Query 048175
Match_columns 134
No_of_seqs 109 out of 192
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 07:04:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048175.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048175hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1688 Golgi proteins involve 100.0 1.6E-60 3.5E-65 379.6 9.3 108 2-109 68-187 (188)
2 PF03248 Rer1: Rer1 family; I 100.0 2.1E-60 4.6E-65 375.6 9.8 107 1-107 52-176 (176)
3 COG5249 RER1 Golgi protein inv 100.0 1.4E-51 3.1E-56 324.7 8.2 105 2-106 62-179 (180)
4 PF09973 DUF2208: Predicted me 89.1 0.6 1.3E-05 39.0 4.2 38 49-90 12-49 (233)
5 PF13260 DUF4051: Protein of u 82.6 1.8 3.8E-05 29.4 3.1 22 71-92 4-25 (54)
6 PRK15432 autoinducer 2 ABC tra 55.5 39 0.00084 29.0 6.0 37 48-84 269-305 (344)
7 PF06703 SPC25: Microsomal sig 52.2 26 0.00056 26.4 4.0 36 48-83 36-76 (162)
8 PRK06531 yajC preprotein trans 51.2 14 0.0003 27.8 2.4 31 61-93 1-31 (113)
9 PRK05886 yajC preprotein trans 47.9 22 0.00048 26.6 3.0 30 63-93 4-33 (109)
10 PF12273 RCR: Chitin synthesis 46.8 27 0.00057 25.7 3.2 27 65-91 3-29 (130)
11 PRK14475 F0F1 ATP synthase sub 46.2 35 0.00076 26.0 3.9 21 56-79 3-23 (167)
12 PF07286 DUF1445: Protein of u 40.7 6 0.00013 31.2 -1.0 8 61-68 107-114 (143)
13 PF11241 DUF3043: Protein of u 40.0 1E+02 0.0023 24.8 5.9 67 26-94 51-134 (170)
14 KOG2887 Membrane protein invol 34.6 1.1E+02 0.0024 25.0 5.3 25 66-90 80-106 (175)
15 PF14373 Imm_superinfect: Supe 30.8 34 0.00074 21.9 1.5 14 2-15 16-29 (43)
16 PHA00736 hypothetical protein 30.8 57 0.0012 23.5 2.7 13 63-75 55-67 (79)
17 CHL00161 secY preprotein trans 30.3 2E+02 0.0043 25.4 6.6 91 5-97 305-415 (417)
18 COG1862 YajC Preprotein transl 30.1 67 0.0015 23.6 3.1 25 69-93 14-38 (97)
19 PF10777 YlaC: Inner membrane 29.6 1.7E+02 0.0037 23.6 5.5 55 40-100 30-92 (155)
20 PRK00968 tetrahydromethanopter 29.3 76 0.0016 27.2 3.7 44 3-58 185-228 (240)
21 PF04109 APG9: Autophagy prote 28.3 60 0.0013 28.8 3.0 36 65-106 130-165 (370)
22 PF10104 Brr6_like_C_C: Di-sul 26.0 1E+02 0.0022 23.3 3.6 25 69-93 15-39 (135)
23 TIGR00908 2A0305 ethanolamine 25.8 1.2E+02 0.0027 25.5 4.4 43 38-82 378-428 (442)
24 COG0817 RuvC Holliday junction 25.7 41 0.00088 27.1 1.4 53 40-92 66-125 (160)
25 PF13677 MotB_plug: Membrane M 25.5 63 0.0014 21.2 2.1 16 69-84 27-42 (58)
26 PF11628 TCR_zetazeta: T-cell 25.3 1.1E+02 0.0023 19.1 2.9 18 69-86 11-28 (33)
27 PRK06771 hypothetical protein; 25.1 1.1E+02 0.0024 22.7 3.5 9 81-89 27-35 (93)
28 PF10524 NfI_DNAbd_pre-N: Nucl 24.7 21 0.00045 23.4 -0.3 12 34-45 6-17 (44)
29 PF08627 CRT-like: CRT-like; 24.6 59 0.0013 25.5 2.1 13 59-71 95-107 (130)
30 COG4168 SapB ABC-type antimicr 24.5 50 0.0011 29.2 1.8 8 61-68 119-126 (321)
31 PF09685 Tic20: Tic20-like pro 23.7 2.4E+02 0.0051 19.1 4.8 9 39-47 34-42 (109)
32 PF05545 FixQ: Cbb3-type cytoc 22.0 1.2E+02 0.0025 18.9 2.7 28 71-98 19-47 (49)
33 PF14002 YniB: YniB-like prote 21.4 1.6E+02 0.0034 24.1 3.9 26 66-91 74-106 (166)
34 PRK05463 hypothetical protein; 21.4 27 0.00058 30.1 -0.4 7 62-68 218-224 (262)
35 PRK15038 autoinducer 2 import 21.3 1.9E+02 0.0041 24.5 4.6 38 48-85 273-310 (330)
36 PF13901 DUF4206: Domain of un 21.1 1.4E+02 0.003 23.8 3.6 36 58-93 51-87 (202)
37 PF02699 YajC: Preprotein tran 20.7 1.7E+02 0.0037 20.2 3.6 23 71-93 9-31 (82)
38 MTH00158 ATP8 ATP synthase F0 20.4 1.4E+02 0.0031 17.5 2.7 19 64-82 6-24 (32)
39 TIGR02796 tolQ TolQ protein. T 20.3 1E+02 0.0022 24.7 2.8 19 65-83 16-34 (215)
No 1
>KOG1688 consensus Golgi proteins involved in ER retention (RER) [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.6e-60 Score=379.59 Aligned_cols=108 Identities=56% Similarity=1.041 Sum_probs=105.2
Q ss_pred cchhHHHHHHHHhhcCCCCCCCC---CCCCCCCCCCCCCCCchhhhhhh---------HHHHHHHhhhhcccccchhhHH
Q 048175 2 NKINHWMLNLLMGFLSPQIDLEY---SDGPTLPTHGSDEFRPFVRCLLE---------SFCIGFLMTFFSAFDVHVFWPI 69 (134)
Q Consensus 2 y~LgIYlLnlfi~FLtPk~Dp~~---~dg~~LP~~~~dEFrPFiRRLPE---------a~~ia~~~TfF~~fDIPVFWPI 69 (134)
||||||+|||||||||||+|||+ +||+.||+++||||||||||||| |+++|++||||++|||||||||
T Consensus 68 Y~LgIYlLNlfiaFLtPk~Dp~~~~~~dg~~Lpt~~~dEFrPFIRRLPEFKFW~s~~ka~~ia~~~tfF~~fdVPVFwPI 147 (188)
T KOG1688|consen 68 YALGIYLLNLFIAFLTPKVDPELQDADDGPSLPTRKSDEFRPFIRRLPEFKFWYSSTKATLIALLCTFFSIFDVPVFWPI 147 (188)
T ss_pred HHHHHHHHHHHHHHhCCCCCchhhcccCCCCCCCCCccccchHHHcCchhHHHHHHHHHHHHHHHHHHHHHhcchhhhHH
Confidence 89999999999999999999996 68999999999999999999999 9999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccCCcccccccCCCCC
Q 048175 70 LLFYWLTLFTLTMRRQIMHMIKYRYVPFSFVKQRYDGKMP 109 (134)
Q Consensus 70 Ll~YFi~Lf~lTMrrqI~HMIKYkYvPf~~gK~~Y~~~~~ 109 (134)
|++||++||++||||||+|||||||+||+.||++|+++++
T Consensus 148 Ll~Y~i~lf~ltmrRqI~HMiKyrY~Pf~~gK~~~~~~~~ 187 (188)
T KOG1688|consen 148 LLMYFIVLFFLTMRRQIAHMIKYRYIPFDIGKKKYGSHSD 187 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccccCchhhhcccc
Confidence 9999999999999999999999999999999999988765
No 2
>PF03248 Rer1: Rer1 family; InterPro: IPR004932 RER1 family proteins are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex [].; GO: 0016021 integral to membrane
Probab=100.00 E-value=2.1e-60 Score=375.55 Aligned_cols=107 Identities=54% Similarity=1.041 Sum_probs=102.8
Q ss_pred CcchhHHHHHHHHhhcCCCCCCCC-------CCCCCCCC--CCCCCCCchhhhhhh---------HHHHHHHhhhhcccc
Q 048175 1 ENKINHWMLNLLMGFLSPQIDLEY-------SDGPTLPT--HGSDEFRPFVRCLLE---------SFCIGFLMTFFSAFD 62 (134)
Q Consensus 1 ~y~LgIYlLnlfi~FLtPk~Dp~~-------~dg~~LP~--~~~dEFrPFiRRLPE---------a~~ia~~~TfF~~fD 62 (134)
.||||||+||+||+|||||+||++ |||+.||+ ++|||||||+||||| |+++|++||||++||
T Consensus 52 tY~LgIylLnlfi~FltP~~Dp~l~~~~~~~~~g~~Lp~~~~~~~EFrPFiRRlPEFkFW~~~tka~~i~~~~tff~~fd 131 (176)
T PF03248_consen 52 TYALGIYLLNLFIAFLTPKFDPELEQDEEDEEEGPELPTTNENDDEFRPFIRRLPEFKFWYSCTKATVISLFCTFFPFFD 131 (176)
T ss_pred hHHHHHHHHHHHHHHhCCcCccccccccccccccccCCCCcccccccCCccccchhhHHHHHHHHHHHHHHHHHHHHhcC
Confidence 389999999999999999999986 35779999 899999999999999 999999999999999
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccccccCCC
Q 048175 63 VHVFWPILLFYWLTLFTLTMRRQIMHMIKYRYVPFSFVKQRYDGK 107 (134)
Q Consensus 63 IPVFWPILl~YFi~Lf~lTMrrqI~HMIKYkYvPf~~gK~~Y~~~ 107 (134)
||||||||++|||+||++||||||+|||||||+|||+||++|++|
T Consensus 132 iPVFWPiLl~Yfi~lf~~tm~~qI~hMiKy~Y~Pf~~gK~~y~~~ 176 (176)
T PF03248_consen 132 IPVFWPILLVYFIVLFVLTMKRQIKHMIKYRYVPFDFGKKKYGRK 176 (176)
T ss_pred CcchhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccccchhccCC
Confidence 999999999999999999999999999999999999999999986
No 3
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.4e-51 Score=324.74 Aligned_cols=105 Identities=40% Similarity=0.825 Sum_probs=98.3
Q ss_pred cchhHHHHHHHHhhcCCCCCCCC---CCCCCCCC-CCCCCCCchhhhhhh---------HHHHHHHhhhhcccccchhhH
Q 048175 2 NKINHWMLNLLMGFLSPQIDLEY---SDGPTLPT-HGSDEFRPFVRCLLE---------SFCIGFLMTFFSAFDVHVFWP 68 (134)
Q Consensus 2 y~LgIYlLnlfi~FLtPk~Dp~~---~dg~~LP~-~~~dEFrPFiRRLPE---------a~~ia~~~TfF~~fDIPVFWP 68 (134)
|+||||+||+|++|||||+||+. +|+..+|. +.||||||||||||| |+++|++.|+|++||||||||
T Consensus 62 Y~LgiyLLn~flaFLTPKfdms~eq~e~d~eieeg~kd~EFrPFIRrLPEFkFWy~s~rat~~aLi~s~F~IfDvPVfwP 141 (180)
T COG5249 62 YCLGIYLLNAFLAFLTPKFDMSFEQIEDDDEIEEGEKDNEFRPFIRRLPEFKFWYFSTRATGMALIGSYFGIFDVPVFWP 141 (180)
T ss_pred HHHHHHHHHHHHHHhCCCCcccHhhhccccccccccccchhhHHHHcCchhHHHHHHHHHHHHHHHHHHHhhhcchhhhH
Confidence 89999999999999999999997 34444554 479999999999999 999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCCcccccccCC
Q 048175 69 ILLFYWLTLFTLTMRRQIMHMIKYRYVPFSFVKQRYDG 106 (134)
Q Consensus 69 ILl~YFi~Lf~lTMrrqI~HMIKYkYvPf~~gK~~Y~~ 106 (134)
|||+|||+|+..|||||||||+||||+|||.||++|++
T Consensus 142 ILvvYfi~l~f~t~rRqIqHM~KYrY~PfdigKkky~s 179 (180)
T COG5249 142 ILVVYFIFLVFYTARRQIQHMKKYRYNPFDIGKKKYKS 179 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhhhhcc
Confidence 99999999999999999999999999999999999975
No 4
>PF09973 DUF2208: Predicted membrane protein (DUF2208); InterPro: IPR009198 There are currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain three or more transmembrane segments.
Probab=89.15 E-value=0.6 Score=38.96 Aligned_cols=38 Identities=13% Similarity=0.561 Sum_probs=32.6
Q ss_pred HHHHHHhhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 048175 49 FCIGFLMTFFSAFDVHVFWPILLFYWLTLFTLTMRRQIMHMI 90 (134)
Q Consensus 49 ~~ia~~~TfF~~fDIPVFWPILl~YFi~Lf~lTMrrqI~HMI 90 (134)
++.|++.++++.- ||++.+.||++.+++||.-.++++-
T Consensus 12 l~fa~Vla~~p~y----~~~~filYfiv~~~i~~~~~~Rs~r 49 (233)
T PF09973_consen 12 LLFAAVLAFFPQY----YFEVFILYFIVFFGIMIVMGIRSYR 49 (233)
T ss_pred HHHHHHHHhccHH----HHHHHHHHHHHHHHHHHHHhhhhcc
Confidence 5678888988754 6799999999999999998888876
No 5
>PF13260 DUF4051: Protein of unknown function (DUF4051)
Probab=82.58 E-value=1.8 Score=29.38 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 048175 71 LFYWLTLFTLTMRRQIMHMIKY 92 (134)
Q Consensus 71 l~YFi~Lf~lTMrrqI~HMIKY 92 (134)
.-|||+|-++..-...-||.+|
T Consensus 4 awywivli~lv~~gy~~hmkry 25 (54)
T PF13260_consen 4 AWYWIVLIVLVVVGYFCHMKRY 25 (54)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3588888888888888899887
No 6
>PRK15432 autoinducer 2 ABC transporter permease LsrC; Provisional
Probab=55.47 E-value=39 Score=29.04 Aligned_cols=37 Identities=8% Similarity=0.218 Sum_probs=28.2
Q ss_pred HHHHHHHhhhhcccccchhhHHHHHHHHHHHHHHHHH
Q 048175 48 SFCIGFLMTFFSAFDVHVFWPILLFYWLTLFTLTMRR 84 (134)
Q Consensus 48 a~~ia~~~TfF~~fDIPVFWPILl~YFi~Lf~lTMrr 84 (134)
|++++.+-+....+++|-.|-.++.+-+++.++...+
T Consensus 269 alll~~l~~~l~~~~~~~~~~~ii~g~lll~vl~~~~ 305 (344)
T PRK15432 269 AYFLTQIDSVLVLLRIPAWWNDFIAGLVLLGVLVFDG 305 (344)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhhhhHHH
Confidence 6677777777777788999988888888777776543
No 7
>PF06703 SPC25: Microsomal signal peptidase 25 kDa subunit (SPC25); InterPro: IPR009582 This family consists of several microsomal signal peptidase 25 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains [].; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=52.20 E-value=26 Score=26.44 Aligned_cols=36 Identities=14% Similarity=0.161 Sum_probs=29.7
Q ss_pred HHHHHHHhhhhcc-----cccchhhHHHHHHHHHHHHHHHH
Q 048175 48 SFCIGFLMTFFSA-----FDVHVFWPILLFYWLTLFTLTMR 83 (134)
Q Consensus 48 a~~ia~~~TfF~~-----fDIPVFWPILl~YFi~Lf~lTMr 83 (134)
|+++|.++.+++. -+-|+-|...+.||++..++|.=
T Consensus 36 a~~iA~~a~~~d~~~~f~~s~~~~~~~v~~YfiLs~il~~~ 76 (162)
T PF06703_consen 36 AVIIAGFAFFYDYKYPFPESKPYLIICVILYFILSGILTLY 76 (162)
T ss_pred HHHHHHHHHHhhhcCCCCccHHHHHHHHHHHHHHHHHHHHH
Confidence 7888888888866 56688899999999999888853
No 8
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=51.20 E-value=14 Score=27.84 Aligned_cols=31 Identities=10% Similarity=0.146 Sum_probs=18.3
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 048175 61 FDVHVFWPILLFYWLTLFTLTMRRQIMHMIKYR 93 (134)
Q Consensus 61 fDIPVFWPILl~YFi~Lf~lTMrrqI~HMIKYk 93 (134)
+|++.++|+.+++-++. +..|.|-|-+.+++
T Consensus 1 ~~~~~il~~vv~~~i~y--f~iRPQkKr~Ke~~ 31 (113)
T PRK06531 1 MGIPTIIMFVVMLGLIF--FMQRQQKKQAQERQ 31 (113)
T ss_pred CchHHHHHHHHHHHHHH--heechHHHHHHHHH
Confidence 35666777666544432 33777777666664
No 9
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=47.88 E-value=22 Score=26.64 Aligned_cols=30 Identities=27% Similarity=0.277 Sum_probs=17.5
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 048175 63 VHVFWPILLFYWLTLFTLTMRRQIMHMIKYR 93 (134)
Q Consensus 63 IPVFWPILl~YFi~Lf~lTMrrqI~HMIKYk 93 (134)
+-.++|++++..++.|. .+|+|-|-+.+++
T Consensus 4 ~~~ll~lv~i~~i~yF~-~iRPQkKr~K~~~ 33 (109)
T PRK05886 4 LVLFLPFLLIMGGFMYF-ASRRQRKAMQATI 33 (109)
T ss_pred HHHHHHHHHHHHHHHHH-HccHHHHHHHHHH
Confidence 34566777765544444 4677766665553
No 10
>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=46.76 E-value=27 Score=25.66 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=14.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 048175 65 VFWPILLFYWLTLFTLTMRRQIMHMIK 91 (134)
Q Consensus 65 VFWPILl~YFi~Lf~lTMrrqI~HMIK 91 (134)
|+|=|+|+-+++++++++++.-|-+.|
T Consensus 3 ~l~~iii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 456666666666666665443333333
No 11
>PRK14475 F0F1 ATP synthase subunit B; Provisional
Probab=46.18 E-value=35 Score=26.01 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=12.4
Q ss_pred hhhcccccchhhHHHHHHHHHHHH
Q 048175 56 TFFSAFDVHVFWPILLFYWLTLFT 79 (134)
Q Consensus 56 TfF~~fDIPVFWPILl~YFi~Lf~ 79 (134)
||++ ++.|.||-+ +-|+++++
T Consensus 3 ~~~~-~~~~~~w~~--i~f~il~~ 23 (167)
T PRK14475 3 SFFN-LSNPEFWVG--AGLLIFFG 23 (167)
T ss_pred CCCC-CCchHHHHH--HHHHHHHH
Confidence 4555 678999954 33444443
No 12
>PF07286 DUF1445: Protein of unknown function (DUF1445); InterPro: IPR009906 This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.; PDB: 3DB9_A 2PIF_A.
Probab=40.66 E-value=6 Score=31.23 Aligned_cols=8 Identities=50% Similarity=1.028 Sum_probs=6.5
Q ss_pred cccchhhH
Q 048175 61 FDVHVFWP 68 (134)
Q Consensus 61 fDIPVFWP 68 (134)
=||||||+
T Consensus 107 gevPVFWa 114 (143)
T PF07286_consen 107 GEVPVFWA 114 (143)
T ss_dssp TEEEEEEE
T ss_pred CCeeeEec
Confidence 36999996
No 13
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=40.02 E-value=1e+02 Score=24.81 Aligned_cols=67 Identities=18% Similarity=0.378 Sum_probs=38.5
Q ss_pred CCCCCCCCCCCCCCchhhhhhh-----------HHHHHHHhhhhcccccc--hhhHHHHHHHHHHHH----HHHHHHHHH
Q 048175 26 DGPTLPTHGSDEFRPFVRCLLE-----------SFCIGFLMTFFSAFDVH--VFWPILLFYWLTLFT----LTMRRQIMH 88 (134)
Q Consensus 26 dg~~LP~~~~dEFrPFiRRLPE-----------a~~ia~~~TfF~~fDIP--VFWPILl~YFi~Lf~----lTMrrqI~H 88 (134)
|+-.||..+...=|-|+|..=. ..++.++++++ ...| ..|-.+++|.+++.+ +.+-|+++.
T Consensus 51 DeryLp~RDrGP~Rr~vRD~VDsR~~i~e~fmP~alv~lv~~~v--~~~~~~~~~~~~~~~~~~~~~iid~~~l~r~vkk 128 (170)
T PF11241_consen 51 DERYLPPRDRGPVRRYVRDYVDSRRNIGEFFMPVALVLLVLSFV--VPSPQVQLYVTLAMYVLLLLVIIDGVILGRRVKK 128 (170)
T ss_pred hhhcCCcccccchhhhhhhhhhcccchHHHHHHHHHHHHHHHHH--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4557777776677778876444 44445555555 1122 234444455444433 346788888
Q ss_pred HHHhcc
Q 048175 89 MIKYRY 94 (134)
Q Consensus 89 MIKYkY 94 (134)
...-||
T Consensus 129 ~v~~kF 134 (170)
T PF11241_consen 129 RVAEKF 134 (170)
T ss_pred HHHHHC
Confidence 887765
No 14
>KOG2887 consensus Membrane protein involved in ER to Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.58 E-value=1.1e+02 Score=25.00 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=16.9
Q ss_pred hhHHHHHHHHHHHHHHH--HHHHHHHH
Q 048175 66 FWPILLFYWLTLFTLTM--RRQIMHMI 90 (134)
Q Consensus 66 FWPILl~YFi~Lf~lTM--rrqI~HMI 90 (134)
+|-+==+-++.-|+..| ++|++||-
T Consensus 80 ~~TlGnll~i~sf~fLmGP~~ql~~m~ 106 (175)
T KOG2887|consen 80 LYTLGNLLAIGSFAFLMGPVSQLKHMF 106 (175)
T ss_pred hHHHHHHHHHHHHHHHHhHHHHHHHhc
Confidence 44444455666666666 89999995
No 15
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=30.83 E-value=34 Score=21.90 Aligned_cols=14 Identities=50% Similarity=0.902 Sum_probs=11.5
Q ss_pred cchhHHHHHHHHhh
Q 048175 2 NKINHWMLNLLMGF 15 (134)
Q Consensus 2 y~LgIYlLnlfi~F 15 (134)
+..+|+++|++++.
T Consensus 16 ~~~~I~~~Nl~lGW 29 (43)
T PF14373_consen 16 NKWAIFLLNLLLGW 29 (43)
T ss_pred cchhhHhHHHHHHh
Confidence 56789999999874
No 16
>PHA00736 hypothetical protein
Probab=30.81 E-value=57 Score=23.51 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=10.6
Q ss_pred cchhhHHHHHHHH
Q 048175 63 VHVFWPILLFYWL 75 (134)
Q Consensus 63 IPVFWPILl~YFi 75 (134)
+|+||-|-+++=+
T Consensus 55 lplfwgi~vifgl 67 (79)
T PHA00736 55 LPLFWGITVIFGL 67 (79)
T ss_pred HHHHHHHHHHHHH
Confidence 7999999887644
No 17
>CHL00161 secY preprotein translocase subunit SecY; Validated
Probab=30.25 E-value=2e+02 Score=25.42 Aligned_cols=91 Identities=11% Similarity=0.205 Sum_probs=41.7
Q ss_pred hHHHHHHHHhhcCCCCCCCC------CCCCCCCCCCCC-CCCchhhhh-hh-----HHHHHHHhhh---hc-ccccchhh
Q 048175 5 NHWMLNLLMGFLSPQIDLEY------SDGPTLPTHGSD-EFRPFVRCL-LE-----SFCIGFLMTF---FS-AFDVHVFW 67 (134)
Q Consensus 5 gIYlLnlfi~FLtPk~Dp~~------~dg~~LP~~~~d-EFrPFiRRL-PE-----a~~ia~~~Tf---F~-~fDIPVFW 67 (134)
-+.+++-+-.+++ +||++ +.|...|..+.. +=+-+++|. +- |+++|+++.. +. .+++++++
T Consensus 305 lii~Fs~f~~~i~--~~p~~iA~~Lkk~g~~IpGvRpG~~T~~yL~~~i~~~t~~Ga~~l~~la~~p~l~~~~~~~~~~~ 382 (417)
T CHL00161 305 LILFFSYFYSTIV--LNPKDISENLQKMAVSIPGIRPGKATTKYLKKTLNRLTLLGALFLAFIALLPNLIESVLNLSVFK 382 (417)
T ss_pred HHHHHHHHHHHHh--cCHHHHHHHHHHCCCcCCCcCCChhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcCccccc
Confidence 3444555666666 88876 345556653332 111222221 11 5555554444 43 22444333
Q ss_pred HH--HHHHHHHHHHHHHHHHHH-HHHHhcccCC
Q 048175 68 PI--LLFYWLTLFTLTMRRQIM-HMIKYRYVPF 97 (134)
Q Consensus 68 PI--Ll~YFi~Lf~lTMrrqI~-HMIKYkYvPf 97 (134)
-+ --+.-++=..+...|||+ |+.+.+|-+|
T Consensus 383 ~~ggtslLI~Vgv~~~~~~qi~a~~~~~~Y~~~ 415 (417)
T CHL00161 383 GLGTTSLLILVGVAIDTSRQIQTYLISNNYENM 415 (417)
T ss_pred ccchhhhhhhHHHHHHHHHHHHHHHHHHhhccc
Confidence 21 001112223333455554 6678888776
No 18
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=30.08 E-value=67 Score=23.63 Aligned_cols=25 Identities=20% Similarity=0.309 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Q 048175 69 ILLFYWLTLFTLTMRRQIMHMIKYR 93 (134)
Q Consensus 69 ILl~YFi~Lf~lTMrrqI~HMIKYk 93 (134)
++++.+.+.+++..|.|-|-|.+++
T Consensus 14 ~~vl~~~ifyFli~RPQrKr~K~~~ 38 (97)
T COG1862 14 PLVLIFAIFYFLIIRPQRKRMKEHQ 38 (97)
T ss_pred HHHHHHHHHHHhhcCHHHHHHHHHH
Confidence 4555566666677888988888875
No 19
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=29.60 E-value=1.7e+02 Score=23.62 Aligned_cols=55 Identities=20% Similarity=0.248 Sum_probs=28.0
Q ss_pred chhhhhhh---HHHHHHHhhh-----hcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccc
Q 048175 40 PFVRCLLE---SFCIGFLMTF-----FSAFDVHVFWPILLFYWLTLFTLTMRRQIMHMIKYRYVPFSFV 100 (134)
Q Consensus 40 PFiRRLPE---a~~ia~~~Tf-----F~~fDIPVFWPILl~YFi~Lf~lTMrrqI~HMIKYkYvPf~~g 100 (134)
-|+|+-|- |..+|.+.|. .+-|-.+-+|=+.+++-++-.++. -=||.+|-=-|+|
T Consensus 30 ~Fi~~HP~L~~~M~~~y~~~~~lm~~spy~G~~s~~~ftv~fv~m~~~ll------fDI~P~YrfEDId 92 (155)
T PF10777_consen 30 SFIRNHPYLCLAMYAAYLAVAALMYYSPYFGLGSVWGFTVFFVVMAAFLL------FDIKPRYRFEDID 92 (155)
T ss_pred HHHHhCcHHHHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHH------hhccceeeecccC
Confidence 58999998 5555554444 444445555544333322222222 2266666555555
No 20
>PRK00968 tetrahydromethanopterin S-methyltransferase subunit D; Provisional
Probab=29.33 E-value=76 Score=27.19 Aligned_cols=44 Identities=14% Similarity=0.344 Sum_probs=25.4
Q ss_pred chhHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhHHHHHHHhhhh
Q 048175 3 KINHWMLNLLMGFLSPQIDLEYSDGPTLPTHGSDEFRPFVRCLLESFCIGFLMTFF 58 (134)
Q Consensus 3 ~LgIYlLnlfi~FLtPk~Dp~~~dg~~LP~~~~dEFrPFiRRLPEa~~ia~~~TfF 58 (134)
+.|+|+.|..++ +.+=+....--.|-.|| |+|.|++-|++.|.+
T Consensus 185 AvG~FfvNAVla--------SYNIgGTIEGfHDPKFK----r~p~~vias~vaS~~ 228 (240)
T PRK00968 185 AVGIFFVNAVLA--------SYNIGGTIEGFHDPKFK----RWPRAVIASFVASLV 228 (240)
T ss_pred HHHHHHHHHHHH--------hhccCceeecCCCcccc----cchHHHHHHHHHHHH
Confidence 678999999887 22211111111244554 888866666666543
No 21
>PF04109 APG9: Autophagy protein Apg9 ; InterPro: IPR007241 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways [].
Probab=28.29 E-value=60 Score=28.84 Aligned_cols=36 Identities=19% Similarity=0.372 Sum_probs=28.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccccccCC
Q 048175 65 VFWPILLFYWLTLFTLTMRRQIMHMIKYRYVPFSFVKQRYDG 106 (134)
Q Consensus 65 VFWPILl~YFi~Lf~lTMrrqI~HMIKYkYvPf~~gK~~Y~~ 106 (134)
++-|++++|.++.+++ +|--.+|-.|-+.|.++|+.
T Consensus 130 ll~Pfi~i~~il~~ff------~y~e~~~~~P~~lg~R~ws~ 165 (370)
T PF04109_consen 130 LLSPFILIYQILYFFF------KYAEEFKKNPGSLGARRWSP 165 (370)
T ss_pred HHhHHHHHHHHHHHHH------HHHHHHhhChHhhcccCCch
Confidence 3569999999998888 46666777888888888753
No 22
>PF10104 Brr6_like_C_C: Di-sulfide bridge nucleocytoplasmic transport domain; InterPro: IPR018767 This entry represents the highly conserved C-terminal region of Brr6-like proteins, including Brl1, which are found in fungi. Brr6 from Saccharomyces cerevisiae (Baker's yeast) is an essential nuclear envelope integral membrane protein that is required for mRNA nuclear export []. Brr6 is involved in the nuclear pore complex (NPC) distribution and nuclear envelope morphology. Brr6 interacts with Brl1, which is also involved in mRNA and protein export from the nucleus []. The conserved C-terminal region carries four highly conserved cysteine residues. It is suggested that members of the family interact with each other via di-sulphide bridges to form a complex that is involved in nucleocytoplasmic transport.; GO: 0015031 protein transport, 0051028 mRNA transport, 0016021 integral to membrane
Probab=26.01 E-value=1e+02 Score=23.26 Aligned_cols=25 Identities=28% Similarity=0.437 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Q 048175 69 ILLFYWLTLFTLTMRRQIMHMIKYR 93 (134)
Q Consensus 69 ILl~YFi~Lf~lTMrrqI~HMIKYk 93 (134)
.+++|++.-|+.|.|+.|+|-+..+
T Consensus 15 ~~~ly~~~~~~~tI~~DI~~k~~~~ 39 (135)
T PF10104_consen 15 SIFLYLVYSFISTIRSDINHKIEQY 39 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999999876544
No 23
>TIGR00908 2A0305 ethanolamine permease. The three genes used as the seed for this model (from Burkholderia pseudomallei, Pseudomonas aeruginosa and Clostridium acetobutylicum are all adjacent to genes for the catabolism of ethanolamine. Most if not all of the hits to this model have a similar arrangement of genes. This group is a member of the Amino Acid-Polyamine-Organocation (APC) Superfamily.
Probab=25.83 E-value=1.2e+02 Score=25.51 Aligned_cols=43 Identities=5% Similarity=0.005 Sum_probs=21.0
Q ss_pred CCchhhhhhh-------HHHHHHHhhhhcccccchhhH-HHHHHHHHHHHHHH
Q 048175 38 FRPFVRCLLE-------SFCIGFLMTFFSAFDVHVFWP-ILLFYWLTLFTLTM 82 (134)
Q Consensus 38 FrPFiRRLPE-------a~~ia~~~TfF~~fDIPVFWP-ILl~YFi~Lf~lTM 82 (134)
-||| |+|- ++++++++....++.=|..|- +.++|.++.....+
T Consensus 378 ~rp~--~~p~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l 428 (442)
T TIGR00908 378 ERPY--RTPGGILTPGVALVLACVALVTGFYVDPRVVVGAVAIFVVLIGYYFL 428 (442)
T ss_pred CCCc--cCCCcchHHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHh
Confidence 3777 6664 555555555444332243453 44444444443333
No 24
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=25.72 E-value=41 Score=27.08 Aligned_cols=53 Identities=17% Similarity=0.106 Sum_probs=37.0
Q ss_pred chhhhhhh-------HHHHHHHhhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 048175 40 PFVRCLLE-------SFCIGFLMTFFSAFDVHVFWPILLFYWLTLFTLTMRRQIMHMIKY 92 (134)
Q Consensus 40 PFiRRLPE-------a~~ia~~~TfF~~fDIPVFWPILl~YFi~Lf~lTMrrqI~HMIKY 92 (134)
.|.++=|- |-.++++.-.=.-.++..|-|-.+==-++=..=.=|+|++||+|.
T Consensus 66 ~F~~kN~~s~lklgQARGv~~la~~~~~l~v~eY~p~~VKkavvG~G~A~K~QVq~MV~~ 125 (160)
T COG0817 66 VFVNKNADSALKLGQARGVALLAAARRGLPVFEYTPNQVKKAVVGNGKADKEQVQHMVKR 125 (160)
T ss_pred HHHhcChHHHHHHHHHHHHHHHHHHHcCCChhhccHHHHHHHhhcCCcccHHHHHHHHHH
Confidence 46665444 556666666667777888888877555554555569999999985
No 25
>PF13677 MotB_plug: Membrane MotB of proton-channel complex MotA/MotB
Probab=25.53 E-value=63 Score=21.18 Aligned_cols=16 Identities=25% Similarity=0.642 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 048175 69 ILLFYWLTLFTLTMRR 84 (134)
Q Consensus 69 ILl~YFi~Lf~lTMrr 84 (134)
+|+++|++|+.+....
T Consensus 27 LLl~fFVlL~s~s~~d 42 (58)
T PF13677_consen 27 LLLAFFVLLFSMSSVD 42 (58)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 5888999999988743
No 26
>PF11628 TCR_zetazeta: T-cell surface glycoprotein CD3 zeta chain; InterPro: IPR021663 The TCR complex of T-lymphocytes consists of either a TCR alpha/beta or TCR gamma/delta heterodimer co-expressed at the cell surface with the invariant subunits of CD3 labelled gamma, delta, epsilon, zeta, and eta []. The zeta subunit forms either homodimers or heterodimers with eta [], but eta homodimers have not been observed. The structure of the zetazeta transmembrane dimer consists of a left-handed coiled coil with polar contacts. Two aspartic acids are critical for zetazeta dimerisation and assembly with TCR []. The high affinity immunoglobulin epsilon receptor (IgE Fc receptor) subunit gamma associates with a variety of FcR alpha chains to form a functional signaling complex. The gamma subunit has a critical role in allowing the IgE Fc receptor to reach the cell surface and regulates several aspects of the immune response []. This family includes both CD3 zeta subunits and IgE Fc receptor gamma subunits. The gamma chain of the high affinity Fc receptor for IgE has significant structural homology to CD3 zeta and the related CD3 eta subunit and can facilitate T cell receptor expression and signaling in the absence of CD3 zeta and CD3 eta [].; PDB: 2HAC_B.
Probab=25.28 E-value=1.1e+02 Score=19.07 Aligned_cols=18 Identities=28% Similarity=0.501 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 048175 69 ILLFYWLTLFTLTMRRQI 86 (134)
Q Consensus 69 ILl~YFi~Lf~lTMrrqI 86 (134)
||++|=|++..+-.|...
T Consensus 11 iL~iYgiiiT~L~~R~K~ 28 (33)
T PF11628_consen 11 ILFIYGIIITALYCREKF 28 (33)
T ss_dssp HHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 799999999999988653
No 27
>PRK06771 hypothetical protein; Provisional
Probab=25.14 E-value=1.1e+02 Score=22.67 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=4.8
Q ss_pred HHHHHHHHH
Q 048175 81 TMRRQIMHM 89 (134)
Q Consensus 81 TMrrqI~HM 89 (134)
++.+++++|
T Consensus 27 ~~~~~~k~i 35 (93)
T PRK06771 27 KTDARLKRM 35 (93)
T ss_pred HHHHHHHHH
Confidence 444466665
No 28
>PF10524 NfI_DNAbd_pre-N: Nuclear factor I protein pre-N-terminus; InterPro: IPR019548 Nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF) [, ] (also known as TGGCA-binding proteins) are a family of vertebrate nuclear proteins which recognise and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. CTF/NF-I binding sites are present in viral and cellular promoters and in the origin of DNA replication of Human adenovirus 2 (HAdV-2). The CTF/NF-I proteins were first identified as nuclear factor I, a collection of proteins that activate the replication of several Adenovirus serotypes (together with NF-II and NF-III) []. The family of proteins was also identified as the CTF transcription factors, before the NFI and CTF families were found to be identical []. The CTF/NF-I proteins are individually capable of activating transcription and DNA replication. In a given species, there are a large number of different CTF/NF-I proteins, generated both by alternative splicing and by the occurrence of four different genes. CTF/NF-1 proteins contain 400 to 600 amino acids. The N-terminal 200 amino-acid sequence, almost perfectly conserved in all species and genes sequenced, mediates site-specific DNA recognition, protein dimerisation and Adenovirus DNA replication. The C-terminal 100 amino acids contain the transcriptional activation domain. This activation domain is the target of gene expression regulatory pathways elicited by growth factors and it interacts with basal transcription factors and with histone H3 []. This entry represents the N terminus, of which 200 residues contain the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication [].
Probab=24.75 E-value=21 Score=23.44 Aligned_cols=12 Identities=50% Similarity=1.046 Sum_probs=9.7
Q ss_pred CCCCCCchhhhh
Q 048175 34 GSDEFRPFVRCL 45 (134)
Q Consensus 34 ~~dEFrPFiRRL 45 (134)
++|||.|||..|
T Consensus 6 ~~de~hpFiEal 17 (44)
T PF10524_consen 6 QQDEFHPFIEAL 17 (44)
T ss_pred hHHHhhhHHHHH
Confidence 578999999765
No 29
>PF08627 CRT-like: CRT-like; InterPro: IPR013936 This region is found in proteins related to Plasmodium falciparum chloroquine resistance transporter (CRT).
Probab=24.62 E-value=59 Score=25.53 Aligned_cols=13 Identities=23% Similarity=0.421 Sum_probs=9.5
Q ss_pred cccccchhhHHHH
Q 048175 59 SAFDVHVFWPILL 71 (134)
Q Consensus 59 ~~fDIPVFWPILl 71 (134)
++-=||||||+++
T Consensus 95 t~gyvpIffaV~l 107 (130)
T PF08627_consen 95 TFGYVPIFFAVVL 107 (130)
T ss_pred ccceehHHHHHHH
Confidence 3445899999875
No 30
>COG4168 SapB ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]
Probab=24.49 E-value=50 Score=29.18 Aligned_cols=8 Identities=50% Similarity=1.323 Sum_probs=6.8
Q ss_pred cccchhhH
Q 048175 61 FDVHVFWP 68 (134)
Q Consensus 61 fDIPVFWP 68 (134)
+.+||||=
T Consensus 119 ~SiPvFWl 126 (321)
T COG4168 119 FSIPVFWL 126 (321)
T ss_pred cCchHHHH
Confidence 67999994
No 31
>PF09685 Tic20: Tic20-like protein; InterPro: IPR019109 This entry represents a group of uncharacterised conserved proteins including a chloroplast protein import component called Tic20. Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. Tic20 is a core member of the Tic complex and is deeply embedded in the inner envelope membrane. It is thought to function as a protein conducting component of the Tic complex [].
Probab=23.74 E-value=2.4e+02 Score=19.08 Aligned_cols=9 Identities=44% Similarity=0.733 Sum_probs=7.2
Q ss_pred Cchhhhhhh
Q 048175 39 RPFVRCLLE 47 (134)
Q Consensus 39 rPFiRRLPE 47 (134)
.||+|+--.
T Consensus 34 ~~~vr~ha~ 42 (109)
T PF09685_consen 34 SPFVRFHAK 42 (109)
T ss_pred CHHHHHHHH
Confidence 688888776
No 32
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=21.97 E-value=1.2e+02 Score=18.92 Aligned_cols=28 Identities=7% Similarity=0.286 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHH-HHHHHHHhcccCCc
Q 048175 71 LFYWLTLFTLTMRR-QIMHMIKYRYVPFS 98 (134)
Q Consensus 71 l~YFi~Lf~lTMrr-qI~HMIKYkYvPf~ 98 (134)
++.|+.+...+.++ +-++.-++..+||+
T Consensus 19 ~~~F~gi~~w~~~~~~k~~~e~aa~lpl~ 47 (49)
T PF05545_consen 19 FVFFIGIVIWAYRPRNKKRFEEAANLPLD 47 (49)
T ss_pred HHHHHHHHHHHHcccchhhHHHHHccCcc
Confidence 33444444444443 47888888888885
No 33
>PF14002 YniB: YniB-like protein
Probab=21.41 E-value=1.6e+02 Score=24.08 Aligned_cols=26 Identities=23% Similarity=0.338 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHHHHHH-------HHHHHHHHHH
Q 048175 66 FWPILLFYWLTLFTLT-------MRRQIMHMIK 91 (134)
Q Consensus 66 FWPILl~YFi~Lf~lT-------MrrqI~HMIK 91 (134)
-|..+++|+++.+.++ |.||+||..+
T Consensus 74 ni~F~vIy~liFvGlAL~aSG~rm~rqvk~ire 106 (166)
T PF14002_consen 74 NIMFWVIYLLIFVGLALQASGARMSRQVKFIRE 106 (166)
T ss_pred cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence 4567778887777665 5789988754
No 34
>PRK05463 hypothetical protein; Provisional
Probab=21.36 E-value=27 Score=30.12 Aligned_cols=7 Identities=43% Similarity=1.407 Sum_probs=5.0
Q ss_pred ccchhhH
Q 048175 62 DVHVFWP 68 (134)
Q Consensus 62 DIPVFWP 68 (134)
+|||||+
T Consensus 218 evPVFWa 224 (262)
T PRK05463 218 EIPVFWA 224 (262)
T ss_pred CcceEec
Confidence 3788885
No 35
>PRK15038 autoinducer 2 import system permease LsrD; Provisional
Probab=21.25 E-value=1.9e+02 Score=24.49 Aligned_cols=38 Identities=16% Similarity=0.046 Sum_probs=32.9
Q ss_pred HHHHHHHhhhhcccccchhhHHHHHHHHHHHHHHHHHH
Q 048175 48 SFCIGFLMTFFSAFDVHVFWPILLFYWLTLFTLTMRRQ 85 (134)
Q Consensus 48 a~~ia~~~TfF~~fDIPVFWPILl~YFi~Lf~lTMrrq 85 (134)
|++++++-+....+++|-+|=-++.+.+++.++..+.|
T Consensus 273 alll~~l~~~l~~~g~~~~~~~~i~G~ili~~v~~~~~ 310 (330)
T PRK15038 273 VLLVGYLQQGLQMAGVPNQISSALSGALLIVVVVGRSV 310 (330)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 77777777777888999999999999999999998865
No 36
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=21.06 E-value=1.4e+02 Score=23.79 Aligned_cols=36 Identities=14% Similarity=0.086 Sum_probs=27.8
Q ss_pred hcccccchhhHHHHHHHH-HHHHHHHHHHHHHHHHhc
Q 048175 58 FSAFDVHVFWPILLFYWL-TLFTLTMRRQIMHMIKYR 93 (134)
Q Consensus 58 F~~fDIPVFWPILl~YFi-~Lf~lTMrrqI~HMIKYk 93 (134)
-+.+||+-.+|-|.-.-= +--+..+|+|+.||.+|-
T Consensus 51 ~Pl~~i~~~np~ly~~v~~L~~v~~lR~~L~~l~~yl 87 (202)
T PF13901_consen 51 KPLINIEALNPSLYSHVKELRKVRELREQLSLLKDYL 87 (202)
T ss_pred CCEeeHHHhCHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 467899999998876543 344578899999998874
No 37
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=20.69 E-value=1.7e+02 Score=20.22 Aligned_cols=23 Identities=13% Similarity=0.281 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Q 048175 71 LFYWLTLFTLTMRRQIMHMIKYR 93 (134)
Q Consensus 71 l~YFi~Lf~lTMrrqI~HMIKYk 93 (134)
++.+++++++.+|.|-|-+.+++
T Consensus 9 v~~~~i~yf~~~rpqkk~~k~~~ 31 (82)
T PF02699_consen 9 VIIFVIFYFLMIRPQKKQQKEHQ 31 (82)
T ss_dssp HHHHHHHHHHTHHHHHHHHHHHT
T ss_pred HHHHHHHhhheecHHHHHHHHHH
Confidence 35555666666677766666554
No 38
>MTH00158 ATP8 ATP synthase F0 subunit 8; Provisional
Probab=20.35 E-value=1.4e+02 Score=17.48 Aligned_cols=19 Identities=32% Similarity=0.562 Sum_probs=14.2
Q ss_pred chhhHHHHHHHHHHHHHHH
Q 048175 64 HVFWPILLFYWLTLFTLTM 82 (134)
Q Consensus 64 PVFWPILl~YFi~Lf~lTM 82 (134)
|.-|=+|.++|++.+.+.+
T Consensus 6 Pm~W~~l~~~f~~~~~~~~ 24 (32)
T MTH00158 6 PMNWLILFILFLITFILFN 24 (32)
T ss_pred cHHHHHHHHHHHHHHHHHH
Confidence 7889888788877776654
No 39
>TIGR02796 tolQ TolQ protein. TolQ is one of the essential components of the Tol-Pal system. Together with TolR, it harnesses protonmotive force to energize TolA, which spans the periplasm to reach the complex of TolB and Pal at the outer member. The tol-pal system proves to be important for maintaining outer membrane integrity. Gene pairs similar to the TolQ and TolR gene pair often number several per genome, but this model describes specificially TolQ per se, as found in tol-pal operons. A close homolog, excluded from this model, is ExbB of the ExbB/ExbD/TonB protein complex, which powers transport of siderophores and vitamin B12 across the bacterial outer membrane. The Tol-Pal system is exploited by colicin and filamentous phage DNA to enter the cell. It is also implicated in pathogenesis in several bacterial species
Probab=20.32 E-value=1e+02 Score=24.67 Aligned_cols=19 Identities=16% Similarity=0.169 Sum_probs=16.0
Q ss_pred hhhHHHHHHHHHHHHHHHH
Q 048175 65 VFWPILLFYWLTLFTLTMR 83 (134)
Q Consensus 65 VFWPILl~YFi~Lf~lTMr 83 (134)
|.||++++-.+.++++.-|
T Consensus 16 vm~~Ll~~Sii~~aviieR 34 (215)
T TIGR02796 16 VMLILLLASIISWAIIFQK 34 (215)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8999999998888877654
Done!