Query 023637
Match_columns 279
No_of_seqs 132 out of 250
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:31:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023637.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023637hhsearch_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 6E-103 1E-107 766.5 22.2 244 6-273 1-247 (478)
2 PRK11677 hypothetical protein; 73.5 7.5 0.00016 33.4 5.1 44 15-62 2-45 (134)
3 PF06305 DUF1049: Protein of u 73.0 17 0.00036 26.4 6.3 47 16-62 18-64 (68)
4 PF07219 HemY_N: HemY protein 70.5 10 0.00022 30.5 5.0 46 12-57 13-65 (108)
5 COG1033 Predicted exporters of 66.8 13 0.00028 39.9 6.2 56 19-74 251-317 (727)
6 TIGR03144 cytochr_II_ccsB cyto 57.0 52 0.0011 30.0 7.6 30 50-79 142-171 (243)
7 TIGR02976 phageshock_pspB phag 56.0 43 0.00093 26.1 5.8 29 15-43 3-31 (75)
8 PF01578 Cytochrom_C_asm: Cyto 53.2 49 0.0011 29.1 6.6 31 49-79 115-145 (214)
9 PF12801 Fer4_5: 4Fe-4S bindin 47.9 34 0.00074 23.3 3.8 25 14-38 1-25 (48)
10 TIGR00540 hemY_coli hemY prote 47.8 33 0.00071 33.2 5.0 45 12-56 38-93 (409)
11 COG3105 Uncharacterized protei 44.6 45 0.00098 28.9 4.8 61 14-78 6-75 (138)
12 PRK10747 putative protoheme IX 43.7 38 0.00083 32.7 4.8 37 12-48 38-81 (398)
13 PF11044 TMEMspv1-c74-12: Plec 42.8 59 0.0013 23.4 4.3 27 14-40 2-33 (49)
14 COG3071 HemY Uncharacterized e 41.9 42 0.00092 33.8 4.8 47 13-59 39-96 (400)
15 PF05568 ASFV_J13L: African sw 41.5 58 0.0013 29.0 5.1 45 11-57 21-65 (189)
16 TIGR00921 2A067 The (Largely A 36.2 1.4E+02 0.0031 30.9 7.8 56 17-72 620-685 (719)
17 PHA03105 EEV glycoprotein; Pro 35.8 42 0.0009 30.2 3.3 33 18-50 9-41 (188)
18 PF14015 DUF4231: Protein of u 35.6 1.2E+02 0.0026 23.7 5.7 42 17-64 53-94 (112)
19 PF13297 Telomere_Sde2_2: Telo 34.5 21 0.00046 26.9 1.1 13 55-67 17-29 (60)
20 PF12273 RCR: Chitin synthesis 33.7 29 0.00063 28.8 1.9 17 16-32 2-18 (130)
21 PF15444 TMEM247: Transmembran 30.7 56 0.0012 29.9 3.3 23 167-189 193-215 (218)
22 PF11742 DUF3302: Protein of u 29.5 2.2E+02 0.0047 22.5 6.0 33 34-73 21-53 (78)
23 PF03176 MMPL: MMPL family; I 27.9 93 0.002 29.0 4.5 50 24-73 208-268 (333)
24 KOG4484 Uncharacterized conser 27.9 1.2E+02 0.0026 27.6 4.9 36 32-67 91-130 (199)
25 PF15050 SCIMP: SCIMP protein 27.2 98 0.0021 26.6 4.0 31 16-48 9-39 (133)
26 PF15167 DUF4581: Domain of un 26.6 57 0.0012 27.7 2.5 29 38-66 66-95 (128)
27 PF11466 Doppel: Prion-like pr 26.0 58 0.0013 21.4 1.9 14 14-27 6-19 (30)
28 TIGR03480 HpnN hopanoid biosyn 25.8 2.4E+02 0.0052 30.5 7.6 56 20-75 325-391 (862)
29 PF06295 DUF1043: Protein of u 25.6 1.5E+02 0.0033 24.7 5.0 50 28-78 8-66 (128)
30 PF00664 ABC_membrane: ABC tra 24.8 2.3E+02 0.005 23.5 5.9 25 15-39 140-164 (275)
31 COG3860 Uncharacterized protei 23.4 60 0.0013 26.2 2.0 22 240-266 54-75 (89)
32 KOG3643 GABA receptor [Signal 22.8 82 0.0018 32.3 3.2 26 19-44 309-334 (459)
33 TIGR01710 typeII_sec_gspG gene 22.3 2.5E+02 0.0055 23.2 5.6 40 22-61 9-48 (134)
34 PRK02935 hypothetical protein; 21.2 2.2E+02 0.0048 23.9 4.9 42 14-73 13-54 (110)
35 TIGR00921 2A067 The (Largely A 21.1 2.5E+02 0.0054 29.1 6.5 53 21-73 250-313 (719)
36 PF12273 RCR: Chitin synthesis 20.6 90 0.0019 25.8 2.6 18 16-33 5-22 (130)
37 PF08041 PetM: PetM family of 20.5 1.9E+02 0.0041 19.2 3.5 22 17-38 5-26 (31)
38 PF14163 SieB: Superinfection 20.3 2.5E+02 0.0054 23.6 5.3 39 20-58 36-75 (151)
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=6.5e-103 Score=766.50 Aligned_cols=244 Identities=63% Similarity=1.035 Sum_probs=227.9
Q ss_pred CCCCcccCCchhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccc
Q 023637 6 GGRSLEETPTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLTVAGSWISKICIP 85 (279)
Q Consensus 6 ~~rsLe~TPTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~ELMLLGFISLLLtv~q~~IskICIp 85 (279)
|+|+||+||||+||+||+|||+||+++||+||++||||+|++||+|+|||||||+|||||||||||||++|++|+|||||
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 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCCCCccccccccccchhhhhhhhHHHHHHHHHhhcCcchhhhhcc--CCCcccCC-CCccccccccchhh
Q 023637 86 ESVANTWHPCDKEREPELNNEKETTEQETTEHENRRRLLEAVAASGGSIRRALAA--GSTTEKCS-KGKVPFVSEDGLHQ 162 (279)
Q Consensus 86 ~~~~~~mlPC~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~rRlLa~--~~~~~~C~-~GkvplvS~egLHQ 162 (279)
++++++|+||+.+++..+. +. ....||+|+. +.+.++|+ ||||||+|.|||||
T Consensus 81 ~~~~~~~lPC~~~~~~~~~---~~---------------------~~~~r~ll~~~~~~~~~~C~~kGkvpliS~egLHQ 136 (478)
T PF03094_consen 81 SSYASTMLPCKPPEESSKE---GS---------------------SHNRRRLLASGAAEGSDYCPKKGKVPLISAEGLHQ 136 (478)
T ss_pred hhHHhcccCCCCccccccc---cc---------------------chhhhhhhhhhcccccCcccccCccccccchhHHH
Confidence 9999999999965543321 00 1136788873 34567897 69999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHhhhhhccccccCCCCceeeeeeeecccccccCCCCCcchHHHHHHHH
Q 023637 163 LHIFIFVLALFHVLYSILTMALSRAKMKKWKKWEKETRTIDYQFSHDPERFRFARETSFGRRHLSSWTKTPVLIWIVCFF 242 (279)
Q Consensus 163 LHIFIFVLAv~HV~ys~lTm~Lg~~Kir~Wk~WE~e~~~~~~~~~~~p~r~r~~~qttF~r~h~~~ws~~~~l~Wi~cFf 242 (279)
||||||||||+||+|||+||+||++|||+||+||+|+++++|+..|||+|+|++|||+|+|+|.++|++++++.|++|||
T Consensus 137 LHIFIFVLAV~HV~Ys~lTm~Lg~~KIr~Wk~WE~e~~~~~~~~~~d~~r~~~~~qt~F~r~h~~~w~~~~~~~wi~~Ff 216 (478)
T PF03094_consen 137 LHIFIFVLAVVHVLYSCLTMLLGRAKIRRWKKWEDEAQTDEYQFSNDPRRFRLTRQTTFVRRHTSFWSKSPVLSWIVCFF 216 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccCcceeeeecccHHHHhhcCCcccChhHHhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCChhHHHHHHhhhhhhhhcCCCcee
Q 023637 243 RQFVRSVPKVDYLTLRHGFVTVIFLCFQSLA 273 (279)
Q Consensus 243 rQF~~SV~k~DYltLR~GFI~~H~~~~~~~~ 273 (279)
||||+||+|+||+|||+|||++|++||+.|.
T Consensus 217 rQF~~SV~k~DYltLR~gFI~~H~~~~~~FD 247 (478)
T PF03094_consen 217 RQFYGSVTKSDYLTLRHGFITAHLLPNPKFD 247 (478)
T ss_pred HHhhccccHHHHHHHHHHHHHhhcCCCCCCC
Confidence 9999999999999999999999999999885
No 2
>PRK11677 hypothetical protein; Provisional
Probab=73.52 E-value=7.5 Score=33.38 Aligned_cols=44 Identities=36% Similarity=0.502 Sum_probs=28.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHH
Q 023637 15 TWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSEL 62 (279)
Q Consensus 15 TWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~EL 62 (279)
+|..|++++|+. +++=.++.+++..=. ++++.|-+-||+.|.||
T Consensus 2 ~W~~a~i~livG---~iiG~~~~R~~~~~~-~~q~~le~eLe~~k~el 45 (134)
T PRK11677 2 TWEYALIGLVVG---IIIGAVAMRFGNRKL-RQQQALQYELEKNKAEL 45 (134)
T ss_pred cHHHHHHHHHHH---HHHHHHHHhhccchh-hHHHHHHHHHHHHHHHH
Confidence 498888766553 334444444433211 35788999999999998
No 3
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=72.96 E-value=17 Score=26.38 Aligned_cols=47 Identities=15% Similarity=0.361 Sum_probs=35.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHH
Q 023637 16 WAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSEL 62 (279)
Q Consensus 16 WaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~EL 62 (279)
+-++++.++..++++++=-.+.....+=.|++-+.+-..+++.+.|+
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 66777777777777777777777766666666688888999988886
No 4
>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=70.53 E-value=10 Score=30.53 Aligned_cols=46 Identities=17% Similarity=0.535 Sum_probs=35.0
Q ss_pred cCCchhhHHHHHHHHHHHHHHHHHHHH-------HHhHhhhhcchHHHHHHHH
Q 023637 12 ETPTWAVAVVCFVLVTISIIIEHIIHL-------IGKWLTKKHKRALYEALEK 57 (279)
Q Consensus 12 ~TPTWaVA~Vc~v~V~iSl~~Er~lH~-------lgk~Lkk~~kkaL~eALeK 57 (279)
+|.-|...+++.+++++-.++.+.+-. +.+|+++++++.-.+||++
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 466688888888888888888888765 5778888888777777764
No 5
>COG1033 Predicted exporters of the RND superfamily [General function prediction only]
Probab=66.85 E-value=13 Score=39.93 Aligned_cols=56 Identities=23% Similarity=0.395 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhcc-----hHHHHHHHHHHHHHHH------HHHHHHHHHH
Q 023637 19 AVVCFVLVTISIIIEHIIHLIGKWLTKKHK-----RALYEALEKIKSELML------LGFISLLLTV 74 (279)
Q Consensus 19 A~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~k-----kaL~eALeKiK~ELML------LGFISLLLtv 74 (279)
.+..++.++|++.++.++|..-.+.+.+++ .|+.||+.++.-=+++ +||+||+.+-
T Consensus 251 ~s~~~~~llIgiGidy~vh~~nr~~ee~~~~~~~~eAv~~ai~~~g~avl~a~lTT~~GF~Sl~~s~ 317 (727)
T COG1033 251 TTSAVPPLLIGIGIDYGVHFHNRYEEERRKGRTVEEAVVEAIKHTGPAVLIAALTTAAGFLSLLTSS 317 (727)
T ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHcc
Confidence 345567788899999999999999987774 5788888887766553 7999998743
No 6
>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=56.99 E-value=52 Score=30.04 Aligned_cols=30 Identities=20% Similarity=0.402 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 023637 50 ALYEALEKIKSELMLLGFISLLLTVAGSWI 79 (279)
Q Consensus 50 aL~eALeKiK~ELMLLGFISLLLtv~q~~I 79 (279)
|=.+.|||+--.....||+-|.++...+.|
T Consensus 142 p~L~~ld~l~~~~~~~Gf~~ltl~li~G~i 171 (243)
T TIGR03144 142 PLLETLDNLSYRTIAIGFPLLTIGIISGAV 171 (243)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 557889999999999999999999887763
No 7
>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=56.00 E-value=43 Score=26.09 Aligned_cols=29 Identities=17% Similarity=0.198 Sum_probs=23.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHhHh
Q 023637 15 TWAVAVVCFVLVTISIIIEHIIHLIGKWL 43 (279)
Q Consensus 15 TWaVA~Vc~v~V~iSl~~Er~lH~lgk~L 43 (279)
.|.+++-.++|+++-..+.-.+||..||=
T Consensus 3 ~~fl~~Pliif~ifVap~wl~lHY~~k~~ 31 (75)
T TIGR02976 3 IFFLAIPLIIFVIFVAPLWLILHYRSKRK 31 (75)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 36778888888888888999999997753
No 8
>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=53.23 E-value=49 Score=29.08 Aligned_cols=31 Identities=32% Similarity=0.493 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 023637 49 RALYEALEKIKSELMLLGFISLLLTVAGSWI 79 (279)
Q Consensus 49 kaL~eALeKiK~ELMLLGFISLLLtv~q~~I 79 (279)
-|-.+.||++-.-++..||+-|.++..-+.+
T Consensus 115 lp~l~~le~~~~~~~~~gf~~lti~l~~G~~ 145 (214)
T PF01578_consen 115 LPSLETLERLSYRLILIGFILLTIGLITGAI 145 (214)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence 4557889999999999999999998887764
No 9
>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=47.93 E-value=34 Score=23.26 Aligned_cols=25 Identities=8% Similarity=0.093 Sum_probs=17.6
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHH
Q 023637 14 PTWAVAVVCFVLVTISIIIEHIIHL 38 (279)
Q Consensus 14 PTWaVA~Vc~v~V~iSl~~Er~lH~ 38 (279)
|.|...+...++++++++..|.--.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~r~~C~ 25 (48)
T PF12801_consen 1 MAWFWLIGFIGFLLLSLFFGRAWCG 25 (48)
T ss_pred CcHHHHHHHHHHHHHHHHHhhhHHh
Confidence 3455666666888999999885433
No 10
>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=47.77 E-value=33 Score=33.22 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=28.7
Q ss_pred cCCchhhHHHHHHHHHHHHHHHHHHH-------HHHhHhhhhcc----hHHHHHHH
Q 023637 12 ETPTWAVAVVCFVLVTISIIIEHIIH-------LIGKWLTKKHK----RALYEALE 56 (279)
Q Consensus 12 ~TPTWaVA~Vc~v~V~iSl~~Er~lH-------~lgk~Lkk~~k----kaL~eALe 56 (279)
+|+=|+..++..+++++.+++++++. .+..|+.++++ +++.+++-
T Consensus 38 e~s~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~r~~~k~~~~~~~gll 93 (409)
T TIGR00540 38 EMSITGLAIFFIIALAIIFAFEWGLRRFFRLGAHSRGWFSGRKRRKAQKQTEEALL 93 (409)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667766666666666668889884 45568877553 34444443
No 11
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.64 E-value=45 Score=28.90 Aligned_cols=61 Identities=31% Similarity=0.434 Sum_probs=37.4
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHH---------HHHHHHHHHHHhhhc
Q 023637 14 PTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELM---------LLGFISLLLTVAGSW 78 (279)
Q Consensus 14 PTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~ELM---------LLGFISLLLtv~q~~ 78 (279)
-+|..|.+-+| |++++-.++-+|++-=- ++|+.+-.-|||+|.+|= .----+||=|..|+|
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---VGIIIGALIARLTNRKL-KQQQKLQYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDY 75 (138)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHHcchhh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46888776543 34444444555544322 245678888999998763 223457788888877
No 12
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=43.66 E-value=38 Score=32.74 Aligned_cols=37 Identities=16% Similarity=0.416 Sum_probs=27.7
Q ss_pred cCCchhhHHHHHHHHHHHHHHHHHHHH-------HHhHhhhhcc
Q 023637 12 ETPTWAVAVVCFVLVTISIIIEHIIHL-------IGKWLTKKHK 48 (279)
Q Consensus 12 ~TPTWaVA~Vc~v~V~iSl~~Er~lH~-------lgk~Lkk~~k 48 (279)
+|+=|..++++.+++++.+++.+++.. +..|+.++|+
T Consensus 38 e~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~rr~ 81 (398)
T PRK10747 38 ETSVTGLAIILILAMVVLFAIEWLLRRIFRTGARTRGWFVGRKR 81 (398)
T ss_pred EehHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhHHHHHHHH
Confidence 567788888888888888888988854 4578877554
No 13
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=42.79 E-value=59 Score=23.41 Aligned_cols=27 Identities=26% Similarity=0.454 Sum_probs=12.5
Q ss_pred CchhhH-----HHHHHHHHHHHHHHHHHHHHH
Q 023637 14 PTWAVA-----VVCFVLVTISIIIEHIIHLIG 40 (279)
Q Consensus 14 PTWaVA-----~Vc~v~V~iSl~~Er~lH~lg 40 (279)
|||.-- .+..+|.-+.+.+=.-+..+.
T Consensus 2 p~wlt~iFsvvIil~If~~iGl~IyQkikqIr 33 (49)
T PF11044_consen 2 PTWLTTIFSVVIILGIFAWIGLSIYQKIKQIR 33 (49)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888532 223333334445545554443
No 14
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=41.95 E-value=42 Score=33.76 Aligned_cols=47 Identities=15% Similarity=0.400 Sum_probs=35.9
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHH-------hHhhhhc----chHHHHHHHHHH
Q 023637 13 TPTWAVAVVCFVLVTISIIIEHIIHLIG-------KWLTKKH----KRALYEALEKIK 59 (279)
Q Consensus 13 TPTWaVA~Vc~v~V~iSl~~Er~lH~lg-------k~Lkk~~----kkaL~eALeKiK 59 (279)
+.-|.+++..++.++|-+++|.+++++. .|+..+| ++++.|+|.|+-
T Consensus 39 ~Sl~~lv~~~ii~lvv~~~l~~~l~~v~~~~~~~~~w~~~rKrrra~~~~~egl~~l~ 96 (400)
T COG3071 39 MSLTTLVIFLIIALVVLYLLEWLLRRVLRTPAHTRGWFSRRKRRRARKALNEGLLKLF 96 (400)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3447777777777888899999999875 4887444 578999998874
No 15
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=41.49 E-value=58 Score=28.98 Aligned_cols=45 Identities=20% Similarity=0.323 Sum_probs=30.3
Q ss_pred ccCCchhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHH
Q 023637 11 EETPTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEK 57 (279)
Q Consensus 11 e~TPTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeK 57 (279)
--+|..--.-.|++++.|-+++--+ --|--|+.+||||+. .|++|
T Consensus 21 ~~~psffsthm~tILiaIvVliiii-ivli~lcssRKkKaa-AAi~e 65 (189)
T PF05568_consen 21 VTPPSFFSTHMYTILIAIVVLIIII-IVLIYLCSSRKKKAA-AAIEE 65 (189)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhhhHHHH-hhhhh
Confidence 3467777777777777666555433 345578888888887 66664
No 16
>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=36.16 E-value=1.4e+02 Score=30.94 Aligned_cols=56 Identities=23% Similarity=0.446 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhHhhhhc----chHHHHHHHHHHHHH------HHHHHHHHHH
Q 023637 17 AVAVVCFVLVTISIIIEHIIHLIGKWLTKKH----KRALYEALEKIKSEL------MLLGFISLLL 72 (279)
Q Consensus 17 aVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~----kkaL~eALeKiK~EL------MLLGFISLLL 72 (279)
.+..+....+++++.++..+|.+.+|.++++ +.++.+|+.+.=.=+ +.+||.+|++
T Consensus 620 ~~~~~~~~~i~lGigvDy~i~~~~r~~~~~~~~~~~~ai~~a~~~~g~ai~~s~lt~~~gf~~l~~ 685 (719)
T TIGR00921 620 FLAMATTISIILGLGMDYSIHLAERYFEERKEHGPKEAITHTMERTGPGILFSGLTTAGGFLSLLL 685 (719)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHh
Confidence 3455556668889999999999999987654 356777777665533 3456666655
No 17
>PHA03105 EEV glycoprotein; Provisional
Probab=35.79 E-value=42 Score=30.16 Aligned_cols=33 Identities=30% Similarity=0.251 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchH
Q 023637 18 VAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRA 50 (279)
Q Consensus 18 VA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kka 50 (279)
+.++|+.++++..++=-.-|.+-|+|+|+++|+
T Consensus 9 ~vv~~SfiiLi~Yll~i~K~~iKKflkkkk~K~ 41 (188)
T PHA03105 9 VVVPLSFIVLILYIFFICKNTIKKFLKKKKGKN 41 (188)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 356788888888888888899999999888765
No 18
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=35.57 E-value=1.2e+02 Score=23.68 Aligned_cols=42 Identities=21% Similarity=0.356 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHH
Q 023637 17 AVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELML 64 (279)
Q Consensus 17 aVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~ELML 64 (279)
.+++++.+++++.-.+...-..=.+|.+.+ .+.|.+|.|.++
T Consensus 53 ~~~~~l~~~~~~~~~~~~~~~~~~~W~~~r------~tae~lk~e~~~ 94 (112)
T PF14015_consen 53 LVAAILSALAAILASLAAFFRFHERWIRYR------ATAESLKREKWL 94 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHhchhHHHHHHH------HHHHHHHHHHHH
Confidence 344566777777777777777777787764 355666666653
No 19
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=34.46 E-value=21 Score=26.88 Aligned_cols=13 Identities=54% Similarity=0.956 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHH
Q 023637 55 LEKIKSELMLLGF 67 (279)
Q Consensus 55 LeKiK~ELMLLGF 67 (279)
+|++|+|||-+|.
T Consensus 17 ldrLK~~L~a~GL 29 (60)
T PF13297_consen 17 LDRLKSALMALGL 29 (60)
T ss_pred HHHHHHHHHHcCC
Confidence 6899999999984
No 20
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=33.75 E-value=29 Score=28.77 Aligned_cols=17 Identities=12% Similarity=0.540 Sum_probs=11.1
Q ss_pred hhhHHHHHHHHHHHHHH
Q 023637 16 WAVAVVCFVLVTISIII 32 (279)
Q Consensus 16 WaVA~Vc~v~V~iSl~~ 32 (279)
|++++|++++++|.|++
T Consensus 2 W~l~~iii~~i~l~~~~ 18 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFL 18 (130)
T ss_pred eeeHHHHHHHHHHHHHH
Confidence 77777766666665554
No 21
>PF15444 TMEM247: Transmembrane protein 247
Probab=30.71 E-value=56 Score=29.94 Aligned_cols=23 Identities=30% Similarity=0.421 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q 023637 167 IFVLALFHVLYSILTMALSRAKM 189 (279)
Q Consensus 167 IFVLAv~HV~ys~lTm~Lg~~Ki 189 (279)
||+|-.-|-+||+.+++|...|-
T Consensus 193 vfflfskhylfciaaillclikt 215 (218)
T PF15444_consen 193 VFFLFSKHYLFCIAAILLCLIKT 215 (218)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHH
Confidence 45666778889999999999884
No 22
>PF11742 DUF3302: Protein of unknown function (DUF3302); InterPro: IPR011223 This is a family of uncharacterised bacterial proteins, restricted to the Gammaproteobacteria.
Probab=29.52 E-value=2.2e+02 Score=22.54 Aligned_cols=33 Identities=27% Similarity=0.395 Sum_probs=26.5
Q ss_pred HHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHH
Q 023637 34 HIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLT 73 (279)
Q Consensus 34 r~lH~lgk~Lkk~~kkaL~eALeKiK~ELMLLGFISLLLt 73 (279)
=.+|-+=.-..|||+.|=.||.. .+|-+||+..
T Consensus 21 ~~lh~lP~~iA~kr~Hpq~eaI~-------v~gwisLft~ 53 (78)
T PF11742_consen 21 WKLHDLPGKIAHKRNHPQAEAIH-------VLGWISLFTL 53 (78)
T ss_pred HHHHhhHHHHHHhcCCchHHHHH-------HHHHHHHHHH
Confidence 46788877888888899888875 6899998764
No 23
>PF03176 MMPL: MMPL family; InterPro: IPR004869 Proteins of this entry are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport [].; GO: 0016020 membrane
Probab=27.94 E-value=93 Score=28.96 Aligned_cols=50 Identities=26% Similarity=0.416 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHhHhhhhc-----chHHHHHHHHHHHH------HHHHHHHHHHHH
Q 023637 24 VLVTISIIIEHIIHLIGKWLTKKH-----KRALYEALEKIKSE------LMLLGFISLLLT 73 (279)
Q Consensus 24 v~V~iSl~~Er~lH~lgk~Lkk~~-----kkaL~eALeKiK~E------LMLLGFISLLLt 73 (279)
..+++++.++.++|.+.+|-.+.+ +.++.+|+.++-.= -+..||.||+++
T Consensus 208 ~~l~lgvgidy~i~l~~r~ree~~~g~~~~~ai~~a~~~~g~~i~~s~ltt~~gf~~L~~s 268 (333)
T PF03176_consen 208 FVLLLGVGIDYSIHLINRYREELRRGMSRKEAIRRAVRSTGRAILLSALTTAIGFGSLLFS 268 (333)
T ss_pred hhhHHHhhhhhHHHHHHHHHHHHHhccchHHHHHHHHhccCchhHHHHHHHHHHHHHHHHh
Confidence 345678888999998877655433 24566666654433 467899998884
No 24
>KOG4484 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.86 E-value=1.2e+02 Score=27.58 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=30.0
Q ss_pred HHHHHHHHHhHhhhhc----chHHHHHHHHHHHHHHHHHH
Q 023637 32 IEHIIHLIGKWLTKKH----KRALYEALEKIKSELMLLGF 67 (279)
Q Consensus 32 ~Er~lH~lgk~Lkk~~----kkaL~eALeKiK~ELMLLGF 67 (279)
+||.+.+|.|-++... .+.+-+-|.|+|++||..-|
T Consensus 91 aeR~irrLeK~~keS~ad~kd~~i~~qlrk~kidL~YVr~ 130 (199)
T KOG4484|consen 91 AERSIRRLEKLIKESGADVKDKQIQQQLRKLKIDLEYVRF 130 (199)
T ss_pred HHHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHHHHHHh
Confidence 6888999988887543 56799999999999999765
No 25
>PF15050 SCIMP: SCIMP protein
Probab=27.19 E-value=98 Score=26.62 Aligned_cols=31 Identities=19% Similarity=0.642 Sum_probs=21.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcc
Q 023637 16 WAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHK 48 (279)
Q Consensus 16 WaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~k 48 (279)
|.+-+|. ||+||+.+--+|--+-+|+-|+.|
T Consensus 9 WiiLAVa--II~vS~~lglIlyCvcR~~lRqGk 39 (133)
T PF15050_consen 9 WIILAVA--IILVSVVLGLILYCVCRWQLRQGK 39 (133)
T ss_pred HHHHHHH--HHHHHHHHHHHHHHHHHHHHHccc
Confidence 7776666 556666666677777777777665
No 26
>PF15167 DUF4581: Domain of unknown function (DUF4581)
Probab=26.60 E-value=57 Score=27.68 Aligned_cols=29 Identities=34% Similarity=0.523 Sum_probs=21.4
Q ss_pred HHHhHhhhhcchHHHHHHHHHHHHH-HHHH
Q 023637 38 LIGKWLTKKHKRALYEALEKIKSEL-MLLG 66 (279)
Q Consensus 38 ~lgk~Lkk~~kkaL~eALeKiK~EL-MLLG 66 (279)
..-.|...-.||.|.+.||||+.-+ ||||
T Consensus 66 laqdyisscGKk~l~e~leKvf~sf~pllg 95 (128)
T PF15167_consen 66 LAQDYISSCGKKTLTESLEKVFKSFRPLLG 95 (128)
T ss_pred HHHHHHHHhchhHHHHHHHHHHHhhhhccC
Confidence 3445666777889999999998765 5555
No 27
>PF11466 Doppel: Prion-like protein Doppel; InterPro: IPR021566 Dpl is a homologue related to the prion protein (PrP). Dpl is toxic to neurons and is expressed in the brains of mice that do not express PrP. In DHPC and SDS micelles, Dpl shoes about 40% alpha-helical structure however in aqueous solution it consists of a random coil. The alpha helical segment can adopt a transmembrane localisation also in a membrane. The unprocessed Dpl protein is thought to posses a possible channel formation mechanism which may be related to toxicity through direct interaction with cell membranes and damage to the cell membrane. ; PDB: 1Z65_A.
Probab=26.03 E-value=58 Score=21.40 Aligned_cols=14 Identities=36% Similarity=0.895 Sum_probs=11.2
Q ss_pred CchhhHHHHHHHHH
Q 023637 14 PTWAVAVVCFVLVT 27 (279)
Q Consensus 14 PTWaVA~Vc~v~V~ 27 (279)
-+|.+|+||..+..
T Consensus 6 g~~~lAi~c~LL~s 19 (30)
T PF11466_consen 6 GGWWLAIVCVLLFS 19 (30)
T ss_dssp SSHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHH
Confidence 47999999987653
No 28
>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.
Probab=25.84 E-value=2.4e+02 Score=30.46 Aligned_cols=56 Identities=23% Similarity=0.406 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhh-----cchHHHHHHHHHHHHHH------HHHHHHHHHHHh
Q 023637 20 VVCFVLVTISIIIEHIIHLIGKWLTKK-----HKRALYEALEKIKSELM------LLGFISLLLTVA 75 (279)
Q Consensus 20 ~Vc~v~V~iSl~~Er~lH~lgk~Lkk~-----~kkaL~eALeKiK~ELM------LLGFISLLLtv~ 75 (279)
++.+.++++.+.++.++|.+..+.+++ +++++.+|+.++-.=++ .+||++|+.+-+
T Consensus 325 s~~~~~lliGi~vD~~I~~~~r~~e~~~~g~~~~~A~~~a~~~~~~~i~~s~lTt~~gf~~l~~~~~ 391 (862)
T TIGR03480 325 SVAFAVLFIGLGVDFAIQFSLRYREERFRGGNHREALSVAARRMGAALLLAALATAAGFFAFLPTDY 391 (862)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 344556678999999999998887653 23566666666555443 468887776643
No 29
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.59 E-value=1.5e+02 Score=24.71 Aligned_cols=50 Identities=22% Similarity=0.285 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHH---------HHHHHHHHHHHhhhc
Q 023637 28 ISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELM---------LLGFISLLLTVAGSW 78 (279)
Q Consensus 28 iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~ELM---------LLGFISLLLtv~q~~ 78 (279)
|.+++=.++.++++-=. ++++.|-+.|++.|+||= +-.-.-||=...+++
T Consensus 8 vG~iiG~~~~r~~~~~~-~~q~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y 66 (128)
T PF06295_consen 8 VGLIIGFLIGRLTSSNQ-QKQAKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDY 66 (128)
T ss_pred HHHHHHHHHHHHhccch-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444455533211 335789999999999983 455555666666654
No 30
>PF00664 ABC_membrane: ABC transporter transmembrane region; InterPro: IPR001140 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). A variety of ATP-binding transport proteins have a six transmembrane helical region. They are all integral membrane proteins involved in a variety of transport systems. Members of this family include; the cystic fibrosis transmembrane conductance regulator (CFTR), bacterial leukotoxin secretion ATP-binding protein, multidrug resistance proteins, the yeast leptomycin B resistance protein, the mammalian sulphonylurea receptor and antigen peptide transporter 2. Many of these proteins have two such regions.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3G61_B 3G5U_B 3G60_A 3B60_D 3QF4_B 2HYD_A 2ONJ_A 4A82_B 4AA3_A 2YL4_A.
Probab=24.76 E-value=2.3e+02 Score=23.53 Aligned_cols=25 Identities=16% Similarity=0.559 Sum_probs=14.7
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHH
Q 023637 15 TWAVAVVCFVLVTISIIIEHIIHLI 39 (279)
Q Consensus 15 TWaVA~Vc~v~V~iSl~~Er~lH~l 39 (279)
.|.++.++.+++.+.+++-..+.+.
T Consensus 140 ~~~l~l~~l~~~~~~~~~~~~~~~~ 164 (275)
T PF00664_consen 140 SWKLALILLIILPLLFLISFIFSKK 164 (275)
T ss_dssp TTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccchhhhhhHhhhhhhccc
Confidence 3666666666666666655554443
No 31
>COG3860 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.43 E-value=60 Score=26.17 Aligned_cols=22 Identities=23% Similarity=0.493 Sum_probs=17.8
Q ss_pred HHHHhhcCCCChhHHHHHHhhhhhhhh
Q 023637 240 CFFRQFVRSVPKVDYLTLRHGFVTVIF 266 (279)
Q Consensus 240 cFfrQF~~SV~k~DYltLR~GFI~~H~ 266 (279)
-..+||+ .||-|+|.-||+.-+
T Consensus 54 ~ii~ryh-----~DyaTvRReli~~~f 75 (89)
T COG3860 54 LIIKRYH-----PDYATVRRELIEYGF 75 (89)
T ss_pred HHHHHhC-----chHHHHHHHHHHcch
Confidence 3457787 899999999998754
No 32
>KOG3643 consensus GABA receptor [Signal transduction mechanisms]
Probab=22.80 E-value=82 Score=32.29 Aligned_cols=26 Identities=27% Similarity=0.354 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhh
Q 023637 19 AVVCFVLVTISIIIEHIIHLIGKWLT 44 (279)
Q Consensus 19 A~Vc~v~V~iSl~~Er~lH~lgk~Lk 44 (279)
-.||+|||.+|++==...|++.+..+
T Consensus 309 L~vCFvfVF~sLLEYA~V~Y~~~~~~ 334 (459)
T KOG3643|consen 309 LGVCFVFVFLSLLEYAAVNYMFKRRG 334 (459)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 46999999999988788899887663
No 33
>TIGR01710 typeII_sec_gspG general secretion pathway protein G. This model represents GspG, protein G of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=22.27 E-value=2.5e+02 Score=23.25 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHH
Q 023637 22 CFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSE 61 (279)
Q Consensus 22 c~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~E 61 (279)
..|+++|++++==++-.+...+++.+.+.....+..++..
T Consensus 9 livlaIigil~~i~~p~~~~~~~~a~~~~~~~~l~~i~~a 48 (134)
T TIGR01710 9 MVVLVILGLLAALVAPKLFSQADKAKAQVAKAQIKALKNA 48 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555444555555566666655555555555443
No 34
>PRK02935 hypothetical protein; Provisional
Probab=21.21 E-value=2.2e+02 Score=23.92 Aligned_cols=42 Identities=21% Similarity=0.545 Sum_probs=25.6
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHH
Q 023637 14 PTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLT 73 (279)
Q Consensus 14 PTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkk~~kkaL~eALeKiK~ELMLLGFISLLLt 73 (279)
-|||...|..-|+ +=|+|-+++. ...+ -.=.|++||++++.+
T Consensus 13 Rt~aL~lvfiG~~---------vMy~Giff~~---~~~~------m~ifm~~G~l~~l~S 54 (110)
T PRK02935 13 RTFALSLVFIGFI---------VMYLGIFFRE---SIII------MTIFMLLGFLAVIAS 54 (110)
T ss_pred HHHHHHHHHHHHH---------HHHHHHHhcc---cHHH------HHHHHHHHHHHHHHH
Confidence 4788776654443 3466655532 2233 344799999998854
No 35
>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=21.08 E-value=2.5e+02 Score=29.14 Aligned_cols=53 Identities=19% Similarity=0.294 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHhhhhc-----chHHHHHHHHHHHHH------HHHHHHHHHHH
Q 023637 21 VCFVLVTISIIIEHIIHLIGKWLTKKH-----KRALYEALEKIKSEL------MLLGFISLLLT 73 (279)
Q Consensus 21 Vc~v~V~iSl~~Er~lH~lgk~Lkk~~-----kkaL~eALeKiK~EL------MLLGFISLLLt 73 (279)
+....+++++.++.++|.+..|.++++ ++++.+|+++.-.=+ ..+||.+|+++
T Consensus 250 ~~~~~l~lgi~vd~~ihl~~r~~~~~~~g~~~~~ai~~a~~~~g~~i~~t~~t~~~gf~~l~~s 313 (719)
T TIGR00921 250 LLAVPMLIGVGIDYGIQTLNRYEEERDIGRAKGEAIVTAVRRTGRAVLIALLTTSAGFAALALS 313 (719)
T ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHHcCCCHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHhc
Confidence 345555678899999999999875432 457777777765544 34688888765
No 36
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=20.59 E-value=90 Score=25.82 Aligned_cols=18 Identities=17% Similarity=0.360 Sum_probs=13.8
Q ss_pred hhhHHHHHHHHHHHHHHH
Q 023637 16 WAVAVVCFVLVTISIIIE 33 (279)
Q Consensus 16 WaVA~Vc~v~V~iSl~~E 33 (279)
|+|.+|+++|++++++.=
T Consensus 5 ~~iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 5 FAIIIVAILLFLFLFYCH 22 (130)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 778888888887777773
No 37
>PF08041 PetM: PetM family of cytochrome b6f complex subunit 7; InterPro: IPR012595 This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta haem's and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin [].; GO: 0009512 cytochrome b6f complex; PDB: 2ZT9_F 1Q90_M 2E76_F 2E75_F 2E74_F 2D2C_S 1VF5_S.
Probab=20.52 E-value=1.9e+02 Score=19.17 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=17.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH
Q 023637 17 AVAVVCFVLVTISIIIEHIIHL 38 (279)
Q Consensus 17 aVA~Vc~v~V~iSl~~Er~lH~ 38 (279)
.+|++|++++++.+.+=-.|=+
T Consensus 5 ~~a~i~~~lvlvGla~Gf~LLk 26 (31)
T PF08041_consen 5 NIAVICFGLVLVGLALGFVLLK 26 (31)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhhe
Confidence 5799999999999887655543
No 38
>PF14163 SieB: Superinfection exclusion protein B
Probab=20.33 E-value=2.5e+02 Score=23.64 Aligned_cols=39 Identities=18% Similarity=0.310 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhh-cchHHHHHHHHH
Q 023637 20 VVCFVLVTISIIIEHIIHLIGKWLTKK-HKRALYEALEKI 58 (279)
Q Consensus 20 ~Vc~v~V~iSl~~Er~lH~lgk~Lkk~-~kkaL~eALeKi 58 (279)
+...+++.+|+++=+.+.++-++.+++ ++|...++++|.
T Consensus 36 i~~~fl~s~s~li~~~~~~~~~~~~~~~~~k~~~~~~~~~ 75 (151)
T PF14163_consen 36 IGLIFLFSVSYLIAQLLSFIYKEAKDRYQRKRKKKKIEKK 75 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556667777777777776654332 234444555544
Done!