Query 033706
Match_columns 113
No_of_seqs 100 out of 237
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:21:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033706hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4455 Uncharacterized conser 100.0 4.4E-31 9.5E-36 180.9 9.4 100 13-112 4-103 (110)
2 PF07019 Rab5ip: Rab5-interact 100.0 3.2E-28 6.9E-33 159.7 7.9 80 33-112 1-80 (81)
3 KOG3415 Putative Rab5-interact 99.8 4.8E-20 1E-24 128.3 8.6 81 32-112 42-122 (129)
4 PF01102 Glycophorin_A: Glycop 83.0 1.5 3.3E-05 30.9 3.1 14 41-54 66-79 (122)
5 PF02439 Adeno_E3_CR2: Adenovi 79.4 4.1 8.9E-05 23.3 3.4 33 40-86 4-36 (38)
6 COG5487 Small integral membran 74.0 14 0.0003 22.5 4.9 19 43-61 8-26 (54)
7 PRK13682 hypothetical protein; 71.7 17 0.00036 22.1 4.9 21 41-61 6-26 (51)
8 PF07043 DUF1328: Protein of u 63.0 27 0.00058 20.0 4.6 21 43-63 3-23 (39)
9 PF11085 YqhR: Conserved membr 59.2 30 0.00065 25.9 5.2 37 41-77 25-90 (173)
10 PF10112 Halogen_Hydrol: 5-bro 47.6 65 0.0014 23.7 5.5 18 39-56 10-27 (199)
11 KOG3195 Uncharacterized membra 44.0 62 0.0013 24.9 4.9 60 27-89 116-182 (213)
12 PRK15049 L-asparagine permease 41.6 1.1E+02 0.0023 25.8 6.5 32 38-69 32-72 (499)
13 PRK12872 ubiA prenyltransferas 40.4 1.7E+02 0.0036 22.4 8.3 19 93-111 266-284 (285)
14 PF03419 Peptidase_U4: Sporula 39.3 1.1E+02 0.0023 24.0 5.8 45 33-77 29-73 (293)
15 PF12650 DUF3784: Domain of un 39.0 1.1E+02 0.0023 19.9 5.2 28 21-48 35-62 (97)
16 PF14015 DUF4231: Protein of u 37.2 1E+02 0.0022 20.0 4.7 23 33-55 15-37 (112)
17 PF04070 DUF378: Domain of unk 31.7 56 0.0012 20.5 2.5 28 32-59 1-28 (62)
18 COG1575 MenA 1,4-dihydroxy-2-n 31.2 1.6E+02 0.0036 23.8 5.8 67 28-95 88-154 (303)
19 PF10112 Halogen_Hydrol: 5-bro 29.3 1.5E+02 0.0033 21.7 5.0 36 38-73 5-41 (199)
20 PRK12884 ubiA prenyltransferas 28.6 2.7E+02 0.0058 21.3 7.5 17 91-107 259-275 (279)
21 COG2149 Predicted membrane pro 28.5 1.5E+02 0.0032 21.0 4.4 27 23-49 14-41 (120)
22 COG2177 FtsX Cell division pro 28.1 2.6E+02 0.0056 22.4 6.4 76 34-111 152-235 (297)
23 PF12576 DUF3754: Protein of u 27.5 1.7E+02 0.0037 20.6 4.8 28 32-59 59-86 (141)
24 PF06916 DUF1279: Protein of u 27.4 1.2E+02 0.0026 19.7 3.7 55 57-111 11-73 (91)
25 TIGR03546 conserved hypothetic 27.4 1.2E+02 0.0027 22.0 4.1 27 39-65 18-44 (154)
26 PF13172 PepSY_TM_1: PepSY-ass 27.0 1.1E+02 0.0023 16.3 2.9 26 33-58 3-28 (34)
27 PRK00665 petG cytochrome b6-f 26.5 29 0.00063 19.6 0.5 15 43-57 4-18 (37)
28 TIGR02840 spore_YtaF putative 26.3 1.9E+02 0.004 21.7 5.1 36 37-72 136-171 (206)
29 PRK11677 hypothetical protein; 25.8 68 0.0015 22.9 2.4 17 37-53 3-19 (134)
30 PF02118 Srg: Srg family chemo 25.6 2E+02 0.0043 21.4 5.2 28 84-111 28-56 (275)
31 CHL00008 petG cytochrome b6/f 25.5 31 0.00066 19.5 0.5 15 43-57 4-18 (37)
32 PF01034 Syndecan: Syndecan do 25.5 23 0.0005 22.4 0.0 12 42-53 12-23 (64)
33 PF03613 EIID-AGA: PTS system 25.4 2.1E+02 0.0045 22.6 5.3 40 33-73 108-147 (264)
34 PF09835 DUF2062: Uncharacteri 25.3 1.5E+02 0.0033 20.6 4.2 28 39-66 21-48 (154)
35 PF02529 PetG: Cytochrome B6-F 25.0 42 0.00091 19.0 1.0 14 43-56 4-17 (37)
36 COG2155 Uncharacterized conser 24.9 72 0.0016 21.0 2.2 27 33-59 4-30 (79)
37 PF12666 PrgI: PrgI family pro 24.9 1.3E+02 0.0029 19.2 3.6 20 37-56 18-37 (93)
38 TIGR02854 spore_II_GA sigma-E 23.3 2.1E+02 0.0045 22.5 5.0 45 33-77 29-73 (288)
39 cd08763 Cyt_b561_CYB561 Verteb 22.9 2.9E+02 0.0062 19.7 8.0 77 29-110 37-130 (143)
40 PF14927 Neurensin: Neurensin 21.9 1.9E+02 0.0041 20.8 4.2 31 16-47 77-107 (140)
41 COG4001 Predicted metal-bindin 21.7 1.2E+02 0.0027 20.6 2.9 31 19-49 70-100 (102)
42 PRK09573 (S)-2,3-di-O-geranylg 21.4 3.8E+02 0.0083 20.5 7.0 20 88-107 255-274 (279)
43 PLN02953 phosphatidate cytidyl 21.3 1.8E+02 0.004 24.5 4.5 32 35-68 97-128 (403)
44 PF14160 FAM110_C: Centrosome- 21.0 60 0.0013 22.6 1.3 23 18-40 84-106 (111)
45 COG4605 CeuC ABC-type enteroch 21.0 3.5E+02 0.0076 22.2 5.9 75 32-106 75-151 (316)
46 PF04829 PT-VENN: Pre-toxin do 20.7 1.3E+02 0.0029 18.1 2.7 19 38-56 13-31 (55)
No 1
>KOG4455 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.97 E-value=4.4e-31 Score=180.90 Aligned_cols=100 Identities=42% Similarity=0.717 Sum_probs=94.1
Q ss_pred CCCCCCcccccchHHHhhchhHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhcCccccccccchh
Q 033706 13 SNDVSNDLQIFNAENLQSNMKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNR 92 (113)
Q Consensus 13 ~~~~~~~~~~~~~~~i~~N~~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~k~~~~~~~yF~~~~~ 92 (113)
..+++.+.+.++.+|++.|.++++++|+.+|+++|++||||||||+.||++|+++..+.+.++..|+++++.+||+++.+
T Consensus 4 s~~~~~~~~~~s~aav~nN~kvl~f~Rt~~s~i~G~aAGILGltg~~GFi~Y~l~~~i~~il~~~K~~~~~~kyf~s~~~ 83 (110)
T KOG4455|consen 4 SKAEEVFIPIYSTAAVRNNKKVLEFVRTSSSAIAGCAAGILGLTGLHGFIFYFLSVLILSILLVLKAGGQWGKYFQSRRN 83 (110)
T ss_pred chhhhcCCcchhHHHHhcCHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHCCCHHhhcCchhH
Confidence 44556677999999999999999999999999999999999999999999999998888888888999999999999999
Q ss_pred HhhhhhhhhhHHHHhHhhhc
Q 033706 93 ILLDGFLGGLMSFVLFWTYF 112 (113)
Q Consensus 93 i~~~g~~~~l~~FvL~Wtl~ 112 (113)
+|++++++++++|||+||+.
T Consensus 84 ~f~~~f~~Gl~tyVl~Wtf~ 103 (110)
T KOG4455|consen 84 LFTESFLGGLTTYVLAWTFF 103 (110)
T ss_pred HHHHHHhchHHHHHHHHHHH
Confidence 99999999999999999985
No 2
>PF07019 Rab5ip: Rab5-interacting protein (Rab5ip)
Probab=99.95 E-value=3.2e-28 Score=159.74 Aligned_cols=80 Identities=46% Similarity=0.920 Sum_probs=78.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhcCccccccccchhHhhhhhhhhhHHHHhHhhhc
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNRILLDGFLGGLMSFVLFWTYF 112 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~k~~~~~~~yF~~~~~i~~~g~~~~l~~FvL~Wtl~ 112 (113)
|+++|+||++|+++|++||||||||+.||++|++++.+++++++.|.++++++||++++|+++||+++++++|||+||++
T Consensus 1 dvi~~~r~~~a~~~Gi~aGILgLtg~~Gf~~f~~~~~~~s~~~~~~~~~~~~~~f~~~~~i~~~g~~~~l~~Fvl~Wtl~ 80 (81)
T PF07019_consen 1 DVIYWCRQIIALLAGIAAGILGLTGLYGFIFFFLSSFLVSLLYYAKAGFPDEDYFGGPWEIFTEGFFSGLSTFVLFWTLF 80 (81)
T ss_pred CHHHHHHHHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHHHhcCChhhhcCCHHHHHHhhhhchHHHHHHHhhee
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999986
No 3
>KOG3415 consensus Putative Rab5-interacting protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.82 E-value=4.8e-20 Score=128.28 Aligned_cols=81 Identities=26% Similarity=0.497 Sum_probs=78.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhcCccccccccchhHhhhhhhhhhHHHHhHhhh
Q 033706 32 MKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNRILLDGFLGGLMSFVLFWTY 111 (113)
Q Consensus 32 ~~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~k~~~~~~~yF~~~~~i~~~g~~~~l~~FvL~Wtl 111 (113)
+|++||.||+++++.|+++||++|+|..|++.|+..+..+.++|+.+..+.+++.|.+.+++.+||+++++++|++.|++
T Consensus 42 lDViyW~rQVi~l~lGviwGi~pL~G~l~iv~f~~issgIvy~y~~~~~~VDEee~GG~weL~kEGf~asfa~FlvtWIi 121 (129)
T KOG3415|consen 42 LDVIYWIRQVIGLILGVIWGIIPLVGFLGIVLFLGISSGIVYLYYANFLKVDEEEYGGHWELLKEGFMASFALFLVTWII 121 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHhhchhhhHHHHHHHHHhhhhHHHHHHHHHHhcCHHHhCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999998888899999999999999999999999999997
Q ss_pred c
Q 033706 112 F 112 (113)
Q Consensus 112 ~ 112 (113)
+
T Consensus 122 ~ 122 (129)
T KOG3415|consen 122 F 122 (129)
T ss_pred H
Confidence 5
No 4
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=82.98 E-value=1.5 Score=30.93 Aligned_cols=14 Identities=50% Similarity=0.975 Sum_probs=12.4
Q ss_pred HHHHHHHHHHhhhc
Q 033706 41 FLSIIGGVIAGILG 54 (113)
Q Consensus 41 ~~sll~Gi~aGILg 54 (113)
++.+++|++|||+|
T Consensus 66 i~~Ii~gv~aGvIg 79 (122)
T PF01102_consen 66 IIGIIFGVMAGVIG 79 (122)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred eeehhHHHHHHHHH
Confidence 58899999999987
No 5
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=79.35 E-value=4.1 Score=23.26 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhcCccccc
Q 033706 40 TFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSY 86 (113)
Q Consensus 40 ~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~k~~~~~~~y 86 (113)
+..|++.|+++|+ +.++++.++|.++.++++.+
T Consensus 4 s~IaIIv~V~vg~--------------~iiii~~~~YaCcykk~~~~ 36 (38)
T PF02439_consen 4 STIAIIVAVVVGM--------------AIIIICMFYYACCYKKHRRQ 36 (38)
T ss_pred chhhHHHHHHHHH--------------HHHHHHHHHHHHHHcccccc
Confidence 4567777777764 33455556777666666543
No 6
>COG5487 Small integral membrane protein [Function unknown]
Probab=74.02 E-value=14 Score=22.50 Aligned_cols=19 Identities=42% Similarity=0.747 Sum_probs=15.1
Q ss_pred HHHHHHHHhhhcccchhHH
Q 033706 43 SIIGGVIAGILGFTGLMGF 61 (113)
Q Consensus 43 sll~Gi~aGILgLtg~~Gf 61 (113)
=++.-++||.+|..|+.|-
T Consensus 8 FlvialIa~~lGFgGiaga 26 (54)
T COG5487 8 FLVIALIAGALGFGGIAGA 26 (54)
T ss_pred HHHHHHHHHHhCcccHHHH
Confidence 3566788999999998874
No 7
>PRK13682 hypothetical protein; Provisional
Probab=71.69 E-value=17 Score=22.05 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhhhcccchhHH
Q 033706 41 FLSIIGGVIAGILGFTGLMGF 61 (113)
Q Consensus 41 ~~sll~Gi~aGILgLtg~~Gf 61 (113)
++-++..++||++|.+|+.|-
T Consensus 6 liFliiA~iA~~lGF~GiAg~ 26 (51)
T PRK13682 6 IIFLVIALIAAVLGFGGIAGA 26 (51)
T ss_pred HHHHHHHHHHHHhccchHHHH
Confidence 345678899999999999984
No 8
>PF07043 DUF1328: Protein of unknown function (DUF1328); InterPro: IPR009760 This entry represents several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown but is thought to be a membrane protein.; GO: 0005886 plasma membrane
Probab=62.96 E-value=27 Score=19.98 Aligned_cols=21 Identities=43% Similarity=0.719 Sum_probs=17.1
Q ss_pred HHHHHHHHhhhcccchhHHHH
Q 033706 43 SIIGGVIAGILGFTGLMGFVF 63 (113)
Q Consensus 43 sll~Gi~aGILgLtg~~Gf~f 63 (113)
-++..++||++|.+|..|-..
T Consensus 3 FliiAliAg~lGF~Giag~a~ 23 (39)
T PF07043_consen 3 FLIIALIAGVLGFGGIAGTAA 23 (39)
T ss_pred hHHHHHHHHHcCcccHHHHHH
Confidence 356788999999999998643
No 9
>PF11085 YqhR: Conserved membrane protein YqhR; InterPro: IPR024563 This family of proteins is conserved in the Bacillaceae family of the Firmicutes. Their function is not known.
Probab=59.23 E-value=30 Score=25.93 Aligned_cols=37 Identities=22% Similarity=0.466 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhhhcc-----------------------------cchhHHHHHHHHHHHHHHHHHH
Q 033706 41 FLSIIGGVIAGILGF-----------------------------TGLMGFVFYFLIMAITSVCLMA 77 (113)
Q Consensus 41 ~~sll~Gi~aGILgL-----------------------------tg~~Gf~fy~~~~~~~s~l~~~ 77 (113)
.++...|+.+|.++. -.+.|.+++.+.+++.+++|++
T Consensus 25 ~iGf~gGliWs~v~yl~y~f~FT~v~P~~ll~Pf~~g~wk~t~~G~~igi~~~gv~Si~aAllY~~ 90 (173)
T PF11085_consen 25 EIGFFGGLIWSLVRYLAYFFHFTEVGPNFLLEPFALGDWKNTWLGNLIGIVFIGVFSIVAALLYYA 90 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccccChhhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888999998763 1245778899999999998886
No 10
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=47.59 E-value=65 Score=23.66 Aligned_cols=18 Identities=22% Similarity=0.331 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHhhhccc
Q 033706 39 RTFLSIIGGVIAGILGFT 56 (113)
Q Consensus 39 r~~~sll~Gi~aGILgLt 56 (113)
|.+++++++++++++..-
T Consensus 10 ~~~~~~~~~~~~~~~~~~ 27 (199)
T PF10112_consen 10 RWILGVLIAAITFLVSFF 27 (199)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455555555555554443
No 11
>KOG3195 consensus Uncharacterized membrane protein NPD008/CGI-148 [General function prediction only]
Probab=44.00 E-value=62 Score=24.90 Aligned_cols=60 Identities=20% Similarity=0.368 Sum_probs=38.3
Q ss_pred HHhhchhHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHH-------HHHhcCcccccccc
Q 033706 27 NLQSNMKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCL-------MAKAKFSVHSYFDS 89 (113)
Q Consensus 27 ~i~~N~~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~-------~~k~~~~~~~yF~~ 89 (113)
++..+.+.+.|.--+ ++-+++||+++..+.+|=+.-+...++...+ |.||.+++.+-+.+
T Consensus 116 ~~n~~dsriFWlgL~---~~pv~W~if~v~al~~fk~~wL~lv~vg~~l~~aN~~Gy~rC~~~a~~~~~q 182 (213)
T KOG3195|consen 116 NVNAIDSRIFWLGLY---LCPVIWIIFAVFALFRFKFKWLILVVVGIALNSANLYGYSRCDKDAKKKFQQ 182 (213)
T ss_pred cchhHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhheeeecCCccchhHHH
Confidence 455666888887554 4456799999999998866644444444332 23677776665543
No 12
>PRK15049 L-asparagine permease; Provisional
Probab=41.59 E-value=1.1e+02 Score=25.77 Aligned_cols=32 Identities=19% Similarity=0.160 Sum_probs=17.7
Q ss_pred HHHHHHHHHH--HHHhhhccc-------chhHHHHHHHHHH
Q 033706 38 SRTFLSIIGG--VIAGILGFT-------GLMGFVFYFLIMA 69 (113)
Q Consensus 38 ~r~~~sll~G--i~aGILgLt-------g~~Gf~fy~~~~~ 69 (113)
.|++..+..| +.+|+.-+. |-.+.+.|+++.+
T Consensus 32 ~~~~~~i~~G~~IGsGiF~~~g~~~~~aGp~~il~~li~~i 72 (499)
T PRK15049 32 NRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGL 72 (499)
T ss_pred HhHhHHHhhhccccchHHHhhHHHHHhcCCHHHHHHHHHHH
Confidence 4677777777 556664443 3344555554433
No 13
>PRK12872 ubiA prenyltransferase; Reviewed
Probab=40.40 E-value=1.7e+02 Score=22.41 Aligned_cols=19 Identities=26% Similarity=0.240 Sum_probs=12.4
Q ss_pred HhhhhhhhhhHHHHhHhhh
Q 033706 93 ILLDGFLGGLMSFVLFWTY 111 (113)
Q Consensus 93 i~~~g~~~~l~~FvL~Wtl 111 (113)
+-..-++.++..|++.|.+
T Consensus 266 ~~~~~~~~g~~~~~~~~~~ 284 (285)
T PRK12872 266 LDKEHMLLGLISMLLGLLV 284 (285)
T ss_pred HhHHHHHHHHHHHHHHHHh
Confidence 3344456778888877764
No 14
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=39.30 E-value=1.1e+02 Score=23.98 Aligned_cols=45 Identities=20% Similarity=0.265 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHH
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMA 77 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~ 77 (113)
+...+.|-+.+..+|....++-+..-.+++...+..++++.+...
T Consensus 29 ~~~~~~Rll~~A~~Gal~~~~~~~p~~~~~~~~~~k~l~s~lmv~ 73 (293)
T PF03419_consen 29 RRASRWRLLLGAAIGALYSLLIFFPPLSFLYSILFKLLISVLMVL 73 (293)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHH
Confidence 346788999999999988877777777777777777777665543
No 15
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=39.00 E-value=1.1e+02 Score=19.86 Aligned_cols=28 Identities=18% Similarity=0.326 Sum_probs=16.2
Q ss_pred cccchHHHhhchhHHHHHHHHHHHHHHH
Q 033706 21 QIFNAENLQSNMKVIYYSRTFLSIIGGV 48 (113)
Q Consensus 21 ~~~~~~~i~~N~~~i~~~r~~~sll~Gi 48 (113)
+.+|.+.+.++......+=.+..++.|+
T Consensus 35 ~~~D~~~l~r~~g~~~~~~~i~~li~~l 62 (97)
T PF12650_consen 35 EKYDKKKLCRFMGKFMLIIGIILLIGGL 62 (97)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577777777765555544444444444
No 16
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=37.23 E-value=1e+02 Score=20.05 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcc
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGF 55 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgL 55 (113)
+..++.-+...++.++.++++|+
T Consensus 15 q~~~~~~~~~~i~~~~~~a~i~~ 37 (112)
T PF14015_consen 15 QRRYRRLRIASIILSVLGAVIPV 37 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666667776666666664
No 17
>PF04070 DUF378: Domain of unknown function (DUF378); InterPro: IPR007211 These are predicted membrane proteins of unknown function. The majority of the proteins have two predicted transmembrane regions.
Probab=31.71 E-value=56 Score=20.47 Aligned_cols=28 Identities=29% Similarity=0.455 Sum_probs=23.5
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhcccchh
Q 033706 32 MKVIYYSRTFLSIIGGVIAGILGFTGLM 59 (113)
Q Consensus 32 ~~~i~~~r~~~sll~Gi~aGILgLtg~~ 59 (113)
++.++|+--+..++.|+=||++|+-++.
T Consensus 1 Mk~ld~ialiLvIIGalNWGliGlf~~n 28 (62)
T PF04070_consen 1 MKILDKIALILVIIGALNWGLIGLFNFN 28 (62)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4678888899999999999999986544
No 18
>COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]
Probab=31.18 E-value=1.6e+02 Score=23.83 Aligned_cols=67 Identities=12% Similarity=0.137 Sum_probs=37.3
Q ss_pred HhhchhHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhcCccccccccchhHhh
Q 033706 28 LQSNMKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNRILL 95 (113)
Q Consensus 28 i~~N~~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~k~~~~~~~yF~~~~~i~~ 95 (113)
.+++++.-..+....++++|.+--.+-+.-.+++.+..++-+.+...+....+..|-.|.+ ..|++.
T Consensus 88 ~~~~~k~~~~l~l~l~~~~g~~llg~~~~~~s~~~~l~lG~l~~~~g~~YTgGp~PlgY~g-LGEi~~ 154 (303)
T COG1575 88 VRQSMKPALILSLALFLLAGLALLGVILAALSDWLVLLLGLLCIAAGILYTGGPFPLGYMG-LGEIFV 154 (303)
T ss_pred ecccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHheeeeccCCcCcccCC-HHHHHH
Confidence 3444555555666666777766666666666777644444443333332344556666654 456553
No 19
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=29.34 E-value=1.5e+02 Score=21.69 Aligned_cols=36 Identities=28% Similarity=0.396 Sum_probs=24.4
Q ss_pred HHHHHHHHHH-HHHhhhcccchhHHHHHHHHHHHHHH
Q 033706 38 SRTFLSIIGG-VIAGILGFTGLMGFVFYFLIMAITSV 73 (113)
Q Consensus 38 ~r~~~sll~G-i~aGILgLtg~~Gf~fy~~~~~~~s~ 73 (113)
.|.+.-.+.| .++++.++..+.|+-.++..+++++.
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~ 41 (199)
T PF10112_consen 5 IRFIFRWILGVLIAAITFLVSFFGFDHSFLLSLLIGA 41 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 4555555555 56667778888888777777776665
No 20
>PRK12884 ubiA prenyltransferase; Reviewed
Probab=28.58 E-value=2.7e+02 Score=21.26 Aligned_cols=17 Identities=35% Similarity=0.583 Sum_probs=8.5
Q ss_pred hhHhhhhhhhhhHHHHh
Q 033706 91 NRILLDGFLGGLMSFVL 107 (113)
Q Consensus 91 ~~i~~~g~~~~l~~FvL 107 (113)
++...-+.+-++..|++
T Consensus 259 ~~~~~~~~~~~~~~~~~ 275 (279)
T PRK12884 259 RKITLTAMLLALVAFAL 275 (279)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444455555555543
No 21
>COG2149 Predicted membrane protein [Function unknown]
Probab=28.46 E-value=1.5e+02 Score=21.01 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=19.9
Q ss_pred cchHHHhhch-hHHHHHHHHHHHHHHHH
Q 033706 23 FNAENLQSNM-KVIYYSRTFLSIIGGVI 49 (113)
Q Consensus 23 ~~~~~i~~N~-~~i~~~r~~~sll~Gi~ 49 (113)
-|+..-..|. .-+-|+|+.++++++-+
T Consensus 14 pd~R~~lAnERTFLAWiRTsLallafGv 41 (120)
T COG2149 14 PDYRFTLANERTFLAWIRTSLALLAFGV 41 (120)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666776 45899999999987644
No 22
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=28.09 E-value=2.6e+02 Score=22.38 Aligned_cols=76 Identities=16% Similarity=0.236 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhc--------CccccccccchhHhhhhhhhhhHHH
Q 033706 34 VIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAK--------FSVHSYFDSWNRILLDGFLGGLMSF 105 (113)
Q Consensus 34 ~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~k~~--------~~~~~yF~~~~~i~~~g~~~~l~~F 105 (113)
--.|++.+.++.-++...-+++.-+..++..++...-+=...+.+.+ +....| . ..+...||..-++.+.
T Consensus 152 ~~~wv~rL~ai~~~~~~v~~~~~~ll~~~~vllI~NtiR~~i~sRr~eIeVmklvGAt~~f-I-~~PFl~~g~~~gl~Ga 229 (297)
T COG2177 152 DREWVDRLFAILRLVRTVGIGLSILLALAAVLLIGNTIRLAIFSRRREIEVMKLVGATDSF-I-RRPFLYEGMLIGLLGA 229 (297)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhccchHH-H-HhHHHHHHHHHHHHHH
Confidence 35788888888887777777777777777776665555555444211 112222 2 3577889888888888
Q ss_pred HhHhhh
Q 033706 106 VLFWTY 111 (113)
Q Consensus 106 vL~Wtl 111 (113)
++.|.+
T Consensus 230 ~~~~~l 235 (297)
T COG2177 230 LIALAL 235 (297)
T ss_pred HHHHHH
Confidence 888876
No 23
>PF12576 DUF3754: Protein of unknown function (DUF3754); InterPro: IPR022227 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=27.51 E-value=1.7e+02 Score=20.62 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhcccchh
Q 033706 32 MKVIYYSRTFLSIIGGVIAGILGFTGLM 59 (113)
Q Consensus 32 ~~~i~~~r~~~sll~Gi~aGILgLtg~~ 59 (113)
++-++|++-..+.+.|.++.+..+-+-.
T Consensus 59 ~~~~D~~~l~~~~vvg~v~~~~~~~~~~ 86 (141)
T PF12576_consen 59 MRPFDRVKLGVSAVVGGVAVFVKLVGMS 86 (141)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 5779999999999999999998866655
No 24
>PF06916 DUF1279: Protein of unknown function (DUF1279); InterPro: IPR009688 This entry represents the C terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.
Probab=27.41 E-value=1.2e+02 Score=19.71 Aligned_cols=55 Identities=13% Similarity=0.105 Sum_probs=28.3
Q ss_pred chhHHHHHHHHHHHHHHHHHH--HhcCcccccccc---c---hhHhhhhhhhhhHHHHhHhhh
Q 033706 57 GLMGFVFYFLIMAITSVCLMA--KAKFSVHSYFDS---W---NRILLDGFLGGLMSFVLFWTY 111 (113)
Q Consensus 57 g~~Gf~fy~~~~~~~s~l~~~--k~~~~~~~yF~~---~---~~i~~~g~~~~l~~FvL~Wtl 111 (113)
|+.++.+|+..+++.-.++|. +.+-+.....+. . .+...+..-+...+|++.|+.
T Consensus 11 G~~~l~vy~~~s~~~~~~~y~~v~~GvDv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lAy~~ 73 (91)
T PF06916_consen 11 GYVALGVYLGLSFISLGSCYLAVSSGVDVIALLESLGISVGWESKVEKKKNSSAGTFALAYAI 73 (91)
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhCCccchhhhhhhcccccHHHHHHHHHH
Confidence 566777887776655444443 444343333322 1 111112123467888888864
No 25
>TIGR03546 conserved hypothetical protein TIGR03546. Members of this family are uncharacterized proteins, usually encoded by a gene adjacent to a member of family TIGR03545, which is also uncharacterized.
Probab=27.41 E-value=1.2e+02 Score=21.97 Aligned_cols=27 Identities=26% Similarity=0.466 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhhhcccchhHHHHHH
Q 033706 39 RTFLSIIGGVIAGILGFTGLMGFVFYF 65 (113)
Q Consensus 39 r~~~sll~Gi~aGILgLtg~~Gf~fy~ 65 (113)
|-..++.+|+..|.+|+-|+.-++..+
T Consensus 18 ~iA~g~a~Gvf~g~~P~~glh~~~~~~ 44 (154)
T TIGR03546 18 QLALAVALGMILGLTPFLNLHNIALLF 44 (154)
T ss_pred HHHHHHHHHHHHHhccchhHHHHHHHH
Confidence 346788899999999987776554443
No 26
>PF13172 PepSY_TM_1: PepSY-associated TM helix
Probab=26.95 E-value=1.1e+02 Score=16.26 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccch
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGFTGL 58 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgLtg~ 58 (113)
+...+++-..++++++..=++.+||.
T Consensus 3 ~~~~~~H~~~g~~~~~~ll~~~lTG~ 28 (34)
T PF13172_consen 3 KFWRKIHRWLGLIAAIFLLLLALTGA 28 (34)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566777777777777666666654
No 27
>PRK00665 petG cytochrome b6-f complex subunit PetG; Reviewed
Probab=26.54 E-value=29 Score=19.58 Aligned_cols=15 Identities=20% Similarity=0.543 Sum_probs=11.6
Q ss_pred HHHHHHHHhhhcccc
Q 033706 43 SIIGGVIAGILGFTG 57 (113)
Q Consensus 43 sll~Gi~aGILgLtg 57 (113)
.+++|++-|.++.|-
T Consensus 4 plL~GiVLGlipiTl 18 (37)
T PRK00665 4 PLLCGIVLGLIPVTL 18 (37)
T ss_pred hhhhhHHHHhHHHHH
Confidence 467899988888763
No 28
>TIGR02840 spore_YtaF putative sporulation protein YtaF. This protein family was identified, at the time of the publication of the Carboxydothermus hydrogenoformans genome, as having a phylogenetic profile that exactly matches the subset of the Firmicutes capable of forming endospores. The species include Bacillus anthracis, Clostridium tetani, Thermoanaerobacter tengcongensis, Geobacillus kaustophilus, etc. This protein, previously named YtaF, is therefore a putative sporulation protein.
Probab=26.28 E-value=1.9e+02 Score=21.69 Aligned_cols=36 Identities=17% Similarity=0.193 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHH
Q 033706 37 YSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITS 72 (113)
Q Consensus 37 ~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s 72 (113)
---++=++..|+.+|++|..-+.-.++-.+++++.+
T Consensus 136 iAlSiDalavG~s~~~~g~~~~~~~~~igivs~i~~ 171 (206)
T TIGR02840 136 IALSLDAFGAGIGASLLGLNPLATSILVAVMSFIFV 171 (206)
T ss_pred HHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 344555778999999999976665555555554444
No 29
>PRK11677 hypothetical protein; Provisional
Probab=25.83 E-value=68 Score=22.91 Aligned_cols=17 Identities=18% Similarity=0.616 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHhhh
Q 033706 37 YSRTFLSIIGGVIAGIL 53 (113)
Q Consensus 37 ~~r~~~sll~Gi~aGIL 53 (113)
|+--++++++|++.|.+
T Consensus 3 W~~a~i~livG~iiG~~ 19 (134)
T PRK11677 3 WEYALIGLVVGIIIGAV 19 (134)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66667777777777643
No 30
>PF02118 Srg: Srg family chemoreceptor; InterPro: IPR000609 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 g (Srg) 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. ; GO: 0004888 transmembrane signaling receptor activity, 0007606 sensory perception of chemical stimulus, 0016020 membrane
Probab=25.63 E-value=2e+02 Score=21.40 Aligned_cols=28 Identities=21% Similarity=0.621 Sum_probs=21.5
Q ss_pred cccccc-chhHhhhhhhhhhHHHHhHhhh
Q 033706 84 HSYFDS-WNRILLDGFLGGLMSFVLFWTY 111 (113)
Q Consensus 84 ~~yF~~-~~~i~~~g~~~~l~~FvL~Wtl 111 (113)
+.||++ ...++.=+...++.+|+..|..
T Consensus 28 ~~~~~~sFy~l~~~d~~~ni~~~ln~~~~ 56 (275)
T PF02118_consen 28 KSYFKSSFYRLYIMDLIMNILTYLNTWIT 56 (275)
T ss_pred ccccCCccHHHHHHHhHHHHHHHHHHHHH
Confidence 556554 5677777778899999999975
No 31
>CHL00008 petG cytochrome b6/f complex subunit V
Probab=25.55 E-value=31 Score=19.50 Aligned_cols=15 Identities=20% Similarity=0.461 Sum_probs=11.6
Q ss_pred HHHHHHHHhhhcccc
Q 033706 43 SIIGGVIAGILGFTG 57 (113)
Q Consensus 43 sll~Gi~aGILgLtg 57 (113)
.+++|++-|.++.|-
T Consensus 4 ~lL~GiVLGlipvTl 18 (37)
T CHL00008 4 VLLFGIVLGLIPITL 18 (37)
T ss_pred hhhhhHHHHhHHHHH
Confidence 467899988888763
No 32
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=25.52 E-value=23 Score=22.38 Aligned_cols=12 Identities=33% Similarity=0.761 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhh
Q 033706 42 LSIIGGVIAGIL 53 (113)
Q Consensus 42 ~sll~Gi~aGIL 53 (113)
.++++|+++|++
T Consensus 12 aavIaG~Vvgll 23 (64)
T PF01034_consen 12 AAVIAGGVVGLL 23 (64)
T ss_dssp ------------
T ss_pred HHHHHHHHHHHH
Confidence 556666666543
No 33
>PF03613 EIID-AGA: PTS system mannose/fructose/sorbose family IID component; InterPro: IPR004704 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=25.41 E-value=2.1e+02 Score=22.57 Aligned_cols=40 Identities=15% Similarity=0.419 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHH
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSV 73 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~ 73 (113)
|++.| -++.-+.+|++++.--=-++.|-++|++.+.+..+
T Consensus 108 Dslf~-~tl~pI~~~i~~~la~~Gn~lGpil~~~~~~~~~~ 147 (264)
T PF03613_consen 108 DSLFW-GTLRPILASIAASLALQGNILGPILFLLLYNIIHF 147 (264)
T ss_pred hHHHH-HHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHH
Confidence 66777 56667777788877777788899999998887754
No 34
>PF09835 DUF2062: Uncharacterized protein conserved in bacteria (DUF2062); InterPro: IPR018639 This domain, found in various prokaryotic proteins, has no known function. It is found at the C-terminal of family 2 glycosyltransferase proteins, in addition to proteins of unknown function.
Probab=25.29 E-value=1.5e+02 Score=20.61 Aligned_cols=28 Identities=29% Similarity=0.300 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHhhhcccchhHHHHHHH
Q 033706 39 RTFLSIIGGVIAGILGFTGLMGFVFYFL 66 (113)
Q Consensus 39 r~~~sll~Gi~aGILgLtg~~Gf~fy~~ 66 (113)
+-..++.+|+..|++|.=|..-++..++
T Consensus 21 ~iA~g~AiG~fig~~P~~g~~~~l~~~l 48 (154)
T PF09835_consen 21 SIALGFAIGVFIGFLPIFGLQTVLAIAL 48 (154)
T ss_pred HHHHHHHHHHHHHHHhcchHHHHHHHHH
Confidence 3456888999999999977776554443
No 35
>PF02529 PetG: Cytochrome B6-F complex subunit 5; InterPro: IPR003683 This family consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].; GO: 0009512 cytochrome b6f complex; PDB: 1Q90_G 2ZT9_G 1VF5_G 2D2C_G 2E74_G 2E75_G 2E76_G.
Probab=25.05 E-value=42 Score=18.98 Aligned_cols=14 Identities=21% Similarity=0.743 Sum_probs=10.9
Q ss_pred HHHHHHHHhhhccc
Q 033706 43 SIIGGVIAGILGFT 56 (113)
Q Consensus 43 sll~Gi~aGILgLt 56 (113)
.+++|++-|.++.|
T Consensus 4 plL~GiVlGli~vt 17 (37)
T PF02529_consen 4 PLLSGIVLGLIPVT 17 (37)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred hhhhhHHHHhHHHH
Confidence 46788888888766
No 36
>COG2155 Uncharacterized conserved protein [Function unknown]
Probab=24.86 E-value=72 Score=20.95 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccchh
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGFTGLM 59 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgLtg~~ 59 (113)
+.+.-+-.+..++.++=||++|++++.
T Consensus 4 ~~i~~~sllLvIiGalNWGLvG~f~fd 30 (79)
T COG2155 4 KIIRGLSLLLVILGALNWGLVGLFGFD 30 (79)
T ss_pred hHHHHHHHHHHHHhhhhhceeeeehhh
Confidence 445556677888899999999999854
No 37
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=24.86 E-value=1.3e+02 Score=19.18 Aligned_cols=20 Identities=15% Similarity=0.310 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHhhhccc
Q 033706 37 YSRTFLSIIGGVIAGILGFT 56 (113)
Q Consensus 37 ~~r~~~sll~Gi~aGILgLt 56 (113)
..||+..+++|+..|+.-.-
T Consensus 18 T~RQl~~l~~~~~~~~~~~~ 37 (93)
T PF12666_consen 18 TLRQLICLAIGALVGVGVYL 37 (93)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 57999999998888765443
No 38
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=23.35 E-value=2.1e+02 Score=22.54 Aligned_cols=45 Identities=16% Similarity=0.120 Sum_probs=36.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHH
Q 033706 33 KVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMA 77 (113)
Q Consensus 33 ~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~ 77 (113)
+...+.|-+.+.++|.+.=++-+..-..++...+.-+++|.+...
T Consensus 29 ~~~~~~Rll~ga~iGa~~~~~~~~p~~~~~~~~~~k~~~s~lmv~ 73 (288)
T TIGR02854 29 DKVSQWRLLLAALIGSLYVLFMFTPKASFFTSPIAKLLYSFLIIF 73 (288)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Confidence 456788999999999988888888877888888887777765553
No 39
>cd08763 Cyt_b561_CYB561 Vertebrate cytochrome b(561), CYB561 gene product. Cytochrome b(561), as found in vertebrates, which might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments.
Probab=22.92 E-value=2.9e+02 Score=19.69 Aligned_cols=77 Identities=6% Similarity=-0.008 Sum_probs=42.8
Q ss_pred hhchhHHHHHHHHHHHHHHHHHhhh-----------c---ccchhHHHHHHHH--HHHHHHHHHHHhcCccccccccchh
Q 033706 29 QSNMKVIYYSRTFLSIIGGVIAGIL-----------G---FTGLMGFVFYFLI--MAITSVCLMAKAKFSVHSYFDSWNR 92 (113)
Q Consensus 29 ~~N~~~i~~~r~~~sll~Gi~aGIL-----------g---Ltg~~Gf~fy~~~--~~~~s~l~~~k~~~~~~~yF~~~~~ 92 (113)
++..+.++|.-+..++++|+++-.. . +-||-|.+.+++. +.+..+..+. . |. ..++.+.
T Consensus 37 k~~~k~~H~~L~~la~~~~~~Gl~av~~~h~~~~~~hf~SlHswlGl~t~~L~~lQ~~~G~~~f~-~---P~-~~~~~r~ 111 (143)
T cd08763 37 KRSTKILHGLLHIMALVISLVGLVAVFDYHQANGYPDMYSLHSWCGILTFVLYFLQWLIGFSFFL-F---PG-ASFTLRS 111 (143)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHccccCCCccccHHHHHHHHHHHHHHHHHHHHHHHHH-c---CC-CchHHHH
Confidence 4456789999999999988875433 2 3355666655433 4444433322 1 11 1122222
Q ss_pred Hhh-hhhhhhhHHHHhHhh
Q 033706 93 ILL-DGFLGGLMSFVLFWT 110 (113)
Q Consensus 93 i~~-~g~~~~l~~FvL~Wt 110 (113)
.+. -..+.+...|+|..+
T Consensus 112 ~~~p~H~~~G~~~f~la~~ 130 (143)
T cd08763 112 QYKPLHEFFGRALFLSSVG 130 (143)
T ss_pred HHhHHHHHHHHHHHHHHHH
Confidence 222 355677888887764
No 40
>PF14927 Neurensin: Neurensin
Probab=21.89 E-value=1.9e+02 Score=20.83 Aligned_cols=31 Identities=6% Similarity=0.046 Sum_probs=22.1
Q ss_pred CCCcccccchHHHhhchhHHHHHHHHHHHHHH
Q 033706 16 VSNDLQIFNAENLQSNMKVIYYSRTFLSIIGG 47 (113)
Q Consensus 16 ~~~~~~~~~~~~i~~N~~~i~~~r~~~sll~G 47 (113)
+..+....++++++.| +.+.-||..-.+++.
T Consensus 77 ~~~~~~~vD~~a~~~n-~~Ld~c~laG~~L~~ 107 (140)
T PF14927_consen 77 EAGEFVVVDSQAARFN-NALDTCKLAGLILLC 107 (140)
T ss_pred ccccccccchHHHHHh-hhHHHHHHHHHHHHH
Confidence 3356788999999999 677777765444443
No 41
>COG4001 Predicted metal-binding protein [General function prediction only]
Probab=21.72 E-value=1.2e+02 Score=20.55 Aligned_cols=31 Identities=19% Similarity=0.358 Sum_probs=26.0
Q ss_pred cccccchHHHhhchhHHHHHHHHHHHHHHHH
Q 033706 19 DLQIFNAENLQSNMKVIYYSRTFLSIIGGVI 49 (113)
Q Consensus 19 ~~~~~~~~~i~~N~~~i~~~r~~~sll~Gi~ 49 (113)
...-.+.|.+++-++-=||-|-+.+.+-||.
T Consensus 70 rAfgVdee~iRE~~~d~ywrrGlasvl~GI~ 100 (102)
T COG4001 70 RAFGVDEEDIREQMHDQYWRRGLASVLRGIG 100 (102)
T ss_pred hhcCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445678889999999999999999999874
No 42
>PRK09573 (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase; Reviewed
Probab=21.43 E-value=3.8e+02 Score=20.55 Aligned_cols=20 Identities=20% Similarity=0.323 Sum_probs=13.0
Q ss_pred ccchhHhhhhhhhhhHHHHh
Q 033706 88 DSWNRILLDGFLGGLMSFVL 107 (113)
Q Consensus 88 ~~~~~i~~~g~~~~l~~FvL 107 (113)
...+.+.+-..+-++.+|++
T Consensus 255 ~~~~~~~~~~m~~g~~~~~~ 274 (279)
T PRK09573 255 SKASKYLKIIMILGLIAFLI 274 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33456666667777777765
No 43
>PLN02953 phosphatidate cytidylyltransferase
Probab=21.26 E-value=1.8e+02 Score=24.55 Aligned_cols=32 Identities=19% Similarity=0.258 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHH
Q 033706 35 IYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIM 68 (113)
Q Consensus 35 i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~ 68 (113)
-.+.|.+.+++.+..+..+=+. .|..|.++..
T Consensus 97 ~l~~RIiSglvl~~l~l~vV~~--GGw~F~~~va 128 (403)
T PLN02953 97 QLKKRVIFGIGIGLPVGCVVLA--GGWFFTVALA 128 (403)
T ss_pred cHHHHHHHHHHHHHHHHheeee--CcHHHHHHHH
Confidence 3468888888887766444333 3444433333
No 44
>PF14160 FAM110_C: Centrosome-associated C terminus
Probab=21.02 E-value=60 Score=22.58 Aligned_cols=23 Identities=9% Similarity=0.195 Sum_probs=16.9
Q ss_pred CcccccchHHHhhchhHHHHHHH
Q 033706 18 NDLQIFNAENLQSNMKVIYYSRT 40 (113)
Q Consensus 18 ~~~~~~~~~~i~~N~~~i~~~r~ 40 (113)
.+..+.-+.-|..|.++|.|+-+
T Consensus 84 ~~r~p~~~SIIERNARIIKWLy~ 106 (111)
T PF14160_consen 84 AERVPYGVSIIERNARIIKWLYG 106 (111)
T ss_pred cccCCCCCceeeehhHHHHHHHh
Confidence 34445667778899999999754
No 45
>COG4605 CeuC ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]
Probab=21.02 E-value=3.5e+02 Score=22.16 Aligned_cols=75 Identities=15% Similarity=0.145 Sum_probs=51.1
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHH--HhcCccccccccchhHhhhhhhhhhHHHH
Q 033706 32 MKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMA--KAKFSVHSYFDSWNRILLDGFLGGLMSFV 106 (113)
Q Consensus 32 ~~~i~~~r~~~sll~Gi~aGILgLtg~~Gf~fy~~~~~~~s~l~~~--k~~~~~~~yF~~~~~i~~~g~~~~l~~Fv 106 (113)
.|.+|-.-|..-+..=-.++.+.+....=|+.=++...+.++++|. ..+...+-|+.=--.+..+.+++++.+|+
T Consensus 75 ~dsLY~liQt~lvf~FG~~~~~~~~~~~~Fl~~l~~mvlFsl~Ly~~lf~~~~r~l~~~lLiGlv~G~lFrSiSsfm 151 (316)
T COG4605 75 FDSLYMLIQTLLVFFFGAASLLALNPNLNFLLELVVMVLFSLLLYYWLFSGGGRDLHLLLLIGLVLGTLFRSISSFM 151 (316)
T ss_pred HHHHHHHHHHHHHheeccceeeeeCchHHHHHHHHHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHHHHHHHH
Confidence 5777776666666555567788888888888888888888877664 33333344443233456777888888886
No 46
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=20.68 E-value=1.3e+02 Score=18.12 Aligned_cols=19 Identities=16% Similarity=0.294 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHhhhccc
Q 033706 38 SRTFLSIIGGVIAGILGFT 56 (113)
Q Consensus 38 ~r~~~sll~Gi~aGILgLt 56 (113)
+..+..++.|+++|+.|-.
T Consensus 13 v~~ls~l~ag~ag~~~g~~ 31 (55)
T PF04829_consen 13 VSALSQLAAGVAGALAGGS 31 (55)
T ss_pred HHHHHHHHHHHHHHHHcCc
Confidence 5667778888888887754
Done!