Query 035000
Match_columns 76
No_of_seqs 102 out of 129
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:22:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035000.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035000hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05251 UPF0197: Uncharacteri 100.0 4.5E-37 9.7E-42 192.7 8.4 74 3-76 4-77 (77)
2 KOG4452 Predicted membrane pro 100.0 7.2E-35 1.6E-39 181.1 6.4 73 4-76 7-79 (79)
3 cd06550 TM_ABC_iron-siderophor 72.7 32 0.00069 24.5 7.9 29 43-71 79-107 (261)
4 COG2116 FocA Formate/nitrite f 68.8 7.4 0.00016 29.4 3.5 29 42-70 22-50 (265)
5 COG1108 ZnuB ABC-type Mn2+/Zn2 67.9 23 0.00051 26.5 6.1 30 42-71 84-113 (274)
6 PF01226 Form_Nir_trans: Forma 63.3 19 0.0004 26.3 4.7 35 37-71 10-44 (250)
7 PRK02919 oxaloacetate decarbox 61.6 14 0.00029 23.2 3.2 26 50-75 5-30 (82)
8 PF11023 DUF2614: Protein of u 61.2 13 0.00028 25.0 3.3 56 5-76 3-58 (114)
9 PRK02935 hypothetical protein; 61.1 14 0.00031 24.7 3.4 54 6-75 5-58 (110)
10 PRK03814 oxaloacetate decarbox 59.9 19 0.0004 22.7 3.7 23 50-72 6-28 (85)
11 PF15038 Jiraiya: Jiraiya 55.4 67 0.0014 23.0 6.2 25 48-72 131-155 (175)
12 PF14256 YwiC: YwiC-like prote 52.4 65 0.0014 21.4 5.5 19 40-58 102-120 (129)
13 PF13807 GNVR: G-rich domain o 49.0 36 0.00078 20.3 3.6 22 47-68 58-79 (82)
14 PRK10805 formate transporter; 48.4 41 0.00089 25.2 4.5 30 40-69 24-53 (285)
15 PF00950 ABC-3: ABC 3 transpor 47.6 65 0.0014 23.5 5.3 27 45-71 78-104 (257)
16 TIGR00790 fnt formate/nitrite 47.4 35 0.00076 24.6 3.9 28 42-69 1-28 (239)
17 PRK09713 focB putative formate 47.2 44 0.00096 25.1 4.5 31 40-70 24-54 (282)
18 COG3630 OadG Na+-transporting 44.2 14 0.0003 23.7 1.2 20 56-75 11-30 (84)
19 COG1007 NuoN NADH:ubiquinone o 43.8 1.4E+02 0.0031 24.3 7.1 27 47-73 153-179 (475)
20 PF07332 DUF1469: Protein of u 43.5 65 0.0014 20.2 4.3 22 47-68 34-55 (121)
21 PF06123 CreD: Inner membrane 42.7 69 0.0015 25.6 5.2 38 21-60 301-338 (430)
22 PRK08378 hypothetical protein; 41.6 95 0.0021 20.0 5.2 34 22-62 10-43 (93)
23 TIGR03017 EpsF chain length de 41.3 43 0.00093 25.4 3.7 25 46-70 395-419 (444)
24 PRK11715 inner membrane protei 40.0 77 0.0017 25.4 5.1 38 21-60 307-344 (436)
25 PF06522 B12D: NADH-ubiquinone 39.9 38 0.00083 20.3 2.7 28 10-39 2-29 (73)
26 TIGR00847 ccoS cytochrome oxid 39.8 63 0.0014 18.6 3.4 21 52-72 5-25 (51)
27 TIGR01195 oadG_fam sodium pump 38.1 52 0.0011 20.3 3.1 17 56-72 8-24 (82)
28 PF14159 CAAD: CAAD domains of 37.4 53 0.0012 20.7 3.2 30 13-42 43-72 (90)
29 PF11712 Vma12: Endoplasmic re 36.1 1.3E+02 0.0028 19.9 6.6 47 20-70 85-132 (142)
30 PRK11562 nitrite transporter N 35.9 59 0.0013 24.2 3.7 27 43-69 20-46 (268)
31 COG3766 Predicted membrane pro 32.7 96 0.0021 21.4 4.0 39 15-53 8-46 (133)
32 PF06295 DUF1043: Protein of u 31.9 67 0.0015 21.2 3.1 15 18-32 1-15 (128)
33 PF00510 COX3: Cytochrome c ox 31.6 2E+02 0.0042 20.9 5.7 19 49-69 154-172 (258)
34 cd02432 Nodulin-21_like_1 Nodu 30.8 2E+02 0.0044 20.6 6.2 48 17-65 168-216 (218)
35 PRK09543 znuB high-affinity zi 30.1 2.2E+02 0.0047 20.7 5.8 27 45-71 78-104 (261)
36 PF04276 DUF443: Protein of un 30.1 2E+02 0.0043 20.2 7.4 68 5-72 78-160 (199)
37 TIGR03007 pepcterm_ChnLen poly 29.4 87 0.0019 24.3 3.8 24 46-69 412-435 (498)
38 TIGR03770 anch_rpt_perm anchor 29.3 1.7E+02 0.0036 21.5 5.1 27 45-71 90-116 (270)
39 COG4975 GlcU Putative glucose 29.1 2.3E+02 0.005 21.9 5.9 50 19-72 181-230 (288)
40 PRK12587 putative monovalent c 28.6 1.2E+02 0.0025 20.2 3.8 23 48-71 2-24 (118)
41 cd02433 Nodulin-21_like_2 Nodu 28.4 2E+02 0.0044 20.9 5.3 49 17-66 183-232 (234)
42 PF07297 DPM2: Dolichol phosph 27.9 1.4E+02 0.0031 18.6 3.9 31 12-42 43-74 (78)
43 PRK13499 rhamnose-proton sympo 27.8 2E+02 0.0044 22.3 5.5 45 16-62 137-187 (345)
44 PF02460 Patched: Patched fami 27.7 2.9E+02 0.0063 23.0 6.7 14 22-35 218-231 (798)
45 TIGR01006 polys_exp_MPA1 polys 27.5 1.1E+02 0.0024 21.2 3.8 24 46-69 173-196 (226)
46 PF06143 Baculo_11_kDa: Baculo 27.1 1.5E+02 0.0033 18.8 3.9 28 43-70 28-55 (84)
47 PF03597 CcoS: Cytochrome oxid 25.6 1.3E+02 0.0029 16.7 3.3 20 53-72 5-24 (45)
48 PF06609 TRI12: Fungal trichot 25.0 3E+02 0.0066 22.9 6.3 32 19-50 273-308 (599)
49 PRK11677 hypothetical protein; 24.9 1.2E+02 0.0026 20.6 3.4 33 17-51 4-38 (134)
50 PF06687 SUR7: SUR7/PalI famil 24.4 2.3E+02 0.005 19.1 7.2 52 17-72 115-168 (212)
51 PF11833 DUF3353: Protein of u 24.3 2.1E+02 0.0045 20.3 4.7 28 23-56 121-148 (194)
52 TIGR02897 QoxC cytochrome aa3 23.7 2.6E+02 0.0055 19.4 6.8 47 14-62 48-95 (190)
53 PF13974 YebO: YebO-like prote 23.7 1.2E+02 0.0027 19.1 3.0 17 21-37 4-20 (80)
54 PF06679 DUF1180: Protein of u 22.8 85 0.0018 22.0 2.4 32 19-50 98-129 (163)
55 PF10966 DUF2768: Protein of u 21.1 2E+02 0.0043 17.1 5.8 44 21-66 5-48 (58)
56 PRK12666 putative monovalent c 20.9 2.8E+02 0.0061 22.3 5.3 28 44-71 158-185 (528)
57 cd02434 Nodulin-21_like_3 Nodu 20.6 3.3E+02 0.0072 19.5 6.7 48 18-66 174-223 (225)
58 TIGR03867 MprA_tail MprA prote 20.6 1.2E+02 0.0026 15.6 2.1 14 16-29 8-21 (27)
59 PF14007 YtpI: YtpI-like prote 20.6 2.4E+02 0.0052 17.9 4.4 36 27-62 5-40 (89)
60 PRK00968 tetrahydromethanopter 20.2 3.1E+02 0.0067 20.6 5.0 26 42-68 211-236 (240)
No 1
>PF05251 UPF0197: Uncharacterised protein family (UPF0197); InterPro: IPR007915 This family of proteins is functionally uncharacterised, but is thought to be a transmembrane protein.
Probab=100.00 E-value=4.5e-37 Score=192.73 Aligned_cols=74 Identities=62% Similarity=0.961 Sum_probs=72.8
Q ss_pred CCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 035000 3 PKPITSPVPDAWYPTLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLGFGSLFLLLASGVYV 76 (76)
Q Consensus 3 ~~py~~pV~~~~~p~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~~GVYV 76 (76)
-+||+|||||+.||++|+++|+||+++++||++||+|++|++||+.||+++|++||+|+|||++|++||+||||
T Consensus 4 m~~Y~sPV~p~~~p~La~vll~iGl~fta~Ffiyevts~k~~r~i~kEl~~a~vAS~flGfG~lFLlL~vGIYV 77 (77)
T PF05251_consen 4 MSRYTSPVNPALYPHLAVVLLAIGLFFTAWFFIYEVTSTKKTRSIAKELLIALVASLFLGFGSLFLLLWVGIYV 77 (77)
T ss_pred ccCcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccccHHHHHHHHHHHHHHHhHHHHHHHHHCCCcC
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG4452 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=7.2e-35 Score=181.07 Aligned_cols=73 Identities=55% Similarity=0.850 Sum_probs=72.2
Q ss_pred CCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 035000 4 KPITSPVPDAWYPTLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLGFGSLFLLLASGVYV 76 (76)
Q Consensus 4 ~py~~pV~~~~~p~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~~GVYV 76 (76)
+||++||||+.+||++.+||.||+++++||+++|||++|+||+++||+++++.||+|+|||++|+++|+||||
T Consensus 7 ~RYtsPVNpAvfPhLttvLl~iG~fftAwFf~~~VtStKy~r~l~KELlIsl~aSvFlGFG~vFLLLwVGIYV 79 (79)
T KOG4452|consen 7 NRYTSPVNPAVFPHLTTVLLGIGLFFTAWFFMIQVTSTKYNRNLLKELLISLTASVFLGFGSVFLLLWVGIYV 79 (79)
T ss_pred hhhcCCCChhHhHHHHHHHHHHHHHHHHHHHheeEecchhhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcC
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999998
No 3
>cd06550 TM_ABC_iron-siderophores_like Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The TMs are bundles of alpha helices that transverse the cytoplasmic membrane multiple times. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Each TM has a prominent cytoplasmic loop which contacts an ABC and represents a conserved motif. The two TMs form either a homodimer (e.g. in the case of the BtuC subunits of the Escherichia coli BtuCD vitamin B12 transporter), a heterodimer (e.g. the TroC and TroD subunits of the Treponema pallidum general transition metal
Probab=72.69 E-value=32 Score=24.53 Aligned_cols=29 Identities=28% Similarity=0.394 Sum_probs=25.7
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 43 QNRSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 43 ~~r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
++++..+|.++|.+-+.+++.|..++...
T Consensus 79 ~~~~~~~~~~iGi~~~~~~~~~~~~ls~~ 107 (261)
T cd06550 79 GGLSPSKLILIGIVLSAFFSAGVILISLL 107 (261)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 36688999999999999999999998765
No 4
>COG2116 FocA Formate/nitrite family of transporters [Inorganic ion transport and metabolism]
Probab=68.83 E-value=7.4 Score=29.35 Aligned_cols=29 Identities=31% Similarity=0.532 Sum_probs=26.0
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 42 RQNRSLGKELITGAVASVFLGFGSLFLLL 70 (76)
Q Consensus 42 k~~r~l~ke~~la~~ASlflGfG~vFl~l 70 (76)
|.+|+..+..+.|..|.++.|+|.+|..-
T Consensus 22 k~~~~~~~~~l~ai~AG~~i~lg~~~~~~ 50 (265)
T COG2116 22 KATKSPLKLLLLAILAGAFIGLGFLFYIT 50 (265)
T ss_pred HHhhcHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45899999999999999999999998753
No 5
>COG1108 ZnuB ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]
Probab=67.89 E-value=23 Score=26.49 Aligned_cols=30 Identities=30% Similarity=0.381 Sum_probs=25.0
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 42 RQNRSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 42 k~~r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
|++.+..+|..++.+.|.++++|.+.+...
T Consensus 84 ~~~~~~~~D~aigiv~s~~~alGlvl~s~~ 113 (274)
T COG1108 84 RRRSKLKEDTAIGIVFSSGLALGLVLLSLV 113 (274)
T ss_pred HhhccchHHHHHHHHHHHHHHHHHHHHhhc
Confidence 334667889999999999999999988754
No 6
>PF01226 Form_Nir_trans: Formate/nitrite transporter; InterPro: IPR000292 Proteins in this entry belong to the Formate-Nitrite Transporter (FNT) family (TC 2.A.44). The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite. The homologous yeast protein may function as a short chain aliphatic carboxylate H+ symporter, transporting formate, acetate and propionate, and functioning primarily as an acetate uptake permease.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 3Q7K_H 3KLY_E 3KLZ_A 3TDX_C 3TE2_B 3TDS_B 3TDR_E 3TDO_C 3TE1_B 3TDP_C ....
Probab=63.27 E-value=19 Score=26.31 Aligned_cols=35 Identities=37% Similarity=0.677 Sum_probs=28.5
Q ss_pred HHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 37 EATSSRQNRSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 37 ~vt~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
+....|.+|+..|.++.|..|-.+.|+|..+..-.
T Consensus 10 ~~g~~k~~~~~~~~~~~~~lAG~~ig~g~~~~~~v 44 (250)
T PF01226_consen 10 EAGEKKANRPPSKLFLRGILAGAFIGFGALLSLVV 44 (250)
T ss_dssp HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455678999999999999999999999876643
No 7
>PRK02919 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=61.62 E-value=14 Score=23.22 Aligned_cols=26 Identities=27% Similarity=0.516 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccc
Q 035000 50 ELITGAVASVFLGFGSLFLLLASGVY 75 (76)
Q Consensus 50 e~~la~~ASlflGfG~vFl~l~~GVY 75 (76)
|++....--..+|.|+||+++.+=||
T Consensus 5 ~ll~~gl~lMvlGMg~VfvFL~lLI~ 30 (82)
T PRK02919 5 ELLGEGFTLMFLGMGFVLAFLFLLIF 30 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666678999999999876544
No 8
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=61.25 E-value=13 Score=25.00 Aligned_cols=56 Identities=20% Similarity=0.377 Sum_probs=32.7
Q ss_pred CCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 035000 5 PITSPVPDAWYPTLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLGFGSLFLLLASGVYV 76 (76)
Q Consensus 5 py~~pV~~~~~p~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~~GVYV 76 (76)
+|++-||.-.-.-+..++..++....+.|+ |..+ .+.++|+=+|.+.++.+.+||+
T Consensus 3 ~~~~KiN~~R~~al~lif~g~~vmy~gi~f-------~~~~---------~im~ifmllG~L~~l~S~~VYf 58 (114)
T PF11023_consen 3 KYSSKINKIRTFALSLIFIGMIVMYIGIFF-------KASP---------IIMVIFMLLGLLAILASTAVYF 58 (114)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHhhhhhh-------cccH---------HHHHHHHHHHHHHHHHHHHHHH
Confidence 455555554444444455555555556554 1111 3567778888888888888873
No 9
>PRK02935 hypothetical protein; Provisional
Probab=61.07 E-value=14 Score=24.67 Aligned_cols=54 Identities=17% Similarity=0.328 Sum_probs=31.5
Q ss_pred CcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 035000 6 ITSPVPDAWYPTLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLGFGSLFLLLASGVY 75 (76)
Q Consensus 6 y~~pV~~~~~p~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~~GVY 75 (76)
|++-||+-.-.-+..++..+++.-.+.|+ ++.. .+.++|+-+|.+.++.+.+||
T Consensus 5 ~ssKINkiRt~aL~lvfiG~~vMy~Giff--------~~~~--------~~m~ifm~~G~l~~l~S~vvY 58 (110)
T PRK02935 5 YSNKINKIRTFALSLVFIGFIVMYLGIFF--------RESI--------IIMTIFMLLGFLAVIASTVVY 58 (110)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHh--------cccH--------HHHHHHHHHHHHHHHHHHHHH
Confidence 44444444433444444444455566665 1111 266788888888888888887
No 10
>PRK03814 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=59.88 E-value=19 Score=22.70 Aligned_cols=23 Identities=26% Similarity=0.585 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 035000 50 ELITGAVASVFLGFGSLFLLLAS 72 (76)
Q Consensus 50 e~~la~~ASlflGfG~vFl~l~~ 72 (76)
|++.-...=.++|.|+||+++..
T Consensus 6 ~~l~~~~~lm~~GM~~VF~fL~l 28 (85)
T PRK03814 6 SLLVDAATLMLTGMGVVFIFLTL 28 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666788999999998865
No 11
>PF15038 Jiraiya: Jiraiya
Probab=55.44 E-value=67 Score=22.97 Aligned_cols=25 Identities=32% Similarity=0.373 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 035000 48 GKELITGAVASVFLGFGSLFLLLAS 72 (76)
Q Consensus 48 ~ke~~la~~ASlflGfG~vFl~l~~ 72 (76)
--|..-|..+|..+|.|++|+.++.
T Consensus 131 ~f~~~~~~~~s~ilG~g~vfl~~~~ 155 (175)
T PF15038_consen 131 QFHSEPGIATSIILGSGAVFLGAAM 155 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677888899999999999987765
No 12
>PF14256 YwiC: YwiC-like protein
Probab=52.35 E-value=65 Score=21.38 Aligned_cols=19 Identities=32% Similarity=0.295 Sum_probs=13.6
Q ss_pred hhccchhHHHHHHHHHHHH
Q 035000 40 SSRQNRSLGKELITGAVAS 58 (76)
Q Consensus 40 ~~k~~r~l~ke~~la~~AS 58 (76)
+.|++|++.+|+.-.+..|
T Consensus 102 ~~~~eRsLlndl~~i~a~~ 120 (129)
T PF14256_consen 102 KRKRERSLLNDLAAIAAFS 120 (129)
T ss_pred HhcCchhHHHhHHHHHHHH
Confidence 5566999999987644443
No 13
>PF13807 GNVR: G-rich domain on putative tyrosine kinase
Probab=49.03 E-value=36 Score=20.33 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 035000 47 LGKELITGAVASVFLGFGSLFL 68 (76)
Q Consensus 47 l~ke~~la~~ASlflGfG~vFl 68 (76)
-..-+.+|++.++++|+|.+|+
T Consensus 58 ~~lil~l~~~~Gl~lgi~~~~~ 79 (82)
T PF13807_consen 58 RALILALGLFLGLILGIGLAFL 79 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3455777788888888887775
No 14
>PRK10805 formate transporter; Provisional
Probab=48.36 E-value=41 Score=25.24 Aligned_cols=30 Identities=17% Similarity=0.284 Sum_probs=25.4
Q ss_pred hhccchhHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 40 SSRQNRSLGKELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 40 ~~k~~r~l~ke~~la~~ASlflGfG~vFl~ 69 (76)
..|.+|+..|.++.|..|-.++|+|.++..
T Consensus 24 ~~k~~~~~~~~~~~ailAG~~Ig~g~~~~~ 53 (285)
T PRK10805 24 VYKATKHPLKTFYLAITAGVFISIAFVFYI 53 (285)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345689999999999999999999997743
No 15
>PF00950 ABC-3: ABC 3 transport family; InterPro: IPR001626 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 number of bacterial transport systems have been found to contain integral membrane components that have similar sequences []: these systems fit the characteristics of ATP-binding cassette transporters []. The proteins form homo- or hetero-oligomeric channels, allowing ATP-mediated transport. Hydropathy analysis of the proteins has revealed the presence of 6 possible transmembrane regions. These proteins belong to family 3 of ABC transporters.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016020 membrane
Probab=47.59 E-value=65 Score=23.50 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=22.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 45 RSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 45 r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
++.-.|..++.+-|.++|.|.+++...
T Consensus 78 ~~~~~d~~igiv~~~~~algvll~s~~ 104 (257)
T PF00950_consen 78 SKISEDAAIGIVFSFSFALGVLLLSLS 104 (257)
T ss_pred cCcchhHHHHHHHHHHHHHHHHHHhhC
Confidence 445789999999999999999987654
No 16
>TIGR00790 fnt formate/nitrite transporter. symport. HCO2 - efflux may be driven by the membrane potential by a uniport mechanism or by H+ antiport.
Probab=47.43 E-value=35 Score=24.62 Aligned_cols=28 Identities=25% Similarity=0.457 Sum_probs=23.1
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 42 RQNRSLGKELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 42 k~~r~l~ke~~la~~ASlflGfG~vFl~ 69 (76)
|-+|+..|.+..|..|..+.|+|..+.+
T Consensus 1 k~~~~~~~~~~~a~~AG~~i~~g~~~~~ 28 (239)
T TIGR00790 1 KAALSLLNLLVLSILAGAFIALGLVFYI 28 (239)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4468889999999999999999986554
No 17
>PRK09713 focB putative formate transporter; Provisional
Probab=47.24 E-value=44 Score=25.10 Aligned_cols=31 Identities=26% Similarity=0.356 Sum_probs=24.2
Q ss_pred hhccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 40 SSRQNRSLGKELITGAVASVFLGFGSLFLLL 70 (76)
Q Consensus 40 ~~k~~r~l~ke~~la~~ASlflGfG~vFl~l 70 (76)
..|.+|+..|.+..|..|-+++|+|..+...
T Consensus 24 ~~k~~~~~~~~~~~~i~AG~~I~~g~~~~~~ 54 (282)
T PRK09713 24 AHKIARSKVSVFLMAMSAGVFMAIGFTFYLS 54 (282)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455788889999999999999988876543
No 18
>COG3630 OadG Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, gamma subunit [Energy production and conversion]
Probab=44.24 E-value=14 Score=23.67 Aligned_cols=20 Identities=35% Similarity=0.732 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHhhccc
Q 035000 56 VASVFLGFGSLFLLLASGVY 75 (76)
Q Consensus 56 ~ASlflGfG~vFl~l~~GVY 75 (76)
+--.++|.|.||++|+.=+|
T Consensus 11 ~~L~vlGmg~VflfL~iLi~ 30 (84)
T COG3630 11 ITLMVLGMGFVFLFLSILIY 30 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34467899999999887655
No 19
>COG1007 NuoN NADH:ubiquinone oxidoreductase subunit 2 (chain N) [Energy production and conversion]
Probab=43.76 E-value=1.4e+02 Score=24.31 Aligned_cols=27 Identities=33% Similarity=0.471 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 035000 47 LGKELITGAVASVFLGFGSLFLLLASG 73 (76)
Q Consensus 47 l~ke~~la~~ASlflGfG~vFl~l~~G 73 (76)
=.|+.+++..+|.++-+|..+.--..|
T Consensus 153 alKYfvlGalsS~~~l~G~al~Y~~tG 179 (475)
T COG1007 153 ALKYFVLGALSSAFLLYGIALVYGATG 179 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 379999999999999999988765554
No 20
>PF07332 DUF1469: Protein of unknown function (DUF1469); InterPro: IPR009937 This entry represents proteins found in hypothetical bacterial proteins where is is annotated as ycf49 or ycf49-like. The function is not known.
Probab=43.46 E-value=65 Score=20.21 Aligned_cols=22 Identities=36% Similarity=0.464 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 035000 47 LGKELITGAVASVFLGFGSLFL 68 (76)
Q Consensus 47 l~ke~~la~~ASlflGfG~vFl 68 (76)
..+-....+.+.++..+|.+|+
T Consensus 34 ~~~~~~~~~~a~vl~~~~l~~l 55 (121)
T PF07332_consen 34 LGRGLALLVLAAVLALLALLFL 55 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333333333
No 21
>PF06123 CreD: Inner membrane protein CreD; InterPro: IPR010364 This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with a Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA [].
Probab=42.68 E-value=69 Score=25.63 Aligned_cols=38 Identities=29% Similarity=0.297 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHH
Q 035000 21 FMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVF 60 (76)
Q Consensus 21 ~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlf 60 (76)
-+|.|++.|++.|+ .|+.+.+ .-..++++++|+.=.+|
T Consensus 301 giLFI~LTF~~ffl-fE~~~~~-~iHpiQY~LVGlAl~lF 338 (430)
T PF06123_consen 301 GILFIGLTFLAFFL-FELLSKL-RIHPIQYLLVGLALVLF 338 (430)
T ss_pred HHHHHHHHHHHHHH-HHHHhcC-cccHHHHHHHHHHHHHH
Confidence 46778888888776 7888766 57789999988765544
No 22
>PRK08378 hypothetical protein; Provisional
Probab=41.55 E-value=95 Score=19.97 Aligned_cols=34 Identities=18% Similarity=0.230 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHH
Q 035000 22 MLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLG 62 (76)
Q Consensus 22 lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflG 62 (76)
.+.+.+..+++..+ ..||+.+..+....=|+++.
T Consensus 10 iLl~~ll~~A~~~v-------~~rdLl~avi~~~~~sll~a 43 (93)
T PRK08378 10 IILALMIISAILAV-------EWRDLLAAAVGMAAVSLFAS 43 (93)
T ss_pred HHHHHHHHHHHHHH-------HHhHHHHHHHHHHHHHHHHH
Confidence 34455666666654 56888887777666666554
No 23
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=41.27 E-value=43 Score=25.43 Aligned_cols=25 Identities=28% Similarity=0.371 Sum_probs=20.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 46 SLGKELITGAVASVFLGFGSLFLLL 70 (76)
Q Consensus 46 ~l~ke~~la~~ASlflGfG~vFl~l 70 (76)
+..+.+.+|++.++++|+|.+|+.-
T Consensus 395 ~~~~~l~~~~~~Gl~lg~~~~~l~e 419 (444)
T TIGR03017 395 RLLLNLVLSIFLGMLLGIGFAFLAE 419 (444)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456778899999999999998753
No 24
>PRK11715 inner membrane protein; Provisional
Probab=39.97 E-value=77 Score=25.43 Aligned_cols=38 Identities=24% Similarity=0.278 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHH
Q 035000 21 FMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVF 60 (76)
Q Consensus 21 ~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlf 60 (76)
-+|.|++-|++.|. .|+.+.+ .--.++++++|+.=.+|
T Consensus 307 giLFI~LTF~~fFl-fE~~~~~-~iHpiQYlLVGlAl~lF 344 (436)
T PRK11715 307 AILFIALTFAAFFL-FELLKKL-RIHPVQYLLVGLALVLF 344 (436)
T ss_pred HHHHHHHHHHHHHH-HHHhcCc-eecHHHHHHHHHHHHHH
Confidence 45778888887775 7888766 56789999988765554
No 25
>PF06522 B12D: NADH-ubiquinone reductase complex 1 MLRQ subunit; InterPro: IPR010530 The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear [] and is found in plants [], insects, fungi and higher metazoans []. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation [].
Probab=39.89 E-value=38 Score=20.35 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=19.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 10 VPDAWYPTLSVFMLAIGLFVTASFFIYEAT 39 (76)
Q Consensus 10 V~~~~~p~la~~lL~igl~~~~~F~i~~vt 39 (76)
.+|+.+|.++++..+.|++ +++..+..+
T Consensus 2 ~~pel~PL~~~vg~a~~~a--~~~~~r~l~ 29 (73)
T PF06522_consen 2 KHPELYPLFVIVGVAVGGA--TFYLYRLLL 29 (73)
T ss_pred CCccccchHHHHHHHHHHH--HHHHHHHHh
Confidence 4789999999877766654 445445554
No 26
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=39.81 E-value=63 Score=18.63 Aligned_cols=21 Identities=29% Similarity=0.113 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 035000 52 ITGAVASVFLGFGSLFLLLAS 72 (76)
Q Consensus 52 ~la~~ASlflGfG~vFl~l~~ 72 (76)
.+=.+.|+++|.+.+..+.|.
T Consensus 5 ~~LIpiSl~l~~~~l~~f~Wa 25 (51)
T TIGR00847 5 TILIPISLLLGGVGLVAFLWS 25 (51)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344678999999999988884
No 27
>TIGR01195 oadG_fam sodium pump decarboxylases, gamma subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
Probab=38.05 E-value=52 Score=20.31 Aligned_cols=17 Identities=35% Similarity=0.657 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHhh
Q 035000 56 VASVFLGFGSLFLLLAS 72 (76)
Q Consensus 56 ~ASlflGfG~vFl~l~~ 72 (76)
..-..+|+|+||++|..
T Consensus 8 ~~l~v~GM~~VF~fL~l 24 (82)
T TIGR01195 8 ATLTVLGMGIVFLFLSL 24 (82)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34457888888888765
No 28
>PF14159 CAAD: CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
Probab=37.44 E-value=53 Score=20.65 Aligned_cols=30 Identities=20% Similarity=0.103 Sum_probs=21.7
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 035000 13 AWYPTLSVFMLAIGLFVTASFFIYEATSSR 42 (76)
Q Consensus 13 ~~~p~la~~lL~igl~~~~~F~i~~vt~~k 42 (76)
+.-|.++-++=.+|+..++||.......++
T Consensus 43 n~iPll~~llElvGlgyt~wF~~ryLL~~~ 72 (90)
T PF14159_consen 43 NSIPLLPGLLELVGLGYTGWFVYRYLLFAE 72 (90)
T ss_pred HcCcchHHHHHHHHHHHHhHHHHHHHcChH
Confidence 345667777888999999999855555443
No 29
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=36.06 E-value=1.3e+02 Score=19.89 Aligned_cols=47 Identities=9% Similarity=0.276 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc-chhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 20 VFMLAIGLFVTASFFIYEATSSRQ-NRSLGKELITGAVASVFLGFGSLFLLL 70 (76)
Q Consensus 20 ~~lL~igl~~~~~F~i~~vt~~k~-~r~l~ke~~la~~ASlflGfG~vFl~l 70 (76)
+++-.++.++.+|+. +.... ..+...-+++|+++++..++.=++++.
T Consensus 85 ilvsv~~~~~~~~~~----~~~~~~~~~~~~Rvllgl~~al~vlvAEv~l~~ 132 (142)
T PF11712_consen 85 ILVSVFAVFFAGWYW----AGYSFGGWSFPYRVLLGLFGALLVLVAEVVLYI 132 (142)
T ss_pred HHHHHHHHHHHHHHH----HHHhhcccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555544 33233 577788889999999888887665543
No 30
>PRK11562 nitrite transporter NirC; Provisional
Probab=35.91 E-value=59 Score=24.23 Aligned_cols=27 Identities=15% Similarity=0.378 Sum_probs=23.7
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 43 QNRSLGKELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 43 ~~r~l~ke~~la~~ASlflGfG~vFl~ 69 (76)
.+++..+.++.|..|-++.|+|.++.+
T Consensus 20 ~~~~~~~~~~~ai~AG~~Ig~g~~~~~ 46 (268)
T PRK11562 20 SANNPLGFWVSSAMAGAYVGLGIILIF 46 (268)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477899999999999999999998754
No 31
>COG3766 Predicted membrane protein [Function unknown]
Probab=32.67 E-value=96 Score=21.38 Aligned_cols=39 Identities=23% Similarity=0.240 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHH
Q 035000 15 YPTLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELIT 53 (76)
Q Consensus 15 ~p~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~l 53 (76)
.|..+--..+-.+++...+++||...+-.+..++||==.
T Consensus 8 l~a~~~~~sv~~l~~i~F~~iy~~vTpyke~elIk~GN~ 46 (133)
T COG3766 8 LLAFAAYFSVGVLMLILFLFIYEKVTPYKEWELIKEGNT 46 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHHHccCH
Confidence 444444455556667777778997766568888888443
No 32
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.88 E-value=67 Score=21.15 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHH
Q 035000 18 LSVFMLAIGLFVTAS 32 (76)
Q Consensus 18 la~~lL~igl~~~~~ 32 (76)
++++.+++|+++..+
T Consensus 1 y~~i~lvvG~iiG~~ 15 (128)
T PF06295_consen 1 YAIIGLVVGLIIGFL 15 (128)
T ss_pred ChHHHHHHHHHHHHH
Confidence 467888888854433
No 33
>PF00510 COX3: Cytochrome c oxidase subunit III This family corresponds to chains c and p.; InterPro: IPR000298 Cytochrome c oxidase (1.9.3.1 from EC) is the terminal enzyme of the respiratory chain of mitochondria and many aerobic bacteria. It catalyses the transfer of electrons from reduced cytochrome c to molecular oxygen: 4 cytochrome c+2 + 4 H+ + O2 --> 4 cytochrome c+3 + 2 H2O This reaction is coupled to the pumping of four additional protons across the mitochondrial or bacterial membrane [, ]. Cytochrome c oxidase is an oligomeric enzymatic complex that is located in the mitochondrial inner membrane of eukaryotes and in the plasma membrane of aerobic prokaryotes. The core structure of prokaryotic and eukaryotic cytochrome c oxidase contains three common subunits, I, II and III. In prokaryotes, subunits I and III can be fused and a fourth subunit is sometimes found, whereas in eukaryotes there are a variable number of additional small polypeptidic subunits []. The functional role of subunit III is not yet understood. As the bacterial respiratory systems are branched, they have a number of distinct terminal oxidases, rather than the single cytochrome c oxidase present in the eukaryotic mitochondrial systems. Although the cytochrome o oxidases do not catalyse the cytochrome c but the quinol (ubiquinol) oxidation they belong to the same haem-copper oxidase superfamily as cytochrome c oxidases. Members of this family share sequence similarities in all three core subunits: subunit I is the most conserved subunit, whereas subunit II is the least conserved [, , ].; GO: 0004129 cytochrome-c oxidase activity, 0006123 mitochondrial electron transport, cytochrome c to oxygen, 0016020 membrane; PDB: 1M57_I 1M56_I 2EIL_P 2OCC_C 2EIM_C 2EIK_P 1OCZ_C 2EIJ_C 3AG2_P 1OCC_P ....
Probab=31.64 E-value=2e+02 Score=20.87 Aligned_cols=19 Identities=32% Similarity=0.450 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 035000 49 KELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 49 ke~~la~~ASlflGfG~vFl~ 69 (76)
|+...++..++.+ |.+|+.
T Consensus 154 ~~~~~~L~~t~~L--G~~Fl~ 172 (258)
T PF00510_consen 154 KAARLWLLLTILL--GLLFLV 172 (258)
T ss_dssp HHHHHHHHHHHHH--HHHHHH
T ss_pred hhhhhhHHHHHHH--HHHHHH
Confidence 4555666666554 444544
No 34
>cd02432 Nodulin-21_like_1 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_1: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=30.76 E-value=2e+02 Score=20.59 Aligned_cols=48 Identities=17% Similarity=0.176 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH-HHHHHH
Q 035000 17 TLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASV-FLGFGS 65 (76)
Q Consensus 17 ~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASl-flGfG~ 65 (76)
..++++..+++++++++- -.++..+..|+..+-++++..|.. ..++|-
T Consensus 168 ~~s~~~~~~aL~~~G~~~-a~~~~~~~~~~~l~~~~iG~~aa~vty~iG~ 216 (218)
T cd02432 168 PVTIIATLLALALTGYVS-ARLGGASVLRAILRNVIWGALAMALTYLIGR 216 (218)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566666666666664 223333345666777777766543 345553
No 35
>PRK09543 znuB high-affinity zinc transporter membrane component; Reviewed
Probab=30.14 E-value=2.2e+02 Score=20.68 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 45 RSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 45 r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
.+..+|..++.+-|.+++.|+.++...
T Consensus 78 ~~~~~d~~iGi~~s~~~a~g~~l~s~~ 104 (261)
T PRK09543 78 PQLAIDTLLGIMAHSALSLGLVVVSLM 104 (261)
T ss_pred cCCchHHHHHHHHHHHHHHHHHHHHhc
Confidence 467889999999999999999988764
No 36
>PF04276 DUF443: Protein of unknown function (DUF443) ; InterPro: IPR005915 The members of this family share 50 % or greater sequence identity. They are found as eleven tandem genes, arranged head-to-tail, in Staphylococcus aureus (strain COL). Distant full-length homologs are found in a Staphylococcus haemolyticus plasmid and in Bacillus halodurans. The function of these proteins is unknown.
Probab=30.09 E-value=2e+02 Score=20.21 Aligned_cols=68 Identities=18% Similarity=0.176 Sum_probs=46.1
Q ss_pred CCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhhcc---c-----------hh-HHHHHHHHHHHHHHHHHHHHHHH
Q 035000 5 PITSPVPDAWYPTLSVFMLAIGLFVTASFFIYEATSSRQ---N-----------RS-LGKELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 5 py~~pV~~~~~p~la~~lL~igl~~~~~F~i~~vt~~k~---~-----------r~-l~ke~~la~~ASlflGfG~vFl~ 69 (76)
||..-.|-+..+.+..+++.++++....+..+--.+.|. + |. -.|+....+.+-+++++.+++++
T Consensus 78 ~~~~~~~i~~~~~i~~~i~~i~~l~v~~l~~~l~kk~k~~i~~~~~~~~~ki~l~P~~~K~~~~~lf~yi~~~~~~i~~~ 157 (199)
T PF04276_consen 78 PYIDYFNIQSSRIINIIICIIVILGVLILRIYLNKKLKKKIYNRNKNSKQKIILIPETFKNFFKNLFAYIFFLFFSIFLF 157 (199)
T ss_pred HHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcceEEEEEEcchHHHHHHHHHHHHHHHHHHHHH
Confidence 344455667778888899999888777665433222221 1 12 47788888899999998888777
Q ss_pred Hhh
Q 035000 70 LAS 72 (76)
Q Consensus 70 l~~ 72 (76)
.++
T Consensus 158 ~~f 160 (199)
T PF04276_consen 158 YMF 160 (199)
T ss_pred HHH
Confidence 654
No 37
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.
Probab=29.41 E-value=87 Score=24.26 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=18.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 46 SLGKELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 46 ~l~ke~~la~~ASlflGfG~vFl~ 69 (76)
+..+.+.+|+++++++|.|.+|+.
T Consensus 412 ~~~~~l~~g~~~Gl~lg~~~~~l~ 435 (498)
T TIGR03007 412 NRPLLMLAGLLGGLGAGIGLAFLL 435 (498)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567888899999999988864
No 38
>TIGR03770 anch_rpt_perm anchored repeat-type ABC transporter, permease subunit. This protein family is the permease subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in the adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous permease subunits outside the scope of this family include manganese transporter MntB in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.
Probab=29.30 E-value=1.7e+02 Score=21.45 Aligned_cols=27 Identities=19% Similarity=0.290 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 45 RSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 45 r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
++.-.|..++.+=|.+++.|.+++...
T Consensus 90 ~~~~~d~~igiv~s~~~algvills~~ 116 (270)
T TIGR03770 90 RRLKEDSIIGIFFVAAFALGLVIISRV 116 (270)
T ss_pred cCCchhHHHHHHHHHHHHHHHhhhhcc
Confidence 566789999999999999999887654
No 39
>COG4975 GlcU Putative glucose uptake permease [Carbohydrate transport and metabolism]
Probab=29.15 E-value=2.3e+02 Score=21.87 Aligned_cols=50 Identities=22% Similarity=0.402 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 035000 19 SVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLGFGSLFLLLAS 72 (76)
Q Consensus 19 a~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~~ 72 (76)
|++=-++|+...+.=+ +..|.++..-|....-.+--+.-|+|-+|++.+-
T Consensus 181 aiLPqAiGMv~~ali~----~~~~~~~~~~K~t~~nii~G~~Wa~GNl~ml~a~ 230 (288)
T COG4975 181 AILPQAIGMVIGALIL----GFFKMEKRFNKYTWLNIIPGLIWAIGNLFMLLAA 230 (288)
T ss_pred hhhHHHHHHHHHHHHH----hhcccccchHHHHHHHHhhHHHHHhhHHHHHHhh
Confidence 4444578887776643 4445567778888888888999999999999873
No 40
>PRK12587 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=28.56 E-value=1.2e+02 Score=20.17 Aligned_cols=23 Identities=30% Similarity=0.297 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 48 GKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 48 ~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
+||. +..++.+++.+|.+|.+.+
T Consensus 2 ~~~~-~~~l~~ill~~G~~~~lig 24 (118)
T PRK12587 2 IKII-LISLALIFVIIGALISALA 24 (118)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHH
Confidence 4555 5567777888888776653
No 41
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=28.40 E-value=2e+02 Score=20.87 Aligned_cols=49 Identities=22% Similarity=0.235 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH-HHHHHHH
Q 035000 17 TLSVFMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASV-FLGFGSL 66 (76)
Q Consensus 17 ~la~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASl-flGfG~v 66 (76)
..++++..+.+++++++. -.++..+.-|+..+-+.+++.|.. ..++|.+
T Consensus 183 ~~s~~~~~~~L~~lG~~~-a~~s~~~~~~~~l~~~~~G~~aa~vsy~iG~l 232 (234)
T cd02433 183 VLSVLLVGLALLATGAVT-GLLSGRSPGISALRQLAIGGGAAAVTYLLGLL 232 (234)
T ss_pred HHHHHHHHHHHHHHHHHH-HhhCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 335555556666666653 222333335666666666666543 3455543
No 42
>PF07297 DPM2: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2); InterPro: IPR009914 This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2 [].; GO: 0009059 macromolecule biosynthetic process, 0030176 integral to endoplasmic reticulum membrane
Probab=27.88 E-value=1.4e+02 Score=18.61 Aligned_cols=31 Identities=29% Similarity=0.458 Sum_probs=21.0
Q ss_pred CCch-HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 035000 12 DAWY-PTLSVFMLAIGLFVTASFFIYEATSSR 42 (76)
Q Consensus 12 ~~~~-p~la~~lL~igl~~~~~F~i~~vt~~k 42 (76)
|..| -.+-.+++.+|+...+.|.-+-..+++
T Consensus 43 Pr~yAi~lP~~lll~~~~~vg~f~g~vmik~~ 74 (78)
T PF07297_consen 43 PREYAIILPIFLLLLGLSGVGTFLGYVMIKSK 74 (78)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3444 356677888999999998755555554
No 43
>PRK13499 rhamnose-proton symporter; Provisional
Probab=27.79 E-value=2e+02 Score=22.31 Aligned_cols=45 Identities=20% Similarity=0.283 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc------cchhHHHHHHHHHHHHHHHH
Q 035000 16 PTLSVFMLAIGLFVTASFFIYEATSSR------QNRSLGKELITGAVASVFLG 62 (76)
Q Consensus 16 p~la~~lL~igl~~~~~F~i~~vt~~k------~~r~l~ke~~la~~ASlflG 62 (76)
-.+++++.++|..++++.-. ....+ .++++.|-+++++++.+..+
T Consensus 137 ~~~gv~liliGi~l~s~Ag~--~k~~~~~~~~~~~~~~~KGi~ialisgi~~~ 187 (345)
T PRK13499 137 TLLGVLVALIGVAIVGRAGQ--LKERKMGIKKAEEFNLKKGLILAVMSGIFSA 187 (345)
T ss_pred HHHHHHHHHHHHHHHHHhhh--hcccccccccccccchHhHHHHHHHHHHHHH
Confidence 46788888899999988642 11111 13578888888887766544
No 44
>PF02460 Patched: Patched family; InterPro: IPR003392 The transmembrane protein, patched, is a receptor for the morphogene Sonic Hedgehog. In Drosophila melanogaster, this protein associates with the smoothened protein to transduce hedgehog signals, leading to the activation of wingless, decapentaplegic and patched itself. It participates in cell interactions that establish pattern within the segment and imaginal disks during development. The mouse homologue may play a role in epidermal development. The human Niemann-Pick C1 protein, defects in which cause Niemann-Pick type II disease, is also a member of this family. This protein is involved in the intracellular trafficking of cholesterol, and may play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural functional integrity of nerve terminals.; GO: 0008158 hedgehog receptor activity, 0016020 membrane
Probab=27.70 E-value=2.9e+02 Score=23.04 Aligned_cols=14 Identities=29% Similarity=0.591 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHH
Q 035000 22 MLAIGLFVTASFFI 35 (76)
Q Consensus 22 lL~igl~~~~~F~i 35 (76)
++.+|..++..|.+
T Consensus 218 ~~~~~~~~~~~f~~ 231 (798)
T PF02460_consen 218 LFAIGFALMFIFVV 231 (798)
T ss_pred HHHHHHHHHHHHHH
Confidence 45556666655554
No 45
>TIGR01006 polys_exp_MPA1 polysaccharide export protein, MPA1 family, Gram-positive type. This family contains members from Low GC Gram-positive bacteria; they are proposed to have a function in the export of complex polysaccharides.
Probab=27.50 E-value=1.1e+02 Score=21.15 Aligned_cols=24 Identities=13% Similarity=0.254 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 46 SLGKELITGAVASVFLGFGSLFLL 69 (76)
Q Consensus 46 ~l~ke~~la~~ASlflGfG~vFl~ 69 (76)
+..+...+|+++.+.+|+|.+|+.
T Consensus 173 ~~~~~~~~g~~~G~~~~~~~~~~~ 196 (226)
T TIGR01006 173 NPKRNLLIGFLLGLVVALIIVLLK 196 (226)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788888888888888888764
No 46
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=27.06 E-value=1.5e+02 Score=18.81 Aligned_cols=28 Identities=25% Similarity=0.363 Sum_probs=19.0
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 035000 43 QNRSLGKELITGAVASVFLGFGSLFLLL 70 (76)
Q Consensus 43 ~~r~l~ke~~la~~ASlflGfG~vFl~l 70 (76)
+||+++|+.++-+.+=+-+=.-++|..+
T Consensus 28 rN~sfirdFvLVic~~lVfVii~lFi~l 55 (84)
T PF06143_consen 28 RNRSFIRDFVLVICCFLVFVIIVLFILL 55 (84)
T ss_pred hChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999955555555555555544
No 47
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=25.55 E-value=1.3e+02 Score=16.71 Aligned_cols=20 Identities=25% Similarity=0.180 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHhh
Q 035000 53 TGAVASVFLGFGSLFLLLAS 72 (76)
Q Consensus 53 la~~ASlflGfG~vFl~l~~ 72 (76)
+-++-|+++|...+..+.|.
T Consensus 5 ~lip~sl~l~~~~l~~f~Wa 24 (45)
T PF03597_consen 5 ILIPVSLILGLIALAAFLWA 24 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34577888888888888774
No 48
>PF06609 TRI12: Fungal trichothecene efflux pump (TRI12); InterPro: IPR010573 This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster. It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes [].
Probab=25.03 E-value=3e+02 Score=22.89 Aligned_cols=32 Identities=22% Similarity=0.382 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh-hcc---chhHHHH
Q 035000 19 SVFMLAIGLFVTASFFIYEATS-SRQ---NRSLGKE 50 (76)
Q Consensus 19 a~~lL~igl~~~~~F~i~~vt~-~k~---~r~l~ke 50 (76)
-+..+++|.++...|.+||.-. +|+ .+++.|+
T Consensus 273 VIa~lviG~~~Lv~F~~wE~~~~~~~Pl~P~~Lf~~ 308 (599)
T PF06609_consen 273 VIAPLVIGFVLLVAFVVWEWFGAPKDPLFPHRLFKD 308 (599)
T ss_pred chhhHHHHHHHHHHHHHhhhhccCCCCcCCHHHhcc
Confidence 4567899999999999999743 332 4555554
No 49
>PRK11677 hypothetical protein; Provisional
Probab=24.94 E-value=1.2e+02 Score=20.57 Aligned_cols=33 Identities=18% Similarity=0.361 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc--cchhHHHHH
Q 035000 17 TLSVFMLAIGLFVTASFFIYEATSSR--QNRSLGKEL 51 (76)
Q Consensus 17 ~la~~lL~igl~~~~~F~i~~vt~~k--~~r~l~ke~ 51 (76)
.++++.++||+++ +++... .+.++ ..+++-+|+
T Consensus 4 ~~a~i~livG~ii-G~~~~R-~~~~~~~~q~~le~eL 38 (134)
T PRK11677 4 EYALIGLVVGIII-GAVAMR-FGNRKLRQQQALQYEL 38 (134)
T ss_pred HHHHHHHHHHHHH-HHHHHh-hccchhhHHHHHHHHH
Confidence 4677888888854 444333 33332 355555554
No 50
>PF06687 SUR7: SUR7/PalI family; InterPro: IPR009571 This family consists of several fungal-specific SUR7 proteins. Its activity regulates expression of RVS161, a homologue of human endophilin, suggesting a function for both in endocytosis [, ]. The protein carries four transmembrane domains and is thus likely to act as an anchoring protein for the eisosome to the plasma membrane. Eisosomes are the immobile protein complexes, that include the proteins Pil1 and Lsp1, which co-localise with sites of protein and lipid endocytosis at the plasma membrane. SUR7 protein may play a role in sporulation []. Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This family also includes PalI which is part of a pH signal transduction cascade. Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH [].
Probab=24.44 E-value=2.3e+02 Score=19.07 Aligned_cols=52 Identities=23% Similarity=0.258 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HH-HhhccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 035000 17 TLSVFMLAIGLFVTASFFIY-EA-TSSRQNRSLGKELITGAVASVFLGFGSLFLLLAS 72 (76)
Q Consensus 17 ~la~~lL~igl~~~~~F~i~-~v-t~~k~~r~l~ke~~la~~ASlflGfG~vFl~l~~ 72 (76)
+...++..+|..+++.-++. -. .-.++.|+ .....+++++-.++.++++.+.
T Consensus 115 ~~~~~l~~ia~~~t~l~~~~~~~~~~~~~~~~----~~~~~~~~~~s~~a~~~~lva~ 168 (212)
T PF06687_consen 115 KAMFILYPIAIVFTFLALILSGLLAFFSRPRN----TILSLVASILSLLAFIFLLVAA 168 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHccchh----HHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777777776666654 22 11122232 3333444444444444444443
No 51
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=24.27 E-value=2.1e+02 Score=20.34 Aligned_cols=28 Identities=32% Similarity=0.504 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHH
Q 035000 23 LAIGLFVTASFFIYEATSSRQNRSLGKELITGAV 56 (76)
Q Consensus 23 L~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ 56 (76)
|++|+...-||. +|++|++.+-.++++.
T Consensus 121 Lal~~~~~iyfl------~~K~~~~~rA~~~~~~ 148 (194)
T PF11833_consen 121 LALGLGACIYFL------NRKERKLGRAFLWTLG 148 (194)
T ss_pred HHHHHHHHHHHH------HHhcchHHHHHHHHHH
Confidence 667777777764 2346777777666543
No 52
>TIGR02897 QoxC cytochrome aa3 quinol oxidase, subunit III. This family (QoxC) encodes subunit III of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site.
Probab=23.71 E-value=2.6e+02 Score=19.37 Aligned_cols=47 Identities=19% Similarity=0.190 Sum_probs=21.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHHHHHH
Q 035000 14 WYPTLSVFMLAIGLFVTASFFIYEATSS-RQNRSLGKELITGAVASVFLG 62 (76)
Q Consensus 14 ~~p~la~~lL~igl~~~~~F~i~~vt~~-k~~r~l~ke~~la~~ASlflG 62 (76)
..+.+...++-..+++++.+.+...... |+++ .++....+.+++.+|
T Consensus 48 ~~~~l~~~~lnT~vLl~SS~~~~~A~~a~~~~~--~~~~~~~L~~tl~lG 95 (190)
T TIGR02897 48 ELFELPLVLIMTFLLLFSSFTCGIAIYEMRKEN--QKLMMFWMIITLLLG 95 (190)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHhCC--HHHHHHHHHHHHHHH
Confidence 3444555555556666666554333222 2111 244555555555444
No 53
>PF13974 YebO: YebO-like protein
Probab=23.66 E-value=1.2e+02 Score=19.06 Aligned_cols=17 Identities=18% Similarity=0.237 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q 035000 21 FMLAIGLFVTASFFIYE 37 (76)
Q Consensus 21 ~lL~igl~~~~~F~i~~ 37 (76)
.++.+=+.++.|||+-.
T Consensus 4 ~~~~~lv~livWFFVnR 20 (80)
T PF13974_consen 4 SVLVLLVGLIVWFFVNR 20 (80)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 34444456789999744
No 54
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=22.75 E-value=85 Score=22.03 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccchhHHHH
Q 035000 19 SVFMLAIGLFVTASFFIYEATSSRQNRSLGKE 50 (76)
Q Consensus 19 a~~lL~igl~~~~~F~i~~vt~~k~~r~l~ke 50 (76)
-.++.++..+.+.||.+..+-..|++|+--|+
T Consensus 98 ~~Vl~g~s~l~i~yfvir~~R~r~~~rktRkY 129 (163)
T PF06679_consen 98 LYVLVGLSALAILYFVIRTFRLRRRNRKTRKY 129 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccccccceee
Confidence 36667777778888887766655545544343
No 55
>PF10966 DUF2768: Protein of unknown function (DUF2768); InterPro: IPR020076 This entry contains proteins with no known function.
Probab=21.06 E-value=2e+02 Score=17.09 Aligned_cols=44 Identities=25% Similarity=0.275 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHH
Q 035000 21 FMLAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASVFLGFGSL 66 (76)
Q Consensus 21 ~lL~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflGfG~v 66 (76)
.+..+|+++.+...+|- .+.| .++=.-+.+++.+|=+.+.+|.+
T Consensus 5 S~~~iglMfisv~~i~~-sR~K-lk~~~lk~i~~~vAy~lli~~gl 48 (58)
T PF10966_consen 5 SFGAIGLMFISVILIYF-SRYK-LKGKFLKFIVSLVAYILLIVSGL 48 (58)
T ss_pred HHHHHHHHHHHHHHHHH-HHHH-HhChHHHHHHHHHHHHHHHHHHH
Confidence 45678888888887643 2333 23324445667777777766653
No 56
>PRK12666 putative monovalent cation/H+ antiporter subunit D; Reviewed
Probab=20.87 E-value=2.8e+02 Score=22.25 Aligned_cols=28 Identities=18% Similarity=0.021 Sum_probs=22.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 035000 44 NRSLGKELITGAVASVFLGFGSLFLLLA 71 (76)
Q Consensus 44 ~r~l~ke~~la~~ASlflGfG~vFl~l~ 71 (76)
.|.-.|+.++..++|.++=+|..++...
T Consensus 158 ~~aa~kY~i~~~vgs~~lL~gi~~ly~~ 185 (528)
T PRK12666 158 VRAGLHYVAINLVASSLFLIGVGLIYGV 185 (528)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998888766443
No 57
>cd02434 Nodulin-21_like_3 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_3: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=20.58 E-value=3.3e+02 Score=19.49 Aligned_cols=48 Identities=29% Similarity=0.270 Sum_probs=25.3
Q ss_pred HHHHH-HHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH-HHHHHHH
Q 035000 18 LSVFM-LAIGLFVTASFFIYEATSSRQNRSLGKELITGAVASV-FLGFGSL 66 (76)
Q Consensus 18 la~~l-L~igl~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASl-flGfG~v 66 (76)
.++.+ ..++++..+++- -..+..+.-|+-.+-++++..|.. ..++|.+
T Consensus 174 ~s~~~~~~~~L~~~G~~~-~~~~~~~~~~~~l~~~~~G~~aa~~ty~iG~l 223 (225)
T cd02434 174 LSILIFVAFTLFLLGSFK-SKLYNGKWIISGIIMLINGAASGGVSFFLGVL 223 (225)
T ss_pred HHHHHHHHHHHHHHHHHH-HHhcCCchHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34444 566666666664 223333334566666666666543 3455544
No 58
>TIGR03867 MprA_tail MprA protease C-terminal sorting domain. This model describes a protein C-terminal domain that occurs in species of the genus Ralstonia and is predicted to play a role in protein targeting. This sequence, though limited to members of the MprA serine in species distribution, resembles C-terminal sorting sequences of the sortase and exosortase systems, as well as a Shewanella-type C-terminal sequence modeled by TIGR03501. For all such cases, member proteins have homologs in other species with essentially full-length homology, save for the lack of the domain modeled here. All members of the present family are predicted serine proteases
Probab=20.57 E-value=1.2e+02 Score=15.55 Aligned_cols=14 Identities=43% Similarity=0.691 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHH
Q 035000 16 PTLSVFMLAIGLFV 29 (76)
Q Consensus 16 p~la~~lL~igl~~ 29 (76)
|..|..++++|++-
T Consensus 8 ~~~A~Lll~aG~~~ 21 (27)
T TIGR03867 8 PWLAALLLAAGLLG 21 (27)
T ss_pred HHHHHHHHHHHhhh
Confidence 78889999998864
No 59
>PF14007 YtpI: YtpI-like protein
Probab=20.56 E-value=2.4e+02 Score=17.88 Aligned_cols=36 Identities=17% Similarity=0.304 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHH
Q 035000 27 LFVTASFFIYEATSSRQNRSLGKELITGAVASVFLG 62 (76)
Q Consensus 27 l~~~~~F~i~~vt~~k~~r~l~ke~~la~~ASlflG 62 (76)
+.++..|.+|--++..++++...--..+.=+++.+|
T Consensus 5 Ii~S~~~yvy~k~k~~Rs~~p~~k~~~~aka~ialG 40 (89)
T PF14007_consen 5 IIISLVFYVYYKIKYFRSKDPMEKKWYSAKANIALG 40 (89)
T ss_pred HHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Confidence 334444444444544444444444444555555555
No 60
>PRK00968 tetrahydromethanopterin S-methyltransferase subunit D; Provisional
Probab=20.24 E-value=3.1e+02 Score=20.62 Aligned_cols=26 Identities=19% Similarity=0.359 Sum_probs=19.9
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHH
Q 035000 42 RQNRSLGKELITGAVASVFLGFGSLFL 68 (76)
Q Consensus 42 k~~r~l~ke~~la~~ASlflGfG~vFl 68 (76)
|+ +++-|-.+-+.+||+.+|+=.+-+
T Consensus 211 KF-Kr~p~~vias~vaS~~~gii~v~~ 236 (240)
T PRK00968 211 KF-KRWPRAVIASFVASLVCGIVAVLM 236 (240)
T ss_pred cc-ccchHHHHHHHHHHHHHHHHHHHH
Confidence 54 677888999999999998755443
Done!