Query 011630
Match_columns 481
No_of_seqs 75 out of 77
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:29:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011630.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011630hhsearch_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 99.1 4.9E-10 1.1E-14 101.4 10.9 103 338-447 16-121 (160)
2 PF13829 DUF4191: Domain of un 93.1 0.052 1.1E-06 53.8 2.0 81 211-293 22-105 (224)
3 PF13567 DUF4131: Domain of un 88.6 15 0.00032 31.5 13.7 21 389-409 147-167 (176)
4 PF12273 RCR: Chitin synthesis 77.8 1.9 4.2E-05 38.5 2.7 21 241-261 1-21 (130)
5 cd06094 RP_Saci_like RP_Saci_l 77.3 2.2 4.7E-05 37.2 2.8 24 353-376 1-24 (89)
6 PF11151 DUF2929: Protein of u 76.9 4.7 0.0001 32.2 4.4 43 216-259 6-48 (57)
7 PRK13254 cytochrome c-type bio 76.0 11 0.00024 35.4 7.2 15 286-300 49-63 (148)
8 COG1200 RecG RecG-like helicas 62.1 20 0.00043 41.1 6.8 48 415-462 104-152 (677)
9 PF03100 CcmE: CcmE; InterPro 53.6 16 0.00035 33.0 3.7 16 286-301 48-63 (131)
10 PF04246 RseC_MucC: Positive r 53.0 14 0.0003 33.0 3.1 41 224-264 77-117 (135)
11 PF13779 DUF4175: Domain of un 52.4 11 0.00024 43.8 3.0 60 218-277 10-71 (820)
12 TIGR02762 TraL_TIGR type IV co 52.0 25 0.00055 30.4 4.4 22 213-234 18-39 (95)
13 PRK14762 membrane protein; Pro 51.9 14 0.0003 26.0 2.2 16 215-230 2-17 (27)
14 PF08114 PMP1_2: ATPase proteo 51.4 12 0.00027 28.9 2.1 26 248-273 17-43 (43)
15 PF06679 DUF1180: Protein of u 50.7 15 0.00032 35.2 3.0 31 246-277 99-129 (163)
16 KOG1571 Predicted E3 ubiquitin 50.4 55 0.0012 35.1 7.4 145 291-446 60-211 (355)
17 PF11292 DUF3093: Protein of u 47.6 31 0.00068 32.4 4.6 52 207-261 3-54 (143)
18 PF10907 DUF2749: Protein of u 46.8 8.3 0.00018 32.2 0.6 47 243-291 4-62 (66)
19 PF11833 DUF3353: Protein of u 44.7 20 0.00043 34.9 3.0 32 210-242 136-167 (194)
20 PF10003 DUF2244: Integral mem 43.8 27 0.00059 31.8 3.5 48 214-263 9-57 (140)
21 PRK00523 hypothetical protein; 42.5 25 0.00053 29.9 2.8 35 242-281 7-41 (72)
22 PTZ00382 Variant-specific surf 42.5 11 0.00024 32.8 0.7 17 252-268 79-95 (96)
23 PRK01844 hypothetical protein; 42.3 25 0.00054 29.9 2.8 33 243-280 7-39 (72)
24 PF11023 DUF2614: Protein of u 41.2 44 0.00096 30.6 4.4 49 213-261 8-57 (114)
25 PF05915 DUF872: Eukaryotic pr 40.7 28 0.0006 31.5 3.0 54 215-268 41-105 (115)
26 PF11712 Vma12: Endoplasmic re 40.7 45 0.00097 30.4 4.4 51 217-267 85-137 (142)
27 PF06645 SPC12: Microsomal sig 40.3 22 0.00047 29.9 2.1 60 216-278 12-71 (76)
28 PRK10862 SoxR reducing system 39.4 26 0.00057 32.7 2.8 23 242-264 102-124 (154)
29 PRK13165 cytochrome c-type bio 39.4 52 0.0011 31.6 4.8 17 285-301 54-70 (160)
30 PF04156 IncA: IncA protein; 37.8 35 0.00076 31.7 3.3 33 232-264 29-61 (191)
31 PF11241 DUF3043: Protein of u 37.4 43 0.00093 32.4 3.9 40 247-286 104-143 (170)
32 PRK13823 conjugal transfer pro 37.1 25 0.00054 30.9 2.1 37 224-261 26-62 (94)
33 PRK13150 cytochrome c-type bio 34.9 66 0.0014 30.9 4.7 17 285-301 54-70 (159)
34 PRK10881 putative hydrogenase 34.2 34 0.00074 36.0 3.0 37 194-239 39-77 (394)
35 PF15050 SCIMP: SCIMP protein 33.6 45 0.00097 31.2 3.2 23 242-264 9-31 (133)
36 PF11808 DUF3329: Domain of un 33.5 1.1E+02 0.0024 26.1 5.4 18 218-235 9-26 (90)
37 cd04488 RecG_wedge_OBF RecG_we 33.4 74 0.0016 23.9 4.0 27 419-445 45-71 (75)
38 PF05425 CopD: Copper resistan 32.2 43 0.00093 28.6 2.8 58 213-270 7-69 (105)
39 COG5015 Uncharacterized conser 31.4 33 0.00072 32.0 2.0 35 267-301 46-81 (132)
40 KOG1016 Predicted DNA helicase 31.0 25 0.00053 41.7 1.4 16 7-22 1199-1214(1387)
41 PF01102 Glycophorin_A: Glycop 30.3 49 0.0011 30.4 2.9 14 275-288 92-105 (122)
42 COG2332 CcmE Cytochrome c-type 29.9 92 0.002 29.9 4.7 54 241-300 8-63 (153)
43 PF06374 NDUF_C2: NADH-ubiquin 29.6 56 0.0012 30.0 3.1 57 222-279 29-96 (117)
44 PF02439 Adeno_E3_CR2: Adenovi 29.5 78 0.0017 24.1 3.3 26 243-268 8-33 (38)
45 PRK08456 flagellar motor prote 29.5 37 0.00081 34.1 2.2 43 232-274 24-67 (257)
46 PF01925 TauE: Sulfite exporte 29.5 56 0.0012 30.7 3.3 42 212-253 60-101 (240)
47 TIGR00540 hemY_coli hemY prote 29.2 1.4E+02 0.003 31.0 6.4 10 233-242 26-35 (409)
48 COG3346 Uncharacterized conser 29.2 3.3E+02 0.0072 28.0 8.8 58 240-297 12-83 (252)
49 KOG0162 Myosin class I heavy c 29.0 3.4E+02 0.0073 32.5 9.6 22 38-59 901-922 (1106)
50 PF04790 Sarcoglycan_1: Sarcog 28.1 6.7E+02 0.015 25.7 14.1 88 346-443 113-220 (264)
51 PRK12869 ubiA protoheme IX far 28.0 1.3E+02 0.0027 30.3 5.6 43 243-289 37-79 (279)
52 TIGR03750 conj_TIGR03750 conju 27.7 54 0.0012 29.7 2.7 46 218-264 24-69 (111)
53 PRK09109 motC flagellar motor 27.7 43 0.00094 33.5 2.3 54 223-276 9-69 (246)
54 PF05961 Chordopox_A13L: Chord 27.4 78 0.0017 26.8 3.3 24 246-269 5-28 (68)
55 PF11846 DUF3366: Domain of un 27.2 92 0.002 28.9 4.2 56 219-274 21-83 (193)
56 PF01957 NfeD: NfeD-like C-ter 26.5 64 0.0014 27.9 2.9 11 284-294 87-97 (144)
57 PF14362 DUF4407: Domain of un 26.2 44 0.00096 33.5 2.1 24 237-263 39-62 (301)
58 PF05090 VKG_Carbox: Vitamin K 26.2 73 0.0016 34.6 3.9 34 333-367 332-366 (446)
59 PF00924 MS_channel: Mechanose 25.8 25 0.00055 32.4 0.3 14 283-296 59-72 (206)
60 PF06703 SPC25: Microsomal sig 25.7 3E+02 0.0065 25.4 7.3 48 241-294 56-103 (162)
61 PRK13159 cytochrome c-type bio 25.6 96 0.0021 29.7 4.1 17 285-301 48-64 (155)
62 TIGR01116 ATPase-IIA1_Ca sarco 25.2 93 0.002 36.5 4.7 59 213-271 5-65 (917)
63 PF00558 Vpu: Vpu protein; In 25.1 72 0.0016 27.7 2.9 24 240-263 2-25 (81)
64 PF01988 VIT1: VIT family; In 24.7 73 0.0016 30.7 3.2 16 219-234 132-147 (213)
65 PF11432 DUF3197: Protein of u 24.2 1.2E+02 0.0027 27.7 4.3 61 351-426 17-87 (113)
66 cd04486 YhcR_OBF_like YhcR_OBF 24.1 1.1E+02 0.0024 25.4 3.8 27 419-445 44-70 (78)
67 COG3763 Uncharacterized protei 24.0 61 0.0013 27.6 2.2 18 263-280 22-39 (71)
68 PF12273 RCR: Chitin synthesis 23.9 46 0.00099 29.8 1.6 6 262-267 19-24 (130)
69 KOG4050 Glutamate transporter 23.8 1E+02 0.0022 30.2 3.9 55 222-282 59-113 (188)
70 PRK10747 putative protoheme IX 23.7 1.5E+02 0.0032 30.8 5.4 10 233-242 26-35 (398)
71 COG0811 TolQ Biopolymer transp 23.6 68 0.0015 31.3 2.8 24 244-267 167-190 (216)
72 PF09788 Tmemb_55A: Transmembr 23.5 53 0.0011 33.8 2.1 70 194-266 182-251 (256)
73 PHA03049 IMV membrane protein; 23.3 89 0.0019 26.4 3.0 24 247-270 6-29 (68)
74 PRK09110 flagellar motor prote 23.3 68 0.0015 33.0 2.8 40 235-274 25-65 (283)
75 COG1463 Ttg2C ABC-type transpo 23.2 1E+02 0.0023 32.0 4.2 19 279-297 47-65 (359)
76 PRK01844 hypothetical protein; 22.9 45 0.00098 28.4 1.2 16 218-233 3-18 (72)
77 TIGR03818 MotA1 flagellar moto 22.7 71 0.0015 32.8 2.8 43 223-265 7-55 (282)
78 PF10112 Halogen_Hydrol: 5-bro 22.5 64 0.0014 30.6 2.3 32 213-244 4-35 (199)
79 PF03419 Peptidase_U4: Sporula 21.9 2.1E+02 0.0046 28.9 5.9 43 281-324 159-201 (293)
80 PRK06743 flagellar motor prote 21.8 64 0.0014 32.7 2.3 28 239-266 28-55 (254)
81 PRK03598 putative efflux pump 21.5 42 0.00092 33.7 1.0 17 240-256 4-20 (331)
82 PF04971 Lysis_S: Lysis protei 21.3 76 0.0016 26.8 2.2 31 242-273 33-63 (68)
83 PRK08124 flagellar motor prote 21.2 80 0.0017 31.9 2.8 31 235-265 27-57 (263)
84 PF04304 DUF454: Protein of un 21.1 1.3E+02 0.0028 24.1 3.4 45 207-253 18-62 (71)
85 PF03916 NrfD: Polysulphide re 20.8 82 0.0018 31.6 2.8 33 198-239 2-34 (313)
86 PRK07118 ferredoxin; Validated 20.8 39 0.00085 34.4 0.5 26 216-241 3-28 (280)
87 PF06609 TRI12: Fungal trichot 20.5 95 0.0021 35.2 3.5 58 219-276 241-308 (599)
88 PRK10917 ATP-dependent DNA hel 20.3 4.1E+02 0.0089 30.2 8.4 29 417-445 105-133 (681)
89 COG5336 Uncharacterized protei 20.3 51 0.0011 30.3 1.1 16 219-234 75-90 (116)
90 PRK12482 flagellar motor prote 20.1 79 0.0017 32.7 2.6 44 222-265 6-55 (287)
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=99.12 E-value=4.9e-10 Score=101.39 Aligned_cols=103 Identities=23% Similarity=0.402 Sum_probs=71.4
Q ss_pred ceeeeeeeeeeeeeeEEEEeCCCceeEEE-ecCCCceeeeeeecceEEc-CCCCCCCCCHHHHHhhhhcCCCCCCceeEE
Q 011630 338 HFTWGLRSLERHVVDFYISDFQSGLRALV-KTGSGARVTPFVDDSVVID-IKPENKDLSPEFIRWLGQKSLSSDDRLMRL 415 (481)
Q Consensus 338 r~~W~l~~~Er~~~dFyIsD~~sG~RALV-kaG~GarVtP~Iees~VvD-~~~~~kd~S~el~~wL~~rnLSsd~r~mRy 415 (481)
...|++++.++..++|||.|.+ | +.+| ....++.+.- .++.| +.+........+..|+...- ..+.+.+||
T Consensus 16 ~~~~~~v~~~~~~vPF~L~D~t-g-~v~V~~~p~~a~l~l----~~v~~~f~p~~~~~~~~~~~~~~~~~-~~~~~G~r~ 88 (160)
T PF12483_consen 16 SSSWRTVSSGTSEVPFYLEDGT-G-RVRVVDDPEGAELDL----ETVYDRFEPSPSSPPDGLFGFFSGER-ELEPKGYRY 88 (160)
T ss_pred cccEEEEEcceeEcCEEEECCc-e-EEEEecCcccCccce----eeEEEEeEECCCCccceeeeeeccce-eccccccEE
Confidence 4569999999999999999975 4 6666 4455665533 34444 22222223333333333222 112677999
Q ss_pred EeeeecCCCEEEEEEEE-EecCceeeEeCCCCc
Q 011630 416 KEGYIKEGSTVSVMGIV-QRNDNVLMIVPPPEP 447 (481)
Q Consensus 416 kEgiI~eGs~VsViGvv-~r~~~vlmI~pP~E~ 447 (481)
+|++|++|++|+|+|.+ .++++.++|.+|.+.
T Consensus 89 ~E~~L~~G~~ltvvGe~~~~~~g~~~i~~p~~g 121 (160)
T PF12483_consen 89 TEEILPVGTPLTVVGELVRDGDGNLVIQPPKDG 121 (160)
T ss_pred EEEEcCCCCEEEEEEEEEEcCCCcEEEeCCCCC
Confidence 99999999999999999 667789999999886
No 2
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=93.08 E-value=0.052 Score=53.82 Aligned_cols=81 Identities=20% Similarity=0.221 Sum_probs=59.7
Q ss_pred cCCcchhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCC---ccccCCC
Q 011630 211 KNFPKPVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDT---DLRTAKS 287 (481)
Q Consensus 211 ~~~p~~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds---~Lrs~~d 287 (481)
+..|+.. |.+++.|+..++++..|-..+++|+++++++.++++++|.+++... ..++..+.+..-|-+ -|++++-
T Consensus 22 k~dp~l~-~~ml~a~l~~~~v~v~ig~l~~~~~~~~i~gi~~g~l~am~vl~rr-a~ra~Y~qieGqpGAa~avL~~lr~ 99 (224)
T PF13829_consen 22 KEDPKLP-WLMLGAFLGPIAVFVLIGLLFGSWWYWLIIGILLGLLAAMIVLSRR-AQRAAYAQIEGQPGAAGAVLDNLRR 99 (224)
T ss_pred HHCcchH-HHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhcCCCchHHHHHHhhcC
Confidence 3445544 8777778777777777777778999999999999999988888443 455667777777765 5667777
Q ss_pred CCEEEE
Q 011630 288 GQFVKV 293 (481)
Q Consensus 288 Gq~VKI 293 (481)
|..++=
T Consensus 100 ~W~~~~ 105 (224)
T PF13829_consen 100 GWRVTE 105 (224)
T ss_pred CcccCC
Confidence 776653
No 3
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=88.59 E-value=15 Score=31.48 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=15.6
Q ss_pred CCCCCCHHHHHhhhhcCCCCC
Q 011630 389 ENKDLSPEFIRWLGQKSLSSD 409 (481)
Q Consensus 389 ~~kd~S~el~~wL~~rnLSsd 409 (481)
..+.-..+.++|+..+|+...
T Consensus 147 ~~Npg~FD~~~yl~~~gI~~~ 167 (176)
T PF13567_consen 147 PTNPGGFDYQRYLRSKGIYAQ 167 (176)
T ss_pred CCCCCCcCHHHHHHHCCCEEE
Confidence 335667778999999996544
No 4
>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=77.75 E-value=1.9 Score=38.48 Aligned_cols=21 Identities=14% Similarity=0.350 Sum_probs=13.8
Q ss_pred chhHHHHHHHHHHHHHHHHhh
Q 011630 241 NPILLIVVLVLFAVIAAIFIW 261 (481)
Q Consensus 241 ~~~ll~~~~~lfa~vaa~~iW 261 (481)
+|+|+++++++|.+++.+++|
T Consensus 1 RW~l~~iii~~i~l~~~~~~~ 21 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLFYC 21 (130)
T ss_pred CeeeHHHHHHHHHHHHHHHHH
Confidence 477777766666666655555
No 5
>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=77.35 E-value=2.2 Score=37.21 Aligned_cols=24 Identities=46% Similarity=0.661 Sum_probs=21.4
Q ss_pred EEEEeCCCceeEEEecCCCceeee
Q 011630 353 FYISDFQSGLRALVKTGSGARVTP 376 (481)
Q Consensus 353 FyIsD~~sG~RALVkaG~GarVtP 376 (481)
|||.|.++|+++||++|..--|.|
T Consensus 1 l~v~D~~s~~~fLVDTGA~vSviP 24 (89)
T cd06094 1 LHVRDRTSGLRFLVDTGAAVSVLP 24 (89)
T ss_pred CeeEECCCCcEEEEeCCCceEeec
Confidence 799999999999999999866655
No 6
>PF11151 DUF2929: Protein of unknown function (DUF2929); InterPro: IPR021324 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=76.94 E-value=4.7 Score=32.21 Aligned_cols=43 Identities=26% Similarity=0.403 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHH
Q 011630 216 PVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIF 259 (481)
Q Consensus 216 ~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~ 259 (481)
.+.|++++..++|++++++-=+.. |...-.++.++|+++++++
T Consensus 6 t~fWs~il~~vvgyI~ssL~~~~~-n~~~~~Ii~vi~~i~~~~~ 48 (57)
T PF11151_consen 6 TFFWSFILGEVVGYIGSSLTGVTY-NFTTAAIIAVIFGIIVANI 48 (57)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHHHHHH
Confidence 568999999999999998876643 4444444444444444333
No 7
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=75.98 E-value=11 Score=35.36 Aligned_cols=15 Identities=27% Similarity=0.543 Sum_probs=12.9
Q ss_pred CCCCEEEEEEEEEeC
Q 011630 286 KSGQFVKVTGVVTCG 300 (481)
Q Consensus 286 ~dGq~VKItGvVtCG 300 (481)
..|+.|+|.|.|.-|
T Consensus 49 ~~g~~vrvgG~V~~g 63 (148)
T PRK13254 49 PAGRRFRLGGLVEKG 63 (148)
T ss_pred cCCCeEEEeEEEecC
Confidence 569999999999874
No 8
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=62.10 E-value=20 Score=41.09 Aligned_cols=48 Identities=23% Similarity=0.220 Sum_probs=36.8
Q ss_pred EEeeeecCCCEEEEEEEEEecCceeeEeCCCCcccccce-eeeeecccc
Q 011630 415 LKEGYIKEGSTVSVMGIVQRNDNVLMIVPPPEPIATGWQ-WTKCIFPAS 462 (481)
Q Consensus 415 ykEgiI~eGs~VsViGvv~r~~~vlmI~pP~E~~stgcq-w~r~~lP~~ 462 (481)
|-+..+++|++|.|.|.+++..+.+-|.-|.=.+...+. ..+.+.|+|
T Consensus 104 ~l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~~~~~~~~~~~i~PvY 152 (677)
T COG1200 104 YLKKKLKVGERVIVYGKVKRFKGGLQITHPEYIVNDDGSELEERLTPVY 152 (677)
T ss_pred HHHhhCCCCCEEEEEEEEeeccCceEEEcceEEecCCCcccccceeeee
Confidence 446678899999999999998888888887666655444 567777775
No 9
>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=53.58 E-value=16 Score=32.97 Aligned_cols=16 Identities=44% Similarity=0.661 Sum_probs=13.2
Q ss_pred CCCCEEEEEEEEEeCC
Q 011630 286 KSGQFVKVTGVVTCGN 301 (481)
Q Consensus 286 ~dGq~VKItGvVtCG~ 301 (481)
..|+.|+|.|.|.-|+
T Consensus 48 ~~~~~vrv~G~V~~gS 63 (131)
T PF03100_consen 48 KVGRKVRVGGLVVEGS 63 (131)
T ss_dssp -TTSEEEEEEEEECTT
T ss_pred cCCceEEEeeEEccCC
Confidence 5899999999998754
No 10
>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=52.96 E-value=14 Score=33.02 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=28.4
Q ss_pred HHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhh
Q 011630 224 IFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTC 264 (481)
Q Consensus 224 ~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~ 264 (481)
+=.++|++|+++..++-...++.+++++.++++++++..++
T Consensus 77 lPll~li~g~~l~~~~~~~e~~~~l~~l~~l~~~~~~~~~~ 117 (135)
T PF04246_consen 77 LPLLALIAGAVLGSYLGGSELWAILGGLLGLALGFLILRLF 117 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455667776666666668888888888888877766665
No 11
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=52.38 E-value=11 Score=43.84 Aligned_cols=60 Identities=15% Similarity=-0.001 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhhheeeeee-eechhHHHHHHHHHHHHHHHHhhhhhhc-ccccccccccC
Q 011630 218 LWLVILIFVMGFIAGGFILGA-VHNPILLIVVLVLFAVIAAIFIWNTCWG-RKAITDFISCH 277 (481)
Q Consensus 218 ~~~~~~~~~~g~~~g~f~l~a-v~~~~ll~~~~~lfa~vaa~~iWn~~~~-~r~l~Rfl~r~ 277 (481)
+|+|+.+|+.-..+|.|-+.. +-.|++|+++++++++.+..-+|++-|- +.++++.|.+.
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 466777777777777776553 2334444444443333333333444443 44456666554
No 12
>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=51.99 E-value=25 Score=30.40 Aligned_cols=22 Identities=18% Similarity=0.338 Sum_probs=12.0
Q ss_pred CcchhHHHHHHHHHHHHhhhee
Q 011630 213 FPKPVLWLVILIFVMGFIAGGF 234 (481)
Q Consensus 213 ~p~~~~~~~~~~~~~g~~~g~f 234 (481)
++.--+-++++.|++|+++|-+
T Consensus 18 ~t~DE~i~~~~~~~~Gi~~~~~ 39 (95)
T TIGR02762 18 LPLDEFLPGATLFGIGILSGKA 39 (95)
T ss_pred eeHHHHHHHHHHHHHHHHHhhH
Confidence 4444444455566666666543
No 13
>PRK14762 membrane protein; Provisional
Probab=51.85 E-value=14 Score=25.97 Aligned_cols=16 Identities=44% Similarity=1.173 Sum_probs=13.6
Q ss_pred chhHHHHHHHHHHHHh
Q 011630 215 KPVLWLVILIFVMGFI 230 (481)
Q Consensus 215 ~~~~~~~~~~~~~g~~ 230 (481)
|.++|++..+|.+|++
T Consensus 2 ki~lw~i~iifligll 17 (27)
T PRK14762 2 KIILWAVLIIFLIGLL 17 (27)
T ss_pred eeHHHHHHHHHHHHHH
Confidence 5689999999999965
No 14
>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=51.36 E-value=12 Score=28.86 Aligned_cols=26 Identities=27% Similarity=0.414 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHhhhhhhc-ccccccc
Q 011630 248 VLVLFAVIAAIFIWNTCWG-RKAITDF 273 (481)
Q Consensus 248 ~~~lfa~vaa~~iWn~~~~-~r~l~Rf 273 (481)
+..+-+.++++|+|+-|.. ++++.||
T Consensus 17 Vglv~i~iva~~iYRKw~aRkr~l~rf 43 (43)
T PF08114_consen 17 VGLVGIGIVALFIYRKWQARKRALQRF 43 (43)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3334445566899988855 5556665
No 15
>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=50.68 E-value=15 Score=35.19 Aligned_cols=31 Identities=19% Similarity=0.059 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHhhhhhhcccccccccccC
Q 011630 246 IVVLVLFAVIAAIFIWNTCWGRKAITDFISCH 277 (481)
Q Consensus 246 ~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~ 277 (481)
+|++++.+++++.|++++|+-|| -.|+.|||
T Consensus 99 ~Vl~g~s~l~i~yfvir~~R~r~-~~rktRkY 129 (163)
T PF06679_consen 99 YVLVGLSALAILYFVIRTFRLRR-RNRKTRKY 129 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcc-ccccceee
Confidence 56667777888888888885554 22344444
No 16
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.37 E-value=55 Score=35.06 Aligned_cols=145 Identities=17% Similarity=0.146 Sum_probs=78.7
Q ss_pred EEEEEEEEeCCcccccccCCCCceEEEEEEEEEeeccCCCCCCCCCcceeee----eeeeeeeeeeEEEEeCCCceeEEE
Q 011630 291 VKVTGVVTCGNVPLESSFRRVPRCVYTSTSLYEYRAWGSKPANPKHRHFTWG----LRSLERHVVDFYISDFQSGLRALV 366 (481)
Q Consensus 291 VKItGvVtCG~~PL~Aplsk~~rCVYYst~L~EYrg~~~K~an~~h~r~~W~----l~~~Er~~~dFyIsD~~sG~RALV 366 (481)
.-+.|-+.-..+|+++.+..+-.=|.---.++|-+.... ..+-|. +.|.-...++|++.+..++ +++-
T Consensus 60 l~~~~~~~~~~~~~~~~~v~~v~gvv~~~~~~~~~~~~~-------~~~~~~~~~k~~~~~~~~~~~~l~~q~~~-~~~~ 131 (355)
T KOG1571|consen 60 LVIRGCAIARKETLRSLCVSNVPGVVQALTLEEPKGRRD-------GGGHWNANSKIFHEGGNEVPFFLRSQTTG-FACE 131 (355)
T ss_pred HHHhhcccccccchHHhhcccCCceEEEeeeccceeeec-------cceeeccceeeccCCCcccceeeccCCcc-eeee
Confidence 446677777778888877766566666666665543221 122233 4555556799999998887 3332
Q ss_pred ecCCCceeeeeeecceEEc-CCCCCCCCCHHHHHhhhhcCCCCCCceeEEEeeeecCCCEEEEEEEEEecC--ceeeEeC
Q 011630 367 KTGSGARVTPFVDDSVVID-IKPENKDLSPEFIRWLGQKSLSSDDRLMRLKEGYIKEGSTVSVMGIVQRND--NVLMIVP 443 (481)
Q Consensus 367 kaG~GarVtP~Iees~VvD-~~~~~kd~S~el~~wL~~rnLSsd~r~mRykEgiI~eGs~VsViGvv~r~~--~vlmI~p 443 (481)
--=.++...-.-.-..+-| +.++ -..++..-....+++---..||..|..|++|.+...+|...+++ +..|+.|
T Consensus 132 ~~~s~~~~~~~l~l~~~~d~f~~s---~p~s~~~~~~~~~sg~~~~~~~~~~~~l~~~~~~t~l~e~v~d~~~~~r~~~~ 208 (355)
T KOG1571|consen 132 VRVSKTLGRLFLPLNVVYDLFEPS---DPCSLVDVGGGYHSGVRRGGFRETERVLPLGTRLTALGELVRDGYCGVRVQPP 208 (355)
T ss_pred eeeecceeeeeecceeeecccccc---CcceeeecccccccceeeecccceEEeeccccceeeeehheecCCCceEecCC
Confidence 1000000100011122222 2211 11222222222333333667899999999999999999886665 4444444
Q ss_pred CCC
Q 011630 444 PPE 446 (481)
Q Consensus 444 P~E 446 (481)
|..
T Consensus 209 ~~g 211 (355)
T KOG1571|consen 209 MQG 211 (355)
T ss_pred ccC
Confidence 543
No 17
>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=47.63 E-value=31 Score=32.44 Aligned_cols=52 Identities=23% Similarity=0.227 Sum_probs=28.3
Q ss_pred cccccCCcchhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhh
Q 011630 207 YSFRKNFPKPVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIW 261 (481)
Q Consensus 207 ~~~~~~~p~~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iW 261 (481)
|+=|.-.|.-. |.+.+++ .|+++..+.+..-. ....+++++++++++++++|
T Consensus 3 Y~ERL~~p~~w-W~~~~~~-~~~~~~~v~~~~~~-~~~~i~~~~~~~~~~~~l~~ 54 (143)
T PF11292_consen 3 YRERLWVPWWW-WLAAAAV-AALLAAEVVLGPPS-LWAWIPYAVVVAVAVWALLS 54 (143)
T ss_pred cccccCCCHHH-HHHHHHH-HHHHHHhhhcCcch-HHHHHHHHHHHHHHHHHHHH
Confidence 66676666553 5555444 67777766665544 33334444444444444444
No 18
>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=46.84 E-value=8.3 Score=32.21 Aligned_cols=47 Identities=30% Similarity=0.440 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhcc-----------cc-cccccccCCCCccccCCCCCEE
Q 011630 243 ILLIVVLVLFAVIAAIFIWNTCWGR-----------KA-ITDFISCHPDTDLRTAKSGQFV 291 (481)
Q Consensus 243 ~ll~~~~~lfa~vaa~~iWn~~~~~-----------r~-l~Rfl~r~Pds~Lrs~~dGq~V 291 (481)
.+||+++++.++.+++..|.+...+ ++ -.+||.. +.+|++.++||--
T Consensus 4 ~viIaL~~avaa~a~~atwviVq~~~a~~p~s~eeQr~~re~ff~~--~~~l~~i~~gqem 62 (66)
T PF10907_consen 4 RVIIALVVAVAAAAGAATWVIVQPRPAGNPASSEEQRAHREKFFGG--DKDLRDIRGGQEM 62 (66)
T ss_pred chhHHHHHHHHhhhceeEEEEECCCCCCCCCChHHHHHHHHHHcCC--CCCCCCCCCCccc
Confidence 4566666667777777777666544 12 2466654 5567888888853
No 19
>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=44.72 E-value=20 Score=34.90 Aligned_cols=32 Identities=19% Similarity=0.434 Sum_probs=25.2
Q ss_pred ccCCcchhHHHHHHHHHHHHhhheeeeeeeech
Q 011630 210 RKNFPKPVLWLVILIFVMGFIAGGFILGAVHNP 242 (481)
Q Consensus 210 ~~~~p~~~~~~~~~~~~~g~~~g~f~l~av~~~ 242 (481)
.++|=|+++|.+..| ++|+++|+++...+...
T Consensus 136 ~~~~~rA~~~~~~~L-~~G~~lGs~l~~~l~~~ 167 (194)
T PF11833_consen 136 ERKLGRAFLWTLGGL-VVGLILGSLLASWLPVD 167 (194)
T ss_pred cchHHHHHHHHHHHH-HHHHHHHHHHHhhcccc
Confidence 456889999999887 78999999887666443
No 20
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=43.79 E-value=27 Score=31.84 Aligned_cols=48 Identities=17% Similarity=0.164 Sum_probs=27.1
Q ss_pred cchhHHHHHHHHHHHHhhhe-eeeeeeechhHHHHHHHHHHHHHHHHhhhh
Q 011630 214 PKPVLWLVILIFVMGFIAGG-FILGAVHNPILLIVVLVLFAVIAAIFIWNT 263 (481)
Q Consensus 214 p~~~~~~~~~~~~~g~~~g~-f~l~av~~~~ll~~~~~lfa~vaa~~iWn~ 263 (481)
|+..+|+++.++++-++++. |.+.-. |.+|..++.-++++..+|-+|+
T Consensus 9 ~~g~~~~~~~~~~~~~~~a~~f~~~Ga--W~Vl~F~glev~~l~~a~~~~~ 57 (140)
T PF10003_consen 9 PRGFLIFIAILAAVSLIIAIAFLLMGA--WPVLPFAGLEVLALWYAFRRNY 57 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhch--HHHHHHHHHHHHHHHHHHHHHH
Confidence 56667777777766644443 333222 6666665555555555555544
No 21
>PRK00523 hypothetical protein; Provisional
Probab=42.52 E-value=25 Score=29.93 Aligned_cols=35 Identities=20% Similarity=0.301 Sum_probs=18.8
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCCc
Q 011630 242 PILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDTD 281 (481)
Q Consensus 242 ~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds~ 281 (481)
||+|++++.+.+++.++|+ +|+-.+.+|++.|-.+
T Consensus 7 ~I~l~i~~li~G~~~Gffi-----ark~~~k~l~~NPpin 41 (72)
T PRK00523 7 ALGLGIPLLIVGGIIGYFV-----SKKMFKKQIRENPPIT 41 (72)
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHCcCCC
Confidence 3444444444444454444 4555677777777543
No 22
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=42.46 E-value=11 Score=32.84 Aligned_cols=17 Identities=12% Similarity=0.221 Sum_probs=9.4
Q ss_pred HHHHHHHHhhhhhhccc
Q 011630 252 FAVIAAIFIWNTCWGRK 268 (481)
Q Consensus 252 fa~vaa~~iWn~~~~~r 268 (481)
++++++++.|-++++||
T Consensus 79 v~~lv~~l~w~f~~r~k 95 (96)
T PTZ00382 79 VGGLVGFLCWWFVCRGK 95 (96)
T ss_pred HHHHHHHHhheeEEeec
Confidence 33444566676665554
No 23
>PRK01844 hypothetical protein; Provisional
Probab=42.34 E-value=25 Score=29.92 Aligned_cols=33 Identities=30% Similarity=0.503 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCC
Q 011630 243 ILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDT 280 (481)
Q Consensus 243 ~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds 280 (481)
|+|++++.+.+++.++|+ +|+-.+.+|++.|-.
T Consensus 7 I~l~I~~li~G~~~Gff~-----ark~~~k~lk~NPpi 39 (72)
T PRK01844 7 ILVGVVALVAGVALGFFI-----ARKYMMNYLQKNPPI 39 (72)
T ss_pred HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHCCCC
Confidence 334444444444444443 455567777777654
No 24
>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=41.25 E-value=44 Score=30.64 Aligned_cols=49 Identities=22% Similarity=0.357 Sum_probs=26.0
Q ss_pred CcchhHHHHHHHHH-HHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhh
Q 011630 213 FPKPVLWLVILIFV-MGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIW 261 (481)
Q Consensus 213 ~p~~~~~~~~~~~~-~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iW 261 (481)
+-|.=.|++.++|+ |++..+++++-+.+....++.++++.+.++...+|
T Consensus 8 iN~~R~~al~lif~g~~vmy~gi~f~~~~~im~ifmllG~L~~l~S~~VY 57 (114)
T PF11023_consen 8 INKIRTFALSLIFIGMIVMYIGIFFKASPIIMVIFMLLGLLAILASTAVY 57 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444688877664 55555665554444444445555555444444443
No 25
>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=40.72 E-value=28 Score=31.49 Aligned_cols=54 Identities=19% Similarity=0.239 Sum_probs=30.8
Q ss_pred chhHHHHHHHHHHH---Hhhheeeeee------eechhHHHHHHHHHHHHH--HHHhhhhhhccc
Q 011630 215 KPVLWLVILIFVMG---FIAGGFILGA------VHNPILLIVVLVLFAVIA--AIFIWNTCWGRK 268 (481)
Q Consensus 215 ~~~~~~~~~~~~~g---~~~g~f~l~a------v~~~~ll~~~~~lfa~va--a~~iWn~~~~~r 268 (481)
.-.+++.++||++| +++|.+++.. .|.+.+|++-+.+|+..+ ..++|.+|.+++
T Consensus 41 wK~I~la~~Lli~G~~li~~g~l~~~~~i~~~~~~~~~llilG~L~fIPG~Y~~~i~y~a~rg~~ 105 (115)
T PF05915_consen 41 WKSIALAVFLLIFGTVLIIIGLLLFFGHIDGDRDRGWALLILGILCFIPGFYHTRIAYYAWRGYK 105 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccchHHHHHHHHHhccHHHHHHHHHHHcCCC
Confidence 44556777777777 5556666544 356777766555555443 344554444443
No 26
>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=40.68 E-value=45 Score=30.40 Aligned_cols=51 Identities=20% Similarity=0.271 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHH-hhheee-eeeeechhHHHHHHHHHHHHHHHHhhhhhhcc
Q 011630 217 VLWLVILIFVMGF-IAGGFI-LGAVHNPILLIVVLVLFAVIAAIFIWNTCWGR 267 (481)
Q Consensus 217 ~~~~~~~~~~~g~-~~g~f~-l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~~ 267 (481)
++-.++..|+.|+ .++... -.-.+.=++|-+++++++++|=+.+++.|..+
T Consensus 85 ilvsv~~~~~~~~~~~~~~~~~~~~~~Rvllgl~~al~vlvAEv~l~~~y~~k 137 (142)
T PF11712_consen 85 ILVSVFAVFFAGWYWAGYSFGGWSFPYRVLLGLFGALLVLVAEVVLYIRYLRK 137 (142)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445555556665 444333 23455557777778888888777777777554
No 27
>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=40.28 E-value=22 Score=29.85 Aligned_cols=60 Identities=13% Similarity=0.365 Sum_probs=38.2
Q ss_pred hhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhhhcccccccccccCC
Q 011630 216 PVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHP 278 (481)
Q Consensus 216 ~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~P 278 (481)
..-+.+++.+++||++| |++--++..+...+++.++++++.+=-|-+| +|.=++++...+
T Consensus 12 l~~~il~~~~iisfi~G-y~~q~~~~~~~~~~~g~~~~~lv~vP~Wp~y--~r~p~~W~~~~~ 71 (76)
T PF06645_consen 12 LMQYILIISAIISFIVG-YITQSFSYTFYIYGAGVVLTLLVVVPPWPFY--NRHPLKWLPPKP 71 (76)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhheeCCcHhh--cCCcccCCCCCc
Confidence 44466666777777776 4556667777777777777776666677666 444455554433
No 28
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=39.45 E-value=26 Score=32.70 Aligned_cols=23 Identities=9% Similarity=0.050 Sum_probs=16.8
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhh
Q 011630 242 PILLIVVLVLFAVIAAIFIWNTC 264 (481)
Q Consensus 242 ~~ll~~~~~lfa~vaa~~iWn~~ 264 (481)
-.++.++.++.++++++++.+++
T Consensus 102 ~e~~~~~~~~~g~~~g~~~~r~~ 124 (154)
T PRK10862 102 SDLAALCGALLGGVGGFLLARGL 124 (154)
T ss_pred chHHHHHHHHHHHHHHHHHHHHH
Confidence 47777777888888877777655
No 29
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=39.41 E-value=52 Score=31.56 Aligned_cols=17 Identities=35% Similarity=0.565 Sum_probs=13.9
Q ss_pred CCCCCEEEEEEEEEeCC
Q 011630 285 AKSGQFVKVTGVVTCGN 301 (481)
Q Consensus 285 ~~dGq~VKItGvVtCG~ 301 (481)
...|+.++|-|.|.-|+
T Consensus 54 ~~~g~~iRvgG~V~~GS 70 (160)
T PRK13165 54 PEVGQRLRVGGMVMPGS 70 (160)
T ss_pred cCCCCEEEEeeEEeCCc
Confidence 34799999999998854
No 30
>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=37.80 E-value=35 Score=31.73 Aligned_cols=33 Identities=27% Similarity=0.067 Sum_probs=20.7
Q ss_pred heeeeeeeechhHHHHHHHHHHHHHHHHhhhhh
Q 011630 232 GGFILGAVHNPILLIVVLVLFAVIAAIFIWNTC 264 (481)
Q Consensus 232 g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~ 264 (481)
+++-|.++...++-++++++.++.+++-+.+++
T Consensus 29 ~~~~l~~~~s~~lg~~~lAlg~vL~~~g~~~~~ 61 (191)
T PF04156_consen 29 FISGLGALISFILGIALLALGVVLLSLGLLCLL 61 (191)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333367777777777777766666555555444
No 31
>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=37.41 E-value=43 Score=32.42 Aligned_cols=40 Identities=20% Similarity=0.307 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHhhhhhhcccccccccccCCCCccccCC
Q 011630 247 VVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDTDLRTAK 286 (481)
Q Consensus 247 ~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds~Lrs~~ 286 (481)
+.+++.+++++++|-.++.+++.-.+-..++|+++-....
T Consensus 104 ~~~~~~~~~~~~iid~~~l~r~vkk~v~~kFp~~~~~~~g 143 (170)
T PF11241_consen 104 VTLAMYVLLLLVIIDGVILGRRVKKRVAEKFPDTTESGRG 143 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCcCCCcc
Confidence 3333344444444444443443345555667885544433
No 32
>PRK13823 conjugal transfer protein TrbD; Provisional
Probab=37.10 E-value=25 Score=30.94 Aligned_cols=37 Identities=16% Similarity=0.152 Sum_probs=21.5
Q ss_pred HHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhh
Q 011630 224 IFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIW 261 (481)
Q Consensus 224 ~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iW 261 (481)
+++.|+++++++++. ++|+-.++.+++..+...++.|
T Consensus 26 ~i~~g~la~~l~~g~-~~~~a~~~gl~lw~v~h~~l~~ 62 (94)
T PRK13823 26 VMFSGLLAGILIFVA-QTWRAALFGIALWFGALFALRL 62 (94)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 445677777777666 6775444444444444445555
No 33
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=34.91 E-value=66 Score=30.89 Aligned_cols=17 Identities=35% Similarity=0.534 Sum_probs=14.1
Q ss_pred CCCCCEEEEEEEEEeCC
Q 011630 285 AKSGQFVKVTGVVTCGN 301 (481)
Q Consensus 285 ~~dGq~VKItGvVtCG~ 301 (481)
...|+.++|-|.|.-|+
T Consensus 54 ~~~g~~iRvgG~V~~GS 70 (159)
T PRK13150 54 PAVGQRLRVGGMVMPGS 70 (159)
T ss_pred cCCCCEEEEeeEEeCCc
Confidence 45799999999998854
No 34
>PRK10881 putative hydrogenase 2 b cytochrome subunit; Provisional
Probab=34.23 E-value=34 Score=35.97 Aligned_cols=37 Identities=19% Similarity=0.542 Sum_probs=25.4
Q ss_pred ccc-cceecccccccccccCCcchhHHHHH-HHHHHHHhhheeeeeee
Q 011630 194 QNQ-AVTTITQEDDYSFRKNFPKPVLWLVI-LIFVMGFIAGGFILGAV 239 (481)
Q Consensus 194 ~~~-avt~l~~~~~~~~~~~~p~~~~~~~~-~~~~~g~~~g~f~l~av 239 (481)
++- +||++|++.-.+ . |... +++.+|+.+|+|++++.
T Consensus 39 ~Glg~vtg~~~~~~WG--------l-~I~~y~~~~vglaag~~~is~~ 77 (394)
T PRK10881 39 FGLGSVSNLNGGYPWG--------I-WIAFDVLIGTGFACGGWALAWL 77 (394)
T ss_pred hcchhhcCCCCCCCch--------H-HHHHHHHHHHHHHHHHHHHHHH
Confidence 465 699999883322 2 5554 55677999999988763
No 35
>PF15050 SCIMP: SCIMP protein
Probab=33.57 E-value=45 Score=31.16 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhh
Q 011630 242 PILLIVVLVLFAVIAAIFIWNTC 264 (481)
Q Consensus 242 ~~ll~~~~~lfa~vaa~~iWn~~ 264 (481)
||+|+|++.++..++++++|-+|
T Consensus 9 WiiLAVaII~vS~~lglIlyCvc 31 (133)
T PF15050_consen 9 WIILAVAIILVSVVLGLILYCVC 31 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 78899998888999999999655
No 36
>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=33.47 E-value=1.1e+02 Score=26.06 Aligned_cols=18 Identities=22% Similarity=0.689 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHhhheee
Q 011630 218 LWLVILIFVMGFIAGGFI 235 (481)
Q Consensus 218 ~~~~~~~~~~g~~~g~f~ 235 (481)
++.++++++.++++|.++
T Consensus 9 l~~l~~~~l~~~lvG~~~ 26 (90)
T PF11808_consen 9 LWRLLLLLLAAALVGWLF 26 (90)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 355555555555555443
No 37
>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=33.42 E-value=74 Score=23.89 Aligned_cols=27 Identities=37% Similarity=0.461 Sum_probs=22.8
Q ss_pred eecCCCEEEEEEEEEecCceeeEeCCC
Q 011630 419 YIKEGSTVSVMGIVQRNDNVLMIVPPP 445 (481)
Q Consensus 419 iI~eGs~VsViGvv~r~~~vlmI~pP~ 445 (481)
.+++|+.+.|.|.+++..+.+-|..|.
T Consensus 45 ~~~~G~~~~v~Gkv~~~~~~~qi~~P~ 71 (75)
T cd04488 45 QLPPGTRVRVSGKVKRFRGGLQIVHPE 71 (75)
T ss_pred cCCCCCEEEEEEEEeecCCeeEEeCCc
Confidence 488999999999999988877777664
No 38
>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=32.19 E-value=43 Score=28.55 Aligned_cols=58 Identities=24% Similarity=0.305 Sum_probs=39.9
Q ss_pred CcchhHHHHHHHHHHHHhhheeeee---eeech--hHHHHHHHHHHHHHHHHhhhhhhccccc
Q 011630 213 FPKPVLWLVILIFVMGFIAGGFILG---AVHNP--ILLIVVLVLFAVIAAIFIWNTCWGRKAI 270 (481)
Q Consensus 213 ~p~~~~~~~~~~~~~g~~~g~f~l~---av~~~--~ll~~~~~lfa~vaa~~iWn~~~~~r~l 270 (481)
|.+...|+++++++.|+..+...+. -+.++ .+|.+=++++++++++-.+|.++-.+.+
T Consensus 7 Fs~~a~~av~~l~~TG~~~a~~~~~~~~l~~t~yG~~Ll~K~~L~~~~l~l~~~~~~~~~p~l 69 (105)
T PF05425_consen 7 FSWIAWAAVAVLVVTGLVMAWLRLGFDALFTTPYGRLLLVKLALVLLMLALAAYNRFRLIPRL 69 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCchhhccChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7788889999999999877665544 22222 4566677777777777777776433333
No 39
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=31.39 E-value=33 Score=32.04 Aligned_cols=35 Identities=20% Similarity=0.306 Sum_probs=30.4
Q ss_pred ccccccccccCCCCcccc-CCCCCEEEEEEEEEeCC
Q 011630 267 RKAITDFISCHPDTDLRT-AKSGQFVKVTGVVTCGN 301 (481)
Q Consensus 267 ~r~l~Rfl~r~Pds~Lrs-~~dGq~VKItGvVtCG~ 301 (481)
.+...+.++++|+.++-+ .++|++|.++|.++..+
T Consensus 46 tK~~yKqik~np~vefcg~~kdg~~vrlrg~a~f~~ 81 (132)
T COG5015 46 TKPYYKQIKKNPEVEFCGMDKDGVMVRLRGRAEFVE 81 (132)
T ss_pred ChHHHHHHhhCCCeEEEEecCCceEEEEeeeEEecc
Confidence 455789999999999998 68999999999998743
No 40
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=30.96 E-value=25 Score=41.67 Aligned_cols=16 Identities=50% Similarity=0.833 Sum_probs=14.6
Q ss_pred ccccCCceeeeCCCCC
Q 011630 7 SHQLSNGLFVSGRPEQ 22 (481)
Q Consensus 7 shqlsnglyvsgrpeq 22 (481)
-|||.|||||+|+|-|
T Consensus 1199 qH~Lps~l~v~~qp~q 1214 (1387)
T KOG1016|consen 1199 QHQLPSGLYVKLQPGQ 1214 (1387)
T ss_pred ccccCccceEecCCcc
Confidence 5999999999999974
No 41
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=30.29 E-value=49 Score=30.41 Aligned_cols=14 Identities=7% Similarity=0.138 Sum_probs=0.4
Q ss_pred ccCCCCccccCCCC
Q 011630 275 SCHPDTDLRTAKSG 288 (481)
Q Consensus 275 ~r~Pds~Lrs~~dG 288 (481)
+|.+..++....++
T Consensus 92 ~Kk~~~~~~p~P~~ 105 (122)
T PF01102_consen 92 RKKSSSDVQPLPEE 105 (122)
T ss_dssp S-------------
T ss_pred hccCCCCCCCCCCC
Confidence 33344455544444
No 42
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=29.93 E-value=92 Score=29.93 Aligned_cols=54 Identities=20% Similarity=0.397 Sum_probs=33.5
Q ss_pred chhHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCCccc--cCCCCCEEEEEEEEEeC
Q 011630 241 NPILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDTDLR--TAKSGQFVKVTGVVTCG 300 (481)
Q Consensus 241 ~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds~Lr--s~~dGq~VKItGvVtCG 300 (481)
++.+++++++..++++.+.+|+. ++++-=| |.-+++. ....||.+++-|-|.-|
T Consensus 8 Rl~~il~~~a~l~~a~~l~Lyal---~~ni~~f---y~Psel~~~~~~~G~rlR~GGlV~~G 63 (153)
T COG2332 8 RLWIILAGLAGLALAVGLVLYAL---RSNIDYF---YTPSELLEGKVETGQRLRLGGLVEAG 63 (153)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhh---ccCceEE---ECHHHhccccccCCcEEEEeeeEeec
Confidence 44555555555666666666654 4444434 4444444 35558999999999884
No 43
>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=29.59 E-value=56 Score=29.98 Aligned_cols=57 Identities=19% Similarity=0.346 Sum_probs=36.9
Q ss_pred HHHHHHHHhhhee--------ee-eeeechhHHHHHHHHHHHHHHHHhhhhhhc--ccccccccccCCC
Q 011630 222 ILIFVMGFIAGGF--------IL-GAVHNPILLIVVLVLFAVIAAIFIWNTCWG--RKAITDFISCHPD 279 (481)
Q Consensus 222 ~~~~~~g~~~g~f--------~l-~av~~~~ll~~~~~lfa~vaa~~iWn~~~~--~r~l~Rfl~r~Pd 279 (481)
+.+..+|+.++-+ ++ +.+|+-+|++.++..++--+ .-.+|+++. ++.++.+++..|.
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 5555577766654 34 66888777776665555444 555677766 4446888888875
No 44
>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=29.52 E-value=78 Score=24.07 Aligned_cols=26 Identities=23% Similarity=0.635 Sum_probs=16.3
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhccc
Q 011630 243 ILLIVVLVLFAVIAAIFIWNTCWGRK 268 (481)
Q Consensus 243 ~ll~~~~~lfa~vaa~~iWn~~~~~r 268 (481)
|+..|++++..+++..++|.+|++|.
T Consensus 8 IIv~V~vg~~iiii~~~~YaCcykk~ 33 (38)
T PF02439_consen 8 IIVAVVVGMAIIIICMFYYACCYKKH 33 (38)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 44455566666666677777776653
No 45
>PRK08456 flagellar motor protein MotA; Validated
Probab=29.52 E-value=37 Score=34.05 Aligned_cols=43 Identities=19% Similarity=0.116 Sum_probs=29.0
Q ss_pred heeeeeeeechhHHHHHHHHHHHHHHHHhhhhhhc-cccccccc
Q 011630 232 GGFILGAVHNPILLIVVLVLFAVIAAIFIWNTCWG-RKAITDFI 274 (481)
Q Consensus 232 g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~-~r~l~Rfl 274 (481)
|+=+..-|+=+.++||+++-+++++..+-|+.... -+.+...|
T Consensus 24 gg~~~~~~~~~~~~IV~Ggt~~a~~i~~~~~~~~~~~~~~~~~f 67 (257)
T PRK08456 24 GGNPLHVIHLSSFIIVVPTALFAAMTATHKKYVKAAYKELKIVF 67 (257)
T ss_pred CCCcHHHhhHhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh
Confidence 43344448888999999999999888887766533 23344444
No 46
>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=29.48 E-value=56 Score=30.72 Aligned_cols=42 Identities=17% Similarity=0.382 Sum_probs=31.2
Q ss_pred CCcchhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHH
Q 011630 212 NFPKPVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFA 253 (481)
Q Consensus 212 ~~p~~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa 253 (481)
++....++.+++..++|..+|++++..+-..++..++..+..
T Consensus 60 ~i~~~~~~~~~~~~~~g~~iG~~l~~~l~~~~l~~~~~~~ll 101 (240)
T PF01925_consen 60 NIDWKIVLPLIIGALIGVVIGAWLLSLLPDDILKLIFGLFLL 101 (240)
T ss_pred ccchhhhhhhhhHhHHHHHHHHhhhcchhHHHHHHHHHHHHH
Confidence 377777788888889999999999997776655555444433
No 47
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=29.18 E-value=1.4e+02 Score=31.02 Aligned_cols=10 Identities=30% Similarity=0.547 Sum_probs=6.7
Q ss_pred eeeeeeeech
Q 011630 233 GFILGAVHNP 242 (481)
Q Consensus 233 ~f~l~av~~~ 242 (481)
|.++.+|-++
T Consensus 26 Gyv~i~~~~~ 35 (409)
T TIGR00540 26 GYVLIETANR 35 (409)
T ss_pred CeEEEEECCE
Confidence 4677777665
No 48
>COG3346 Uncharacterized conserved protein [Function unknown]
Probab=29.15 E-value=3.3e+02 Score=28.03 Aligned_cols=58 Identities=24% Similarity=0.415 Sum_probs=32.8
Q ss_pred echhHHHHHHHHHHHHHHHHhh---hhhhccccc--ccccccCCCCccccCCCC-------CE--EEEEEEE
Q 011630 240 HNPILLIVVLVLFAVIAAIFIW---NTCWGRKAI--TDFISCHPDTDLRTAKSG-------QF--VKVTGVV 297 (481)
Q Consensus 240 ~~~~ll~~~~~lfa~vaa~~iW---n~~~~~r~l--~Rfl~r~Pds~Lrs~~dG-------q~--VKItGvV 297 (481)
.+++++++++++|++.+++=.| +..|..+-+ ...-...|-..+...-+- || |+++|+-
T Consensus 12 ~~~~l~~l~~~~~~il~~LGtWQl~Rl~wK~~lia~ie~r~~appv~l~~~~~~~~~~~~~eyrrV~ltG~f 83 (252)
T COG3346 12 WLALLLLLVLATFAILLGLGTWQLQRLHWKLALIARIEARLHAPPVPLPKLLDWADSGADLEYRRVTLTGTF 83 (252)
T ss_pred hhHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHhcCCCCCcccccchhhcCcccceEEEEEEEEE
Confidence 3456677777788888888888 333443222 333344555555543333 44 7777764
No 49
>KOG0162 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=28.98 E-value=3.4e+02 Score=32.51 Aligned_cols=22 Identities=14% Similarity=0.188 Sum_probs=18.3
Q ss_pred cCCcccccccccceecccCCcc
Q 011630 38 TGGDIKKSGELGKMFDIPMDSA 59 (481)
Q Consensus 38 tggdikksgelgkmfdi~~~~~ 59 (481)
.++|.|+-++.+|-+.|+|-.-
T Consensus 901 ~~~~~~~~k~~~Ks~tvsvg~G 922 (1106)
T KOG0162|consen 901 DFEDLKVLKDIYKSLTVSVGTG 922 (1106)
T ss_pred CccchhhhccccceeEEEecCC
Confidence 4589999999999999987643
No 50
>PF04790 Sarcoglycan_1: Sarcoglycan complex subunit protein; InterPro: IPR006875 The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle. The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains. This family contains beta, gamma and delta members [, ].; GO: 0007010 cytoskeleton organization, 0016012 sarcoglycan complex, 0016021 integral to membrane
Probab=28.11 E-value=6.7e+02 Score=25.73 Aligned_cols=88 Identities=18% Similarity=0.242 Sum_probs=48.3
Q ss_pred eeeeeeeEEEEeCCCceeEEEecCCCceee-------ee-----eecceEEcCCCCCCCCCHHHHHhhhhcCCCCCCc--
Q 011630 346 LERHVVDFYISDFQSGLRALVKTGSGARVT-------PF-----VDDSVVIDIKPENKDLSPEFIRWLGQKSLSSDDR-- 411 (481)
Q Consensus 346 ~Er~~~dFyIsD~~sG~RALVkaG~GarVt-------P~-----Iees~VvD~~~~~kd~S~el~~wL~~rnLSsd~r-- 411 (481)
-|.....|-|.|..+| +.|-.+.+- +|+ -. +.+..|....= ..++..+| .|++++|
T Consensus 113 v~~~~~~F~V~d~~~g-~~lFsad~~-~v~v~~~~lrv~~~~G~l~~~~v~T~~I-rs~~~~~L-------~leS~trsL 182 (264)
T PF04790_consen 113 VEAQSNRFEVKDPRDG-KTLFSADRP-EVVVGAEKLRVTGPEGALFEKSVQTPRI-RSPPNEDL-------RLESPTRSL 182 (264)
T ss_pred EEEecCeEEEEcCCCC-ceEEEecCC-ceEEeeeeEEecCCccEEEeeeEEeccc-cCCCCccc-------ccccCCcEE
Confidence 5677888999998555 455544443 332 11 22222221000 02344444 7888888
Q ss_pred eeEEEeeeecCCCE--EEEEE----EEEecCceeeEeC
Q 011630 412 LMRLKEGYIKEGST--VSVMG----IVQRNDNVLMIVP 443 (481)
Q Consensus 412 ~mRykEgiI~eGs~--VsViG----vv~r~~~vlmI~p 443 (481)
.||--||+-=++.. |.+-. .++-.++.+++..
T Consensus 183 ~~~a~egV~i~a~ag~I~~~a~~di~L~S~~G~i~Lda 220 (264)
T PF04790_consen 183 SMRAPEGVHIEAKAGDIEASARQDISLNSTDGSIVLDA 220 (264)
T ss_pred EEECCCCeEEEeccCcEEEEecCCEEEEecCCeEEEec
Confidence 77888887766666 55533 2233466666666
No 51
>PRK12869 ubiA protoheme IX farnesyltransferase; Reviewed
Probab=28.01 E-value=1.3e+02 Score=30.27 Aligned_cols=43 Identities=14% Similarity=0.110 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCCccccCCCCC
Q 011630 243 ILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDTDLRTAKSGQ 289 (481)
Q Consensus 243 ~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds~Lrs~~dGq 289 (481)
.++.+.++.+.+..+..+||-|+ |+++-+..+|.++ |-...|+
T Consensus 37 ~~~l~~~~~~l~~~a~~~~Nd~~-D~~iD~~~~Rt~~---RPl~sG~ 79 (279)
T PRK12869 37 PLIPLLIGGTLASGGSAAFNHGI-ERDIDKVMSRTSK---RPTPVGL 79 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHhchH-hcCCCCCCCCCCC---CCcCCCC
Confidence 34555666666788889999886 5555554444433 4444444
No 52
>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=27.73 E-value=54 Score=29.75 Aligned_cols=46 Identities=17% Similarity=0.101 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhh
Q 011630 218 LWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTC 264 (481)
Q Consensus 218 ~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~ 264 (481)
.|++.+=+++|+++|..+..... .+.++-++++...++++++...+
T Consensus 24 ~~~~~~~~~~gl~~g~~l~~~~~-~w~~~p~~~lig~~l~v~~gg~~ 69 (111)
T TIGR03750 24 GVAAGVGLAAGLVLGLLLALLAG-PWALIPTGALLGPILVVLIGGKL 69 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhHHH
Confidence 35666678888888876544444 55566666677777767776443
No 53
>PRK09109 motC flagellar motor protein; Reviewed
Probab=27.73 E-value=43 Score=33.45 Aligned_cols=54 Identities=20% Similarity=0.163 Sum_probs=34.6
Q ss_pred HHHHHHHhhheeee------eeeechhHHHHHHHHHHHHHHHHhhhhhhc-cccccccccc
Q 011630 223 LIFVMGFIAGGFIL------GAVHNPILLIVVLVLFAVIAAIFIWNTCWG-RKAITDFISC 276 (481)
Q Consensus 223 ~~~~~g~~~g~f~l------~av~~~~ll~~~~~lfa~vaa~~iWn~~~~-~r~l~Rfl~r 276 (481)
++++++.++++|++ .-++=+.+++|+++-++++...+-|+..+. -+.+...+++
T Consensus 9 ~~~~~~~v~~~~~~~gg~~~~~~~~~~~lIV~Ggt~~a~~i~~~~~~~~~~~~~~~~~f~~ 69 (246)
T PRK09109 9 LILAFVAIIGGQVLEGGHLGSLLNGPAFLIVIGGTLGAVLLQTPLAVFKRAFKILRWVFFP 69 (246)
T ss_pred HHHHHHHHHHHHHhcCCChHHHhhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcc
Confidence 34444444444443 347788899999999999888888866643 3334455543
No 54
>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].
Probab=27.35 E-value=78 Score=26.79 Aligned_cols=24 Identities=8% Similarity=0.412 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHhhhhhhcccc
Q 011630 246 IVVLVLFAVIAAIFIWNTCWGRKA 269 (481)
Q Consensus 246 ~~~~~lfa~vaa~~iWn~~~~~r~ 269 (481)
++++++.++++++++|.+|.++++
T Consensus 5 ~iLi~ICVaii~lIlY~iYnr~~~ 28 (68)
T PF05961_consen 5 FILIIICVAIIGLILYGIYNRKKT 28 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccc
Confidence 345566677888999999866554
No 55
>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=27.16 E-value=92 Score=28.94 Aligned_cols=56 Identities=16% Similarity=0.271 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhhheeee--eeee-----chhHHHHHHHHHHHHHHHHhhhhhhccccccccc
Q 011630 219 WLVILIFVMGFIAGGFIL--GAVH-----NPILLIVVLVLFAVIAAIFIWNTCWGRKAITDFI 274 (481)
Q Consensus 219 ~~~~~~~~~g~~~g~f~l--~av~-----~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl 274 (481)
|-...++.++|++|...- ..++ -...|.++++++++++.+++|+.|..-..+.+|-
T Consensus 21 ~ysyfl~~~~l~Lg~~~~~~~~~~~~~~~~~~~l~~~~~l~~l~~~~~~~~~~~~~~~l~~~~ 83 (193)
T PF11846_consen 21 WYSYFLWPFALLLGLLPDPARRLRRIPRSLAFALRAAALLIALAALGFMLTDYHTNEQLTRFE 83 (193)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 555555556666665544 2222 2244556666667777777776665443344443
No 56
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=26.47 E-value=64 Score=27.93 Aligned_cols=11 Identities=18% Similarity=-0.009 Sum_probs=7.2
Q ss_pred cCCCCCEEEEE
Q 011630 284 TAKSGQFVKVT 294 (481)
Q Consensus 284 s~~dGq~VKIt 294 (481)
+--.|+..+++
T Consensus 87 ~~liG~~g~v~ 97 (144)
T PF01957_consen 87 DDLIGKEGTVI 97 (144)
T ss_dssp GGGTTSEEEEE
T ss_pred HHHcCCeEEEE
Confidence 34478877775
No 57
>PF14362 DUF4407: Domain of unknown function (DUF4407)
Probab=26.23 E-value=44 Score=33.47 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=12.1
Q ss_pred eeeechhHHHHHHHHHHHHHHHHhhhh
Q 011630 237 GAVHNPILLIVVLVLFAVIAAIFIWNT 263 (481)
Q Consensus 237 ~av~~~~ll~~~~~lfa~vaa~~iWn~ 263 (481)
-+.+++. .+..+|+++.+++|+|+
T Consensus 39 ~~~~~~~---~~ai~~glvwgl~I~~l 62 (301)
T PF14362_consen 39 TVFGGPV---WAAIPFGLVWGLVIFNL 62 (301)
T ss_pred HHhccch---HHHHHHHHHHHHHHHHH
Confidence 3444443 33344445556666655
No 58
>PF05090 VKG_Carbox: Vitamin K-dependent gamma-carboxylase; InterPro: IPR007782 Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase [].; GO: 0008488 gamma-glutamyl carboxylase activity, 0017187 peptidyl-glutamic acid carboxylation
Probab=26.17 E-value=73 Score=34.60 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=25.7
Q ss_pred CCCCcceeee-eeeeeeeeeeEEEEeCCCceeEEEe
Q 011630 333 NPKHRHFTWG-LRSLERHVVDFYISDFQSGLRALVK 367 (481)
Q Consensus 333 n~~h~r~~W~-l~~~Er~~~dFyIsD~~sG~RALVk 367 (481)
+..| |++|+ ++++....+.|++.|.++|.+-.|+
T Consensus 332 e~g~-r~SWrmMl~~~~~~~~~~v~d~~tg~~~~v~ 366 (446)
T PF05090_consen 332 EEGY-RFSWRMMLRSKSGYVQFKVVDKKTGERFYVD 366 (446)
T ss_pred cccc-cceeEEEEEEcceeEEEEEEeCCCCceEEEC
Confidence 5667 79999 4455556789999999998765554
No 59
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=25.81 E-value=25 Score=32.38 Aligned_cols=14 Identities=36% Similarity=0.603 Sum_probs=8.2
Q ss_pred ccCCCCCEEEEEEE
Q 011630 283 RTAKSGQFVKVTGV 296 (481)
Q Consensus 283 rs~~dGq~VKItGv 296 (481)
+-++.||+|+|.|.
T Consensus 59 ~pf~vGD~I~i~~~ 72 (206)
T PF00924_consen 59 RPFKVGDRIEIGGV 72 (206)
T ss_dssp -SS-TT-EEESSS-
T ss_pred CCccCCCEEEEEEe
Confidence 35889999998743
No 60
>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=25.70 E-value=3e+02 Score=25.36 Aligned_cols=48 Identities=15% Similarity=0.265 Sum_probs=26.8
Q ss_pred chhHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCCccccCCCCCEEEEE
Q 011630 241 NPILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDTDLRTAKSGQFVKVT 294 (481)
Q Consensus 241 ~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds~Lrs~~dGq~VKIt 294 (481)
.+++++.+++=|++..++.+|+.|+-+..+....++-+ ...++.+.|.
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 45555555666666666777777765544443333222 4456666665
No 61
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=25.62 E-value=96 Score=29.68 Aligned_cols=17 Identities=29% Similarity=0.427 Sum_probs=13.4
Q ss_pred CCCCCEEEEEEEEEeCC
Q 011630 285 AKSGQFVKVTGVVTCGN 301 (481)
Q Consensus 285 ~~dGq~VKItGvVtCG~ 301 (481)
...++.++|-|.|.-|+
T Consensus 48 ~~~~~~~RlGG~V~~GS 64 (155)
T PRK13159 48 AAGYQQFRLGGMVKAGS 64 (155)
T ss_pred cccCCeEEEccEEecCc
Confidence 45678899999998754
No 62
>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=25.17 E-value=93 Score=36.47 Aligned_cols=59 Identities=20% Similarity=0.330 Sum_probs=30.4
Q ss_pred CcchhHHHHHHHHHHHHhhheeee--eeeechhHHHHHHHHHHHHHHHHhhhhhhcccccc
Q 011630 213 FPKPVLWLVILIFVMGFIAGGFIL--GAVHNPILLIVVLVLFAVIAAIFIWNTCWGRKAIT 271 (481)
Q Consensus 213 ~p~~~~~~~~~~~~~g~~~g~f~l--~av~~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~ 271 (481)
|-.++.|.+++.+++-|+.|.... -...+|+.-+++++++.+.+++-.|.-+.+++.+.
T Consensus 5 f~~~~~~iL~~aa~ls~~~~~~~~~~~~~~~~~~~~~Il~vi~~~~~i~~~qe~~a~~~~~ 65 (917)
T TIGR01116 5 FEDLLVRILLLAACVSFVLAWFEEGEETVTAFVEPFVILLILVANAIVGVWQERNAEKAIE 65 (917)
T ss_pred HhCHHHHHHHHHHHHHHHHhcccccccccccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444566777666666676664321 12235544444444444444455565555555543
No 63
>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=25.10 E-value=72 Score=27.67 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=11.6
Q ss_pred echhHHHHHHHHHHHHHHHHhhhh
Q 011630 240 HNPILLIVVLVLFAVIAAIFIWNT 263 (481)
Q Consensus 240 ~~~~ll~~~~~lfa~vaa~~iWn~ 263 (481)
|...++.+++.++++++|.++|.+
T Consensus 2 ~~l~i~~iialiv~~iiaIvvW~i 25 (81)
T PF00558_consen 2 QSLEILAIIALIVALIIAIVVWTI 25 (81)
T ss_dssp ------HHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555666666667777744
No 64
>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=24.74 E-value=73 Score=30.73 Aligned_cols=16 Identities=38% Similarity=0.848 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHhhhee
Q 011630 219 WLVILIFVMGFIAGGF 234 (481)
Q Consensus 219 ~~~~~~~~~g~~~g~f 234 (481)
|.-.+.-.++|++|++
T Consensus 132 ~~~al~~~~sf~lg~l 147 (213)
T PF01988_consen 132 WKAALATFLSFILGGL 147 (213)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5555555666666663
No 65
>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=24.19 E-value=1.2e+02 Score=27.75 Aligned_cols=61 Identities=21% Similarity=0.412 Sum_probs=34.6
Q ss_pred eeEEEEeCCCc-----eeEEEecCCCceeeeeeecceEEc-CCCCC----CCCCHHHHHhhhhcCCCCCCceeEEEeeee
Q 011630 351 VDFYISDFQSG-----LRALVKTGSGARVTPFVDDSVVID-IKPEN----KDLSPEFIRWLGQKSLSSDDRLMRLKEGYI 420 (481)
Q Consensus 351 ~dFyIsD~~sG-----~RALVkaG~GarVtP~Iees~VvD-~~~~~----kd~S~el~~wL~~rnLSsd~r~mRykEgiI 420 (481)
.-.+|+|.|+. ..++|..|... -...| +.|.. ..+=.||..||.+++ . |.+|-+|
T Consensus 17 ~v~liTDwQd~R~~ARYa~ll~~gk~~--------llt~dAFGPafG~~G~~ALaELv~wl~~~G------~-~f~EaVl 81 (113)
T PF11432_consen 17 KVYLITDWQDQRPQARYALLLRGGKEP--------LLTPDAFGPAFGPEGERALAELVRWLQERG------A-RFYEAVL 81 (113)
T ss_dssp EEEEEEE--SSCCC--EEEEEE-SS-E--------EEEEEEESTTS-TTHHHHHHHHHHHHHHTT--------EEEEEEE
T ss_pred eEEEEeccccchhhhhhhhheecCCcc--------cccccccCcccCccHHHHHHHHHHHHHHcC------C-chhheec
Confidence 34578887764 23344433321 12233 55554 244568999999999 4 8999999
Q ss_pred cCCCEE
Q 011630 421 KEGSTV 426 (481)
Q Consensus 421 ~eGs~V 426 (481)
.+|+-.
T Consensus 82 ~p~e~~ 87 (113)
T PF11432_consen 82 SPSEFA 87 (113)
T ss_dssp -GGGHH
T ss_pred CHHHHH
Confidence 988643
No 66
>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=24.06 E-value=1.1e+02 Score=25.39 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.2
Q ss_pred eecCCCEEEEEEEEEecCceeeEeCCC
Q 011630 419 YIKEGSTVSVMGIVQRNDNVLMIVPPP 445 (481)
Q Consensus 419 iI~eGs~VsViGvv~r~~~vlmI~pP~ 445 (481)
-+++|++|.|-|+++...+..=|.+++
T Consensus 44 ~~~~Gd~V~vtG~v~ey~g~tql~~~~ 70 (78)
T cd04486 44 DVAVGDLVRVTGTVTEYYGLTQLTAVS 70 (78)
T ss_pred CCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence 467899999999999999888777775
No 67
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.99 E-value=61 Score=27.59 Aligned_cols=18 Identities=17% Similarity=0.207 Sum_probs=13.0
Q ss_pred hhhcccccccccccCCCC
Q 011630 263 TCWGRKAITDFISCHPDT 280 (481)
Q Consensus 263 ~~~~~r~l~Rfl~r~Pds 280 (481)
+|.++|-..+.|++.|.-
T Consensus 22 ~fiark~~~k~lk~NPpi 39 (71)
T COG3763 22 FFIARKQMKKQLKDNPPI 39 (71)
T ss_pred HHHHHHHHHHHHhhCCCC
Confidence 455677778888888754
No 68
>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=23.91 E-value=46 Score=29.79 Aligned_cols=6 Identities=33% Similarity=0.601 Sum_probs=2.4
Q ss_pred hhhhcc
Q 011630 262 NTCWGR 267 (481)
Q Consensus 262 n~~~~~ 267 (481)
-+|+++
T Consensus 19 ~~~~~r 24 (130)
T PF12273_consen 19 FYCHNR 24 (130)
T ss_pred HHHHHH
Confidence 444443
No 69
>KOG4050 consensus Glutamate transporter EAAC1-interacting protein GTRAP3-18 [Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=23.83 E-value=1e+02 Score=30.23 Aligned_cols=55 Identities=25% Similarity=0.535 Sum_probs=35.0
Q ss_pred HHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhhhcccccccccccCCCCcc
Q 011630 222 ILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTCWGRKAITDFISCHPDTDL 282 (481)
Q Consensus 222 ~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rfl~r~Pds~L 282 (481)
.++|+|+|..-+|+ |+.=.++-+.+.+++++.+||... .+++++|--+++|.+-+
T Consensus 59 fv~~it~~~l~~f~-----sp~~iilglivvvlvi~~liwa~~-~~a~~krmr~~hp~~~l 113 (188)
T KOG4050|consen 59 FVTFITLFLLHGFI-----SPQDIILGLIVVVLVIGTLIWAAS-ADANIKRMRTDHPLVTL 113 (188)
T ss_pred HHHHHHHHHHHHHc-----CHHHHHHHHHHHHHHHHHHHHHHh-ccHHHHHHhhcCcHHHH
Confidence 45677777666665 455555555566777788999554 56666665566666544
No 70
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=23.72 E-value=1.5e+02 Score=30.82 Aligned_cols=10 Identities=30% Similarity=0.507 Sum_probs=6.6
Q ss_pred eeeeeeeech
Q 011630 233 GFILGAVHNP 242 (481)
Q Consensus 233 ~f~l~av~~~ 242 (481)
|.++.+|-++
T Consensus 26 Gyv~i~~~~~ 35 (398)
T PRK10747 26 GYVLIQTDNY 35 (398)
T ss_pred CeEEEEECCE
Confidence 4677777665
No 71
>COG0811 TolQ Biopolymer transport proteins [Intracellular trafficking and secretion]
Probab=23.56 E-value=68 Score=31.31 Aligned_cols=24 Identities=25% Similarity=0.451 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhcc
Q 011630 244 LLIVVLVLFAVIAAIFIWNTCWGR 267 (481)
Q Consensus 244 ll~~~~~lfa~vaa~~iWn~~~~~ 267 (481)
|+.-+++||+++.|+++||++.++
T Consensus 167 L~aTA~GL~vAIPAvi~yn~l~r~ 190 (216)
T COG0811 167 LIATAIGLFVAIPAVVAYNVLRRK 190 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566789999999999999998443
No 72
>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=23.53 E-value=53 Score=33.79 Aligned_cols=70 Identities=16% Similarity=0.274 Sum_probs=35.3
Q ss_pred ccccceecccccccccccCCcchhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhhhc
Q 011630 194 QNQAVTTITQEDDYSFRKNFPKPVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTCWG 266 (481)
Q Consensus 194 ~~~avt~l~~~~~~~~~~~~p~~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~ 266 (481)
|=..|++..+ +|.-++.+=..++=++.+++++|+.+|.+-.+--|+.+.. +-+++|.+.+.+++-.+||.
T Consensus 182 HCrKvSSVG~--~faRkR~i~f~llgllfliiaigltvGT~~~A~~~~giY~-~wv~~~l~a~~~~~rs~yy~ 251 (256)
T PF09788_consen 182 HCRKVSSVGP--RFARKRAIIFFLLGLLFLIIAIGLTVGTWTYAKTYGGIYV-SWVGLFLIALICLIRSIYYC 251 (256)
T ss_pred CCceeccccc--hHhhhHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcEeH-HHHHHHHHHHHHHHHhheeE
Confidence 3445555544 3444433333344444455566677777666555554443 33344444443555566664
No 73
>PHA03049 IMV membrane protein; Provisional
Probab=23.33 E-value=89 Score=26.42 Aligned_cols=24 Identities=8% Similarity=0.382 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHhhhhhhccccc
Q 011630 247 VVLVLFAVIAAIFIWNTCWGRKAI 270 (481)
Q Consensus 247 ~~~~lfa~vaa~~iWn~~~~~r~l 270 (481)
+++++.++++++++|.+|.++++.
T Consensus 6 ~l~iICVaIi~lIvYgiYnkk~~~ 29 (68)
T PHA03049 6 ILVIICVVIIGLIVYGIYNKKTTT 29 (68)
T ss_pred HHHHHHHHHHHHHHHHHHhccccc
Confidence 345566778888999988665543
No 74
>PRK09110 flagellar motor protein MotA; Validated
Probab=23.30 E-value=68 Score=33.00 Aligned_cols=40 Identities=13% Similarity=0.009 Sum_probs=28.4
Q ss_pred eeeeeechhHHHHHHHHHHHHHHHHhhhhhhc-cccccccc
Q 011630 235 ILGAVHNPILLIVVLVLFAVIAAIFIWNTCWG-RKAITDFI 274 (481)
Q Consensus 235 ~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~-~r~l~Rfl 274 (481)
+.+-+|=+.+|||+++-+++++..+-++.... -+.+.+-|
T Consensus 25 ~~~l~~~~~~lIV~Ggtlga~lv~~p~~~i~~~~k~~~~~f 65 (283)
T PRK09110 25 LGALIQPAELLIIGGAALGAFIVGNPGKAIKATLKALPKLF 65 (283)
T ss_pred hhHhhchhHHHHHHHhHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence 34448888999999999999988888876643 33343333
No 75
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.22 E-value=1e+02 Score=32.02 Aligned_cols=19 Identities=26% Similarity=0.155 Sum_probs=15.0
Q ss_pred CCccccCCCCCEEEEEEEE
Q 011630 279 DTDLRTAKSGQFVKVTGVV 297 (481)
Q Consensus 279 ds~Lrs~~dGq~VKItGvV 297 (481)
-.+...+..|..|++.|+.
T Consensus 47 f~~~~GL~~gs~V~~~GV~ 65 (359)
T COG1463 47 FDDAGGLYVGSPVRYRGVK 65 (359)
T ss_pred ecccccCCCCCceEEcCEE
Confidence 3466778999999999864
No 76
>PRK01844 hypothetical protein; Provisional
Probab=22.94 E-value=45 Score=28.39 Aligned_cols=16 Identities=44% Similarity=0.831 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHhhhe
Q 011630 218 LWLVILIFVMGFIAGG 233 (481)
Q Consensus 218 ~~~~~~~~~~g~~~g~ 233 (481)
+|..|+|.+++|++|+
T Consensus 3 ~~~~I~l~I~~li~G~ 18 (72)
T PRK01844 3 IWLGILVGVVALVAGV 18 (72)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5777777777777765
No 77
>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=22.66 E-value=71 Score=32.82 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=29.9
Q ss_pred HHHHHHHhhheeee------eeeechhHHHHHHHHHHHHHHHHhhhhhh
Q 011630 223 LIFVMGFIAGGFIL------GAVHNPILLIVVLVLFAVIAAIFIWNTCW 265 (481)
Q Consensus 223 ~~~~~g~~~g~f~l------~av~~~~ll~~~~~lfa~vaa~~iWn~~~ 265 (481)
++++.|+++++|++ .-++=+.++||+++-+++++..+-++..+
T Consensus 7 li~~~~~v~~g~~l~Gg~~~~l~~~~~~lIV~Ggtlga~lis~p~~~~~ 55 (282)
T TIGR03818 7 LVVVLGCVFGGYLLAGGHLAALWQPAELLIIGGAAIGAFIIANPPKVLK 55 (282)
T ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence 34444444444444 34778889999999999998888886664
No 78
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=22.50 E-value=64 Score=30.59 Aligned_cols=32 Identities=9% Similarity=0.122 Sum_probs=15.4
Q ss_pred CcchhHHHHHHHHHHHHhhheeeeeeeechhH
Q 011630 213 FPKPVLWLVILIFVMGFIAGGFILGAVHNPIL 244 (481)
Q Consensus 213 ~p~~~~~~~~~~~~~g~~~g~f~l~av~~~~l 244 (481)
+-+.+.|.++.++++.++.-..+++.-++.++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 35 (199)
T PF10112_consen 4 IIRFIFRWILGVLIAAITFLVSFFGFDHSFLL 35 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 34556666666555544433333334444433
No 79
>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=21.91 E-value=2.1e+02 Score=28.85 Aligned_cols=43 Identities=12% Similarity=0.177 Sum_probs=32.3
Q ss_pred ccccCCCCCEEEEEEEEEeCCcccccccCCCCceEEEEEEEEEe
Q 011630 281 DLRTAKSGQFVKVTGVVTCGNVPLESSFRRVPRCVYTSTSLYEY 324 (481)
Q Consensus 281 ~Lrs~~dGq~VKItGvVtCG~~PL~Aplsk~~rCVYYst~L~EY 324 (481)
++.=-.+|..++++|-+-- +.-|.=|+++.|=||--...++++
T Consensus 159 ~v~i~~~~~~~~~~allDT-GN~L~DPitg~PV~Vve~~~~~~~ 201 (293)
T PF03419_consen 159 PVTIEIGGKKIELKALLDT-GNQLRDPITGRPVIVVEYEALEKL 201 (293)
T ss_pred EEEEEECCEEEEEEEEEEC-CCcccCCCCCCcEEEEEHHHHHhh
Confidence 3444567789999999999 556899999997777666655555
No 80
>PRK06743 flagellar motor protein MotP; Reviewed
Probab=21.75 E-value=64 Score=32.74 Aligned_cols=28 Identities=18% Similarity=0.138 Sum_probs=23.8
Q ss_pred eechhHHHHHHHHHHHHHHHHhhhhhhc
Q 011630 239 VHNPILLIVVLVLFAVIAAIFIWNTCWG 266 (481)
Q Consensus 239 v~~~~ll~~~~~lfa~vaa~~iWn~~~~ 266 (481)
||=+.++||+++-++++...+-++..+.
T Consensus 28 ~~~~~~lIV~GGt~ga~li~~p~~~i~~ 55 (254)
T PRK06743 28 LDVSSILIVIGGTTATIVVAYRFGEIKK 55 (254)
T ss_pred hCHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 7888999999999999998888877643
No 81
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=21.49 E-value=42 Score=33.73 Aligned_cols=17 Identities=35% Similarity=0.233 Sum_probs=9.1
Q ss_pred echhHHHHHHHHHHHHH
Q 011630 240 HNPILLIVVLVLFAVIA 256 (481)
Q Consensus 240 ~~~~ll~~~~~lfa~va 256 (481)
+.|+.|++++.++++++
T Consensus 4 ~~~~~~~~~~~~~~~~~ 20 (331)
T PRK03598 4 KVVIGLAVVVLAAAVAG 20 (331)
T ss_pred eEEEEhHHHHHHHHHHH
Confidence 34666665555554444
No 82
>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=21.31 E-value=76 Score=26.83 Aligned_cols=31 Identities=13% Similarity=-0.025 Sum_probs=16.9
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhcccccccc
Q 011630 242 PILLIVVLVLFAVIAAIFIWNTCWGRKAITDF 273 (481)
Q Consensus 242 ~~ll~~~~~lfa~vaa~~iWn~~~~~r~l~Rf 273 (481)
|..+-++.+++..++ .++-|.||..++-+|.
T Consensus 33 W~aIGvi~gi~~~~l-t~ltN~YFK~k~drr~ 63 (68)
T PF04971_consen 33 WAAIGVIGGIFFGLL-TYLTNLYFKIKEDRRK 63 (68)
T ss_pred chhHHHHHHHHHHHH-HHHhHhhhhhhHhhhH
Confidence 444444444443333 4555999887665554
No 83
>PRK08124 flagellar motor protein MotA; Validated
Probab=21.17 E-value=80 Score=31.91 Aligned_cols=31 Identities=13% Similarity=0.178 Sum_probs=24.3
Q ss_pred eeeeeechhHHHHHHHHHHHHHHHHhhhhhh
Q 011630 235 ILGAVHNPILLIVVLVLFAVIAAIFIWNTCW 265 (481)
Q Consensus 235 ~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~ 265 (481)
+..-||=+.+|+|+++-+++++..+-++..+
T Consensus 27 ~~~~~~~~~~lIV~Ggt~~a~~i~~~~~~~~ 57 (263)
T PRK08124 27 LAVLLNPAAILIIIVGTIAAVMIAFPMSELK 57 (263)
T ss_pred hHHHhhHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence 3344788889999999999998888886654
No 84
>PF04304 DUF454: Protein of unknown function (DUF454); InterPro: IPR007401 This is a predicted membrane protein.
Probab=21.08 E-value=1.3e+02 Score=24.07 Aligned_cols=45 Identities=16% Similarity=0.304 Sum_probs=28.7
Q ss_pred cccccCCcchhHHHHHHHHHHHHhhheeeeeeeechhHHHHHHHHHH
Q 011630 207 YSFRKNFPKPVLWLVILIFVMGFIAGGFILGAVHNPILLIVVLVLFA 253 (481)
Q Consensus 207 ~~~~~~~p~~~~~~~~~~~~~g~~~g~f~l~av~~~~ll~~~~~lfa 253 (481)
|.-++.+|+..=+..++.....++..+|++ +.+..+.++++++.+
T Consensus 18 w~~~r~i~~k~K~~a~~~m~~~~~~s~~~~--~~~~~~~~~l~~~~~ 62 (71)
T PF04304_consen 18 WEEHRGIPRKAKIRALLMMWLSMGISAFFF--VPNLWVRIVLAAILL 62 (71)
T ss_pred HHHCCCcCHHHHHHHHHHHHHHHHHHHHHH--ccHHHHHHHHHHHHH
Confidence 666788999888877777777777665553 345444444444443
No 85
>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=20.82 E-value=82 Score=31.59 Aligned_cols=33 Identities=24% Similarity=0.566 Sum_probs=21.2
Q ss_pred ceecccccccccccCCcchhHHHHHHHHHHHHhhheeeeeee
Q 011630 198 VTTITQEDDYSFRKNFPKPVLWLVILIFVMGFIAGGFILGAV 239 (481)
Q Consensus 198 vt~l~~~~~~~~~~~~p~~~~~~~~~~~~~g~~~g~f~l~av 239 (481)
||++|++.-.+ . |...-+|..|+.+|+|++++.
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 77877773322 2 344567777888888776553
No 86
>PRK07118 ferredoxin; Validated
Probab=20.78 E-value=39 Score=34.38 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHHHHhhheeeeeeeec
Q 011630 216 PVLWLVILIFVMGFIAGGFILGAVHN 241 (481)
Q Consensus 216 ~~~~~~~~~~~~g~~~g~f~l~av~~ 241 (481)
.|++++++|.++||++|.++..|-+.
T Consensus 3 ~i~~~~~~~~~~g~~~g~~l~~a~~~ 28 (280)
T PRK07118 3 MILFAVLSLGALGLVFGILLAFASKK 28 (280)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHeee
Confidence 47899999999999999887666553
No 87
>PF06609 TRI12: Fungal trichothecene efflux pump (TRI12); InterPro: IPR010573 This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster. It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes [].
Probab=20.52 E-value=95 Score=35.17 Aligned_cols=58 Identities=16% Similarity=0.449 Sum_probs=39.3
Q ss_pred HHHHHHHHHH-------HhhheeeeeeeechhHHHHHHHHHHHHHHHHhhhhhhc-ccc-c-cccccc
Q 011630 219 WLVILIFVMG-------FIAGGFILGAVHNPILLIVVLVLFAVIAAIFIWNTCWG-RKA-I-TDFISC 276 (481)
Q Consensus 219 ~~~~~~~~~g-------~~~g~f~l~av~~~~ll~~~~~lfa~vaa~~iWn~~~~-~r~-l-~Rfl~r 276 (481)
|+=++||+.| |-.|+-----|+++-++.-++..+++++++.+|-.|.. +.- + .|.+++
T Consensus 241 ~IG~~L~~~Gl~LfLlgl~wgG~~~~~W~Sa~VIa~lviG~~~Lv~F~~wE~~~~~~~Pl~P~~Lf~~ 308 (599)
T PF06609_consen 241 WIGIFLFIAGLALFLLGLSWGGYPYYPWKSAHVIAPLVIGFVLLVAFVVWEWFGAPKDPLFPHRLFKD 308 (599)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCCCCCCccchhhHHHHHHHHHHHHHhhhhccCCCCcCCHHHhcc
Confidence 5555555555 44444433468999999999999999999999977644 333 3 555553
No 88
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=20.35 E-value=4.1e+02 Score=30.19 Aligned_cols=29 Identities=34% Similarity=0.471 Sum_probs=21.8
Q ss_pred eeeecCCCEEEEEEEEEecCceeeEeCCC
Q 011630 417 EGYIKEGSTVSVMGIVQRNDNVLMIVPPP 445 (481)
Q Consensus 417 EgiI~eGs~VsViGvv~r~~~vlmI~pP~ 445 (481)
+..+++|+++.|-|.++...+.+-|..|.
T Consensus 105 ~~~l~~G~~~~v~Gkv~~~~~~~qm~~P~ 133 (681)
T PRK10917 105 KKQLKVGKRVAVYGKVKRGKYGLEMVHPE 133 (681)
T ss_pred HhhCCCCCEEEEEEEEEecCCeEEEEcCE
Confidence 34578999999999998876655555553
No 89
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.26 E-value=51 Score=30.31 Aligned_cols=16 Identities=38% Similarity=0.870 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHhhhee
Q 011630 219 WLVILIFVMGFIAGGF 234 (481)
Q Consensus 219 ~~~~~~~~~g~~~g~f 234 (481)
|-+|++..+||+||.|
T Consensus 75 wglIv~lllGf~AG~l 90 (116)
T COG5336 75 WGLIVFLLLGFGAGVL 90 (116)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5566666666666544
No 90
>PRK12482 flagellar motor protein MotA; Provisional
Probab=20.10 E-value=79 Score=32.71 Aligned_cols=44 Identities=16% Similarity=0.181 Sum_probs=30.7
Q ss_pred HHHHHHHHhhheeee------eeeechhHHHHHHHHHHHHHHHHhhhhhh
Q 011630 222 ILIFVMGFIAGGFIL------GAVHNPILLIVVLVLFAVIAAIFIWNTCW 265 (481)
Q Consensus 222 ~~~~~~g~~~g~f~l------~av~~~~ll~~~~~lfa~vaa~~iWn~~~ 265 (481)
-+++++|+++++|++ .-+|=+.++||+++-+++++..+-|+...
T Consensus 6 Glv~~~~~v~~g~~l~Gg~~~~~~~~~~~lIV~GGt~ga~lis~p~~~~~ 55 (287)
T PRK12482 6 GLLVVMGCVFGGYLMSGGSLSSIWQPGEIIIILGAGIGAMILGNPKSVLK 55 (287)
T ss_pred HHHHHHHHHHHHHHHhCCChHHHHhHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence 344455555555544 33777889999999999998888886664
Done!