276 hkYi~RsLE~DFk~VVGIS~~lW~~vviFlLlnv~Gw~~yfW 317 (510)
+.|=-| +||+-.++| +..||-||+|++|.=. .+.++|
T Consensus 25 qdyEc~--KDdsc~~iG-~fLlWyfviilvLm~~--~ras~W 61 (243)
T PF15468_consen 25 QDYECR--KDDSCGAIG-SFLLWYFVIILVLMFF--SRASVW 61 (243)
T ss_pred cchhhc--cCCccchhh-hHHHHHHHHHHHHHHH--HHHHHH
Confidence 344333 899998888 7899999988776522 255555
No 13
>PF12801 Fer4_5: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=26.25 E-value=1.2e+02 Score=22.58 Aligned_cols=24 Identities=17% Similarity=0.032 Sum_probs=16.8
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHH
Q 010450 15 TWVVAAVCTVIVAISLGAERLLHY 38 (510)
Q Consensus 15 TWaVA~Vc~v~v~iSl~~Er~lH~ 38 (510)
.|...+...++++++++..|.-..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~r~~C~ 25 (48)
T PF12801_consen 2 AWFWLIGFIGFLLLSLFFGRAWCG 25 (48)
T ss_pred cHHHHHHHHHHHHHHHHHhhhHHh
Confidence 455556666888888998885443
No 14
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=25.60 E-value=99 Score=32.76 Aligned_cols=38 Identities=16% Similarity=0.119 Sum_probs=24.3
Q ss_pred CCCchhhhHHHHHHHHHHHHHHHHHH-------HHHHHHhhcCch
Q 010450 12 YTPTWVVAAVCTVIVAISLGAERLLH-------YLGRYLKNKKQK 49 (510)
Q Consensus 12 ~TPTWaVA~Vc~v~v~iSl~~Er~lH-------~lgk~lkkk~kk 49 (510)
+|+-|+..++..+++++-+++++++. .+.+|+.++|++
T Consensus 38 e~s~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~r~~~ 82 (409)
T TIGR00540 38 EMSITGLAIFFIIALAIIFAFEWGLRRFFRLGAHSRGWFSGRKRR 82 (409)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHH
Confidence 45566666666666666667888885 445687775553
No 15
>TIGR00921 2A067 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family. Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea.
Probab=24.54 E-value=2.5e+02 Score=31.89 Aligned_cols=57 Identities=25% Similarity=0.525 Sum_probs=39.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCc----hHHHHHHHHHHHHH------HHHHHHHHHHH
Q 010450 17 VVAAVCTVIVAISLGAERLLHYLGRYLKNKKQ----KSLFEALQKVKEEL------MLLGFISLLLT 73 (510)
Q Consensus 17 aVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~k----kaL~eALeKiK~EL------MLLGFISLLLt 73 (510)
.+..+....+++++.++..+|.+.+|.+++++ .++.+|+.+.=.=+ +.+||.+|+++
T Consensus 620 ~~~~~~~~~i~lGigvDy~i~~~~r~~~~~~~~~~~~ai~~a~~~~g~ai~~s~lt~~~gf~~l~~s 686 (719)
T TIGR00921 620 FLAMATTISIILGLGMDYSIHLAERYFEERKEHGPKEAITHTMERTGPGILFSGLTTAGGFLSLLLS 686 (719)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhc
Confidence 34555566688889999999999999876543 56666666655533 44577776664
No 16
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=23.92 E-value=2e+02 Score=24.26 Aligned_cols=39 Identities=26% Similarity=0.573 Sum_probs=22.3
Q ss_pred hhccCcchhhHhh----hhHHHHHHHHhhhH------HHHHHHHHHHHHH
Q 010450 306 LLNINEWHTYFWI----AFIPFILLLAVGAK------LEHVISQLAHEVA 345 (510)
Q Consensus 306 Llnv~Gw~~yfWl----sfiPlillL~VGtK------Lq~IIt~lalei~ 345 (510)
++|..|...|-|+ +.+|+++++ |-+- |+.|.-+.|.|..
T Consensus 9 FfaMGgyafyVWlA~~~tll~l~~l~-v~sv~qrr~iL~~v~r~~aReaR 57 (67)
T COG3114 9 FFAMGGYAFYVWLAVGMTLLPLAVLV-VHSVLQRRAILRGVARQRAREAR 57 (67)
T ss_pred HHHccCchHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556677777787 556766444 4433 4445555555543
No 17
>PF01956 DUF106: Integral membrane protein DUF106; InterPro: IPR002809 This entry represents a group of eukaryotic and archaeal proteins that have no known function. Members are predicted to be integral membrane proteins.; GO: 0016020 membrane
Probab=23.70 E-value=61 Score=30.39 Aligned_cols=135 Identities=19% Similarity=0.267 Sum_probs=0.0
Q ss_pred ccccchhhhHHHHHHHHHH-HHHHHHHHHHHHH-----HHHHHhhhHhHhhHhhhccCCccccccceEEE------eeec
Q 010450 152 PLLSTEALHHLHIFIFVLA-IVHVTFCVLTILF-----AGARIRQWKNWEDSIAKQDFDPEQVLKTKVTH------VHQH 219 (510)
Q Consensus 152 pliS~e~LHQLHIFIFvLA-v~HV~ys~~Tm~L-----g~~Kir~Wk~WE~e~~~~~~~~~p~~~~r~r~------~~qt 219 (510)
|++. -.+.-+++.||++| +.|.+-..++-.+ ...|.+. +..+++.+..+...|....+++.- .-|.
T Consensus 6 p~i~-~~~~P~~i~v~~~~~~~~~~s~l~~~~~i~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~ 83 (168)
T PF01956_consen 6 PLIR-WVLLPITIVVFLIAILRGLISELLQKFLIDRKMDKYQKRM-KEFQKRYRELRKNGDFKKPKKLEKRQMELMEKQQ 83 (168)
T ss_pred chHh-hhhcCHHHHHHHHHHHHHHHHHHHhccccccccHHHHHHH-HHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHH
Q ss_pred chhhhhccC----CCCCchhHHHHHHHHHhhccCCchhhHHHHHHHHHhhhcCCCCCCchHHHHHHHhhhhcccccchhh
Q 010450 220 AFIKEHFLG----YGKDSALLGWMLSFFKQFYASITKADYVTLRLGFIMTHCRGSPKFNFHKYMIRALEDDFKRVVGISW 295 (510)
Q Consensus 220 ~F~~~h~~~----~~~~s~~l~Wi~cFfrQF~~SV~k~DYltLR~gFI~~H~~~~~~FdFhkYi~RsLE~DFk~VVGIS~ 295 (510)
+.-..+.++ .--..+++.|+-.||. ||+-.-.+-++...|+.-..|.+ +=-.+--.||
T Consensus 84 ~~~~~~mK~~~~~~v~~i~i~~wi~~~f~----------------g~vv~klPFpl~~~f~~~~qrgl--~~~d~~~~s~ 145 (168)
T PF01956_consen 84 EMMMMMMKPMFVTMVPQIPIFYWINYFFS----------------GFVVAKLPFPLTGRFKSMLQRGL--EGLDVSYVSS 145 (168)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHhh----------------hcceEEeeccccHHHhHHhhcCC--CCCcccHhHH
Q ss_pred HHHHHHHHHhh
Q 010450 296 YLWIFVVIFLL 306 (510)
Q Consensus 296 ~lW~~vviFlL 306 (510)
..|-|.+.|-+
T Consensus 146 i~wYfL~s~~~ 156 (168)
T PF01956_consen 146 ISWYFLCSFGL 156 (168)
T ss_pred HHHHHHHHHHH
No 18
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=23.60 E-value=1e+02 Score=32.56 Aligned_cols=37 Identities=16% Similarity=0.190 Sum_probs=27.1
Q ss_pred CCCchhhhHHHHHHHHHHHHHHHHHHH-------HHHHHhhcCc
Q 010450 12 YTPTWVVAAVCTVIVAISLGAERLLHY-------LGRYLKNKKQ 48 (510)
Q Consensus 12 ~TPTWaVA~Vc~v~v~iSl~~Er~lH~-------lgk~lkkk~k 48 (510)
+|+=|..++++.+++++.+++++++.. +..|+.++|+
T Consensus 38 e~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~rr~ 81 (398)
T PRK10747 38 ETSVTGLAIILILAMVVLFAIEWLLRRIFRTGARTRGWFVGRKR 81 (398)
T ss_pred EehHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhHHHHHHHH
Confidence 577787777777777777788888854 4568777555
No 19
>PHA03105 EEV glycoprotein; Provisional
Probab=23.30 E-value=96 Score=30.29 Aligned_cols=33 Identities=27% Similarity=0.200 Sum_probs=27.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhcCchH
Q 010450 18 VAAVCTVIVAISLGAERLLHYLGRYLKNKKQKS 50 (510)
Q Consensus 18 VA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~kka 50 (510)
+.++|..++++..++--.-|.+.|+|+|+++|+
T Consensus 9 ~vv~~SfiiLi~Yll~i~K~~iKKflkkkk~K~ 41 (188)
T PHA03105 9 VVVPLSFIVLILYIFFICKNTIKKFLKKKKGKN 41 (188)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 346788888888888888999999999888763
No 20
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.71 E-value=1.6e+02 Score=27.96 Aligned_cols=61 Identities=31% Similarity=0.298 Sum_probs=37.8
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHH---------HHHHHHHHHHhhhhc
Q 010450 14 PTWVVAAVCTVIVAISLGAERLLHYLGRYLKNKKQKSLFEALQKVKEELM---------LLGFISLLLTVFQNT 78 (510)
Q Consensus 14 PTWaVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~kkaL~eALeKiK~ELM---------LLGFISLLLtv~q~~ 78 (510)
-+|..|.+-+| +++++-.++-+|++- +-|+++.+..-|||+|.+|= .----+||=|..|++
T Consensus 6 ~~W~~a~igLv---vGi~IG~li~Rlt~~-~~k~q~~~q~ELe~~K~~ld~~rqel~~HFa~sAeLlktl~~dY 75 (138)
T COG3105 6 MTWEYALIGLV---VGIIIGALIARLTNR-KLKQQQKLQYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDY 75 (138)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHHcch-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46887766543 344444555555554 23456688888999998763 223456777777776
No 21
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.22 E-value=1.6e+02 Score=27.03 Aligned_cols=49 Identities=27% Similarity=0.192 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHH---------HHHHHHHHHHhhhhc
Q 010450 29 SLGAERLLHYLGRYLKNKKQKSLFEALQKVKEELM---------LLGFISLLLTVFQNT 78 (510)
Q Consensus 29 Sl~~Er~lH~lgk~lkkk~kkaL~eALeKiK~ELM---------LLGFISLLLtv~q~~ 78 (510)
++++=.++.++.+.= .++++.|-+.|++.|+||= +-.-.-||=...+++
T Consensus 9 G~iiG~~~~r~~~~~-~~~q~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y 66 (128)
T PF06295_consen 9 GLIIGFLIGRLTSSN-QQKQAKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDY 66 (128)
T ss_pred HHHHHHHHHHHhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444445554431 1345789999999999983 555555666666554
No 22
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=20.47 E-value=1.9e+02 Score=28.02 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=30.7
Q ss_pred cccCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHH
Q 010450 9 TLEYTPTWVVAAVCTVIVAISLGAERLLHYLGRYLKNKKQKSLFEALQK 57 (510)
Q Consensus 9 sLe~TPTWaVA~Vc~v~v~iSl~~Er~lH~lgk~lkkk~kkaL~eALeK 57 (510)
+--.+|+.--.-.|++++.|-+++--+ -.|--|+.+||||+. .|+|+
T Consensus 19 s~~~~psffsthm~tILiaIvVliiii-ivli~lcssRKkKaa-AAi~e 65 (189)
T PF05568_consen 19 SPVTPPSFFSTHMYTILIAIVVLIIII-IVLIYLCSSRKKKAA-AAIEE 65 (189)
T ss_pred CCCCCccHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhhhHHHH-hhhhh
Confidence 334567777777777777665555433 345567778888877 66664
Done!