Query 025359
Match_columns 254
No_of_seqs 136 out of 249
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:01:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025359.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025359hhsearch_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 4.5E-93 9.6E-98 688.2 19.4 221 6-250 1-224 (478)
2 PRK11677 hypothetical protein; 82.3 2.8 6.1E-05 35.4 5.0 44 15-62 2-45 (134)
3 PF06305 DUF1049: Protein of u 77.3 12 0.00026 26.8 6.3 47 16-62 18-64 (68)
4 PF07219 HemY_N: HemY protein 73.4 7.7 0.00017 30.7 4.9 46 12-57 13-65 (108)
5 COG1033 Predicted exporters of 70.6 10 0.00022 40.2 6.3 56 19-74 251-317 (727)
6 TIGR02976 phageshock_pspB phag 65.7 23 0.0005 27.2 5.8 28 15-42 3-30 (75)
7 TIGR03144 cytochr_II_ccsB cyto 60.0 46 0.00099 30.0 7.7 30 50-79 142-171 (243)
8 COG3105 Uncharacterized protei 55.3 24 0.00053 30.1 4.7 61 14-78 6-75 (138)
9 PF01578 Cytochrom_C_asm: Cyto 55.1 47 0.001 28.7 6.7 30 50-79 116-145 (214)
10 PF12801 Fer4_5: 4Fe-4S bindin 53.7 24 0.00053 23.6 3.8 25 14-38 1-25 (48)
11 TIGR00540 hemY_coli hemY prote 51.0 27 0.00059 33.3 4.9 37 12-48 38-81 (409)
12 PF11044 TMEMspv1-c74-12: Plec 50.3 38 0.00083 24.0 4.3 28 14-41 2-34 (49)
13 PHA03105 EEV glycoprotein; Pro 48.0 21 0.00046 31.6 3.3 33 18-50 9-41 (188)
14 PRK10747 putative protoheme IX 47.2 31 0.00067 32.9 4.7 37 12-48 38-81 (398)
15 PF12273 RCR: Chitin synthesis 45.0 22 0.00048 29.0 2.9 17 16-32 2-18 (130)
16 PF06295 DUF1043: Protein of u 44.4 50 0.0011 27.3 4.9 51 27-78 7-66 (128)
17 PF14015 DUF4231: Protein of u 42.7 88 0.0019 24.1 5.9 42 17-64 53-94 (112)
18 TIGR00921 2A067 The (Largely A 41.5 1.1E+02 0.0024 31.2 7.9 56 17-72 620-685 (719)
19 PF05568 ASFV_J13L: African sw 40.6 62 0.0013 28.4 5.0 45 11-57 21-65 (189)
20 PF13297 Telomere_Sde2_2: Telo 37.4 18 0.00039 26.9 1.1 13 55-67 17-29 (60)
21 PF12273 RCR: Chitin synthesis 37.1 24 0.00053 28.8 2.0 18 16-33 5-22 (130)
22 PF15050 SCIMP: SCIMP protein 33.9 65 0.0014 27.3 4.0 32 16-49 9-40 (133)
23 PF15167 DUF4581: Domain of un 33.1 40 0.00086 28.2 2.6 30 37-66 65-95 (128)
24 PF03176 MMPL: MMPL family; I 32.1 75 0.0016 29.1 4.5 50 24-73 208-268 (333)
25 PRK02935 hypothetical protein; 31.3 1E+02 0.0022 25.5 4.6 42 14-73 13-54 (110)
26 KOG3643 GABA receptor [Signal 30.7 39 0.00084 34.1 2.5 25 19-43 309-333 (459)
27 TIGR03480 HpnN hopanoid biosyn 30.5 1.9E+02 0.004 30.8 7.7 56 20-75 325-391 (862)
28 PF15444 TMEM247: Transmembran 30.5 59 0.0013 29.4 3.4 23 167-189 193-215 (218)
29 PF11742 DUF3302: Protein of u 29.7 2.3E+02 0.0051 22.0 6.2 33 34-73 21-53 (78)
30 PF00664 ABC_membrane: ABC tra 27.8 2E+02 0.0043 23.6 6.0 27 15-41 140-166 (275)
31 PF08041 PetM: PetM family of 26.3 1.3E+02 0.0027 19.7 3.5 22 17-38 5-26 (31)
32 PF11466 Doppel: Prion-like pr 26.3 55 0.0012 21.2 1.8 14 14-27 6-19 (30)
33 TIGR01710 typeII_sec_gspG gene 25.5 2.1E+02 0.0046 23.4 5.7 40 22-61 9-48 (134)
34 TIGR00921 2A067 The (Largely A 25.4 1.9E+02 0.0042 29.5 6.5 53 21-73 250-313 (719)
35 COG3071 HemY Uncharacterized e 24.5 1.3E+02 0.0028 30.0 4.8 47 13-59 39-96 (400)
36 KOG4484 Uncharacterized conser 24.3 1.6E+02 0.0034 26.5 4.9 36 32-67 91-130 (199)
37 PF07950 DUF1691: Protein of u 22.8 2.5E+02 0.0054 22.4 5.5 53 18-75 43-95 (110)
38 PF04145 Ctr: Ctr copper trans 22.3 49 0.0011 26.6 1.3 30 8-37 17-46 (144)
39 PF03032 Brevenin: Brevenin/es 21.6 40 0.00086 23.7 0.6 10 62-71 10-19 (46)
40 PLN02250 lipid phosphate phosp 21.3 2.5E+02 0.0054 26.9 6.0 22 11-32 64-85 (314)
41 PF14163 SieB: Superinfection 20.9 2.5E+02 0.0054 23.3 5.3 67 20-96 36-103 (151)
42 PF04883 HK97-gp10_like: Bacte 20.8 1.7E+02 0.0038 20.5 3.9 32 32-63 3-34 (78)
43 KOG1357 Serine palmitoyltransf 20.6 1.3E+02 0.0027 30.9 4.0 48 9-56 32-88 (519)
44 PRK08326 ribonucleotide-diphos 20.5 6E+02 0.013 23.8 8.4 61 16-76 162-224 (311)
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=4.5e-93 Score=688.20 Aligned_cols=221 Identities=61% Similarity=0.991 Sum_probs=205.0
Q ss_pred CCCCcccCCCchhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccc
Q 025359 6 GGRSLEETPTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLTVAGSWISKICIP 85 (254)
Q Consensus 6 ~~rsLe~TPTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELMLLGFISLLLtv~q~~IskICIp 85 (254)
|+|+||+|||||||+||+|||+||+++||+||++||||+|++||+|+|||||||+||||||||||||||+|++|+|||||
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 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCCCCCccccccccccchhhhhhhHHHHHHHHHHhcCcchhhhhcc--CCCcccC-CCCccccccccchhH
Q 025359 86 ESVANTWHPCDKEREPELNNEKETTEQETTEHENRRRLLEAVAASGGSIRRALAA--GSTTEKC-SKGKVPFVSEDGLHQ 162 (254)
Q Consensus 86 ~~~~~~mlPC~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~RRlLa~--~~~~~~C-~~GkvplvS~eglhQ 162 (254)
++++++|+||+.+++.++. + ....+||+|+. +.+.++| +||||||+|.|||||
T Consensus 81 ~~~~~~~lPC~~~~~~~~~---~---------------------~~~~~r~ll~~~~~~~~~~C~~kGkvpliS~egLHQ 136 (478)
T PF03094_consen 81 SSYASTMLPCKPPEESSKE---G---------------------SSHNRRRLLASGAAEGSDYCPKKGKVPLISAEGLHQ 136 (478)
T ss_pred hhHHhcccCCCCccccccc---c---------------------cchhhhhhhhhhcccccCcccccCccccccchhHHH
Confidence 9999999999865543321 0 01136777763 3457799 679999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHhhhhccccccCCCCceeeeeeeccccccccCCCCCCchhhhHHhhh
Q 025359 163 LHIFIFVLALFHVLYSILTMALSRAKMKKWKKWEKETRTIDYQFSHDPERFRFARETSFGRRHLSSWTKTPVLIWIVRNS 242 (254)
Q Consensus 163 LHiFIFVLAv~HV~ys~lTm~Lg~~Kir~Wk~WE~e~~~~~~~~~~dp~r~r~~~qttF~~~h~~~ws~~~~l~Wi~cFf 242 (254)
||||||||||+||+|||+||+||++|||+||+||+|+++++||..|||+|+|++|||+|+|+|.++|++++++.|++|||
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 hhhccccc
Q 025359 243 LSFLSCYQ 250 (254)
Q Consensus 243 rQF~~~~~ 250 (254)
||||+||+
T Consensus 217 rQF~~SV~ 224 (478)
T PF03094_consen 217 RQFYGSVT 224 (478)
T ss_pred HHhhcccc
Confidence 99999994
No 2
>PRK11677 hypothetical protein; Provisional
Probab=82.28 E-value=2.8 Score=35.44 Aligned_cols=44 Identities=36% Similarity=0.524 Sum_probs=29.0
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHH
Q 025359 15 TWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSEL 62 (254)
Q Consensus 15 TWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~EL 62 (254)
+|..|++++|+ .+++=.++.+++..= .++++.|-+-||+.|.||
T Consensus 2 ~W~~a~i~liv---G~iiG~~~~R~~~~~-~~~q~~le~eLe~~k~el 45 (134)
T PRK11677 2 TWEYALIGLVV---GIIIGAVAMRFGNRK-LRQQQALQYELEKNKAEL 45 (134)
T ss_pred cHHHHHHHHHH---HHHHHHHHHhhccch-hhHHHHHHHHHHHHHHHH
Confidence 48888866654 344444444543311 146788999999999998
No 3
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=77.29 E-value=12 Score=26.78 Aligned_cols=47 Identities=15% Similarity=0.361 Sum_probs=37.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHH
Q 025359 16 WAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSEL 62 (254)
Q Consensus 16 WaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~EL 62 (254)
+-++++.++..++++++=-.+.....+=.|++.+.+-..+++.+.|+
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 67777777777888888777777777777777788889999998886
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=73.45 E-value=7.7 Score=30.72 Aligned_cols=46 Identities=17% Similarity=0.535 Sum_probs=35.2
Q ss_pred cCCCchhHHHHHHHHHHHHHHHHHHHH-------HHhHhhhhcchHHHHHHHH
Q 025359 12 ETPTWAVAVVCFVLVTISIIIEHIIHL-------IGKWLTKKHKRALYEALEK 57 (254)
Q Consensus 12 ~TPTWaVA~Vc~v~V~iSl~~Er~lH~-------lgk~Lkkk~kkaL~eALeK 57 (254)
+|.-|...++..+++++-.++.+.+-. +.+|+++++++.-.+||++
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 456677777777777777788887755 6788888888888877764
No 5
>COG1033 Predicted exporters of the RND superfamily [General function prediction only]
Probab=70.57 E-value=10 Score=40.15 Aligned_cols=56 Identities=23% Similarity=0.395 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhcc-----hHHHHHHHHHHHHHHH------HHHHHHHHHH
Q 025359 19 AVVCFVLVTISIIIEHIIHLIGKWLTKKHK-----RALYEALEKIKSELML------LGFISLLLTV 74 (254)
Q Consensus 19 A~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~k-----kaL~eALeKiK~ELML------LGFISLLLtv 74 (254)
....++.++|++.+++++|..-.+.+.+++ .|+.||+.++.-=+++ +||+||+.+-
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 345567788999999999999999987766 4777888887766553 7999998753
No 6
>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=65.71 E-value=23 Score=27.20 Aligned_cols=28 Identities=18% Similarity=0.230 Sum_probs=23.2
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHhH
Q 025359 15 TWAVAVVCFVLVTISIIIEHIIHLIGKW 42 (254)
Q Consensus 15 TWaVA~Vc~v~V~iSl~~Er~lH~lgk~ 42 (254)
.|.+++-..+|+++-..+.-.+||..||
T Consensus 3 ~~fl~~Pliif~ifVap~wl~lHY~~k~ 30 (75)
T TIGR02976 3 IFFLAIPLIIFVIFVAPLWLILHYRSKR 30 (75)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3677778888888888899999999884
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=59.98 E-value=46 Score=29.98 Aligned_cols=30 Identities=20% Similarity=0.402 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 025359 50 ALYEALEKIKSELMLLGFISLLLTVAGSWI 79 (254)
Q Consensus 50 aL~eALeKiK~ELMLLGFISLLLtv~q~~I 79 (254)
|=.+.|||+--.....||+-|.+++..+.|
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 556789999999999999999999887763
No 8
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.26 E-value=24 Score=30.11 Aligned_cols=61 Identities=31% Similarity=0.441 Sum_probs=37.7
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHH---------HHHHHHHHHHHhhhc
Q 025359 14 PTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELM---------LLGFISLLLTVAGSW 78 (254)
Q Consensus 14 PTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELM---------LLGFISLLLtv~q~~ 78 (254)
-+|..|.+-+| |.++|-.++-+|++- +-|+++.+-.-|||+|.+|= .----+||=|..|+|
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 36888776543 344444444455542 22355678888999998763 223457888888877
No 9
>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=55.06 E-value=47 Score=28.74 Aligned_cols=30 Identities=33% Similarity=0.534 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 025359 50 ALYEALEKIKSELMLLGFISLLLTVAGSWI 79 (254)
Q Consensus 50 aL~eALeKiK~ELMLLGFISLLLtv~q~~I 79 (254)
+-.+.||++-.-++..||+.|.++..-+.+
T Consensus 116 p~l~~le~~~~~~~~~gf~~lti~l~~G~~ 145 (214)
T PF01578_consen 116 PSLETLERLSYRLILIGFILLTIGLITGAI 145 (214)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence 446888999999999999999998887765
No 10
>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=53.73 E-value=24 Score=23.64 Aligned_cols=25 Identities=8% Similarity=0.093 Sum_probs=17.8
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHH
Q 025359 14 PTWAVAVVCFVLVTISIIIEHIIHL 38 (254)
Q Consensus 14 PTWaVA~Vc~v~V~iSl~~Er~lH~ 38 (254)
|.|...+...++++++++..|.-..
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~r~~C~ 25 (48)
T PF12801_consen 1 MAWFWLIGFIGFLLLSLFFGRAWCG 25 (48)
T ss_pred CcHHHHHHHHHHHHHHHHHhhhHHh
Confidence 3455666666889999999985443
No 11
>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=50.96 E-value=27 Score=33.27 Aligned_cols=37 Identities=14% Similarity=0.304 Sum_probs=24.7
Q ss_pred cCCCchhHHHHHHHHHHHHHHHHHHH-------HHHhHhhhhcc
Q 025359 12 ETPTWAVAVVCFVLVTISIIIEHIIH-------LIGKWLTKKHK 48 (254)
Q Consensus 12 ~TPTWaVA~Vc~v~V~iSl~~Er~lH-------~lgk~Lkkk~k 48 (254)
+|+=|...++..+++++.+++++++. .+..|+.++|+
T Consensus 38 e~s~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~r~~ 81 (409)
T TIGR00540 38 EMSITGLAIFFIIALAIIFAFEWGLRRFFRLGAHSRGWFSGRKR 81 (409)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence 45556666666666666667888884 45668877554
No 12
>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=50.31 E-value=38 Score=24.03 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=12.9
Q ss_pred CCchhH-----HHHHHHHHHHHHHHHHHHHHHh
Q 025359 14 PTWAVA-----VVCFVLVTISIIIEHIIHLIGK 41 (254)
Q Consensus 14 PTWaVA-----~Vc~v~V~iSl~~Er~lH~lgk 41 (254)
|||.-- .+..+|.-+.+.+=.-+..+..
T Consensus 2 p~wlt~iFsvvIil~If~~iGl~IyQkikqIrg 34 (49)
T PF11044_consen 2 PTWLTTIFSVVIILGIFAWIGLSIYQKIKQIRG 34 (49)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 788532 2223333344555555555444
No 13
>PHA03105 EEV glycoprotein; Provisional
Probab=48.02 E-value=21 Score=31.56 Aligned_cols=33 Identities=30% Similarity=0.251 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchH
Q 025359 18 VAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRA 50 (254)
Q Consensus 18 VA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kka 50 (254)
+.++|+.++++..++=-.-|.+.|+|+|+++|+
T Consensus 9 ~vv~~SfiiLi~Yll~i~K~~iKKflkkkk~K~ 41 (188)
T PHA03105 9 VVVPLSFIVLILYIFFICKNTIKKFLKKKKGKN 41 (188)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 356788889999999889999999999988876
No 14
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=47.22 E-value=31 Score=32.88 Aligned_cols=37 Identities=16% Similarity=0.416 Sum_probs=27.4
Q ss_pred cCCCchhHHHHHHHHHHHHHHHHHHHH-------HHhHhhhhcc
Q 025359 12 ETPTWAVAVVCFVLVTISIIIEHIIHL-------IGKWLTKKHK 48 (254)
Q Consensus 12 ~TPTWaVA~Vc~v~V~iSl~~Er~lH~-------lgk~Lkkk~k 48 (254)
+|+=|..++++.+++++.+++.+++.. +..|+.++|+
T Consensus 38 e~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~rr~ 81 (398)
T PRK10747 38 ETSVTGLAIILILAMVVLFAIEWLLRRIFRTGARTRGWFVGRKR 81 (398)
T ss_pred EehHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhHHHHHHHH
Confidence 567788888888887877788888854 4578877555
No 15
>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=45.00 E-value=22 Score=29.01 Aligned_cols=17 Identities=12% Similarity=0.540 Sum_probs=10.8
Q ss_pred chhHHHHHHHHHHHHHH
Q 025359 16 WAVAVVCFVLVTISIII 32 (254)
Q Consensus 16 WaVA~Vc~v~V~iSl~~ 32 (254)
|++++|++++++|-|++
T Consensus 2 W~l~~iii~~i~l~~~~ 18 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFL 18 (130)
T ss_pred eeeHHHHHHHHHHHHHH
Confidence 77777666666655554
No 16
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=44.35 E-value=50 Score=27.25 Aligned_cols=51 Identities=22% Similarity=0.289 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHH---------HHHHHHHHHHHhhhc
Q 025359 27 TISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELM---------LLGFISLLLTVAGSW 78 (254)
Q Consensus 27 ~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELM---------LLGFISLLLtv~q~~ 78 (254)
+|.+++=.++.++.+-= .++++.|-+.|++.|.||= +-.-.-||=...++|
T Consensus 7 vvG~iiG~~~~r~~~~~-~~~q~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y 66 (128)
T PF06295_consen 7 VVGLIIGFLIGRLTSSN-QQKQAKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDY 66 (128)
T ss_pred HHHHHHHHHHHHHhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444455554421 1345789999999999983 455555666666654
No 17
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=42.73 E-value=88 Score=24.08 Aligned_cols=42 Identities=21% Similarity=0.356 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHH
Q 025359 17 AVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELML 64 (254)
Q Consensus 17 aVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELML 64 (254)
.+++++.+++++.-.+...-..=.+|.+-+ .+.|.+|.|.++
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 344567777777777777777777887744 456667777664
No 18
>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=41.46 E-value=1.1e+02 Score=31.20 Aligned_cols=56 Identities=21% Similarity=0.434 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcc----hHHHHHHHHHHHHH------HHHHHHHHHH
Q 025359 17 AVAVVCFVLVTISIIIEHIIHLIGKWLTKKHK----RALYEALEKIKSEL------MLLGFISLLL 72 (254)
Q Consensus 17 aVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~k----kaL~eALeKiK~EL------MLLGFISLLL 72 (254)
.+..+....+++++.++..+|.+.+|.+++++ .++.+|+.+.=.=+ +.+||.+|++
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 34555666788899999999999999876543 56677777665533 3456666655
No 19
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=40.61 E-value=62 Score=28.44 Aligned_cols=45 Identities=22% Similarity=0.369 Sum_probs=29.6
Q ss_pred ccCCCchhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHH
Q 025359 11 EETPTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEK 57 (254)
Q Consensus 11 e~TPTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeK 57 (254)
--+|..--.-.|+++|.|-+++--++ -|--|+.+||||+. .|++|
T Consensus 21 ~~~psffsthm~tILiaIvVliiiii-vli~lcssRKkKaa-AAi~e 65 (189)
T PF05568_consen 21 VTPPSFFSTHMYTILIAIVVLIIIII-VLIYLCSSRKKKAA-AAIEE 65 (189)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhhHHHH-hhhhh
Confidence 34677777777777776665554333 44567888888887 66664
No 20
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=37.38 E-value=18 Score=26.89 Aligned_cols=13 Identities=54% Similarity=0.956 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHH
Q 025359 55 LEKIKSELMLLGF 67 (254)
Q Consensus 55 LeKiK~ELMLLGF 67 (254)
||++|+|||-+|.
T Consensus 17 ldrLK~~L~a~GL 29 (60)
T PF13297_consen 17 LDRLKSALMALGL 29 (60)
T ss_pred HHHHHHHHHHcCC
Confidence 6899999999984
No 21
>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=37.15 E-value=24 Score=28.77 Aligned_cols=18 Identities=17% Similarity=0.360 Sum_probs=13.7
Q ss_pred chhHHHHHHHHHHHHHHH
Q 025359 16 WAVAVVCFVLVTISIIIE 33 (254)
Q Consensus 16 WaVA~Vc~v~V~iSl~~E 33 (254)
|+|.+|+++|++++++.=
T Consensus 5 ~~iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 5 FAIIIVAILLFLFLFYCH 22 (130)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 778888888887777764
No 22
>PF15050 SCIMP: SCIMP protein
Probab=33.90 E-value=65 Score=27.31 Aligned_cols=32 Identities=19% Similarity=0.650 Sum_probs=23.3
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcch
Q 025359 16 WAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKR 49 (254)
Q Consensus 16 WaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kk 49 (254)
|++-+|. ||+||+.+--+|--+-+|+-|+.||
T Consensus 9 WiiLAVa--II~vS~~lglIlyCvcR~~lRqGkk 40 (133)
T PF15050_consen 9 WIILAVA--IILVSVVLGLILYCVCRWQLRQGKK 40 (133)
T ss_pred HHHHHHH--HHHHHHHHHHHHHHHHHHHHHcccc
Confidence 7666665 6667777777888888888777664
No 23
>PF15167 DUF4581: Domain of unknown function (DUF4581)
Probab=33.12 E-value=40 Score=28.23 Aligned_cols=30 Identities=33% Similarity=0.518 Sum_probs=22.0
Q ss_pred HHHHhHhhhhcchHHHHHHHHHHHHH-HHHH
Q 025359 37 HLIGKWLTKKHKRALYEALEKIKSEL-MLLG 66 (254)
Q Consensus 37 H~lgk~Lkkk~kkaL~eALeKiK~EL-MLLG 66 (254)
...-.|...-.||.|.+.||||+.-+ ||||
T Consensus 65 qlaqdyisscGKk~l~e~leKvf~sf~pllg 95 (128)
T PF15167_consen 65 QLAQDYISSCGKKTLTESLEKVFKSFRPLLG 95 (128)
T ss_pred HHHHHHHHHhchhHHHHHHHHHHHhhhhccC
Confidence 33445666677889999999998765 5555
No 24
>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=32.10 E-value=75 Score=29.15 Aligned_cols=50 Identities=26% Similarity=0.416 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHhHhhhhc-----chHHHHHHHHHHHH------HHHHHHHHHHHH
Q 025359 24 VLVTISIIIEHIIHLIGKWLTKKH-----KRALYEALEKIKSE------LMLLGFISLLLT 73 (254)
Q Consensus 24 v~V~iSl~~Er~lH~lgk~Lkkk~-----kkaL~eALeKiK~E------LMLLGFISLLLt 73 (254)
..+++++.++..+|.+.+|-.+.+ +.++.+|+.++-.= -+..||.||+++
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 345678888999998877654332 23566666654433 467889998874
No 25
>PRK02935 hypothetical protein; Provisional
Probab=31.34 E-value=1e+02 Score=25.50 Aligned_cols=42 Identities=24% Similarity=0.582 Sum_probs=25.4
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHH
Q 025359 14 PTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLT 73 (254)
Q Consensus 14 PTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELMLLGFISLLLt 73 (254)
-|||...|..-|+ +-++|-+++. ... +-.=.|++||++++..
T Consensus 13 Rt~aL~lvfiG~~---------vMy~Giff~~---~~~------~m~ifm~~G~l~~l~S 54 (110)
T PRK02935 13 RTFALSLVFIGFI---------VMYLGIFFRE---SII------IMTIFMLLGFLAVIAS 54 (110)
T ss_pred HHHHHHHHHHHHH---------HHHHHHHhcc---cHH------HHHHHHHHHHHHHHHH
Confidence 4787766654443 3466655522 223 3345799999998854
No 26
>KOG3643 consensus GABA receptor [Signal transduction mechanisms]
Probab=30.67 E-value=39 Score=34.08 Aligned_cols=25 Identities=28% Similarity=0.382 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHh
Q 025359 19 AVVCFVLVTISIIIEHIIHLIGKWL 43 (254)
Q Consensus 19 A~Vc~v~V~iSl~~Er~lH~lgk~L 43 (254)
-.||+|||.+|++==...|++.+..
T Consensus 309 L~vCFvfVF~sLLEYA~V~Y~~~~~ 333 (459)
T KOG3643|consen 309 LGVCFVFVFLSLLEYAAVNYMFKRR 333 (459)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhH
Confidence 4599999999998888889988866
No 27
>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=30.52 E-value=1.9e+02 Score=30.79 Aligned_cols=56 Identities=23% Similarity=0.406 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhh-----cchHHHHHHHHHHHHHH------HHHHHHHHHHHh
Q 025359 20 VVCFVLVTISIIIEHIIHLIGKWLTKK-----HKRALYEALEKIKSELM------LLGFISLLLTVA 75 (254)
Q Consensus 20 ~Vc~v~V~iSl~~Er~lH~lgk~Lkkk-----~kkaL~eALeKiK~ELM------LLGFISLLLtv~ 75 (254)
++.+.++++.+.++.++|.+..+.+++ +++++.+|+.++-.=++ .+||++|+.+-+
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 344556678999999999998887643 33566666666555443 468877776633
No 28
>PF15444 TMEM247: Transmembrane protein 247
Probab=30.49 E-value=59 Score=29.44 Aligned_cols=23 Identities=30% Similarity=0.421 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhHhh
Q 025359 167 IFVLALFHVLYSILTMALSRAKM 189 (254)
Q Consensus 167 IFVLAv~HV~ys~lTm~Lg~~Ki 189 (254)
||+|-.=|-+||+.+++|...|.
T Consensus 193 vfflfskhylfciaaillclikt 215 (218)
T PF15444_consen 193 VFFLFSKHYLFCIAAILLCLIKT 215 (218)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHH
Confidence 45666668888999999999884
No 29
>PF11742 DUF3302: Protein of unknown function (DUF3302); InterPro: IPR011223 This is a family of uncharacterised bacterial proteins, restricted to the Gammaproteobacteria.
Probab=29.71 E-value=2.3e+02 Score=22.03 Aligned_cols=33 Identities=27% Similarity=0.395 Sum_probs=26.3
Q ss_pred HHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHH
Q 025359 34 HIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLT 73 (254)
Q Consensus 34 r~lH~lgk~Lkkk~kkaL~eALeKiK~ELMLLGFISLLLt 73 (254)
=.+|-+=.-..|||+.|=.||.. .+|-+||+..
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 56787777778888899888875 6899998764
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=27.77 E-value=2e+02 Score=23.57 Aligned_cols=27 Identities=15% Similarity=0.496 Sum_probs=15.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHh
Q 025359 15 TWAVAVVCFVLVTISIIIEHIIHLIGK 41 (254)
Q Consensus 15 TWaVA~Vc~v~V~iSl~~Er~lH~lgk 41 (254)
.|.+++++.+++.+.+++-..+.+..+
T Consensus 140 ~~~l~l~~l~~~~~~~~~~~~~~~~~~ 166 (275)
T PF00664_consen 140 SWKLALILLIILPLLFLISFIFSKKIR 166 (275)
T ss_dssp TTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccchhhhhhHhhhhhhccccc
Confidence 366666666666666666555544433
No 31
>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=26.35 E-value=1.3e+02 Score=19.72 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=17.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH
Q 025359 17 AVAVVCFVLVTISIIIEHIIHL 38 (254)
Q Consensus 17 aVA~Vc~v~V~iSl~~Er~lH~ 38 (254)
.+|++|++++++.+.+=-.|=+
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 4799999999999887655533
No 32
>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=26.32 E-value=55 Score=21.21 Aligned_cols=14 Identities=36% Similarity=0.895 Sum_probs=11.2
Q ss_pred CCchhHHHHHHHHH
Q 025359 14 PTWAVAVVCFVLVT 27 (254)
Q Consensus 14 PTWaVA~Vc~v~V~ 27 (254)
-+|.+|+||..+..
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 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=25.53 E-value=2.1e+02 Score=23.35 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHH
Q 025359 22 CFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSE 61 (254)
Q Consensus 22 c~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~E 61 (254)
..|+++|++++==++-.+....++.+.+.....+..++..
T Consensus 9 livlaIigil~~i~~p~~~~~~~~a~~~~~~~~l~~i~~a 48 (134)
T TIGR01710 9 MVVLVILGLLAALVAPKLFSQADKAKAQVAKAQIKALKNA 48 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555554555555666666655555555555443
No 34
>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=25.41 E-value=1.9e+02 Score=29.50 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHhhhh-----cchHHHHHHHHHHHHHH------HHHHHHHHHH
Q 025359 21 VCFVLVTISIIIEHIIHLIGKWLTKK-----HKRALYEALEKIKSELM------LLGFISLLLT 73 (254)
Q Consensus 21 Vc~v~V~iSl~~Er~lH~lgk~Lkkk-----~kkaL~eALeKiK~ELM------LLGFISLLLt 73 (254)
+....+++++.++.++|.+..|.+++ +++++.+|+.+.-.=+. .+||.||+++
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 44555568889999999999987543 23577777776655443 4588887765
No 35
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=24.51 E-value=1.3e+02 Score=30.03 Aligned_cols=47 Identities=15% Similarity=0.400 Sum_probs=34.4
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHH-------hHhhhhc----chHHHHHHHHHH
Q 025359 13 TPTWAVAVVCFVLVTISIIIEHIIHLIG-------KWLTKKH----KRALYEALEKIK 59 (254)
Q Consensus 13 TPTWaVA~Vc~v~V~iSl~~Er~lH~lg-------k~Lkkk~----kkaL~eALeKiK 59 (254)
+.-|.+++...+.++|-+++|.+++++. .|+..+| ++++.|+|.|+-
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 3346677777777788889999999864 5777333 467888888873
No 36
>KOG4484 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.31 E-value=1.6e+02 Score=26.51 Aligned_cols=36 Identities=22% Similarity=0.401 Sum_probs=29.4
Q ss_pred HHHHHHHHHhHhhhh----cchHHHHHHHHHHHHHHHHHH
Q 025359 32 IEHIIHLIGKWLTKK----HKRALYEALEKIKSELMLLGF 67 (254)
Q Consensus 32 ~Er~lH~lgk~Lkkk----~kkaL~eALeKiK~ELMLLGF 67 (254)
+||.+.+|.|-++.. +.+.+-+-|.|+|++||..-|
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 688888888877743 456799999999999999765
No 37
>PF07950 DUF1691: Protein of unknown function (DUF1691); InterPro: IPR012472 This family of fungal proteins is uncharacterised. Each protein contains two copies of this region.
Probab=22.84 E-value=2.5e+02 Score=22.37 Aligned_cols=53 Identities=15% Similarity=0.253 Sum_probs=29.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025359 18 VAVVCFVLVTISIIIEHIIHLIGKWLTKKHKRALYEALEKIKSELMLLGFISLLLTVA 75 (254)
Q Consensus 18 VA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELMLLGFISLLLtv~ 75 (254)
++..+.+-+..-=++-...-+++++-+++||+.-. ....+..+|++||.+.=.
T Consensus 43 ~~~~~Lv~~~~~Hv~sG~a~~~~~~~~~~rr~~~~-----~~~~~~~iG~~sl~~~g~ 95 (110)
T PF07950_consen 43 LEYLLLVGSGVYHVVSGIALRLGRRSRRRRRRGWW-----VINGQSAIGLISLWRLGG 95 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc-----ccchhHHHHHHHHHHhcc
Confidence 34444444444444555555555554444443322 227888999999887433
No 38
>PF04145 Ctr: Ctr copper transporter family; InterPro: IPR007274 The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionines probably coordinate copper during the process of metal transport.; GO: 0005375 copper ion transmembrane transporter activity, 0035434 copper ion transmembrane transport, 0016021 integral to membrane; PDB: 2LS4_A 2LS2_A 2LS3_A.
Probab=22.29 E-value=49 Score=26.58 Aligned_cols=30 Identities=13% Similarity=0.255 Sum_probs=17.8
Q ss_pred CCcccCCCchhHHHHHHHHHHHHHHHHHHH
Q 025359 8 RSLEETPTWAVAVVCFVLVTISIIIEHIIH 37 (254)
Q Consensus 8 rsLe~TPTWaVA~Vc~v~V~iSl~~Er~lH 37 (254)
+++.-+.+|..+..|+++++++++.|-+-.
T Consensus 17 ~~W~~~s~~~~~~sci~~f~lav~~e~L~~ 46 (144)
T PF04145_consen 17 KSWKPSSAGAYVGSCIGVFLLAVLYEFLKA 46 (144)
T ss_dssp --------HHHHHHHHHHHHHHHHTTT---
T ss_pred CCcEECCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667889999999999999999886543
No 39
>PF03032 Brevenin: Brevenin/esculentin/gaegurin/rugosin family; InterPro: IPR004275 In addition to the highly specific cell-mediated immune system, vertebrates possess an efficient host-defence mechanism against invading microorganisms which involves the synthesis of highly potent antimicrobial peptides with a large spectrum of activity. This entry represents a number of these defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins.; GO: 0006952 defense response, 0042742 defense response to bacterium, 0005576 extracellular region
Probab=21.63 E-value=40 Score=23.68 Aligned_cols=10 Identities=60% Similarity=0.803 Sum_probs=5.1
Q ss_pred HHHHHHHHHH
Q 025359 62 LMLLGFISLL 71 (254)
Q Consensus 62 LMLLGFISLL 71 (254)
|..||+|||-
T Consensus 10 lfflG~ISlS 19 (46)
T PF03032_consen 10 LFFLGTISLS 19 (46)
T ss_pred HHHHHHcccc
Confidence 3455555553
No 40
>PLN02250 lipid phosphate phosphatase
Probab=21.29 E-value=2.5e+02 Score=26.85 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=16.0
Q ss_pred ccCCCchhHHHHHHHHHHHHHH
Q 025359 11 EETPTWAVAVVCFVLVTISIII 32 (254)
Q Consensus 11 e~TPTWaVA~Vc~v~V~iSl~~ 32 (254)
+--|+|++.+++.++-++.+++
T Consensus 64 ~tVp~~~l~ii~~~iP~~vilv 85 (314)
T PLN02250 64 NTIPFWAVPLIAILLPFAVILV 85 (314)
T ss_pred CeecHHHHHHHHHHHHHHHHHH
Confidence 5669999988877666665554
No 41
>PF14163 SieB: Superinfection exclusion protein B
Probab=20.90 E-value=2.5e+02 Score=23.26 Aligned_cols=67 Identities=15% Similarity=0.141 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhh-hcchHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccccccccccCC
Q 025359 20 VVCFVLVTISIIIEHIIHLIGKWLTK-KHKRALYEALEKIKSELMLLGFISLLLTVAGSWISKICIPESVANTWHPCD 96 (254)
Q Consensus 20 ~Vc~v~V~iSl~~Er~lH~lgk~Lkk-k~kkaL~eALeKiK~ELMLLGFISLLLtv~q~~IskICIp~~~~~~mlPC~ 96 (254)
+...+++.+|+++=+.+.++-++.++ .++|...++++|.=. .||--|..|-+-.+-.+-..-.+|+.
T Consensus 36 i~~~fl~s~s~li~~~~~~~~~~~~~~~~~k~~~~~~~~~l~----------~Lt~~EkavL~~~~~~~~~~~~lp~~ 103 (151)
T PF14163_consen 36 IGLIFLFSVSYLIAQLLSFIYKEAKDRYQRKRKKKKIEKKLN----------SLTPEEKAVLREFYIQGNNTLTLPYN 103 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------hCCHHHHHHHHHHHHCCCCeEEecCC
Confidence 34455666777777777777665333 333444455554411 12333444444444444333466664
No 42
>PF04883 HK97-gp10_like: Bacteriophage HK97-gp10, putative tail-component; InterPro: IPR010064 This entry represents a family of highly divergent putative prophage and bacteriophage proteins of unknown function. The family includes Gp10 from phages HK022 and HK97.
Probab=20.83 E-value=1.7e+02 Score=20.52 Aligned_cols=32 Identities=31% Similarity=0.340 Sum_probs=24.0
Q ss_pred HHHHHHHHHhHhhhhcchHHHHHHHHHHHHHH
Q 025359 32 IEHIIHLIGKWLTKKHKRALYEALEKIKSELM 63 (254)
Q Consensus 32 ~Er~lH~lgk~Lkkk~kkaL~eALeKiK~ELM 63 (254)
+++-|..+++-..+.-+++|-++.+.+++|+-
T Consensus 3 l~~~l~~~~~~~~~~~~~~l~~~a~~~~~~~k 34 (78)
T PF04883_consen 3 LERQLEKLQDKAEKAAKKALREAAEEIEDEAK 34 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35556667766777778889999999888764
No 43
>KOG1357 consensus Serine palmitoyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=20.62 E-value=1.3e+02 Score=30.93 Aligned_cols=48 Identities=23% Similarity=0.433 Sum_probs=40.0
Q ss_pred CcccCCCchhHHHHHHHHHHHHHHHHHHHHHHhHhhhhc---------chHHHHHHH
Q 025359 9 SLEETPTWAVAVVCFVLVTISIIIEHIIHLIGKWLTKKH---------KRALYEALE 56 (254)
Q Consensus 9 sLe~TPTWaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~---------kkaL~eALe 56 (254)
.++.||.|-|++.-.+.-.|-+++-++..++|+|+-+++ .-|||.+.|
T Consensus 32 ~~~~~~~~~v~l~ty~~y~~l~~~ghvrd~~~~~f~~~~~~~~~~~~g~~ply~~Fe 88 (519)
T KOG1357|consen 32 KFEDTIPYLVALATYLSYLLLFVFGHVRDFFGKIFFVKKYKKDNEMDGYAPLYSSFE 88 (519)
T ss_pred hhhcccccHHHHHHHHHHHHHHHHHHHHHHHhhheehhhhcccccccCccchhhhHH
Confidence 478999999999999999999999999999999997422 236777766
No 44
>PRK08326 ribonucleotide-diphosphate reductase subunit beta; Validated
Probab=20.49 E-value=6e+02 Score=23.81 Aligned_cols=61 Identities=15% Similarity=0.026 Sum_probs=49.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHhHhhhhcc-hHHHHHHHHH-HHHHHHHHHHHHHHHHhh
Q 025359 16 WAVAVVCFVLVTISIIIEHIIHLIGKWLTKKHK-RALYEALEKI-KSELMLLGFISLLLTVAG 76 (254)
Q Consensus 16 WaVA~Vc~v~V~iSl~~Er~lH~lgk~Lkkk~k-kaL~eALeKi-K~ELMLLGFISLLLtv~q 76 (254)
.++|+|++-+++=++++.-+.+.+-.||+++++ +.+.++.+.| ++|.+=+.|...++.-..
T Consensus 162 ~~~a~v~~~~~iEGi~f~sgF~~~~~~l~~~~~mpgl~~~i~~I~RDE~~H~~fg~~l~~~l~ 224 (311)
T PRK08326 162 QVRASVTYNHVVEGVLAETGYYAWRKICVTRGILPGLQELVRRIGDDERRHIAWGTYTCRRLV 224 (311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566777777888888888888999999998776 5688999876 689999999988885443
Done!