Query 045035
Match_columns 95
No_of_seqs 137 out of 1170
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:15:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045035.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045035hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0537 Cytochrome b5 [Energy 99.8 4.4E-20 9.6E-25 127.9 0.1 84 1-92 29-122 (124)
2 PF00173 Cyt-b5: Cytochrome b5 99.2 8.7E-13 1.9E-17 81.7 -1.4 37 1-37 24-60 (76)
3 KOG0536 Flavohemoprotein b5+b5 99.1 1.2E-11 2.5E-16 87.5 0.9 36 1-37 92-127 (145)
4 COG5274 CYB5 Cytochrome b invo 99.1 2.9E-11 6.3E-16 87.6 0.2 37 1-37 74-110 (164)
5 KOG4232 Delta 6-fatty acid des 99.0 1.6E-10 3.5E-15 93.6 3.6 44 1-45 31-86 (430)
6 PLN03199 delta6-acyl-lipid des 99.0 1.2E-10 2.6E-15 95.0 2.6 44 1-47 48-101 (485)
7 PLN03198 delta6-acyl-lipid des 99.0 9E-11 2E-15 97.0 0.6 43 1-45 128-180 (526)
8 PLN02252 nitrate reductase [NA 99.0 1.7E-10 3.6E-15 100.2 2.2 46 1-47 542-597 (888)
9 KOG4576 Sulfite oxidase, heme- 98.4 3.7E-08 8.1E-13 70.4 -1.3 46 1-48 105-163 (167)
10 PF11698 V-ATPase_H_C: V-ATPas 67.2 0.51 1.1E-05 32.6 -2.7 24 2-25 66-89 (119)
11 KOG1110 Putative steroid membr 57.9 8.8 0.00019 28.5 2.2 30 1-32 83-113 (183)
12 cd00256 VATPase_H VATPase_H, r 57.8 2.4 5.3E-05 34.9 -0.8 33 2-36 376-408 (429)
13 PRK14758 hypothetical protein; 56.4 22 0.00049 18.6 3.0 19 74-92 8-26 (27)
14 COG4892 Predicted heme/steroid 56.1 5.3 0.00011 25.9 0.7 28 1-33 27-58 (81)
15 PRK10920 putative uroporphyrin 55.3 24 0.00051 28.9 4.5 19 75-93 41-59 (390)
16 KOG2759 Vacuolar H+-ATPase V1 54.3 4.3 9.4E-05 33.8 0.1 34 2-37 389-422 (442)
17 PHA02844 putative transmembran 52.6 26 0.00057 22.5 3.5 11 82-92 59-69 (75)
18 PF04375 HemX: HemX; InterPro 52.1 50 0.0011 26.4 5.8 10 82-91 41-50 (372)
19 COG3424 BcsA Predicted naringe 46.5 9.7 0.00021 30.9 1.0 20 3-23 270-289 (356)
20 PHA02819 hypothetical protein; 45.1 40 0.00088 21.5 3.4 12 82-93 57-68 (71)
21 COG3088 CcmH Uncharacterized p 44.9 32 0.0007 24.9 3.4 18 71-88 105-122 (153)
22 COG3197 FixS Uncharacterized p 44.8 19 0.00042 22.1 1.9 16 73-88 4-19 (58)
23 PF02797 Chal_sti_synt_C: Chal 44.7 10 0.00022 26.7 0.8 15 8-22 63-77 (151)
24 PHA02650 hypothetical protein; 44.5 54 0.0012 21.4 4.0 11 82-92 60-70 (81)
25 PF14283 DUF4366: Domain of un 44.3 23 0.00049 26.7 2.6 9 84-92 172-180 (218)
26 PF12652 CotJB: CotJB protein; 44.3 8.2 0.00018 24.8 0.2 39 2-44 16-59 (78)
27 PF07533 BRK: BRK domain; Int 44.0 3.3 7.1E-05 24.1 -1.5 11 3-13 29-39 (46)
28 TIGR03147 cyt_nit_nrfF cytochr 43.9 35 0.00076 23.8 3.3 16 72-87 102-117 (126)
29 PF02046 COX6A: Cytochrome c o 40.1 1E+02 0.0023 21.0 5.2 26 64-89 40-66 (116)
30 TIGR00847 ccoS cytochrome oxid 39.6 56 0.0012 19.4 3.3 11 73-83 4-14 (51)
31 PRK10807 paraquat-inducible pr 39.0 33 0.00072 29.0 3.0 21 73-93 19-41 (547)
32 PRK07021 fliL flagellar basal 38.9 65 0.0014 22.6 4.2 7 87-93 35-41 (162)
33 TIGR03068 srtB_sig_NPQTN sorta 38.2 40 0.00087 18.5 2.3 10 73-82 11-20 (33)
34 TIGR03521 GldG gliding-associa 36.9 48 0.001 27.8 3.7 29 66-94 521-549 (552)
35 PF15086 UPF0542: Uncharacteri 36.7 81 0.0018 20.3 3.9 25 66-90 20-44 (74)
36 PF03597 CcoS: Cytochrome oxid 35.4 65 0.0014 18.5 3.0 10 73-82 3-12 (45)
37 KOG1108 Predicted heme/steroid 35.3 9.5 0.00021 29.8 -0.7 31 1-33 87-118 (281)
38 smart00592 BRK domain in trans 35.2 8.1 0.00018 22.3 -0.8 12 3-14 27-38 (45)
39 PF07423 DUF1510: Protein of u 33.7 53 0.0011 24.9 3.1 21 72-92 15-36 (217)
40 PF10661 EssA: WXG100 protein 33.4 45 0.00098 23.5 2.6 14 80-93 128-141 (145)
41 PTZ00208 65 kDa invariant surf 33.2 38 0.00083 28.3 2.5 19 72-90 389-407 (436)
42 PF12575 DUF3753: Protein of u 31.5 96 0.0021 19.8 3.6 7 86-92 63-69 (72)
43 PRK10144 formate-dependent nit 31.3 69 0.0015 22.4 3.2 14 72-85 102-115 (126)
44 PF03918 CcmH: Cytochrome C bi 30.9 16 0.00035 25.8 0.0 18 72-89 102-119 (148)
45 PRK13415 flagella biosynthesis 30.8 1.7E+02 0.0037 22.3 5.5 9 72-80 68-76 (219)
46 PF01708 Gemini_mov: Geminivir 30.2 28 0.00061 23.2 1.0 29 65-93 30-60 (91)
47 KOG4827 Uncharacterized conser 28.9 29 0.00062 26.7 1.0 21 64-84 237-257 (279)
48 PF11346 DUF3149: Protein of u 28.5 98 0.0021 17.6 3.0 22 72-93 13-35 (42)
49 PF09451 ATG27: Autophagy-rela 28.4 1.5E+02 0.0032 22.5 4.9 11 73-83 203-213 (268)
50 PHA03054 IMV membrane protein; 28.1 1.4E+02 0.003 19.1 3.9 13 81-93 58-70 (72)
51 cd00925 Cyt_c_Oxidase_VIa Cyto 27.6 1.2E+02 0.0026 19.8 3.7 24 66-89 13-37 (86)
52 PHA02975 hypothetical protein; 25.5 1.2E+02 0.0027 19.2 3.3 13 81-93 54-66 (69)
53 PHA03240 envelope glycoprotein 25.3 85 0.0018 24.4 3.0 18 73-90 213-230 (258)
54 PF04246 RseC_MucC: Positive r 24.3 1.9E+02 0.0041 19.4 4.3 14 70-83 70-83 (135)
55 PF05283 MGC-24: Multi-glycosy 23.4 2.4E+02 0.0052 20.9 5.0 20 73-92 165-184 (186)
56 PF14756 Pdase_C33_assoc: Pept 23.3 8.5 0.00018 27.2 -2.5 24 1-24 51-74 (147)
57 PF11694 DUF3290: Protein of u 23.0 1.5E+02 0.0033 21.0 3.8 13 81-93 27-39 (149)
58 PF02419 PsbL: PsbL protein; 22.9 1.5E+02 0.0034 16.5 3.2 19 73-91 17-36 (37)
59 PF13260 DUF4051: Protein of u 21.5 1.3E+02 0.0029 18.0 2.7 15 74-90 6-20 (54)
No 1
>KOG0537 consensus Cytochrome b5 [Energy production and conversion]
Probab=99.77 E-value=4.4e-20 Score=127.90 Aligned_cols=84 Identities=45% Similarity=0.664 Sum_probs=59.9
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC----------CCCCCCCCCCCCCCCCCCCCCCCcCCCChhHHH
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP----------IGEIDVSTIPKKKVCTPPKQPHYNQDKTSEFII 70 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~----------VG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 (95)
|||||+|+++||||.++|+++||||||+.|++++||. ||+|.+.+.+...... +....+ ...
T Consensus 29 VYDvT~Fl~eHPGG~~vLl~~AGkDaT~~F~~~gHS~~A~~ml~~y~ig~~~~~~~~~~~~~~----~~~~~~----~~~ 100 (124)
T KOG0537|consen 29 VYDVTSFLDEHPGGEDVLLEYAGKDATEAFEDVGHSKDAREMLEEYYIGEVPTTARPVVWSNT----AGYEVD----RLT 100 (124)
T ss_pred EEeccchhhhCCChHHHHHHHhchhhHHhccccCCcHHHHHHhhhcccccccCCCccceeccc----cccccc----ccc
Confidence 7999999999999999999999999999999999999 9999988765543322 000101 111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 045035 71 RLLQFLVPLAILGLAVGIRIYT 92 (95)
Q Consensus 71 ~~~~~~vpl~~~~~~~~~~~~~ 92 (95)
....+.++++++.++..++.+.
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~ 122 (124)
T KOG0537|consen 101 VSGGLLVAILILPLQEHILGLT 122 (124)
T ss_pred ccccceeeeeechhhhhhhhcc
Confidence 1233556666666665555554
No 2
>PF00173 Cyt-b5: Cytochrome b5-like Heme/Steroid binding domain This prints entry is a subset of the Pfam entry; InterPro: IPR001199 Cytochromes b5 are ubiquitous electron transport proteins found in animals, plants and yeasts []. The microsomal and mitochondrial variants are membrane-bound, while those from erythrocytes and other animal tissues are water-soluble [, ]. The 3D structure of bovine cyt b5 is known, the fold belonging to the alpha+beta class, with 5 strands and 5 short helices forming a framework for supporting a central haem group []. The cytochrome b5 domain is similar to that of a number of oxidoreductases, such as plant and fungal nitrate reductases, sulphite oxidase, yeast flavocytochrome b2 (L-lactate dehydrogenase) and plant cyt b5/acyl lipid desaturase fusion protein.; GO: 0020037 heme binding; PDB: 2I96_A 3KS0_A 1KBI_B 1KBJ_B 1LTD_A 1SZG_B 1SZF_A 1LDC_B 2OZ0_B 1LCO_A ....
Probab=99.21 E-value=8.7e-13 Score=81.73 Aligned_cols=37 Identities=51% Similarity=0.902 Sum_probs=32.8
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP 37 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~ 37 (95)
|||||+|+..||||.++|..++|+|+|+.|....|+.
T Consensus 24 VYDvt~~~~~hpgg~~~~~~~aG~D~T~~f~~~~h~~ 60 (76)
T PF00173_consen 24 VYDVTDFLDRHPGGADILKKYAGRDATDAFEEAFHSW 60 (76)
T ss_dssp EEECTTTTTTSTTTSHHHHTTTTSBTHHHHHHHTHHH
T ss_pred EcccccccccccchhHHHHHhccccccHHHhhccCcH
Confidence 7999999999999999999999999999993333754
No 3
>KOG0536 consensus Flavohemoprotein b5+b5R [Energy production and conversion]
Probab=99.13 E-value=1.2e-11 Score=87.53 Aligned_cols=36 Identities=42% Similarity=0.721 Sum_probs=34.9
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP 37 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~ 37 (95)
|||||.||+.||||...|++++|+|+|..|+.+ |.+
T Consensus 92 VYnVt~Yl~fHPgG~d~lmk~aGrD~T~~Fnk~-H~W 127 (145)
T KOG0536|consen 92 VYNVTAYLDFHPGGVDELMKHAGRDATKLFNKY-HAW 127 (145)
T ss_pred EEecccccccCCCCHHHHHHhcCcchHHHHHHH-HHH
Confidence 799999999999999999999999999999999 877
No 4
>COG5274 CYB5 Cytochrome b involved in lipid metabolism [Energy production and conversion / Lipid metabolism]
Probab=99.05 E-value=2.9e-11 Score=87.57 Aligned_cols=37 Identities=46% Similarity=0.923 Sum_probs=35.6
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP 37 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~ 37 (95)
|||||.|+++||||+.+|+.++|+|||..|+..+|+.
T Consensus 74 VyDvs~fl~~HPGGe~ii~~~~g~Dat~~f~~~~~~~ 110 (164)
T COG5274 74 VYDVSQFLDEHPGGEDIIKDTAGKDATKAFNFLHHSH 110 (164)
T ss_pred EEEhhhccccCCCcceeehhccCchhhhhhcccccch
Confidence 7999999999999999999999999999999998866
No 5
>KOG4232 consensus Delta 6-fatty acid desaturase/delta-8 sphingolipid desaturase [Lipid transport and metabolism]
Probab=99.03 E-value=1.6e-10 Score=93.62 Aligned_cols=44 Identities=41% Similarity=0.814 Sum_probs=40.3
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC------------CCCCCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP------------IGEIDVST 45 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~------------VG~l~~~~ 45 (95)
|||+|+|++.||||+.+|..++|.|||++|+.. |.. +|+..++.
T Consensus 31 vYd~s~~~~~HPGG~~~I~~~~g~DaTdaF~Af-H~~~~~~~~~l~~l~~~~~~pe~ 86 (430)
T KOG4232|consen 31 VYDISDWIKRHPGGSRVIEHYAGQDATDAFEAF-HPGTAFAYKHLKPLLIGELSPEI 86 (430)
T ss_pred cccHHHHHHhCCCchhHHHHhcCCccchHHHHh-CCChHHHHHHHHHHHcCCcCccc
Confidence 899999999999999999999999999999999 866 77777764
No 6
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=99.02 E-value=1.2e-10 Score=95.02 Aligned_cols=44 Identities=41% Similarity=0.804 Sum_probs=39.0
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC----------CCCCCCCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP----------IGEIDVSTIP 47 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~----------VG~l~~~~~~ 47 (95)
|||||+|+ +||||+ +|+.++|+|||+.|+.. ||. ||+|++++.+
T Consensus 48 vYDvt~f~-~HPGG~-~i~~~aG~DaT~~F~~~-H~~~~~~~l~~~~iG~l~~~~~~ 101 (485)
T PLN03199 48 VYDVSNWH-DHPGGA-VIFTHAGDDMTDIFAAF-HAPGSQALMKKFYIGDLIPESTE 101 (485)
T ss_pred EEcCCCcC-cCCCch-HHHhhCCCChhHHHHHh-cCHHHHHHHHhcccccccccccc
Confidence 79999997 899997 88899999999999998 975 9999776543
No 7
>PLN03198 delta6-acyl-lipid desaturase; Provisional
Probab=98.99 E-value=9e-11 Score=97.01 Aligned_cols=43 Identities=42% Similarity=0.852 Sum_probs=39.2
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC----------CCCCCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP----------IGEIDVST 45 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~----------VG~l~~~~ 45 (95)
|||+|+|+++||||+ +|+.++|+|||+.|+.. |+. ||+|++.+
T Consensus 128 VYDvT~fl~~HPGG~-~i~~~aG~DaT~~F~~~-H~~~~~~~l~~~~IG~l~~~~ 180 (526)
T PLN03198 128 VYDVSDFAAEHPGGS-VISTYFGRDGTDAFSSF-HAASTWKILQDFYIGDVDNVE 180 (526)
T ss_pred EEecHHHHHhCCCch-HHHHhcCCcHhHHHHHh-cCHHHHHHHhhCcceecCCcc
Confidence 799999999999997 89999999999999999 875 99997643
No 8
>PLN02252 nitrate reductase [NADPH]
Probab=98.99 E-value=1.7e-10 Score=100.21 Aligned_cols=46 Identities=43% Similarity=0.866 Sum_probs=42.2
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC----------CCCCCCCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP----------IGEIDVSTIP 47 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~----------VG~l~~~~~~ 47 (95)
|||+|+|++.||||.++|+.++|+|||+.|+.+ ||. ||+|......
T Consensus 542 VYDvT~fl~~HPGG~~~I~~~aG~DaT~~F~~~-Hs~~a~~~L~~~~IG~l~~~~~~ 597 (888)
T PLN02252 542 VYDCTRFLKDHPGGADSILINAGTDCTEEFDAI-HSDKAKKMLEDYRIGELVTTGAA 597 (888)
T ss_pred EEeCHHHHHHCCChHHHHHhhcCCCcHHHHhhh-hhHHHHHHHHhCcCCcccccccc
Confidence 799999999999999999999999999999998 886 9999876543
No 9
>KOG4576 consensus Sulfite oxidase, heme-binding component [Energy production and conversion]
Probab=98.37 E-value=3.7e-08 Score=70.42 Aligned_cols=46 Identities=41% Similarity=0.801 Sum_probs=35.9
Q ss_pred CcccccCcccCCChHHHHHhhcCCCcchhhhhc--CCCC-----------CCCCCCCCCCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGKDATDDFEDV--GHSP-----------IGEIDVSTIPK 48 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~--~Hs~-----------VG~l~~~~~~~ 48 (95)
|||||+|++.||||+++|+. ||. +.+.|+.. .|.. ||+|.+.+.++
T Consensus 105 VyDVTdFv~~HPGGdKillA-AG~-a~dPFWalY~qHnt~eVlElLegyrIG~L~~~dv~~ 163 (167)
T KOG4576|consen 105 VYDVTDFVDLHPGGDKILLA-AGG-ALDPFWALYAQHNTSEVLELLEGYRIGELNPEDVVA 163 (167)
T ss_pred ceeHHHHHHhCCCcceeeee-cCC-CcCcHHHHHHHhhHHHHHHHHhhcccccCChhhccc
Confidence 89999999999999765554 453 78888877 3433 99999887654
No 10
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 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 []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=67.19 E-value=0.51 Score=32.65 Aligned_cols=24 Identities=17% Similarity=0.484 Sum_probs=20.5
Q ss_pred cccccCcccCCChHHHHHhhcCCC
Q 045035 2 YEVTKFLEDHPGGDEVFLSVTGKD 25 (95)
Q Consensus 2 YDvt~fl~~HPGG~~vi~~~aGkD 25 (95)
+|+..|+..||.|..+|....+|+
T Consensus 66 ~Dig~~vr~~p~gr~ii~~lg~K~ 89 (119)
T PF11698_consen 66 HDIGEFVRHYPNGRNIIEKLGAKE 89 (119)
T ss_dssp HHHHHHHHH-GGGHHHHHHHSHHH
T ss_pred cchHHHHHHChhHHHHHHhcChHH
Confidence 799999999999999998887764
No 11
>KOG1110 consensus Putative steroid membrane receptor Hpr6.6/25-Dx [General function prediction only]
Probab=57.93 E-value=8.8 Score=28.54 Aligned_cols=30 Identities=40% Similarity=0.546 Sum_probs=21.1
Q ss_pred CcccccCcc-cCCChHHHHHhhcCCCcchhhhh
Q 045035 1 VYEVTKFLE-DHPGGDEVFLSVTGKDATDDFED 32 (95)
Q Consensus 1 VYDvt~fl~-~HPGG~~vi~~~aGkDaT~~f~~ 32 (95)
|||||+=-. .=|||.- -.+||+||+.....
T Consensus 83 VYDVT~Gr~FYGp~GpY--~~fAG~DASR~La~ 113 (183)
T KOG1110|consen 83 VYDVTRGREFYGPGGPY--SLFAGKDASRGLAK 113 (183)
T ss_pred EEEecCCccccCCCCCc--hhhcccchHHHHHh
Confidence 789986221 5788874 45799999876543
No 12
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=57.81 E-value=2.4 Score=34.94 Aligned_cols=33 Identities=18% Similarity=0.413 Sum_probs=25.8
Q ss_pred cccccCcccCCChHHHHHhhcCCCcchhhhhcCCC
Q 045035 2 YEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHS 36 (95)
Q Consensus 2 YDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs 36 (95)
+|+..|+..||.|..++.+..||+. .++=.+|+
T Consensus 376 ~Dige~vr~~P~gr~i~~~lg~K~~--vM~Lm~h~ 408 (429)
T cd00256 376 HDIGEYVRHYPRGKDVVEQLGGKQR--VMRLLNHE 408 (429)
T ss_pred hhHHHHHHHCccHHHHHHHcCcHHH--HHHHhcCC
Confidence 7999999999999999999988754 33333453
No 13
>PRK14758 hypothetical protein; Provisional
Probab=56.40 E-value=22 Score=18.60 Aligned_cols=19 Identities=26% Similarity=0.543 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 045035 74 QFLVPLAILGLAVGIRIYT 92 (95)
Q Consensus 74 ~~~vpl~~~~~~~~~~~~~ 92 (95)
.+++.++|+++.++.++|.
T Consensus 8 EliLivlIlCalia~~fy~ 26 (27)
T PRK14758 8 EFILIILILCALIAARFYL 26 (27)
T ss_pred HHHHHHHHHHHHHHHHhcc
Confidence 4555666677767888775
No 14
>COG4892 Predicted heme/steroid binding protein [General function prediction only]
Probab=56.12 E-value=5.3 Score=25.86 Aligned_cols=28 Identities=32% Similarity=0.544 Sum_probs=18.4
Q ss_pred CcccccCcc----cCCChHHHHHhhcCCCcchhhhhc
Q 045035 1 VYEVTKFLE----DHPGGDEVFLSVTGKDATDDFEDV 33 (95)
Q Consensus 1 VYDvt~fl~----~HPGG~~vi~~~aGkDaT~~f~~~ 33 (95)
||||+.=-. .|-|+ .-+|+|.++.|+.-
T Consensus 27 VYDvS~s~~W~dGtHqgl-----hsaG~DLs~~~~~~ 58 (81)
T COG4892 27 VYDVSLSPSWGDGTHQGL-----HSAGKDLSSEFNSC 58 (81)
T ss_pred EEeeccCcccCCCccccc-----cccchhHHHHHhhc
Confidence 678875322 34443 34799999999865
No 15
>PRK10920 putative uroporphyrinogen III C-methyltransferase; Provisional
Probab=55.33 E-value=24 Score=28.87 Aligned_cols=19 Identities=11% Similarity=0.079 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 045035 75 FLVPLAILGLAVGIRIYTR 93 (95)
Q Consensus 75 ~~vpl~~~~~~~~~~~~~~ 93 (95)
.++.+++++++.++|||..
T Consensus 41 ~~aili~la~g~g~y~~~~ 59 (390)
T PRK10920 41 AVAIAIALAAGAGLYYHGK 59 (390)
T ss_pred HHHHHHHHHHhhHHHHHHH
Confidence 3444445677777777753
No 16
>KOG2759 consensus Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=54.30 E-value=4.3 Score=33.81 Aligned_cols=34 Identities=18% Similarity=0.366 Sum_probs=27.6
Q ss_pred cccccCcccCCChHHHHHhhcCCCcchhhhhcCCCC
Q 045035 2 YEVTKFLEDHPGGDEVFLSVTGKDATDDFEDVGHSP 37 (95)
Q Consensus 2 YDvt~fl~~HPGG~~vi~~~aGkDaT~~f~~~~Hs~ 37 (95)
.|++.|...||.|..++..+.||. ..++-.+|++
T Consensus 389 ~DIge~Vr~yP~gk~vv~k~ggKe--~vM~Llnh~d 422 (442)
T KOG2759|consen 389 HDIGEYVRHYPEGKAVVEKYGGKE--RVMNLLNHED 422 (442)
T ss_pred hhHHHHHHhCchHhHHHHHhchHH--HHHHHhcCCC
Confidence 599999999999999999999984 4455556643
No 17
>PHA02844 putative transmembrane protein; Provisional
Probab=52.62 E-value=26 Score=22.54 Aligned_cols=11 Identities=9% Similarity=-0.082 Sum_probs=5.1
Q ss_pred HHHHHHHHHHh
Q 045035 82 LGLAVGIRIYT 92 (95)
Q Consensus 82 ~~~~~~~~~~~ 92 (95)
+++++..++|.
T Consensus 59 ~~~~~~~flYL 69 (75)
T PHA02844 59 VFATFLTFLYL 69 (75)
T ss_pred HHHHHHHHHHH
Confidence 34444444554
No 18
>PF04375 HemX: HemX; InterPro: IPR007470 The majority of proteins in this family are annotated as uroporphyrin-III C-methyltransferase (2.1.1.107 from EC) []; however, there is no direct evidence to support this annotation for these proteins, which come from mainly pathogenic Gram-negative organisms. There is some evidence to suggest that the proteins are membrane anchored as they have a predicted N-terminal signal peptide and transmembrane domain and may be involved in haem transport [].
Probab=52.11 E-value=50 Score=26.36 Aligned_cols=10 Identities=30% Similarity=0.435 Sum_probs=5.9
Q ss_pred HHHHHHHHHH
Q 045035 82 LGLAVGIRIY 91 (95)
Q Consensus 82 ~~~~~~~~~~ 91 (95)
++++.++|+|
T Consensus 41 ~alg~~~~~~ 50 (372)
T PF04375_consen 41 LALGAGGWYW 50 (372)
T ss_pred HHHHHHHHHH
Confidence 5555566665
No 19
>COG3424 BcsA Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=46.47 E-value=9.7 Score=30.88 Aligned_cols=20 Identities=25% Similarity=0.577 Sum_probs=15.2
Q ss_pred ccccCcccCCChHHHHHhhcC
Q 045035 3 EVTKFLEDHPGGDEVFLSVTG 23 (95)
Q Consensus 3 Dvt~fl~~HPGG~~vi~~~aG 23 (95)
|+.-|+ -||||.+||..+.+
T Consensus 270 dI~~w~-~HPGG~KVida~~~ 289 (356)
T COG3424 270 DIEAWV-VHPGGPKVIDAYEE 289 (356)
T ss_pred hhceee-eCCCCchHHHHHHH
Confidence 455555 69999999988754
No 20
>PHA02819 hypothetical protein; Provisional
Probab=45.12 E-value=40 Score=21.48 Aligned_cols=12 Identities=17% Similarity=0.204 Sum_probs=5.5
Q ss_pred HHHHHHHHHHhc
Q 045035 82 LGLAVGIRIYTR 93 (95)
Q Consensus 82 ~~~~~~~~~~~~ 93 (95)
+.+++..++|.|
T Consensus 57 ~~~~~~~flYLK 68 (71)
T PHA02819 57 VFVIIFIIFYLK 68 (71)
T ss_pred HHHHHHHHHHHH
Confidence 334445555543
No 21
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=44.93 E-value=32 Score=24.90 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 045035 71 RLLQFLVPLAILGLAVGI 88 (95)
Q Consensus 71 ~~~~~~vpl~~~~~~~~~ 88 (95)
++.-|..|++++.+++..
T Consensus 105 T~lLW~~Pv~llllG~~~ 122 (153)
T COG3088 105 TLLLWGLPVVLLLLGGVL 122 (153)
T ss_pred HHHHHHhHHHHHHHHHHH
Confidence 356799999966555543
No 22
>COG3197 FixS Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]
Probab=44.84 E-value=19 Score=22.08 Aligned_cols=16 Identities=50% Similarity=0.735 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 045035 73 LQFLVPLAILGLAVGI 88 (95)
Q Consensus 73 ~~~~vpl~~~~~~~~~ 88 (95)
++++||+.+++++++.
T Consensus 4 l~~Lipvsi~l~~v~l 19 (58)
T COG3197 4 LYILIPVSILLGAVGL 19 (58)
T ss_pred eeeHHHHHHHHHHHHH
Confidence 4577888865544433
No 23
>PF02797 Chal_sti_synt_C: Chalcone and stilbene synthases, C-terminal domain; InterPro: IPR012328 Synonym(s): Chalcone synthase, Flavonone synthase, 6'-deoxychalcone synthase Naringenin-chalcone synthases (2.3.1.74 from EC) and stilbene synthases (STS) (formerly known as resveratrol synthases) are related plant enzymes. CHS is an important enzyme in flavanoid biosynthesis and STS is a key enzyme in stilbene-type phyloalexin biosynthesis. Both enzymes catalyze the addition of three molecules of malonyl-CoA to a starter CoA ester (a typical example is 4-coumaroyl-CoA), producing either a chalcone (with CHS) or stilbene (with STS) []. These enzymes have a conserved cysteine residue, located in the central section of the protein sequence, which is essential for the catalytic activity of both enzymes and probably represents the binding site for the 4-coumaryl-CoA group []. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 3OV2_A 3OV3_B 1Z1F_A 1Z1E_A 3ALE_C 3OIT_A 2H84_A 1TEE_D 1TED_A 2P0U_A ....
Probab=44.68 E-value=10 Score=26.74 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=10.5
Q ss_pred cccCCChHHHHHhhc
Q 045035 8 LEDHPGGDEVFLSVT 22 (95)
Q Consensus 8 l~~HPGG~~vi~~~a 22 (95)
---||||.+||....
T Consensus 63 wavHPGG~~ILd~v~ 77 (151)
T PF02797_consen 63 WAVHPGGRKILDAVE 77 (151)
T ss_dssp EEEE-SSHHHHHHHH
T ss_pred eeecCChHHHHHHHH
Confidence 346999999987664
No 24
>PHA02650 hypothetical protein; Provisional
Probab=44.48 E-value=54 Score=21.40 Aligned_cols=11 Identities=9% Similarity=-0.245 Sum_probs=4.6
Q ss_pred HHHHHHHHHHh
Q 045035 82 LGLAVGIRIYT 92 (95)
Q Consensus 82 ~~~~~~~~~~~ 92 (95)
+.+++..++|.
T Consensus 60 ~i~~l~~flYL 70 (81)
T PHA02650 60 IIVALFSFFVF 70 (81)
T ss_pred HHHHHHHHHHH
Confidence 33444444443
No 25
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=44.33 E-value=23 Score=26.73 Aligned_cols=9 Identities=22% Similarity=0.331 Sum_probs=3.8
Q ss_pred HHHHHHHHh
Q 045035 84 LAVGIRIYT 92 (95)
Q Consensus 84 ~~~~~~~~~ 92 (95)
++.++++|+
T Consensus 172 ~gGGa~yYf 180 (218)
T PF14283_consen 172 IGGGAYYYF 180 (218)
T ss_pred hhcceEEEE
Confidence 333444444
No 26
>PF12652 CotJB: CotJB protein; InterPro: IPR024207 The cotJ operon proteins affect spore coat composition, and is controlled by sigma E. The genes, which include CotJB, are either required for the normal formation of the inner layers of the coat or are themselves structural components of the coat []. CotJB has been identified as a spore coat protein [].
Probab=44.25 E-value=8.2 Score=24.76 Aligned_cols=39 Identities=18% Similarity=0.380 Sum_probs=27.3
Q ss_pred cccccCcccCCChHHHHHhhc-----CCCcchhhhhcCCCCCCCCCCC
Q 045035 2 YEVTKFLEDHPGGDEVFLSVT-----GKDATDDFEDVGHSPIGEIDVS 44 (95)
Q Consensus 2 YDvt~fl~~HPGG~~vi~~~a-----GkDaT~~f~~~~Hs~VG~l~~~ 44 (95)
.|++=||+-||.-.+.|..+- =+.+...|+.. -|.|...
T Consensus 16 ~dl~LyLDTHP~d~~Al~~y~~~~~~~~~l~~~Ye~~----yGPLt~~ 59 (78)
T PF12652_consen 16 VDLNLYLDTHPDDQEALEYYNEYSKQRKQLKKEYEKR----YGPLTNF 59 (78)
T ss_pred HHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHH----hCCCcCC
Confidence 578889999999998887663 23455667666 5666443
No 27
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=43.96 E-value=3.3 Score=24.06 Aligned_cols=11 Identities=55% Similarity=1.229 Sum_probs=8.4
Q ss_pred ccccCcccCCC
Q 045035 3 EVTKFLEDHPG 13 (95)
Q Consensus 3 Dvt~fl~~HPG 13 (95)
|++.||++|||
T Consensus 29 ~L~~WL~~~P~ 39 (46)
T PF07533_consen 29 ELEEWLEEHPG 39 (46)
T ss_dssp CHHHHHHH-TT
T ss_pred HHHHHHHHCcC
Confidence 57789999997
No 28
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=43.91 E-value=35 Score=23.82 Aligned_cols=16 Identities=44% Similarity=0.617 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 045035 72 LLQFLVPLAILGLAVG 87 (95)
Q Consensus 72 ~~~~~vpl~~~~~~~~ 87 (95)
+..|+.|+++++++++
T Consensus 102 ~~LW~~P~lll~~G~~ 117 (126)
T TIGR03147 102 LLLWLLPVLLLLLAFV 117 (126)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4569999987665543
No 29
>PF02046 COX6A: Cytochrome c oxidase subunit VIa; InterPro: IPR001349 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as VIa in vertebrates and fungi. Mammals have two tissue-specific isoforms of VIa, a liver and a heart form. Only one form is found in fish [].; GO: 0004129 cytochrome-c oxidase activity, 0005743 mitochondrial inner membrane, 0005751 mitochondrial respiratory chain complex IV; PDB: 2DYR_G 2EIM_G 2Y69_T 1OCC_G 3AG4_G 3AG2_G 3ASN_G 3ABL_G 1V55_T 2EIJ_T ....
Probab=40.06 E-value=1e+02 Score=21.02 Aligned_cols=26 Identities=15% Similarity=0.232 Sum_probs=16.4
Q ss_pred CChhHHHHHHHH-HHHHHHHHHHHHHH
Q 045035 64 KTSEFIIRLLQF-LVPLAILGLAVGIR 89 (95)
Q Consensus 64 ~~~~~~~~~~~~-~vpl~~~~~~~~~~ 89 (95)
.....|.++..+ .+|+++++...+|+
T Consensus 40 ~~~~~Wk~iS~~v~iP~i~l~~~n~~~ 66 (116)
T PF02046_consen 40 ETAKLWKKISFFVAIPAIALCMLNAYY 66 (116)
T ss_dssp SSHHHHHHHHHHTHHHHHHHHHHHHH-
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346678877664 67877766655553
No 30
>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=39.56 E-value=56 Score=19.38 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=7.3
Q ss_pred HHHHHHHHHHH
Q 045035 73 LQFLVPLAILG 83 (95)
Q Consensus 73 ~~~~vpl~~~~ 83 (95)
.+++||+.++.
T Consensus 4 l~~LIpiSl~l 14 (51)
T TIGR00847 4 LTILIPISLLL 14 (51)
T ss_pred HHHHHHHHHHH
Confidence 56788887533
No 31
>PRK10807 paraquat-inducible protein B; Provisional
Probab=38.96 E-value=33 Score=29.01 Aligned_cols=21 Identities=10% Similarity=0.320 Sum_probs=14.2
Q ss_pred HHHHHHHHH--HHHHHHHHHHhc
Q 045035 73 LQFLVPLAI--LGLAVGIRIYTR 93 (95)
Q Consensus 73 ~~~~vpl~~--~~~~~~~~~~~~ 93 (95)
.-|+||+++ ++++++|+.|..
T Consensus 19 ~iWlvP~~a~~i~~~l~~~~~~~ 41 (547)
T PRK10807 19 PVWIFPIVTALIGAWILFYHFSH 41 (547)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Confidence 359999995 455556666654
No 32
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=38.87 E-value=65 Score=22.62 Aligned_cols=7 Identities=14% Similarity=0.311 Sum_probs=3.5
Q ss_pred HHHHHhc
Q 045035 87 GIRIYTR 93 (95)
Q Consensus 87 ~~~~~~~ 93 (95)
++++|+.
T Consensus 35 g~~~~~~ 41 (162)
T PRK07021 35 GYSWWLS 41 (162)
T ss_pred HHHHHhh
Confidence 4555544
No 33
>TIGR03068 srtB_sig_NPQTN sortase B signal domain, NPQTN class. This model represents one of the boutique (rare) sortase signals, recognized by sortase B (SrtB) rather than by the housekeeping-type SrtA class sortase. This sequence, beginning NPQTN, shows little similarity to several other SrtB substrates.
Probab=38.19 E-value=40 Score=18.47 Aligned_cols=10 Identities=30% Similarity=0.637 Sum_probs=5.9
Q ss_pred HHHHHHHHHH
Q 045035 73 LQFLVPLAIL 82 (95)
Q Consensus 73 ~~~~vpl~~~ 82 (95)
+.++||++.+
T Consensus 11 y~y~Ip~v~l 20 (33)
T TIGR03068 11 YIYAIPVASL 20 (33)
T ss_pred hhhHHHHHHH
Confidence 4466776653
No 34
>TIGR03521 GldG gliding-associated putative ABC transporter substrate-binding component GldG. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldG is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldG abolish the gliding phenotype. GldG, along with GldA and GldF are believed to compose an ABC transporter and are observed as an operon. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=36.87 E-value=48 Score=27.79 Aligned_cols=29 Identities=10% Similarity=-0.049 Sum_probs=17.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 045035 66 SEFIIRLLQFLVPLAILGLAVGIRIYTRS 94 (95)
Q Consensus 66 ~~~~~~~~~~~vpl~~~~~~~~~~~~~~~ 94 (95)
...|.-+..+++|++++++++..++..++
T Consensus 521 ~~~~~~~~i~~pp~~~l~~G~~~~~~Rrr 549 (552)
T TIGR03521 521 RTTWQLINIGLPILLLLLFGLSFTYIRKR 549 (552)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45555444444446677787777766554
No 35
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=36.73 E-value=81 Score=20.25 Aligned_cols=25 Identities=28% Similarity=0.550 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Q 045035 66 SEFIIRLLQFLVPLAILGLAVGIRI 90 (95)
Q Consensus 66 ~~~~~~~~~~~vpl~~~~~~~~~~~ 90 (95)
-++...++..+-|++++++.+.+++
T Consensus 20 ~~Fl~~vll~LtPlfiisa~lSwkL 44 (74)
T PF15086_consen 20 YEFLTTVLLILTPLFIISAVLSWKL 44 (74)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 4555556677888888888777664
No 36
>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=35.39 E-value=65 Score=18.51 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=6.5
Q ss_pred HHHHHHHHHH
Q 045035 73 LQFLVPLAIL 82 (95)
Q Consensus 73 ~~~~vpl~~~ 82 (95)
.++++|+.++
T Consensus 3 l~~lip~sl~ 12 (45)
T PF03597_consen 3 LYILIPVSLI 12 (45)
T ss_pred hhHHHHHHHH
Confidence 4577887743
No 37
>KOG1108 consensus Predicted heme/steroid binding protein [General function prediction only]
Probab=35.32 E-value=9.5 Score=29.82 Aligned_cols=31 Identities=23% Similarity=0.390 Sum_probs=22.4
Q ss_pred CcccccCcc-cCCChHHHHHhhcCCCcchhhhhc
Q 045035 1 VYEVTKFLE-DHPGGDEVFLSVTGKDATDDFEDV 33 (95)
Q Consensus 1 VYDvt~fl~-~HPGG~~vi~~~aGkDaT~~f~~~ 33 (95)
||||++=.. .-||+. -..+||+||+.+|-..
T Consensus 87 VfdVs~gk~hYgsG~s--YnhFaGRDASrAFvsG 118 (281)
T KOG1108|consen 87 VFDVSRGKKHYGSGCS--YNHFAGRDASRAFVSG 118 (281)
T ss_pred eeeccCCeeeeCCCCC--cccccccccchheecc
Confidence 788887542 335554 4788999999999665
No 38
>smart00592 BRK domain in transcription and CHROMO domain helicases.
Probab=35.15 E-value=8.1 Score=22.30 Aligned_cols=12 Identities=25% Similarity=0.695 Sum_probs=9.6
Q ss_pred ccccCcccCCCh
Q 045035 3 EVTKFLEDHPGG 14 (95)
Q Consensus 3 Dvt~fl~~HPGG 14 (95)
|+..||+.||+=
T Consensus 27 ~l~~WL~~~p~y 38 (45)
T smart00592 27 DLERWLEENPEY 38 (45)
T ss_pred HHHHHHhcCCCc
Confidence 567899999985
No 39
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=33.73 E-value=53 Score=24.85 Aligned_cols=21 Identities=10% Similarity=0.344 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHH-HHHHHh
Q 045035 72 LLQFLVPLAILGLAV-GIRIYT 92 (95)
Q Consensus 72 ~~~~~vpl~~~~~~~-~~~~~~ 92 (95)
++.++|.+++|+|.+ +|.+|+
T Consensus 15 iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 15 ILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred hHHHHHHHHHHHHHHHhhhhee
Confidence 456777777555444 444554
No 40
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=33.43 E-value=45 Score=23.55 Aligned_cols=14 Identities=29% Similarity=0.494 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHhc
Q 045035 80 AILGLAVGIRIYTR 93 (95)
Q Consensus 80 ~~~~~~~~~~~~~~ 93 (95)
+++++++++|...+
T Consensus 128 ~ll~i~~giy~~~r 141 (145)
T PF10661_consen 128 ILLAICGGIYVVLR 141 (145)
T ss_pred HHHHHHHHHHHHHH
Confidence 35666666665543
No 41
>PTZ00208 65 kDa invariant surface glycoprotein; Provisional
Probab=33.16 E-value=38 Score=28.27 Aligned_cols=19 Identities=32% Similarity=0.422 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 045035 72 LLQFLVPLAILGLAVGIRI 90 (95)
Q Consensus 72 ~~~~~vpl~~~~~~~~~~~ 90 (95)
++.++||.+||++..+.++
T Consensus 389 ~~avl~p~~il~~~~~~~~ 407 (436)
T PTZ00208 389 ILAVLVPAIILAIIAVAFF 407 (436)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 4678999998885544343
No 42
>PF12575 DUF3753: Protein of unknown function (DUF3753); InterPro: IPR009175 This group represents an uncharacterised conserved protein belonging to poxvirus family I2.
Probab=31.52 E-value=96 Score=19.77 Aligned_cols=7 Identities=14% Similarity=0.140 Sum_probs=3.0
Q ss_pred HHHHHHh
Q 045035 86 VGIRIYT 92 (95)
Q Consensus 86 ~~~~~~~ 92 (95)
+...+|.
T Consensus 63 ~l~flYL 69 (72)
T PF12575_consen 63 LLTFLYL 69 (72)
T ss_pred HHHHHHh
Confidence 3344444
No 43
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=31.31 E-value=69 Score=22.37 Aligned_cols=14 Identities=29% Similarity=0.562 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHH
Q 045035 72 LLQFLVPLAILGLA 85 (95)
Q Consensus 72 ~~~~~vpl~~~~~~ 85 (95)
+..|+.|+++++++
T Consensus 102 ~~LW~~P~~lll~g 115 (126)
T PRK10144 102 LVLWALPVVLLLLM 115 (126)
T ss_pred HHHHHHHHHHHHHH
Confidence 45699998865544
No 44
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=30.88 E-value=16 Score=25.81 Aligned_cols=18 Identities=28% Similarity=0.355 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 045035 72 LLQFLVPLAILGLAVGIR 89 (95)
Q Consensus 72 ~~~~~vpl~~~~~~~~~~ 89 (95)
+..|+.|+++++++++..
T Consensus 102 ~~lW~~P~~~l~~g~~~~ 119 (148)
T PF03918_consen 102 WLLWLGPFLLLLLGGALL 119 (148)
T ss_dssp ------------------
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 456999999766555433
No 45
>PRK13415 flagella biosynthesis protein FliZ; Provisional
Probab=30.84 E-value=1.7e+02 Score=22.33 Aligned_cols=9 Identities=0% Similarity=0.172 Sum_probs=5.0
Q ss_pred HHHHHHHHH
Q 045035 72 LLQFLVPLA 80 (95)
Q Consensus 72 ~~~~~vpl~ 80 (95)
+..+++.|+
T Consensus 68 l~qmi~aL~ 76 (219)
T PRK13415 68 FVKLIGATL 76 (219)
T ss_pred HHHHHHHHH
Confidence 555555555
No 46
>PF01708 Gemini_mov: Geminivirus putative movement protein ; InterPro: IPR002621 This family consists of putative movement proteins from Maize streak virus and Wheat dwarf virus [].; GO: 0046740 spread of virus in host, cell to cell, 0016021 integral to membrane
Probab=30.16 E-value=28 Score=23.20 Aligned_cols=29 Identities=10% Similarity=0.067 Sum_probs=13.6
Q ss_pred ChhHHHHHHHHHHHH--HHHHHHHHHHHHhc
Q 045035 65 TSEFIIRLLQFLVPL--AILGLAVGIRIYTR 93 (95)
Q Consensus 65 ~~~~~~~~~~~~vpl--~~~~~~~~~~~~~~ 93 (95)
+.-.|+++...+|.+ .+++++++|..+.+
T Consensus 30 s~~~ws~vv~v~i~~lvaVg~~YL~y~~fLk 60 (91)
T PF01708_consen 30 SGLPWSRVVEVAIFTLVAVGCLYLAYTWFLK 60 (91)
T ss_pred CCCcceeEeeeeehHHHHHHHHHHHHHHHHH
Confidence 344455443322222 24556666665543
No 47
>KOG4827 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.89 E-value=29 Score=26.74 Aligned_cols=21 Identities=19% Similarity=0.616 Sum_probs=16.4
Q ss_pred CChhHHHHHHHHHHHHHHHHH
Q 045035 64 KTSEFIIRLLQFLVPLAILGL 84 (95)
Q Consensus 64 ~~~~~~~~~~~~~vpl~~~~~ 84 (95)
...++|.+..+++||+-++++
T Consensus 237 ~eRSF~AKYWMYiiPlglVVl 257 (279)
T KOG4827|consen 237 DERSFLAKYWMYIIPLGLVVL 257 (279)
T ss_pred cchhHHHHHHHhhccchhhhh
Confidence 347899999999999876554
No 48
>PF11346 DUF3149: Protein of unknown function (DUF3149); InterPro: IPR021494 This bacterial family of proteins has no known function.
Probab=28.55 E-value=98 Score=17.65 Aligned_cols=22 Identities=27% Similarity=0.436 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH-HHHHHHHHhc
Q 045035 72 LLQFLVPLAILG-LAVGIRIYTR 93 (95)
Q Consensus 72 ~~~~~vpl~~~~-~~~~~~~~~~ 93 (95)
+..+++.+++++ +++.+++|.+
T Consensus 13 L~Sl~vI~~~igm~~~~~~~F~~ 35 (42)
T PF11346_consen 13 LMSLIVIVFTIGMGVFFIRYFIR 35 (42)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555433 3344445543
No 49
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=28.44 E-value=1.5e+02 Score=22.52 Aligned_cols=11 Identities=18% Similarity=0.259 Sum_probs=4.9
Q ss_pred HHHHHHHHHHH
Q 045035 73 LQFLVPLAILG 83 (95)
Q Consensus 73 ~~~~vpl~~~~ 83 (95)
+.|++.+++++
T Consensus 203 f~wl~i~~~l~ 213 (268)
T PF09451_consen 203 FTWLFIILFLF 213 (268)
T ss_pred HHHHHHHHHHH
Confidence 34555444333
No 50
>PHA03054 IMV membrane protein; Provisional
Probab=28.13 E-value=1.4e+02 Score=19.10 Aligned_cols=13 Identities=31% Similarity=0.437 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHhc
Q 045035 81 ILGLAVGIRIYTR 93 (95)
Q Consensus 81 ~~~~~~~~~~~~~ 93 (95)
++.+++..++|.|
T Consensus 58 v~~~~l~~flYLK 70 (72)
T PHA03054 58 VLILLLLIYLYLK 70 (72)
T ss_pred HHHHHHHHHHHHh
Confidence 3444455555543
No 51
>cd00925 Cyt_c_Oxidase_VIa Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform. Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip i
Probab=27.55 E-value=1.2e+02 Score=19.77 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=14.1
Q ss_pred hhHHHHHHH-HHHHHHHHHHHHHHH
Q 045035 66 SEFIIRLLQ-FLVPLAILGLAVGIR 89 (95)
Q Consensus 66 ~~~~~~~~~-~~vpl~~~~~~~~~~ 89 (95)
+..|.++.. ..+|.++|+..-+|.
T Consensus 13 ~~~WkkiS~~va~P~v~l~~~n~y~ 37 (86)
T cd00925 13 SELWKKISFYVALPAVALCMLNAYL 37 (86)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHh
Confidence 566766644 456766666554543
No 52
>PHA02975 hypothetical protein; Provisional
Probab=25.45 E-value=1.2e+02 Score=19.15 Aligned_cols=13 Identities=31% Similarity=0.317 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHhc
Q 045035 81 ILGLAVGIRIYTR 93 (95)
Q Consensus 81 ~~~~~~~~~~~~~ 93 (95)
++.+++..++|.|
T Consensus 54 v~~~~~~~flYLK 66 (69)
T PHA02975 54 ITCIAVFTFLYLK 66 (69)
T ss_pred HHHHHHHHHHHHH
Confidence 3444445555543
No 53
>PHA03240 envelope glycoprotein M; Provisional
Probab=25.27 E-value=85 Score=24.36 Aligned_cols=18 Identities=6% Similarity=0.167 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 045035 73 LQFLVPLAILGLAVGIRI 90 (95)
Q Consensus 73 ~~~~vpl~~~~~~~~~~~ 90 (95)
..|+|+++|+.+.+.+.+
T Consensus 213 ~~WIiilIIiIiIIIL~c 230 (258)
T PHA03240 213 IAWIFIAIIIIIVIILFF 230 (258)
T ss_pred HhHHHHHHHHHHHHHHHH
Confidence 347777776544444433
No 54
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=24.30 E-value=1.9e+02 Score=19.37 Aligned_cols=14 Identities=36% Similarity=0.550 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHH
Q 045035 70 IRLLQFLVPLAILG 83 (95)
Q Consensus 70 ~~~~~~~vpl~~~~ 83 (95)
..++.+++|++++.
T Consensus 70 aa~l~Y~lPll~li 83 (135)
T PF04246_consen 70 AAFLVYLLPLLALI 83 (135)
T ss_pred HHHHHHHHHHHHHH
Confidence 44677899999433
No 55
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=23.42 E-value=2.4e+02 Score=20.87 Aligned_cols=20 Identities=10% Similarity=0.198 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 045035 73 LQFLVPLAILGLAVGIRIYT 92 (95)
Q Consensus 73 ~~~~vpl~~~~~~~~~~~~~ 92 (95)
.-+++-|-+++++|+.|.|-
T Consensus 165 GGIVL~LGv~aI~ff~~KF~ 184 (186)
T PF05283_consen 165 GGIVLTLGVLAIIFFLYKFC 184 (186)
T ss_pred hHHHHHHHHHHHHHHHhhhc
Confidence 34555555677666655543
No 56
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=23.31 E-value=8.5 Score=27.23 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=17.1
Q ss_pred CcccccCcccCCChHHHHHhhcCC
Q 045035 1 VYEVTKFLEDHPGGDEVFLSVTGK 24 (95)
Q Consensus 1 VYDvt~fl~~HPGG~~vi~~~aGk 24 (95)
||.|++|...|-||+..=....||
T Consensus 51 vwtvsqf~arh~gg~hpdq~~lgk 74 (147)
T PF14756_consen 51 VWTVSQFFARHRGGEHPDQVCLGK 74 (147)
T ss_pred eeeHHHHHHHhcCCCCcchhHHHH
Confidence 689999999999996333333344
No 57
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=23.02 E-value=1.5e+02 Score=20.97 Aligned_cols=13 Identities=31% Similarity=0.240 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHhc
Q 045035 81 ILGLAVGIRIYTR 93 (95)
Q Consensus 81 ~~~~~~~~~~~~~ 93 (95)
++++.++...|++
T Consensus 27 l~~l~~~~~~Y~r 39 (149)
T PF11694_consen 27 LLVLIFFFIKYLR 39 (149)
T ss_pred HHHHHHHHHHHHH
Confidence 4444444444443
No 58
>PF02419 PsbL: PsbL protein; InterPro: IPR003372 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (IPR002682 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex []. In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_L 3A0B_l 3ARC_l 1S5L_l 2AXT_l 3BZ2_L 4FBY_L 3PRQ_L 3PRR_L 3KZI_L ....
Probab=22.86 E-value=1.5e+02 Score=16.55 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=10.4
Q ss_pred HHHHHHHH-HHHHHHHHHHH
Q 045035 73 LQFLVPLA-ILGLAVGIRIY 91 (95)
Q Consensus 73 ~~~~vpl~-~~~~~~~~~~~ 91 (95)
++|-+.++ ++++.|.-|+|
T Consensus 17 LY~GLllifvl~vLFssyff 36 (37)
T PF02419_consen 17 LYWGLLLIFVLAVLFSSYFF 36 (37)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhhhc
Confidence 45555555 45665655554
No 59
>PF13260 DUF4051: Protein of unknown function (DUF4051)
Probab=21.53 E-value=1.3e+02 Score=17.96 Aligned_cols=15 Identities=13% Similarity=0.299 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 045035 74 QFLVPLAILGLAVGIRI 90 (95)
Q Consensus 74 ~~~vpl~~~~~~~~~~~ 90 (95)
+|+|-++++++ +|++
T Consensus 6 ywivli~lv~~--gy~~ 20 (54)
T PF13260_consen 6 YWIVLIVLVVV--GYFC 20 (54)
T ss_pred HHHHHHHHHHH--HHHH
Confidence 46555444444 4443
Done!