Query 014676
Match_columns 420
No_of_seqs 56 out of 58
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 07:27:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12483 GIDE: E3 Ubiquitin li 97.9 0.00013 2.7E-09 64.8 10.1 102 278-386 17-121 (160)
2 PF13567 DUF4131: Domain of un 91.7 6.8 0.00015 32.5 13.1 21 329-349 148-168 (176)
3 PF13829 DUF4191: Domain of un 90.6 0.33 7.3E-06 47.3 4.4 74 156-230 27-103 (224)
4 cd06094 RP_Saci_like RP_Saci_l 79.0 1.7 3.7E-05 37.2 2.6 24 292-315 1-24 (89)
5 PF12273 RCR: Chitin synthesis 78.0 1.5 3.3E-05 38.2 2.1 28 180-207 1-29 (130)
6 PF10907 DUF2749: Protein of u 73.6 1.7 3.7E-05 35.6 1.2 49 181-231 3-63 (66)
7 TIGR02762 TraL_TIGR type IV co 73.1 11 0.00023 32.0 5.8 32 141-174 8-40 (95)
8 PF11151 DUF2929: Protein of u 72.7 9.3 0.0002 30.0 5.0 40 155-195 6-45 (57)
9 PF10003 DUF2244: Integral mem 70.3 13 0.00028 33.2 6.0 62 153-234 9-70 (140)
10 PRK13254 cytochrome c-type bio 70.1 8.3 0.00018 35.4 4.8 57 179-241 7-65 (148)
11 PF03100 CcmE: CcmE; InterPro 66.7 5.7 0.00012 35.1 3.0 17 225-241 48-64 (131)
12 PRK01844 hypothetical protein; 61.8 9.6 0.00021 31.8 3.3 33 182-219 7-39 (72)
13 COG3763 Uncharacterized protei 61.6 9.3 0.0002 31.9 3.1 34 182-220 7-40 (71)
14 PF15050 SCIMP: SCIMP protein 61.4 8.9 0.00019 35.1 3.2 25 181-205 9-33 (133)
15 PRK00523 hypothetical protein; 59.5 11 0.00024 31.4 3.3 35 181-220 7-41 (72)
16 PRK10881 putative hydrogenase 58.6 12 0.00027 38.2 4.2 37 135-178 39-77 (394)
17 PF04246 RseC_MucC: Positive r 57.9 27 0.00059 30.4 5.6 42 164-205 78-119 (135)
18 COG5015 Uncharacterized conser 57.2 9.4 0.0002 35.0 2.7 35 206-240 46-81 (132)
19 TIGR03750 conj_TIGR03750 conju 57.1 18 0.00039 32.2 4.3 71 158-235 25-106 (111)
20 PF08114 PMP1_2: ATPase proteo 56.4 12 0.00026 28.5 2.7 29 184-212 14-43 (43)
21 COG1200 RecG RecG-like helicas 52.6 47 0.001 37.5 7.6 46 356-401 106-152 (677)
22 PRK13707 conjugal transfer pil 51.7 70 0.0015 27.7 7.0 26 198-223 71-98 (101)
23 PF11833 DUF3353: Protein of u 51.5 22 0.00048 33.9 4.3 30 151-181 138-167 (194)
24 PRK13823 conjugal transfer pro 50.2 24 0.00053 30.4 4.0 38 163-201 26-63 (94)
25 PRK08456 flagellar motor prote 48.0 30 0.00064 34.0 4.7 55 161-215 8-69 (257)
26 PRK13165 cytochrome c-type bio 47.9 40 0.00087 31.7 5.3 18 224-241 54-71 (160)
27 PF04156 IncA: IncA protein; 46.1 34 0.00073 31.0 4.5 35 171-205 29-63 (191)
28 PF05425 CopD: Copper resistan 45.4 37 0.0008 28.3 4.3 59 151-209 6-69 (105)
29 PF11241 DUF3043: Protein of u 45.0 41 0.00088 32.0 4.9 36 187-222 105-140 (170)
30 PF14362 DUF4407: Domain of un 44.2 25 0.00053 34.4 3.5 27 186-215 46-72 (301)
31 PRK09109 motC flagellar motor 43.7 38 0.00083 33.1 4.7 55 161-215 8-69 (246)
32 PF06305 DUF1049: Protein of u 43.4 29 0.00063 26.5 3.2 21 152-172 16-36 (68)
33 PRK10862 SoxR reducing system 43.4 41 0.00088 30.8 4.6 57 144-202 63-123 (154)
34 PF00558 Vpu: Vpu protein; In 42.6 24 0.00052 30.0 2.7 27 179-205 2-28 (81)
35 PTZ00382 Variant-specific surf 42.2 9.8 0.00021 32.5 0.4 17 191-207 79-95 (96)
36 PF05915 DUF872: Eukaryotic pr 42.0 28 0.00061 30.8 3.2 55 152-206 39-104 (115)
37 PF13779 DUF4175: Domain of un 41.9 34 0.00073 39.2 4.6 60 157-216 10-71 (820)
38 PF11712 Vma12: Endoplasmic re 41.7 70 0.0015 28.5 5.7 51 156-206 85-137 (142)
39 PRK14762 membrane protein; Pro 41.6 24 0.00053 24.5 2.1 16 154-169 2-17 (27)
40 PRK13150 cytochrome c-type bio 41.6 58 0.0013 30.6 5.4 18 224-241 54-71 (159)
41 PF11990 DUF3487: Protein of u 41.2 43 0.00093 29.9 4.3 63 149-218 20-82 (121)
42 PF03916 NrfD: Polysulphide re 40.9 35 0.00076 33.3 4.0 33 139-178 2-34 (313)
43 PF06703 SPC25: Microsomal sig 38.9 2.9E+02 0.0064 24.8 10.0 48 180-233 56-103 (162)
44 PRK13159 cytochrome c-type bio 38.8 45 0.00097 31.3 4.1 18 224-241 48-65 (155)
45 PF06645 SPC12: Microsomal sig 37.8 40 0.00086 27.7 3.3 49 155-204 12-60 (76)
46 PF03672 UPF0154: Uncharacteri 37.6 26 0.00057 28.6 2.2 30 184-218 2-31 (64)
47 KOG0887 60S ribosomal protein 35.7 27 0.00058 31.3 2.1 47 225-283 29-75 (111)
48 TIGR01116 ATPase-IIA1_Ca sarco 35.6 86 0.0019 35.9 6.5 79 153-232 6-86 (917)
49 TIGR03818 MotA1 flagellar moto 35.6 62 0.0013 32.5 4.8 45 161-205 6-56 (282)
50 PF02439 Adeno_E3_CR2: Adenovi 35.4 54 0.0012 24.6 3.3 26 182-207 8-33 (38)
51 PF06374 NDUF_C2: NADH-ubiquin 35.3 84 0.0018 28.3 5.1 57 161-218 29-96 (117)
52 PRK06743 flagellar motor prote 34.9 47 0.001 33.0 3.8 28 178-205 28-55 (254)
53 PF11808 DUF3329: Domain of un 33.5 1.4E+02 0.0029 25.0 5.8 21 195-216 38-58 (90)
54 KOG1016 Predicted DNA helicase 32.9 22 0.00047 41.4 1.4 16 7-22 1199-1214(1387)
55 PF06679 DUF1180: Protein of u 32.7 39 0.00085 31.8 2.8 31 185-216 99-129 (163)
56 PF11023 DUF2614: Protein of u 32.0 82 0.0018 28.5 4.5 47 148-194 4-51 (114)
57 PRK10747 putative protoheme IX 31.8 1.2E+02 0.0026 30.8 6.2 10 172-181 26-35 (398)
58 PF11846 DUF3366: Domain of un 31.7 1.4E+02 0.003 27.1 6.1 57 157-213 20-83 (193)
59 COG0811 TolQ Biopolymer transp 31.5 45 0.00097 31.8 3.0 23 183-205 167-189 (216)
60 PRK09110 flagellar motor prote 31.4 74 0.0016 32.0 4.6 44 162-205 7-56 (283)
61 PF05834 Lycopene_cycl: Lycope 31.0 1.7E+02 0.0037 29.3 7.2 44 317-361 198-243 (374)
62 PRK08124 flagellar motor prote 29.9 90 0.0019 30.8 4.9 45 161-205 8-58 (263)
63 PF03419 Peptidase_U4: Sporula 29.6 1.5E+02 0.0032 29.2 6.3 43 220-263 159-201 (293)
64 COG2332 CcmE Cytochrome c-type 29.4 96 0.0021 29.3 4.7 56 180-241 8-65 (153)
65 PRK12482 flagellar motor prote 29.1 88 0.0019 31.7 4.7 46 160-205 5-56 (287)
66 PRK08990 flagellar motor prote 28.6 98 0.0021 30.6 4.9 40 166-205 18-57 (254)
67 PF10281 Ish1: Putative stress 28.6 45 0.00097 23.7 1.9 17 333-349 6-22 (38)
68 PF01988 VIT1: VIT family; In 28.4 1E+02 0.0023 29.0 4.9 16 158-173 132-147 (213)
69 PRK10490 sensor protein KdpD; 28.3 35 0.00077 38.7 2.0 15 190-204 449-463 (895)
70 PF12273 RCR: Chitin synthesis 28.1 41 0.00089 29.4 2.0 26 186-211 4-29 (130)
71 TIGR01523 ATPase-IID_K-Na pota 27.8 1.3E+02 0.0029 35.2 6.4 52 180-232 80-131 (1053)
72 PF05545 FixQ: Cbb3-type cytoc 27.4 78 0.0017 23.5 3.1 32 184-215 12-43 (49)
73 KOG0558 Dihydrolipoamide trans 27.2 20 0.00044 38.1 -0.1 18 350-367 77-94 (474)
74 PRK13629 threonine/serine tran 26.8 67 0.0014 34.5 3.6 63 156-224 22-87 (443)
75 PF13869 NUDIX_2: Nucleotide h 26.7 11 0.00024 36.2 -1.9 35 342-376 21-55 (188)
76 cd04486 YhcR_OBF_like YhcR_OBF 26.3 93 0.002 25.3 3.6 28 357-384 43-70 (78)
77 PF11292 DUF3093: Protein of u 26.2 1.4E+02 0.003 27.7 5.1 43 156-199 11-53 (143)
78 PF04971 Lysis_S: Lysis protei 26.2 63 0.0014 26.8 2.6 25 186-210 35-61 (68)
79 COG1291 MotA Flagellar motor c 26.1 56 0.0012 33.1 2.8 53 171-223 24-77 (266)
80 COG4303 EutB Ethanolamine ammo 26.0 54 0.0012 34.8 2.7 27 330-357 421-447 (453)
81 COG1585 Membrane protein impli 25.4 2.3E+02 0.0051 25.7 6.3 24 156-179 6-31 (140)
82 TIGR01789 lycopene_cycl lycope 25.3 1.4E+02 0.0029 30.3 5.3 81 263-360 149-236 (370)
83 cd04488 RecG_wedge_OBF RecG_we 25.1 1.2E+02 0.0025 22.2 3.7 27 358-384 45-71 (75)
84 PRK01122 potassium-transportin 24.7 1.6E+02 0.0035 33.1 6.2 34 136-173 19-52 (679)
85 PRK14992 tetrathionate reducta 24.4 91 0.002 32.2 4.0 23 157-179 16-38 (335)
86 PF02037 SAP: SAP domain; Int 23.4 65 0.0014 22.6 1.9 17 334-350 7-23 (35)
87 PF14110 DUF4282: Domain of un 23.2 1.2E+02 0.0025 25.4 3.7 21 152-172 13-33 (90)
88 PF07790 DUF1628: Protein of u 22.9 82 0.0018 25.2 2.7 22 181-202 9-30 (80)
89 PRK07118 ferredoxin; Validated 22.8 46 0.001 33.1 1.5 26 155-180 3-28 (280)
90 KOG2362 Uncharacterized Fe-S p 22.8 55 0.0012 34.2 2.0 17 354-370 316-332 (336)
91 TIGR02916 PEP_his_kin putative 22.7 1.2E+02 0.0025 32.9 4.6 19 149-167 221-239 (679)
92 PF05934 MCLC: Mid-1-related c 22.1 1.1E+02 0.0023 34.0 4.1 85 118-205 146-230 (549)
93 PF09788 Tmemb_55A: Transmembr 22.0 82 0.0018 31.9 3.0 46 159-205 206-251 (256)
94 cd04478 RPA2_DBD_D RPA2_DBD_D: 21.8 79 0.0017 25.3 2.4 20 219-238 43-62 (95)
95 PF05454 DAG1: Dystroglycan (D 21.8 30 0.00066 35.1 0.0 11 195-205 161-171 (290)
96 PF11432 DUF3197: Protein of u 21.8 95 0.0021 28.0 3.0 58 292-363 19-85 (113)
97 PRK01844 hypothetical protein; 21.3 65 0.0014 27.0 1.8 16 157-172 3-18 (72)
98 PF14023 DUF4239: Protein of u 21.2 1.9E+02 0.0041 26.7 5.0 10 152-162 135-144 (209)
99 TIGR02302 aProt_lowcomp conser 21.0 1.1E+02 0.0025 35.4 4.2 67 159-228 26-99 (851)
100 PF06993 DUF1304: Protein of u 20.7 2E+02 0.0044 25.2 4.9 41 162-203 52-92 (113)
101 TIGR01944 rnfB electron transp 20.7 52 0.0011 30.0 1.3 22 156-177 2-23 (165)
102 COG4965 TadB Flp pilus assembl 20.6 1.1E+02 0.0024 31.6 3.6 14 206-219 128-141 (309)
103 PF10969 DUF2771: Protein of u 20.4 84 0.0018 29.2 2.6 49 182-238 6-54 (161)
104 PF07291 MauE: Methylamine uti 20.3 1.8E+02 0.0038 27.4 4.7 57 152-208 45-102 (184)
105 PF01925 TauE: Sulfite exporte 20.2 1.7E+02 0.0037 26.8 4.5 44 152-195 61-104 (240)
106 PF12576 DUF3754: Protein of u 20.2 2E+02 0.0043 25.9 4.8 18 196-213 106-124 (141)
107 COG3601 Predicted membrane pro 20.2 96 0.0021 30.1 2.9 55 156-212 40-110 (186)
108 PF03144 GTP_EFTU_D2: Elongati 20.2 85 0.0019 23.8 2.2 19 351-369 5-23 (74)
109 PF05879 RHD3: Root hair defec 20.1 94 0.002 35.1 3.3 45 152-202 649-693 (742)
No 1
>PF12483 GIDE: E3 Ubiquitin ligase; InterPro: IPR022170 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis. ; GO: 0016881 acid-amino acid ligase activity
Probab=97.86 E-value=0.00013 Score=64.76 Aligned_cols=102 Identities=20% Similarity=0.267 Sum_probs=68.6
Q ss_pred ccccceeeeeEeeceEEEecCCceeEEE-EecCCCeeeeeeeeceEEeecCCCCCCCHHHHHHHhhcC-CCCccceeEEe
Q 014676 278 FSWGSRHLEKYVSDFYISDFQSGLRALV-KAGYGAKVAPFVKPATVVNITKGNRDLSPSFLRWLADRN-LSSDDRIMRLK 355 (420)
Q Consensus 278 f~W~l~~~E~~~~DFYIsD~~sG~RAlV-KaG~G~kVtp~V~e~~vv~~~~~~~dlS~~f~~WL~erN-LSsd~r~mRlk 355 (420)
-.|++.+..+..+.||+.| ..-|.+| ....|+.+.--.+-+..... .......+..|+..+- +. .+-.||+
T Consensus 17 ~~~~~v~~~~~~vPF~L~D--~tg~v~V~~~p~~a~l~l~~v~~~f~p~---~~~~~~~~~~~~~~~~~~~--~~G~r~~ 89 (160)
T PF12483_consen 17 SSWRTVSSGTSEVPFYLED--GTGRVRVVDDPEGAELDLETVYDRFEPS---PSSPPDGLFGFFSGERELE--PKGYRYT 89 (160)
T ss_pred ccEEEEEcceeEcCEEEEC--CceEEEEecCcccCccceeeEEEEeEEC---CCCccceeeeeeccceecc--ccccEEE
Confidence 3499999999999999999 4455555 56667665432333332111 1133444444433322 11 3347999
Q ss_pred cceeeeCCEEEEEEEE-EeeCceeEEeCCCCc
Q 014676 356 EGYIKEGSTVSVMGVV-RRHDNVLMIVPSTEP 386 (420)
Q Consensus 356 EGyIkEGstvSVmGvv-kr~~~~~mi~pP~e~ 386 (420)
|-.|.+|++|.|+|.+ ..+|..++|-+|.+.
T Consensus 90 E~~L~~G~~ltvvGe~~~~~~g~~~i~~p~~g 121 (160)
T PF12483_consen 90 EEILPVGTPLTVVGELVRDGDGNLVIQPPKDG 121 (160)
T ss_pred EEEcCCCCEEEEEEEEEEcCCCcEEEeCCCCC
Confidence 9999999999999999 555678999999986
No 2
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=91.73 E-value=6.8 Score=32.54 Aligned_cols=21 Identities=10% Similarity=0.241 Sum_probs=16.9
Q ss_pred CCCCCHHHHHHHhhcCCCCcc
Q 014676 329 NRDLSPSFLRWLADRNLSSDD 349 (420)
Q Consensus 329 ~~dlS~~f~~WL~erNLSsd~ 349 (420)
.|.=.-++++||..+|+....
T Consensus 148 ~Npg~FD~~~yl~~~gI~~~~ 168 (176)
T PF13567_consen 148 TNPGGFDYQRYLRSKGIYAQG 168 (176)
T ss_pred CCCCCcCHHHHHHHCCCEEEE
Confidence 455667799999999998765
No 3
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=90.58 E-value=0.33 Score=47.35 Aligned_cols=74 Identities=12% Similarity=0.161 Sum_probs=54.0
Q ss_pred hHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCc---ccccCcCCcEE
Q 014676 156 VAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDT---ELRGAIDGQYV 230 (420)
Q Consensus 156 vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~---~lr~a~dGq~V 230 (420)
+.|.+++.|+..++++..|-..+++|++++++++++++++|+|+++- +..++....+..-|.+ .|++++-|=.+
T Consensus 27 l~~~ml~a~l~~~~v~v~ig~l~~~~~~~~i~gi~~g~l~am~vl~r-ra~ra~Y~qieGqpGAa~avL~~lr~~W~~ 103 (224)
T PF13829_consen 27 LPWLMLGAFLGPIAVFVLIGLLFGSWWYWLIIGILLGLLAAMIVLSR-RAQRAAYAQIEGQPGAAGAVLDNLRRGWRV 103 (224)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhcCCCchHHHHHHhhcCCccc
Confidence 45877777887788877777778899999999999999998887753 2356666777777765 45555544333
No 4
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=79.04 E-value=1.7 Score=37.18 Aligned_cols=24 Identities=42% Similarity=0.595 Sum_probs=20.4
Q ss_pred eEEEecCCceeEEEEecCCCeeee
Q 014676 292 FYISDFQSGLRALVKAGYGAKVAP 315 (420)
Q Consensus 292 FYIsD~~sG~RAlVKaG~G~kVtp 315 (420)
|||.|++||+|+||-||..-.|-|
T Consensus 1 l~v~D~~s~~~fLVDTGA~vSviP 24 (89)
T cd06094 1 LHVRDRTSGLRFLVDTGAAVSVLP 24 (89)
T ss_pred CeeEECCCCcEEEEeCCCceEeec
Confidence 799999999999999988754444
No 5
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=78.04 E-value=1.5 Score=38.24 Aligned_cols=28 Identities=14% Similarity=0.138 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHHHHHHHhhhh-hhhhchh
Q 014676 180 KAVVLVAVAAVVGPLFIGMIW-NCVWGRR 207 (420)
Q Consensus 180 ~~~ll~~~~~~f~~v~a~~iw-N~~~~~~ 207 (420)
+|+|+++++++|.+++.++++ |-.++|+
T Consensus 1 RW~l~~iii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred CeeeHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 466776666666555555555 4433343
No 6
>PF10907 DUF2749: Protein of unknown function (DUF2749); InterPro: IPR024475 This bacterial family of proteins represent the TrbJ and TrbK genes of the Ti plasmid conjugative transfer operon [].
Probab=73.64 E-value=1.7 Score=35.61 Aligned_cols=49 Identities=27% Similarity=0.292 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhhch------------hhhhhccccCCCcccccCcCCcEEE
Q 014676 181 AVVLVAVAAVVGPLFIGMIWNCVWGR------------RGLLGFVKKYPDTELRGAIDGQYVK 231 (420)
Q Consensus 181 ~~ll~~~~~~f~~v~a~~iwN~~~~~------------~~i~rfl~k~Pd~~lr~a~dGq~VK 231 (420)
..+||++++++++.+++..|.+...+ +.=++||.. |.+|++.++||.-|
T Consensus 3 ~~viIaL~~avaa~a~~atwviVq~~~a~~p~s~eeQr~~re~ff~~--~~~l~~i~~gqem~ 63 (66)
T PF10907_consen 3 RRVIIALVVAVAAAAGAATWVIVQPRPAGNPASSEEQRAHREKFFGG--DKDLRDIRGGQEMK 63 (66)
T ss_pred cchhHHHHHHHHhhhceeEEEEECCCCCCCCCChHHHHHHHHHHcCC--CCCCCCCCCCcccC
Confidence 34567777778888888888766554 334567765 55688889999654
No 7
>TIGR02762 TraL_TIGR type IV conjugative transfer system protein TraL. This protein is part of the type IV secretion system for conjugative plasmid transfer. The function of the TraL protein is unknown.
Probab=73.06 E-value=11 Score=32.04 Aligned_cols=32 Identities=19% Similarity=0.345 Sum_probs=17.8
Q ss_pred ccCccee-eeeEechhhHHHHHHHHHHHHHhhhee
Q 014676 141 SLGEDVK-VGFRVSRAVAWVVMVVVAMGVMVGAFL 174 (420)
Q Consensus 141 ~l~~~~~-~~~~vpk~vlw~vi~l~~~g~~~G~f~ 174 (420)
.||++.+ +++... -+-++++.|++|+++|-++
T Consensus 8 ~Ld~~~~i~g~t~D--E~i~~~~~~~~Gi~~~~~l 40 (95)
T TIGR02762 8 YLDEQPRILGLPLD--EFLPGATLFGIGILSGKAL 40 (95)
T ss_pred ccCCCCeEEEeeHH--HHHHHHHHHHHHHHHhhHH
Confidence 4566644 453344 4445666677777776543
No 8
>PF11151 DUF2929: Protein of unknown function (DUF2929); InterPro: IPR021324 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=72.67 E-value=9.3 Score=30.00 Aligned_cols=40 Identities=13% Similarity=0.261 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHH
Q 014676 155 AVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLF 195 (420)
Q Consensus 155 ~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~ 195 (420)
.+.|.+++..++|+++++.-=+.. |..--.++.++|+.++
T Consensus 6 t~fWs~il~~vvgyI~ssL~~~~~-n~~~~~Ii~vi~~i~~ 45 (57)
T PF11151_consen 6 TFFWSFILGEVVGYIGSSLTGVTY-NFTTAAIIAVIFGIIV 45 (57)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHHH
Confidence 468999999999999999876644 3333333333344333
No 9
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=70.28 E-value=13 Score=33.18 Aligned_cols=62 Identities=16% Similarity=0.193 Sum_probs=40.3
Q ss_pred chhhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccccCcCCcEEEE
Q 014676 153 SRAVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELRGAIDGQYVKV 232 (420)
Q Consensus 153 pk~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr~a~dGq~VKI 232 (420)
|+..+|+++.++++-++++..++.. -.|.+|.-+++-++++..+|-+|+ +.+.+.|.+.|
T Consensus 9 ~~g~~~~~~~~~~~~~~~a~~f~~~-GaW~Vl~F~glev~~l~~a~~~~~-------------------r~~~~~E~I~l 68 (140)
T PF10003_consen 9 PRGFLIFIAILAAVSLIIAIAFLLM-GAWPVLPFAGLEVLALWYAFRRNY-------------------RHARDYERITL 68 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh-chHHHHHHHHHHHHHHHHHHHHHH-------------------hhCcCcEEEEE
Confidence 5667777777777765444333222 228888777777777777777776 34566777777
Q ss_pred EE
Q 014676 233 TG 234 (420)
Q Consensus 233 tG 234 (420)
+.
T Consensus 69 ~~ 70 (140)
T PF10003_consen 69 SP 70 (140)
T ss_pred eC
Confidence 76
No 10
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=70.08 E-value=8.3 Score=35.42 Aligned_cols=57 Identities=21% Similarity=0.453 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccc--cCcCCcEEEEEEEEEeccc
Q 014676 179 KKAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELR--GAIDGQYVKVTGVVTCGSI 241 (420)
Q Consensus 179 ~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr--~a~dGq~VKItG~VtcG~~ 241 (420)
++..+++++++++++++++++++. +..+.-|+. | +++. ....|+.|+|.|.|.-|++
T Consensus 7 ~rl~~~~~~~~~~~~~~~L~~~a~---~~~~~yf~t--p-se~~~~~~~~g~~vrvgG~V~~gSi 65 (148)
T PRK13254 7 RRLLIILGALAALGLAVALVLYAL---RQNIVFFYT--P-SEVAEGEAPAGRRFRLGGLVEKGSV 65 (148)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH---HhCCceeeC--H-HHHhcCCccCCCeEEEeEEEecCcE
Confidence 344455555555555555555543 222222221 1 1222 1356999999999998855
No 11
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=66.66 E-value=5.7 Score=35.09 Aligned_cols=17 Identities=41% Similarity=0.591 Sum_probs=14.6
Q ss_pred cCCcEEEEEEEEEeccc
Q 014676 225 IDGQYVKVTGVVTCGSI 241 (420)
Q Consensus 225 ~dGq~VKItG~VtcG~~ 241 (420)
+.|+.|+|.|.|.-|++
T Consensus 48 ~~~~~vrv~G~V~~gSv 64 (131)
T PF03100_consen 48 KVGRKVRVGGLVVEGSV 64 (131)
T ss_dssp -TTSEEEEEEEEECTTE
T ss_pred cCCceEEEeeEEccCCE
Confidence 48999999999998874
No 12
>PRK01844 hypothetical protein; Provisional
Probab=61.76 E-value=9.6 Score=31.80 Aligned_cols=33 Identities=21% Similarity=0.342 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCc
Q 014676 182 VVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDT 219 (420)
Q Consensus 182 ~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~ 219 (420)
|+|++++.+.+++.++| ..|+-.+.+|++.|--
T Consensus 7 I~l~I~~li~G~~~Gff-----~ark~~~k~lk~NPpi 39 (72)
T PRK01844 7 ILVGVVALVAGVALGFF-----IARKYMMNYLQKNPPI 39 (72)
T ss_pred HHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHCCCC
Confidence 44444444555555544 3477788899998754
No 13
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.58 E-value=9.3 Score=31.85 Aligned_cols=34 Identities=18% Similarity=0.267 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcc
Q 014676 182 VVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTE 220 (420)
Q Consensus 182 ~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~ 220 (420)
+|++++..+++++.+ +|.+|+-+.++|++.|--.
T Consensus 7 il~ivl~ll~G~~~G-----~fiark~~~k~lk~NPpin 40 (71)
T COG3763 7 ILLIVLALLAGLIGG-----FFIARKQMKKQLKDNPPIN 40 (71)
T ss_pred HHHHHHHHHHHHHHH-----HHHHHHHHHHHHhhCCCCC
Confidence 344444444444444 5556899999999999653
No 14
>PF15050 SCIMP: SCIMP protein
Probab=61.36 E-value=8.9 Score=35.09 Aligned_cols=25 Identities=8% Similarity=0.082 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 181 AVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 181 ~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
||+|+|+.+++..++++++|-+|+.
T Consensus 9 WiiLAVaII~vS~~lglIlyCvcR~ 33 (133)
T PF15050_consen 9 WIILAVAIILVSVVLGLILYCVCRW 33 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999977664
No 15
>PRK00523 hypothetical protein; Provisional
Probab=59.48 E-value=11 Score=31.43 Aligned_cols=35 Identities=14% Similarity=0.123 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcc
Q 014676 181 AVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTE 220 (420)
Q Consensus 181 ~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~ 220 (420)
||+|++++.+.+++.++| ..|+-.+.+|++.|--+
T Consensus 7 ~I~l~i~~li~G~~~Gff-----iark~~~k~l~~NPpin 41 (72)
T PRK00523 7 ALGLGIPLLIVGGIIGYF-----VSKKMFKKQIRENPPIT 41 (72)
T ss_pred HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHCcCCC
Confidence 445555555555555544 34777888899888643
No 16
>PRK10881 putative hydrogenase 2 b cytochrome subunit; Provisional
Probab=58.58 E-value=12 Score=38.23 Aligned_cols=37 Identities=22% Similarity=0.591 Sum_probs=27.3
Q ss_pred ccc-cccccCcceeeeeEechhhHHHHH-HHHHHHHHhhheeeeee
Q 014676 135 YGS-AVTSLGEDVKVGFRVSRAVAWVVM-VVVAMGVMVGAFLMVAV 178 (420)
Q Consensus 135 ~~~-avt~l~~~~~~~~~vpk~vlw~vi-~l~~~g~~~G~f~l~av 178 (420)
+|- +||++|++.-.| +|... +++.+|+.+|+|++++.
T Consensus 39 ~Glg~vtg~~~~~~WG-------l~I~~y~~~~vglaag~~~is~~ 77 (394)
T PRK10881 39 FGLGSVSNLNGGYPWG-------IWIAFDVLIGTGFACGGWALAWL 77 (394)
T ss_pred hcchhhcCCCCCCCch-------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 565 699999997777 35454 55677888888888763
No 17
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=57.90 E-value=27 Score=30.39 Aligned_cols=42 Identities=12% Similarity=0.089 Sum_probs=28.0
Q ss_pred HHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 164 VAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 164 ~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
=.++|++|+++..++-...+..+++++.++++++++.-.+.+
T Consensus 78 Pll~li~g~~l~~~~~~~e~~~~l~~l~~l~~~~~~~~~~~~ 119 (135)
T PF04246_consen 78 PLLALIAGAVLGSYLGGSELWAILGGLLGLALGFLILRLFDR 119 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345577777777776666777777777777776665544433
No 18
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=57.17 E-value=9.4 Score=34.99 Aligned_cols=35 Identities=26% Similarity=0.394 Sum_probs=31.1
Q ss_pred hhhhhhccccCCCccccc-CcCCcEEEEEEEEEecc
Q 014676 206 RRGLLGFVKKYPDTELRG-AIDGQYVKVTGVVTCGS 240 (420)
Q Consensus 206 ~~~i~rfl~k~Pd~~lr~-a~dGq~VKItG~VtcG~ 240 (420)
-+...+.++++|+.++.+ .+|||+|.++|.++.-+
T Consensus 46 tK~~yKqik~np~vefcg~~kdg~~vrlrg~a~f~~ 81 (132)
T COG5015 46 TKPYYKQIKKNPEVEFCGMDKDGVMVRLRGRAEFVE 81 (132)
T ss_pred ChHHHHHHhhCCCeEEEEecCCceEEEEeeeEEecc
Confidence 567899999999999997 79999999999988643
No 19
>TIGR03750 conj_TIGR03750 conjugative transfer region protein, TIGR03750 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=57.07 E-value=18 Score=32.18 Aligned_cols=71 Identities=18% Similarity=0.237 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhh-hhhhc-hh---------hhhhccccCCCcccccCcC
Q 014676 158 WVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIW-NCVWG-RR---------GLLGFVKKYPDTELRGAID 226 (420)
Q Consensus 158 w~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iw-N~~~~-~~---------~i~rfl~k~Pd~~lr~a~d 226 (420)
|++.+=+++|+++|..+..... .+.++-++++.+.++++++. .+..+ || .+..++.+++ +..
T Consensus 25 ~~~~~~~~~gl~~g~~l~~~~~-~w~~~p~~~lig~~l~v~~gg~~l~rlKRGrPe~yl~r~l~~~~~~~~------l~~ 97 (111)
T TIGR03750 25 VAAGVGLAAGLVLGLLLALLAG-PWALIPTGALLGPILVVLIGGKLLARLKRGKPEGYLYRKLEWKLARLG------LGR 97 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhHHHHHHHHcCCCchHHHHHHHHHHHHcC------CCC
Confidence 7777888889999977544444 56666777777777777777 43333 32 2333334433 345
Q ss_pred CcEEEEEEE
Q 014676 227 GQYVKVTGV 235 (420)
Q Consensus 227 Gq~VKItG~ 235 (420)
.+|+.-.|.
T Consensus 98 ~~lI~~sg~ 106 (111)
T TIGR03750 98 HRLILRSGG 106 (111)
T ss_pred CCeEEEecc
Confidence 677766664
No 20
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=56.44 E-value=12 Score=28.54 Aligned_cols=29 Identities=21% Similarity=0.162 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHhhhhhhhhc-hhhhhhc
Q 014676 184 LVAVAAVVGPLFIGMIWNCVWG-RRGLLGF 212 (420)
Q Consensus 184 l~~~~~~f~~v~a~~iwN~~~~-~~~i~rf 212 (420)
++.++++...++++|||+-+-. +|++.||
T Consensus 14 F~lVglv~i~iva~~iYRKw~aRkr~l~rf 43 (43)
T PF08114_consen 14 FCLVGLVGIGIVALFIYRKWQARKRALQRF 43 (43)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4455566667778999955544 7888776
No 21
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=52.58 E-value=47 Score=37.51 Aligned_cols=46 Identities=28% Similarity=0.335 Sum_probs=32.7
Q ss_pred cceeeeCCEEEEEEEEEeeCceeEEeCCCCcccccce-eceeccccc
Q 014676 356 EGYIKEGSTVSVMGVVRRHDNVLMIVPSTEPVSTGCQ-WSRCLLPTY 401 (420)
Q Consensus 356 EGyIkEGstvSVmGvvkr~~~~~mi~pP~e~vstGcq-w~~~llP~~ 401 (420)
+..+++|+++.|.|-++|.++.+=|.-|.=-+-..+. ..+.+.|+|
T Consensus 106 ~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~~~~~~~~~~~i~PvY 152 (677)
T COG1200 106 KKKLKVGERVIVYGKVKRFKGGLQITHPEYIVNDDGSELEERLTPVY 152 (677)
T ss_pred HhhCCCCCEEEEEEEEeeccCceEEEcceEEecCCCcccccceeeee
Confidence 4457899999999999998877666666544433333 566677775
No 22
>PRK13707 conjugal transfer pilus assembly protein TraL; Provisional
Probab=51.75 E-value=70 Score=27.73 Aligned_cols=26 Identities=23% Similarity=0.316 Sum_probs=17.1
Q ss_pred hhhhhhhc-hhhhhh-ccccCCCccccc
Q 014676 198 MIWNCVWG-RRGLLG-FVKKYPDTELRG 223 (420)
Q Consensus 198 ~iwN~~~~-~~~i~r-fl~k~Pd~~lr~ 223 (420)
++.-+||- -..+.+ ++|+.|++-.|.
T Consensus 71 l~h~~YW~lP~~~~~~~~k~~P~S~~R~ 98 (101)
T PRK13707 71 LRDLIYWYLPTALLRGIFHNVPDSCFRQ 98 (101)
T ss_pred HHHHHHHhcchhhcccccCcCCcHHHHH
Confidence 33345555 455554 799999998774
No 23
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=51.48 E-value=22 Score=33.87 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=23.8
Q ss_pred EechhhHHHHHHHHHHHHHhhheeeeeehhH
Q 014676 151 RVSRAVAWVVMVVVAMGVMVGAFLMVAVKKA 181 (420)
Q Consensus 151 ~vpk~vlw~vi~l~~~g~~~G~f~l~av~~~ 181 (420)
++=|+++|.+..| +.|+++|+++...+...
T Consensus 138 ~~~rA~~~~~~~L-~~G~~lGs~l~~~l~~~ 167 (194)
T PF11833_consen 138 KLGRAFLWTLGGL-VVGLILGSLLASWLPVD 167 (194)
T ss_pred hHHHHHHHHHHHH-HHHHHHHHHHHhhcccc
Confidence 3669999999887 78999999887766443
No 24
>PRK13823 conjugal transfer protein TrbD; Provisional
Probab=50.17 E-value=24 Score=30.41 Aligned_cols=38 Identities=16% Similarity=0.138 Sum_probs=22.8
Q ss_pred HHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhh
Q 014676 163 VVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWN 201 (420)
Q Consensus 163 l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN 201 (420)
++..|+++++++++. ++|.-.++.+++..+...++.|-
T Consensus 26 ~i~~g~la~~l~~g~-~~~~a~~~gl~lw~v~h~~l~~m 63 (94)
T PRK13823 26 VMFSGLLAGILIFVA-QTWRAALFGIALWFGALFALRLM 63 (94)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 445777777776666 77764444445545555556664
No 25
>PRK08456 flagellar motor protein MotA; Validated
Probab=47.95 E-value=30 Score=33.97 Aligned_cols=55 Identities=11% Similarity=0.064 Sum_probs=36.0
Q ss_pred HHHHHHHHHhhheee------eeehhHHHHHHHHHHHHHHHHhhhhhhhhc-hhhhhhcccc
Q 014676 161 MVVVAMGVMVGAFLM------VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG-RRGLLGFVKK 215 (420)
Q Consensus 161 i~l~~~g~~~G~f~l------~av~~~~ll~~~~~~f~~v~a~~iwN~~~~-~~~i~rfl~k 215 (420)
.+++++++++++|++ .-|+=+.++||+++.+++++..+-++.... -+.+...+++
T Consensus 8 G~~~~~~~i~~~~~~~gg~~~~~~~~~~~~IV~Ggt~~a~~i~~~~~~~~~~~~~~~~~f~~ 69 (257)
T PRK08456 8 GMVLAVASISVGDILEGGNPLHVIHLSSFIIVVPTALFAAMTATHKKYVKAAYKELKIVFKN 69 (257)
T ss_pred HHHHHHHHHHHHHHhcCCCcHHHhhHhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhcc
Confidence 344445555544444 448888999999999999888887766665 4444445533
No 26
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=47.94 E-value=40 Score=31.69 Aligned_cols=18 Identities=39% Similarity=0.534 Sum_probs=15.6
Q ss_pred CcCCcEEEEEEEEEeccc
Q 014676 224 AIDGQYVKVTGVVTCGSI 241 (420)
Q Consensus 224 a~dGq~VKItG~VtcG~~ 241 (420)
+..|+.+.|-|.|.-|++
T Consensus 54 ~~~g~~iRvgG~V~~GSi 71 (160)
T PRK13165 54 PEVGQRLRVGGMVMPGSV 71 (160)
T ss_pred cCCCCEEEEeeEEeCCcE
Confidence 357999999999998876
No 27
>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=46.05 E-value=34 Score=31.02 Aligned_cols=35 Identities=11% Similarity=-0.177 Sum_probs=22.1
Q ss_pred hheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 171 GAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 171 G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
+++-+.++.+.++-+++++++++.+++-+.+++.+
T Consensus 29 ~~~~l~~~~s~~lg~~~lAlg~vL~~~g~~~~~~~ 63 (191)
T PF04156_consen 29 FISGLGALISFILGIALLALGVVLLSLGLLCLLSK 63 (191)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 33336777777777777776666666666555544
No 28
>PF05425 CopD: Copper resistance protein D; InterPro: IPR008457 Copper sequestering activity displayed by some bacteria is determined by copper-binding protein products of the copper resistance operon (cop). CopD, together with CopC, perform copper uptake into the cytoplasm [].; GO: 0016021 integral to membrane
Probab=45.44 E-value=37 Score=28.27 Aligned_cols=59 Identities=19% Similarity=0.098 Sum_probs=39.6
Q ss_pred EechhhHHHHHHHHHHHHHhhheeee---eehhH--HHHHHHHHHHHHHHHhhhhhhhhchhhh
Q 014676 151 RVSRAVAWVVMVVVAMGVMVGAFLMV---AVKKA--VVLVAVAAVVGPLFIGMIWNCVWGRRGL 209 (420)
Q Consensus 151 ~vpk~vlw~vi~l~~~g~~~G~f~l~---av~~~--~ll~~~~~~f~~v~a~~iwN~~~~~~~i 209 (420)
||++...++++++++.|+..+...+. -+.++ .+|.+=.+++++++++-.+|.++-...+
T Consensus 6 rFs~~a~~av~~l~~TG~~~a~~~~~~~~l~~t~yG~~Ll~K~~L~~~~l~l~~~~~~~~~p~l 69 (105)
T PF05425_consen 6 RFSWIAWAAVAVLVVTGLVMAWLRLGFDALFTTPYGRLLLVKLALVLLMLALAAYNRFRLIPRL 69 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCchhhccChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 37788899999999999887766644 12222 3466666777777777777876543333
No 29
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=44.95 E-value=41 Score=31.97 Aligned_cols=36 Identities=28% Similarity=0.322 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccc
Q 014676 187 VAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELR 222 (420)
Q Consensus 187 ~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr 222 (420)
.+++.+++++++|--++-+++.=.+-..||||++-.
T Consensus 105 ~~~~~~~~~~~iid~~~l~r~vkk~v~~kFp~~~~~ 140 (170)
T PF11241_consen 105 TLAMYVLLLLVIIDGVILGRRVKKRVAEKFPDTTES 140 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCcCC
Confidence 333344444444554444455555556789995433
No 30
>PF14362 DUF4407: Domain of unknown function (DUF4407)
Probab=44.22 E-value=25 Score=34.39 Aligned_cols=27 Identities=22% Similarity=0.237 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHhhhhhhhhchhhhhhcccc
Q 014676 186 AVAAVVGPLFIGMIWNCVWGRRGLLGFVKK 215 (420)
Q Consensus 186 ~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k 215 (420)
...++|+++.+++|+|+ .|.|.--.++
T Consensus 46 ~~ai~~glvwgl~I~~l---DR~ivss~~~ 72 (301)
T PF14362_consen 46 WAAIPFGLVWGLVIFNL---DRFIVSSIRK 72 (301)
T ss_pred HHHHHHHHHHHHHHHHH---HHHHHhcccc
Confidence 55566778888889988 4444444443
No 31
>PRK09109 motC flagellar motor protein; Reviewed
Probab=43.70 E-value=38 Score=33.06 Aligned_cols=55 Identities=9% Similarity=0.151 Sum_probs=36.8
Q ss_pred HHHHHHHHHhhheee------eeehhHHHHHHHHHHHHHHHHhhhhhhhhc-hhhhhhcccc
Q 014676 161 MVVVAMGVMVGAFLM------VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG-RRGLLGFVKK 215 (420)
Q Consensus 161 i~l~~~g~~~G~f~l------~av~~~~ll~~~~~~f~~v~a~~iwN~~~~-~~~i~rfl~k 215 (420)
.++++++.++++|++ .-++=+.++|++++.+++++..+-++..+. -+.+...+++
T Consensus 8 G~~~~~~~v~~~~~~~gg~~~~~~~~~~~lIV~Ggt~~a~~i~~~~~~~~~~~~~~~~~f~~ 69 (246)
T PRK09109 8 GLILAFVAIIGGQVLEGGHLGSLLNGPAFLIVIGGTLGAVLLQTPLAVFKRAFKILRWVFFP 69 (246)
T ss_pred HHHHHHHHHHHHHHhcCCChHHHhhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcc
Confidence 344455555555544 337888899999999998888888876665 4445555544
No 32
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=43.45 E-value=29 Score=26.53 Aligned_cols=21 Identities=10% Similarity=0.431 Sum_probs=9.8
Q ss_pred echhhHHHHHHHHHHHHHhhh
Q 014676 152 VSRAVAWVVMVVVAMGVMVGA 172 (420)
Q Consensus 152 vpk~vlw~vi~l~~~g~~~G~ 172 (420)
++-+...++++.|++|+++|.
T Consensus 16 ~~~pl~l~il~~f~~G~llg~ 36 (68)
T PF06305_consen 16 FPLPLGLLILIAFLLGALLGW 36 (68)
T ss_pred ccchHHHHHHHHHHHHHHHHH
Confidence 443444444445555554443
No 33
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=43.43 E-value=41 Score=30.78 Aligned_cols=57 Identities=21% Similarity=0.262 Sum_probs=28.0
Q ss_pred cceeeeeE---echhhHHHHH-HHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhh
Q 014676 144 EDVKVGFR---VSRAVAWVVM-VVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNC 202 (420)
Q Consensus 144 ~~~~~~~~---vpk~vlw~vi-~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~ 202 (420)
++..+++. +=|+.+|+-+ +|+ +|++|+++...+..-.++.++.+++++++++++...
T Consensus 63 D~V~v~i~e~~llkaa~lvYllPLl--~li~ga~l~~~~~~~e~~~~~~~~~g~~~g~~~~r~ 123 (154)
T PRK10862 63 QKVELGIAEGSLLRSALLVYMTPLV--GLFLGAALFQLLFGSDLAALCGALLGGVGGFLLARG 123 (154)
T ss_pred CEEEEecchhhHHHHHHHHHHHHHH--HHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHH
Confidence 33446654 4444444322 222 333343333333334666677777777776665543
No 34
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=42.65 E-value=24 Score=30.02 Aligned_cols=27 Identities=19% Similarity=0.417 Sum_probs=13.4
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 179 KKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 179 ~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
|...++..++.+++++.|.++|.+.|.
T Consensus 2 ~~l~i~~iialiv~~iiaIvvW~iv~i 28 (81)
T PF00558_consen 2 QSLEILAIIALIVALIIAIVVWTIVYI 28 (81)
T ss_dssp ------HHHHHHHHHHHHHHHHHHH--
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666666677778888855544
No 35
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=42.21 E-value=9.8 Score=32.47 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=9.5
Q ss_pred HHHHHHhhhhhhhhchh
Q 014676 191 VGPLFIGMIWNCVWGRR 207 (420)
Q Consensus 191 f~~v~a~~iwN~~~~~~ 207 (420)
++++++++.|-++++||
T Consensus 79 v~~lv~~l~w~f~~r~k 95 (96)
T PTZ00382 79 VGGLVGFLCWWFVCRGK 95 (96)
T ss_pred HHHHHHHHhheeEEeec
Confidence 33444556676666644
No 36
>PF05915 DUF872: Eukaryotic protein of unknown function (DUF872); InterPro: IPR008590 This entry represents several uncharacterised eukaryotic transmembrane proteins. The function of this currently unknown.
Probab=42.02 E-value=28 Score=30.81 Aligned_cols=55 Identities=13% Similarity=0.251 Sum_probs=31.4
Q ss_pred echhhHHHHHHHHHHH---HHhhheeeeee------hhHHHHHHHHHHHHHHH--Hhhhhhhhhch
Q 014676 152 VSRAVAWVVMVVVAMG---VMVGAFLMVAV------KKAVVLVAVAAVVGPLF--IGMIWNCVWGR 206 (420)
Q Consensus 152 vpk~vlw~vi~l~~~g---~~~G~f~l~av------~~~~ll~~~~~~f~~v~--a~~iwN~~~~~ 206 (420)
.|.=.+++.+.|+++| +++|.+++..- |.+.+|++-..+|...+ ..++|.++.++
T Consensus 39 ~pwK~I~la~~Lli~G~~li~~g~l~~~~~i~~~~~~~~~llilG~L~fIPG~Y~~~i~y~a~rg~ 104 (115)
T PF05915_consen 39 IPWKSIALAVFLLIFGTVLIIIGLLLFFGHIDGDRDRGWALLILGILCFIPGFYHTRIAYYAWRGY 104 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccchHHHHHHHHHhccHHHHHHHHHHHcCC
Confidence 3444556667777777 55666665543 56777776666665543 23444444443
No 37
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=41.89 E-value=34 Score=39.23 Aligned_cols=60 Identities=15% Similarity=0.161 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhhheeeee-ehhHHHHHHHHHHHHHHHHhhhhhhhhc-hhhhhhccccC
Q 014676 157 AWVVMVVVAMGVMVGAFLMVA-VKKAVVLVAVAAVVGPLFIGMIWNCVWG-RRGLLGFVKKY 216 (420)
Q Consensus 157 lw~vi~l~~~g~~~G~f~l~a-v~~~~ll~~~~~~f~~v~a~~iwN~~~~-~~~i~rfl~k~ 216 (420)
+|+|+.+|..-..+|.|-+.. +-.|++|+++++++++.+..-+|.+.|- +.++++=|.+-
T Consensus 10 ~~~v~~lflal~~lGl~~~lp~~~~~~~l~~~~~a~~~al~~~lrrfr~Pt~~ea~~RLe~~ 71 (820)
T PF13779_consen 10 LLSVLALFLALSWLGLWDLLPDWLRWALLAAFAAAALAALVRGLRRFRWPTRAEALRRLERA 71 (820)
T ss_pred HHHHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHhhh
Confidence 456666666667777776553 2333444433333333332333455444 66666666543
No 38
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=41.67 E-value=70 Score=28.51 Aligned_cols=51 Identities=14% Similarity=0.035 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHHH-Hhhhee-eeeehhHHHHHHHHHHHHHHHHhhhhhhhhch
Q 014676 156 VAWVVMVVVAMGV-MVGAFL-MVAVKKAVVLVAVAAVVGPLFIGMIWNCVWGR 206 (420)
Q Consensus 156 vlw~vi~l~~~g~-~~G~f~-l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~~ 206 (420)
++-.++..|+.|+ .++... -.-.+.=++|-++++++++++=+.+++.|..+
T Consensus 85 ilvsv~~~~~~~~~~~~~~~~~~~~~~Rvllgl~~al~vlvAEv~l~~~y~~k 137 (142)
T PF11712_consen 85 ILVSVFAVFFAGWYWAGYSFGGWSFPYRVLLGLFGALLVLVAEVVLYIRYLRK 137 (142)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445555566665 444333 34455556777777777777777777777664
No 39
>PRK14762 membrane protein; Provisional
Probab=41.59 E-value=24 Score=24.50 Aligned_cols=16 Identities=19% Similarity=0.897 Sum_probs=13.4
Q ss_pred hhhHHHHHHHHHHHHH
Q 014676 154 RAVAWVVMVVVAMGVM 169 (420)
Q Consensus 154 k~vlw~vi~l~~~g~~ 169 (420)
|.++|++..+|..|++
T Consensus 2 ki~lw~i~iifligll 17 (27)
T PRK14762 2 KIILWAVLIIFLIGLL 17 (27)
T ss_pred eeHHHHHHHHHHHHHH
Confidence 5678999999999965
No 40
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=41.57 E-value=58 Score=30.64 Aligned_cols=18 Identities=39% Similarity=0.569 Sum_probs=15.8
Q ss_pred CcCCcEEEEEEEEEeccc
Q 014676 224 AIDGQYVKVTGVVTCGSI 241 (420)
Q Consensus 224 a~dGq~VKItG~VtcG~~ 241 (420)
...|+.+.|-|.|.-|++
T Consensus 54 ~~~g~~iRvgG~V~~GSv 71 (159)
T PRK13150 54 PAVGQRLRVGGMVMPGSV 71 (159)
T ss_pred cCCCCEEEEeeEEeCCcE
Confidence 457999999999999886
No 41
>PF11990 DUF3487: Protein of unknown function (DUF3487); InterPro: IPR021877 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.
Probab=41.24 E-value=43 Score=29.93 Aligned_cols=63 Identities=17% Similarity=0.260 Sum_probs=34.9
Q ss_pred eeEechhhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCC
Q 014676 149 GFRVSRAVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPD 218 (420)
Q Consensus 149 ~~~vpk~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd 218 (420)
|+..+-. .+++.+=+++|+++|.++......+ .++..++++.+++.+++. .+-+-|.=+.-||
T Consensus 20 GlT~~El-~~~a~~~~~~g~~~gl~la~~~g~~-a~~pt~~ll~~~~~v~~g-----g~~l~rlKRGKP~ 82 (121)
T PF11990_consen 20 GLTADEL-GLAAGVGFVAGLVVGLPLALLTGWW-AMIPTGALLGPILGVFVG-----GKLLARLKRGKPE 82 (121)
T ss_pred CCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHh-----HHHHHHHHcCCch
Confidence 4444443 3666667788888888876665554 344445555555544443 3334444444555
No 42
>PF03916 NrfD: Polysulphide reductase, NrfD; InterPro: IPR005614 NrfD is an integral transmembrane protein with loops in both the periplasm and the cytoplasm. NrfD is thought to participate in the transfer of electrons, from the quinone pool into the terminal components of the Nrf pathway [].
Probab=40.85 E-value=35 Score=33.31 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=22.3
Q ss_pred ccccCcceeeeeEechhhHHHHHHHHHHHHHhhheeeeee
Q 014676 139 VTSLGEDVKVGFRVSRAVAWVVMVVVAMGVMVGAFLMVAV 178 (420)
Q Consensus 139 vt~l~~~~~~~~~vpk~vlw~vi~l~~~g~~~G~f~l~av 178 (420)
||++|++.-.| . |...-+|..|+.+|+|++++.
T Consensus 2 vt~~~~~~~WG--l-----~i~~y~f~~glaaG~~~~a~~ 34 (313)
T PF03916_consen 2 VTGMSDQVPWG--L-----PIAVYLFFGGLAAGAFLLASL 34 (313)
T ss_pred CCCCCCCCCcc--c-----HHHHHHHHHHHHHHHHHHHHH
Confidence 78899887777 2 344466666777777766543
No 43
>PF06703 SPC25: Microsomal signal peptidase 25 kDa subunit (SPC25); InterPro: IPR009582 This family consists of several microsomal signal peptidase 25 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains [].; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=38.85 E-value=2.9e+02 Score=24.83 Aligned_cols=48 Identities=10% Similarity=0.036 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccccCcCCcEEEEE
Q 014676 180 KAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELRGAIDGQYVKVT 233 (420)
Q Consensus 180 ~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr~a~dGq~VKIt 233 (420)
.+++++.+++=|++-.++.+|+.++-+..+.-.-++-+ ...++.+.|.
T Consensus 56 ~~~~~~~v~~YfiLs~il~~~~~~~ek~~~~~g~~~~~------~~~~~~i~i~ 103 (162)
T PF06703_consen 56 KPYLIICVILYFILSGILTLYSYFVEKDIFYVGKRKDG------SSSGEKITIS 103 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEeccCC------CCCCCEEEEE
Confidence 34445555555555555666688777777665555433 3455566655
No 44
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=38.77 E-value=45 Score=31.27 Aligned_cols=18 Identities=39% Similarity=0.505 Sum_probs=15.0
Q ss_pred CcCCcEEEEEEEEEeccc
Q 014676 224 AIDGQYVKVTGVVTCGSI 241 (420)
Q Consensus 224 a~dGq~VKItG~VtcG~~ 241 (420)
.+.++.++|-|.|.-|++
T Consensus 48 ~~~~~~~RlGG~V~~GSv 65 (155)
T PRK13159 48 AAGYQQFRLGGMVKAGSI 65 (155)
T ss_pred cccCCeEEEccEEecCcE
Confidence 456799999999998876
No 45
>PF06645 SPC12: Microsomal signal peptidase 12 kDa subunit (SPC12); InterPro: IPR009542 This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12).; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=37.85 E-value=40 Score=27.73 Aligned_cols=49 Identities=10% Similarity=0.305 Sum_probs=34.6
Q ss_pred hhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhh
Q 014676 155 AVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVW 204 (420)
Q Consensus 155 ~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~ 204 (420)
..-+++++.+++||++| |+.--++..+...++++++++++.+=-|-+|.
T Consensus 12 l~~~il~~~~iisfi~G-y~~q~~~~~~~~~~~g~~~~~lv~vP~Wp~y~ 60 (76)
T PF06645_consen 12 LMQYILIISAIISFIVG-YITQSFSYTFYIYGAGVVLTLLVVVPPWPFYN 60 (76)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhheeCCcHhhc
Confidence 34455666667777776 55667777888888888888777777786654
No 46
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=37.57 E-value=26 Score=28.61 Aligned_cols=30 Identities=27% Similarity=0.371 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCC
Q 014676 184 LVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPD 218 (420)
Q Consensus 184 l~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd 218 (420)
+++++.+.++++++|+ .|+....+|++.|-
T Consensus 2 ~iilali~G~~~Gff~-----ar~~~~k~l~~NPp 31 (64)
T PF03672_consen 2 LIILALIVGAVIGFFI-----ARKYMEKQLKENPP 31 (64)
T ss_pred hHHHHHHHHHHHHHHH-----HHHHHHHHHHHCCC
Confidence 4555555566665544 47777888888875
No 47
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=35.65 E-value=27 Score=31.31 Aligned_cols=47 Identities=30% Similarity=0.475 Sum_probs=35.1
Q ss_pred cCCcEEEEEEEEEeccccccCccCCCCceeEEeeeEEEecCCCCCCCCCCCccccccce
Q 014676 225 IDGQYVKVTGVVTCGSIPLESSYQRVPRCVYVSTELHEYKGCGGKPANPKHRCFSWGSR 283 (420)
Q Consensus 225 ~dGq~VKItG~VtcG~~PL~ss~qkv~rCVYtst~LyE~rgw~~k~an~kh~~f~W~l~ 283 (420)
++-.++||.|+ ...=|++|-.-.||+|.+-.=.+-|+ ++.+-.|+..
T Consensus 29 ~~t~llkIEGv----~skeEa~fYlGkR~~yvYKa~~~~~~--------~k~RvIWGkV 75 (111)
T KOG0887|consen 29 PNTSLLKIEGV----YSKEEASFYLGKRCVYVYKAKPEVRG--------SKTRVIWGKV 75 (111)
T ss_pred CCcEEEEEecc----cchhhhheeecCcEEEEEecCCCCCC--------ceEEEEEEEE
Confidence 44458999997 45678899989999998765544444 7888888864
No 48
>TIGR01116 ATPase-IIA1_Ca sarco/endoplasmic reticulum calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1, the latter of which is modelled by TIGR01522.
Probab=35.64 E-value=86 Score=35.88 Aligned_cols=79 Identities=9% Similarity=0.143 Sum_probs=40.4
Q ss_pred chhhHHHHHHHHHHHHHhhheee--eeehhHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccccCcCCcEE
Q 014676 153 SRAVAWVVMVVVAMGVMVGAFLM--VAVKKAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELRGAIDGQYV 230 (420)
Q Consensus 153 pk~vlw~vi~l~~~g~~~G~f~l--~av~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr~a~dGq~V 230 (420)
-.++.|.+++.++.-++.|.... -...+|+.-+++++++.+.+++-.|.-+..++.+....+..|. .....|||+..
T Consensus 6 ~~~~~~iL~~aa~ls~~~~~~~~~~~~~~~~~~~~~Il~vi~~~~~i~~~qe~~a~~~~~~L~~~~~~-~~~ViRdg~~~ 84 (917)
T TIGR01116 6 EDLLVRILLLAACVSFVLAWFEEGEETVTAFVEPFVILLILVANAIVGVWQERNAEKAIEALKEYESE-HAKVLRDGRWS 84 (917)
T ss_pred hCHHHHHHHHHHHHHHHHhcccccccccccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC-ceEEEECCEEE
Confidence 34566666666666666663321 1123454444444444444445566666667666665544443 23334455444
Q ss_pred EE
Q 014676 231 KV 232 (420)
Q Consensus 231 KI 232 (420)
+|
T Consensus 85 ~I 86 (917)
T TIGR01116 85 VI 86 (917)
T ss_pred EE
Confidence 44
No 49
>TIGR03818 MotA1 flagellar motor stator protein MotA. This model represents one family of MotA proteins which are often not identified by the "transporter, MotA/TolQ/ExbB proton channel family" model, pfam01618.
Probab=35.58 E-value=62 Score=32.52 Aligned_cols=45 Identities=22% Similarity=0.348 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhheee------eeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 161 MVVVAMGVMVGAFLM------VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 161 i~l~~~g~~~G~f~l------~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
.++++.|+++|+|++ .-++=+.++||+++.+++++..+-++..+.
T Consensus 6 Gli~~~~~v~~g~~l~Gg~~~~l~~~~~~lIV~Ggtlga~lis~p~~~~~~ 56 (282)
T TIGR03818 6 GLVVVLGCVFGGYLLAGGHLAALWQPAELLIIGGAAIGAFIIANPPKVLKE 56 (282)
T ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 344455555555554 337788899999999999888888866665
No 50
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=35.41 E-value=54 Score=24.57 Aligned_cols=26 Identities=8% Similarity=0.367 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhhchh
Q 014676 182 VVLVAVAAVVGPLFIGMIWNCVWGRR 207 (420)
Q Consensus 182 ~ll~~~~~~f~~v~a~~iwN~~~~~~ 207 (420)
++..|++++...+...|+|.+|++|.
T Consensus 8 IIv~V~vg~~iiii~~~~YaCcykk~ 33 (38)
T PF02439_consen 8 IIVAVVVGMAIIIICMFYYACCYKKH 33 (38)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 34445555555666677777877753
No 51
>PF06374 NDUF_C2: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2); InterPro: IPR009423 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 family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport, NADH to ubiquinone, 0005743 mitochondrial inner membrane
Probab=35.25 E-value=84 Score=28.34 Aligned_cols=57 Identities=11% Similarity=0.271 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhhe--------ee-eeehhHHHHHHHHHHHHHHHHhhhhhhhhc--hhhhhhccccCCC
Q 014676 161 MVVVAMGVMVGAF--------LM-VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG--RRGLLGFVKKYPD 218 (420)
Q Consensus 161 i~l~~~g~~~G~f--------~l-~av~~~~ll~~~~~~f~~v~a~~iwN~~~~--~~~i~rfl~k~Pd 218 (420)
+.+..+|++.+-+ ++ +.+|+-+|++.++..++-.+ .=..|++.. .+.++.+++..|+
T Consensus 29 ~~~g~~G~~~~ll~N~~~rRP~~~sGihr~ll~~t~g~~~Gy~~-~k~~n~~~A~rD~~m~~YI~lHPE 96 (117)
T PF06374_consen 29 IWLGFLGFCTALLDNAINRRPPLKSGIHRQLLLATIGWFIGYYI-TKYRNYYYAERDADMRHYIKLHPE 96 (117)
T ss_pred HHHHHHHHHHHHHHHHHhcCCchhhccHHHHHHHHHHHHHHHHH-HHHHHHHHHHhchhHHHHHHhCcc
Confidence 4445566666544 34 77888888888777666554 233466665 7889999999886
No 52
>PRK06743 flagellar motor protein MotP; Reviewed
Probab=34.91 E-value=47 Score=33.01 Aligned_cols=28 Identities=4% Similarity=0.229 Sum_probs=24.1
Q ss_pred ehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 178 VKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 178 v~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
|+=+.++||+++.+++++..+=++..+.
T Consensus 28 ~~~~~~lIV~GGt~ga~li~~p~~~i~~ 55 (254)
T PRK06743 28 LDVSSILIVIGGTTATIVVAYRFGEIKK 55 (254)
T ss_pred hCHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 7888999999999999998888877665
No 53
>PF11808 DUF3329: Domain of unknown function (DUF3329); InterPro: IPR021766 This family of proteins are functionally uncharacterised. This family is only found in bacteria. ; GO: 0004673 protein histidine kinase activity
Probab=33.48 E-value=1.4e+02 Score=24.97 Aligned_cols=21 Identities=10% Similarity=0.216 Sum_probs=10.9
Q ss_pred HHhhhhhhhhchhhhhhccccC
Q 014676 195 FIGMIWNCVWGRRGLLGFVKKY 216 (420)
Q Consensus 195 ~a~~iwN~~~~~~~i~rfl~k~ 216 (420)
++.++|+++.= ..+.+.+++-
T Consensus 38 ~~~l~wh~~~l-~rL~~WL~~~ 58 (90)
T PF11808_consen 38 LLYLFWHLYQL-YRLERWLRNP 58 (90)
T ss_pred HHHHHHHHHHH-HHHHHHHhCC
Confidence 34556765532 3455666543
No 54
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=32.87 E-value=22 Score=41.43 Aligned_cols=16 Identities=63% Similarity=0.916 Sum_probs=14.4
Q ss_pred ccccCCceeEeCCCCc
Q 014676 7 SHQLSSGLYVSGRPEQ 22 (420)
Q Consensus 7 sHqlsnGlyVSGrpeq 22 (420)
-|||.|||||+|+|-|
T Consensus 1199 qH~Lps~l~v~~qp~q 1214 (1387)
T KOG1016|consen 1199 QHQLPSGLYVKLQPGQ 1214 (1387)
T ss_pred ccccCccceEecCCcc
Confidence 5999999999999874
No 55
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=32.73 E-value=39 Score=31.77 Aligned_cols=31 Identities=13% Similarity=0.116 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHhhhhhhhhchhhhhhccccC
Q 014676 185 VAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKY 216 (420)
Q Consensus 185 ~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~ 216 (420)
+|++++.+++++.|++.+|+.|+. .|..|||
T Consensus 99 ~Vl~g~s~l~i~yfvir~~R~r~~-~rktRkY 129 (163)
T PF06679_consen 99 YVLVGLSALAILYFVIRTFRLRRR-NRKTRKY 129 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccc-cccceee
Confidence 455666777777888888877552 2444555
No 56
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=31.98 E-value=82 Score=28.48 Aligned_cols=47 Identities=13% Similarity=0.207 Sum_probs=25.5
Q ss_pred eeeEechhhHHHHHHHHH-HHHHhhheeeeeehhHHHHHHHHHHHHHH
Q 014676 148 VGFRVSRAVAWVVMVVVA-MGVMVGAFLMVAVKKAVVLVAVAAVVGPL 194 (420)
Q Consensus 148 ~~~~vpk~vlw~vi~l~~-~g~~~G~f~l~av~~~~ll~~~~~~f~~v 194 (420)
|+=++-|.=.|++.++|+ |++..++++.-+.+....+..++++.+.+
T Consensus 4 ~~~KiN~~R~~al~lif~g~~vmy~gi~f~~~~~im~ifmllG~L~~l 51 (114)
T PF11023_consen 4 YSSKINKIRTFALSLIFIGMIVMYIGIFFKASPIIMVIFMLLGLLAIL 51 (114)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHHHHH
Confidence 343455666788877764 66666666554444444444444444333
No 57
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=31.81 E-value=1.2e+02 Score=30.77 Aligned_cols=10 Identities=0% Similarity=0.408 Sum_probs=5.9
Q ss_pred heeeeeehhH
Q 014676 172 AFLMVAVKKA 181 (420)
Q Consensus 172 ~f~l~av~~~ 181 (420)
+.++.+|-++
T Consensus 26 Gyv~i~~~~~ 35 (398)
T PRK10747 26 GYVLIQTDNY 35 (398)
T ss_pred CeEEEEECCE
Confidence 3567776554
No 58
>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 200 amino acids in length.
Probab=31.71 E-value=1.4e+02 Score=27.11 Aligned_cols=57 Identities=16% Similarity=0.233 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHhhheee--eee-----hhHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhcc
Q 014676 157 AWVVMVVVAMGVMVGAFLM--VAV-----KKAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFV 213 (420)
Q Consensus 157 lw~vi~l~~~g~~~G~f~l--~av-----~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl 213 (420)
+|-...+..++|++|...- ..+ .....|.++++++++++..++|+-+..-..+.+|-
T Consensus 20 L~ysyfl~~~~l~Lg~~~~~~~~~~~~~~~~~~~l~~~~~l~~l~~~~~~~~~~~~~~~l~~~~ 83 (193)
T PF11846_consen 20 LWYSYFLWPFALLLGLLPDPARRLRRIPRSLAFALRAAALLIALAALGFMLTDYHTNEQLTRFE 83 (193)
T ss_pred HHHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4656666666666666554 222 22345556677777777788887776655555555
No 59
>COG0811 TolQ Biopolymer transport proteins [Intracellular trafficking and secretion]
Probab=31.49 E-value=45 Score=31.84 Aligned_cols=23 Identities=4% Similarity=0.101 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhc
Q 014676 183 VLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 183 ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
|+.-+++||+++.|+++||++.+
T Consensus 167 L~aTA~GL~vAIPAvi~yn~l~r 189 (216)
T COG0811 167 LIATAIGLFVAIPAVVAYNVLRR 189 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 55678899999999999999887
No 60
>PRK09110 flagellar motor protein MotA; Validated
Probab=31.38 E-value=74 Score=32.05 Aligned_cols=44 Identities=20% Similarity=0.454 Sum_probs=31.6
Q ss_pred HHHHHHHHhhheee------eeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 162 VVVAMGVMVGAFLM------VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 162 ~l~~~g~~~G~f~l------~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
++++.|+++|+|++ +-++-+.++||+++.+++++..+=++....
T Consensus 7 li~~~~~i~~g~~l~gg~~~~l~~~~~~lIV~Ggtlga~lv~~p~~~i~~ 56 (283)
T PRK09110 7 YIVVLGSVFGGYLLAGGHLGALIQPAELLIIGGAALGAFIVGNPGKAIKA 56 (283)
T ss_pred HHHHHHHHHHHHHHcCCChhHhhchhHHHHHHHhHHHHHHHcCCHHHHHH
Confidence 34445555555444 347888999999999999988888876665
No 61
>PF05834 Lycopene_cycl: Lycopene cyclase protein; InterPro: IPR008671 This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare [].; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0016117 carotenoid biosynthetic process
Probab=30.98 E-value=1.7e+02 Score=29.33 Aligned_cols=44 Identities=16% Similarity=0.247 Sum_probs=32.9
Q ss_pred eeeceEEeecC--CCCCCCHHHHHHHhhcCCCCccceeEEecceeee
Q 014676 317 VKPATVVNITK--GNRDLSPSFLRWLADRNLSSDDRIMRLKEGYIKE 361 (420)
Q Consensus 317 V~e~~vv~~~~--~~~dlS~~f~~WL~erNLSsd~r~mRlkEGyIkE 361 (420)
++|.|.++... +..++...+.+||+++|+.... ++|-|.|+|--
T Consensus 198 lvE~T~fs~~~~~~~~~~~~~l~~~l~~~g~~~~~-i~~~E~G~IPm 243 (374)
T PF05834_consen 198 LVEETSFSPRPALPEEELKARLRRYLERLGIDDYE-ILEEERGVIPM 243 (374)
T ss_pred EEEEEEEcCCCCCCHHHHHHHHHHHHHHcCCCcee-EEEeecceeec
Confidence 56666666544 2346778899999998888765 88999998876
No 62
>PRK08124 flagellar motor protein MotA; Validated
Probab=29.90 E-value=90 Score=30.85 Aligned_cols=45 Identities=11% Similarity=0.254 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhheee------eeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 161 MVVVAMGVMVGAFLM------VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 161 i~l~~~g~~~G~f~l------~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
.+++++|.+++++++ .-||=+.+|||+++.+++++..+-++....
T Consensus 8 G~~~~~~~i~~g~~~~gg~~~~~~~~~~~lIV~Ggt~~a~~i~~~~~~~~~ 58 (263)
T PRK08124 8 GLILGLIAVVVGMVVKGASLAVLLNPAAILIIIVGTIAAVMIAFPMSELKK 58 (263)
T ss_pred HHHHHHHHHHHHHHhcCCChHHHhhHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 344445545544443 347888899999999999888888866655
No 63
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=29.56 E-value=1.5e+02 Score=29.17 Aligned_cols=43 Identities=16% Similarity=0.251 Sum_probs=36.0
Q ss_pred ccccCcCCcEEEEEEEEEeccccccCccCCCCceeEEeeeEEEe
Q 014676 220 ELRGAIDGQYVKVTGVVTCGSIPLESSYQRVPRCVYVSTELHEY 263 (420)
Q Consensus 220 ~lr~a~dGq~VKItG~VtcG~~PL~ss~qkv~rCVYtst~LyE~ 263 (420)
++.--.+|+.++++|.+-=||. |..|+++.|=||-....+++.
T Consensus 159 ~v~i~~~~~~~~~~allDTGN~-L~DPitg~PV~Vve~~~~~~~ 201 (293)
T PF03419_consen 159 PVTIEIGGKKIELKALLDTGNQ-LRDPITGRPVIVVEYEALEKL 201 (293)
T ss_pred EEEEEECCEEEEEEEEEECCCc-ccCCCCCCcEEEEEHHHHHhh
Confidence 3445678999999999999996 788999999888888777776
No 64
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=29.35 E-value=96 Score=29.30 Aligned_cols=56 Identities=23% Similarity=0.324 Sum_probs=35.8
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccc--cCcCCcEEEEEEEEEeccc
Q 014676 180 KAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELR--GAIDGQYVKVTGVVTCGSI 241 (420)
Q Consensus 180 ~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr--~a~dGq~VKItG~VtcG~~ 241 (420)
++.+++++++..++++++.+||. +..|-=| |+-+++. ....||-+.+-|.|.-|++
T Consensus 8 Rl~~il~~~a~l~~a~~l~Lyal---~~ni~~f---y~Psel~~~~~~~G~rlR~GGlV~~GSv 65 (153)
T COG2332 8 RLWIILAGLAGLALAVGLVLYAL---RSNIDYF---YTPSELLEGKVETGQRLRLGGLVEAGSV 65 (153)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhh---ccCceEE---ECHHHhccccccCCcEEEEeeeEeeceE
Confidence 45566666666677777777765 3333222 3444554 3455899999999998864
No 65
>PRK12482 flagellar motor protein MotA; Provisional
Probab=29.08 E-value=88 Score=31.72 Aligned_cols=46 Identities=20% Similarity=0.398 Sum_probs=32.6
Q ss_pred HHHHHHHHHHhhheee------eeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 160 VMVVVAMGVMVGAFLM------VAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 160 vi~l~~~g~~~G~f~l------~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
+.+++++|+++++|++ .-++=+.++|++++.+++++..+=|+....
T Consensus 5 iGlv~~~~~v~~g~~l~Gg~~~~~~~~~~~lIV~GGt~ga~lis~p~~~~~~ 56 (287)
T PRK12482 5 FGLLVVMGCVFGGYLMSGGSLSSIWQPGEIIIILGAGIGAMILGNPKSVLKE 56 (287)
T ss_pred HHHHHHHHHHHHHHHHhCCChHHHHhHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 3445555656655554 337778899999999999888888866665
No 66
>PRK08990 flagellar motor protein PomA; Reviewed
Probab=28.61 E-value=98 Score=30.64 Aligned_cols=40 Identities=13% Similarity=0.240 Sum_probs=28.0
Q ss_pred HHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 166 MGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 166 ~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
.|+..|+=+..-|+=+.++|++++.+++++..+-+.-.++
T Consensus 18 ~g~~~gg~~~~l~~~~~~lIV~GGt~ga~l~~~~~~~~~~ 57 (254)
T PRK08990 18 MAMVLGGGIGMFVDVPSILIVFGGSLFVVLMKFNLGQFFG 57 (254)
T ss_pred HHHHhcCcHHHHhCHHHHHHHHHHHHHHHHhhccHHHHHH
Confidence 3455555555558888899999999888886666654444
No 67
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=28.61 E-value=45 Score=23.67 Aligned_cols=17 Identities=12% Similarity=0.440 Sum_probs=14.7
Q ss_pred CHHHHHHHhhcCCCCcc
Q 014676 333 SPSFLRWLADRNLSSDD 349 (420)
Q Consensus 333 S~~f~~WL~erNLSsd~ 349 (420)
..+|+.||.++|+....
T Consensus 6 ~~~L~~wL~~~gi~~~~ 22 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPK 22 (38)
T ss_pred HHHHHHHHHHcCCCCCC
Confidence 47899999999998775
No 68
>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=28.36 E-value=1e+02 Score=28.96 Aligned_cols=16 Identities=13% Similarity=0.588 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHhhhe
Q 014676 158 WVVMVVVAMGVMVGAF 173 (420)
Q Consensus 158 w~vi~l~~~g~~~G~f 173 (420)
|.-.+.-..++++|++
T Consensus 132 ~~~al~~~~sf~lg~l 147 (213)
T PF01988_consen 132 WKAALATFLSFILGGL 147 (213)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5566666666666663
No 69
>PRK10490 sensor protein KdpD; Provisional
Probab=28.28 E-value=35 Score=38.67 Aligned_cols=15 Identities=13% Similarity=0.215 Sum_probs=6.9
Q ss_pred HHHHHHHhhhhhhhh
Q 014676 190 VVGPLFIGMIWNCVW 204 (420)
Q Consensus 190 ~f~~v~a~~iwN~~~ 204 (420)
++++++++++|||+|
T Consensus 449 i~aavls~l~~nfFF 463 (895)
T PRK10490 449 VVATVINVASFDLFF 463 (895)
T ss_pred HHHHHHHHHHHHhee
Confidence 344444444555544
No 70
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=28.06 E-value=41 Score=29.40 Aligned_cols=26 Identities=12% Similarity=0.107 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHhhhhhhhhchhhhhh
Q 014676 186 AVAAVVGPLFIGMIWNCVWGRRGLLG 211 (420)
Q Consensus 186 ~~~~~f~~v~a~~iwN~~~~~~~i~r 211 (420)
++++++++++.+|+.-+|+.||...+
T Consensus 4 l~~iii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 4 LFAIIIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred eHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34445555554444466666666655
No 71
>TIGR01523 ATPase-IID_K-Na potassium and/or sodium efflux P-type ATPase, fungal-type. The Leishmania sequence (GP|3192903), which falls between trusted and noise in this model, may very well turn out to be an active potassium pump.
Probab=27.79 E-value=1.3e+02 Score=35.24 Aligned_cols=52 Identities=6% Similarity=-0.035 Sum_probs=23.1
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccccCcCCcEEEE
Q 014676 180 KAVVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELRGAIDGQYVKV 232 (420)
Q Consensus 180 ~~~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr~a~dGq~VKI 232 (420)
.|+--+++++++.+.+++-.|+-++.++.+.. |++.-...-+..|||+...|
T Consensus 80 ~~~~~~iIl~vv~in~~i~~~QE~~aekal~a-L~~l~~~~~~ViRdg~~~~I 131 (1053)
T TIGR01523 80 DWIEGGVISAIIALNILIGFIQEYKAEKTMDS-LKNLASPMAHVIRNGKSDAI 131 (1053)
T ss_pred hHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH-HhccCCCceEEEeCCeeeec
Confidence 34433333333333443445566666665554 44433333334444444433
No 72
>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=27.42 E-value=78 Score=23.54 Aligned_cols=32 Identities=6% Similarity=-0.039 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHhhhhhhhhchhhhhhcccc
Q 014676 184 LVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKK 215 (420)
Q Consensus 184 l~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k 215 (420)
.+..+.++++-+++++|.+..+++.-..-.++
T Consensus 12 ~~~~v~~~~~F~gi~~w~~~~~~k~~~e~aa~ 43 (49)
T PF05545_consen 12 SIGTVLFFVFFIGIVIWAYRPRNKKRFEEAAN 43 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHcccchhhHHHHHc
Confidence 33444445555556666664444433333333
No 73
>KOG0558 consensus Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion]
Probab=27.15 E-value=20 Score=38.08 Aligned_cols=18 Identities=39% Similarity=0.545 Sum_probs=15.8
Q ss_pred ceeEEecceeeeCCEEEE
Q 014676 350 RIMRLKEGYIKEGSTVSV 367 (420)
Q Consensus 350 r~mRlkEGyIkEGstvSV 367 (420)
|-..+||.|+||||||+=
T Consensus 77 ~Ev~vkeWfVKEGDtVeq 94 (474)
T KOG0558|consen 77 AEVTVKEWFVKEGDTVEQ 94 (474)
T ss_pred eeeeeeeehhhcCCcHHH
Confidence 668999999999999863
No 74
>PRK13629 threonine/serine transporter TdcC; Provisional
Probab=26.84 E-value=67 Score=34.46 Aligned_cols=63 Identities=10% Similarity=0.207 Sum_probs=48.5
Q ss_pred hHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhh-hhhhchhhhhhccccC--CCcccccC
Q 014676 156 VAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIW-NCVWGRRGLLGFVKKY--PDTELRGA 224 (420)
Q Consensus 156 vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iw-N~~~~~~~i~rfl~k~--Pd~~lr~a 224 (420)
..|+ ..++.+.++||.+.| ++.....+.....++.+++| -.|++.+.+.|+.-.+ +++++.++
T Consensus 22 ~~W~-l~l~GTAIGAGmLfL-----PI~~g~~Gf~p~lillll~~p~m~~s~l~L~e~~L~~~~~~~~i~~v 87 (443)
T PRK13629 22 TTWT-LGLFGTAIGAGVLFF-----PIRAGFGGLIPILLMLVLAYPIAFYCHRALARLCLSGSNPSGNITET 87 (443)
T ss_pred chHH-HHHHHHHHhHHHHHH-----HHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCHHHH
Confidence 3488 667888899998876 67777777788888889999 7788888888988776 34555543
No 75
>PF13869 NUDIX_2: Nucleotide hydrolase; PDB: 3MDG_B 2J8Q_B 3Q2S_A 3P5T_D 3BAP_A 2CL3_A 3P6Y_A 3Q2T_B 3BHO_A 3N9U_A ....
Probab=26.72 E-value=11 Score=36.23 Aligned_cols=35 Identities=43% Similarity=0.613 Sum_probs=28.4
Q ss_pred hcCCCCccceeEEecceeeeCCEEEEEEEEEeeCc
Q 014676 342 DRNLSSDDRIMRLKEGYIKEGSTVSVMGVVRRHDN 376 (420)
Q Consensus 342 erNLSsd~r~mRlkEGyIkEGstvSVmGvvkr~~~ 376 (420)
|+..+..+|.+|++|-|-++|++-||-||+==|..
T Consensus 21 ekd~s~~~rl~rl~~~y~~~GmRrsVe~Vllvh~h 55 (188)
T PF13869_consen 21 EKDPSVAARLQRLKENYEKEGMRRSVEGVLLVHEH 55 (188)
T ss_dssp -SSSSHHHHHHHHHHHHHHHSSEEEEEEEEEEEET
T ss_pred ccccCHHHHHHHHHHHHHHhCCceEEEEEEEEecC
Confidence 34566678999999999999999999998755544
No 76
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=26.33 E-value=93 Score=25.33 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=24.1
Q ss_pred ceeeeCCEEEEEEEEEeeCceeEEeCCC
Q 014676 357 GYIKEGSTVSVMGVVRRHDNVLMIVPST 384 (420)
Q Consensus 357 GyIkEGstvSVmGvvkr~~~~~mi~pP~ 384 (420)
.-+++|++|.|-|.++...+..=|.++.
T Consensus 43 ~~~~~Gd~V~vtG~v~ey~g~tql~~~~ 70 (78)
T cd04486 43 ADVAVGDLVRVTGTVTEYYGLTQLTAVS 70 (78)
T ss_pred CCCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence 4568999999999999999987777776
No 77
>PF11292 DUF3093: Protein of unknown function (DUF3093); InterPro: IPR021443 This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed.
Probab=26.24 E-value=1.4e+02 Score=27.67 Aligned_cols=43 Identities=9% Similarity=0.135 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhh
Q 014676 156 VAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMI 199 (420)
Q Consensus 156 vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~i 199 (420)
..|-++.+++.|+++..+.+..-.-+.. +++++++++++++++
T Consensus 11 ~~wW~~~~~~~~~~~~~v~~~~~~~~~~-i~~~~~~~~~~~~l~ 53 (143)
T PF11292_consen 11 WWWWLAAAAVAALLAAEVVLGPPSLWAW-IPYAVVVAVAVWALL 53 (143)
T ss_pred HHHHHHHHHHHHHHHHhhhcCcchHHHH-HHHHHHHHHHHHHHH
Confidence 3344444555777777777655544444 333333333333333
No 78
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=26.18 E-value=63 Score=26.85 Aligned_cols=25 Identities=16% Similarity=0.179 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHhhhh--hhhhchhhhh
Q 014676 186 AVAAVVGPLFIGMIW--NCVWGRRGLL 210 (420)
Q Consensus 186 ~~~~~f~~v~a~~iw--N~~~~~~~i~ 210 (420)
+++++.+++++++.| |.||..++=.
T Consensus 35 aIGvi~gi~~~~lt~ltN~YFK~k~dr 61 (68)
T PF04971_consen 35 AIGVIGGIFFGLLTYLTNLYFKIKEDR 61 (68)
T ss_pred hHHHHHHHHHHHHHHHhHhhhhhhHhh
Confidence 344444444444444 9999844433
No 79
>COG1291 MotA Flagellar motor component [Cell motility and secretion]
Probab=26.13 E-value=56 Score=33.07 Aligned_cols=53 Identities=17% Similarity=0.236 Sum_probs=40.4
Q ss_pred hheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhc-hhhhhhccccCCCccccc
Q 014676 171 GAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWG-RRGLLGFVKKYPDTELRG 223 (420)
Q Consensus 171 G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~-~~~i~rfl~k~Pd~~lr~ 223 (420)
|+=+.+-+|=+.++|++++.++++...+=++.... -+.+...++++...++.+
T Consensus 24 Gg~~~~l~~~~s~lII~gg~i~A~~~~~p~~~vk~~~k~~~~~F~~~k~~~~~~ 77 (266)
T COG1291 24 GGSLGALIQPSSLLIIVGGGIGAFMVGNPGKVVKATPKALKEAFRKPKKEDYVD 77 (266)
T ss_pred CCceeeeeccchhheeechhhHHHHhcCcHHHHHHHHHHHHHHHhcCchhhHHH
Confidence 33366778999999999999888888888888777 666777777777565543
No 80
>COG4303 EutB Ethanolamine ammonia-lyase, large subunit [Amino acid transport and metabolism]
Probab=26.04 E-value=54 Score=34.80 Aligned_cols=27 Identities=26% Similarity=0.569 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhhcCCCCccceeEEecc
Q 014676 330 RDLSPSFLRWLADRNLSSDDRIMRLKEG 357 (420)
Q Consensus 330 ~dlS~~f~~WL~erNLSsd~r~mRlkEG 357 (420)
....|||++||.+.++..++|+ +...|
T Consensus 421 lrP~~EFe~wl~~mGi~~~Grl-t~~ag 447 (453)
T COG4303 421 LRPIPEFERWLERMGIMANGRL-TKRAG 447 (453)
T ss_pred CCCchHHHHHHHHhCcccCCce-eccCC
Confidence 5678999999999999988863 44443
No 81
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=25.43 E-value=2.3e+02 Score=25.72 Aligned_cols=24 Identities=4% Similarity=0.296 Sum_probs=11.3
Q ss_pred hHHHHHHHHHHH--HHhhheeeeeeh
Q 014676 156 VAWVVMVVVAMG--VMVGAFLMVAVK 179 (420)
Q Consensus 156 vlw~vi~l~~~g--~~~G~f~l~av~ 179 (420)
..|.++.++... ++.++|++..+.
T Consensus 6 ~~wli~g~~ll~~E~l~~~~~ll~~g 31 (140)
T COG1585 6 WIWLILGLLLLIAEILGPGVFLLWLG 31 (140)
T ss_pred HHHHHHHHHHHHHHHhcccHHHHHHH
Confidence 345444333333 555555555555
No 82
>TIGR01789 lycopene_cycl lycopene cyclase. This model represents a family of bacterial lycopene cyclases catalyzing the transformation of lycopene to carotene. These enzymes are found in a limited spectrum of alpha and gamma proteobacteria as well as Flavobacterium.
Probab=25.31 E-value=1.4e+02 Score=30.29 Aligned_cols=81 Identities=16% Similarity=0.222 Sum_probs=44.7
Q ss_pred ecCCCCCCCCCCCccccccceeeeeEeeceEEEecCCceeEEEEecCCCeeeee-----eeeceEEeecC--CCCCCCHH
Q 014676 263 YKGCGGKPANPKHRCFSWGSRHLEKYVSDFYISDFQSGLRALVKAGYGAKVAPF-----VKPATVVNITK--GNRDLSPS 335 (420)
Q Consensus 263 ~rgw~~k~an~kh~~f~W~l~~~E~~~~DFYIsD~~sG~RAlVKaG~G~kVtp~-----V~e~~vv~~~~--~~~dlS~~ 335 (420)
..||-.+...| |.--+ -..-||.+.+ ..|.|++- |.|+ .+|+|.++-.+ +..++...
T Consensus 149 f~G~~~r~~~p-~~~~~-------~~lMD~~~~q-~~g~~F~Y-------~lP~~~~~~lvE~T~~s~~~~l~~~~l~~~ 212 (370)
T TIGR01789 149 FLGREMRLQEP-HGLEN-------PIIMDATVDQ-LAGYRFVY-------VLPLGSHDLLIEDTYYADDPLLDRNALSQR 212 (370)
T ss_pred EEEEEEEEcCC-CCCCc-------cEEEeeeccC-CCCceEEE-------ECcCCCCeEEEEEEeccCCCCCCHHHHHHH
Confidence 46665555555 53211 1234566643 34556554 4444 34565554321 12345567
Q ss_pred HHHHHhhcCCCCccceeEEecceee
Q 014676 336 FLRWLADRNLSSDDRIMRLKEGYIK 360 (420)
Q Consensus 336 f~~WL~erNLSsd~r~mRlkEGyIk 360 (420)
|.+|++++++.... +++.|.|.|-
T Consensus 213 l~~~~~~~g~~~~~-i~~~e~g~iP 236 (370)
T TIGR01789 213 IDQYARANGWQNGT-PVRHEQGVLP 236 (370)
T ss_pred HHHHHHHhCCCceE-EEEeeeeEEe
Confidence 88999888776555 7777777664
No 83
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=25.14 E-value=1.2e+02 Score=22.22 Aligned_cols=27 Identities=33% Similarity=0.434 Sum_probs=22.7
Q ss_pred eeeeCCEEEEEEEEEeeCceeEEeCCC
Q 014676 358 YIKEGSTVSVMGVVRRHDNVLMIVPST 384 (420)
Q Consensus 358 yIkEGstvSVmGvvkr~~~~~mi~pP~ 384 (420)
.+++|+++.|.|.+++..+.+-|..|.
T Consensus 45 ~~~~G~~~~v~Gkv~~~~~~~qi~~P~ 71 (75)
T cd04488 45 QLPPGTRVRVSGKVKRFRGGLQIVHPE 71 (75)
T ss_pred cCCCCCEEEEEEEEeecCCeeEEeCCc
Confidence 478999999999999988877777664
No 84
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=24.71 E-value=1.6e+02 Score=33.11 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=18.6
Q ss_pred cccccccCcceeeeeEechhhHHHHHHHHHHHHHhhhe
Q 014676 136 GSAVTSLGEDVKVGFRVSRAVAWVVMVVVAMGVMVGAF 173 (420)
Q Consensus 136 ~~avt~l~~~~~~~~~vpk~vlw~vi~l~~~g~~~G~f 173 (420)
-.|...|+.+. -|+=| ++|++.+..+.-+++|.+
T Consensus 19 ~~~~~~~~~~~--~~~~p--~~~vl~~~a~ls~~~~~~ 52 (679)
T PRK01122 19 KDAFKKLDPRV--QIRNP--VMFVVEVGSILTTILTIA 52 (679)
T ss_pred HHHHHcCCHHH--HhhCh--HHHHHHHHHHHHHHHHhh
Confidence 44555666653 33333 556666666666666643
No 85
>PRK14992 tetrathionate reductase subunit C; Provisional
Probab=24.41 E-value=91 Score=32.21 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHhhheeeeeeh
Q 014676 157 AWVVMVVVAMGVMVGAFLMVAVK 179 (420)
Q Consensus 157 lw~vi~l~~~g~~~G~f~l~av~ 179 (420)
.|++.-+|..|+.+|+|++++.+
T Consensus 16 ~~iv~YlFl~GlaaGa~lla~~~ 38 (335)
T PRK14992 16 PWAVQYFFFIGIAACAALFACYL 38 (335)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 48889999999999999998653
No 86
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=23.35 E-value=65 Score=22.62 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=14.4
Q ss_pred HHHHHHHhhcCCCCccc
Q 014676 334 PSFLRWLADRNLSSDDR 350 (420)
Q Consensus 334 ~~f~~WL~erNLSsd~r 350 (420)
++|+.+|+++||+..|+
T Consensus 7 ~eLk~~l~~~gL~~~G~ 23 (35)
T PF02037_consen 7 AELKEELKERGLSTSGK 23 (35)
T ss_dssp HHHHHHHHHTTS-STSS
T ss_pred HHHHHHHHHCCCCCCCC
Confidence 68999999999999983
No 87
>PF14110 DUF4282: Domain of unknown function (DUF4282)
Probab=23.22 E-value=1.2e+02 Score=25.35 Aligned_cols=21 Identities=10% Similarity=0.553 Sum_probs=14.1
Q ss_pred echhhHHHHHHHHHHHHHhhh
Q 014676 152 VSRAVAWVVMVVVAMGVMVGA 172 (420)
Q Consensus 152 vpk~vlw~vi~l~~~g~~~G~ 172 (420)
+=+.++|+.+++.+.+.+.+.
T Consensus 13 ii~~~Y~l~li~i~l~~~~~~ 33 (90)
T PF14110_consen 13 IIKVLYWLGLILIVLSGLSGI 33 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 446778888777776655544
No 88
>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=22.91 E-value=82 Score=25.15 Aligned_cols=22 Identities=9% Similarity=0.442 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHhhhhhh
Q 014676 181 AVVLVAVAAVVGPLFIGMIWNC 202 (420)
Q Consensus 181 ~~ll~~~~~~f~~v~a~~iwN~ 202 (420)
-+||+++.++.++++++|.++.
T Consensus 9 viLliaitVilaavv~~~~~~~ 30 (80)
T PF07790_consen 9 VILLIAITVILAAVVGAFVFGL 30 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4677777778888888877765
No 89
>PRK07118 ferredoxin; Validated
Probab=22.81 E-value=46 Score=33.11 Aligned_cols=26 Identities=31% Similarity=0.551 Sum_probs=22.0
Q ss_pred hhHHHHHHHHHHHHHhhheeeeeehh
Q 014676 155 AVAWVVMVVVAMGVMVGAFLMVAVKK 180 (420)
Q Consensus 155 ~vlw~vi~l~~~g~~~G~f~l~av~~ 180 (420)
.+++++++|.++||++|.++.+|-+.
T Consensus 3 ~i~~~~~~~~~~g~~~g~~l~~a~~~ 28 (280)
T PRK07118 3 MILFAVLSLGALGLVFGILLAFASKK 28 (280)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHeee
Confidence 47899999999999999988777654
No 90
>KOG2362 consensus Uncharacterized Fe-S protein [General function prediction only]
Probab=22.78 E-value=55 Score=34.16 Aligned_cols=17 Identities=47% Similarity=0.546 Sum_probs=14.9
Q ss_pred EecceeeeCCEEEEEEE
Q 014676 354 LKEGYIKEGSTVSVMGV 370 (420)
Q Consensus 354 lkEGyIkEGstvSVmGv 370 (420)
++||||+.|++|.|+.-
T Consensus 316 ~~~g~I~vGd~Vyv~~k 332 (336)
T KOG2362|consen 316 VNEGTIKVGDTVYVLYK 332 (336)
T ss_pred cccceEEeCCEEEEEec
Confidence 56899999999999864
No 91
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=22.73 E-value=1.2e+02 Score=32.87 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=15.1
Q ss_pred eeEechhhHHHHHHHHHHH
Q 014676 149 GFRVSRAVAWVVMVVVAMG 167 (420)
Q Consensus 149 ~~~vpk~vlw~vi~l~~~g 167 (420)
.+.++|.+++-...+++.|
T Consensus 221 ~~~~sr~~~~~~~~~~~~g 239 (679)
T TIGR02916 221 RIAVSREMAFHSATLLGAG 239 (679)
T ss_pred ceeechHHHHHHHHHHHHH
Confidence 3449999998888888777
No 92
>PF05934 MCLC: Mid-1-related chloride channel (MCLC); InterPro: IPR009231 This entry consists of several Chloride channel CLIC-like proteins, which function as a chloride channel when incorporated in the planar lipid bilayer [].
Probab=22.14 E-value=1.1e+02 Score=33.98 Aligned_cols=85 Identities=11% Similarity=0.028 Sum_probs=39.5
Q ss_pred CCCCCCCCCCCCCccccccccccccCcceeeeeEechhhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHh
Q 014676 118 SGQLDYSGSGSGSVKAGYGSAVTSLGEDVKVGFRVSRAVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIG 197 (420)
Q Consensus 118 Sg~l~~~~s~~~~~~~~~~~avt~l~~~~~~~~~vpk~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~ 197 (420)
+|-||.+-|--.-....|..-.=.-.-+|-||+..--....++.+|..+.++| +-|...-.|...+.-..++.+++ -
T Consensus 146 ~gaLddALs~iLin~k~hd~e~wkwrfeD~fGVD~~t~l~v~l~lL~IV~iVA--teLwt~V~W~~Ql~R~fvisFLi-S 222 (549)
T PF05934_consen 146 PGALDDALSDILINFKPHDYEAWKWRFEDTFGVDPYTVLMVLLCLLCIVAIVA--TELWTYVSWFTQLRRMFVISFLI-S 222 (549)
T ss_pred cchHHHHHHHHhhcCCcchhHHhhhhhccccCCchhHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH-H
Confidence 56666655522222222332222235677888764333322333444444443 33433444554444443333333 6
Q ss_pred hhhhhhhc
Q 014676 198 MIWNCVWG 205 (420)
Q Consensus 198 ~iwN~~~~ 205 (420)
|+||.++=
T Consensus 223 ~~WNWiyL 230 (549)
T PF05934_consen 223 FGWNWIYL 230 (549)
T ss_pred HHHHHHHH
Confidence 78877654
No 93
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=22.02 E-value=82 Score=31.86 Aligned_cols=46 Identities=15% Similarity=0.309 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhc
Q 014676 159 VVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWG 205 (420)
Q Consensus 159 ~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~ 205 (420)
++.+++++|+.+|.+-.+--++.+..+-+ ++|.+.+.+++-.+||.
T Consensus 206 llfliiaigltvGT~~~A~~~~giY~~wv-~~~l~a~~~~~rs~yy~ 251 (256)
T PF09788_consen 206 LLFLIIAIGLTVGTWTYAKTYGGIYVSWV-GLFLIALICLIRSIYYC 251 (256)
T ss_pred HHHHHHHHHHhhhhHHHHhhcCcEeHHHH-HHHHHHHHHHHHhheeE
Confidence 34444556666666655444444333333 33333333555566665
No 94
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=21.84 E-value=79 Score=25.35 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=16.7
Q ss_pred cccccCcCCcEEEEEEEEEe
Q 014676 219 TELRGAIDGQYVKVTGVVTC 238 (420)
Q Consensus 219 ~~lr~a~dGq~VKItG~Vtc 238 (420)
.....++.|+||||.|.+..
T Consensus 43 ~~~~~~~~g~~v~v~G~v~~ 62 (95)
T cd04478 43 SEVEPIEEGTYVRVFGNLKS 62 (95)
T ss_pred ccccccccCCEEEEEEEEcc
Confidence 35778999999999998764
No 95
>PF05454 DAG1: Dystroglycan (Dystrophin-associated glycoprotein 1); InterPro: IPR008465 Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5.5 kb transcript in Homo sapiens. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in Mus musculus brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear [].; PDB: 1EG4_P.
Probab=21.81 E-value=30 Score=35.13 Aligned_cols=11 Identities=18% Similarity=0.302 Sum_probs=0.0
Q ss_pred HHhhhhhhhhc
Q 014676 195 FIGMIWNCVWG 205 (420)
Q Consensus 195 ~a~~iwN~~~~ 205 (420)
+|++|+-+|++
T Consensus 161 IA~iIa~icyr 171 (290)
T PF05454_consen 161 IAGIIACICYR 171 (290)
T ss_dssp -----------
T ss_pred HHHHHHHHhhh
Confidence 34455544444
No 96
>PF11432 DUF3197: Protein of unknown function (DUF3197); InterPro: IPR024443 This domain, whose function is unknown, is found in bacterial proteins.; PDB: 1WN9_A 1WNA_A.
Probab=21.79 E-value=95 Score=28.04 Aligned_cols=58 Identities=22% Similarity=0.517 Sum_probs=33.4
Q ss_pred eEEEecCC-----ceeEEEEecCCCeeeeeeeeceEEeecCCC----CCCCHHHHHHHhhcCCCCccceeEEecceeeeC
Q 014676 292 FYISDFQS-----GLRALVKAGYGAKVAPFVKPATVVNITKGN----RDLSPSFLRWLADRNLSSDDRIMRLKEGYIKEG 362 (420)
Q Consensus 292 FYIsD~~s-----G~RAlVKaG~G~kVtp~V~e~~vv~~~~~~----~dlS~~f~~WL~erNLSsd~r~mRlkEGyIkEG 362 (420)
.+|||.|. +..++|..|. ++.+.+|. .|+-. ..+=.||.+||.+++. +.+|-.+-.|
T Consensus 19 ~liTDwQd~R~~ARYa~ll~~gk----~~llt~dA---FGPafG~~G~~ALaELv~wl~~~G~-------~f~EaVl~p~ 84 (113)
T PF11432_consen 19 YLITDWQDQRPQARYALLLRGGK----EPLLTPDA---FGPAFGPEGERALAELVRWLQERGA-------RFYEAVLSPS 84 (113)
T ss_dssp EEEEE--SSCCC--EEEEEE-SS-----EEEEEEE---ESTTS-TTHHHHHHHHHHHHHHTT--------EEEEEEE-GG
T ss_pred EEEeccccchhhhhhhhheecCC----cccccccc---cCcccCccHHHHHHHHHHHHHHcCC-------chhheecCHH
Confidence 68999886 3456665554 45666655 23322 2345689999999984 6678766655
Q ss_pred C
Q 014676 363 S 363 (420)
Q Consensus 363 s 363 (420)
+
T Consensus 85 e 85 (113)
T PF11432_consen 85 E 85 (113)
T ss_dssp G
T ss_pred H
Confidence 4
No 97
>PRK01844 hypothetical protein; Provisional
Probab=21.32 E-value=65 Score=27.01 Aligned_cols=16 Identities=19% Similarity=0.598 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHhhh
Q 014676 157 AWVVMVVVAMGVMVGA 172 (420)
Q Consensus 157 lw~vi~l~~~g~~~G~ 172 (420)
+|..+++.+.+|++|+
T Consensus 3 ~~~~I~l~I~~li~G~ 18 (72)
T PRK01844 3 IWLGILVGVVALVAGV 18 (72)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4666666666666664
No 98
>PF14023 DUF4239: Protein of unknown function (DUF4239)
Probab=21.22 E-value=1.9e+02 Score=26.68 Aligned_cols=10 Identities=20% Similarity=0.956 Sum_probs=6.0
Q ss_pred echhhHHHHHH
Q 014676 152 VSRAVAWVVMV 162 (420)
Q Consensus 152 vpk~vlw~vi~ 162 (420)
+|... |.+++
T Consensus 135 lp~~~-w~vl~ 144 (209)
T PF14023_consen 135 LPPPL-WIVLL 144 (209)
T ss_pred CChhH-HHHHH
Confidence 88766 55433
No 99
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=21.03 E-value=1.1e+02 Score=35.40 Aligned_cols=67 Identities=12% Similarity=0.058 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHH---hhhhhhhhc-hhhhhhccccC---CCcccccCcCCc
Q 014676 159 VVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFI---GMIWNCVWG-RRGLLGFVKKY---PDTELRGAIDGQ 228 (420)
Q Consensus 159 ~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a---~~iwN~~~~-~~~i~rfl~k~---Pd~~lr~a~dGq 228 (420)
+|+.+|..-..+|.|-+.-.--+++++++ |++++. ..+|++.|= +.++++=|.+- +..-|....|-+
T Consensus 26 ~v~~lfla~~~~Gl~~~lp~~~~~~~l~~---~~~~~~~~l~~~~rfr~P~~~ea~~Rle~~s~l~hrP~~al~D~~ 99 (851)
T TIGR02302 26 SLVGLFLSLGWAGLFLALPFWLHIAGLVL---FAALALVALIPAIRFRWPSRDEALARLERNNGLKHRPATVQGDAL 99 (851)
T ss_pred HHHHHHHHHHHHhHHHhhHHHHHHHHHHH---HHHHHHHHHhhhhhcCCCCHHHHHHHHHHhCCCCCCCchhhcccc
Confidence 34444444455666655522112222222 333332 233454444 66666655432 244444444443
No 100
>PF06993 DUF1304: Protein of unknown function (DUF1304); InterPro: IPR009732 This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=20.73 E-value=2e+02 Score=25.25 Aligned_cols=41 Identities=15% Similarity=0.028 Sum_probs=26.9
Q ss_pred HHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhh
Q 014676 162 VVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCV 203 (420)
Q Consensus 162 ~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~ 203 (420)
..+++|++.|.++.-. .-..-+++..+.+.+++|+..+-+.
T Consensus 52 gfLavgll~gl~~~~~-~~~~~~~~~~l~~~~~aa~yg~~T~ 92 (113)
T PF06993_consen 52 GFLAVGLLWGLFILNS-VAGLTLVLFFLGCMIVAAIYGALTS 92 (113)
T ss_pred HHHHHHHHHHHHhccc-hHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5678889999888877 2233444555566666666666444
No 101
>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit.
Probab=20.68 E-value=52 Score=29.95 Aligned_cols=22 Identities=32% Similarity=0.439 Sum_probs=15.4
Q ss_pred hHHHHHHHHHHHHHhhheeeee
Q 014676 156 VAWVVMVVVAMGVMVGAFLMVA 177 (420)
Q Consensus 156 vlw~vi~l~~~g~~~G~f~l~a 177 (420)
++++++++.++|+++|.++..|
T Consensus 2 ~~~~~~~~~~~g~~~~~~l~~~ 23 (165)
T TIGR01944 2 IIAAVAALSALGLALGAILGYA 23 (165)
T ss_pred hHHHHHHHHHHHHHHHHHHHHh
Confidence 4677788888887777665444
No 102
>COG4965 TadB Flp pilus assembly protein TadB [Intracellular trafficking and secretion]
Probab=20.65 E-value=1.1e+02 Score=31.62 Aligned_cols=14 Identities=29% Similarity=0.515 Sum_probs=11.9
Q ss_pred hhhhhhccccCCCc
Q 014676 206 RRGLLGFVKKYPDT 219 (420)
Q Consensus 206 ~~~i~rfl~k~Pd~ 219 (420)
+|...||...+|++
T Consensus 128 ~rr~krf~~qlP~a 141 (309)
T COG4965 128 ARRLKRFGQQLPEA 141 (309)
T ss_pred HHHHHHHHHHhhHH
Confidence 67788999999986
No 103
>PF10969 DUF2771: Protein of unknown function (DUF2771); InterPro: IPR024495 This bacterial family of proteins has no known function.
Probab=20.42 E-value=84 Score=29.16 Aligned_cols=49 Identities=22% Similarity=0.325 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhhchhhhhhccccCCCcccccCcCCcEEEEEEEEEe
Q 014676 182 VVLVAVAAVVGPLFIGMIWNCVWGRRGLLGFVKKYPDTELRGAIDGQYVKVTGVVTC 238 (420)
Q Consensus 182 ~ll~~~~~~f~~v~a~~iwN~~~~~~~i~rfl~k~Pd~~lr~a~dGq~VKItG~Vtc 238 (420)
+|++++++++++++++..|+...+. -.+.| ++.-.-+|+++.|.=.--|
T Consensus 6 ~i~avvvV~~~a~~g~~~~~~~~~~------~p~~p--~It~~s~g~~~~V~P~~~C 54 (161)
T PF10969_consen 6 LIAAVVVVVAAAVVGVGWWQLRRGS------DPQDP--EITAYSDGELVEVGPYQYC 54 (161)
T ss_pred hhHHHHHHHHHHHHHHHHHHhCCCC------CCCCc--EEEEEECCcEEEECCeeee
Confidence 3445556666666666667642221 12233 4444569999998766666
No 104
>PF07291 MauE: Methylamine utilisation protein MauE; InterPro: IPR009908 This entry consists of several bacterial methylamine utilisation MauE proteins. Synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (MADH) is encoded by genes present in the mau cluster. MauE and MauD are specifically involved in the processing, transport, and/or maturation of the beta-subunit and that the absence of each of these proteins leads to production of a non-functional beta-subunit which becomes rapidly degraded [].; GO: 0030416 methylamine metabolic process, 0016021 integral to membrane
Probab=20.35 E-value=1.8e+02 Score=27.41 Aligned_cols=57 Identities=14% Similarity=0.162 Sum_probs=27.5
Q ss_pred echhhHHHHHHHH-HHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhhhhchhh
Q 014676 152 VSRAVAWVVMVVV-AMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNCVWGRRG 208 (420)
Q Consensus 152 vpk~vlw~vi~l~-~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~~~~~~~ 208 (420)
+|......++.++ ..=+++|..++.-.-+..-.+++.++++.-.+.+.+|..++++.
T Consensus 45 lP~~~~~~~A~~lP~~El~~gl~Ll~~~~~~~a~~~a~~Ll~~F~~ai~~~~~rg~~~ 102 (184)
T PF07291_consen 45 LPDWLVRPVAWALPWLELALGLLLLFPPTRRWAALLAAALLLVFTAAIAINLLRGRTD 102 (184)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 5765443333333 33355555554444333333444444444444566787666543
No 105
>PF01925 TauE: Sulfite exporter TauE/SafE; InterPro: IPR002781 This family is found in integral membrane proteins of prokaryotes which are uncharacterised.; GO: 0016021 integral to membrane
Probab=20.24 E-value=1.7e+02 Score=26.76 Aligned_cols=44 Identities=14% Similarity=0.314 Sum_probs=31.0
Q ss_pred echhhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHH
Q 014676 152 VSRAVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLF 195 (420)
Q Consensus 152 vpk~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~ 195 (420)
+....++.+++..++|..+|++++..+-..++..+++++..+.+
T Consensus 61 i~~~~~~~~~~~~~~g~~iG~~l~~~l~~~~l~~~~~~~ll~~~ 104 (240)
T PF01925_consen 61 IDWKIVLPLIIGALIGVVIGAWLLSLLPDDILKLIFGLFLLLLA 104 (240)
T ss_pred cchhhhhhhhhHhHHHHHHHHhhhcchhHHHHHHHHHHHHHHHH
Confidence 44456677788888999999999998877765555555443333
No 106
>PF12576 DUF3754: Protein of unknown function (DUF3754); InterPro: IPR022227 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=20.21 E-value=2e+02 Score=25.89 Aligned_cols=18 Identities=11% Similarity=0.136 Sum_probs=10.0
Q ss_pred Hhhhhhhhhc-hhhhhhcc
Q 014676 196 IGMIWNCVWG-RRGLLGFV 213 (420)
Q Consensus 196 a~~iwN~~~~-~~~i~rfl 213 (420)
+.+++..|.+ ++.-.||.
T Consensus 106 ~~~~~r~~~~~~~~~~ry~ 124 (141)
T PF12576_consen 106 GGYAFRQYTGYKNNRARYQ 124 (141)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3556666666 55544443
No 107
>COG3601 Predicted membrane protein [Function unknown]
Probab=20.18 E-value=96 Score=30.12 Aligned_cols=55 Identities=13% Similarity=0.201 Sum_probs=34.2
Q ss_pred hHHHHHHHHHHHHHhhheeeeeehhHHHHHH---------------HHHHHHHHHHhhhhhhhhc-hhhhhhc
Q 014676 156 VAWVVMVVVAMGVMVGAFLMVAVKKAVVLVA---------------VAAVVGPLFIGMIWNCVWG-RRGLLGF 212 (420)
Q Consensus 156 vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~---------------~~~~f~~v~a~~iwN~~~~-~~~i~rf 212 (420)
.+=+++..|.||+.||-|++ +++|...++. ++..|..++ .++|+.-++ ++.+..+
T Consensus 40 ~iP~Lig~~~lGp~ag~~vl-lvk~iL~~l~~g~~~~~iG~~mNfiag~~fv~~~-~~~~k~~ks~~~~i~~~ 110 (186)
T COG3601 40 DIPALIGYFLLGPGAGIFVL-LVKNILLYLLSGPVGDPIGPPMNFIAGGSFVLIA-ALIYKKKKSTKNLIVGL 110 (186)
T ss_pred HhHHHHHHHHhccchHHHHH-HHHHHHHHHHcCCCCCCccHHHHHHHHHHHHHHH-HHHHHHHhHHHHHHHHH
Confidence 44577889999999998876 4666655543 344444443 566766555 4444443
No 108
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=20.16 E-value=85 Score=23.83 Aligned_cols=19 Identities=32% Similarity=0.482 Sum_probs=17.3
Q ss_pred eeEEecceeeeCCEEEEEE
Q 014676 351 IMRLKEGYIKEGSTVSVMG 369 (420)
Q Consensus 351 ~mRlkEGyIkEGstvSVmG 369 (420)
..|+..|-|+.||+|.+++
T Consensus 5 ~grV~sG~l~~gd~v~~~~ 23 (74)
T PF03144_consen 5 TGRVYSGTLKKGDKVRVLP 23 (74)
T ss_dssp EEEEEESEEETTEEEEEES
T ss_pred EEEEEEeEEcCCCEEEECc
Confidence 3689999999999999988
No 109
>PF05879 RHD3: Root hair defective 3 GTP-binding protein (RHD3); InterPro: IPR008803 This family consists of several eukaryotic root hair defective 3 like GTP-binding proteins. It has been speculated that the RHD3 protein is a member of a novel class of GTP-binding proteins that is widespread in eukaryotes and required for regulated cell enlargement []. The family also contains the homologous Saccharomyces cerevisiae synthetic construct enhancement of YOP1 (SEY1) protein which is involved in membrane trafficking [].; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=20.10 E-value=94 Score=35.10 Aligned_cols=45 Identities=11% Similarity=0.369 Sum_probs=30.1
Q ss_pred echhhHHHHHHHHHHHHHhhheeeeeehhHHHHHHHHHHHHHHHHhhhhhh
Q 014676 152 VSRAVAWVVMVVVAMGVMVGAFLMVAVKKAVVLVAVAAVVGPLFIGMIWNC 202 (420)
Q Consensus 152 vpk~vlw~vi~l~~~g~~~G~f~l~av~~~~ll~~~~~~f~~v~a~~iwN~ 202 (420)
+| +|+.+++++.|+= =+++.++|+++|++++++++++.+++--|.
T Consensus 649 iP---~w~~~ll~vLGwN---E~m~vLrnPl~~~l~li~~~~~~~~~~l~l 693 (742)
T PF05879_consen 649 IP---PWMYLLLLVLGWN---EFMAVLRNPLYFTLLLILGGGFYVLYQLNL 693 (742)
T ss_pred CC---HHHHHHHHHHhHH---HHHHHHHChHHHHHHHHHHHHHHHHHHhcc
Confidence 77 4777777777742 235577899999998887766555443344
Done!