Query psy674
Match_columns 70
No_of_seqs 100 out of 126
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:13:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy674.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/674hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00918 2A060602 The Eukaryo 99.9 5.4E-28 1.2E-32 200.7 5.6 70 1-70 25-94 (1145)
2 KOG1935|consensus 99.9 9.8E-25 2.1E-29 178.6 4.6 69 1-69 41-109 (1143)
3 TIGR00917 2A060601 Niemann-Pic 99.4 2E-13 4.2E-18 114.5 5.6 60 11-70 301-360 (1204)
4 KOG1933|consensus 99.0 3.5E-10 7.5E-15 95.7 3.6 56 14-69 282-337 (1201)
5 TIGR00921 2A067 The (Largely A 96.3 0.0067 1.5E-07 47.7 4.3 49 17-65 366-414 (719)
6 KOG1934|consensus 95.0 0.029 6.3E-07 47.2 3.9 53 14-66 4-56 (868)
7 TIGR00833 actII Transport prot 94.2 0.073 1.6E-06 44.2 4.3 46 19-64 346-391 (910)
8 TIGR03480 HpnN hopanoid biosyn 94.1 0.063 1.4E-06 44.0 3.8 42 23-64 2-44 (862)
9 COG1033 Predicted exporters of 93.7 0.11 2.5E-06 43.0 4.5 52 16-68 365-416 (727)
10 COG1033 Predicted exporters of 93.3 0.13 2.8E-06 42.7 4.2 41 23-63 2-42 (727)
11 TIGR00921 2A067 The (Largely A 93.0 0.074 1.6E-06 41.9 2.4 33 32-64 2-34 (719)
12 TIGR03480 HpnN hopanoid biosyn 91.5 0.27 5.8E-06 40.4 4.0 45 21-65 435-479 (862)
13 TIGR00920 2A060605 3-hydroxy-3 89.1 0.2 4.4E-06 42.6 1.4 28 19-46 2-29 (886)
14 PF05957 DUF883: Bacterial pro 82.0 6.4 0.00014 24.0 5.3 41 10-50 49-89 (94)
15 TIGR00914 2A0601 heavy metal e 72.4 9.9 0.00022 32.3 5.4 46 16-61 519-564 (1051)
16 PF08496 Peptidase_S49_N: Pept 70.8 9.1 0.0002 26.2 4.1 34 21-54 2-35 (155)
17 PRK10614 multidrug efflux syst 70.8 9.1 0.0002 32.5 4.8 44 18-61 510-553 (1025)
18 PF00873 ACR_tran: AcrB/AcrD/A 69.0 17 0.00037 30.5 6.0 42 15-56 508-549 (1021)
19 PF01004 Flavi_M: Flavivirus e 61.7 10 0.00022 23.4 2.6 41 12-52 17-58 (75)
20 PRK10404 hypothetical protein; 60.2 38 0.00083 21.5 5.2 29 20-48 66-94 (101)
21 COG2409 Predicted drug exporte 59.5 7.9 0.00017 32.8 2.4 33 22-54 2-34 (937)
22 PF14980 TIP39: TIP39 peptide 59.5 7.4 0.00016 22.5 1.6 10 14-23 38-47 (51)
23 PF11139 DUF2910: Protein of u 57.2 42 0.0009 23.0 5.4 38 13-50 172-209 (214)
24 PRK07118 ferredoxin; Validated 49.5 19 0.00041 26.5 2.8 24 39-62 13-36 (280)
25 TIGR00914 2A0601 heavy metal e 47.7 31 0.00066 29.4 4.1 39 24-62 3-41 (1051)
26 PF13323 HPIH: N-terminal doma 47.6 12 0.00026 25.4 1.5 37 18-54 3-39 (153)
27 PRK05113 electron transport co 46.1 24 0.00051 24.5 2.7 23 40-62 14-36 (191)
28 PRK10132 hypothetical protein; 46.1 80 0.0017 20.4 5.2 29 20-48 72-100 (108)
29 TIGR01760 tape_meas_TP901 phag 46.0 56 0.0012 23.5 4.8 35 15-49 313-347 (350)
30 PF06363 Picorna_P3A: Picornav 41.7 94 0.002 20.2 4.8 35 10-44 45-79 (100)
31 COG2878 Predicted NADH:ubiquin 41.7 26 0.00057 25.3 2.4 24 39-62 13-36 (198)
32 KOG2322|consensus 39.7 41 0.00089 24.9 3.2 37 24-60 126-162 (237)
33 PHA02662 ORF131 putative membr 39.6 31 0.00068 25.4 2.6 40 1-42 150-194 (226)
34 PF02460 Patched: Patched fami 39.2 65 0.0014 26.4 4.6 47 20-66 422-470 (798)
35 PRK11114 cellulose synthase re 38.6 41 0.00089 27.9 3.4 31 24-54 714-744 (756)
36 TIGR00915 2A0602 The (Largely 38.6 67 0.0015 27.5 4.7 35 18-52 522-556 (1044)
37 KOG4489|consensus 38.0 76 0.0016 20.1 3.8 27 10-36 18-44 (87)
38 PF10777 YlaC: Inner membrane 36.6 51 0.0011 23.0 3.2 24 28-51 30-53 (155)
39 COG4575 ElaB Uncharacterized c 35.7 44 0.00096 21.9 2.6 25 24-48 73-97 (104)
40 PF13456 RVT_3: Reverse transc 35.5 45 0.00098 18.5 2.4 19 44-62 13-31 (87)
41 PRK10503 multidrug efflux syst 34.9 39 0.00085 28.9 2.8 37 26-62 12-48 (1040)
42 PRK10503 multidrug efflux syst 33.2 1E+02 0.0022 26.5 5.0 31 18-48 520-550 (1040)
43 PRK11778 putative inner membra 33.0 64 0.0014 24.6 3.5 33 22-54 1-33 (330)
44 PF15086 UPF0542: Uncharacteri 32.8 89 0.0019 19.4 3.5 25 20-44 5-29 (74)
45 PRK10370 formate-dependent nit 32.7 48 0.001 22.5 2.6 22 33-54 6-27 (198)
46 PF06936 Selenoprotein_S: Sele 32.6 15 0.00032 26.1 0.0 30 19-48 22-51 (190)
47 PF00873 ACR_tran: AcrB/AcrD/A 31.7 67 0.0014 27.1 3.7 35 28-62 3-37 (1021)
48 PF13124 DUF3963: Protein of u 31.6 95 0.0021 17.0 4.7 31 17-50 7-37 (40)
49 PF10031 DUF2273: Small integr 31.5 76 0.0017 17.9 2.9 26 28-53 2-30 (51)
50 PRK10614 multidrug efflux syst 30.4 48 0.001 28.3 2.7 38 25-62 2-39 (1025)
51 TIGR01944 rnfB electron transp 30.2 63 0.0014 21.6 2.8 22 40-61 12-33 (165)
52 COG1811 Uncharacterized membra 28.6 81 0.0018 23.3 3.3 34 18-51 74-109 (228)
53 PF09911 DUF2140: Uncharacteri 27.8 78 0.0017 21.9 3.0 28 33-60 1-28 (187)
54 PF05781 MRVI1: MRVI1 protein; 27.5 1.6E+02 0.0035 24.3 5.1 32 18-50 461-492 (538)
55 cd03383 PAP2_diacylglycerolkin 26.7 66 0.0014 20.4 2.3 33 30-62 5-37 (109)
56 TIGR00915 2A0602 The (Largely 25.5 63 0.0014 27.7 2.5 35 28-62 3-37 (1044)
57 PF05915 DUF872: Eukaryotic pr 25.1 92 0.002 20.3 2.8 34 32-65 38-77 (115)
58 PF06692 MNSV_P7B: Melon necro 24.4 84 0.0018 18.7 2.2 19 34-52 16-34 (61)
59 PRK09579 multidrug efflux prot 23.7 82 0.0018 27.0 2.9 37 26-62 3-39 (1017)
60 PF11455 DUF3018: Protein of 23.6 39 0.00084 20.3 0.7 10 60-69 18-27 (65)
61 PRK11901 hypothetical protein; 23.5 78 0.0017 24.5 2.5 21 34-54 36-56 (327)
62 PF14066 DUF4256: Protein of u 23.5 15 0.00032 26.1 -1.3 27 28-66 11-37 (173)
63 COG3337 CRISPR system related 23.3 67 0.0015 21.9 1.9 27 22-48 26-52 (134)
64 PRK13836 conjugal transfer pro 23.2 2E+02 0.0043 20.1 4.3 34 20-53 16-51 (220)
65 PF01456 Mucin: Mucin-like gly 23.1 64 0.0014 20.6 1.7 13 38-50 6-18 (143)
66 PF12911 OppC_N: N-terminal TM 23.0 1.4E+02 0.003 16.0 3.1 19 28-46 10-28 (56)
67 PRK15127 multidrug efflux syst 22.8 80 0.0017 27.1 2.7 35 28-62 3-37 (1049)
68 COG2409 Predicted drug exporte 21.9 43 0.00094 28.5 0.9 38 19-56 357-394 (937)
69 KOG0860|consensus 21.7 1.4E+02 0.0031 19.8 3.2 27 29-55 87-113 (116)
70 PRK01207 methionine synthase; 21.5 38 0.00082 25.9 0.5 10 60-69 305-314 (343)
71 PRK06052 5-methyltetrahydropte 21.4 35 0.00076 26.4 0.3 10 60-69 305-314 (344)
72 PF02117 7TM_GPCR_Sra: Serpent 20.9 3.1E+02 0.0066 20.3 5.2 52 11-65 120-171 (328)
73 PF11174 DUF2970: Protein of u 20.9 1.2E+02 0.0027 17.4 2.5 26 29-54 25-50 (56)
74 TIGR02120 GspF general secreti 20.8 2.1E+02 0.0045 21.3 4.3 37 10-48 349-385 (399)
75 PRK10555 aminoglycoside/multid 20.4 3E+02 0.0064 23.7 5.5 30 19-48 522-551 (1037)
76 PF15464 DUF4633: Domain of un 20.4 83 0.0018 20.9 1.8 31 7-39 81-111 (115)
77 TIGR03746 conj_TIGR03746 integ 20.2 1.4E+02 0.0029 21.7 3.0 25 42-69 23-47 (202)
78 PF06422 PDR_CDR: CDR ABC tran 20.1 1.5E+02 0.0032 18.5 2.9 43 18-60 36-78 (103)
No 1
>TIGR00918 2A060602 The Eukaryotic (Putative) Sterol Transporter (EST) Family.
Probab=99.94 E-value=5.4e-28 Score=200.73 Aligned_cols=70 Identities=47% Similarity=0.935 Sum_probs=68.4
Q ss_pred CCcccccccchhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccccCCC
Q psy674 1 MFKGKAEGQRTALWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWIEGRH 70 (70)
Q Consensus 1 i~~g~a~G~r~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWVsp~~ 70 (70)
|+||||+|||+|||+|+++|++|+++|++|||||++||+++++++++||+||++++||||||||||||+.
T Consensus 25 ~~~g~a~g~~~~l~~~~~~q~~~~~~G~~~~~~p~~vl~~~~~~~~~~~~Gl~~~~ietdp~~LWv~~~s 94 (1145)
T TIGR00918 25 IDKGKATGRRAPLWLRAKFQRLLFTLGCYIQKHCGKVLFVGLLVFSAFAVGLRAANIETNVEQLWVEVGG 94 (1145)
T ss_pred hhhhhccCccccHHHHHHHHHHHHHHHHHHHHCchhhhhHHHHHHHHHHhhHhheEEEecHHHhccCCCC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999973
No 2
>KOG1935|consensus
Probab=99.90 E-value=9.8e-25 Score=178.65 Aligned_cols=69 Identities=51% Similarity=0.904 Sum_probs=67.9
Q ss_pred CCcccccccchhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccccCC
Q psy674 1 MFKGKAEGQRTALWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWIEGR 69 (70)
Q Consensus 1 i~~g~a~G~r~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWVsp~ 69 (70)
|+||||+|||+|||+|+++|+++|+|||++|||+|+|||++++++++||+||+.++||||.|||||+.|
T Consensus 41 i~kGKA~g~r~al~lRa~fQ~lLf~lGc~vqr~agkvlfv~~lif~~~~~GLr~a~IeT~~~qLWV~~G 109 (1143)
T KOG1935|consen 41 IKKGKATGNRAALYLRAFFQLLLFRLGCFVQRHAGKVLFVGLLIFGAFCVGLRHATIETDLVQLWVEEG 109 (1143)
T ss_pred HhhccccCchhhHHHHHHHHHHHHHhhhHHHhhhhhhHHHHHHHHHHHHhhhhheeeeccHHHHHHHhc
Confidence 789999999999999999999999999999999999999999999999999999999999999999986
No 3
>TIGR00917 2A060601 Niemann-Pick C type protein family. The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis.
Probab=99.42 E-value=2e-13 Score=114.48 Aligned_cols=60 Identities=22% Similarity=0.356 Sum_probs=57.4
Q ss_pred hhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccccCCC
Q psy674 11 TALWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWIEGRH 70 (70)
Q Consensus 11 ~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWVsp~~ 70 (70)
..-+++.+++++|+++|.+++|||+++|+++++++++||+|+.++++||||++||++|+.
T Consensus 301 ~~~~~~~~l~~~F~~~G~~var~P~~vi~isllv~~~l~~Gl~~~~vetDpv~Lw~~~~s 360 (1204)
T TIGR00917 301 QLATVEGHLARFFTKYGIWVARNPGLVLCLSVSVVLLLGVGLIFFEVETDPVKLWVAPGS 360 (1204)
T ss_pred hhhHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHhCcccCChhhhcCCCCc
Confidence 477899999999999999999999999999999999999999999999999999999973
No 4
>KOG1933|consensus
Probab=98.97 E-value=3.5e-10 Score=95.71 Aligned_cols=56 Identities=23% Similarity=0.378 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccccCC
Q psy674 14 WFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWIEGR 69 (70)
Q Consensus 14 ~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWVsp~ 69 (70)
+.+++++.+|.++|.|+++||.+++++++.+++.||.|+.+++++|||++||++|+
T Consensus 282 ~~~~~l~~~F~~~g~~~~~~P~~~~~~~~~~~i~~s~gli~~~v~T~pv~lW~~~~ 337 (1201)
T KOG1933|consen 282 STETFLEVFFRRWGTFCARNPLIVLYIILFVVIALSSGLIYFMVTTDPVDLWSLAR 337 (1201)
T ss_pred hHHHHHHHHhhhcccceecCchhhhHHHHHHHHHhccchhheeeeccchhhccCCc
Confidence 68899999999999999999999999999999999999999999999999999986
No 5
>TIGR00921 2A067 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family. Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea.
Probab=96.25 E-value=0.0067 Score=47.74 Aligned_cols=49 Identities=22% Similarity=0.165 Sum_probs=43.9
Q ss_pred HHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCcccc
Q psy674 17 SKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLW 65 (70)
Q Consensus 17 ~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLW 65 (70)
+.+++.+.++|.++.|||+.++.+.++++++..+|..++++|.|+.++.
T Consensus 366 ~~~~~~l~~~~~~~~r~~~~vl~v~lll~~~~~~~~~~l~~~~d~~~~~ 414 (719)
T TIGR00921 366 SEIEEELSKVLSITVRHPVPALVAALIITGLGLYGAAGIKPEVNIEKFI 414 (719)
T ss_pred hHHHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhccCCCcccChhhcC
Confidence 3567789999999999999999999999999999999999999998763
No 6
>KOG1934|consensus
Probab=95.04 E-value=0.029 Score=47.15 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccc
Q psy674 14 WFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWI 66 (70)
Q Consensus 14 ~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWV 66 (70)
++......+|+++|.+++|||+..|.+.++.++.|+.|+..+..|.|+-.+.=
T Consensus 4 ~~~r~~~~~f~~~g~~v~~~p~~~ii~~l~lt~~~s~g~~~~~~~~d~~~~yt 56 (868)
T KOG1934|consen 4 RLERILKVLFRKYGLFVARYPWFFIIIPLLLTAVLSVGILPLLTEDDARYLYT 56 (868)
T ss_pred hHHHHHHHHHHHhCceeeecchHHHHHHHHHHHHHhcCchhheecCCcceeeC
Confidence 34556778899999999999999999999999999999988899999877643
No 7
>TIGR00833 actII Transport protein. Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This sub-family includes the S. coelicolor ActII3 protein, which may play a role in drug resistance, and the M. tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate.
Probab=94.18 E-value=0.073 Score=44.17 Aligned_cols=46 Identities=15% Similarity=0.080 Sum_probs=40.7
Q ss_pred HHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccc
Q psy674 19 LQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDL 64 (70)
Q Consensus 19 lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kL 64 (70)
.+..+.+++.++.|||+.++.+++++++++.++..++++|.|+.+.
T Consensus 346 ~~~~~~~l~~~v~r~p~~vl~v~~~ll~~~~~~~~~l~~~~~~~~~ 391 (910)
T TIGR00833 346 IRFIWRRLGTAVVRRPWPILVTTLIISGVSLLALPLIRTGYDDEKM 391 (910)
T ss_pred HhHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCcCCCcHhh
Confidence 4457889999999999999999999999999999999999887663
No 8
>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.
Probab=94.12 E-value=0.063 Score=43.96 Aligned_cols=42 Identities=31% Similarity=0.354 Sum_probs=36.5
Q ss_pred HHHHcHHHHhhhhHHHHHHHHHHHHHHh-hhhceeeeccCccc
Q psy674 23 LFSLGRFLQRHAGKVIFVALLILLTFCV-GLKTHVVHSKIEDL 64 (70)
Q Consensus 23 f~~lG~~var~p~~vi~~~ll~~~~l~~-Gl~~~~iETdp~kL 64 (70)
|.++-.++.|||+.++.++++++++++. +..+++++||..+|
T Consensus 2 ~~~~~~~~~~~~~~vl~~~~~lt~~~~~~~~~~l~i~td~~~L 44 (862)
T TIGR03480 2 LVRLVGFCARHAWWVLAIALLLTALSVIYTVTNLSVNTDTSDL 44 (862)
T ss_pred hHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHhceecCCHHHh
Confidence 4567789999999999988888888885 78899999999887
No 9
>COG1033 Predicted exporters of the RND superfamily [General function prediction only]
Probab=93.67 E-value=0.11 Score=43.00 Aligned_cols=52 Identities=25% Similarity=0.447 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccccC
Q psy674 16 RSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWIEG 68 (70)
Q Consensus 16 ~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWVsp 68 (70)
.+.+.+.+.+.+....|||..++.+.+++++..-.|..+.++|+|.+| -.+|
T Consensus 365 ~~~~~~~l~~i~~~~~~~~~~~L~vali~~~~~~yg~~~v~~~~d~~k-~~p~ 416 (727)
T COG1033 365 KGKLEKRLSKIAKIIARHPVTVLVVALIIVGVSLYGASKVKIETDIEK-YLPQ 416 (727)
T ss_pred chhHHHHHHHHHHHhHhhhHHHHHHHHHHHHHHHhhhhhcccccchHh-hcCC
Confidence 356888999999999999999999999999999999999999999988 4443
No 10
>COG1033 Predicted exporters of the RND superfamily [General function prediction only]
Probab=93.32 E-value=0.13 Score=42.72 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=38.4
Q ss_pred HHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCcc
Q psy674 23 LFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIED 63 (70)
Q Consensus 23 f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~k 63 (70)
|.+++.++++||+.++++.++++.+...|.+++++++|-++
T Consensus 2 ~~kl~~fi~~~r~~i~~~~~~l~i~~~~~a~~l~~~s~~~~ 42 (727)
T COG1033 2 FEKLARFIIRRRKSIILIFLLLTILSAFGAQNLEFDSGTET 42 (727)
T ss_pred hHHHHHHHHhCccHHHHHHHHHHHHHHHhhheeeecCCccc
Confidence 78999999999999999999999999999999999999544
No 11
>TIGR00921 2A067 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family. Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea.
Probab=93.01 E-value=0.074 Score=41.93 Aligned_cols=33 Identities=27% Similarity=0.318 Sum_probs=31.2
Q ss_pred hhhhHHHHHHHHHHHHHHhhhhceeeeccCccc
Q psy674 32 RHAGKVIFVALLILLTFCVGLKTHVVHSKIEDL 64 (70)
Q Consensus 32 r~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kL 64 (70)
|||++++.+.+++++++..|+.++++++|++++
T Consensus 2 ~~~~~v~~~~~~l~~~~~~g~~~l~~~~~~~~~ 34 (719)
T TIGR00921 2 RFRTAIILVFLALLILSAYGAQHLNVESDTEKQ 34 (719)
T ss_pred CCchhhHHHHHHHHHHHHHhcccceeccChhhh
Confidence 799999999999999999999999999999864
No 12
>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.
Probab=91.53 E-value=0.27 Score=40.38 Aligned_cols=45 Identities=24% Similarity=0.205 Sum_probs=39.7
Q ss_pred HHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCcccc
Q psy674 21 RELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLW 65 (70)
Q Consensus 21 ~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLW 65 (70)
+++.+++.++.|||..++.++++++++...++...++|.||.++.
T Consensus 435 ~~~~~~~~~~~~~~~~v~~~~l~l~~~~~~~~~~~~~~~~~~~~~ 479 (862)
T TIGR03480 435 ATLAPLDAFLRRHRRPVLGVTLILGIAALALLPQLRFDFNPLNLQ 479 (862)
T ss_pred hhHHHHHHHHHhccHHHHHHHHHHHHHHHHHhccCCCCCCchhcc
Confidence 467788999999999999999999999999999999999986654
No 13
>TIGR00920 2A060605 3-hydroxy-3-methylglutaryl-coenzyme A reductase.
Probab=89.14 E-value=0.2 Score=42.56 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=23.0
Q ss_pred HHHHHHHHcHHHHhhhhHHHHHHHHHHH
Q psy674 19 LQRELFSLGRFLQRHAGKVIFVALLILL 46 (70)
Q Consensus 19 lq~~f~~lG~~var~p~~vi~~~ll~~~ 46 (70)
+.++|+..|.||+.|||=||.-.+-+++
T Consensus 2 ~~rlf~~hg~fcashpweviv~~~tlt~ 29 (886)
T TIGR00920 2 LSRLFRAHGQFCASHPWEVIVATLTLTI 29 (886)
T ss_pred chhHhhhhcchhcCCCceehhhHHHHHH
Confidence 4678999999999999999876655544
No 14
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=82.01 E-value=6.4 Score=24.00 Aligned_cols=41 Identities=7% Similarity=-0.003 Sum_probs=31.4
Q ss_pred chhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHh
Q psy674 10 RTALWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCV 50 (70)
Q Consensus 10 r~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~ 50 (70)
..+--++...+..-.....+|..||+..+.+++.+=++++.
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~V~e~P~~svgiAagvG~llG~ 89 (94)
T PF05957_consen 49 DAADQAREQAREAAEQTEDYVRENPWQSVGIAAGVGFLLGL 89 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHH
Confidence 33445667788888999999999999999888776555543
No 15
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=72.43 E-value=9.9 Score=32.26 Aligned_cols=46 Identities=11% Similarity=-0.143 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccC
Q psy674 16 RSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKI 61 (70)
Q Consensus 16 ~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp 61 (70)
+.++++.|.++=.|+-|||+.+++++++++++....+.++..|--|
T Consensus 519 ~~~~~~~Y~~~l~~~l~~~~~~i~~~~~ll~~~~~~~~~l~~~f~P 564 (1051)
T TIGR00914 519 MRVLKRRYEPLLERVLAWPAVVLGAAAVSIVLVVWIASRVGGEFIP 564 (1051)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcCcCcCC
Confidence 3367888999999999999999998888877665555554444443
No 16
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=70.84 E-value=9.1 Score=26.18 Aligned_cols=34 Identities=21% Similarity=0.300 Sum_probs=28.6
Q ss_pred HHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhc
Q psy674 21 RELFSLGRFLQRHAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 21 ~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
.+|+.||-|.++=-.+|+.+.+++.++.+++-+.
T Consensus 2 efl~~yglFlaK~vTvVvaI~~vv~~I~~~~~k~ 35 (155)
T PF08496_consen 2 EFLYEYGLFLAKIVTVVVAILAVVGLIVAAAQKK 35 (155)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 4789999999998888888888888888877654
No 17
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=70.75 E-value=9.1 Score=32.49 Aligned_cols=44 Identities=14% Similarity=-0.155 Sum_probs=32.6
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccC
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKI 61 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp 61 (70)
++++.+.++=.++-|||+.++++++++++++.....+...|--|
T Consensus 510 ~l~~~Y~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~f~P 553 (1025)
T PRK10614 510 ALQQGYGRSLKWVLNHTRWVGVVLLGTIALNVWLYISIPKTFFP 553 (1025)
T ss_pred HHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHhCCCCcCC
Confidence 46777888888999999999998888777666655555545444
No 18
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=69.00 E-value=17 Score=30.52 Aligned_cols=42 Identities=31% Similarity=0.350 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhcee
Q psy674 15 FRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHV 56 (70)
Q Consensus 15 ~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~ 56 (70)
...++++.|.++=.++-+||++++.+.++++++....+....
T Consensus 508 ~~~~l~~~Y~~lL~~~L~~~~~~l~i~l~l~i~s~~l~~~l~ 549 (1021)
T PF00873_consen 508 FFDRLQRGYRRLLRWALRHPKLVLLIALLLLILSLFLFPFLP 549 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHCTSE
T ss_pred cccccccchhhhhhhhhhcccchhhhhhhhhhhhhcccccCC
Confidence 445688888889999999999999998877776444443333
No 19
>PF01004 Flavi_M: Flavivirus envelope glycoprotein M; InterPro: IPR000069 Flaviviruses are small enveloped viruses with virions comprised of three proteins called C, M and E [, , ]. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.; GO: 0019058 viral infectious cycle, 0019028 viral capsid
Probab=61.69 E-value=10 Score=23.35 Aligned_cols=41 Identities=15% Similarity=0.238 Sum_probs=30.4
Q ss_pred hHHHHH-HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhh
Q psy674 12 ALWFRS-KLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGL 52 (70)
Q Consensus 12 al~~~~-~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl 52 (70)
..|+.+ ...+.+.|.=.|+-|||+.++...++.-.+.+--.
T Consensus 17 ~~Wl~~~~~~~hl~rvE~WilrNp~~al~a~~l~w~lg~s~~ 58 (75)
T PF01004_consen 17 ETWLDSDSAWKHLTRVESWILRNPGYALAAVALAWMLGSSTT 58 (75)
T ss_pred cccccCccHHHHHHHHHHHHhcCchHHHHHHHHHHHHcCCch
Confidence 355443 56778888999999999999998887765554433
No 20
>PRK10404 hypothetical protein; Provisional
Probab=60.19 E-value=38 Score=21.53 Aligned_cols=29 Identities=10% Similarity=0.196 Sum_probs=20.3
Q ss_pred HHHHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 20 QRELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 20 q~~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
+..-..--.+|+.|||..+.++..+=+++
T Consensus 66 k~aa~~td~yV~e~Pw~avGiaagvGlll 94 (101)
T PRK10404 66 KQAVYRADDYVHEKPWQGIGVGAAVGLVL 94 (101)
T ss_pred HHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence 44445556779999999998877644443
No 21
>COG2409 Predicted drug exporters of the RND superfamily [General function prediction only]
Probab=59.53 E-value=7.9 Score=32.76 Aligned_cols=33 Identities=30% Similarity=0.476 Sum_probs=26.7
Q ss_pred HHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhc
Q psy674 22 ELFSLGRFLQRHAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 22 ~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
.++++|+++.||++.+|..-+++.+++.+-.-.
T Consensus 2 ~~~~~~r~i~r~~~~vi~~Wi~~~~~~~~~~p~ 34 (937)
T COG2409 2 GLFPIGRFIRRFAWAVILAWIALAVVLNLFAPT 34 (937)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHhccch
Confidence 356799999999999999999888877654433
No 22
>PF14980 TIP39: TIP39 peptide
Probab=59.51 E-value=7.4 Score=22.54 Aligned_cols=10 Identities=40% Similarity=0.866 Sum_probs=8.6
Q ss_pred HHHHHHHHHH
Q psy674 14 WFRSKLQREL 23 (70)
Q Consensus 14 ~~~~~lq~~f 23 (70)
|+||++|+.+
T Consensus 38 WLnSYMqkLL 47 (51)
T PF14980_consen 38 WLNSYMQKLL 47 (51)
T ss_pred HHHHHHHHHH
Confidence 8899999876
No 23
>PF11139 DUF2910: Protein of unknown function (DUF2910); InterPro: IPR021315 Some members in this bacterial family annotate the proteins as cytochrome C biogenesis proteins however this cannot be confirmed. Currently no function for this family is known.
Probab=57.18 E-value=42 Score=23.03 Aligned_cols=38 Identities=26% Similarity=0.343 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHh
Q psy674 13 LWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCV 50 (70)
Q Consensus 13 l~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~ 50 (70)
+....+.++.+.++-.|.++|...++.+.+.++++.-+
T Consensus 172 ~~~~~r~~~~l~r~~~wl~~~~~~i~~~i~~i~G~~l~ 209 (214)
T PF11139_consen 172 LVAPERAEPWLERLRSWLRRHSRQILAVILLIVGALLL 209 (214)
T ss_pred HHhHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHH
Confidence 34567899999999999999999998877777765543
No 24
>PRK07118 ferredoxin; Validated
Probab=49.46 E-value=19 Score=26.46 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHhhhhceeeeccCc
Q psy674 39 FVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 39 ~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
.+++++-++|.+.=++|.||+||-
T Consensus 13 ~~g~~~g~~l~~a~~~f~v~~d~~ 36 (280)
T PRK07118 13 ALGLVFGILLAFASKKFAVEEDPR 36 (280)
T ss_pred HHHHHHHHHHHHHeeeeeccCCCc
Confidence 356666667777779999999994
No 25
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=47.70 E-value=31 Score=29.42 Aligned_cols=39 Identities=8% Similarity=0.004 Sum_probs=33.5
Q ss_pred HHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 24 FSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 24 ~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
.++-.|+-+||..++.+.++++++-.+.+.+..+|-.|+
T Consensus 3 ~~l~~~~l~~~~~~~~~~~~l~~~G~~~~~~lp~~~~P~ 41 (1051)
T TIGR00914 3 ERIISFSVAQRWLVLLATLVMAILGIWSYNRLPIDAVPD 41 (1051)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhCCcccCCC
Confidence 467788999999999998888888888888888998886
No 26
>PF13323 HPIH: N-terminal domain with HPIH motif
Probab=47.59 E-value=12 Score=25.39 Aligned_cols=37 Identities=27% Similarity=0.377 Sum_probs=31.0
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhc
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
++-+.+..+.++.++||.=||++..++..+-=+|+..
T Consensus 3 ~vt~~l~~lsr~aa~hPIHtIvv~aLLAS~aYlsvle 39 (153)
T PF13323_consen 3 QVTKPLQALSRFAARHPIHTIVVTALLASTAYLSVLE 39 (153)
T ss_pred cccHHHHHHHHHHccCCCeehHHHHHHHHHHHHHHHH
Confidence 4567788899999999999999988888877777664
No 27
>PRK05113 electron transport complex protein RnfB; Provisional
Probab=46.09 E-value=24 Score=24.47 Aligned_cols=23 Identities=13% Similarity=0.052 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhhhhceeeeccCc
Q psy674 40 VALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 40 ~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
+++++-.+|.+.=+.|.||+||-
T Consensus 14 lg~~~g~~l~~a~~~~~ve~dp~ 36 (191)
T PRK05113 14 LALVFGAILGFASRRFKVEGDPI 36 (191)
T ss_pred HHHHHHHHHHHHhcCccccCCCh
Confidence 45555566666778899999984
No 28
>PRK10132 hypothetical protein; Provisional
Probab=46.06 E-value=80 Score=20.36 Aligned_cols=29 Identities=7% Similarity=-0.014 Sum_probs=19.3
Q ss_pred HHHHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 20 QRELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 20 q~~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
+.....-=.+|+.|||..+.++..+=+++
T Consensus 72 ~~a~~~~~~~V~~~Pw~svgiaagvG~ll 100 (108)
T PRK10132 72 RDAVGCADTFVRERPWCSVGTAAAVGIFI 100 (108)
T ss_pred HHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence 33444444588999999998876654443
No 29
>TIGR01760 tape_meas_TP901 phage tail tape measure protein, TP901 family, core region. This model represents a reasonably well conserved core region of a family of phage tail proteins. The member from phage TP901-1 was characterized as a tail length tape measure protein in that a shortened form of the protein leads to phage with proportionately shorter tails.
Probab=45.98 E-value=56 Score=23.48 Aligned_cols=35 Identities=6% Similarity=0.132 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHH
Q psy674 15 FRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFC 49 (70)
Q Consensus 15 ~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~ 49 (70)
+-..+.++..+++.|+..||..+-.+..++.++..
T Consensus 313 ~~~~~~~~~~~~~~~~~~~p~l~~~i~~~~aa~~~ 347 (350)
T TIGR01760 313 LAQALTKLINAINGLAKENPQLAVTLAAVAAAILA 347 (350)
T ss_pred HHHHHHHHHHHHHHhhHhChHHHHHHHHHHHHHHh
Confidence 34577888899999999999999888887777554
No 30
>PF06363 Picorna_P3A: Picornaviridae P3A protein; InterPro: IPR009419 The viral polyprotein of parechoviruses contains: coat protein VP0 (P1AB); coat protein VP3 (P1C); coat protein VP1 (P1D); picornain 2A (3.4.22.29 from EC, core protein P2A); core protein P2B; core protein P2C; core protein P3A; genome-linked protein VPg (P3B); picornain 3C (3.4.22.28 from EC, MEROPS peptidase subfamily 3CF: parechovirus picornain 3C (P3C))[]. This entry consists of the parechovirus P3A protein. P3A has been identified as a genome-linked protein (VPg), which is involved in replication [].; GO: 0019012 virion
Probab=41.75 E-value=94 Score=20.24 Aligned_cols=35 Identities=14% Similarity=0.161 Sum_probs=26.7
Q ss_pred chhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHH
Q psy674 10 RTALWFRSKLQRELFSLGRFLQRHAGKVIFVALLI 44 (70)
Q Consensus 10 r~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~ 44 (70)
+++=.+-+|+.+-+.+.+.|+-||.++.-++|.+-
T Consensus 45 ~a~~kv~~W~~~k~k~~~~FV~RNk~W~T~~S~~t 79 (100)
T PF06363_consen 45 TACDKVKSWVKNKMKSMLSFVERNKAWFTVVSAVT 79 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcchHhhHHHHHH
Confidence 45556778888889999999999988766555543
No 31
>COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]
Probab=41.65 E-value=26 Score=25.32 Aligned_cols=24 Identities=8% Similarity=0.001 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHhhhhceeeeccCc
Q psy674 39 FVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 39 ~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
++++++=++++..=++|++|.||.
T Consensus 13 ~l~~~~G~~L~~As~rFkve~DP~ 36 (198)
T COG2878 13 LLGLAFGAMLGYASRRFKVEEDPV 36 (198)
T ss_pred HHHHHHHHHHHhhhhhhccccCcH
Confidence 456666677778889999999996
No 32
>KOG2322|consensus
Probab=39.66 E-value=41 Score=24.90 Aligned_cols=37 Identities=24% Similarity=0.352 Sum_probs=33.1
Q ss_pred HHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeecc
Q psy674 24 FSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSK 60 (70)
Q Consensus 24 ~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETd 60 (70)
+.+|-.++.+-+++++.++.+++++++++.-+.+.|.
T Consensus 126 ~~~g~~~a~~~~~~VL~Al~IT~~V~~slt~~t~qtK 162 (237)
T KOG2322|consen 126 FMTGLVTAFYDAKVVLLALIITTVVVLSLTLFTLQTK 162 (237)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHhheeeEEEEEEeec
Confidence 5678889999999999999999999999999888874
No 33
>PHA02662 ORF131 putative membrane protein; Provisional
Probab=39.63 E-value=31 Score=25.40 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=20.8
Q ss_pred CCcccccccchhHHHHHHHHHHH--HHHcHHHHhh---hhHHHHHHH
Q psy674 1 MFKGKAEGQRTALWFRSKLQREL--FSLGRFLQRH---AGKVIFVAL 42 (70)
Q Consensus 1 i~~g~a~G~r~al~~~~~lq~~f--~~lG~~var~---p~~vi~~~l 42 (70)
|+.|.|+||=+--.+-..+.+-. .++| .+.- ||.+++..+
T Consensus 150 INSGtA~aNCgl~~I~~~ltkr~~~nr~~--~~~~~~~~W~i~~~v~ 194 (226)
T PHA02662 150 VNSGHAAANCALARVATALTRRVPASRHG--LAEGGTPPWTLLLAVA 194 (226)
T ss_pred EecCchhhhhhHHHHHHHHhhhccccccc--cccCCCCcchhHHHHH
Confidence 46788888843222222222222 4454 3333 888777655
No 34
>PF02460 Patched: Patched family; InterPro: IPR003392 The transmembrane protein, patched, is a receptor for the morphogene Sonic Hedgehog. In Drosophila melanogaster, this protein associates with the smoothened protein to transduce hedgehog signals, leading to the activation of wingless, decapentaplegic and patched itself. It participates in cell interactions that establish pattern within the segment and imaginal disks during development. The mouse homologue may play a role in epidermal development. The human Niemann-Pick C1 protein, defects in which cause Niemann-Pick type II disease, is also a member of this family. This protein is involved in the intracellular trafficking of cholesterol, and may play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural functional integrity of nerve terminals.; GO: 0008158 hedgehog receptor activity, 0016020 membrane
Probab=39.18 E-value=65 Score=26.43 Aligned_cols=47 Identities=17% Similarity=0.001 Sum_probs=33.5
Q ss_pred HHHHHHHcHHHHhhhhHHHHHH--HHHHHHHHhhhhceeeeccCccccc
Q psy674 20 QRELFSLGRFLQRHAGKVIFVA--LLILLTFCVGLKTHVVHSKIEDLWI 66 (70)
Q Consensus 20 q~~f~~lG~~var~p~~vi~~~--ll~~~~l~~Gl~~~~iETdp~kLWV 66 (70)
..+...|+.++.+.+.+++.+. +..+++...|..+++..-||++|=.
T Consensus 422 ~~~~~~y~~~l~~~~~k~~vll~~~~yl~~siyG~~~i~~gld~~~l~p 470 (798)
T PF02460_consen 422 RFFRDYYAPFLTSPWVKIFVLLLFLIYLGVSIYGCTQIKEGLDPEKLFP 470 (798)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHhhcccCCCCChhhccC
Confidence 4445789999999888765433 3334456688888888999987643
No 35
>PRK11114 cellulose synthase regulator protein; Provisional
Probab=38.61 E-value=41 Score=27.89 Aligned_cols=31 Identities=23% Similarity=0.125 Sum_probs=25.1
Q ss_pred HHHcHHHHhhhhHHHHHHHHHHHHHHhhhhc
Q psy674 24 FSLGRFLQRHAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 24 ~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
.++-.++.+||.+..+++++.++++++.+.+
T Consensus 714 ~~l~~~ls~hp~~l~~~~~~~~~l~~~~~~~ 744 (756)
T PRK11114 714 ERLWWALSNHPVLLALLAALSVLLLALVLWR 744 (756)
T ss_pred HHHHHHHccChHHHHHHHHHHHHHHHHHHHH
Confidence 4555699999999999998888888777654
No 36
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=38.57 E-value=67 Score=27.53 Aligned_cols=35 Identities=9% Similarity=0.050 Sum_probs=25.9
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhh
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGL 52 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl 52 (70)
++++.+.++-.++=+||+++++++++++++..+..
T Consensus 522 ~l~~~y~~~l~~~l~~~~~~~~~~~~~~~~~~~~~ 556 (1044)
T TIGR00915 522 RSTHGYENGVGKILKRRGRYLLVYVLLVGGMVWLF 556 (1044)
T ss_pred HHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHH
Confidence 45677888888999999999998776655443333
No 37
>KOG4489|consensus
Probab=38.03 E-value=76 Score=20.09 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=23.7
Q ss_pred chhHHHHHHHHHHHHHHcHHHHhhhhH
Q psy674 10 RTALWFRSKLQRELFSLGRFLQRHAGK 36 (70)
Q Consensus 10 r~al~~~~~lq~~f~~lG~~var~p~~ 36 (70)
..|+|....+=-+||-+|-+..|.|-.
T Consensus 18 nPal~~~h~mFm~fYlvgFfLERkPCt 44 (87)
T KOG4489|consen 18 NPALLVEHAMFMWFYLVGFFLERKPCT 44 (87)
T ss_pred ChHHHHHHHHHHHHHHHHHHhccCCce
Confidence 468888888888999999999999974
No 38
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=36.62 E-value=51 Score=23.02 Aligned_cols=24 Identities=13% Similarity=0.109 Sum_probs=14.5
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHhh
Q psy674 28 RFLQRHAGKVIFVALLILLTFCVG 51 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~~~~l~~G 51 (70)
.|+.+||++.+..-+.-++++.+.
T Consensus 30 ~Fi~~HP~L~~~M~~~y~~~~~lm 53 (155)
T PF10777_consen 30 SFIRNHPYLCLAMYAAYLAVAALM 53 (155)
T ss_pred HHHHhCcHHHHHHHHHHHHHHHHH
Confidence 467888888766554444444443
No 39
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=35.69 E-value=44 Score=21.87 Aligned_cols=25 Identities=12% Similarity=0.060 Sum_probs=17.3
Q ss_pred HHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 24 FSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 24 ~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
..-=.+|+.|||..+.++-.+=+++
T Consensus 73 ~~tD~yV~e~PWq~VGvaAaVGlll 97 (104)
T COG4575 73 DATDDYVRENPWQGVGVAAAVGLLL 97 (104)
T ss_pred HHHHHHHHcCCchHHHHHHHHHHHH
Confidence 3334578899999998876554443
No 40
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=35.50 E-value=45 Score=18.49 Aligned_cols=19 Identities=21% Similarity=0.487 Sum_probs=13.1
Q ss_pred HHHHHHhhhhceeeeccCc
Q psy674 44 ILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 44 ~~~~l~~Gl~~~~iETdp~ 62 (70)
+-.+...|+.++.+|||-.
T Consensus 13 l~~a~~~g~~~i~v~sDs~ 31 (87)
T PF13456_consen 13 LQLAWELGIRKIIVESDSQ 31 (87)
T ss_dssp HHHHHCCT-SCEEEEES-H
T ss_pred HHHHHHCCCCEEEEEecCc
Confidence 3445678999999999953
No 41
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=34.88 E-value=39 Score=28.92 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=31.4
Q ss_pred HcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 26 LGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 26 lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
+-+|+.+||-.++.+.++++++--+++.+..+|.+|+
T Consensus 12 ~~~~~i~~p~~~~~l~~~l~~~Gi~s~~~lp~~~~P~ 48 (1040)
T PRK10503 12 PSRLFILRPVATTLLMVAILLAGIIGYRALPVSALPE 48 (1040)
T ss_pred HHHHHhcCcHHHHHHHHHHHHHHHHHHHhCCHhhCCC
Confidence 4578899999999888888887778888888999886
No 42
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=33.16 E-value=1e+02 Score=26.54 Aligned_cols=31 Identities=19% Similarity=-0.038 Sum_probs=22.3
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
++.+.|.++=.++-+||+.+++++++++++.
T Consensus 520 ~l~~~y~~~l~~~l~~~~~~~~~~~~~~~~s 550 (1040)
T PRK10503 520 RVIAAYGRGLAKVLNHPWLTLSVALSTLLLT 550 (1040)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 3456666777778899999998777665543
No 43
>PRK11778 putative inner membrane peptidase; Provisional
Probab=32.98 E-value=64 Score=24.58 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=26.3
Q ss_pred HHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhc
Q psy674 22 ELFSLGRFLQRHAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 22 ~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
+|+.||-|.++--..|+.+.+++.++.+++-+.
T Consensus 1 ~~~~y~~f~~k~~t~~~~~~~~~~~~~~~~~~~ 33 (330)
T PRK11778 1 FLSEYGLFLAKTVTVVVAIAAVVALIVSLAQRK 33 (330)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 478899999998888888888887777776544
No 44
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=32.77 E-value=89 Score=19.38 Aligned_cols=25 Identities=12% Similarity=0.125 Sum_probs=19.3
Q ss_pred HHHHHHHcHHHHhhhhHHHHHHHHH
Q psy674 20 QRELFSLGRFLQRHAGKVIFVALLI 44 (70)
Q Consensus 20 q~~f~~lG~~var~p~~vi~~~ll~ 44 (70)
..++..+-.|+++.|+-.|...+++
T Consensus 5 k~w~~~~v~~vAkdP~~Fl~~vll~ 29 (74)
T PF15086_consen 5 KAWASYIVEWVAKDPYEFLTTVLLI 29 (74)
T ss_pred HHHHHHHHHHHHcChHHHHHHHHHH
Confidence 4567777899999999887766554
No 45
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=32.67 E-value=48 Score=22.53 Aligned_cols=22 Identities=18% Similarity=0.360 Sum_probs=18.4
Q ss_pred hhhHHHHHHHHHHHHHHhhhhc
Q psy674 33 HAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 33 ~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
-|.++.+++++++.++|+|+-.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~Y~ 27 (198)
T PRK10370 6 IPVKMLTTLTILMVFLCVGSYL 27 (198)
T ss_pred CchHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999998754
No 46
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=32.64 E-value=15 Score=26.05 Aligned_cols=30 Identities=23% Similarity=0.364 Sum_probs=0.0
Q ss_pred HHHHHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 19 LQRELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 19 lq~~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
++-+-..+|.+++.|.|.+++++++++.+.
T Consensus 22 ~~~l~~tv~~~L~~yGWyil~~~I~ly~l~ 51 (190)
T PF06936_consen 22 LSFLQSTVGSFLSSYGWYILFGCILLYLLW 51 (190)
T ss_dssp ------------------------------
T ss_pred HHHHHHHHHHHHHHhCHHHHHHHHHHHHHH
Confidence 344447789999999999999888877654
No 47
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=31.71 E-value=67 Score=27.12 Aligned_cols=35 Identities=14% Similarity=0.162 Sum_probs=29.7
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 28 RFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
.|.-+||-.++.+.+++++.-.+++.+..+|..|.
T Consensus 3 ~~~i~~~~~~~~l~~~~~~~G~~~~~~l~~~~~P~ 37 (1021)
T PF00873_consen 3 KFFIKRPVAVLLLFLALILFGIFSFFSLPVELFPD 37 (1021)
T ss_dssp HHHHCTHHHHHHHHHHHHHHHHHHHHTSSBESSSS
T ss_pred HHHHhChHHHHHHHHHHHHHHHHHhhcCChhhCCC
Confidence 46778999998888888888888888999999986
No 48
>PF13124 DUF3963: Protein of unknown function (DUF3963)
Probab=31.62 E-value=95 Score=17.03 Aligned_cols=31 Identities=13% Similarity=0.335 Sum_probs=20.4
Q ss_pred HHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHh
Q psy674 17 SKLQRELFSLGRFLQRHAGKVIFVALLILLTFCV 50 (70)
Q Consensus 17 ~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~ 50 (70)
.++++.|--+-+|+.. ++.+.+++++++.++
T Consensus 7 ~fieryfddiqkwirn---it~cfal~vv~lvsl 37 (40)
T PF13124_consen 7 AFIERYFDDIQKWIRN---ITFCFALLVVVLVSL 37 (40)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 3567777777777653 567777777766553
No 49
>PF10031 DUF2273: Small integral membrane protein (DUF2273); InterPro: IPR018730 Members of this family of hypothetical bacterial proteins have no known function.
Probab=31.45 E-value=76 Score=17.88 Aligned_cols=26 Identities=31% Similarity=0.468 Sum_probs=14.6
Q ss_pred HHHHhhhhHHHHHHHHH---HHHHHhhhh
Q psy674 28 RFLQRHAGKVIFVALLI---LLTFCVGLK 53 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~---~~~l~~Gl~ 53 (70)
.+.++|+++++...+-+ +..+++|+.
T Consensus 2 e~~~~~~~~iiG~~~G~ila~l~l~~GF~ 30 (51)
T PF10031_consen 2 EFWKNHRGKIIGGLIGLILALLILTFGFW 30 (51)
T ss_pred hHHHHCcchHHHHHHHHHHHHHHHHHHHH
Confidence 35678888887654332 334445543
No 50
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=30.42 E-value=48 Score=28.27 Aligned_cols=38 Identities=16% Similarity=0.120 Sum_probs=32.2
Q ss_pred HHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 25 SLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 25 ~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
++-.++.|||-.++++.++++++-.+.+.+..+|-+|+
T Consensus 2 ~~~~~~i~~~~~~~~l~~~l~~~G~~~~~~lp~~~~P~ 39 (1025)
T PRK10614 2 KFFALFIYRPVATILLSLAITLCGILGFRLLPVAPLPQ 39 (1025)
T ss_pred CccHHHhcCCHHHHHHHHHHHHHHHHHHhcCCHhhCCC
Confidence 35678999999999988888888888888888888886
No 51
>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit.
Probab=30.21 E-value=63 Score=21.62 Aligned_cols=22 Identities=9% Similarity=0.052 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhhhhceeeeccC
Q psy674 40 VALLILLTFCVGLKTHVVHSKI 61 (70)
Q Consensus 40 ~~ll~~~~l~~Gl~~~~iETdp 61 (70)
+++++-++|.+.=+.+.||+||
T Consensus 12 ~g~~~~~~l~~~~~~~~ve~~p 33 (165)
T TIGR01944 12 LGLALGAILGYAARRFPVEADP 33 (165)
T ss_pred HHHHHHHHHHHheeeeeccCCC
Confidence 4555666677777889999999
No 52
>COG1811 Uncharacterized membrane protein, possible Na+ channel or pump [General function prediction only]
Probab=28.61 E-value=81 Score=23.29 Aligned_cols=34 Identities=26% Similarity=0.664 Sum_probs=23.4
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHH--HHHHHhh
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLI--LLTFCVG 51 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~--~~~l~~G 51 (70)
-+++.+.++|.+++|+|+.=-|..=.+ +.++|+|
T Consensus 74 niek~in~~g~~~~~~~~~~~f~e~fVta~lLfcig 109 (228)
T COG1811 74 NIEKRINNLGQKLEDKPGHGSFAEGFVTAILLFCIG 109 (228)
T ss_pred hHHHHHHHHHHHHHhCcCcchHHHHHHHHHHHHHhc
Confidence 378999999999999887655543332 3345554
No 53
>PF09911 DUF2140: Uncharacterized protein conserved in bacteria (DUF2140); InterPro: IPR018672 This family of conserved hypothetical proteins has no known function.
Probab=27.84 E-value=78 Score=21.92 Aligned_cols=28 Identities=21% Similarity=0.017 Sum_probs=21.2
Q ss_pred hhhHHHHHHHHHHHHHHhhhhceeeecc
Q psy674 33 HAGKVIFVALLILLTFCVGLKTHVVHSK 60 (70)
Q Consensus 33 ~p~~vi~~~ll~~~~l~~Gl~~~~iETd 60 (70)
++|+..|..|+.+.+..+++..+.+=+.
T Consensus 1 N~WK~aF~~Lla~~l~~~~~~~~~~~~~ 28 (187)
T PF09911_consen 1 NWWKWAFLILLALNLAFVIVVFFRLFQP 28 (187)
T ss_pred ChHHHHHHHHHHHHHHHHhheeeEEEcc
Confidence 5789999999888888888766555433
No 54
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=27.52 E-value=1.6e+02 Score=24.26 Aligned_cols=32 Identities=9% Similarity=0.268 Sum_probs=17.9
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHh
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLILLTFCV 50 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~ 50 (70)
.++.+...|...+.+-. ++|.+++.++++||+
T Consensus 461 rves~~~~Lk~s~pKan-K~LWIsvAliVLLAa 492 (538)
T PF05781_consen 461 RVESWASYLKTSFPKAN-KVLWISVALIVLLAA 492 (538)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 35555555555555444 666666666555554
No 55
>cd03383 PAP2_diacylglycerolkinase PAP2_like proteins, diacylglycerol_kinase like sub-family. In some prokaryotes, PAP2_like phosphatase domains appear fused to E. coli DAGK-like trans-membrane diacylglycerol kinase domains. The cellular function of these architectures remains to be determined.
Probab=26.69 E-value=66 Score=20.40 Aligned_cols=33 Identities=27% Similarity=0.291 Sum_probs=27.4
Q ss_pred HHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 30 LQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 30 var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
+.++|+-+.+.++++..+++..+|.+-=..+|.
T Consensus 5 ~~~~~~~~~~~~~~~~~~i~~~lK~~~~r~RP~ 37 (109)
T cd03383 5 IGESPPHVTFVSLLIVIIVVVILKAYFGRGTPL 37 (109)
T ss_pred hcCCchHHHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 568899999999999999999988876666665
No 56
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=25.54 E-value=63 Score=27.70 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=29.6
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 28 RFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
.|+-+||..++++.++++++--+.+.+..+|..|+
T Consensus 3 ~~~i~~~~~~~~l~v~ll~~G~~~~~~lp~~~~P~ 37 (1044)
T TIGR00915 3 KFFIDRPIFAWVIAIIIMLAGALSILSLPVAQYPS 37 (1044)
T ss_pred chhhcCCHHHHHHHHHHHHHHHHHHHhCCHhhCCC
Confidence 46788999999988888888888888888988886
No 57
>PF05915 DUF872: Eukaryotic protein of unknown function (DUF872); InterPro: IPR008590 This entry represents several uncharacterised eukaryotic transmembrane proteins. The function of this currently unknown.
Probab=25.06 E-value=92 Score=20.25 Aligned_cols=34 Identities=21% Similarity=0.386 Sum_probs=17.0
Q ss_pred hhhhHHHHHHHHHHH----HHHhhhhce--eeeccCcccc
Q psy674 32 RHAGKVIFVALLILL----TFCVGLKTH--VVHSKIEDLW 65 (70)
Q Consensus 32 r~p~~vi~~~ll~~~----~l~~Gl~~~--~iETdp~kLW 65 (70)
|.|+|+|..+++.++ ++.+|...+ .++.|..+-|
T Consensus 38 k~pwK~I~la~~Lli~G~~li~~g~l~~~~~i~~~~~~~~ 77 (115)
T PF05915_consen 38 KIPWKSIALAVFLLIFGTVLIIIGLLLFFGHIDGDRDRGW 77 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccc
Confidence 345888776654433 223332221 3456666555
No 58
>PF06692 MNSV_P7B: Melon necrotic spot virus P7B protein; InterPro: IPR009575 This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown.
Probab=24.44 E-value=84 Score=18.75 Aligned_cols=19 Identities=11% Similarity=0.349 Sum_probs=14.0
Q ss_pred hhHHHHHHHHHHHHHHhhh
Q psy674 34 AGKVIFVALLILLTFCVGL 52 (70)
Q Consensus 34 p~~vi~~~ll~~~~l~~Gl 52 (70)
|-++|+++++++.+-++|=
T Consensus 16 ~lLiliis~~f~lI~~l~q 34 (61)
T PF06692_consen 16 PLLILIISFVFFLITSLGQ 34 (61)
T ss_pred HHHHHHHHHHHHHHhhhcc
Confidence 4567888888888777763
No 59
>PRK09579 multidrug efflux protein; Reviewed
Probab=23.67 E-value=82 Score=26.99 Aligned_cols=37 Identities=16% Similarity=0.061 Sum_probs=31.0
Q ss_pred HcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 26 LGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 26 lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
+-++..|||-.++++.++++.+=-+.+.+..+|.+|+
T Consensus 3 l~~~~i~~~~~~~~l~~~l~i~G~~~~~~lp~~~~P~ 39 (1017)
T PRK09579 3 FTDPFIRRPVLASVVSLLIVLLGFQAWSKLQIRQYPQ 39 (1017)
T ss_pred hhHHHHcCCHHHHHHHHHHHHHHHHHHHcCCHhhCCC
Confidence 4567889999999888888887778888888999886
No 60
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=23.57 E-value=39 Score=20.34 Aligned_cols=10 Identities=10% Similarity=0.621 Sum_probs=7.8
Q ss_pred cCccccccCC
Q psy674 60 KIEDLWIEGR 69 (70)
Q Consensus 60 dp~kLWVsp~ 69 (70)
.|+++||+-+
T Consensus 18 RPVqiWVPDt 27 (65)
T PF11455_consen 18 RPVQIWVPDT 27 (65)
T ss_pred CcceeeCCCC
Confidence 5899999753
No 61
>PRK11901 hypothetical protein; Reviewed
Probab=23.48 E-value=78 Score=24.49 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=16.7
Q ss_pred hhHHHHHHHHHHHHHHhhhhc
Q psy674 34 AGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 34 p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
-...|.++|||+++|-+|+-.
T Consensus 36 Qh~MiGiGilVLlLLIi~IgS 56 (327)
T PRK11901 36 QHMMIGIGILVLLLLIIAIGS 56 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 356788999999999888754
No 62
>PF14066 DUF4256: Protein of unknown function (DUF4256)
Probab=23.46 E-value=15 Score=26.11 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=17.6
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCccccc
Q psy674 28 RFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLWI 66 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLWV 66 (70)
....|||++.--- ...++|.||+|||.
T Consensus 11 kn~~RH~~l~W~~------------V~~kL~~~p~kLws 37 (173)
T PF14066_consen 11 KNMNRHPGLEWAK------------VQAKLEANPEKLWS 37 (173)
T ss_pred hchhccCCCcHHH------------HHHHHHcChHHHHH
Confidence 3456787654321 12368999999995
No 63
>COG3337 CRISPR system related protein [Defense mechanisms]
Probab=23.28 E-value=67 Score=21.90 Aligned_cols=27 Identities=11% Similarity=0.232 Sum_probs=22.6
Q ss_pred HHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 22 ELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 22 ~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
+=.++|..|.++|..++.=+|..++.+
T Consensus 26 ~~~ky~Sy~~k~PsmI~~NGL~~TvAF 52 (134)
T COG3337 26 FKTKYGSYCHKFPSMIRLNGLRLTVAF 52 (134)
T ss_pred HHHHHHHHHHhccHHHHhccchHHHHH
Confidence 346899999999999999888877655
No 64
>PRK13836 conjugal transfer protein TrbF; Provisional
Probab=23.23 E-value=2e+02 Score=20.06 Aligned_cols=34 Identities=12% Similarity=-0.004 Sum_probs=19.4
Q ss_pred HHHHHHHcHHHH-hhhhHHHHHHHHHHHHH-Hhhhh
Q psy674 20 QRELFSLGRFLQ-RHAGKVIFVALLILLTF-CVGLK 53 (70)
Q Consensus 20 q~~f~~lG~~va-r~p~~vi~~~ll~~~~l-~~Gl~ 53 (70)
|.+..++|...+ ++.|.+.+++.++++++ ..|+.
T Consensus 16 ~~w~er~g~~~~~~~~W~~~a~~~l~~a~~~v~~~~ 51 (220)
T PRK13836 16 QEWNERYGSYVKAAAAWRIVGILGLTMAVIGFGYAL 51 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555577776654 56677777744444433 44444
No 65
>PF01456 Mucin: Mucin-like glycoprotein; InterPro: IPR000458 This family of trypanosomal proteins resemble vertebrate mucins. The protein consists of three regions. The N and C terminii are conserved between all members of the family, whereas the central region is not well conserved and contains a large number of threonine residues which can be glycosylated []. Indirect evidence suggested that these genes might encode the core protein of parasite mucins, glycoproteins that were proposed to be involved in the interaction with, and invasion of, mammalian host cells.
Probab=23.08 E-value=64 Score=20.63 Aligned_cols=13 Identities=38% Similarity=0.782 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHh
Q psy674 38 IFVALLILLTFCV 50 (70)
Q Consensus 38 i~~~ll~~~~l~~ 50 (70)
|+..|||+++||.
T Consensus 6 LLCalLvlaLcCC 18 (143)
T PF01456_consen 6 LLCALLVLALCCC 18 (143)
T ss_pred HHHHHHHHHHHcC
Confidence 4567888888764
No 66
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=22.98 E-value=1.4e+02 Score=16.00 Aligned_cols=19 Identities=32% Similarity=0.445 Sum_probs=9.7
Q ss_pred HHHHhhhhHHHHHHHHHHH
Q psy674 28 RFLQRHAGKVIFVALLILL 46 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~~~ 46 (70)
+..-||+.-++...++++.
T Consensus 10 ~~f~~nk~a~~gl~il~~~ 28 (56)
T PF12911_consen 10 RRFRRNKLAVIGLIILLIL 28 (56)
T ss_pred HHHHhCchHHHHHHHHHHH
Confidence 3345666666554444433
No 67
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=22.76 E-value=80 Score=27.14 Aligned_cols=35 Identities=14% Similarity=0.110 Sum_probs=30.2
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCc
Q psy674 28 RFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIE 62 (70)
Q Consensus 28 ~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~ 62 (70)
.++-+||-.++.+.++++++-.+++.+..+|.+|+
T Consensus 3 ~~~i~~pv~~~~l~~~l~i~G~~s~~~lp~~~~P~ 37 (1049)
T PRK15127 3 NFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPT 37 (1049)
T ss_pred chhhcCcHHHHHHHHHHHHHHHHHHHcCCHhhCCC
Confidence 46779999999988888888888888999999886
No 68
>COG2409 Predicted drug exporters of the RND superfamily [General function prediction only]
Probab=21.87 E-value=43 Score=28.47 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=31.3
Q ss_pred HHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhcee
Q psy674 19 LQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHV 56 (70)
Q Consensus 19 lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~ 56 (70)
-++..++.|.++.|+|..++..++++++++.+-....+
T Consensus 357 ~~~~w~~~~~~v~~~P~~~l~~s~~ill~~~l~~~~~~ 394 (937)
T COG2409 357 ESRFWRRVGTLVVRRPLAILVASLAILLVLALPLPLVR 394 (937)
T ss_pred hcchhhhheeEEeeccHHHHHHHHHHHHHHHHHhcccc
Confidence 56677899999999999999999988888776655543
No 69
>KOG0860|consensus
Probab=21.75 E-value=1.4e+02 Score=19.84 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=19.3
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhhhce
Q psy674 29 FLQRHAGKVIFVALLILLTFCVGLKTH 55 (70)
Q Consensus 29 ~var~p~~vi~~~ll~~~~l~~Gl~~~ 55 (70)
+..++....+++++++++++.+++..+
T Consensus 87 ~wWkn~Km~~il~~v~~i~l~iiii~~ 113 (116)
T KOG0860|consen 87 MWWKNCKMRIILGLVIIILLVVIIIYI 113 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667777888888888887776653
No 70
>PRK01207 methionine synthase; Provisional
Probab=21.45 E-value=38 Score=25.91 Aligned_cols=10 Identities=10% Similarity=-0.014 Sum_probs=9.0
Q ss_pred cCccccccCC
Q psy674 60 KIEDLWIEGR 69 (70)
Q Consensus 60 dp~kLWVsp~ 69 (70)
+|++|||.|+
T Consensus 305 ~~e~l~vnpD 314 (343)
T PRK01207 305 DPELVRLNPD 314 (343)
T ss_pred CcceEEEcCC
Confidence 8999999986
No 71
>PRK06052 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=21.40 E-value=35 Score=26.44 Aligned_cols=10 Identities=0% Similarity=-0.193 Sum_probs=8.0
Q ss_pred cCccccccCC
Q psy674 60 KIEDLWIEGR 69 (70)
Q Consensus 60 dp~kLWVsp~ 69 (70)
+|++|||.|+
T Consensus 305 ~~e~lwVNPD 314 (344)
T PRK06052 305 GDRIKYVGPD 314 (344)
T ss_pred ChhhEEECCC
Confidence 6888888886
No 72
>PF02117 7TM_GPCR_Sra: Serpentine type 7TM GPCR chemoreceptor Sra; InterPro: IPR000344 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 a (Sra) from the Sra superfamily []. Sra receptors contain 6-7 hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.; GO: 0004888 transmembrane signaling receptor activity, 0007606 sensory perception of chemical stimulus, 0016021 integral to membrane
Probab=20.93 E-value=3.1e+02 Score=20.31 Aligned_cols=52 Identities=12% Similarity=-0.038 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeeccCcccc
Q psy674 11 TALWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSKIEDLW 65 (70)
Q Consensus 11 ~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETdp~kLW 65 (70)
.||.+.-.+...+.++...-+..+|.+|.+ ++.+++++.-..-.-.||-+=.
T Consensus 120 ~aL~idRl~at~~~~~~~~~~~~~g~~l~i---~~li~s~~~~~~i~~~~p~~gy 171 (328)
T PF02117_consen 120 FALTIDRLLATFFPKYYSKKSYIIGIILSI---LVLILSFITGFIIYWDDPLDGY 171 (328)
T ss_pred HHHHHHHHHHHhchhhhhhhhHHHHHHHHH---HHHHHHHHHeeEEEeCCCCccc
Confidence 466666666666666665556666666543 3334566665666667775433
No 73
>PF11174 DUF2970: Protein of unknown function (DUF2970); InterPro: IPR021344 This short family is conserved in Proteobacteria. The function is not known.
Probab=20.85 E-value=1.2e+02 Score=17.38 Aligned_cols=26 Identities=27% Similarity=0.428 Sum_probs=20.9
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhhhc
Q psy674 29 FLQRHAGKVIFVALLILLTFCVGLKT 54 (70)
Q Consensus 29 ~var~p~~vi~~~ll~~~~l~~Gl~~ 54 (70)
+-+-+|.-.|+++++..+++-.++.-
T Consensus 25 f~~~~p~~~Ii~gii~~~~fV~~Lv~ 50 (56)
T PF11174_consen 25 FAQGSPVHFIIVGIILAALFVAGLVL 50 (56)
T ss_pred HHcCCCchHHHHHHHHHHHHHHHHHH
Confidence 44567999999999999988887753
No 74
>TIGR02120 GspF general secretion pathway protein F. This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the"Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. This model was constructed from the broader subfamily model, pfam00482 which includes components of pilin complexes (PilC) as well as other related genes. GspF is nearly always gene clustered with other GSP subunits. Some genes from Xylella and Xanthomonas strains score below the trusted cutoff due to excessive divergence from the family such that a sequence from Deinococcus which does not appear to be GspF scores higher.
Probab=20.84 E-value=2.1e+02 Score=21.26 Aligned_cols=37 Identities=16% Similarity=0.253 Sum_probs=23.6
Q ss_pred chhHHHHHHHHHHHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 10 RTALWFRSKLQRELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 10 r~al~~~~~lq~~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
+.|=+.....+....++...++ |..++++++++..+.
T Consensus 349 ~~a~~~~~~~~~~~~~~~~lie--P~~il~ig~~v~~i~ 385 (399)
T TIGR02120 349 RAADNQEREFERRIATLTALLE--PLLIVVMGGVVLFIV 385 (399)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence 4444455555666666666664 888888887766554
No 75
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=20.44 E-value=3e+02 Score=23.74 Aligned_cols=30 Identities=10% Similarity=-0.031 Sum_probs=21.9
Q ss_pred HHHHHHHHcHHHHhhhhHHHHHHHHHHHHH
Q psy674 19 LQRELFSLGRFLQRHAGKVIFVALLILLTF 48 (70)
Q Consensus 19 lq~~f~~lG~~var~p~~vi~~~ll~~~~l 48 (70)
+++.+.++=.++-+||+.+++++++++++.
T Consensus 522 ~~~~Y~~~L~~~l~~~~~~l~~~~~~~~~~ 551 (1037)
T PRK10555 522 NAERYEKGVAKILHRSLRWILIYVLLLGGM 551 (1037)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 456666666778899999998887665543
No 76
>PF15464 DUF4633: Domain of unknown function (DUF4633)
Probab=20.40 E-value=83 Score=20.93 Aligned_cols=31 Identities=19% Similarity=0.318 Sum_probs=25.3
Q ss_pred cccchhHHHHHHHHHHHHHHcHHHHhhhhHHHH
Q psy674 7 EGQRTALWFRSKLQRELFSLGRFLQRHAGKVIF 39 (70)
Q Consensus 7 ~G~r~al~~~~~lq~~f~~lG~~var~p~~vi~ 39 (70)
.|+| =|++-+=|..=.+--.||+.||.+|+-
T Consensus 81 ~~sr--rwlrqYqQ~vrrrw~~FVa~fp~VtlS 111 (115)
T PF15464_consen 81 RGSR--RWLRQYQQQVRRRWESFVASFPSVTLS 111 (115)
T ss_pred cchH--HHHHHHHHHHHHHHHHHHhcCCceeec
Confidence 3555 588988888888888999999998863
No 77
>TIGR03746 conj_TIGR03746 integrating conjugative element protein, PFL_4703 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown.
Probab=20.23 E-value=1.4e+02 Score=21.72 Aligned_cols=25 Identities=28% Similarity=0.355 Sum_probs=13.4
Q ss_pred HHHHHHHHhhhhceeeeccCccccccCC
Q psy674 42 LLILLTFCVGLKTHVVHSKIEDLWIEGR 69 (70)
Q Consensus 42 ll~~~~l~~Gl~~~~iETdp~kLWVsp~ 69 (70)
+++++++++||..+ -+-...|++|+
T Consensus 23 ~~i~~~l~~gw~~a---P~~ltih~PPD 47 (202)
T TIGR03746 23 ALILLALWFGWRTA---PKDLTIHVPPD 47 (202)
T ss_pred HHHHHHHHHHHHhC---CCccEEECCCc
Confidence 44455567777764 22233456664
No 78
>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=20.09 E-value=1.5e+02 Score=18.51 Aligned_cols=43 Identities=9% Similarity=-0.028 Sum_probs=30.7
Q ss_pred HHHHHHHHHcHHHHhhhhHHHHHHHHHHHHHHhhhhceeeecc
Q psy674 18 KLQRELFSLGRFLQRHAGKVIFVALLILLTFCVGLKTHVVHSK 60 (70)
Q Consensus 18 ~lq~~f~~lG~~var~p~~vi~~~ll~~~~l~~Gl~~~~iETd 60 (70)
+++..|.-.=....|+=++++...++++++-++++..++.+..
T Consensus 36 YL~~~y~y~~sh~WRN~GIli~f~i~f~~~~~~~~e~~~~~~~ 78 (103)
T PF06422_consen 36 YLEESYGYSYSHRWRNFGILIAFWIFFIVLTLLATEFIKFEKS 78 (103)
T ss_pred HHhhhccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 5555544444457889999999888888888888776665543
Done!