Query 035538
Match_columns 171
No_of_seqs 20 out of 22
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 03:51:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08229 SHR3_chaperone: ER me 94.8 0.041 8.8E-07 46.1 4.2 39 105-146 138-176 (196)
2 PF14880 COX14: Cytochrome oxi 89.7 0.39 8.4E-06 32.8 2.9 42 106-147 16-57 (59)
3 smart00786 SHR3_chaperone ER m 89.5 0.48 1E-05 40.2 3.9 38 105-145 138-175 (196)
4 PF11770 GAPT: GRB2-binding ad 86.6 0.98 2.1E-05 37.6 4.0 44 90-136 1-53 (158)
5 PF11044 TMEMspv1-c74-12: Plec 83.9 3.3 7.2E-05 28.8 4.9 31 109-148 18-48 (49)
6 PF14981 FAM165: FAM165 family 82.3 1.7 3.7E-05 30.4 3.0 26 122-147 23-48 (51)
7 PF10669 Phage_Gp23: Protein g 78.7 3.8 8.2E-05 32.7 4.3 19 102-120 18-36 (121)
8 PRK09173 F0F1 ATP synthase sub 73.0 3.8 8.3E-05 31.4 2.9 13 126-138 27-39 (159)
9 PRK13460 F0F1 ATP synthase sub 70.2 5.2 0.00011 31.3 3.2 16 122-137 37-52 (173)
10 PLN02777 photosystem I P subun 67.7 7.8 0.00017 32.5 3.8 15 26-40 22-36 (167)
11 PRK14475 F0F1 ATP synthase sub 66.4 11 0.00023 29.5 4.2 35 102-137 12-46 (167)
12 PF10183 ESSS: ESSS subunit of 65.8 7.9 0.00017 29.0 3.2 36 107-142 64-102 (105)
13 PF12606 RELT: Tumour necrosis 65.1 7.7 0.00017 26.6 2.8 20 101-120 5-24 (50)
14 TIGR02209 ftsL_broad cell divi 65.0 8.8 0.00019 26.3 3.1 22 106-127 4-25 (85)
15 PF15002 ERK-JNK_inhib: ERK an 64.7 6.2 0.00013 33.4 2.7 17 145-161 186-202 (207)
16 PF08507 COPI_assoc: COPI asso 64.4 1.4 3.1E-05 33.4 -1.0 26 107-132 86-111 (136)
17 PRK07353 F0F1 ATP synthase sub 64.2 9.7 0.00021 28.3 3.4 29 109-137 13-41 (140)
18 CHL00118 atpG ATP synthase CF0 63.0 9.9 0.00022 29.4 3.4 36 106-141 27-62 (156)
19 KOG2302 T-type voltage-gated C 62.5 12 0.00026 39.9 4.8 44 99-148 1362-1405(1956)
20 PRK13455 F0F1 ATP synthase sub 61.7 9.2 0.0002 30.2 3.0 15 126-140 52-66 (184)
21 COG2245 Predicted membrane pro 60.9 4.5 9.7E-05 34.4 1.2 39 98-137 140-178 (182)
22 KOG4326 Mitochondrial F1F0-ATP 59.6 7.2 0.00016 29.5 2.0 32 109-141 12-43 (81)
23 PRK04125 murein hydrolase regu 59.0 14 0.00031 29.6 3.7 9 127-135 113-121 (141)
24 PRK11778 putative inner membra 58.6 15 0.00033 32.9 4.2 20 129-148 60-79 (330)
25 PF06930 DUF1282: Protein of u 58.3 5 0.00011 31.1 1.0 28 110-137 128-155 (170)
26 cd02437 CCC1_like_1 CCC1-relat 57.4 11 0.00025 29.7 2.9 13 122-134 48-60 (175)
27 CHL00114 psbX photosystem II p 56.1 21 0.00046 23.8 3.5 34 98-131 4-37 (39)
28 PF08229 SHR3_chaperone: ER me 56.0 7.4 0.00016 32.8 1.7 41 110-150 136-176 (196)
29 PRK13454 F0F1 ATP synthase sub 55.3 15 0.00033 29.3 3.4 31 107-137 37-67 (181)
30 PRK14472 F0F1 ATP synthase sub 53.2 18 0.00039 28.3 3.4 17 122-138 39-55 (175)
31 PF04999 FtsL: Cell division p 53.2 20 0.00043 25.4 3.3 14 112-125 21-34 (97)
32 PRK08475 F0F1 ATP synthase sub 52.6 15 0.00033 29.0 2.9 36 101-139 25-60 (167)
33 KOG1156 N-terminal acetyltrans 52.0 12 0.00025 37.3 2.5 37 135-171 597-639 (700)
34 PRK13453 F0F1 ATP synthase sub 51.4 23 0.0005 27.9 3.7 31 108-138 25-55 (173)
35 PF10278 Med19: Mediator of RN 51.2 8.6 0.00019 32.3 1.4 8 155-162 171-178 (178)
36 PRK05759 F0F1 ATP synthase sub 51.2 23 0.0005 26.6 3.6 37 109-145 12-48 (156)
37 PRK13461 F0F1 ATP synthase sub 48.8 26 0.00056 26.9 3.6 32 109-140 13-44 (159)
38 PF04882 Peroxin-3: Peroxin-3; 47.3 8.8 0.00019 34.8 0.9 31 117-148 20-50 (432)
39 TIGR00267 conserved hypothetic 47.2 17 0.00037 29.0 2.4 34 112-145 33-66 (169)
40 PF06375 BLVR: Bovine leukaemi 46.7 5.7 0.00012 32.4 -0.3 17 155-171 96-112 (154)
41 PF08496 Peptidase_S49_N: Pept 45.5 51 0.0011 26.6 4.9 21 100-120 12-32 (155)
42 PF03268 DUF267: Caenorhabditi 44.2 25 0.00055 32.3 3.4 49 100-148 150-199 (353)
43 PRK09174 F0F1 ATP synthase sub 44.0 29 0.00062 28.7 3.4 30 108-137 60-89 (204)
44 PF15122 TMEM206: TMEM206 prot 42.5 20 0.00044 32.4 2.4 34 99-132 9-42 (298)
45 PRK14473 F0F1 ATP synthase sub 42.5 41 0.00089 25.9 3.8 33 109-141 16-48 (164)
46 TIGR00990 3a0801s09 mitochondr 42.3 14 0.00031 33.3 1.5 27 99-125 26-57 (615)
47 PF10066 DUF2304: Uncharacteri 42.2 42 0.00091 25.0 3.7 23 97-119 60-82 (115)
48 PRK14471 F0F1 ATP synthase sub 41.8 40 0.00086 26.0 3.7 30 109-138 16-45 (164)
49 KOG4727 U1-like Zn-finger prot 40.2 32 0.00069 29.6 3.1 20 127-146 135-154 (193)
50 PF11214 Med2: Mediator comple 40.0 26 0.00056 27.5 2.4 18 130-147 82-99 (105)
51 PF07790 DUF1628: Protein of u 39.5 20 0.00044 24.7 1.6 30 97-126 1-30 (80)
52 PF11688 DUF3285: Protein of u 39.3 13 0.00027 25.6 0.5 31 89-125 14-44 (45)
53 PRK06568 F0F1 ATP synthase sub 39.3 48 0.001 26.7 3.9 30 109-138 12-41 (154)
54 TIGR01144 ATP_synt_b ATP synth 38.6 36 0.00078 25.4 2.9 31 110-140 4-34 (147)
55 TIGR03065 srtB_sig_QVPTGV sort 38.4 4.8 0.0001 26.0 -1.5 16 110-125 12-28 (32)
56 PF10883 DUF2681: Protein of u 36.8 67 0.0015 24.2 4.1 18 103-120 2-19 (87)
57 PF13908 Shisa: Wnt and FGF in 36.6 17 0.00036 28.5 0.9 17 96-112 75-91 (179)
58 TIGR03321 alt_F1F0_F0_B altern 34.9 47 0.001 27.5 3.3 32 110-141 14-45 (246)
59 PF13105 DUF3959: Protein of u 32.9 27 0.00059 30.7 1.6 44 105-148 124-169 (239)
60 KOG2827 Uncharacterized conser 32.7 29 0.00063 31.8 1.9 40 126-165 111-150 (322)
61 PRK13415 flagella biosynthesis 32.6 32 0.00069 29.8 2.0 33 96-135 62-94 (219)
62 PF03823 Neurokinin_B: Neuroki 32.4 38 0.00083 24.4 2.1 14 104-117 3-16 (59)
63 PF01597 GCV_H: Glycine cleava 31.9 28 0.00061 26.4 1.4 16 120-135 16-31 (122)
64 PF12409 P5-ATPase: P5-type AT 31.7 17 0.00036 27.1 0.1 17 108-124 17-33 (119)
65 MTH00057 ND6 NADH dehydrogenas 31.4 25 0.00053 28.6 1.1 17 102-118 148-164 (186)
66 PF03596 Cad: Cadmium resistan 31.0 12 0.00025 31.2 -0.9 39 98-136 35-81 (191)
67 PF05545 FixQ: Cbb3-type cytoc 30.9 65 0.0014 20.8 2.8 17 101-117 12-28 (49)
68 PF08725 Integrin_b_cyt: Integ 30.9 32 0.00069 23.0 1.4 18 126-143 3-20 (47)
69 PF15240 Pro-rich: Proline-ric 30.8 31 0.00068 29.1 1.7 25 104-128 3-30 (179)
70 PF13755 Sensor_TM1: Sensor N- 30.6 24 0.00053 26.2 0.9 21 105-125 17-37 (79)
71 PF07946 DUF1682: Protein of u 30.6 39 0.00085 29.3 2.2 6 16-21 128-133 (321)
72 PF00430 ATP-synt_B: ATP synth 30.1 40 0.00087 24.2 1.9 30 109-138 7-36 (132)
73 PF03004 Transposase_24: Plant 30.0 48 0.001 24.5 2.3 40 127-166 6-47 (141)
74 PF04789 DUF621: Protein of un 29.7 52 0.0011 30.0 2.9 22 99-120 21-42 (305)
75 PF09428 DUF2011: Fungal prote 29.7 46 0.00099 26.3 2.3 12 149-160 118-129 (131)
76 PF03839 Sec62: Translocation 29.5 56 0.0012 28.1 3.0 29 99-127 110-145 (224)
77 KOG4848 Extracellular matrix-a 29.5 47 0.001 29.2 2.5 26 127-152 192-217 (225)
78 PF01988 VIT1: VIT family; In 29.3 46 0.001 26.9 2.3 35 111-145 35-69 (213)
79 PRK08808 general secretion pat 28.9 49 0.0011 27.8 2.5 33 101-136 10-42 (211)
80 PF01405 PsbT: Photosystem II 28.8 15 0.00033 23.2 -0.4 18 109-126 4-21 (29)
81 PF09125 COX2-transmemb: Cytoc 28.8 66 0.0014 21.5 2.6 17 102-118 21-37 (38)
82 PF04999 FtsL: Cell division p 27.0 1E+02 0.0022 21.8 3.5 30 102-131 14-43 (97)
83 TIGR02537 arch_flag_Nterm arch 27.0 99 0.0021 18.6 2.9 19 96-114 1-19 (26)
84 PF00664 ABC_membrane: ABC tra 26.7 63 0.0014 23.4 2.4 32 113-144 144-175 (275)
85 COG0711 AtpF F0F1-type ATP syn 26.5 1E+02 0.0022 24.3 3.7 37 108-144 13-49 (161)
86 KOG1608 Protein transporter of 26.4 1.7E+02 0.0038 27.4 5.7 34 133-166 321-354 (374)
87 KOG1313 DHHC-type Zn-finger pr 26.0 1.6E+02 0.0034 27.1 5.3 48 100-147 211-258 (309)
88 PF09425 CCT_2: Divergent CCT 25.8 29 0.00063 21.5 0.5 11 125-135 7-17 (27)
89 PF08374 Protocadherin: Protoc 25.5 8.1 0.00017 33.6 -2.8 8 66-73 12-19 (221)
90 KOG1226 Integrin beta subunit 24.9 79 0.0017 32.1 3.4 21 122-142 734-754 (783)
91 PF03219 TLC: TLC ATP/ADP tran 24.7 26 0.00056 32.6 0.1 21 120-140 233-253 (491)
92 PF12955 DUF3844: Domain of un 24.6 48 0.0011 25.7 1.6 28 96-123 63-90 (103)
93 PF13150 DUF3989: Protein of u 24.2 74 0.0016 23.5 2.4 21 101-121 28-48 (85)
94 PRK06569 F0F1 ATP synthase sub 24.2 1E+02 0.0022 25.1 3.5 31 107-137 16-46 (155)
95 PRK00888 ftsB cell division pr 24.2 1.3E+02 0.0028 22.6 3.8 10 128-137 28-37 (105)
96 PF01917 Arch_flagellin: Archa 24.2 58 0.0013 25.5 2.0 35 104-139 7-41 (190)
97 PF12569 NARP1: NMDA receptor- 24.2 88 0.0019 29.4 3.5 7 122-128 384-390 (517)
98 PF07219 HemY_N: HemY protein 24.0 1.3E+02 0.0028 21.9 3.7 37 103-139 22-60 (108)
99 PF12158 DUF3592: Protein of u 23.6 57 0.0012 23.4 1.7 24 100-123 121-145 (148)
100 PF08113 CoxIIa: Cytochrome c 23.4 98 0.0021 20.3 2.6 22 103-124 6-29 (34)
101 PF04277 OAD_gamma: Oxaloaceta 23.4 19 0.00041 24.6 -0.8 13 108-120 13-25 (79)
102 PF07741 BRF1: Brf1-like TBP-b 23.2 21 0.00046 26.2 -0.6 15 127-141 26-40 (97)
103 PRK14474 F0F1 ATP synthase sub 22.8 1E+02 0.0023 26.0 3.4 30 109-138 13-42 (250)
104 PRK08541 flagellin; Validated 22.7 87 0.0019 26.8 2.9 34 103-137 9-42 (211)
105 PF06305 DUF1049: Protein of u 22.6 2.3E+02 0.005 18.5 4.6 13 129-141 44-56 (68)
106 CHL00019 atpF ATP synthase CF0 22.4 1.1E+02 0.0023 24.2 3.2 18 122-139 45-62 (184)
107 CHL00031 psbT photosystem II p 22.2 30 0.00064 22.5 0.0 17 110-126 5-21 (33)
108 PF14358 DUF4405: Domain of un 22.2 1.1E+02 0.0024 20.2 2.8 22 100-121 2-23 (64)
109 PRK08476 F0F1 ATP synthase sub 21.6 1.1E+02 0.0024 23.5 3.1 32 110-141 16-47 (141)
110 PRK13428 F0F1 ATP synthase sub 21.4 97 0.0021 28.3 3.1 17 121-137 21-37 (445)
111 cd06848 GCS_H Glycine cleavage 21.3 58 0.0013 23.2 1.4 14 120-133 14-27 (96)
112 KOG0052 Translation elongation 21.1 38 0.00082 31.6 0.5 21 128-148 29-49 (391)
113 PF13800 Sigma_reg_N: Sigma fa 21.1 2.2E+02 0.0048 20.2 4.3 23 102-125 18-40 (96)
114 PF04156 IncA: IncA protein; 21.1 93 0.002 24.1 2.6 18 113-130 49-66 (191)
115 KOG1631 Translocon-associated 21.0 76 0.0016 28.5 2.3 26 105-134 185-210 (261)
116 PF11820 DUF3339: Protein of u 20.7 1.4E+02 0.003 22.0 3.2 25 97-121 40-64 (68)
117 COG2165 PulG Type II secretory 20.2 1.4E+02 0.003 20.7 3.1 30 101-130 11-40 (149)
No 1
>PF08229 SHR3_chaperone: ER membrane protein SH3 ; InterPro: IPR013248 This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) []. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=94.79 E-value=0.041 Score=46.15 Aligned_cols=39 Identities=28% Similarity=0.472 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHhh
Q 035538 105 VLLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAATK 146 (171)
Q Consensus 105 ~LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak~ 146 (171)
+++.++++|..+|=+|--| .+..+.++.++|++||++++
T Consensus 138 ~Ii~~~LvGVLvLQaG~~Y---Ae~~~~~~~~~~~~~e~~~~ 176 (196)
T PF08229_consen 138 TIIALVLVGVLVLQAGQWY---AERKDAKELEEFEKEEAEAA 176 (196)
T ss_pred HHHHHHHHHHHHHHhhHHH---HhhhhHHHHHHHHHHHHHHH
Confidence 4667788899999999998 78888889998888874333
No 2
>PF14880 COX14: Cytochrome oxidase c assembly
Probab=89.70 E-value=0.39 Score=32.80 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHhhh
Q 035538 106 LLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAATKK 147 (171)
Q Consensus 106 LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak~k 147 (171)
+...+.+|+++...|++-..+-++.+.+++++.+-+|.++++
T Consensus 16 ~tV~~Lig~T~~~g~~~~~~~y~~~~~~r~~~~~~~e~~~~~ 57 (59)
T PF14880_consen 16 TTVLGLIGFTVYGGGLTVYTVYSYFKYNRRRRAEWIEREKQK 57 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566778888888777789999999988887666665554
No 3
>smart00786 SHR3_chaperone ER membrane protein SH3. This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) PUBMED:15623581. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=89.49 E-value=0.48 Score=40.15 Aligned_cols=38 Identities=21% Similarity=0.482 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHh
Q 035538 105 VLLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAAT 145 (171)
Q Consensus 105 ~LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak 145 (171)
+++.++++|..+|=.|--| .+..+.++.|+|.|||+++
T Consensus 138 ~Il~~vLvGVL~LQaG~wY---Aer~~~~~~~~~~~~~~~~ 175 (196)
T smart00786 138 TILLFVLVGVLVLQAGLWY---AERKDAKQKEEFAAEERKE 175 (196)
T ss_pred hhHHHHHHHHHHHHhhHHH---HHHhHHHHHHHHHHHHHHH
Confidence 4667778888899999887 5788888888887776544
No 4
>PF11770 GAPT: GRB2-binding adapter (GAPT); InterPro: IPR021082 This entry represents a family of transmembrane proteins which bind the growth factor receptor-bound protein 2 (GRB2) in B cells []. In contrast to other transmembrane adaptor proteins, GAPT, which this entry represents, is not phosphorylated upon BCR ligation. It associates with GRB2 constitutively through its proline-rich region [].
Probab=86.65 E-value=0.98 Score=37.55 Aligned_cols=44 Identities=32% Similarity=0.527 Sum_probs=30.3
Q ss_pred hhhccCCcchHHHHHHHHHHHHHHHHHhhheeeee---------ehhhhhhhHHHH
Q 035538 90 MVSSTGDESLSSVISVLLFAAFIALSILTIGVVYI---------GVTDFLQKRERE 136 (171)
Q Consensus 90 ~~~s~~d~g~a~vis~LlfvAfvgLsilTiGViYL---------~VtdFlqKRe~E 136 (171)
|..+-+...++..|.+.|++ -|.|..||+++- .+--|||+|-..
T Consensus 1 mL~s~gn~sv~i~igi~Ll~---lLl~cgiGcvwhwkhr~~~~ftLPkflqRRssk 53 (158)
T PF11770_consen 1 MLKSCGNTSVAISIGISLLL---LLLLCGIGCVWHWKHRDSTRFTLPKFLQRRSSK 53 (158)
T ss_pred CcccccCchHHHHHHHHHHH---HHHHHhcceEEEeeccCccccchHHHHHhhhhh
Confidence 34444555666666665554 577888998875 777899998764
No 5
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=83.95 E-value=3.3 Score=28.81 Aligned_cols=31 Identities=39% Similarity=0.448 Sum_probs=17.6
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHhhhh
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAATKKK 148 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak~kk 148 (171)
+|.+||+| |-.+ =|=|-+.|++||.+.|+.+
T Consensus 18 f~~iGl~I------yQki---kqIrgKkk~KKeie~ke~~ 48 (49)
T PF11044_consen 18 FAWIGLSI------YQKI---KQIRGKKKEKKEIERKEDK 48 (49)
T ss_pred HHHHHHHH------HHHH---HHHHhhhhhHHHHHHHhhc
Confidence 34467664 4333 3456666777776666554
No 6
>PF14981 FAM165: FAM165 family
Probab=82.32 E-value=1.7 Score=30.43 Aligned_cols=26 Identities=38% Similarity=0.530 Sum_probs=20.1
Q ss_pred eeeehhhhhhhHHHHHHHHHHHHhhh
Q 035538 122 VYIGVTDFLQKREREKFEKEEAATKK 147 (171)
Q Consensus 122 iYL~VtdFlqKRe~EkfeKeEaak~k 147 (171)
.+-||.=|=.||+++|.+|+|++|++
T Consensus 23 aFAgvK~yQ~krlEak~~k~~aekk~ 48 (51)
T PF14981_consen 23 AFAGVKMYQRKRLEAKLKKLEAEKKK 48 (51)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 34467778889999999999888754
No 7
>PF10669 Phage_Gp23: Protein gp23 (Bacteriophage A118); InterPro: IPR018926 This entry is represented by the major tail subunit protein, Gp23 of Listeria phage A118 and prophage found in Bacilli. The function is currently unknown.
Probab=78.66 E-value=3.8 Score=32.73 Aligned_cols=19 Identities=32% Similarity=0.513 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHhhhe
Q 035538 102 VISVLLFAAFIALSILTIG 120 (171)
Q Consensus 102 vis~LlfvAfvgLsilTiG 120 (171)
+..+|+.+.|+-|.|+|--
T Consensus 18 ~FA~L~i~~FiILLIi~~~ 36 (121)
T PF10669_consen 18 FFAFLFIVVFIILLIITKS 36 (121)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3455666667666666543
No 8
>PRK09173 F0F1 ATP synthase subunit B; Validated
Probab=73.00 E-value=3.8 Score=31.43 Aligned_cols=13 Identities=15% Similarity=0.117 Sum_probs=10.6
Q ss_pred hhhhhhhHHHHHH
Q 035538 126 VTDFLQKREREKF 138 (171)
Q Consensus 126 VtdFlqKRe~Ekf 138 (171)
|.++|++|+..=.
T Consensus 27 i~~~l~~R~~~I~ 39 (159)
T PRK09173 27 IARSLDARADRIK 39 (159)
T ss_pred HHHHHHHHHHHHH
Confidence 8999999987543
No 9
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=70.24 E-value=5.2 Score=31.33 Aligned_cols=16 Identities=13% Similarity=0.111 Sum_probs=11.9
Q ss_pred eeeehhhhhhhHHHHH
Q 035538 122 VYIGVTDFLQKREREK 137 (171)
Q Consensus 122 iYL~VtdFlqKRe~Ek 137 (171)
+|=-|.++|++|+..=
T Consensus 37 ~~kpi~~~l~~R~~~I 52 (173)
T PRK13460 37 AWDVILKALDERASGV 52 (173)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 3334999999998654
No 10
>PLN02777 photosystem I P subunit (PSI-P)
Probab=67.72 E-value=7.8 Score=32.53 Aligned_cols=15 Identities=20% Similarity=-0.011 Sum_probs=8.7
Q ss_pred Ccccccccceeeeec
Q 035538 26 RHFHRCTVSFSTIYC 40 (171)
Q Consensus 26 s~lh~~~~sl~~L~~ 40 (171)
+....+-.+||.||-
T Consensus 22 ~a~~~~~~~lp~lpp 36 (167)
T PLN02777 22 AAASPQCVSLPTLPP 36 (167)
T ss_pred cccCCccccCCCCCC
Confidence 333445667777773
No 11
>PRK14475 F0F1 ATP synthase subunit B; Provisional
Probab=66.44 E-value=11 Score=29.50 Aligned_cols=35 Identities=11% Similarity=0.040 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 102 VISVLLFAAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 102 vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
+..++-|+.|+++.++ ..+.|=-|+.+|++|..+=
T Consensus 12 ~w~~i~f~il~~iL~~-~k~l~~pi~~~le~R~~~I 46 (167)
T PRK14475 12 FWVGAGLLIFFGILIA-LKVLPKALAGALDAYAAKI 46 (167)
T ss_pred HHHHHHHHHHHHHHHH-HHHhHHHHHHHHHHHHHHH
Confidence 3344444444443332 4666777999999998754
No 12
>PF10183 ESSS: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) ; InterPro: IPR019329 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents the ESSS subunit from mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences [].
Probab=65.78 E-value=7.9 Score=29.00 Aligned_cols=36 Identities=14% Similarity=0.271 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhhheeeee---ehhhhhhhHHHHHHHHHH
Q 035538 107 LFAAFIALSILTIGVVYI---GVTDFLQKREREKFEKEE 142 (171)
Q Consensus 107 lfvAfvgLsilTiGViYL---~VtdFlqKRe~EkfeKeE 142 (171)
|+.-+++++++++++.|. .++|+=++.+.+..+.-|
T Consensus 64 f~~~~~~~v~~~~~~~y~PD~~i~~WA~rEA~~rl~~rE 102 (105)
T PF10183_consen 64 FFGFSGSLVFGGVFLAYKPDTSIQTWARREAYRRLERRE 102 (105)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhHHh
Confidence 334456778888899998 566666555555444333
No 13
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=65.11 E-value=7.7 Score=26.63 Aligned_cols=20 Identities=25% Similarity=0.428 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHhhhe
Q 035538 101 SVISVLLFAAFIALSILTIG 120 (171)
Q Consensus 101 ~vis~LlfvAfvgLsilTiG 120 (171)
.+|++++.++.+|++|+|+-
T Consensus 5 ~iV~i~iv~~lLg~~I~~~~ 24 (50)
T PF12606_consen 5 LIVSIFIVMGLLGLSICTTL 24 (50)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 57899999999999999874
No 14
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=65.01 E-value=8.8 Score=26.26 Aligned_cols=22 Identities=23% Similarity=0.255 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHhhheeeeeehh
Q 035538 106 LLFAAFIALSILTIGVVYIGVT 127 (171)
Q Consensus 106 LlfvAfvgLsilTiGViYL~Vt 127 (171)
|.++.++.+.++.+++||.-..
T Consensus 4 l~~~l~~~v~~~~~~~v~~~~~ 25 (85)
T TIGR02209 4 LYVLLLLAILVSAISVVSAQHQ 25 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555555666665443
No 15
>PF15002 ERK-JNK_inhib: ERK and JNK pathways, inhibitor
Probab=64.68 E-value=6.2 Score=33.44 Aligned_cols=17 Identities=53% Similarity=0.663 Sum_probs=9.9
Q ss_pred hhhhhhccccccCCCCC
Q 035538 145 TKKKKKVKAKPRAGPRG 161 (171)
Q Consensus 145 k~kkkkk~~raraGprG 161 (171)
+++|||++++.+-|||+
T Consensus 186 ~~~kKk~kkk~kKgPrl 202 (207)
T PF15002_consen 186 RRKKKKKKKKIKKGPRL 202 (207)
T ss_pred HHHHHHHHHHhccCCCc
Confidence 33334444446778887
No 16
>PF08507 COPI_assoc: COPI associated protein; InterPro: IPR013714 Proteins in this family co-localise with COPI vesicle coat proteins []. In yeast it is a Golgi membrane protein involved in vesicular trafficking, interacting with TVP18 [].
Probab=64.40 E-value=1.4 Score=33.39 Aligned_cols=26 Identities=27% Similarity=0.499 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhhheeeeeehhhhhhh
Q 035538 107 LFAAFIALSILTIGVVYIGVTDFLQK 132 (171)
Q Consensus 107 lfvAfvgLsilTiGViYL~VtdFlqK 132 (171)
++--++|+.++.+|++|+.+-=+--.
T Consensus 86 ~~~~i~g~~~~~~G~~~i~l~~~~~~ 111 (136)
T PF08507_consen 86 ILSIIIGLLLFLVGVIYIILGFFCPI 111 (136)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44456788899999999877544333
No 17
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=64.23 E-value=9.7 Score=28.27 Aligned_cols=29 Identities=21% Similarity=0.361 Sum_probs=22.7
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
|.|+.|.++---++|=.|+++|++|+..=
T Consensus 13 i~flil~~ll~~~l~~pi~~~l~~R~~~I 41 (140)
T PRK07353 13 VQFVLLTFILNALFYKPVGKVVEEREDYI 41 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666777766778888999999998653
No 18
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=63.02 E-value=9.9 Score=29.39 Aligned_cols=36 Identities=19% Similarity=0.247 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHH
Q 035538 106 LLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKE 141 (171)
Q Consensus 106 LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKe 141 (171)
++.+.|+.|.++.--++|=-|+++|++|+..=....
T Consensus 27 ~~~inFliL~~lL~k~l~~Pi~~~l~~R~~~I~~~l 62 (156)
T CHL00118 27 LMALQFLLLMVLLNIILYKPLLKVLDERKEYIRKNL 62 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566677777777888899999999987654443
No 19
>KOG2302 consensus T-type voltage-gated Ca2+ channel, pore-forming alpha1I subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=62.47 E-value=12 Score=39.87 Aligned_cols=44 Identities=39% Similarity=0.594 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHhhhh
Q 035538 99 LSSVISVLLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAATKKK 148 (171)
Q Consensus 99 ~a~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak~kk 148 (171)
.-++||.||.|+|..|.++. ||+ |+.|..-|+. +|.|||+++.+
T Consensus 1362 llYfIsfllIvsffVlnmfV-gvv---venfhKcrqh--qe~EeArRreE 1405 (1956)
T KOG2302|consen 1362 LLYFISFLLIVSFFVLNMFV-GVV---VENFHKCRQH--QEAEEARRREE 1405 (1956)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHH---HHHHHHHHHH--HHHHHHHHHHH
Confidence 45899999999999998874 553 6778766654 44455555444
No 20
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=61.74 E-value=9.2 Score=30.19 Aligned_cols=15 Identities=20% Similarity=0.273 Sum_probs=11.4
Q ss_pred hhhhhhhHHHHHHHH
Q 035538 126 VTDFLQKREREKFEK 140 (171)
Q Consensus 126 VtdFlqKRe~EkfeK 140 (171)
|.++|++|...=...
T Consensus 52 v~~~L~~R~~~I~~~ 66 (184)
T PRK13455 52 IGGMLDKRAEGIRSE 66 (184)
T ss_pred HHHHHHHHHHHHHHH
Confidence 799999998754333
No 21
>COG2245 Predicted membrane protein [Function unknown]
Probab=60.91 E-value=4.5 Score=34.39 Aligned_cols=39 Identities=26% Similarity=0.331 Sum_probs=33.6
Q ss_pred chHHHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 98 SLSSVISVLLFAAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 98 g~a~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
|+-+.|.+++.+.++|+.|+-||-|...| -|++.+.+||
T Consensus 140 gl~Y~iGaiLlIV~vG~iIi~Ia~IL~iV-affslp~e~~ 178 (182)
T COG2245 140 GLLYFIGAILLIVAVGLIIILIAAILEIV-AFFSLPPEEK 178 (182)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhcCChhhc
Confidence 67899999999999999999999887666 5788888776
No 22
>KOG4326 consensus Mitochondrial F1F0-ATP synthase, subunit e [Energy production and conversion]
Probab=59.55 E-value=7.2 Score=29.50 Aligned_cols=32 Identities=34% Similarity=0.419 Sum_probs=19.8
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKFEKE 141 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~EkfeKe 141 (171)
+-|---+.|.+||+| |.+-.-|=|+.++..+|
T Consensus 12 IkfGRysaL~lGvaY-Ga~r~~~l~~~~e~~Re 43 (81)
T KOG4326|consen 12 IKFGRYSALSLGVAY-GAFRLRQLREYHEDIRE 43 (81)
T ss_pred HHhhHHHHHHHHHHH-hHHHHHHHhHHHHHHHH
Confidence 345556778889999 44444455555555555
No 23
>PRK04125 murein hydrolase regulator LrgA; Provisional
Probab=58.98 E-value=14 Score=29.61 Aligned_cols=9 Identities=11% Similarity=0.464 Sum_probs=5.6
Q ss_pred hhhhhhHHH
Q 035538 127 TDFLQKRER 135 (171)
Q Consensus 127 tdFlqKRe~ 135 (171)
.+|+.+|++
T Consensus 113 ~~~l~r~~~ 121 (141)
T PRK04125 113 SQFILGKTE 121 (141)
T ss_pred HHHHHHhhh
Confidence 467777644
No 24
>PRK11778 putative inner membrane peptidase; Provisional
Probab=58.57 E-value=15 Score=32.89 Aligned_cols=20 Identities=25% Similarity=0.486 Sum_probs=10.2
Q ss_pred hhhhHHHHHHHHHHHHhhhh
Q 035538 129 FLQKREREKFEKEEAATKKK 148 (171)
Q Consensus 129 FlqKRe~EkfeKeEaak~kk 148 (171)
.|.|.|..+++|++..+.|+
T Consensus 60 ~~~~~~~k~~~k~~~~~~k~ 79 (330)
T PRK11778 60 LLDKKELKAWHKAQKKKEKQ 79 (330)
T ss_pred hCCHHHHHHHHHHHHHHHHH
Confidence 34555555555555443333
No 25
>PF06930 DUF1282: Protein of unknown function (DUF1282); InterPro: IPR009698 This entry represents several hypothetical proteins of around 200 residues in length. The function of is unknown although a number of the members are thought to be putative membrane proteins.
Probab=58.29 E-value=5 Score=31.09 Aligned_cols=28 Identities=25% Similarity=0.471 Sum_probs=21.2
Q ss_pred HHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 110 AFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 110 AfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
++..+.+-++.++|+||..+.+=||+++
T Consensus 128 ~~~~~~~~~~~Lly~Gv~~~~~i~~~~~ 155 (170)
T PF06930_consen 128 VGLIALIYSVYLLYLGVPIFMNISEKER 155 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCcCcccc
Confidence 4455566778889999999997766654
No 26
>cd02437 CCC1_like_1 CCC1-related protein family. CCC1_like_1: This is a protein family closely related to CCC1, a family of proteins involved in iron and manganese transport. Yeast CCC1 is a vacuole transmembrane protein responsible for the iron and manganese accumulation in vacuole.
Probab=57.35 E-value=11 Score=29.74 Aligned_cols=13 Identities=8% Similarity=0.143 Sum_probs=7.4
Q ss_pred eeeehhhhhhhHH
Q 035538 122 VYIGVTDFLQKRE 134 (171)
Q Consensus 122 iYL~VtdFlqKRe 134 (171)
+=.++.+|+..|+
T Consensus 48 ~Sma~g~yvs~~~ 60 (175)
T cd02437 48 ISNGLGAAVAEEG 60 (175)
T ss_pred HHHHHHHHHHHHH
Confidence 4455667775443
No 27
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=56.10 E-value=21 Score=23.83 Aligned_cols=34 Identities=29% Similarity=0.476 Sum_probs=27.6
Q ss_pred chHHHHHHHHHHHHHHHHHhhheeeeeehhhhhh
Q 035538 98 SLSSVISVLLFAAFIALSILTIGVVYIGVTDFLQ 131 (171)
Q Consensus 98 g~a~vis~LlfvAfvgLsilTiGViYL~VtdFlq 131 (171)
+.+.++.-|+.-|++...-+|++.|+++-+|=++
T Consensus 4 SLsnF~~SL~~Ga~ivvipi~~aLifvSq~D~v~ 37 (39)
T CHL00114 4 SLSAFINSLLLGAIIVVIPITLALLFVSQKDRTT 37 (39)
T ss_pred hHHHHHHHHHHHHHHhHHHhhhheEEEeccceec
Confidence 3567888888888887778899999999888654
No 28
>PF08229 SHR3_chaperone: ER membrane protein SH3 ; InterPro: IPR013248 This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) []. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=56.01 E-value=7.4 Score=32.84 Aligned_cols=41 Identities=12% Similarity=0.226 Sum_probs=29.7
Q ss_pred HHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHhhhhhh
Q 035538 110 AFIALSILTIGVVYIGVTDFLQKREREKFEKEEAATKKKKK 150 (171)
Q Consensus 110 AfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak~kkkk 150 (171)
.=+-+.++.+||+=|=..-|.-+|+.++.++|..+++++++
T Consensus 136 Sn~Ii~~~LvGVLvLQaG~~YAe~~~~~~~~~~~~~e~~~~ 176 (196)
T PF08229_consen 136 SNTIIALVLVGVLVLQAGQWYAERKDAKELEEFEKEEAEAA 176 (196)
T ss_pred hhHHHHHHHHHHHHHHhhHHHHhhhhHHHHHHHHHHHHHHH
Confidence 34446667778888888888888888887777666665544
No 29
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=55.27 E-value=15 Score=29.31 Aligned_cols=31 Identities=16% Similarity=0.269 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 107 LFAAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 107 lfvAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
++|.|+.|.++.--++|==|..+|++|...=
T Consensus 37 ~lI~F~iL~~ll~k~l~~PI~~~l~~R~~~I 67 (181)
T PRK13454 37 LLVTLVAIYFVLTRVALPRIGAVLAERQGTI 67 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777777778888999999998654
No 30
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=53.22 E-value=18 Score=28.34 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=12.7
Q ss_pred eeeehhhhhhhHHHHHH
Q 035538 122 VYIGVTDFLQKREREKF 138 (171)
Q Consensus 122 iYL~VtdFlqKRe~Ekf 138 (171)
+|=-|.++|++|+..=.
T Consensus 39 l~kpi~~~l~~R~~~I~ 55 (175)
T PRK14472 39 AWGPILSALEEREKGIQ 55 (175)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 45559999999986543
No 31
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=53.15 E-value=20 Score=25.41 Aligned_cols=14 Identities=43% Similarity=0.655 Sum_probs=6.1
Q ss_pred HHHHHhhheeeeee
Q 035538 112 IALSILTIGVVYIG 125 (171)
Q Consensus 112 vgLsilTiGViYL~ 125 (171)
+++.++.+|++|..
T Consensus 21 ~~v~~~a~~~v~~~ 34 (97)
T PF04999_consen 21 IVVLISALGVVYSR 34 (97)
T ss_pred HHHHHHHHHHHHHH
Confidence 33333444555544
No 32
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=52.56 E-value=15 Score=28.99 Aligned_cols=36 Identities=11% Similarity=0.182 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHH
Q 035538 101 SVISVLLFAAFIALSILTIGVVYIGVTDFLQKREREKFE 139 (171)
Q Consensus 101 ~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~Ekfe 139 (171)
.+.+++-|+.|++|... ++|==++++|++|+..=.+
T Consensus 25 ~~~~~inflil~~lL~~---fl~kPi~~~l~~R~~~I~~ 60 (167)
T PRK08475 25 IIERTINFLIFVGILWY---FAAKPLKNFYKSRINKISK 60 (167)
T ss_pred HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Confidence 44444444444433332 3455599999999876433
No 33
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=51.97 E-value=12 Score=37.34 Aligned_cols=37 Identities=38% Similarity=0.561 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhhhhhhccccccCCCC------CCCcccCCCCC
Q 035538 135 REKFEKEEAATKKKKKVKAKPRAGPR------GFGQKIDDDDD 171 (171)
Q Consensus 135 ~EkfeKeEaak~kkkkk~~raraGpr------GFGqKi~eddd 171 (171)
++|.+||++.+.+++++..+-..|.+ =||+|+...||
T Consensus 597 ~kk~~~e~~~~~~~~~~~~~s~~~~~~~~d~~~~gekL~~t~~ 639 (700)
T KOG1156|consen 597 KKKAKKEAKKKKDKKKKEAKSQSGKPVDIDEDPFGEKLLKTED 639 (700)
T ss_pred HHHHHHHHHHHHHHHHhhhccccCCCCCCCCcchhhhHhhcCC
Confidence 33344444333333444333334443 46666665554
No 34
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=51.39 E-value=23 Score=27.89 Aligned_cols=31 Identities=29% Similarity=0.362 Sum_probs=19.8
Q ss_pred HHHHHHHHHhhheeeeeehhhhhhhHHHHHH
Q 035538 108 FAAFIALSILTIGVVYIGVTDFLQKREREKF 138 (171)
Q Consensus 108 fvAfvgLsilTiGViYL~VtdFlqKRe~Ekf 138 (171)
+|.|+.|.+|-.=++|=-|.++|++|+..=.
T Consensus 25 iInFliL~~lL~~~l~~pi~~~l~~R~~~I~ 55 (173)
T PRK13453 25 VLTFIVLLALLKKFAWGPLKDVMDKRERDIN 55 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445544444444556669999999987543
No 35
>PF10278 Med19: Mediator of RNA pol II transcription subunit 19 ; InterPro: IPR019403 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=51.22 E-value=8.6 Score=32.28 Aligned_cols=8 Identities=38% Similarity=0.663 Sum_probs=3.3
Q ss_pred ccCCCCCC
Q 035538 155 PRAGPRGF 162 (171)
Q Consensus 155 araGprGF 162 (171)
+.-.|-||
T Consensus 171 ~~~~~~~~ 178 (178)
T PF10278_consen 171 PEHPGMGF 178 (178)
T ss_pred CcCCCCCC
Confidence 33344444
No 36
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=51.17 E-value=23 Score=26.64 Aligned_cols=37 Identities=22% Similarity=0.317 Sum_probs=21.0
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHh
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAAT 145 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak 145 (171)
|.|+-|.++--=.+|=-+.+||++|+..=.+..+++.
T Consensus 12 i~Flil~~il~~~~~~pi~~~l~~R~~~I~~~l~~a~ 48 (156)
T PRK05759 12 IAFLILVWFIMKFVWPPIMKALEERQKKIADGLAAAE 48 (156)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444333332233455599999999876554443333
No 37
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=48.83 E-value=26 Score=26.88 Aligned_cols=32 Identities=19% Similarity=0.276 Sum_probs=19.8
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKFEK 140 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~EkfeK 140 (171)
|.|+.|.++..=++|=-|.++|++|...=...
T Consensus 13 inF~il~~iL~~f~~kpi~~~l~~R~~~I~~~ 44 (159)
T PRK13461 13 INFIILLLILKHFFFDKIKAVIDSRQSEIDNK 44 (159)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 34444444444445666999999998754333
No 38
>PF04882 Peroxin-3: Peroxin-3; InterPro: IPR006966 Peroxin 3 (Pex3p), also known as Peroxisomal biogenesis factor 3, has been identified and characterised as a peroxisomal membrane protein in yeasts and mammals []. Two putative peroxisomal membrane-bound Pex3p homologues have also been found in Arabidopsis thaliana []. They possess a membrane peroxisomal targeting signal. Pex3p is an integral membrane protein of peroxisomes, exposing its N- and C-terminal parts to the cytosol []. Peroxin is involved in peroxisome biosynthesis and integrity; it assembles membrane vesicles before the matrix proteins are translocated. In humans, defects in PEX3 are the cause of peroxisome biogenesis disorders [], which include Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). These are peroxisomal disorders that are the result of proteins failing to be imported into the peroxisome.; GO: 0007031 peroxisome organization, 0005779 integral to peroxisomal membrane; PDB: 3MK4_A 3AJB_A.
Probab=47.28 E-value=8.8 Score=34.75 Aligned_cols=31 Identities=26% Similarity=0.331 Sum_probs=5.4
Q ss_pred hhheeeeeehhhhhhhHHHHHHHHHHHHhhhh
Q 035538 117 LTIGVVYIGVTDFLQKREREKFEKEEAATKKK 148 (171)
Q Consensus 117 lTiGViYL~VtdFlqKRe~EkfeKeEaak~kk 148 (171)
..+|.+|+ +.-|.++|-+|-.+++.+++--|
T Consensus 20 ~v~g~~y~-~~~y~~~kl~e~q~~~~~e~~~k 50 (432)
T PF04882_consen 20 GVVGGGYL-LYQYAQKKLREQQERMAEERFAK 50 (432)
T ss_dssp ---------------------HHHHHHHHHHH
T ss_pred cccccccc-ccccccccccccccccccccccc
Confidence 45677788 77799998655555554444444
No 39
>TIGR00267 conserved hypothetical protein TIGR00267. This family is represented in three of the first four completed archaeal genomes, with two members in A. fulgidus.
Probab=47.16 E-value=17 Score=28.97 Aligned_cols=34 Identities=18% Similarity=0.062 Sum_probs=18.1
Q ss_pred HHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHh
Q 035538 112 IALSILTIGVVYIGVTDFLQKREREKFEKEEAAT 145 (171)
Q Consensus 112 vgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak 145 (171)
.||.-+.-|-+=.+.-+|+..|++.+.|++|-+|
T Consensus 33 ~Gla~~vA~a~Sma~GeYv~e~ae~~~e~~ele~ 66 (169)
T TIGR00267 33 AGLGGGVANGMSNAFGAFTAERAEEEREMRELEK 66 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444556677888655555555544433
No 40
>PF06375 BLVR: Bovine leukaemia virus receptor (BLVR); InterPro: IPR010474 Bovine leukemia virus (BLV) is one of the most common infectious cattle viruses, with between 30 and 40% of cows in the United States being infected. It is closely related to the human T-cell leukaemia virus type 1 (HTLV-1) and has highly conserved envelope glycoprotein functional domains []. BLV is an oncogenic C-type retrovirus, which results in the animals developing a malignant lymphoma. BLV, like the human and simian T cell leukaemia viruses, is a deltaretrovirus. 182 residues at the amino-terminal of the BLV envelope glycoprotein surface unit encompass the receptor-binding domain. The metabolic activity in B cells, T cells, and thymocytes is indicated by the expression of the BLV-binding receptor []. A candidate gene of the receptor (BLVR) is related, but unique, to a gene family of the delta subunit of the adaptor protein (AP) complex 3, AP-3 []. The AP-3 complex is not clathrin-associated but is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. ; PDB: 4AFI_B.
Probab=46.68 E-value=5.7 Score=32.42 Aligned_cols=17 Identities=18% Similarity=0.503 Sum_probs=0.0
Q ss_pred ccCCCCCCCcccCCCCC
Q 035538 155 PRAGPRGFGQKIDDDDD 171 (171)
Q Consensus 155 araGprGFGqKi~eddd 171 (171)
-+++.+.+.-.=++|||
T Consensus 96 Kk~~k~~~~~sse~~ed 112 (154)
T PF06375_consen 96 KKSKKRHYSESSESDED 112 (154)
T ss_dssp -----------------
T ss_pred ccCCCCCCCCCCccccc
Confidence 44444455555444443
No 41
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=45.55 E-value=51 Score=26.60 Aligned_cols=21 Identities=10% Similarity=0.194 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhe
Q 035538 100 SSVISVLLFAAFIALSILTIG 120 (171)
Q Consensus 100 a~vis~LlfvAfvgLsilTiG 120 (171)
+-+|++++.|++|...|+.++
T Consensus 12 aK~vTvVvaI~~vv~~I~~~~ 32 (155)
T PF08496_consen 12 AKIVTVVVAILAVVGLIVAAA 32 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 445666666666655666654
No 42
>PF03268 DUF267: Caenorhabditis protein of unknown function, DUF267; InterPro: IPR004950 This family of proteins, from Caenorhabditis species, have not been characterised though a number are annotated as 'serpentine receptor, class r' proteins.
Probab=44.23 E-value=25 Score=32.27 Aligned_cols=49 Identities=29% Similarity=0.242 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHH-HHHhhhh
Q 035538 100 SSVISVLLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKE-EAATKKK 148 (171)
Q Consensus 100 a~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKe-Eaak~kk 148 (171)
+..-....+++|++--+-++-++|-++--.-=.||=|.|.+| |+|++.|
T Consensus 150 ~~~~~~~~~i~~l~~~is~i~L~~y~lv~~al~REi~yFN~ELe~A~keK 199 (353)
T PF03268_consen 150 SWYYILDPFINFLCWYISFICLAIYFLVNSALNREIEYFNEELEKASKEK 199 (353)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 444455556666666566665555555555668999999999 7776666
No 43
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=44.01 E-value=29 Score=28.70 Aligned_cols=30 Identities=10% Similarity=0.157 Sum_probs=22.1
Q ss_pred HHHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 108 FAAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 108 fvAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
.|.|+.|.+|.--++|==|.++|++|...=
T Consensus 60 ~I~FliL~~lL~k~~~~pI~~vLe~R~~~I 89 (204)
T PRK09174 60 AITFGLFYLFMSRVILPRIGGIIETRRDRI 89 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356666666666677777899999998654
No 44
>PF15122 TMEM206: TMEM206 protein family
Probab=42.47 E-value=20 Score=32.41 Aligned_cols=34 Identities=32% Similarity=0.544 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhheeeeeehhhhhhh
Q 035538 99 LSSVISVLLFAAFIALSILTIGVVYIGVTDFLQK 132 (171)
Q Consensus 99 ~a~vis~LlfvAfvgLsilTiGViYL~VtdFlqK 132 (171)
.-.+.|+||..-++.|.++.+=.+|--++||++|
T Consensus 9 lkn~fsvlLi~iYllLmaVAvflayqTI~df~ek 42 (298)
T PF15122_consen 9 LKNVFSVLLIFIYLLLMAVAVFLAYQTISDFREK 42 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence 4578999999999999999999999999999876
No 45
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=42.45 E-value=41 Score=25.90 Aligned_cols=33 Identities=27% Similarity=0.329 Sum_probs=20.8
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKFEKE 141 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~EkfeKe 141 (171)
|.|+.|.+|-.=++|=-+.++|++|+..=.+.-
T Consensus 16 inflil~~lL~~fl~kpi~~~l~~R~~~I~~~l 48 (164)
T PRK14473 16 INFLLLIFLLRTFLYRPVLNLLNERTRRIEESL 48 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444556669999999987544433
No 46
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=42.28 E-value=14 Score=33.27 Aligned_cols=27 Identities=30% Similarity=0.303 Sum_probs=20.3
Q ss_pred hHHHHH----HHHHHHHHHHHHhhheeee-ee
Q 035538 99 LSSVIS----VLLFAAFIALSILTIGVVY-IG 125 (171)
Q Consensus 99 ~a~vis----~LlfvAfvgLsilTiGViY-L~ 125 (171)
++.+|+ +++++|-++.++-++|++| +.
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (615)
T TIGR00990 26 MSNWISENKTAVYTIAGVTVVATGAGVVYYQR 57 (615)
T ss_pred HHHHHHhcchHhhhhhhhHhheeccceEEEee
Confidence 555554 6677888888888999888 65
No 47
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=42.22 E-value=42 Score=24.96 Aligned_cols=23 Identities=9% Similarity=0.277 Sum_probs=15.0
Q ss_pred cchHHHHHHHHHHHHHHHHHhhh
Q 035538 97 ESLSSVISVLLFAAFIALSILTI 119 (171)
Q Consensus 97 ~g~a~vis~LlfvAfvgLsilTi 119 (171)
-|+.+-...+|+++++.+.++++
T Consensus 60 lGi~~~~n~lf~~~i~~ll~~~~ 82 (115)
T PF10066_consen 60 LGIGRPPNLLFYLGILFLLVIIF 82 (115)
T ss_pred HCCCchhHHHHHHHHHHHHHHHH
Confidence 35666667777777777666543
No 48
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=41.78 E-value=40 Score=25.98 Aligned_cols=30 Identities=17% Similarity=0.224 Sum_probs=20.1
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKF 138 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~Ekf 138 (171)
|.|+.|.+|.-=.+|==|..+|++|+..=.
T Consensus 16 i~Flil~~ll~~~l~~pi~~~l~~R~~~I~ 45 (164)
T PRK14471 16 ILFLILLLLLAKFAWKPILGAVKEREDSIK 45 (164)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 445555555444567779999999987543
No 49
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=40.16 E-value=32 Score=29.60 Aligned_cols=20 Identities=30% Similarity=0.265 Sum_probs=14.8
Q ss_pred hhhhhhHHHHHHHHHHHHhh
Q 035538 127 TDFLQKREREKFEKEEAATK 146 (171)
Q Consensus 127 tdFlqKRe~EkfeKeEaak~ 146 (171)
.+|++.|-+|-+|+||..+.
T Consensus 135 e~~vE~r~~e~qeee~rlkd 154 (193)
T KOG4727|consen 135 EYDVEERLRETQEEEERLKD 154 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 46888888888888765543
No 50
>PF11214 Med2: Mediator complex subunit 2; InterPro: IPR021017 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression [, ].
Probab=40.03 E-value=26 Score=27.51 Aligned_cols=18 Identities=44% Similarity=0.595 Sum_probs=9.6
Q ss_pred hhhHHHHHHHHHHHHhhh
Q 035538 130 LQKREREKFEKEEAATKK 147 (171)
Q Consensus 130 lqKRe~EkfeKeEaak~k 147 (171)
=++||++|.++||+.+++
T Consensus 82 ~q~~ee~K~keE~E~~rk 99 (105)
T PF11214_consen 82 KQKQEEEKIKEEEERKRK 99 (105)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 356676674444444443
No 51
>PF07790 DUF1628: Protein of unknown function (DUF1628); InterPro: IPR012859 The sequences making up this family are derived from hypothetical proteins of unknown function expressed by various archaeal species. The region in question is approximately 160 residues long.
Probab=39.51 E-value=20 Score=24.68 Aligned_cols=30 Identities=27% Similarity=0.500 Sum_probs=21.8
Q ss_pred cchHHHHHHHHHHHHHHHHHhhheeeeeeh
Q 035538 97 ESLSSVISVLLFAAFIALSILTIGVVYIGV 126 (171)
Q Consensus 97 ~g~a~vis~LlfvAfvgLsilTiGViYL~V 126 (171)
+|++-+|.++|.+|..-+..-++|+.-++.
T Consensus 1 ~avS~viGviLliaitVilaavv~~~~~~~ 30 (80)
T PF07790_consen 1 RAVSPVIGVILLIAITVILAAVVGAFVFGL 30 (80)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 478889999998887776666666655554
No 52
>PF11688 DUF3285: Protein of unknown function (DUF3285); InterPro: IPR021702 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=39.33 E-value=13 Score=25.63 Aligned_cols=31 Identities=19% Similarity=0.237 Sum_probs=17.5
Q ss_pred hhhhccCCcchHHHHHHHHHHHHHHHHHhhheeeeee
Q 035538 89 EMVSSTGDESLSSVISVLLFAAFIALSILTIGVVYIG 125 (171)
Q Consensus 89 ~~~~s~~d~g~a~vis~LlfvAfvgLsilTiGViYL~ 125 (171)
.||. ..|++..= |++-++||.-+-||+.||+
T Consensus 14 NMVR---Kg~~SL~H---F~LT~~gll~~lv~la~l~ 44 (45)
T PF11688_consen 14 NMVR---KGGTSLFH---FGLTAVGLLGFLVGLAYLT 44 (45)
T ss_pred HHHH---ccCcchhH---HHHHHHHHHHHHHHHHHhc
Confidence 5555 34455443 4444555555667788875
No 53
>PRK06568 F0F1 ATP synthase subunit B; Validated
Probab=39.27 E-value=48 Score=26.71 Aligned_cols=30 Identities=13% Similarity=0.112 Sum_probs=19.2
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKF 138 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~Ekf 138 (171)
|+|+.|.+|.--..|=-++.+|++|+..=.
T Consensus 12 I~FlIll~ll~kfawkPI~~~LeeR~~~I~ 41 (154)
T PRK06568 12 VSFVIFVYLIYRPAKKAILNSLDAKILEVQ 41 (154)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 334444444344557789999999987543
No 54
>TIGR01144 ATP_synt_b ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase.
Probab=38.58 E-value=36 Score=25.43 Aligned_cols=31 Identities=16% Similarity=0.323 Sum_probs=18.8
Q ss_pred HHHHHHHhhheeeeeehhhhhhhHHHHHHHH
Q 035538 110 AFIALSILTIGVVYIGVTDFLQKREREKFEK 140 (171)
Q Consensus 110 AfvgLsilTiGViYL~VtdFlqKRe~EkfeK 140 (171)
.|+.|.+|--=++|=-|..||++|+..=...
T Consensus 4 ~Flil~~il~~~~~~pi~~~l~~R~~~I~~~ 34 (147)
T TIGR01144 4 SFILLVWFCMKYVWPPLAKAIETRQKKIADG 34 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444433345666999999998754333
No 55
>TIGR03065 srtB_sig_QVPTGV sortase B signal domain, QVPTGV class. This model represents a boutique (unusual) sorting signal, recognized by a member of the sortase SrtB family rather than by the housekeeping sortase, SrtA.
Probab=38.43 E-value=4.8 Score=25.96 Aligned_cols=16 Identities=44% Similarity=0.858 Sum_probs=11.9
Q ss_pred HHHHHHHhhh-eeeeee
Q 035538 110 AFIALSILTI-GVVYIG 125 (171)
Q Consensus 110 AfvgLsilTi-GViYL~ 125 (171)
-|++|+|+.+ |++|+-
T Consensus 12 pf~al~iva~gg~~y~t 28 (32)
T TIGR03065 12 PFAALGIVAIGGAIYFT 28 (32)
T ss_pred cceeEEEEEeccEEEEE
Confidence 4788888866 588873
No 56
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=36.79 E-value=67 Score=24.19 Aligned_cols=18 Identities=17% Similarity=0.255 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHhhhe
Q 035538 103 ISVLLFAAFIALSILTIG 120 (171)
Q Consensus 103 is~LlfvAfvgLsilTiG 120 (171)
|+..++++++|+.++-+|
T Consensus 2 i~l~iv~~~~~v~~~i~~ 19 (87)
T PF10883_consen 2 INLQIVGGVGAVVALILA 19 (87)
T ss_pred hhHHHHHHHHHHHHHHHH
Confidence 344555555555555544
No 57
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=36.61 E-value=17 Score=28.52 Aligned_cols=17 Identities=12% Similarity=-0.078 Sum_probs=12.3
Q ss_pred CcchHHHHHHHHHHHHH
Q 035538 96 DESLSSVISVLLFAAFI 112 (171)
Q Consensus 96 d~g~a~vis~LlfvAfv 112 (171)
+..+..+|++++||+||
T Consensus 75 ~~~~~iivgvi~~Vi~I 91 (179)
T PF13908_consen 75 YFITGIIVGVICGVIAI 91 (179)
T ss_pred cceeeeeeehhhHHHHH
Confidence 44566778888888777
No 58
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=34.89 E-value=47 Score=27.52 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=19.0
Q ss_pred HHHHHHHhhheeeeeehhhhhhhHHHHHHHHH
Q 035538 110 AFIALSILTIGVVYIGVTDFLQKREREKFEKE 141 (171)
Q Consensus 110 AfvgLsilTiGViYL~VtdFlqKRe~EkfeKe 141 (171)
.|+.|.++..=.+|=-|..+|++|+..=...-
T Consensus 14 nFlil~~lL~kfl~kPi~~~l~~R~~~I~~~l 45 (246)
T TIGR03321 14 NFLILVWLLKRFLYRPILDAMDAREKKIAGEL 45 (246)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 34434333333445559999999987644333
No 59
>PF13105 DUF3959: Protein of unknown function (DUF3959)
Probab=32.91 E-value=27 Score=30.68 Aligned_cols=44 Identities=25% Similarity=0.379 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHH--HHHhhhh
Q 035538 105 VLLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKE--EAATKKK 148 (171)
Q Consensus 105 ~LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKe--Eaak~kk 148 (171)
-|++--++=|.+|..|.|.=|+-.-+-+|.+..+.|| .-=|+||
T Consensus 124 sLmTs~~~YlllLvgGli~GGLlA~~~hRke~d~~kEn~nlf~qKK 169 (239)
T PF13105_consen 124 SLMTSHYLYLLLLVGGLILGGLLAMLIHRKEKDNNKENINLFKQKK 169 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhhHHHhhHh
Confidence 3556666666666777777676666667765555555 3344444
No 60
>KOG2827 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.74 E-value=29 Score=31.80 Aligned_cols=40 Identities=23% Similarity=0.194 Sum_probs=27.2
Q ss_pred hhhhhhhHHHHHHHHHHHHhhhhhhccccccCCCCCCCcc
Q 035538 126 VTDFLQKREREKFEKEEAATKKKKKVKAKPRAGPRGFGQK 165 (171)
Q Consensus 126 VtdFlqKRe~EkfeKeEaak~kkkkk~~raraGprGFGqK 165 (171)
|..||+|+..|+.+++|..|+|=.|--+-+.++.++=-|+
T Consensus 111 Lk~wLeKqa~eere~kE~kK~KlEKllA~p~~kHdFdD~~ 150 (322)
T KOG2827|consen 111 LKIWLEKQAVEERESKESKKEKLEKLLALPNGKHDFDDSG 150 (322)
T ss_pred HHHHHHhcchhhhhhHHHHHHHHHHHcccCCccccccchh
Confidence 5678999999998888877776666555455555543333
No 61
>PRK13415 flagella biosynthesis protein FliZ; Provisional
Probab=32.62 E-value=32 Score=29.83 Aligned_cols=33 Identities=24% Similarity=0.371 Sum_probs=16.7
Q ss_pred CcchHHHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHH
Q 035538 96 DESLSSVISVLLFAAFIALSILTIGVVYIGVTDFLQKRER 135 (171)
Q Consensus 96 d~g~a~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~ 135 (171)
..++..++.+++.++|| |+.||.. .-||-||-.
T Consensus 62 ~~s~~~l~qmi~aL~~V------I~Liy~l-~rwL~rR~~ 94 (219)
T PRK13415 62 SVSAFDFVKLIGATLFV------IFLIYAL-VKWLNKRNR 94 (219)
T ss_pred CccHHHHHHHHHHHHHH------HHHHHHH-HHHHHHhcc
Confidence 33455566666555555 2333322 237777643
No 62
>PF03823 Neurokinin_B: Neurokinin B; InterPro: IPR003635 Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. This family includes neurokinins, as well as many other peptides. Like other tachykinins, neurokinins are synthesized as larger protein precursors that are enzymatically converted to their mature forms.; GO: 0007217 tachykinin receptor signaling pathway
Probab=32.38 E-value=38 Score=24.44 Aligned_cols=14 Identities=64% Similarity=0.857 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHh
Q 035538 104 SVLLFAAFIALSIL 117 (171)
Q Consensus 104 s~LlfvAfvgLsil 117 (171)
+.|||+|+++|++-
T Consensus 3 ~~lLf~aiLalsla 16 (59)
T PF03823_consen 3 STLLFAAILALSLA 16 (59)
T ss_pred hHHHHHHHHHHHHH
Confidence 57999999999875
No 63
>PF01597 GCV_H: Glycine cleavage H-protein; InterPro: IPR002930 This is a family of glycine cleavage H-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein [].; GO: 0006546 glycine catabolic process, 0005960 glycine cleavage complex; PDB: 3KLR_A 2EDG_A 1ONL_B 2KA7_A 1ZKO_A 3TZU_C 3MXU_A 3A8I_F 3A8J_E 3A7A_B ....
Probab=31.88 E-value=28 Score=26.36 Aligned_cols=16 Identities=50% Similarity=0.775 Sum_probs=12.4
Q ss_pred eeeeeehhhhhhhHHH
Q 035538 120 GVVYIGVTDFLQKRER 135 (171)
Q Consensus 120 GViYL~VtdFlqKRe~ 135 (171)
|++.||+|||.|++--
T Consensus 16 g~~~vGit~~a~~~lG 31 (122)
T PF01597_consen 16 GVVRVGITDFAQDELG 31 (122)
T ss_dssp TEEEEEE-HHHHHHH-
T ss_pred CEEEEEECchHhhcCC
Confidence 6999999999998753
No 64
>PF12409 P5-ATPase: P5-type ATPase cation transporter
Probab=31.72 E-value=17 Score=27.13 Aligned_cols=17 Identities=35% Similarity=0.708 Sum_probs=12.9
Q ss_pred HHHHHHHHHhhheeeee
Q 035538 108 FAAFIALSILTIGVVYI 124 (171)
Q Consensus 108 fvAfvgLsilTiGViYL 124 (171)
.+.+..|+|+|.|+.||
T Consensus 17 ~~l~~~l~ilT~Gll~L 33 (119)
T PF12409_consen 17 TILYYFLCILTLGLLYL 33 (119)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45667788888888776
No 65
>MTH00057 ND6 NADH dehydrogenase subunit 6; Provisional
Probab=31.43 E-value=25 Score=28.62 Aligned_cols=17 Identities=35% Similarity=0.536 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHhh
Q 035538 102 VISVLLFAAFIALSILT 118 (171)
Q Consensus 102 vis~LlfvAfvgLsilT 118 (171)
++|+||.+|.+|-.+||
T Consensus 148 ~~s~lLLvAmIGAIvLa 164 (186)
T MTH00057 148 LASFILLVAMIGAIVLT 164 (186)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 34555555555544443
No 66
>PF03596 Cad: Cadmium resistance transporter; InterPro: IPR004676 These proteins are members of the Cadmium Resistance (CadD) Family. To date, this family of proteins has only been found in Gram-positive bacteria. The CadD family includes two close orthologues in two Staphylococcus species that have been reported to function in cadmium resistance, and another staphylococcal protein that has been reported to possibly function in quaternary ammonium ion export.
Probab=30.97 E-value=12 Score=31.19 Aligned_cols=39 Identities=21% Similarity=0.506 Sum_probs=21.1
Q ss_pred chHHHHHHHHHHHHHHHHHhh---hee-----eeeehhhhhhhHHHH
Q 035538 98 SLSSVISVLLFAAFIALSILT---IGV-----VYIGVTDFLQKRERE 136 (171)
Q Consensus 98 g~a~vis~LlfvAfvgLsilT---iGV-----iYL~VtdFlqKRe~E 136 (171)
|...+|.+=++.|+.+..+.. +|. ||||+.-+++.++.|
T Consensus 35 G~~~Lv~~Sl~~~~~l~~ip~~wiLGlLGliPI~lGi~~l~~~~~~~ 81 (191)
T PF03596_consen 35 GFTILVLASLLGAFGLLFIPPEWILGLLGLIPIYLGIKALFSGEDDD 81 (191)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 555555555555554433221 232 788888777655333
No 67
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=30.95 E-value=65 Score=20.76 Aligned_cols=17 Identities=41% Similarity=0.649 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHh
Q 035538 101 SVISVLLFAAFIALSIL 117 (171)
Q Consensus 101 ~vis~LlfvAfvgLsil 117 (171)
.+..++||+.|+|+.+-
T Consensus 12 ~~~~v~~~~~F~gi~~w 28 (49)
T PF05545_consen 12 SIGTVLFFVFFIGIVIW 28 (49)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34455666666666544
No 68
>PF08725 Integrin_b_cyt: Integrin beta cytoplasmic domain; InterPro: IPR014836 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]. The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus. Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits []. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another. The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane []. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices. This entry represents the cytoplasmic domain of integrin beta subunits. ; GO: 0004872 receptor activity, 0005488 binding, 0007155 cell adhesion, 0007160 cell-matrix adhesion, 0007229 integrin-mediated signaling pathway, 0008305 integrin complex; PDB: 3G9W_C 2JF1_T 2BRQ_D 1MK9_E 1KUZ_B 2LJF_A 1MK7_C 2RN0_A 1M8O_B 2LJE_A ....
Probab=30.93 E-value=32 Score=23.02 Aligned_cols=18 Identities=39% Similarity=0.575 Sum_probs=14.8
Q ss_pred hhhhhhhHHHHHHHHHHH
Q 035538 126 VTDFLQKREREKFEKEEA 143 (171)
Q Consensus 126 VtdFlqKRe~EkfeKeEa 143 (171)
++...++||=+|||+|-.
T Consensus 3 l~~i~DrrEy~kFe~E~~ 20 (47)
T PF08725_consen 3 LITIHDRREYAKFEKERK 20 (47)
T ss_dssp HHHHHHHCHCHHHHHHHH
T ss_pred EEEEehHHHHHHHHHHHH
Confidence 456789999999999954
No 69
>PF15240 Pro-rich: Proline-rich
Probab=30.83 E-value=31 Score=29.06 Aligned_cols=25 Identities=32% Similarity=0.183 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHh---hheeeeeehhh
Q 035538 104 SVLLFAAFIALSIL---TIGVVYIGVTD 128 (171)
Q Consensus 104 s~LlfvAfvgLsil---TiGViYL~Vtd 128 (171)
-|||+||.||||-. -=.|+|-.+++
T Consensus 3 lVLLSvALLALSSAQ~~dEdv~~e~~~~ 30 (179)
T PF15240_consen 3 LVLLSVALLALSSAQSTDEDVSQEESPS 30 (179)
T ss_pred hHHHHHHHHHhhhccccccccccccCcc
Confidence 47999999999853 22345544333
No 70
>PF13755 Sensor_TM1: Sensor N-terminal transmembrane domain
Probab=30.60 E-value=24 Score=26.18 Aligned_cols=21 Identities=29% Similarity=0.592 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHhhheeeeee
Q 035538 105 VLLFAAFIALSILTIGVVYIG 125 (171)
Q Consensus 105 ~LlfvAfvgLsilTiGViYL~ 125 (171)
-++++=.+||.+|..|+.||-
T Consensus 17 rIl~~Nl~aL~vLv~G~LyLn 37 (79)
T PF13755_consen 17 RILAFNLLALAVLVGGILYLN 37 (79)
T ss_pred HHHHHHHHHHHHHHHHHHhhh
Confidence 357778899999999999985
No 71
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=30.56 E-value=39 Score=29.30 Aligned_cols=6 Identities=33% Similarity=0.645 Sum_probs=2.2
Q ss_pred ceeecC
Q 035538 16 ITSILN 21 (171)
Q Consensus 16 ~~si~~ 21 (171)
+..|.+
T Consensus 128 V~Aiv~ 133 (321)
T PF07946_consen 128 VFAIVN 133 (321)
T ss_pred EEEEEc
Confidence 333333
No 72
>PF00430 ATP-synt_B: ATP synthase B/B' CF(0); InterPro: IPR002146 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunits B and B' from the F0 complex in F-ATPases found in chloroplasts and in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial and chloroplast F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o); PDB: 1L2P_A 2KHK_A 1B9U_A.
Probab=30.06 E-value=40 Score=24.17 Aligned_cols=30 Identities=23% Similarity=0.373 Sum_probs=15.7
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKF 138 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~Ekf 138 (171)
|.|+-|.++-.-.+|=-+..||++|...=.
T Consensus 7 i~Flil~~~l~~~~~~pi~~~l~~R~~~I~ 36 (132)
T PF00430_consen 7 INFLILFFLLNKFLYKPIKKFLDERKAKIQ 36 (132)
T ss_dssp HHHHHHHHHHHHHTHHHHHHHCS--S-HHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444456678899999976543
No 73
>PF03004 Transposase_24: Plant transposase (Ptta/En/Spm family); InterPro: IPR004252 Transposase proteins are necessary for efficient DNA transposition. This family includes various plant transposases from the Ptta and En/Spm families []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=30.03 E-value=48 Score=24.46 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=28.3
Q ss_pred hhhhhhHHHHHHHHH-HHHhhhh-hhccccccCCCCCCCccc
Q 035538 127 TDFLQKREREKFEKE-EAATKKK-KKVKAKPRAGPRGFGQKI 166 (171)
Q Consensus 127 tdFlqKRe~EkfeKe-Eaak~kk-kkk~~raraGprGFGqKi 166 (171)
..|++.+..+||++. +..+.-+ .+....-++|.++|.+..
T Consensus 6 ~~lv~~w~s~~~~~~S~~nk~nR~~~~~~~H~~Gs~s~~~~~ 47 (141)
T PF03004_consen 6 NWLVEYWSSPEFKKRSEKNKANRSAKGKHPHTTGSKSFAAHR 47 (141)
T ss_pred HHHHHHhCCHHHHHHHHHHHHhhhcCCCcccCcCCchHHHHH
Confidence 357778888888887 4444444 456677899999997654
No 74
>PF04789 DUF621: Protein of unknown function (DUF621); InterPro: IPR006874 This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans, and is noted to have possible G-protein-coupled receptor-like activity.
Probab=29.72 E-value=52 Score=30.02 Aligned_cols=22 Identities=45% Similarity=0.623 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHHHhhhe
Q 035538 99 LSSVISVLLFAAFIALSILTIG 120 (171)
Q Consensus 99 ~a~vis~LlfvAfvgLsilTiG 120 (171)
+++++|.||+.+|+.|+++--|
T Consensus 21 ~st~~stlLt~~Flv~~i~lW~ 42 (305)
T PF04789_consen 21 LSTIASTLLTGAFLVLSIILWS 42 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5788899999999998886544
No 75
>PF09428 DUF2011: Fungal protein of unknown function (DUF2011); InterPro: IPR018555 This is a family of fungal proteins whose function is unknown.
Probab=29.68 E-value=46 Score=26.29 Aligned_cols=12 Identities=33% Similarity=0.387 Sum_probs=5.8
Q ss_pred hhccccccCCCC
Q 035538 149 KKVKAKPRAGPR 160 (171)
Q Consensus 149 kkk~~raraGpr 160 (171)
++|+-+-|+|-|
T Consensus 118 r~KK~kkR~~~K 129 (131)
T PF09428_consen 118 RKKKFKKRGKKK 129 (131)
T ss_pred HHHHHHhhcccc
Confidence 344444566543
No 76
>PF03839 Sec62: Translocation protein Sec62; InterPro: IPR004728 Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins have been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane
Probab=29.53 E-value=56 Score=28.06 Aligned_cols=29 Identities=31% Similarity=0.602 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHHHh-------hheeeeeehh
Q 035538 99 LSSVISVLLFAAFIALSIL-------TIGVVYIGVT 127 (171)
Q Consensus 99 ~a~vis~LlfvAfvgLsil-------TiGViYL~Vt 127 (171)
..+++++++.++++++.+. =.||-||++.
T Consensus 110 ~~~l~~~~~~~~v~a~~lFPlWP~~~r~gv~YlS~~ 145 (224)
T PF03839_consen 110 MQYLIGALLLVGVIAICLFPLWPRWMRQGVYYLSVG 145 (224)
T ss_pred HHHHHHHHHHHHHHHHHhhhcChHHHhheeehhHHH
Confidence 5677888888887776653 3577777754
No 77
>KOG4848 consensus Extracellular matrix-associated peroxidase [Extracellular structures; Defense mechanisms]
Probab=29.48 E-value=47 Score=29.17 Aligned_cols=26 Identities=31% Similarity=0.496 Sum_probs=19.0
Q ss_pred hhhhhhHHHHHHHHHHHHhhhhhhcc
Q 035538 127 TDFLQKREREKFEKEEAATKKKKKVK 152 (171)
Q Consensus 127 tdFlqKRe~EkfeKeEaak~kkkkk~ 152 (171)
.+.||..|+|+-++-.+||+|.|+.+
T Consensus 192 ~emLqqkEkeekK~~KeaKrk~k~ek 217 (225)
T KOG4848|consen 192 EEMLQQKEKEEKKAVKEAKRKEKQEK 217 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57788888888777777777775543
No 78
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=29.33 E-value=46 Score=26.91 Aligned_cols=35 Identities=17% Similarity=0.343 Sum_probs=21.0
Q ss_pred HHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHh
Q 035538 111 FIALSILTIGVVYIGVTDFLQKREREKFEKEEAAT 145 (171)
Q Consensus 111 fvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak 145 (171)
..||..+.-|-+=.|+.+|+-.|.+.+.++.|.++
T Consensus 35 ~~gla~~iAga~SMa~G~yls~~se~~~~~~e~~r 69 (213)
T PF01988_consen 35 LAGLAGLIAGAISMAVGEYLSVKSERDLYEAERER 69 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhHH
Confidence 34555555566667788888766665544444433
No 79
>PRK08808 general secretion pathway protein J; Validated
Probab=28.89 E-value=49 Score=27.78 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHH
Q 035538 101 SVISVLLFAAFIALSILTIGVVYIGVTDFLQKRERE 136 (171)
Q Consensus 101 ~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~E 136 (171)
|+|=+|+.+|++|+ ..+++|.+++++.++.++-
T Consensus 10 TLiEllia~ai~~i---l~~~a~~s~~~~~~~~~r~ 42 (211)
T PRK08808 10 TLIEVLLATVLLVG---GLALAFATLRSASAVSQRG 42 (211)
T ss_pred eHHHHHHHHHHHHH---HHHHHHHHHHHHHhhhHHH
Confidence 57778888887773 3345899999999886543
No 80
>PF01405 PsbT: Photosystem II reaction centre T protein; InterPro: IPR001743 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 PsbT found in PSII, which is thought to be associated with the D1 (PsbA) - D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3BZ1_T 1S5L_t 2AXT_t 3KZI_T 3PRQ_T 3BZ2_T 3PRR_T 4FBY_g 3A0H_t 3A0B_T ....
Probab=28.84 E-value=15 Score=23.18 Aligned_cols=18 Identities=22% Similarity=0.539 Sum_probs=11.6
Q ss_pred HHHHHHHHhhheeeeeeh
Q 035538 109 AAFIALSILTIGVVYIGV 126 (171)
Q Consensus 109 vAfvgLsilTiGViYL~V 126 (171)
++.+-|.+.|+|+++.+|
T Consensus 4 ~vY~~ll~~tlgilffAI 21 (29)
T PF01405_consen 4 LVYTFLLIGTLGILFFAI 21 (29)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHhhh
Confidence 345556667777777665
No 81
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=28.75 E-value=66 Score=21.51 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHhh
Q 035538 102 VISVLLFAAFIALSILT 118 (171)
Q Consensus 102 vis~LlfvAfvgLsilT 118 (171)
++.++.|++++|-++.|
T Consensus 21 l~mi~vFi~li~ytl~t 37 (38)
T PF09125_consen 21 LAMILVFIALIGYTLAT 37 (38)
T ss_dssp HHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 45667788888877765
No 82
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=26.99 E-value=1e+02 Score=21.81 Aligned_cols=30 Identities=10% Similarity=0.051 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHhhheeeeeehhhhhh
Q 035538 102 VISVLLFAAFIALSILTIGVVYIGVTDFLQ 131 (171)
Q Consensus 102 vis~LlfvAfvgLsilTiGViYL~VtdFlq 131 (171)
.+.++|+++++++.+..+.+-|-....+-+
T Consensus 14 ~l~i~l~~~v~~~a~~~v~~~~~~~~~~~~ 43 (97)
T PF04999_consen 14 KLIILLVIVVLISALGVVYSRHQSRQLFYE 43 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445557777777777777777666666654
No 83
>TIGR02537 arch_flag_Nterm archaeal flagellin N-terminal-like domain. This model describes a hydrophobic N-terminal sequence of archaeal flagellins and other archaeal proteins. The sequence is directly analogous to bacterial sequences recognized by TIGR02532, which has cleavage motif resembling G^FxxxE followed by strongly hydrophobic sequence. Such sequences are the recognized for cleavage and methylation, and include pilins and other pilus components and competence and type II secretion secretion proteins. In the present family, the E is not conversed and sequence differs enough that there is no overlap between this family and TIGR02532.
Probab=26.96 E-value=99 Score=18.64 Aligned_cols=19 Identities=16% Similarity=0.436 Sum_probs=14.3
Q ss_pred CcchHHHHHHHHHHHHHHH
Q 035538 96 DESLSSVISVLLFAAFIAL 114 (171)
Q Consensus 96 d~g~a~vis~LlfvAfvgL 114 (171)
+.|.+-++.+++++|++-.
T Consensus 1 ~rgis~I~~~iiliai~iv 19 (26)
T TIGR02537 1 RKGISPIIGTIILIAITIV 19 (26)
T ss_pred CCcchhHHHHHHHHHHHHH
Confidence 3577888888888887643
No 84
>PF00664 ABC_membrane: ABC transporter transmembrane region; InterPro: IPR001140 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). A variety of ATP-binding transport proteins have a six transmembrane helical region. They are all integral membrane proteins involved in a variety of transport systems. Members of this family include; the cystic fibrosis transmembrane conductance regulator (CFTR), bacterial leukotoxin secretion ATP-binding protein, multidrug resistance proteins, the yeast leptomycin B resistance protein, the mammalian sulphonylurea receptor and antigen peptide transporter 2. Many of these proteins have two such regions.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3G61_B 3G5U_B 3G60_A 3B60_D 3QF4_B 2HYD_A 2ONJ_A 4A82_B 4AA3_A 2YL4_A.
Probab=26.71 E-value=63 Score=23.37 Aligned_cols=32 Identities=25% Similarity=0.213 Sum_probs=20.8
Q ss_pred HHHHhhheeeeeehhhhhhhHHHHHHHHHHHH
Q 035538 113 ALSILTIGVVYIGVTDFLQKREREKFEKEEAA 144 (171)
Q Consensus 113 gLsilTiGViYL~VtdFlqKRe~EkfeKeEaa 144 (171)
++.++.+.++++.+.-++.|+-++..++..++
T Consensus 144 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 175 (275)
T PF00664_consen 144 ALILLIILPLLFLISFIFSKKIRKLSKKYQEA 175 (275)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchhhhhhHhhhhhhcccccccccccccc
Confidence 44455556678888888888777665555333
No 85
>COG0711 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion]
Probab=26.50 E-value=1e+02 Score=24.29 Aligned_cols=37 Identities=22% Similarity=0.253 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHH
Q 035538 108 FAAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAA 144 (171)
Q Consensus 108 fvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaa 144 (171)
.++|+.|.++..=.+|=-+..+|++|...=-+....|
T Consensus 13 ~i~F~ill~ll~~~~~~pi~~~l~~R~~~I~~~l~~A 49 (161)
T COG0711 13 LIAFVILLWLLKKFVWKPILKALDERQAKIADDLAEA 49 (161)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444445555567778999999987654444333
No 86
>KOG1608 consensus Protein transporter of the TRAM (translocating chain-associating membrane) superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.41 E-value=1.7e+02 Score=27.38 Aligned_cols=34 Identities=26% Similarity=0.313 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHhhhhhhccccccCCCCCCCccc
Q 035538 133 REREKFEKEEAATKKKKKVKAKPRAGPRGFGQKI 166 (171)
Q Consensus 133 Re~EkfeKeEaak~kkkkk~~raraGprGFGqKi 166 (171)
|.-.+..+|.+.+.|||.-++++|+--++-+.|-
T Consensus 321 rrwrE~sn~qa~~~Kkk~t~~~sr~~k~~~~~~~ 354 (374)
T KOG1608|consen 321 RRWREASNEQAKKEKKKLTKKPSRSSKKAVENKE 354 (374)
T ss_pred HHHHHhhhhhhHHhhcccccCcccchhhhccccc
Confidence 3333344444555555444555666555555554
No 87
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=25.98 E-value=1.6e+02 Score=27.08 Aligned_cols=48 Identities=17% Similarity=0.038 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHHHHHHHhhh
Q 035538 100 SSVISVLLFAAFIALSILTIGVVYIGVTDFLQKREREKFEKEEAATKK 147 (171)
Q Consensus 100 a~vis~LlfvAfvgLsilTiGViYL~VtdFlqKRe~EkfeKeEaak~k 147 (171)
..++++.+.|+..+|++--+=.||+|++.|=|--...++++--+.+++
T Consensus 211 ~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~ 258 (309)
T KOG1313|consen 211 LWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRS 258 (309)
T ss_pred HHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccC
Confidence 567777777777788888888899999998666555555555555553
No 88
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=25.78 E-value=29 Score=21.49 Aligned_cols=11 Identities=36% Similarity=0.709 Sum_probs=7.5
Q ss_pred ehhhhhhhHHH
Q 035538 125 GVTDFLQKRER 135 (171)
Q Consensus 125 ~VtdFlqKRe~ 135 (171)
+++-|||||..
T Consensus 7 SLqRFLeKRK~ 17 (27)
T PF09425_consen 7 SLQRFLEKRKD 17 (27)
T ss_dssp HHHHHHHHH--
T ss_pred HHHHHHHHHHH
Confidence 56789999853
No 89
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=25.45 E-value=8.1 Score=33.64 Aligned_cols=8 Identities=38% Similarity=0.347 Sum_probs=3.2
Q ss_pred cccccCCC
Q 035538 66 IWRSNATS 73 (171)
Q Consensus 66 Lwr~~a~p 73 (171)
+.|...+|
T Consensus 12 v~rs~~tP 19 (221)
T PF08374_consen 12 VRRSLETP 19 (221)
T ss_pred HHhhccCC
Confidence 34444344
No 90
>KOG1226 consensus Integrin beta subunit (N-terminal portion of extracellular region) [Signal transduction mechanisms; Extracellular structures]
Probab=24.87 E-value=79 Score=32.13 Aligned_cols=21 Identities=38% Similarity=0.537 Sum_probs=17.0
Q ss_pred eeeehhhhhhhHHHHHHHHHH
Q 035538 122 VYIGVTDFLQKREREKFEKEE 142 (171)
Q Consensus 122 iYL~VtdFlqKRe~EkfeKeE 142 (171)
||=.++-+-++||--|||||.
T Consensus 734 iwkll~~~~DrrE~akFe~er 754 (783)
T KOG1226|consen 734 IWKLLTTIHDRREFAKFEKER 754 (783)
T ss_pred HHHHhheecccHHhhhhhHHH
Confidence 344677888999999999983
No 91
>PF03219 TLC: TLC ATP/ADP transporter; InterPro: IPR004667 These proteins are members of the ATP:ADP Antiporter (AAA) family, which consists of nucleotide transporters that have 12 GES predicted transmembrane regions. One protein from Rickettsia prowazekii functions to take up ATP from the eukaryotic cell cytoplasm into the bacterium in exchange for ADP. Five AAA family paralogues are encoded within the genome of R. prowazekii. This organism transports UMP and GMP but not CMP, and it seems likely that one or more of the AAA family paralogues are responsible. The genome of Chlamydia trachomatis encodes two AAA family members, Npt1 and Npt2, which catalyse ATP/ADP exchange and GTP, CTP, ATP and UTP uptake probably employing a proton symport mechanism. Two homologous adenylate translocators of Arabidopsis thaliana are postulated to be localized to the intracellular plastid membrane where they function as ATP importers.; GO: 0005471 ATP:ADP antiporter activity, 0005524 ATP binding, 0006810 transport, 0016021 integral to membrane
Probab=24.67 E-value=26 Score=32.55 Aligned_cols=21 Identities=19% Similarity=0.213 Sum_probs=12.2
Q ss_pred eeeeeehhhhhhhHHHHHHHH
Q 035538 120 GVVYIGVTDFLQKREREKFEK 140 (171)
Q Consensus 120 GViYL~VtdFlqKRe~EkfeK 140 (171)
|++.+.+.-+++++..++.+.
T Consensus 233 g~~i~~~~~~~~~~vl~~~~~ 253 (491)
T PF03219_consen 233 GIVIILLYRYMNKNVLTDPRF 253 (491)
T ss_pred HHHHHHHHHHHHHHccCcccc
Confidence 344445566777777655443
No 92
>PF12955 DUF3844: Domain of unknown function (DUF3844); InterPro: IPR024382 This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins thought to be located in the endoplasmic reticulum.
Probab=24.63 E-value=48 Score=25.67 Aligned_cols=28 Identities=21% Similarity=0.261 Sum_probs=19.2
Q ss_pred CcchHHHHHHHHHHHHHHHHHhhheeee
Q 035538 96 DESLSSVISVLLFAAFIALSILTIGVVY 123 (171)
Q Consensus 96 d~g~a~vis~LlfvAfvgLsilTiGViY 123 (171)
|-++.-.+-+.++|+.|++.+..||..|
T Consensus 63 DvS~~F~L~~~~ti~lv~~~~~~I~lL~ 90 (103)
T PF12955_consen 63 DVSVPFWLFAGFTIALVVLVAGAIGLLF 90 (103)
T ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 5556666666777777777777777655
No 93
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=24.24 E-value=74 Score=23.52 Aligned_cols=21 Identities=14% Similarity=0.244 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHhhhee
Q 035538 101 SVISVLLFAAFIALSILTIGV 121 (171)
Q Consensus 101 ~vis~LlfvAfvgLsilTiGV 121 (171)
..|-+++|+.|.+|++.+++-
T Consensus 28 ~~vvl~ml~~fa~l~ly~~~~ 48 (85)
T PF13150_consen 28 LRVVLVMLVLFAALCLYMTVS 48 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 345667788888888877653
No 94
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=24.23 E-value=1e+02 Score=25.13 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 107 LFAAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 107 lfvAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
++|.|+.|.++--=++|=-|+..|++|+..=
T Consensus 16 ~iI~FlILy~ll~kf~~ppI~~iLe~R~~~I 46 (155)
T PRK06569 16 LIVTFGLLYIFVYKFITPKAEEIFNNRQTNI 46 (155)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 4466666666666677888999999998654
No 95
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=24.20 E-value=1.3e+02 Score=22.56 Aligned_cols=10 Identities=10% Similarity=0.371 Sum_probs=4.4
Q ss_pred hhhhhHHHHH
Q 035538 128 DFLQKREREK 137 (171)
Q Consensus 128 dFlqKRe~Ek 137 (171)
.+.+.+++-.
T Consensus 28 ~~~~l~~q~~ 37 (105)
T PRK00888 28 DYWRVNDQVA 37 (105)
T ss_pred HHHHHHHHHH
Confidence 4444444433
No 96
>PF01917 Arch_flagellin: Archaebacterial flagellin; InterPro: IPR002774 Archaeal motility occurs by the rotation of flagella that are different to bacterial flagella, but show similarity to bacterial type IV pili. These similarities include the multiflagellin nature of the flagellar filament, N-terminal sequence similarities, as well as the presence of homologous proteins in the two systems [, ]. Also unlike bacterial flagellins but similar to type IV pilins, archaeal flagellins are initially synthesised with a short leader peptide that is cleaved by a membrane-located peptidase [, ]. The enzyme responsible for the removal of the this leader peptide is FlaK [].; GO: 0005198 structural molecule activity, 0006928 cellular component movement
Probab=24.19 E-value=58 Score=25.51 Aligned_cols=35 Identities=26% Similarity=0.561 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHHHH
Q 035538 104 SVLLFAAFIALSILTIGVVYIGVTDFLQKREREKFE 139 (171)
Q Consensus 104 s~LlfvAfvgLsilTiGViYL~VtdFlqKRe~Ekfe 139 (171)
.+++|+|||-...+-.||+ |.-..|||.+.++.-+
T Consensus 7 t~IvfIA~VlVAAv~a~vl-i~t~~~l~~~a~~~~~ 41 (190)
T PF01917_consen 7 TAIVFIAFVLVAAVAAGVL-INTGGFLQQKAQSTGQ 41 (190)
T ss_pred hHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 4567888877777777765 4566789988877633
No 97
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=24.18 E-value=88 Score=29.43 Aligned_cols=7 Identities=29% Similarity=0.909 Sum_probs=3.1
Q ss_pred eeeehhh
Q 035538 122 VYIGVTD 128 (171)
Q Consensus 122 iYL~Vtd 128 (171)
|||-+-|
T Consensus 384 iYl~l~d 390 (517)
T PF12569_consen 384 IYLELHD 390 (517)
T ss_pred HHHHHhc
Confidence 4544443
No 98
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=24.02 E-value=1.3e+02 Score=21.94 Aligned_cols=37 Identities=24% Similarity=0.374 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHhhheeeee--ehhhhhhhHHHHHHH
Q 035538 103 ISVLLFAAFIALSILTIGVVYI--GVTDFLQKREREKFE 139 (171)
Q Consensus 103 is~LlfvAfvgLsilTiGViYL--~VtdFlqKRe~Ekfe 139 (171)
+-+++|+++..+.-+-..++.+ .+..++++|-++|-.
T Consensus 22 ~l~~~~~~l~ll~~ll~~~~~~p~~~~~~~~~rr~~ka~ 60 (108)
T PF07219_consen 22 LLLLLFVVLYLLLRLLRRLLSLPSRVRRWRRRRRRRKAQ 60 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHH
Confidence 3333344443333333344333 467777777766643
No 99
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=23.59 E-value=57 Score=23.40 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHH-HHHHhhheeee
Q 035538 100 SSVISVLLFAAFI-ALSILTIGVVY 123 (171)
Q Consensus 100 a~vis~LlfvAfv-gLsilTiGViY 123 (171)
...+..+++++|+ |+.++.+|++.
T Consensus 121 ~~~~~~~~~~~~~lG~~~~~~gl~~ 145 (148)
T PF12158_consen 121 GLWLMFIFGFGFILGLIFFLVGLFM 145 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555543 77777777654
No 100
>PF08113 CoxIIa: Cytochrome c oxidase subunit IIa family; InterPro: IPR012538 This family consists of the cytochrome c oxidase subunit IIa family. The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix, subunit IIa, spans the membrane. This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases [].; PDB: 2QPD_C 3QJR_C 3EH5_C 3BVD_C 3S39_C 3QJU_C 3QJS_C 4EV3_C 3QJT_C 4FA7_C ....
Probab=23.45 E-value=98 Score=20.26 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHhhh--eeeee
Q 035538 103 ISVLLFAAFIALSILTI--GVVYI 124 (171)
Q Consensus 103 is~LlfvAfvgLsilTi--GViYL 124 (171)
+.+|+.|++++++||++ ||.|+
T Consensus 6 ~Gal~vv~iLt~~ILvFWfgvf~~ 29 (34)
T PF08113_consen 6 KGALGVVMILTAFILVFWFGVFAL 29 (34)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cceeeeHHHHHHHHHHHHHHHHHh
Confidence 35677888888888864 55443
No 101
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=23.36 E-value=19 Score=24.60 Aligned_cols=13 Identities=23% Similarity=0.306 Sum_probs=6.9
Q ss_pred HHHHHHHHHhhhe
Q 035538 108 FAAFIALSILTIG 120 (171)
Q Consensus 108 fvAfvgLsilTiG 120 (171)
.+.|++|.+|.+.
T Consensus 13 ~iVF~~L~lL~~~ 25 (79)
T PF04277_consen 13 GIVFLVLILLILV 25 (79)
T ss_pred HHHHHHHHHHHHH
Confidence 3446666655543
No 102
>PF07741 BRF1: Brf1-like TBP-binding domain; InterPro: IPR011665 The Vaccinia virus has an infection-induced host cell cycle control mechanism. p53 and Rb, which are associated with the is inactivated Rb, which are associated with the RNA polymerase III transcription factor B (TFIIIB) subunits, TBP and Brf1, are inactivated [, ]. TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound pre-initiation complex, whereas Brf1 and Brf2 are involved in the recruitment of Pol III. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1 []. It is suggested that the structure of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. Entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box []. This region covers both the Brf homology II and III regions []. ; GO: 0008270 zinc ion binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NGM_J.
Probab=23.17 E-value=21 Score=26.23 Aligned_cols=15 Identities=20% Similarity=0.638 Sum_probs=9.5
Q ss_pred hhhhhhHHHHHHHHH
Q 035538 127 TDFLQKREREKFEKE 141 (171)
Q Consensus 127 tdFlqKRe~EkfeKe 141 (171)
.|||++.++.+++.+
T Consensus 26 kdyL~~~~~K~~~~~ 40 (97)
T PF07741_consen 26 KDYLEEQEEKELKAK 40 (97)
T ss_dssp HHHHHHHHHCCCCT-
T ss_pred HHHHHHHHHHHHHHH
Confidence 488887776665544
No 103
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=22.81 E-value=1e+02 Score=26.01 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=20.6
Q ss_pred HHHHHHHHhhheeeeeehhhhhhhHHHHHH
Q 035538 109 AAFIALSILTIGVVYIGVTDFLQKREREKF 138 (171)
Q Consensus 109 vAfvgLsilTiGViYL~VtdFlqKRe~Ekf 138 (171)
|.|+.|..|-.=+.|=-|.++|++|+..=.
T Consensus 13 InFlILv~lL~~fl~kPi~~~l~eR~~~I~ 42 (250)
T PRK14474 13 INFLILVYLLRRFLYKPIIQVMKKRQQRIA 42 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555667779999999987543
No 104
>PRK08541 flagellin; Validated
Probab=22.74 E-value=87 Score=26.80 Aligned_cols=34 Identities=18% Similarity=0.460 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHhhheeeeeehhhhhhhHHHHH
Q 035538 103 ISVLLFAAFIALSILTIGVVYIGVTDFLQKREREK 137 (171)
Q Consensus 103 is~LlfvAfvgLsilTiGViYL~VtdFlqKRe~Ek 137 (171)
=+++.|+|||-...+.-+|+ |+-.-|||.++++-
T Consensus 9 GTLIVFIAmVLVAAVAA~VL-InTsgfLQQKA~~t 42 (211)
T PRK08541 9 GTLIVFIAMVLVAAVAAAVL-INTSGYLQQKASAT 42 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHh-hcchhhhhHHHHHH
Confidence 34456777766666655554 67788999988775
No 105
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.64 E-value=2.3e+02 Score=18.46 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=5.6
Q ss_pred hhhhHHHHHHHHH
Q 035538 129 FLQKREREKFEKE 141 (171)
Q Consensus 129 FlqKRe~EkfeKe 141 (171)
+=.+|+..+.+|+
T Consensus 44 ~~~r~~~~~~~k~ 56 (68)
T PF06305_consen 44 LRLRRRIRRLRKE 56 (68)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444444
No 106
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=22.36 E-value=1.1e+02 Score=24.24 Aligned_cols=18 Identities=17% Similarity=0.198 Sum_probs=12.9
Q ss_pred eeeehhhhhhhHHHHHHH
Q 035538 122 VYIGVTDFLQKREREKFE 139 (171)
Q Consensus 122 iYL~VtdFlqKRe~Ekfe 139 (171)
.|=-|.++|++|...=..
T Consensus 45 l~kPI~~~l~~R~~~I~~ 62 (184)
T CHL00019 45 GKGVLSDLLDNRKQTILN 62 (184)
T ss_pred hHhHHHHHHHHHHHHHHH
Confidence 345689999999875433
No 107
>CHL00031 psbT photosystem II protein T
Probab=22.23 E-value=30 Score=22.51 Aligned_cols=17 Identities=18% Similarity=0.647 Sum_probs=10.8
Q ss_pred HHHHHHHhhheeeeeeh
Q 035538 110 AFIALSILTIGVVYIGV 126 (171)
Q Consensus 110 AfvgLsilTiGViYL~V 126 (171)
+.+-|.+.|+|+++.++
T Consensus 5 vYtfll~~tlgilFFAI 21 (33)
T CHL00031 5 VYTFLLVSTLGIIFFAI 21 (33)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 44455667777777665
No 108
>PF14358 DUF4405: Domain of unknown function (DUF4405)
Probab=22.19 E-value=1.1e+02 Score=20.22 Aligned_cols=22 Identities=32% Similarity=0.547 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhee
Q 035538 100 SSVISVLLFAAFIALSILTIGV 121 (171)
Q Consensus 100 a~vis~LlfvAfvgLsilTiGV 121 (171)
.++++.+++++|+++.+-.+..
T Consensus 2 ~~~i~~~l~~~~~~~~iSGi~l 23 (64)
T PF14358_consen 2 RYIINLLLLVSFLVLAISGILL 23 (64)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 3688999999999887766543
No 109
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=21.63 E-value=1.1e+02 Score=23.49 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=19.9
Q ss_pred HHHHHHHhhheeeeeehhhhhhhHHHHHHHHH
Q 035538 110 AFIALSILTIGVVYIGVTDFLQKREREKFEKE 141 (171)
Q Consensus 110 AfvgLsilTiGViYL~VtdFlqKRe~EkfeKe 141 (171)
.|+.|.++.-=++|==|..+|++|+..=.+..
T Consensus 16 ~Flil~~~l~kfl~kPi~~~l~~R~~~I~~~l 47 (141)
T PRK08476 16 VFLLLIVILNSWLYKPLLKFMDNRNASIKNDL 47 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444567788999999987544333
No 110
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=21.38 E-value=97 Score=28.31 Aligned_cols=17 Identities=18% Similarity=0.190 Sum_probs=12.5
Q ss_pred eeeeehhhhhhhHHHHH
Q 035538 121 VVYIGVTDFLQKREREK 137 (171)
Q Consensus 121 ViYL~VtdFlqKRe~Ek 137 (171)
++|=-|.++|++|+..=
T Consensus 21 fl~~Pi~~~l~~R~~~I 37 (445)
T PRK13428 21 FVVPPVRRLMAARQDTV 37 (445)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34445999999998653
No 111
>cd06848 GCS_H Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-proteins) which catalyzes the oxidative cleavage of glycine. The H-protein shuttles the methylamine group of glycine from the P-protein (glycine dehydrogenase) to the T-protein (aminomethyltransferase) via a lipoyl group, attached to a completely conserved lysine residue.
Probab=21.29 E-value=58 Score=23.19 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=12.3
Q ss_pred eeeeeehhhhhhhH
Q 035538 120 GVVYIGVTDFLQKR 133 (171)
Q Consensus 120 GViYL~VtdFlqKR 133 (171)
|.++||+|||.|+.
T Consensus 14 ~~~~lGlt~~~~~~ 27 (96)
T cd06848 14 GIATVGITDYAQDL 27 (96)
T ss_pred cEEEEeeCHHHHhh
Confidence 78999999999865
No 112
>KOG0052 consensus Translation elongation factor EF-1 alpha/Tu [Translation, ribosomal structure and biogenesis]
Probab=21.15 E-value=38 Score=31.61 Aligned_cols=21 Identities=48% Similarity=0.493 Sum_probs=18.0
Q ss_pred hhhhhHHHHHHHHHHHHhhhh
Q 035538 128 DFLQKREREKFEKEEAATKKK 148 (171)
Q Consensus 128 dFlqKRe~EkfeKeEaak~kk 148 (171)
.+++||..||||||.+...|-
T Consensus 29 g~id~~~~~k~~keaa~~~kg 49 (391)
T KOG0052|consen 29 GGIDKRTIEKFEKEAAEMGKG 49 (391)
T ss_pred ccccchhhhhhchHHHhhccc
Confidence 678999999999998876654
No 113
>PF13800 Sigma_reg_N: Sigma factor regulator N-terminal
Probab=21.09 E-value=2.2e+02 Score=20.18 Aligned_cols=23 Identities=22% Similarity=0.392 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHhhheeeeee
Q 035538 102 VISVLLFAAFIALSILTIGVVYIG 125 (171)
Q Consensus 102 vis~LlfvAfvgLsilTiGViYL~ 125 (171)
+|++++++.+++|..+-- .+|++
T Consensus 18 ~isi~~~lvi~~i~~~~~-~l~y~ 40 (96)
T PF13800_consen 18 VISIISALVIFIISFIIS-ALYYN 40 (96)
T ss_pred HHHHhhhhhhHHHHHHhh-hheee
Confidence 455555555555444322 34444
No 114
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=21.08 E-value=93 Score=24.10 Aligned_cols=18 Identities=11% Similarity=0.322 Sum_probs=9.1
Q ss_pred HHHHhhheeeeeehhhhh
Q 035538 113 ALSILTIGVVYIGVTDFL 130 (171)
Q Consensus 113 gLsilTiGViYL~VtdFl 130 (171)
|+.++.+|+.|+-..-..
T Consensus 49 g~vL~~~g~~~~~~~~~~ 66 (191)
T PF04156_consen 49 GVVLLSLGLLCLLSKRPV 66 (191)
T ss_pred HHHHHHHHHHHHHHcccc
Confidence 355555566555444433
No 115
>KOG1631 consensus Translocon-associated complex TRAP, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.95 E-value=76 Score=28.46 Aligned_cols=26 Identities=35% Similarity=0.571 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHhhheeeeeehhhhhhhHH
Q 035538 105 VLLFAAFIALSILTIGVVYIGVTDFLQKRE 134 (171)
Q Consensus 105 ~LlfvAfvgLsilTiGViYL~VtdFlqKRe 134 (171)
+.|++-++||++|-+ +..+.||+++-
T Consensus 185 vFL~~lligl~llll----v~~~q~L~~~s 210 (261)
T KOG1631|consen 185 VFLYILLIGLSLLLL----VLSQQFLSKLS 210 (261)
T ss_pred hHHHHHHHHHHHHHH----HHHHHHHHHhh
Confidence 344445556555432 23477888885
No 116
>PF11820 DUF3339: Protein of unknown function (DUF3339); InterPro: IPR021775 This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length.
Probab=20.69 E-value=1.4e+02 Score=21.96 Aligned_cols=25 Identities=28% Similarity=0.539 Sum_probs=22.4
Q ss_pred cchHHHHHHHHHHHHHHHHHhhhee
Q 035538 97 ESLSSVISVLLFAAFIALSILTIGV 121 (171)
Q Consensus 97 ~g~a~vis~LlfvAfvgLsilTiGV 121 (171)
.|.+.+|=+++|.+++.+.++.+||
T Consensus 40 sg~si~vHa~iff~l~~i~~va~~v 64 (68)
T PF11820_consen 40 SGKSILVHALIFFALFTIFLVAIGV 64 (68)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhee
Confidence 4688889999999999999999997
No 117
>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.18 E-value=1.4e+02 Score=20.71 Aligned_cols=30 Identities=20% Similarity=0.164 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHhhheeeeeehhhhh
Q 035538 101 SVISVLLFAAFIALSILTIGVVYIGVTDFL 130 (171)
Q Consensus 101 ~vis~LlfvAfvgLsilTiGViYL~VtdFl 130 (171)
|+|=.|+.+++||+....+.--+.+-.+.-
T Consensus 11 TLiElLVvl~Iigil~~~~~p~~~~~~~~~ 40 (149)
T COG2165 11 TLIELLVVLAIIGILAALALPSLQGSIDKA 40 (149)
T ss_pred chHHHHHHHHHHHHHHHHHHhhhhhHHHHH
Confidence 456666677777666555554444444443
Done!