Query 034024
Match_columns 106
No_of_seqs 12 out of 14
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 08:56:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034024.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034024hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12273 RCR: Chitin synthesis 85.8 0.61 1.3E-05 32.7 2.1 25 65-89 1-25 (130)
2 PF15099 PIRT: Phosphoinositid 74.8 2.9 6.3E-05 31.6 2.6 35 50-84 59-98 (129)
3 PF05393 Hum_adeno_E3A: Human 70.5 6.8 0.00015 28.4 3.5 26 67-99 38-63 (94)
4 PF11044 TMEMspv1-c74-12: Plec 69.4 15 0.00032 23.9 4.5 20 68-87 7-26 (49)
5 TIGR01129 secD protein-export 67.8 25 0.00053 29.5 6.8 30 39-68 244-273 (397)
6 PF03554 Herpes_UL73: UL73 vir 67.4 6.5 0.00014 27.3 2.8 21 46-67 51-71 (82)
7 PRK10755 sensor protein BasS/P 66.3 33 0.00072 25.8 6.6 21 46-66 9-29 (356)
8 PF10323 7TM_GPCR_Srv: Serpent 65.0 36 0.00078 26.4 6.8 48 42-102 166-213 (283)
9 PF12273 RCR: Chitin synthesis 57.2 10 0.00023 26.5 2.4 20 70-89 3-22 (130)
10 COG5232 SEC62 Preprotein trans 55.9 33 0.00072 28.6 5.4 26 28-58 144-169 (259)
11 PF11696 DUF3292: Protein of u 55.7 38 0.00083 31.2 6.2 35 26-60 303-338 (642)
12 KOG0033 Ca2+/calmodulin-depend 54.2 4.1 9E-05 34.9 -0.0 38 1-38 279-316 (355)
13 PRK05812 secD preprotein trans 54.0 89 0.0019 27.3 8.0 36 36-71 326-361 (498)
14 PF11120 DUF2636: Protein of u 53.9 45 0.00097 22.3 4.9 33 71-103 9-41 (62)
15 PRK11176 lipid transporter ATP 52.6 1.1E+02 0.0025 25.4 8.1 21 58-78 156-176 (582)
16 PRK13024 bifunctional preprote 51.3 1.2E+02 0.0026 27.6 8.6 47 21-72 560-607 (755)
17 PF07264 EI24: Etoposide-induc 50.9 90 0.002 22.4 7.4 34 66-100 162-195 (219)
18 PF14851 FAM176: FAM176 family 50.7 51 0.0011 25.1 5.3 19 70-88 26-44 (153)
19 COG4965 TadB Flp pilus assembl 49.4 1.1E+02 0.0024 25.7 7.6 50 36-85 74-123 (309)
20 KOG1583 UDP-N-acetylglucosamin 48.9 26 0.00057 30.1 3.9 61 39-99 158-229 (330)
21 PF02932 Neur_chan_memb: Neuro 48.5 58 0.0013 20.9 4.6 49 25-74 14-68 (237)
22 PHA03156 hypothetical protein; 48.2 16 0.00034 26.3 2.1 23 44-67 57-79 (90)
23 PRK08343 secD preprotein trans 46.4 82 0.0018 26.9 6.4 35 38-72 256-290 (417)
24 TIGR03424 urea_degr_1 urea car 46.3 14 0.00031 28.6 1.8 28 4-31 115-142 (198)
25 PF06305 DUF1049: Protein of u 45.2 70 0.0015 19.4 5.1 11 80-90 40-50 (68)
26 PF06799 DUF1230: Protein of u 44.7 95 0.0021 23.6 6.0 59 27-86 21-83 (144)
27 PF07010 Endomucin: Endomucin; 43.8 39 0.00085 28.2 4.1 25 40-64 188-212 (259)
28 PRK11174 cysteine/glutathione 43.8 1.9E+02 0.0042 24.1 8.1 28 58-85 154-181 (588)
29 PF09435 DUF2015: Fungal prote 42.7 47 0.001 25.0 4.0 25 46-71 5-29 (128)
30 PF12729 4HB_MCP_1: Four helix 42.0 51 0.0011 21.3 3.7 22 42-63 7-28 (181)
31 PF02355 SecD_SecF: Protein ex 41.8 76 0.0017 23.9 5.1 29 38-66 26-54 (189)
32 cd02865 Heme_Cu_Oxidase_III_2 41.7 1.4E+02 0.003 21.8 7.8 66 32-97 4-77 (184)
33 PRK13743 conjugal transfer pro 41.4 37 0.0008 26.2 3.3 22 65-86 39-60 (141)
34 cd02863 Ubiquinol_oxidase_III 41.3 1.5E+02 0.0032 22.0 7.7 67 32-98 4-79 (186)
35 PRK13023 bifunctional preprote 40.9 2E+02 0.0044 26.7 8.5 34 39-72 574-608 (758)
36 PF10960 DUF2762: Protein of u 40.7 21 0.00046 23.9 1.8 11 46-56 14-24 (71)
37 PF11045 YbjM: Putative inner 40.6 1E+02 0.0022 23.1 5.5 29 68-96 96-125 (125)
38 COG0341 SecF Preprotein transl 40.4 48 0.001 27.4 4.1 39 25-68 121-159 (305)
39 PHA03163 hypothetical protein; 40.3 26 0.00056 25.3 2.2 23 44-67 58-80 (92)
40 PF10281 Ish1: Putative stress 39.8 23 0.00049 20.3 1.6 12 3-14 26-37 (38)
41 PF10066 DUF2304: Uncharacteri 39.2 1.3E+02 0.0028 20.8 8.3 55 39-93 28-95 (115)
42 PF14163 SieB: Superinfection 39.0 1.4E+02 0.003 21.1 6.8 22 61-83 30-51 (151)
43 PF02932 Neur_chan_memb: Neuro 38.6 1E+02 0.0022 19.8 4.6 26 39-64 57-82 (237)
44 PF00664 ABC_membrane: ABC tra 38.3 1.2E+02 0.0026 20.3 8.4 40 56-95 130-170 (275)
45 cd00386 Heme_Cu_Oxidase_III_li 37.4 1.5E+02 0.0033 21.2 8.5 31 33-63 5-35 (183)
46 PRK10774 cell division protein 36.3 1E+02 0.0023 25.9 5.6 32 58-89 291-322 (404)
47 PF06072 Herpes_US9: Alphaherp 36.1 33 0.00071 23.1 2.1 18 84-101 16-33 (60)
48 PF09347 DUF1989: Domain of un 35.2 23 0.00049 26.6 1.4 28 4-31 109-136 (166)
49 PRK13024 bifunctional preprote 35.1 1.6E+02 0.0034 27.0 6.8 32 39-70 262-293 (755)
50 TIGR01193 bacteriocin_ABC ABC- 34.9 3E+02 0.0065 23.8 8.7 26 60-85 288-313 (708)
51 TIGR00916 2A0604s01 protein-ex 34.9 1.9E+02 0.0041 21.5 7.1 27 40-66 44-70 (192)
52 TIGR02203 MsbA_lipidA lipid A 34.1 2.7E+02 0.0058 23.0 9.6 31 56-86 143-173 (571)
53 PF10328 7TM_GPCR_Srx: Serpent 34.0 1.3E+02 0.0028 22.6 5.2 11 91-101 199-209 (274)
54 PRK13022 secF preprotein trans 33.7 2.5E+02 0.0054 22.4 8.9 27 39-65 123-149 (289)
55 PF10176 DUF2370: Protein of u 33.4 70 0.0015 25.9 3.9 18 66-83 193-210 (233)
56 PF02699 YajC: Preprotein tran 33.1 1.1E+02 0.0025 20.2 4.4 10 91-100 24-33 (82)
57 PF07172 GRP: Glycine rich pro 32.5 60 0.0013 22.6 3.0 11 76-86 13-23 (95)
58 TIGR00966 3a0501s07 protein-ex 32.2 2.3E+02 0.0051 21.7 8.9 32 38-70 93-124 (246)
59 PF08222 HTH_CodY: CodY helix- 31.6 39 0.00085 22.9 1.9 15 1-15 15-29 (61)
60 PTZ00265 multidrug resistance 31.5 4.7E+02 0.01 25.8 9.6 36 54-89 184-219 (1466)
61 PF08355 EF_assoc_1: EF hand a 31.3 9.3 0.0002 25.8 -1.1 17 82-98 59-75 (76)
62 PLN00084 photosystem II subuni 31.1 79 0.0017 25.7 3.9 23 7-30 19-41 (214)
63 PRK12933 secD preprotein trans 31.1 2.6E+02 0.0056 25.6 7.5 48 23-70 420-467 (604)
64 PRK12468 flhB flagellar biosyn 30.9 3.4E+02 0.0073 23.1 7.8 11 83-93 219-229 (386)
65 PF12307 DUF3631: Protein of u 29.9 26 0.00056 27.3 0.9 19 2-20 143-161 (184)
66 PRK14726 bifunctional preprote 29.9 2.1E+02 0.0046 27.0 6.9 39 38-79 367-405 (855)
67 PHA02819 hypothetical protein; 29.9 1.4E+02 0.0031 20.6 4.5 27 29-55 35-62 (71)
68 PRK11371 hypothetical protein; 28.8 1.3E+02 0.0028 22.7 4.5 60 25-89 2-62 (126)
69 PF11808 DUF3329: Domain of un 28.4 1.9E+02 0.004 19.3 6.8 39 52-93 14-52 (90)
70 PF12270 Cyt_c_ox_IV: Cytochro 28.1 2.6E+02 0.0057 21.0 6.3 27 24-55 80-106 (137)
71 PRK05702 flhB flagellar biosyn 27.9 2.2E+02 0.0047 23.9 6.1 11 83-93 219-229 (359)
72 PF11241 DUF3043: Protein of u 27.8 2.9E+02 0.0063 21.4 8.1 35 57-91 97-131 (170)
73 PF08006 DUF1700: Protein of u 27.5 2.4E+02 0.0052 20.3 8.2 13 7-19 56-69 (181)
74 PF04387 PTPLA: Protein tyrosi 27.4 1.3E+02 0.0029 22.3 4.3 32 66-97 132-163 (164)
75 COG3326 Predicted membrane pro 27.3 1.2E+02 0.0025 21.9 3.8 25 74-100 13-37 (94)
76 PF15086 UPF0542: Uncharacteri 27.1 1.7E+02 0.0038 20.4 4.5 14 86-99 48-61 (74)
77 PRK11246 hypothetical protein; 26.5 93 0.002 25.2 3.5 24 60-83 4-27 (218)
78 PF11694 DUF3290: Protein of u 26.4 2.8E+02 0.006 20.7 8.7 33 60-92 34-71 (149)
79 PF09594 DUF2029: Protein of u 26.3 1.2E+02 0.0027 21.3 3.8 34 47-80 76-109 (241)
80 PF06422 PDR_CDR: CDR ABC tran 26.2 97 0.0021 21.2 3.2 23 44-66 53-75 (103)
81 TIGR01404 FlhB_rel_III type II 25.9 2.5E+02 0.0055 23.3 6.1 12 83-94 211-222 (342)
82 PF10268 Tmemb_161AB: Predicte 25.8 2.3E+02 0.005 25.1 6.1 28 38-65 130-160 (486)
83 PRK04307 putative disulfide ox 25.6 1.8E+02 0.0039 23.1 5.0 22 46-67 25-47 (218)
84 PRK15127 multidrug efflux syst 25.1 5E+02 0.011 24.4 8.3 32 42-73 337-368 (1049)
85 TIGR00077 lspA lipoprotein sig 24.9 2.4E+02 0.0052 20.9 5.3 14 17-30 51-65 (166)
86 TIGR03796 NHPM_micro_ABC1 NHPM 24.8 4.6E+02 0.0099 22.7 9.1 17 61-77 287-303 (710)
87 PRK10663 cytochrome o ubiquino 24.7 3.2E+02 0.0068 20.8 7.4 58 39-98 27-95 (204)
88 PLN02838 3-hydroxyacyl-CoA deh 24.5 1.4E+02 0.003 23.7 4.2 21 78-98 199-219 (221)
89 TIGR00328 flhB flagellar biosy 24.5 2.8E+02 0.006 23.2 6.1 11 83-93 212-222 (347)
90 PRK09759 small toxic polypepti 24.5 66 0.0014 20.6 1.9 19 66-84 5-23 (50)
91 PRK09776 putative diguanylate 24.2 2E+02 0.0044 25.2 5.4 35 68-103 140-174 (1092)
92 PF10032 Pho88: Phosphate tran 24.2 1.7E+02 0.0038 22.7 4.6 30 60-89 28-57 (192)
93 COG0586 DedA Uncharacterized m 24.1 3.2E+02 0.0069 20.6 7.8 17 39-55 145-161 (208)
94 PF11511 RhodobacterPufX: Intr 23.5 1.3E+02 0.0028 20.6 3.3 26 38-63 17-46 (67)
95 PF15192 TMEM213: TMEM213 fami 23.5 1.1E+02 0.0025 21.7 3.1 18 41-58 48-65 (82)
96 PF02009 Rifin_STEVOR: Rifin/s 23.5 2.4E+02 0.0053 23.3 5.5 42 56-97 248-289 (299)
97 KOG1746 Defender against cell 23.4 96 0.0021 23.2 2.9 19 68-86 58-77 (115)
98 PRK09738 small toxic polypepti 23.2 64 0.0014 20.9 1.7 19 66-84 7-25 (52)
99 COG1377 FlhB Flagellar biosynt 22.8 1.9E+02 0.0041 24.9 4.9 12 83-94 219-230 (363)
100 KOG4050 Glutamate transporter 22.8 2.8E+02 0.006 22.3 5.5 30 56-85 115-144 (188)
101 PRK09108 type III secretion sy 22.8 3.1E+02 0.0068 22.9 6.1 11 83-93 214-224 (353)
102 COG3887 Predicted signaling pr 22.6 4.5E+02 0.0097 24.8 7.4 44 45-88 12-55 (655)
103 PRK14776 lipoprotein signal pe 22.6 2.2E+02 0.0048 21.4 4.8 15 16-30 49-64 (170)
104 PRK14413 membrane protein; Pro 22.5 3.7E+02 0.008 20.8 6.3 38 36-73 114-151 (197)
105 PF13268 DUF4059: Protein of u 22.0 1.7E+02 0.0038 20.2 3.7 31 59-89 5-35 (72)
106 PRK08156 type III secretion sy 21.9 3.3E+02 0.0071 23.1 6.1 11 83-93 207-217 (361)
107 TIGR02868 CydC thiol reductant 21.7 4.6E+02 0.01 21.6 7.2 13 64-76 150-162 (529)
108 PF15339 Afaf: Acrosome format 21.0 1.4E+02 0.003 24.2 3.5 18 46-63 139-156 (200)
109 TIGR03425 urea_degr_2 urea car 20.9 71 0.0015 25.6 1.9 28 4-31 120-147 (233)
110 PF11840 DUF3360: Protein of u 20.8 86 0.0019 28.3 2.6 30 68-105 206-235 (492)
111 TIGR01652 ATPase-Plipid phosph 20.8 3.7E+02 0.008 25.1 6.6 19 66-84 1021-1039(1057)
112 PRK14412 membrane protein; Pro 20.8 4.1E+02 0.0088 20.6 6.4 38 36-73 106-143 (198)
113 PF05875 Ceramidase: Ceramidas 20.7 3.1E+02 0.0068 20.9 5.3 50 51-100 119-173 (262)
114 KOG0812 SNARE protein SED5/Syn 20.7 1.1E+02 0.0024 26.2 3.1 26 32-57 283-309 (311)
115 PF12583 TPPII_N: Tripeptidyl 20.6 57 0.0012 25.0 1.2 12 7-18 75-86 (139)
116 PF07782 DC_STAMP: DC-STAMP-li 20.6 2.3E+02 0.0049 21.0 4.4 36 30-69 137-172 (191)
117 PRK13592 ubiA prenyltransferas 20.5 3.6E+02 0.0077 22.6 5.9 35 56-90 231-266 (299)
118 COG0342 SecD Preprotein transl 20.4 5.4E+02 0.012 22.7 7.2 30 40-69 340-369 (506)
119 PRK14726 bifunctional preprote 20.1 7.6E+02 0.016 23.5 8.6 34 38-71 667-701 (855)
No 1
>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=85.81 E-value=0.61 Score=32.70 Aligned_cols=25 Identities=32% Similarity=0.526 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 65 RHMRLAIILVSITMLLLLCMKVTKQ 89 (106)
Q Consensus 65 r~~~Ls~~~ic~~ilL~~~lkitrq 89 (106)
||.-++++++++-|++.+++.++|.
T Consensus 1 RW~l~~iii~~i~l~~~~~~~~~rR 25 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLFYCHNRR 25 (130)
T ss_pred CeeeHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666667777777766554
No 2
>PF15099 PIRT: Phosphoinositide-interacting protein family
Probab=74.82 E-value=2.9 Score=31.56 Aligned_cols=35 Identities=29% Similarity=0.517 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHH
Q 034024 50 VILAFLVFSAVSLYFR-----HMRLAIILVSITMLLLLCM 84 (106)
Q Consensus 50 lf~~l~v~s~vtlYfr-----~~~Ls~~~ic~~ilL~~~l 84 (106)
+++|=++-++++.-|. .=-++-+++|.|.+|++|=
T Consensus 59 ili~GvvvT~vays~n~~~si~~~~G~vlLs~GLmlL~~~ 98 (129)
T PF15099_consen 59 ILIAGVVVTAVAYSFNSHGSIISIFGPVLLSLGLMLLACS 98 (129)
T ss_pred HHHHhhHhheeeEeecCCcchhhhehHHHHHHHHHHHHhh
Confidence 4455566666665543 1123456789999998876
No 3
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=70.53 E-value=6.8 Score=28.38 Aligned_cols=26 Identities=27% Similarity=0.605 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 034024 67 MRLAIILVSITMLLLLCMKVTKQVRLARKKKRR 99 (106)
Q Consensus 67 ~~Ls~~~ic~~ilL~~~lkitrq~rlarkreRr 99 (106)
+-++++|+|+-|+-.+|- +||||-||
T Consensus 38 lvI~~iFil~VilwfvCC-------~kRkrsRr 63 (94)
T PF05393_consen 38 LVICGIFILLVILWFVCC-------KKRKRSRR 63 (94)
T ss_pred HHHHHHHHHHHHHHHHHH-------HHhhhccC
Confidence 344566777777777775 46666666
No 4
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=69.36 E-value=15 Score=23.94 Aligned_cols=20 Identities=0% Similarity=0.233 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034024 68 RLAIILVSITMLLLLCMKVT 87 (106)
Q Consensus 68 ~Ls~~~ic~~ilL~~~lkit 87 (106)
++..+++.+|||++++|-|-
T Consensus 7 ~iFsvvIil~If~~iGl~Iy 26 (49)
T PF11044_consen 7 TIFSVVIILGIFAWIGLSIY 26 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34567778888888888764
No 5
>TIGR01129 secD protein-export membrane protein SecD. SecD from Mycobacterium tuberculosis has a long Pro-rich insert.
Probab=67.81 E-value=25 Score=29.50 Aligned_cols=30 Identities=27% Similarity=0.237 Sum_probs=25.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYFRHMR 68 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYfr~~~ 68 (106)
.|.+-..++++++.+++|+-++.+|||.+.
T Consensus 244 ~~~i~~~~~a~~ig~ilV~l~~~~~yr~~g 273 (397)
T TIGR01129 244 ADSIEAGIKAGLIGLVLVLVFMILYYRLFG 273 (397)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 456667899999999999999999999443
No 6
>PF03554 Herpes_UL73: UL73 viral envelope glycoprotein ; InterPro: IPR005211 This entry represents a conserved region found in a number of viral proteins: BLRF1, U46, 53, and UL73, collectively known as glycoprotein N. These UL73-like envelope glycoproteins, which associate in a high molecular mass complex with their counterpart protein gM, induce neutralizing antibody responses in the host. These glycoproteins are highly polymorphic, particularly in the N-terminal region [].; GO: 0019031 viral envelope
Probab=67.40 E-value=6.5 Score=27.27 Aligned_cols=21 Identities=24% Similarity=0.757 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 034024 46 IWELVILAFLVFSAVSLYFRHM 67 (106)
Q Consensus 46 ~w~llf~~l~v~s~vtlYfr~~ 67 (106)
+|+++= .++++.+-.+|+||.
T Consensus 51 IW~iiN-~~il~~A~~vyLry~ 71 (82)
T PF03554_consen 51 IWAIIN-VVILLCAFCVYLRYL 71 (82)
T ss_pred HHHHHH-HHHHHHHHHHHHHHH
Confidence 788764 445566678899985
No 7
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=66.25 E-value=33 Score=25.82 Aligned_cols=21 Identities=5% Similarity=0.237 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 034024 46 IWELVILAFLVFSAVSLYFRH 66 (106)
Q Consensus 46 ~w~llf~~l~v~s~vtlYfr~ 66 (106)
.|-+++++++.+....+|+.|
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~ 29 (356)
T PRK10755 9 LLTIGLILLVFQLISVFWLWH 29 (356)
T ss_pred HHHHHHHHHHHHHHHHHHhcc
Confidence 344444444545555555544
No 8
>PF10323 7TM_GPCR_Srv: Serpentine type 7TM GPCR chemoreceptor Srv; InterPro: IPR019426 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class v (Srv) from the Srg superfamily [, ]. Srg receptors contain seven hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.
Probab=64.97 E-value=36 Score=26.35 Aligned_cols=48 Identities=17% Similarity=0.188 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 034024 42 VIFVIWELVILAFLVFSAVSLYFRHMRLAIILVSITMLLLLCMKVTKQVRLARKKKRRMLL 102 (106)
Q Consensus 42 vv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq~rlarkreRrllL 102 (106)
.++.+...++|...+.+|..++... |-..= +-+++....+|||.|+..
T Consensus 166 ~~~~~~~~~~cv~~iv~Y~~i~~~i-Rk~~k------------~~s~~~s~~~~rE~~L~~ 213 (283)
T PF10323_consen 166 LIAFIFVSVTCVICIVCYGIIFIFI-RKRNK------------KKSKSSSRSRRREIRLAI 213 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHhhh------------hhhHhhhhhhhHhHHHHH
Confidence 3455556666666666666555321 11100 566677888999998754
No 9
>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=57.19 E-value=10 Score=26.48 Aligned_cols=20 Identities=15% Similarity=0.247 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034024 70 AIILVSITMLLLLCMKVTKQ 89 (106)
Q Consensus 70 s~~~ic~~ilL~~~lkitrq 89 (106)
++++++|.+++.+.+=+...
T Consensus 3 ~l~~iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFYCH 22 (130)
T ss_pred eeHHHHHHHHHHHHHHHHHH
Confidence 34556666666666666555
No 10
>COG5232 SEC62 Preprotein translocase subunit Sec62 [Intracellular trafficking and secretion]
Probab=55.86 E-value=33 Score=28.56 Aligned_cols=26 Identities=38% Similarity=0.687 Sum_probs=21.2
Q ss_pred ecCCCCCCcchhHHHHHHHHHHHHHHHHHHH
Q 034024 28 FSSTSNISSSRVDVVIFVIWELVILAFLVFS 58 (106)
Q Consensus 28 fS~~~~~~~sr~dvvv~v~w~llf~~l~v~s 58 (106)
.-|+|++ |.++++.++++.+|++.|-
T Consensus 144 yep~~~~-----~~~l~~~fvlv~lalVlfp 169 (259)
T COG5232 144 YEPTSNI-----SLVLCGVFVLVTLALVLFP 169 (259)
T ss_pred cCCCccc-----hhhHHHHHHHHHHHHHHHh
Confidence 3566777 8999999999999998864
No 11
>PF11696 DUF3292: Protein of unknown function (DUF3292); InterPro: IPR021709 This eukaryotic family of proteins has no known function.
Probab=55.70 E-value=38 Score=31.20 Aligned_cols=35 Identities=14% Similarity=0.199 Sum_probs=20.2
Q ss_pred eeecCCCCCCcchhHHHH-HHHHHHHHHHHHHHHHH
Q 034024 26 SFFSSTSNISSSRVDVVI-FVIWELVILAFLVFSAV 60 (106)
Q Consensus 26 s~fS~~~~~~~sr~dvvv-~v~w~llf~~l~v~s~v 60 (106)
+.+||||+.+...--.-+ +++--+++..++++|||
T Consensus 303 NaLSPTpPFp~~~~RlRLa~~l~p~~l~Sl~~ssy~ 338 (642)
T PF11696_consen 303 NALSPTPPFPRHTPRLRLAAILAPLLLASLFVSSYM 338 (642)
T ss_pred hccCCCCCCCCccHHHHHHHHHHHHHHHHHHhhHHH
Confidence 578999998754333333 33444444555566655
No 12
>KOG0033 consensus Ca2+/calmodulin-dependent protein kinase, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=54.23 E-value=4.1 Score=34.94 Aligned_cols=38 Identities=24% Similarity=0.351 Sum_probs=29.7
Q ss_pred CcchhHHHHHHHHHhhhhhcccceeeeecCCCCCCcch
Q 034024 1 MITRSNLAEQLREYQNRSKHEWASVSFFSSTSNISSSR 38 (106)
Q Consensus 1 mITRskLvEQLReyQiRs~h~~aals~fS~~~~~~~sr 38 (106)
||-|+.-|||||.|..|.|-+=|-++.-+++.+.+++.
T Consensus 279 ~~H~~dtvd~lrkfNarRKLKgavLtav~s~r~~s~~~ 316 (355)
T KOG0033|consen 279 AIHRQDTVDCLKKFNARRKLKGAILTTVIATRNLSTTP 316 (355)
T ss_pred HhhhHHHHHHHHHhhHHHHHHHHHHHHHHhccccccCC
Confidence 46788999999999999999987777666655554443
No 13
>PRK05812 secD preprotein translocase subunit SecD; Reviewed
Probab=54.03 E-value=89 Score=27.30 Aligned_cols=36 Identities=25% Similarity=0.187 Sum_probs=29.3
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 36 SSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAI 71 (106)
Q Consensus 36 ~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~ 71 (106)
+=..|.+=..++++++.+++|+-||.+|||.+.+..
T Consensus 326 slG~~~i~~~~~A~lig~ilV~i~m~~~yr~~glia 361 (498)
T PRK05812 326 SLGADSIRAGLIAGLIGLALVLLFMILYYRLFGLIA 361 (498)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence 344577778899999999999999999999655443
No 14
>PF11120 DUF2636: Protein of unknown function (DUF2636); InterPro: IPR019995 Members of this protein family are found invariably together with genes of bacterial cellulose biosynthesis, and are presumed to be involved in the process []. Members average about 63 amino acids in length and are not uncharacterised. The gene has been designated both YhjT and BcsF (bacterial cellulose synthesis F).
Probab=53.88 E-value=45 Score=22.29 Aligned_cols=33 Identities=24% Similarity=0.395 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccC
Q 034024 71 IILVSITMLLLLCMKVTKQVRLARKKKRRMLLP 103 (106)
Q Consensus 71 ~~~ic~~ilL~~~lkitrq~rlarkreRrllLP 103 (106)
.+++|.-|++|.+.-.-+--+--++.-|++++|
T Consensus 9 ii~l~AlI~~pLGyl~~~~~~r~~~~lr~~l~~ 41 (62)
T PF11120_consen 9 IIILCALIFFPLGYLARRWLPRIRRTLRRRLFP 41 (62)
T ss_pred HHHHHHHHHHhHHHHHHHHhHHHHHHHHHHhcC
Confidence 355666666666666655555566666666655
No 15
>PRK11176 lipid transporter ATP-binding/permease protein; Provisional
Probab=52.57 E-value=1.1e+02 Score=25.37 Aligned_cols=21 Identities=19% Similarity=0.461 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 034024 58 SAVSLYFRHMRLAIILVSITM 78 (106)
Q Consensus 58 s~vtlYfr~~~Ls~~~ic~~i 78 (106)
+.+.+++-..+++.+.++...
T Consensus 156 ~~~~l~~~~~~l~l~~l~~~~ 176 (582)
T PRK11176 156 LFIMMFYYSWQLSLILIVIAP 176 (582)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333334444555555554433
No 16
>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=51.29 E-value=1.2e+02 Score=27.63 Aligned_cols=47 Identities=15% Similarity=0.137 Sum_probs=32.9
Q ss_pred ccceeeeecCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH
Q 034024 21 EWASVSFFSSTSNISSSRVDVVIFVIWELVILAFLVFSAVSLYFRH-MRLAII 72 (106)
Q Consensus 21 ~~aals~fS~~~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~-~~Ls~~ 72 (106)
+..+....+|+ -..|..=--++++++.++.++-|++++|+| |.++.+
T Consensus 560 ~~~~~~~Vgp~-----~g~~~~~~~~~a~~~a~~~i~iyi~~rF~~~~~~~ai 607 (755)
T PRK13024 560 TIPSSETVGPT-----VGKELARNAIIAVLIALIGILLYILIRFEWTFSLGAI 607 (755)
T ss_pred ceeEEEEECHh-----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566663 334666666788999999999999999987 455444
No 17
>PF07264 EI24: Etoposide-induced protein 2.4 (EI24); PDB: 3TX3_B.
Probab=50.86 E-value=90 Score=22.37 Aligned_cols=34 Identities=12% Similarity=0.034 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 034024 66 HMRLAIILVSITMLLLLCMKVTKQVRLARKKKRRM 100 (106)
Q Consensus 66 ~~~Ls~~~ic~~ilL~~~lkitrq~rlarkreRrl 100 (106)
++++..-..|+..+-...-+ ++++|++..+|+|.
T Consensus 162 ~~~l~~~~~~~e~~~~~~~~-~~~er~~~~~~~~~ 195 (219)
T PF07264_consen 162 WFWLNAYFLGFEYLWSSLGR-SFEERKRFLERNRG 195 (219)
T ss_dssp HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHCTHH
T ss_pred HHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHhHH
Confidence 44555555777766666555 88888888888875
No 18
>PF14851 FAM176: FAM176 family
Probab=50.72 E-value=51 Score=25.09 Aligned_cols=19 Identities=32% Similarity=0.481 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034024 70 AIILVSITMLLLLCMKVTK 88 (106)
Q Consensus 70 s~~~ic~~ilL~~~lkitr 88 (106)
+..=||+|++|.+|+=+.|
T Consensus 26 Fv~gVC~GLlLtLcllV~r 44 (153)
T PF14851_consen 26 FVSGVCAGLLLTLCLLVIR 44 (153)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 3556899999999986654
No 19
>COG4965 TadB Flp pilus assembly protein TadB [Intracellular trafficking and secretion]
Probab=49.37 E-value=1.1e+02 Score=25.70 Aligned_cols=50 Identities=16% Similarity=0.020 Sum_probs=38.5
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 36 SSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAIILVSITMLLLLCMK 85 (106)
Q Consensus 36 ~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lk 85 (106)
++-.++-+.=.|.+.+++.++..++..|.--.+.+.+++..+.++|.-..
T Consensus 74 q~G~~~~~~~~~~l~~~~~l~~~~v~~~~~~l~v~~~~~~~~~llp~~~~ 123 (309)
T COG4965 74 QAGLRVSLARLILLSAGAGLAVALVAWLGLSLLVALVALIGAALLPRLVL 123 (309)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Confidence 34556777778888889999888888888888888877777777776443
No 20
>KOG1583 consensus UDP-N-acetylglucosamine transporter [Carbohydrate transport and metabolism]
Probab=48.86 E-value=26 Score=30.09 Aligned_cols=61 Identities=20% Similarity=0.320 Sum_probs=43.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYF--------RHMRLAII---LVSITMLLLLCMKVTKQVRLARKKKRR 99 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYf--------r~~~Ls~~---~ic~~ilL~~~lkitrq~rlarkreRr 99 (106)
.|.--.+.-++|-+++++++||++|- ||-+=+.. ++.+-.+|.+.=-|--|-+++.|.|+-
T Consensus 158 ~~~~w~iGi~lL~~al~~sa~mgiyqE~~Y~kyGKh~~EalFytH~LsLP~Flf~~~div~~~~~~~~se~~ 229 (330)
T KOG1583|consen 158 DFFWWLIGIALLVFALLLSAYMGIYQETTYQKYGKHWKEALFYTHFLSLPLFLFMGDDIVSHWRLAFKSESY 229 (330)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHhccchHHHhcchHHHHHHHHhcCcce
Confidence 34555677889999999999999874 33333332 355666777777777888888888864
No 21
>PF02932 Neur_chan_memb: Neurotransmitter-gated ion-channel transmembrane region ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006029 Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily: Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits []. Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits []. Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known []. Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) []. Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) []. These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ]. This domain represents four transmembrane helices of a variety of neurotransmitter-gated ion-channels.; GO: 0006811 ion transport, 0016020 membrane; PDB: 1DXZ_A 3MRA_A 1EQ8_C 1OED_C 2PR9_P 1A11_A 1CEK_A 2BG9_E 2KSR_A 2K59_B ....
Probab=48.52 E-value=58 Score=20.88 Aligned_cols=49 Identities=16% Similarity=0.242 Sum_probs=27.6
Q ss_pred eeeecCCCCCCcchhHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHH
Q 034024 25 VSFFSSTSNISSSRVDVVIFVIWELVILAFLV------FSAVSLYFRHMRLAIILV 74 (106)
Q Consensus 25 ls~fS~~~~~~~sr~dvvv~v~w~llf~~l~v------~s~vtlYfr~~~Ls~~~i 74 (106)
++||=| +.....|.-+.|.++=++.++.+++ .||..-..-++-...+++
T Consensus 14 ~~f~~~-~~~~~~rv~l~it~lL~~~~~~~~~~~~lP~~s~~~pl~~~~~~~~~~v 68 (237)
T PF02932_consen 14 LSFWLP-PESGPERVTLGITTLLAMTVFLLMVAENLPPTSYAKPLDGWYFICTMFV 68 (237)
T ss_dssp HHHHHH-HHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHH
T ss_pred hheEeC-ccccccccccchhHHHHHHHHHhhhhhhhcccccccchhhhhccccchh
Confidence 345555 3332367777777777777777766 344444444444444443
No 22
>PHA03156 hypothetical protein; Provisional
Probab=48.17 E-value=16 Score=26.31 Aligned_cols=23 Identities=26% Similarity=0.648 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 44 FVIWELVILAFLVFSAVSLYFRHM 67 (106)
Q Consensus 44 ~v~w~llf~~l~v~s~vtlYfr~~ 67 (106)
+-+|+++=. +++.+...+|+||.
T Consensus 57 SSIWallN~-~i~~~A~~ifL~y~ 79 (90)
T PHA03156 57 SSIWAILNG-IIFFCASLFFLRHL 79 (90)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHH
Confidence 448887654 45556677899984
No 23
>PRK08343 secD preprotein translocase subunit SecD; Reviewed
Probab=46.42 E-value=82 Score=26.86 Aligned_cols=35 Identities=17% Similarity=0.074 Sum_probs=27.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 38 RVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAII 72 (106)
Q Consensus 38 r~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~ 72 (106)
..|..-..+++.++.+++|..+|-+|||..++++.
T Consensus 256 g~~~~~~~l~a~ii~~ilVl~~m~~~yr~~~~i~~ 290 (417)
T PRK08343 256 GEQFKKGSLIAGLLALLAVALVVFLRYREPRIALP 290 (417)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444467788999999999999999999777653
No 24
>TIGR03424 urea_degr_1 urea carboxylase-associated protein 1. A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes.
Probab=46.27 E-value=14 Score=28.61 Aligned_cols=28 Identities=18% Similarity=0.363 Sum_probs=26.1
Q ss_pred hhHHHHHHHHHhhhhhcccceeeeecCC
Q 034024 4 RSNLAEQLREYQNRSKHEWASVSFFSST 31 (106)
Q Consensus 4 RskLvEQLReyQiRs~h~~aals~fS~~ 31 (106)
|.|+.+.|.+|-+..++-|+++++|+.+
T Consensus 115 ~dN~~~al~~~Gl~~rdi~~~iN~Fm~v 142 (198)
T TIGR03424 115 RDNFLLAIAKYGLGKRDIVSNINFFMNV 142 (198)
T ss_pred HHHHHHHHHHhCCCccccCCcEeeeeec
Confidence 6799999999999999999999999984
No 25
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=45.20 E-value=70 Score=19.43 Aligned_cols=11 Identities=9% Similarity=0.359 Sum_probs=4.5
Q ss_pred HHHHHHHHHHH
Q 034024 80 LLLCMKVTKQV 90 (106)
Q Consensus 80 L~~~lkitrq~ 90 (106)
++..+|..++.
T Consensus 40 ~~~~~~~r~~~ 50 (68)
T PF06305_consen 40 LPSRLRLRRRI 50 (68)
T ss_pred HHHHHHHHHHH
Confidence 33344444443
No 26
>PF06799 DUF1230: Protein of unknown function (DUF1230); InterPro: IPR009631 This family represents Ycf36, which is found in plants, encoded in the genomes of algal chloroplasts and in cyanobacteria. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=44.71 E-value=95 Score=23.63 Aligned_cols=59 Identities=22% Similarity=0.300 Sum_probs=34.7
Q ss_pred eecCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Q 034024 27 FFSSTSNISSSRVDVVIFVIWELVILAFLVFSAVSLYFR----HMRLAIILVSITMLLLLCMKV 86 (106)
Q Consensus 27 ~fS~~~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr----~~~Ls~~~ic~~ilL~~~lki 86 (106)
+||= +..........++.+|.+.+......+..+++.+ ++-+++.+....+.+.+.+|+
T Consensus 21 ~FsW-~~~~~~~y~~~l~~~w~~~~~~~~pia~~S~~~~~~~~~~~l~~~~ga~~~~~l~llRl 83 (144)
T PF06799_consen 21 FFSW-PTLELKSYLKRLLWIWLISFLVFGPIAAGSFPPEKDPLEFILSGAVGALLLLLLVLLRL 83 (144)
T ss_pred CccC-ccCChHHHHHHHHHHHHHHHHHHHhhheeecCccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5665 3333455677788888876666555555556443 555665555555555555543
No 27
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=43.83 E-value=39 Score=28.20 Aligned_cols=25 Identities=32% Similarity=0.631 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 40 DVVIFVIWELVILAFLVFSAVSLYF 64 (106)
Q Consensus 40 dvvv~v~w~llf~~l~v~s~vtlYf 64 (106)
++++-|.-+++..-+++|..|+||-
T Consensus 188 ~vilpvvIaliVitl~vf~LvgLyr 212 (259)
T PF07010_consen 188 SVILPVVIALIVITLSVFTLVGLYR 212 (259)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778888899999999999999984
No 28
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=43.79 E-value=1.9e+02 Score=24.15 Aligned_cols=28 Identities=18% Similarity=0.275 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 58 SAVSLYFRHMRLAIILVSITMLLLLCMK 85 (106)
Q Consensus 58 s~vtlYfr~~~Ls~~~ic~~ilL~~~lk 85 (106)
+.+.++.-..+++.++++...+.++..+
T Consensus 154 ~~~~l~~~~~~l~l~~l~~~~~~~~~~~ 181 (588)
T PRK11174 154 ILIAVFPINWAAGLILLGTAPLIPLFMA 181 (588)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555666666666555544443
No 29
>PF09435 DUF2015: Fungal protein of unknown function (DUF2015); InterPro: IPR018559 This entry represents uncharacterised proteins found in fungi.
Probab=42.72 E-value=47 Score=24.98 Aligned_cols=25 Identities=16% Similarity=0.489 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 46 IWELVILAFLVFSAVSLYFRHMRLAI 71 (106)
Q Consensus 46 ~w~llf~~l~v~s~vtlYfr~~~Ls~ 71 (106)
+|.+.++++++. .+.+++||.|+..
T Consensus 5 ly~~~~~~~i~~-t~lf~~R~r~~~~ 29 (128)
T PF09435_consen 5 LYSLTFFVLIIG-TLLFFTRHRWLPL 29 (128)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHhh
Confidence 444444443333 3667777777654
No 30
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=42.04 E-value=51 Score=21.32 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 034024 42 VIFVIWELVILAFLVFSAVSLY 63 (106)
Q Consensus 42 vv~v~w~llf~~l~v~s~vtlY 63 (106)
.+.+.++++++++++.+.+++|
T Consensus 7 KL~~~f~~~~~l~~~~~~~~~~ 28 (181)
T PF12729_consen 7 KLILGFGLIILLLLIVGIVGLY 28 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666666666666665
No 31
>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.
Probab=41.78 E-value=76 Score=23.90 Aligned_cols=29 Identities=21% Similarity=0.295 Sum_probs=23.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 38 RVDVVIFVIWELVILAFLVFSAVSLYFRH 66 (106)
Q Consensus 38 r~dvvv~v~w~llf~~l~v~s~vtlYfr~ 66 (106)
..|..=.-++++++.++++.-|+.++||+
T Consensus 26 g~~~~~~~~~a~~~al~~i~iyi~~rf~~ 54 (189)
T PF02355_consen 26 GSDLLKSALIALIIALIAILIYIFLRFRW 54 (189)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCTH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34666666788888888899999999997
No 32
>cd02865 Heme_Cu_Oxidase_III_2 Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. Although not required for catalytic activity, subunit III is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the in
Probab=41.73 E-value=1.4e+02 Score=21.82 Aligned_cols=66 Identities=14% Similarity=0.112 Sum_probs=39.5
Q ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 034024 32 SNISSSRVDVVIFVIWELVILAFLVFSAVSLYFR--------HMRLAIILVSITMLLLLCMKVTKQVRLARKKK 97 (106)
Q Consensus 32 ~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr--------~~~Ls~~~ic~~ilL~~~lkitrq~rlarkre 97 (106)
++-+..++-..+++.=|..+++.++++|.-+... ...+...++.-.+++.-+.-+..-++-+|+++
T Consensus 4 ~~~~~~~~g~w~fi~se~~~F~~l~~~y~~~~~~~~~~p~~~~~~~~~~~~nT~lLl~Ss~~~~~A~~a~~~~~ 77 (184)
T cd02865 4 GARSPGWWGLWVFMAVEGTLFALLISAYFMRMTSGDWQPGAPLPLPNLLSLNTAVLAASSVAMQWARRAARRNR 77 (184)
T ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCccccCchHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3444577888889888999999999988644321 12223334444455555555555545444433
No 33
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=41.44 E-value=37 Score=26.17 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 034024 65 RHMRLAIILVSITMLLLLCMKV 86 (106)
Q Consensus 65 r~~~Ls~~~ic~~ilL~~~lki 86 (106)
++++|+++|+--|++|..-|++
T Consensus 39 ~Y~~LfiVFl~AG~vLw~vM~~ 60 (141)
T PRK13743 39 IYFDLFIVFLTAGIVLWVIMHS 60 (141)
T ss_pred HHHHHHHHHHHhhHHHHHHHHH
Confidence 5788899999999999888875
No 34
>cd02863 Ubiquinol_oxidase_III Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Ubiquinol oxidases feature four subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of bovine CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in bovine CcO. Although not required for catalytic activity, subunit III appears to be involved in assembly of the multimer complex.
Probab=41.26 E-value=1.5e+02 Score=22.02 Aligned_cols=67 Identities=15% Similarity=0.219 Sum_probs=39.9
Q ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 034024 32 SNISSSRVDVVIFVIWELVILAFLVFSAVSLYFRH---------MRLAIILVSITMLLLLCMKVTKQVRLARKKKR 98 (106)
Q Consensus 32 ~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~---------~~Ls~~~ic~~ilL~~~lkitrq~rlarkreR 98 (106)
+++...+.-..+++.-|..+++.++++|.-.-..+ ..+...++.-.+|+.-+.-+..-++-+|+.+|
T Consensus 4 ~~~~~~~~G~w~fi~sE~~~F~~l~~ay~~~~~~~~~~~~~~~~~~~~~~~~nT~vLl~SS~~~~~a~~a~~~~~~ 79 (186)
T cd02863 4 NTGSKKILGFWIYLMSDCILFATLFATYAVLSGNTAGGPPGHELFELPLVFIETFLLLLSSFTCGLAMIAMNKNNK 79 (186)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHccccCCCCccccccchHHHHHHHHHHHHHHHHHHHHHHHHhCCH
Confidence 45556777889999999999999999985322111 12223344445555555555555444444443
No 35
>PRK13023 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=40.90 E-value=2e+02 Score=26.75 Aligned_cols=34 Identities=15% Similarity=0.212 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYFRH-MRLAII 72 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYfr~-~~Ls~~ 72 (106)
.|..---+||+++.++.+.-|+++.|+| |.++.+
T Consensus 574 ~el~~~ai~Av~ia~i~IliYI~~RF~~~fav~Av 608 (758)
T PRK13023 574 EQLSRAGVLAVILSLIGIFIYVWFRFRWQLALGAV 608 (758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 4667777899999999999999999997 566544
No 36
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=40.73 E-value=21 Score=23.93 Aligned_cols=11 Identities=18% Similarity=0.501 Sum_probs=8.0
Q ss_pred HHHHHHHHHHH
Q 034024 46 IWELVILAFLV 56 (106)
Q Consensus 46 ~w~llf~~l~v 56 (106)
+||.||+.|++
T Consensus 14 ~fA~LFv~Ll~ 24 (71)
T PF10960_consen 14 IFAVLFVWLLF 24 (71)
T ss_pred cHHHHHHHHHH
Confidence 58888777665
No 37
>PF11045 YbjM: Putative inner membrane protein of Enterobacteriaceae; InterPro: IPR020368 This entry contains membrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=40.63 E-value=1e+02 Score=23.07 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=21.7
Q ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Q 034024 68 RLAIILVS-ITMLLLLCMKVTKQVRLARKK 96 (106)
Q Consensus 68 ~Ls~~~ic-~~ilL~~~lkitrq~rlarkr 96 (106)
-.|++|-| +|.++...++.-.|++.++||
T Consensus 96 ~~SAvFWc~lGAL~~lf~~~l~~~~~~~~r 125 (125)
T PF11045_consen 96 LFSAVFWCALGALLVLFLRSLLQRRRHHKR 125 (125)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHhccC
Confidence 35778877 589999999988886655543
No 38
>COG0341 SecF Preprotein translocase subunit SecF [Intracellular trafficking and secretion]
Probab=40.38 E-value=48 Score=27.39 Aligned_cols=39 Identities=15% Similarity=0.123 Sum_probs=30.5
Q ss_pred eeeecCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 25 VSFFSSTSNISSSRVDVVIFVIWELVILAFLVFSAVSLYFRHMR 68 (106)
Q Consensus 25 ls~fS~~~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~ 68 (106)
..+=||+ =..+..-.-++|+++.+..+.-|+++.|+|.-
T Consensus 121 ~~~Vgp~-----vg~eL~~~~~~Al~~alv~I~iYV~~RFe~~~ 159 (305)
T COG0341 121 VEFVGPT-----VGKELARQGLLALLLALVGILIYVFFRFEWRF 159 (305)
T ss_pred eeEECcc-----hHHHHHHHHHHHHHHHHHHHHHhhheeeehHH
Confidence 3455663 23377777889999999999999999999876
No 39
>PHA03163 hypothetical protein; Provisional
Probab=40.26 E-value=26 Score=25.33 Aligned_cols=23 Identities=22% Similarity=0.457 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 44 FVIWELVILAFLVFSAVSLYFRHM 67 (106)
Q Consensus 44 ~v~w~llf~~l~v~s~vtlYfr~~ 67 (106)
+-+|+++=.+ ++...-.+|+||.
T Consensus 58 SSIWaliNv~-Ivl~A~~iyL~y~ 80 (92)
T PHA03163 58 SSIWAILNVL-IMLIACIIYCIYM 80 (92)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHH
Confidence 4488877554 4445567888884
No 40
>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=39.80 E-value=23 Score=20.34 Aligned_cols=12 Identities=25% Similarity=0.343 Sum_probs=10.8
Q ss_pred chhHHHHHHHHH
Q 034024 3 TRSNLAEQLREY 14 (106)
Q Consensus 3 TRskLvEQLRey 14 (106)
||..|++++|+|
T Consensus 26 ~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 26 TRDELLKLAKKN 37 (38)
T ss_pred CHHHHHHHHHHh
Confidence 799999999986
No 41
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=39.16 E-value=1.3e+02 Score=20.75 Aligned_cols=55 Identities=11% Similarity=0.268 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH---HHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 39 VDVVIFVIWELVILAFLVFSAV---SLYFRH----------MRLAIILVSITMLLLLCMKVTKQVRLA 93 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~v---tlYfr~----------~~Ls~~~ic~~ilL~~~lkitrq~rla 93 (106)
-+..-++.|.++...+++.+.. .-++-+ .-+.++++++.+.+....+++|+++.=
T Consensus 28 l~~~~~l~Wl~~~i~~l~~~ifP~~~~~vA~~lGi~~~~n~lf~~~i~~ll~~~~~l~~~is~le~~i 95 (115)
T PF10066_consen 28 LRLKYSLLWLVFSIILLILSIFPNILDWVAKLLGIGRPPNLLFYLGILFLLVIIFSLYVRISRLEEKI 95 (115)
T ss_pred ccHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555566777766666665532 112111 223456666677777888888876543
No 42
>PF14163 SieB: Superinfection exclusion protein B
Probab=39.04 E-value=1.4e+02 Score=21.15 Aligned_cols=22 Identities=18% Similarity=0.292 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 034024 61 SLYFRHMRLAIILVSITMLLLLC 83 (106)
Q Consensus 61 tlYfr~~~Ls~~~ic~~ilL~~~ 83 (106)
+.|--|+++.|++ |++.++-..
T Consensus 30 ~~y~~~i~~~fl~-s~s~li~~~ 51 (151)
T PF14163_consen 30 IKYQPWIGLIFLF-SVSYLIAQL 51 (151)
T ss_pred HhcchHHHHHHHH-HHHHHHHHH
Confidence 4566777776654 444444333
No 43
>PF02932 Neur_chan_memb: Neurotransmitter-gated ion-channel transmembrane region ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006029 Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily: Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits []. Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits []. Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known []. Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) []. Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) []. These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ]. This domain represents four transmembrane helices of a variety of neurotransmitter-gated ion-channels.; GO: 0006811 ion transport, 0016020 membrane; PDB: 1DXZ_A 3MRA_A 1EQ8_C 1OED_C 2PR9_P 1A11_A 1CEK_A 2BG9_E 2KSR_A 2K59_B ....
Probab=38.61 E-value=1e+02 Score=19.76 Aligned_cols=26 Identities=27% Similarity=0.253 Sum_probs=14.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYF 64 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYf 64 (106)
-|+..++.-.++|++++.++.+.+.+
T Consensus 57 l~~~~~~~~~~v~~~~~~~avv~~~~ 82 (237)
T PF02932_consen 57 LDGWYFICTMFVFSASLEFAVVVYNI 82 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhccccchhhhHHHHhhhhhhhh
Confidence 35555555555555666666665555
No 44
>PF00664 ABC_membrane: ABC transporter transmembrane region; InterPro: IPR001140 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). A variety of ATP-binding transport proteins have a six transmembrane helical region. They are all integral membrane proteins involved in a variety of transport systems. Members of this family include; the cystic fibrosis transmembrane conductance regulator (CFTR), bacterial leukotoxin secretion ATP-binding protein, multidrug resistance proteins, the yeast leptomycin B resistance protein, the mammalian sulphonylurea receptor and antigen peptide transporter 2. Many of these proteins have two such regions.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3G61_B 3G5U_B 3G60_A 3B60_D 3QF4_B 2HYD_A 2ONJ_A 4A82_B 4AA3_A 2YL4_A.
Probab=38.34 E-value=1.2e+02 Score=20.25 Aligned_cols=40 Identities=33% Similarity=0.637 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
Q 034024 56 VFSAVSLYFRHMRLAIILV-SITMLLLLCMKVTKQVRLARK 95 (106)
Q Consensus 56 v~s~vtlYfr~~~Ls~~~i-c~~ilL~~~lkitrq~rlark 95 (106)
+.+.+.+++-..+++.+.+ ++.+..++.....|..+...+
T Consensus 130 i~~~~~~~~~~~~l~l~~l~~~~~~~~~~~~~~~~~~~~~~ 170 (275)
T PF00664_consen 130 IFSLILLFFISWKLALILLIILPLLFLISFIFSKKIRKLSK 170 (275)
T ss_dssp HHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhcccccccccccccchhhhhhHhhhhhhccccccccc
Confidence 3334444444556666555 444555555555554443333
No 45
>cd00386 Heme_Cu_Oxidase_III_like Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. This group additionally contains proteins which are fusions between subunits I and III, such as Sulfolobus acidocaldarius SoxM, a subunit of the SoxM terminal oxidase complex
Probab=37.38 E-value=1.5e+02 Score=21.18 Aligned_cols=31 Identities=13% Similarity=0.286 Sum_probs=24.1
Q ss_pred CCCcchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 33 NISSSRVDVVIFVIWELVILAFLVFSAVSLY 63 (106)
Q Consensus 33 ~~~~sr~dvvv~v~w~llf~~l~v~s~vtlY 63 (106)
+.+..++-..++++=|..+++.++++|.-+.
T Consensus 5 ~~~~~~~g~~~fi~se~~~F~~l~~~y~~~~ 35 (183)
T cd00386 5 VRSGGRLGMWLFILSEVMLFGSFFWAYFHSR 35 (183)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345778888999999999999999986443
No 46
>PRK10774 cell division protein FtsW; Provisional
Probab=36.32 E-value=1e+02 Score=25.94 Aligned_cols=32 Identities=9% Similarity=0.231 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 58 SAVSLYFRHMRLAIILVSITMLLLLCMKVTKQ 89 (106)
Q Consensus 58 s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq 89 (106)
++++=.+-+++..++++++..++.-++++.++
T Consensus 291 avi~EE~GfiG~~~vl~Lf~~li~r~~~ia~~ 322 (404)
T PRK10774 291 SIIGEELGYIGVVLALLMVFFVAFRAMSIGRK 322 (404)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344445555555555555555555555543
No 47
>PF06072 Herpes_US9: Alphaherpesvirus tegument protein US9; InterPro: IPR009278 This family consists of several US9 and related proteins from the Alphaherpesviruses. The function of the US9 protein is unknown although in Bovine herpesvirus 5 Us9 is essential for the anterograde spread of the virus from the olfactory mucosa to the bulb [].; GO: 0019033 viral tegument
Probab=36.10 E-value=33 Score=23.08 Aligned_cols=18 Identities=28% Similarity=0.497 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHhhhhhc
Q 034024 84 MKVTKQVRLARKKKRRML 101 (106)
Q Consensus 84 lkitrq~rlarkreRrll 101 (106)
.||.||....|+|+||-.
T Consensus 16 ~RvGr~q~~~r~RrRrc~ 33 (60)
T PF06072_consen 16 RRVGRQQHASRRRRRRCR 33 (60)
T ss_pred HHHhHHHHHHHHHHHHHH
Confidence 588999866666777643
No 48
>PF09347 DUF1989: Domain of unknown function (DUF1989); InterPro: IPR018959 This entry represents proteins that are functionally uncharacterised. ; PDB: 3ORU_A 3SIY_C 3DI4_A.
Probab=35.16 E-value=23 Score=26.58 Aligned_cols=28 Identities=25% Similarity=0.362 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHhhhhhcccceeeeecCC
Q 034024 4 RSNLAEQLREYQNRSKHEWASVSFFSST 31 (106)
Q Consensus 4 RskLvEQLReyQiRs~h~~aals~fS~~ 31 (106)
+.|+.+.|.+|.+..++-++.+++|+.+
T Consensus 109 ~dnl~~al~~~Gl~~~di~~~lNlFm~v 136 (166)
T PF09347_consen 109 RDNLLEALAKYGLGPRDIPPPLNLFMNV 136 (166)
T ss_dssp HHHHHHHHHTCCHHHCC----EEECEEE
T ss_pred HHHHHHHHHHhCCCccccCCcEEeeECC
Confidence 6899999999999999999999999974
No 49
>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=35.12 E-value=1.6e+02 Score=26.98 Aligned_cols=32 Identities=22% Similarity=0.145 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYFRHMRLA 70 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls 70 (106)
.|..=..+++++..+++++-++.+|||++.+.
T Consensus 262 ~~a~~~~~~a~~ial~lV~i~l~~~fr~~~li 293 (755)
T PRK13024 262 QDAIDAGIIAGIIGFALIFLFMLVYYGLPGLI 293 (755)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence 35555678888888899999999999974443
No 50
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=34.94 E-value=3e+02 Score=23.82 Aligned_cols=26 Identities=12% Similarity=0.070 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 60 VSLYFRHMRLAIILVSITMLLLLCMK 85 (106)
Q Consensus 60 vtlYfr~~~Ls~~~ic~~ilL~~~lk 85 (106)
+.+++-..+++.+++++.++..+...
T Consensus 288 ~~l~~~~~~l~li~l~~~~l~~~~~~ 313 (708)
T TIGR01193 288 LFLVRQNMLLFLLSLLSIPVYAVIII 313 (708)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 33444555677666655544444333
No 51
>TIGR00916 2A0604s01 protein-export membrane protein, SecD/SecF family. The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins.
Probab=34.94 E-value=1.9e+02 Score=21.52 Aligned_cols=27 Identities=22% Similarity=0.223 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 40 DVVIFVIWELVILAFLVFSAVSLYFRH 66 (106)
Q Consensus 40 dvvv~v~w~llf~~l~v~s~vtlYfr~ 66 (106)
|..--..++++..++++.-++.++||+
T Consensus 44 ~~~~~~~~~l~~a~~lv~l~l~~~~r~ 70 (192)
T TIGR00916 44 ELIKAGIIALLIGLVLVLLYMLLRYEW 70 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555667777777888888899984
No 52
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.
Probab=34.12 E-value=2.7e+02 Score=23.01 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 56 VFSAVSLYFRHMRLAIILVSITMLLLLCMKV 86 (106)
Q Consensus 56 v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lki 86 (106)
+.+.+.+++-..+++++++++.++..+..++
T Consensus 143 ~~~~~~l~~~~~~l~~i~l~~~~l~~~~~~~ 173 (571)
T TIGR02203 143 IGLFIVLLYYSWQLTLIVVVMLPVLSILMRR 173 (571)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3333434444455666665554443333333
No 53
>PF10328 7TM_GPCR_Srx: Serpentine type 7TM GPCR chemoreceptor Srx; InterPro: IPR019430 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class x (Srx) from the Srg superfamily [, ]. Srg receptors contain seven hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.
Probab=33.95 E-value=1.3e+02 Score=22.60 Aligned_cols=11 Identities=27% Similarity=0.537 Sum_probs=6.7
Q ss_pred HHHHHhhhhhc
Q 034024 91 RLARKKKRRML 101 (106)
Q Consensus 91 rlarkreRrll 101 (106)
+..||||++++
T Consensus 199 ~~r~rke~~f~ 209 (274)
T PF10328_consen 199 KKRRRKEIRFF 209 (274)
T ss_pred HHHHHHHHHHH
Confidence 35666677653
No 54
>PRK13022 secF preprotein translocase subunit SecF; Reviewed
Probab=33.69 E-value=2.5e+02 Score=22.44 Aligned_cols=27 Identities=7% Similarity=0.145 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYFR 65 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYfr 65 (106)
.|..--.++++++.+++++-|+..+|+
T Consensus 123 ~~~~~~~~~a~~~al~~i~i~l~~~F~ 149 (289)
T PRK13022 123 KELAQKGLLALLVALVGILIYIAFRFE 149 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577778889999999999999999998
No 55
>PF10176 DUF2370: Protein of unknown function (DUF2370); InterPro: IPR019325 Proteins in this family are conserved from fungi to humans. They include the human NEDD4 family-interacting proteins and the yeast BSD2 metal homeostatis proteins.
Probab=33.37 E-value=70 Score=25.93 Aligned_cols=18 Identities=22% Similarity=0.370 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 034024 66 HMRLAIILVSITMLLLLC 83 (106)
Q Consensus 66 ~~~Ls~~~ic~~ilL~~~ 83 (106)
.-|++.+++.+|+|+.+.
T Consensus 193 ~~wla~~Lm~~G~fI~ir 210 (233)
T PF10176_consen 193 NPWLAYILMAFGWFIFIR 210 (233)
T ss_pred CcHHHHHHHHHHHHHHHH
Confidence 346777777778776554
No 56
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=33.09 E-value=1.1e+02 Score=20.20 Aligned_cols=10 Identities=20% Similarity=0.438 Sum_probs=4.0
Q ss_pred HHHHHhhhhh
Q 034024 91 RLARKKKRRM 100 (106)
Q Consensus 91 rlarkreRrl 100 (106)
++++|+.+.|
T Consensus 24 kk~~k~~~~m 33 (82)
T PF02699_consen 24 KKQQKEHQEM 33 (82)
T ss_dssp HHHHHHHTTG
T ss_pred HHHHHHHHHH
Confidence 3344444433
No 57
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=32.50 E-value=60 Score=22.56 Aligned_cols=11 Identities=36% Similarity=0.631 Sum_probs=4.4
Q ss_pred HHHHHHHHHHH
Q 034024 76 ITMLLLLCMKV 86 (106)
Q Consensus 76 ~~ilL~~~lki 86 (106)
++++|+++--+
T Consensus 13 LA~lLlisSev 23 (95)
T PF07172_consen 13 LAALLLISSEV 23 (95)
T ss_pred HHHHHHHHhhh
Confidence 33444444333
No 58
>TIGR00966 3a0501s07 protein-export membrane protein SecF. This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein.
Probab=32.20 E-value=2.3e+02 Score=21.74 Aligned_cols=32 Identities=16% Similarity=0.262 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 38 RVDVVIFVIWELVILAFLVFSAVSLYFRHMRLA 70 (106)
Q Consensus 38 r~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls 70 (106)
-.|+.--.+.++.+..++++-++.++|+ ++.+
T Consensus 93 ~~~~~~~~~~~~~la~i~i~l~l~~~f~-~r~~ 124 (246)
T TIGR00966 93 GGELARKAVLALLAALVLILIYITVRFE-WRFA 124 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Confidence 3567777788888888888888999888 4444
No 59
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=31.65 E-value=39 Score=22.85 Aligned_cols=15 Identities=40% Similarity=0.510 Sum_probs=11.3
Q ss_pred CcchhHHHHHHHHHh
Q 034024 1 MITRSNLAEQLREYQ 15 (106)
Q Consensus 1 mITRskLvEQLReyQ 15 (106)
.||||.+|..||...
T Consensus 15 GiTRSvIVNALRKle 29 (61)
T PF08222_consen 15 GITRSVIVNALRKLE 29 (61)
T ss_dssp T--HHHHHHHHHHHH
T ss_pred CccHHHHHHHHHHHH
Confidence 589999999999865
No 60
>PTZ00265 multidrug resistance protein (mdr1); Provisional
Probab=31.50 E-value=4.7e+02 Score=25.78 Aligned_cols=36 Identities=14% Similarity=0.308 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 54 FLVFSAVSLYFRHMRLAIILVSITMLLLLCMKVTKQ 89 (106)
Q Consensus 54 l~v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq 89 (106)
.++.+++.+++...+|+.+++|+..++.++..+...
T Consensus 184 ~~i~~~i~~~~~sw~Lalv~l~~~pl~~~~~~~~~~ 219 (1466)
T PTZ00265 184 AFLGLYIWSLFKNARLTLCITCVFPLIYICGVICNK 219 (1466)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355666666677888888888877666666655544
No 61
>PF08355 EF_assoc_1: EF hand associated; InterPro: IPR013566 This region typically appears on the C terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis[]). The EF hand associated region is found in yeast, vertebrates and plants.
Probab=31.26 E-value=9.3 Score=25.76 Aligned_cols=17 Identities=41% Similarity=0.536 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHhhh
Q 034024 82 LCMKVTKQVRLARKKKR 98 (106)
Q Consensus 82 ~~lkitrq~rlarkreR 98 (106)
-+++|||.||+.|||+|
T Consensus 59 ~Ai~VTr~R~~d~~k~~ 75 (76)
T PF08355_consen 59 SAITVTRPRRLDRKKGQ 75 (76)
T ss_pred hheEEcCchhhhhhccC
Confidence 36789999888888765
No 62
>PLN00084 photosystem II subunit S (PsbS); Provisional
Probab=31.12 E-value=79 Score=25.71 Aligned_cols=23 Identities=30% Similarity=0.224 Sum_probs=16.9
Q ss_pred HHHHHHHHhhhhhcccceeeeecC
Q 034024 7 LAEQLREYQNRSKHEWASVSFFSS 30 (106)
Q Consensus 7 LvEQLReyQiRs~h~~aals~fS~ 30 (106)
=+|||+|-|.= --.+|+...|-|
T Consensus 19 p~eql~de~~~-igahassvlfhp 41 (214)
T PLN00084 19 PLEQLRDEEMF-IGAHASSVLFHP 41 (214)
T ss_pred cHHHhhhhHHH-hhhcccccccCC
Confidence 37999997753 345578888888
No 63
>PRK12933 secD preprotein translocase subunit SecD; Reviewed
Probab=31.05 E-value=2.6e+02 Score=25.59 Aligned_cols=48 Identities=13% Similarity=0.100 Sum_probs=31.3
Q ss_pred ceeeeecCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 23 ASVSFFSSTSNISSSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRLA 70 (106)
Q Consensus 23 aals~fS~~~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls 70 (106)
+.+.+.+..+=..+=..|.+-..++++++-+++++-+|..|||.+.+.
T Consensus 420 a~~~i~~~~tVgpsLG~~~i~~gl~A~iig~vlV~lFm~~~Yr~~glv 467 (604)
T PRK12933 420 APVTIVEERTIGPSLGAENIENGFAALALGMGITLLFMALWYRRLGWV 467 (604)
T ss_pred CCeEEEEeeecchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444443211234557777788888888888888999888865543
No 64
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=30.92 E-value=3.4e+02 Score=23.13 Aligned_cols=11 Identities=27% Similarity=0.151 Sum_probs=8.4
Q ss_pred HHHHHHHHHHH
Q 034024 83 CMKVTKQVRLA 93 (106)
Q Consensus 83 ~lkitrq~rla 93 (106)
.||||||+-+.
T Consensus 219 ~lkMSkqEvKd 229 (386)
T PRK12468 219 KLRMTKQDIRD 229 (386)
T ss_pred HCCCCHHHHHH
Confidence 47999997654
No 65
>PF12307 DUF3631: Protein of unknown function (DUF3631); InterPro: IPR022081 This domain is found in uncharacterised proteins and in tripartite motif containing (TRIM) protein 41. This protein functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C [].
Probab=29.94 E-value=26 Score=27.30 Aligned_cols=19 Identities=47% Similarity=0.641 Sum_probs=16.9
Q ss_pred cchhHHHHHHHHHhhhhhc
Q 034024 2 ITRSNLAEQLREYQNRSKH 20 (106)
Q Consensus 2 ITRskLvEQLReyQiRs~h 20 (106)
||-.+|...|+||.|||+.
T Consensus 143 Lt~r~La~~L~~ygI~s~~ 161 (184)
T PF12307_consen 143 LTPRQLAKLLKEYGIRSKN 161 (184)
T ss_pred CCHHHHHHHHHHCCCCCCc
Confidence 6778899999999999985
No 66
>PRK14726 bifunctional preprotein translocase subunit SecD/SecF; Provisional
Probab=29.88 E-value=2.1e+02 Score=27.01 Aligned_cols=39 Identities=15% Similarity=0.192 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 38 RVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAIILVSITML 79 (106)
Q Consensus 38 r~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ic~~il 79 (106)
-.|.+=..++++++-+.+|.-+|-+|+++ ++++.++++.
T Consensus 367 g~~~i~~~~~aliig~ilV~l~m~lfyr~---~glia~ial~ 405 (855)
T PRK14726 367 GADSIAAGLVAGLIAAILVAALMIGFYGF---LGVIAVIALI 405 (855)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH
Confidence 34555667788888888888888888886 4444444443
No 67
>PHA02819 hypothetical protein; Provisional
Probab=29.86 E-value=1.4e+02 Score=20.59 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=10.4
Q ss_pred cCCCCCC-cchhHHHHHHHHHHHHHHHH
Q 034024 29 SSTSNIS-SSRVDVVIFVIWELVILAFL 55 (106)
Q Consensus 29 S~~~~~~-~sr~dvvv~v~w~llf~~l~ 55 (106)
||+++++ ++.|-....++.+.++.+++
T Consensus 35 s~~~~~~~~~~~~~~ii~l~~~~~~~~~ 62 (71)
T PHA02819 35 NYNKKTKKSFLRYYLIIGLVTIVFVIIF 62 (71)
T ss_pred CCcccccCChhHHHHHHHHHHHHHHHHH
Confidence 3444333 34443333333333333333
No 68
>PRK11371 hypothetical protein; Provisional
Probab=28.85 E-value=1.3e+02 Score=22.73 Aligned_cols=60 Identities=28% Similarity=0.367 Sum_probs=37.4
Q ss_pred eeeecCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q 034024 25 VSFFSSTSNISSSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAIILVSITMLL-LLCMKVTKQ 89 (106)
Q Consensus 25 ls~fS~~~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ic~~ilL-~~~lkitrq 89 (106)
+++|=|+++--.||.--+...+..=++|++++.- |-.-.-.+..+..+|+| +.-..+.-|
T Consensus 2 l~ifipts~~~isr~ryi~sf~lin~if~~li~~-----~~~~~~~~l~i~~tillhylvinmncq 62 (126)
T PRK11371 2 LRIFIPTSNGKISRRRYIFSFILINFIFAFLIIF-----FNDGEAGFLVIVSTILLHYLVINMNCQ 62 (126)
T ss_pred eeEEeecCCCceehhHHHHHHHHHHHHHHHHHHH-----HhcCCceehhHHHHHHHHHHheecchH
Confidence 5788898877778887777766666666666542 33334455566677776 333344444
No 69
>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=28.38 E-value=1.9e+02 Score=19.35 Aligned_cols=39 Identities=28% Similarity=0.402 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 52 LAFLVFSAVSLYFRHMRLAIILVSITMLLLLCMKVTKQVRLA 93 (106)
Q Consensus 52 ~~l~v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq~rla 93 (106)
+.++++..++.++-+...+ +++|.+++++--.--..|+.
T Consensus 14 ~~~l~~~lvG~~~g~~~~~---l~~~l~~~l~wh~~~l~rL~ 52 (90)
T PF11808_consen 14 LLLLAAALVGWLFGHLWWA---LLLGLLLYLFWHLYQLYRLE 52 (90)
T ss_pred HHHHHHHHHHHHHhHHHHH---HHHHHHHHHHHHHHHHHHHH
Confidence 3444555677777777654 44455555554443333443
No 70
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=28.11 E-value=2.6e+02 Score=21.02 Aligned_cols=27 Identities=30% Similarity=0.386 Sum_probs=19.9
Q ss_pred eeeeecCCCCCCcchhHHHHHHHHHHHHHHHH
Q 034024 24 SVSFFSSTSNISSSRVDVVIFVIWELVILAFL 55 (106)
Q Consensus 24 als~fS~~~~~~~sr~dvvv~v~w~llf~~l~ 55 (106)
-+.|||| .|.|-++++..=++++.-+.
T Consensus 80 e~GfFsP-----~SwWPl~la~~~al~~lGla 106 (137)
T PF12270_consen 80 ELGFFSP-----HSWWPLVLAAAAALVFLGLA 106 (137)
T ss_pred CcCcCCC-----ccHhHHHHHHHHHHHHHHHH
Confidence 4789999 68888888877666665544
No 71
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=27.95 E-value=2.2e+02 Score=23.90 Aligned_cols=11 Identities=36% Similarity=0.211 Sum_probs=8.4
Q ss_pred HHHHHHHHHHH
Q 034024 83 CMKVTKQVRLA 93 (106)
Q Consensus 83 ~lkitrq~rla 93 (106)
.||||||+-+.
T Consensus 219 ~lkMskqEVKd 229 (359)
T PRK05702 219 KLKMTKQEVKD 229 (359)
T ss_pred hCCCCHHHHHH
Confidence 58999997553
No 72
>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=27.78 E-value=2.9e+02 Score=21.41 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 57 FSAVSLYFRHMRLAIILVSITMLLLLCMKVTKQVR 91 (106)
Q Consensus 57 ~s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq~r 91 (106)
+..+.+|.-...+.++++++.=-..++-++.|+.+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~iid~~~l~r~vkk~v~ 131 (170)
T PF11241_consen 97 SPQVQLYVTLAMYVLLLLVIIDGVILGRRVKKRVA 131 (170)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777777777777777777666677777777643
No 73
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=27.46 E-value=2.4e+02 Score=20.35 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=5.4
Q ss_pred HHHHHH-HHhhhhh
Q 034024 7 LAEQLR-EYQNRSK 19 (106)
Q Consensus 7 LvEQLR-eyQiRs~ 19 (106)
+++|+. ||.++..
T Consensus 56 iA~~i~~~~~i~~~ 69 (181)
T PF08006_consen 56 IAREILAEYSIKEE 69 (181)
T ss_pred HHHHHHHhhhhhhh
Confidence 344433 4444443
No 74
>PF04387 PTPLA: Protein tyrosine phosphatase-like protein, PTPLA; InterPro: IPR007482 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types [].
Probab=27.39 E-value=1.3e+02 Score=22.34 Aligned_cols=32 Identities=25% Similarity=0.231 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 034024 66 HMRLAIILVSITMLLLLCMKVTKQVRLARKKK 97 (106)
Q Consensus 66 ~~~Ls~~~ic~~ilL~~~lkitrq~rlarkre 97 (106)
++-.+..++-+-.+..+=..|-||||++-+|+
T Consensus 132 ~~~~~~l~~y~pg~~~ly~hM~~qRrK~l~~~ 163 (164)
T PF04387_consen 132 YFLIFVLLLYIPGFPFLYSHMLKQRRKKLGKK 163 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 33333343434445555667789987776554
No 75
>COG3326 Predicted membrane protein [Function unknown]
Probab=27.25 E-value=1.2e+02 Score=21.88 Aligned_cols=25 Identities=28% Similarity=0.426 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 034024 74 VSITMLLLLCMKVTKQVRLARKKKRRM 100 (106)
Q Consensus 74 ic~~ilL~~~lkitrq~rlarkreRrl 100 (106)
..++++-..-+-+.|+ .|||+.+|.
T Consensus 13 ~~~nl~~F~ly~iDK~--kA~~~~wRI 37 (94)
T COG3326 13 AILNLLVFALYGIDKR--KARKGKWRI 37 (94)
T ss_pred HHHHHHHHHHHHhhHH--HHHccCCCC
Confidence 3344444444555654 788877775
No 76
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=27.05 E-value=1.7e+02 Score=20.37 Aligned_cols=14 Identities=36% Similarity=0.563 Sum_probs=7.5
Q ss_pred HHHHHHHHHHhhhh
Q 034024 86 VTKQVRLARKKKRR 99 (106)
Q Consensus 86 itrq~rlarkreRr 99 (106)
|-+|+|-+++|+.|
T Consensus 48 ie~~ere~K~k~Kr 61 (74)
T PF15086_consen 48 IEKEEREKKKKAKR 61 (74)
T ss_pred HHHHHHHHHHHHHH
Confidence 44566655555444
No 77
>PRK11246 hypothetical protein; Provisional
Probab=26.48 E-value=93 Score=25.15 Aligned_cols=24 Identities=38% Similarity=0.620 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 60 VSLYFRHMRLAIILVSITMLLLLC 83 (106)
Q Consensus 60 vtlYfr~~~Ls~~~ic~~ilL~~~ 83 (106)
+.++||--|.+.+++|++++-.+-
T Consensus 4 ~~~~fRl~r~~iiliclallv~l~ 27 (218)
T PRK11246 4 AKLKFRLHRTAIVLICLALLVALM 27 (218)
T ss_pred hHHHhHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999887543
No 78
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=26.38 E-value=2.8e+02 Score=20.69 Aligned_cols=33 Identities=21% Similarity=0.320 Sum_probs=24.0
Q ss_pred HHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 60 VSLYFRH-----MRLAIILVSITMLLLLCMKVTKQVRL 92 (106)
Q Consensus 60 vtlYfr~-----~~Ls~~~ic~~ilL~~~lkitrq~rl 92 (106)
...|+|| +|=-+++..+.+++.+++.++.=...
T Consensus 34 ~~~Y~r~r~~tKyRDL~II~~L~ll~l~giq~~~y~~~ 71 (149)
T PF11694_consen 34 FIKYLRNRLDTKYRDLSIIALLLLLLLIGIQYSDYQQN 71 (149)
T ss_pred HHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578886 56667777788888899998865433
No 79
>PF09594 DUF2029: Protein of unknown function (DUF2029); InterPro: IPR018584 This is a putative transmembrane protein from prokaryotes. It is likely to be conserved between Mycobacterium species []. ; GO: 0016758 transferase activity, transferring hexosyl groups
Probab=26.30 E-value=1.2e+02 Score=21.30 Aligned_cols=34 Identities=21% Similarity=0.384 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 47 WELVILAFLVFSAVSLYFRHMRLAIILVSITMLL 80 (106)
Q Consensus 47 w~llf~~l~v~s~vtlYfr~~~Ls~~~ic~~ilL 80 (106)
++++..++++.++..+.=++-+++++++.+++..
T Consensus 76 ~~~l~~~l~~~a~~~~~r~r~~~agv~lgla~~~ 109 (241)
T PF09594_consen 76 FDLLVAALLLLALLALRRGRPWLAGVLLGLAAAI 109 (241)
T ss_pred HHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence 4455566666666655556677888888776543
No 80
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=26.24 E-value=97 Score=21.20 Aligned_cols=23 Identities=4% Similarity=0.127 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 034024 44 FVIWELVILAFLVFSAVSLYFRH 66 (106)
Q Consensus 44 ~v~w~llf~~l~v~s~vtlYfr~ 66 (106)
.++|++.++++++....+-|+++
T Consensus 53 GIli~f~i~f~~~~~~~~e~~~~ 75 (103)
T PF06422_consen 53 GILIAFWIFFIVLTLLATEFIKF 75 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 34455555555555444444444
No 81
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=25.89 E-value=2.5e+02 Score=23.26 Aligned_cols=12 Identities=17% Similarity=0.108 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHH
Q 034024 83 CMKVTKQVRLAR 94 (106)
Q Consensus 83 ~lkitrq~rlar 94 (106)
.||||||+-+..
T Consensus 211 ~lkMskqEvKdE 222 (342)
T TIGR01404 211 DLKMSKDEVKRE 222 (342)
T ss_pred hCCCCHHHHHHH
Confidence 589999976543
No 82
>PF10268 Tmemb_161AB: Predicted transmembrane protein 161AB; InterPro: IPR019395 This entry represents a family of conserved eukaryotic proteins. Members are putative transmembrane proteins but otherwise the function is not known.
Probab=25.84 E-value=2.3e+02 Score=25.07 Aligned_cols=28 Identities=32% Similarity=0.612 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHHHHHHHHHH---HHHHHHHH
Q 034024 38 RVDVVIFVIWELVILAFLVF---SAVSLYFR 65 (106)
Q Consensus 38 r~dvvv~v~w~llf~~l~v~---s~vtlYfr 65 (106)
..|+-+.++|.++.+++.+- +....||+
T Consensus 130 ~~e~Nisv~w~lL~v~F~lk~L~sLt~~yf~ 160 (486)
T PF10268_consen 130 STEFNISVVWCLLVVFFALKVLFSLTRLYFS 160 (486)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34677778898887776554 77778887
No 83
>PRK04307 putative disulfide oxidoreductase; Provisional
Probab=25.57 E-value=1.8e+02 Score=23.15 Aligned_cols=22 Identities=18% Similarity=0.448 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHH
Q 034024 46 IWELVILAFLVFSAVS-LYFRHM 67 (106)
Q Consensus 46 ~w~llf~~l~v~s~vt-lYfr~~ 67 (106)
.|.+++++-+..-..+ +||-|.
T Consensus 25 ~wlll~l~~~~L~~~Al~yfQ~v 47 (218)
T PRK04307 25 LWLLMAIAMGGLIILAHSFFQIY 47 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 7777776666666677 688775
No 84
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=25.11 E-value=5e+02 Score=24.42 Aligned_cols=32 Identities=28% Similarity=0.415 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 42 VIFVIWELVILAFLVFSAVSLYFRHMRLAIIL 73 (106)
Q Consensus 42 vv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ 73 (106)
+--+.+.+++.+++++-.+.+.|+.+|.+++.
T Consensus 337 ~~~~~~~l~~~~~lv~~vl~l~l~~~r~~li~ 368 (1049)
T PRK15127 337 IHEVVKTLVEAIILVFLVMYLFLQNFRATLIP 368 (1049)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence 44556666677777777777778877766544
No 85
>TIGR00077 lspA lipoprotein signal peptidase. Alternate name: lipoprotein signal peptidase
Probab=24.93 E-value=2.4e+02 Score=20.92 Aligned_cols=14 Identities=14% Similarity=0.135 Sum_probs=9.1
Q ss_pred hhhccc-ceeeeecC
Q 034024 17 RSKHEW-ASVSFFSS 30 (106)
Q Consensus 17 Rs~h~~-aals~fS~ 30 (106)
++-|+- +|.++|+.
T Consensus 51 ~~v~N~GaAFg~~~~ 65 (166)
T TIGR00077 51 TYVRNTGAAFSLLAD 65 (166)
T ss_pred EEEecCceEEecccC
Confidence 344444 88888876
No 86
>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
Probab=24.85 E-value=4.6e+02 Score=22.69 Aligned_cols=17 Identities=12% Similarity=0.192 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q 034024 61 SLYFRHMRLAIILVSIT 77 (106)
Q Consensus 61 tlYfr~~~Ls~~~ic~~ 77 (106)
.+++-..+++.+.+++.
T Consensus 287 ~l~~~~~~l~li~l~~~ 303 (710)
T TIGR03796 287 LMLLYDPVLTLIGIAFA 303 (710)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444445555554443
No 87
>PRK10663 cytochrome o ubiquinol oxidase subunit III; Provisional
Probab=24.70 E-value=3.2e+02 Score=20.78 Aligned_cols=58 Identities=14% Similarity=0.242 Sum_probs=34.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 034024 39 VDVVIFVIWELVILAFLVFSAVSLYFR-----------HMRLAIILVSITMLLLLCMKVTKQVRLARKKKR 98 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~v~s~vtlYfr-----------~~~Ls~~~ic~~ilL~~~lkitrq~rlarkreR 98 (106)
.-..+++.=|..+++.++++| +|.+ .+.+...++.-.+|+.-+.-+..-.+-+|+.+|
T Consensus 27 ~G~wlFi~sE~~~F~~lf~ay--~~~~~~~~~~p~~~~~~~lp~~~~nT~iLl~SS~~~~~A~~a~~~~~~ 95 (204)
T PRK10663 27 FGFWIYLMSDCILFSILFATY--AVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNK 95 (204)
T ss_pred ehhHHHHHHHHHHHHHHHHHH--HHHHhccCCCCCccccccccHHHHHHHHHHHHHHHHHHHHHHHHhCCH
Confidence 567888888888888888888 3333 222233345555566666666655555444333
No 88
>PLN02838 3-hydroxyacyl-CoA dehydratase subunit of elongase
Probab=24.53 E-value=1.4e+02 Score=23.69 Aligned_cols=21 Identities=14% Similarity=-0.064 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 034024 78 MLLLLCMKVTKQVRLARKKKR 98 (106)
Q Consensus 78 ilL~~~lkitrq~rlarkreR 98 (106)
.+..+-..|-||||++=++|+
T Consensus 199 g~~~ly~hM~~QRkK~l~~k~ 219 (221)
T PLN02838 199 GSPHMYSYMLGQRKKALSKSK 219 (221)
T ss_pred hHHHHHHHHHHHHHHHhcccc
Confidence 344566788899887765543
No 89
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=24.51 E-value=2.8e+02 Score=23.18 Aligned_cols=11 Identities=36% Similarity=0.299 Sum_probs=8.4
Q ss_pred HHHHHHHHHHH
Q 034024 83 CMKVTKQVRLA 93 (106)
Q Consensus 83 ~lkitrq~rla 93 (106)
.||||||+-+.
T Consensus 212 ~lrMskqEVKd 222 (347)
T TIGR00328 212 SLKMTKQEVKD 222 (347)
T ss_pred hCCCCHHHHHH
Confidence 58999997543
No 90
>PRK09759 small toxic polypeptide; Provisional
Probab=24.49 E-value=66 Score=20.64 Aligned_cols=19 Identities=26% Similarity=0.476 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034024 66 HMRLAIILVSITMLLLLCM 84 (106)
Q Consensus 66 ~~~Ls~~~ic~~ilL~~~l 84 (106)
+.-++.+++|++++..+-|
T Consensus 5 ~~l~~liivCiTvL~f~~l 23 (50)
T PRK09759 5 YRLLSLIVICFTLLFFTWM 23 (50)
T ss_pred eeHHHHHHHHHHHHHHHHH
Confidence 3446778899999876644
No 91
>PRK09776 putative diguanylate cyclase; Provisional
Probab=24.25 E-value=2e+02 Score=25.21 Aligned_cols=35 Identities=17% Similarity=0.251 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccC
Q 034024 68 RLAIILVSITMLLLLCMKVTKQVRLARKKKRRMLLP 103 (106)
Q Consensus 68 ~Ls~~~ic~~ilL~~~lkitrq~rlarkreRrllLP 103 (106)
|.++-.+..-+++|+.+-+... ++.+++.+++++|
T Consensus 140 w~~~~~~g~l~~~p~~l~~~~~-~~~~~~~~~~~~~ 174 (1092)
T PRK09776 140 WVLSEAIGMLALVPLGLLFKPH-YLLRHRNPRLLFE 174 (1092)
T ss_pred HHHHHHHHHHHHhhHhhhcchH-HHhhhcccchHHH
Confidence 6566666777778888866443 4555555555443
No 92
>PF10032 Pho88: Phosphate transport (Pho88); InterPro: IPR019263 This entry represents proteins involved in inorganic phosphate transport, as well as telomere length regulation and maintenance [, , , ].
Probab=24.21 E-value=1.7e+02 Score=22.71 Aligned_cols=30 Identities=27% Similarity=0.401 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 60 VSLYFRHMRLAIILVSITMLLLLCMKVTKQ 89 (106)
Q Consensus 60 vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq 89 (106)
+-.|.|..-.+..++|+++.+++..||.+.
T Consensus 28 v~~~vR~~y~~s~~i~~~~y~yi~~~I~~k 57 (192)
T PF10032_consen 28 VLFYVRIAYVASQLIILGVYLYIFSKIKKK 57 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 457888888888999999999998888654
No 93
>COG0586 DedA Uncharacterized membrane-associated protein [Function unknown]
Probab=24.08 E-value=3.2e+02 Score=20.59 Aligned_cols=17 Identities=18% Similarity=0.458 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHHHHHH
Q 034024 39 VDVVIFVIWELVILAFL 55 (106)
Q Consensus 39 ~dvvv~v~w~llf~~l~ 55 (106)
.|.+-+++|+.++..+-
T Consensus 145 ~n~~ga~iW~~~~~~lG 161 (208)
T COG0586 145 YNILGALLWALVLTLLG 161 (208)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 47888899998876654
No 94
>PF11511 RhodobacterPufX: Intrinsic membrane protein PufX; InterPro: IPR020169 PufX organises RC-LH1, the photosynthesis reaction centre-light harvesting complex 1 core complex of Rhodobacter sphaeroides []. It also facilitates the exchange of quinol for quinone between the reaction centre and cytochrome bc(1) complexes. In organic solvent, PufX contains two hydrophobic helices which are flanked by unstructured regions and connected by a helical bend [].; PDB: 2DW3_A 2ITA_A 2NRG_A.
Probab=23.51 E-value=1.3e+02 Score=20.59 Aligned_cols=26 Identities=27% Similarity=0.313 Sum_probs=16.7
Q ss_pred hhHHHHHH----HHHHHHHHHHHHHHHHHH
Q 034024 38 RVDVVIFV----IWELVILAFLVFSAVSLY 63 (106)
Q Consensus 38 r~dvvv~v----~w~llf~~l~v~s~vtlY 63 (106)
|.|+.-.. .|+-++|+...+..+++|
T Consensus 17 ~~~~~~qMlkGag~Aav~~~~~~~~l~~~~ 46 (67)
T PF11511_consen 17 RAWILFQMLKGAGYAAVFFLGLWFLLVALY 46 (67)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHHHHH
Confidence 44554443 466777777777777766
No 95
>PF15192 TMEM213: TMEM213 family
Probab=23.50 E-value=1.1e+02 Score=21.68 Aligned_cols=18 Identities=22% Similarity=0.539 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 034024 41 VVIFVIWELVILAFLVFS 58 (106)
Q Consensus 41 vvv~v~w~llf~~l~v~s 58 (106)
+.-+|.|.|.|+-|++.|
T Consensus 48 IAAAVGWSLwFLTLILLC 65 (82)
T PF15192_consen 48 IAAAVGWSLWFLTLILLC 65 (82)
T ss_pred HHHHHhHHHHHHHHHHHH
Confidence 467899999988776544
No 96
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=23.47 E-value=2.4e+02 Score=23.32 Aligned_cols=42 Identities=17% Similarity=0.184 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 034024 56 VFSAVSLYFRHMRLAIILVSITMLLLLCMKVTKQVRLARKKK 97 (106)
Q Consensus 56 v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq~rlarkre 97 (106)
=++++++|.--+.-...++++-+.+.+-.-|-|-||++|.+|
T Consensus 248 ~~~~~~~~t~I~aSiiaIliIVLIMvIIYLILRYRRKKKmkK 289 (299)
T PF02009_consen 248 NSTYASLTTAIIASIIAILIIVLIMVIIYLILRYRRKKKMKK 289 (299)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH
Confidence 344666776555555555555556666677888877555444
No 97
>KOG1746 consensus Defender against cell death protein/oligosaccharyltransferase, epsilon subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=23.36 E-value=96 Score=23.23 Aligned_cols=19 Identities=16% Similarity=0.492 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHH-HHHHHHH
Q 034024 68 RLAIILVSITML-LLLCMKV 86 (106)
Q Consensus 68 ~Ls~~~ic~~il-L~~~lki 86 (106)
-||+++.|+|-+ |.+|+||
T Consensus 58 FLSGfIscVg~fVLavclR~ 77 (115)
T KOG1746|consen 58 FLSGFISCVGQFVLAVCLRI 77 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 489999999965 6678876
No 98
>PRK09738 small toxic polypeptide; Provisional
Probab=23.20 E-value=64 Score=20.87 Aligned_cols=19 Identities=16% Similarity=0.520 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034024 66 HMRLAIILVSITMLLLLCM 84 (106)
Q Consensus 66 ~~~Ls~~~ic~~ilL~~~l 84 (106)
.+-++.++||++++..+-|
T Consensus 7 ~~~~~livvCiTvL~f~~l 25 (52)
T PRK09738 7 PLVWCVLIVCLTLLIFTYL 25 (52)
T ss_pred eehhhHHHHHHHHHHHHHH
Confidence 3446778899998876644
No 99
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.85 E-value=1.9e+02 Score=24.94 Aligned_cols=12 Identities=33% Similarity=0.205 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHH
Q 034024 83 CMKVTKQVRLAR 94 (106)
Q Consensus 83 ~lkitrq~rlar 94 (106)
.||||||+.+..
T Consensus 219 ~lkMtKqEVKdE 230 (363)
T COG1377 219 KLKMTKQEVKDE 230 (363)
T ss_pred HccCcHHHHHHH
Confidence 489999987643
No 100
>KOG4050 consensus Glutamate transporter EAAC1-interacting protein GTRAP3-18 [Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=22.78 E-value=2.8e+02 Score=22.34 Aligned_cols=30 Identities=7% Similarity=0.162 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 56 VFSAVSLYFRHMRLAIILVSITMLLLLCMK 85 (106)
Q Consensus 56 v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lk 85 (106)
.--.++..+-|.--+.....|+|+.|+.+-
T Consensus 115 gvllv~yfli~v~~~vlv~~F~il~Pv~L~ 144 (188)
T KOG4050|consen 115 GVLLVGYFLISVFGGVLVFAFAILFPVLLV 144 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566666676667777889999998653
No 101
>PRK09108 type III secretion system protein HrcU; Validated
Probab=22.77 E-value=3.1e+02 Score=22.94 Aligned_cols=11 Identities=9% Similarity=-0.061 Sum_probs=8.5
Q ss_pred HHHHHHHHHHH
Q 034024 83 CMKVTKQVRLA 93 (106)
Q Consensus 83 ~lkitrq~rla 93 (106)
.||||||+-+.
T Consensus 214 ~lkMSkqEvK~ 224 (353)
T PRK09108 214 DNRMSKDEVKR 224 (353)
T ss_pred HCCCCHHHHHH
Confidence 58999997653
No 102
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=22.59 E-value=4.5e+02 Score=24.77 Aligned_cols=44 Identities=18% Similarity=0.233 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 45 VIWELVILAFLVFSAVSLYFRHMRLAIILVSITMLLLLCMKVTK 88 (106)
Q Consensus 45 v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ic~~ilL~~~lkitr 88 (106)
.+.-.+|.+.++..++++++-|..-....+.+++++-..++.-+
T Consensus 12 ~~~~~lI~~~iiliiv~f~~~~~l~~i~~l~~~~~~i~~l~~~~ 55 (655)
T COG3887 12 YIFLGLIAFSIILIIVSFSFNWWLSAIAVLLLVVFLIFLLLAFT 55 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455667777888889999888777777777766666555443
No 103
>PRK14776 lipoprotein signal peptidase; Provisional
Probab=22.57 E-value=2.2e+02 Score=21.37 Aligned_cols=15 Identities=20% Similarity=0.125 Sum_probs=9.5
Q ss_pred hhhhccc-ceeeeecC
Q 034024 16 NRSKHEW-ASVSFFSS 30 (106)
Q Consensus 16 iRs~h~~-aals~fS~ 30 (106)
+++-|+- +|.|.|+.
T Consensus 49 l~~v~N~GaAFgll~~ 64 (170)
T PRK14776 49 WVHLWNTGAAFSLFAN 64 (170)
T ss_pred EEEEEeccEEEECCCC
Confidence 3444444 78888875
No 104
>PRK14413 membrane protein; Provisional
Probab=22.46 E-value=3.7e+02 Score=20.77 Aligned_cols=38 Identities=18% Similarity=0.307 Sum_probs=25.4
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 36 SSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAIIL 73 (106)
Q Consensus 36 ~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ 73 (106)
.+..-+..++-|....+++.++-.+.+..|+.-++.++
T Consensus 114 At~~Gvll~l~p~~~l~~~~~~~i~~~~tr~vSl~Si~ 151 (197)
T PRK14413 114 NTTLGVFIFIAPIPTLTGLAVYFILGLFTRIVSIRSIA 151 (197)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 45556666677777777777777777777777666543
No 105
>PF13268 DUF4059: Protein of unknown function (DUF4059)
Probab=22.02 E-value=1.7e+02 Score=20.23 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 59 AVSLYFRHMRLAIILVSITMLLLLCMKVTKQ 89 (106)
Q Consensus 59 ~vtlYfr~~~Ls~~~ic~~ilL~~~lkitrq 89 (106)
..++|.+-.-++++++.+--.+.+..|..|.
T Consensus 5 if~lYlqgL~ls~i~V~~~~~~wi~~Ra~~~ 35 (72)
T PF13268_consen 5 IFSLYLQGLLLSSILVLLVSGIWILWRALRK 35 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3579999999999998888888888887665
No 106
>PRK08156 type III secretion system protein SpaS; Validated
Probab=21.89 E-value=3.3e+02 Score=23.07 Aligned_cols=11 Identities=36% Similarity=0.160 Sum_probs=8.3
Q ss_pred HHHHHHHHHHH
Q 034024 83 CMKVTKQVRLA 93 (106)
Q Consensus 83 ~lkitrq~rla 93 (106)
.||||||+-+.
T Consensus 207 ~lkMSkqEvKd 217 (361)
T PRK08156 207 DMKMDKQEVKR 217 (361)
T ss_pred HCCCCHHHHHH
Confidence 58999997543
No 107
>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.
Probab=21.69 E-value=4.6e+02 Score=21.61 Aligned_cols=13 Identities=15% Similarity=0.209 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHH
Q 034024 64 FRHMRLAIILVSI 76 (106)
Q Consensus 64 fr~~~Ls~~~ic~ 76 (106)
.-...++.++++.
T Consensus 150 ~~~~~l~l~~l~~ 162 (529)
T TIGR02868 150 LLSVPAALVLAAG 162 (529)
T ss_pred HHhHHHHHHHHHH
Confidence 3344455544433
No 108
>PF15339 Afaf: Acrosome formation-associated factor
Probab=21.02 E-value=1.4e+02 Score=24.22 Aligned_cols=18 Identities=22% Similarity=0.551 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 034024 46 IWELVILAFLVFSAVSLY 63 (106)
Q Consensus 46 ~w~llf~~l~v~s~vtlY 63 (106)
.=-++|..|+.||+++||
T Consensus 139 mTl~lfv~Ll~~c~atly 156 (200)
T PF15339_consen 139 MTLFLFVILLAFCSATLY 156 (200)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334566777788888887
No 109
>TIGR03425 urea_degr_2 urea carboxylase-associated protein 2. A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes.
Probab=20.88 E-value=71 Score=25.55 Aligned_cols=28 Identities=32% Similarity=0.442 Sum_probs=25.8
Q ss_pred hhHHHHHHHHHhhhhhcccceeeeecCC
Q 034024 4 RSNLAEQLREYQNRSKHEWASVSFFSST 31 (106)
Q Consensus 4 RskLvEQLReyQiRs~h~~aals~fS~~ 31 (106)
+.|+.+.|.+|.+-.++-++++++|+..
T Consensus 120 ~dNl~~alak~Gl~~rdv~~~lNlFm~V 147 (233)
T TIGR03425 120 RDNLLLELGKYGLGRRDLVPNVNFFSKV 147 (233)
T ss_pred HHHHHHHHHHhCCCccccCCceeeeecc
Confidence 5799999999999999999999999984
No 110
>PF11840 DUF3360: Protein of unknown function (DUF3360); InterPro: IPR021794 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 489 to 517 amino acids in length.
Probab=20.85 E-value=86 Score=28.28 Aligned_cols=30 Identities=30% Similarity=0.579 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCC
Q 034024 68 RLAIILVSITMLLLLCMKVTKQVRLARKKKRRMLLPLS 105 (106)
Q Consensus 68 ~Ls~~~ic~~ilL~~~lkitrq~rlarkreRrllLPLS 105 (106)
+++|+++..+|.+|. -|++++||-+..|++
T Consensus 206 ~i~fvvi~~tiv~Ya--------~L~k~~KrWLaIPl~ 235 (492)
T PF11840_consen 206 YIAFVVIIVTIVLYA--------YLAKIEKRWLAIPLC 235 (492)
T ss_pred HHHHHHHHHHHHHHH--------HHHHhccchhhhhHH
Confidence 568888888888886 468889999999975
No 111
>TIGR01652 ATPase-Plipid phospholipid-translocating P-type ATPase, flippase. This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes.
Probab=20.83 E-value=3.7e+02 Score=25.11 Aligned_cols=19 Identities=16% Similarity=0.267 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034024 66 HMRLAIILVSITMLLLLCM 84 (106)
Q Consensus 66 ~~~Ls~~~ic~~ilL~~~l 84 (106)
.||+..+++++..++|.-.
T Consensus 1021 ~f~l~~ll~~~~~l~p~~~ 1039 (1057)
T TIGR01652 1021 GFWLVLLVIVLISLLPRFT 1039 (1057)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4777777777777777443
No 112
>PRK14412 membrane protein; Provisional
Probab=20.81 E-value=4.1e+02 Score=20.64 Aligned_cols=38 Identities=26% Similarity=0.195 Sum_probs=21.1
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 36 SSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRLAIIL 73 (106)
Q Consensus 36 ~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~Ls~~~ 73 (106)
.|..-+..++.|....++++++-.+.+..|+.-++.++
T Consensus 106 At~~Gvll~l~p~~~l~~~~v~~~~~~~tr~vSl~Si~ 143 (198)
T PRK14412 106 ATSVGVVMTVSPLLGIIALAIGVAIIALTKYVSLGSIT 143 (198)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555655555566665555566665555443
No 113
>PF05875 Ceramidase: Ceramidase; InterPro: IPR008901 This entry consists of several ceramidases. Ceramidases are enzymes involved in regulating cellular levels of ceramides, sphingoid bases, and their phosphates.; GO: 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides, 0006672 ceramide metabolic process, 0016021 integral to membrane
Probab=20.69 E-value=3.1e+02 Score=20.89 Aligned_cols=50 Identities=16% Similarity=0.324 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhhhhh
Q 034024 51 ILAFLVFSAVSLYF---RHMRLAIILVSITMLLLLCMKVTKQVR--LARKKKRRM 100 (106)
Q Consensus 51 f~~l~v~s~vtlYf---r~~~Ls~~~ic~~ilL~~~lkitrq~r--larkreRrl 100 (106)
+.+.+++++..++. .....++..+-+.+.+....-+.+..+ .+|++-+|+
T Consensus 119 ~~~~~~~t~~~~~~~~p~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 173 (262)
T PF05875_consen 119 FIYAVVVTVLYFVLDNPVFHQIAFASLVLLVILRSIYLIRRRVRDACRRRRARRL 173 (262)
T ss_pred HHHHHHHHHHHhhhccchhhhhhHHHHHHHHHHHHHHHHHHhcCchhhchHHHHH
Confidence 33444455555552 223344444333333333333333111 344444444
No 114
>KOG0812 consensus SNARE protein SED5/Syntaxin 5 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.68 E-value=1.1e+02 Score=26.21 Aligned_cols=26 Identities=38% Similarity=0.534 Sum_probs=14.0
Q ss_pred CCCCcchhH-HHHHHHHHHHHHHHHHH
Q 034024 32 SNISSSRVD-VVIFVIWELVILAFLVF 57 (106)
Q Consensus 32 ~~~~~sr~d-vvv~v~w~llf~~l~v~ 57 (106)
.++|+.||= +.++.+|-++|+.+++|
T Consensus 283 e~vSSNRwLmvkiF~i~ivFflvfvlf 309 (311)
T KOG0812|consen 283 ERVSSNRWLMVKIFGILIVFFLVFVLF 309 (311)
T ss_pred HHhccchHHHHHHHHHHHHHHHHHHHh
Confidence 355666663 44555555555554443
No 115
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=20.60 E-value=57 Score=25.02 Aligned_cols=12 Identities=33% Similarity=0.512 Sum_probs=9.4
Q ss_pred HHHHHHHHhhhh
Q 034024 7 LAEQLREYQNRS 18 (106)
Q Consensus 7 LvEQLReyQiRs 18 (106)
--|.|||||+-.
T Consensus 75 Y~EaLRDfq~~~ 86 (139)
T PF12583_consen 75 YSEALRDFQCSW 86 (139)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 468999999853
No 116
>PF07782 DC_STAMP: DC-STAMP-like protein; InterPro: IPR012858 This group of sequences is similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP, Q9H295 from SWISSPROT). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins []. It is thought to have seven putative transmembrane regions [], two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC [], but these are not conserved. ; GO: 0016021 integral to membrane
Probab=20.57 E-value=2.3e+02 Score=20.99 Aligned_cols=36 Identities=17% Similarity=0.171 Sum_probs=16.1
Q ss_pred CCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 30 STSNISSSRVDVVIFVIWELVILAFLVFSAVSLYFRHMRL 69 (106)
Q Consensus 30 ~~~~~~~sr~dvvv~v~w~llf~~l~v~s~vtlYfr~~~L 69 (106)
|+|+...+..=+.+.++|.++++. +...-|....|-
T Consensus 137 p~P~~p~~~~~~~i~~l~~l~~ll----~~le~Y~~RLR~ 172 (191)
T PF07782_consen 137 PQPSPPDYSVYIQIGLLYLLLWLL----VLLEPYALRLRR 172 (191)
T ss_pred CCCcCCChHHHHHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence 333333344444445555544444 444445544443
No 117
>PRK13592 ubiA prenyltransferase; Provisional
Probab=20.52 E-value=3.6e+02 Score=22.58 Aligned_cols=35 Identities=9% Similarity=0.259 Sum_probs=23.2
Q ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 56 VFSAVSLY-FRHMRLAIILVSITMLLLLCMKVTKQV 90 (106)
Q Consensus 56 v~s~vtlY-fr~~~Ls~~~ic~~ilL~~~lkitrq~ 90 (106)
+.|..-+. +-+++...+.+|..++++-|.+.-|..
T Consensus 231 ~~s~lp~~~~g~~g~~~l~~~~~~~l~~~~~~lk~p 266 (299)
T PRK13592 231 LTNFALLWNISHVGVVVLVLNVIWMTVQFEQFIKSP 266 (299)
T ss_pred HHhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcCC
Confidence 33443333 456666777789999998888776653
No 118
>COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion]
Probab=20.35 E-value=5.4e+02 Score=22.75 Aligned_cols=30 Identities=23% Similarity=0.165 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034024 40 DVVIFVIWELVILAFLVFSAVSLYFRHMRL 69 (106)
Q Consensus 40 dvvv~v~w~llf~~l~v~s~vtlYfr~~~L 69 (106)
|-+-.-+-|.++-+.+|.-+|.+|+|.+++
T Consensus 340 ~~i~~gi~Agl~g~~~V~vfm~~~Yr~~Gv 369 (506)
T COG0342 340 DSIKAGLIAGLIGLALVAVFMLLYYRLAGV 369 (506)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 444444555555566777788999996554
No 119
>PRK14726 bifunctional preprotein translocase subunit SecD/SecF; Provisional
Probab=20.06 E-value=7.6e+02 Score=23.48 Aligned_cols=34 Identities=3% Similarity=0.072 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Q 034024 38 RVDVVIFVIWELVILAFLVFSAVSLYFRH-MRLAI 71 (106)
Q Consensus 38 r~dvvv~v~w~llf~~l~v~s~vtlYfr~-~~Ls~ 71 (106)
..+..---+||+++.++.++-|++++|+| |.++.
T Consensus 667 G~el~~~ai~Al~iAli~IliYI~~RF~~~fa~~a 701 (855)
T PRK14726 667 SGELTMAATLGVLAALAAILIYIWIRFEWQFAVGA 701 (855)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 34666677889999999999999999985 44443
Done!