Query 032884
Match_columns 131
No_of_seqs 117 out of 199
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 07:07:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032884.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032884hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06749 DUF1218: Protein of u 99.8 1.6E-18 3.4E-23 122.4 6.6 63 57-119 1-65 (97)
2 PF05478 Prominin: Prominin; 91.8 0.82 1.8E-05 42.7 8.0 74 43-117 406-492 (806)
3 cd07912 Tweety_N N-terminal do 88.2 3.1 6.6E-05 36.6 8.1 31 51-81 38-69 (418)
4 PF09788 Tmemb_55A: Transmembr 86.5 0.9 1.9E-05 37.6 3.7 50 72-122 177-230 (256)
5 PF07344 Amastin: Amastin surf 80.9 18 0.00039 27.1 8.4 89 4-109 66-155 (155)
6 KOG4684 Uncharacterized conser 76.9 5.9 0.00013 32.6 5.0 60 67-126 184-246 (275)
7 PF04906 Tweety: Tweety; Inte 74.6 7.6 0.00016 33.7 5.5 31 54-84 22-52 (406)
8 KOG4433 Tweety transmembrane/c 65.5 9.9 0.00021 34.4 4.3 63 40-103 30-99 (526)
9 PF05478 Prominin: Prominin; 57.0 70 0.0015 30.1 8.5 24 89-112 141-164 (806)
10 PF05360 YiaAB: yiaA/B two hel 54.7 14 0.0003 23.2 2.4 20 95-114 2-21 (53)
11 PF13903 Claudin_2: PMP-22/EMP 47.2 1E+02 0.0022 21.9 8.4 27 89-115 102-128 (172)
12 PF11169 DUF2956: Protein of u 46.4 17 0.00036 26.3 2.1 18 90-107 85-102 (103)
13 PF07172 GRP: Glycine rich pro 44.1 48 0.001 23.3 4.1 15 1-15 1-15 (95)
14 PF14798 Ca_hom_mod: Calcium h 43.9 60 0.0013 26.6 5.2 61 47-118 13-73 (251)
15 PF13903 Claudin_2: PMP-22/EMP 34.0 1.7E+02 0.0037 20.7 6.6 25 45-69 146-170 (172)
16 PF10320 7TM_GPCR_Srsx: Serpen 33.4 1.3E+02 0.0027 23.9 5.5 88 41-128 132-229 (257)
17 PF10624 TraS: Plasmid conjuga 26.2 68 0.0015 24.6 2.6 26 6-31 73-98 (164)
18 PRK05113 electron transport co 26.2 1.6E+02 0.0036 22.7 4.9 46 7-52 5-60 (191)
19 PRK11383 hypothetical protein; 25.7 1.8E+02 0.0039 22.2 4.8 35 93-127 11-50 (145)
20 PF03597 CcoS: Cytochrome oxid 24.4 1.6E+02 0.0035 17.9 3.6 27 93-119 5-31 (45)
21 KOG4112 Signal peptidase subun 24.1 1.3E+02 0.0028 21.7 3.5 25 104-128 35-59 (101)
22 COG4682 Predicted membrane pro 22.4 1.3E+02 0.0028 22.5 3.5 26 88-113 6-31 (128)
23 PF15048 OSTbeta: Organic solu 22.4 1.3E+02 0.0027 22.5 3.4 32 90-121 35-66 (125)
24 PF13623 SurA_N_2: SurA N-term 22.1 92 0.002 23.3 2.7 18 6-23 10-27 (145)
25 PF06750 DiS_P_DiS: Bacterial 20.7 91 0.002 21.5 2.2 14 72-85 58-71 (92)
26 PF10267 Tmemb_cc2: Predicted 20.5 2.5E+02 0.0055 24.6 5.4 46 52-97 338-383 (395)
No 1
>PF06749 DUF1218: Protein of unknown function (DUF1218); InterPro: IPR009606 This family contains hypothetical plant proteins of unknown function. Family members contain a number of conserved cysteine residues.
Probab=99.76 E-value=1.6e-18 Score=122.41 Aligned_cols=63 Identities=35% Similarity=0.677 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHHHHHHhhccccCCCCCC--CccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcch
Q 032884 57 GAFLFLLASQVLIMLASRCFCCGKPLSP--GGSRAWAVILFIICWYVRISSDWIAFYWTLLDRFG 119 (131)
Q Consensus 57 ~A~v~Ll~aqvv~~~~~~C~Ccg~~~~~--~~~r~~av~~~v~SWi~f~iA~~lLl~gt~~~~~~ 119 (131)
+|+++|+++|+++|+++||+||+++.+| +++|+++++||++||++|++||++|++|+++|+..
T Consensus 1 ~A~~~L~~aqvi~~~~~gC~cc~~~~~~~~~~~r~~a~~~~v~SWi~f~ia~~~ll~ga~~n~~~ 65 (97)
T PF06749_consen 1 AAAVFLLAAQVIANVAGGCLCCGKRVSPKSSRNRTLAVVFFVLSWIVFIIAEALLLAGASMNARH 65 (97)
T ss_pred CHHHHHHHHHHHHHHHhcceEeCCCCCCcccccchhhhhhHHHHHHHHHHHHHHHHHHHhccccc
Confidence 4899999999999999999999998766 37999999999999999999999999999888763
No 2
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=91.77 E-value=0.82 Score=42.66 Aligned_cols=74 Identities=22% Similarity=0.332 Sum_probs=44.8
Q ss_pred eeecCCChhhhhHHHHHHHHHHHHHHHHHHhhccccC-CC-CCCC--------ccH---HHHHHHHHHHHHHHHHHHHHH
Q 032884 43 YCIYDSDISTGMGVGAFLFLLASQVLIMLASRCFCCG-KP-LSPG--------GSR---AWAVILFIICWYVRISSDWIA 109 (131)
Q Consensus 43 ~C~Yps~~A~~LGv~A~v~Ll~aqvv~~~~~~C~Ccg-~~-~~~~--------~~r---~~av~~~v~SWi~f~iA~~lL 109 (131)
+-+|.++.-.+.-+...+++++. ++.....-|+||| ++ ..|+ +.+ .-..+.|++||+..+++...|
T Consensus 406 ~~~y~~yR~~~~lil~~~llLIv-~~~~lGLl~G~~G~~~~~~p~~r~c~~~tGg~~Lm~gv~~~Flf~~~l~l~~~~~F 484 (806)
T PF05478_consen 406 YEKYDSYRWIVGLILCCVLLLIV-LCLLLGLLCGCCGYRRRADPTDRGCSSNTGGNFLMAGVGLSFLFSWFLMLLVLFYF 484 (806)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhccCCCCCCCcccCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44565555444333333333333 4444555678898 43 1221 222 234567889999999999999
Q ss_pred HHHHhhhc
Q 032884 110 FYWTLLDR 117 (131)
Q Consensus 110 l~gt~~~~ 117 (131)
+.|..+++
T Consensus 485 l~G~~~~~ 492 (806)
T PF05478_consen 485 LVGGNTYT 492 (806)
T ss_pred HHHhhhhe
Confidence 99998865
No 3
>cd07912 Tweety_N N-terminal domain of the protein encoded by the Drosophila tweety gene and related proteins, a family of chloride ion channels. The protein product of the Drosophila tweety (tty) gene is thought to form a trans-membrane protein with five membrane-spanning regions and a cytoplasmic C-terminus. This N-terminal domain contains the putative transmembrane spanning regions. Tweety has been suggested as a candidate for a large conductance chloride channel, both in vertebrate and insect cells. Three human homologs have been identified and designated TTYH1-3. TTYH2 has been associated with the progression of cancer, and Drosophila melanogaster tweety has been assumed to play a role in development. TTYH2, and TTYH3 bind to and are ubiquinated by Nedd4-2, a HECT type E3 ubiquitin ligase, which most likely plays a role in controlling the cellular levels of tweety family proteins.
Probab=88.17 E-value=3.1 Score=36.55 Aligned_cols=31 Identities=16% Similarity=0.240 Sum_probs=18.6
Q ss_pred hhhh-HHHHHHHHHHHHHHHHHHhhccccCCC
Q 032884 51 STGM-GVGAFLFLLASQVLIMLASRCFCCGKP 81 (131)
Q Consensus 51 A~~L-Gv~A~v~Ll~aqvv~~~~~~C~Ccg~~ 81 (131)
++++ |..|++.+++.-+...+...|.||+++
T Consensus 38 Sv~~~a~iaavwlil~ll~ll~~~~~~CCcr~ 69 (418)
T cd07912 38 SLLILASIPAACLILSLLFLLVYLITRCCDRK 69 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 5554 455555665665666666667766554
No 4
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=86.49 E-value=0.9 Score=37.58 Aligned_cols=50 Identities=28% Similarity=0.373 Sum_probs=36.9
Q ss_pred HhhccccCCCCCCC--ccHHHHHHHHHHHHHHHHHHHHHHHHHH--hhhcchhHH
Q 032884 72 ASRCFCCGKPLSPG--GSRAWAVILFIICWYVRISSDWIAFYWT--LLDRFGQIL 122 (131)
Q Consensus 72 ~~~C~Ccg~~~~~~--~~r~~av~~~v~SWi~f~iA~~lLl~gt--~~~~~~~~~ 122 (131)
..+|+-|+|..+-+ -.|..++.||+++-+.+++|..+- +|| ..+++|.|.
T Consensus 177 lARCPHCrKvSSVG~~faRkR~i~f~llgllfliiaiglt-vGT~~~A~~~~giY 230 (256)
T PF09788_consen 177 LARCPHCRKVSSVGPRFARKRAIIFFLLGLLFLIIAIGLT-VGTWTYAKTYGGIY 230 (256)
T ss_pred cccCCCCceeccccchHhhhHHHHHHHHHHHHHHHHHHHh-hhhHHHHhhcCcEe
Confidence 37999888765444 478899999999988888887764 566 556776543
No 5
>PF07344 Amastin: Amastin surface glycoprotein; InterPro: IPR009944 This family contains the eukaryotic surface glycoprotein amastin (approximately 180 residues long).In Trypanosoma cruzi, amastin is particularly abundant during the amastigote stage.
Probab=80.87 E-value=18 Score=27.06 Aligned_cols=89 Identities=17% Similarity=0.153 Sum_probs=57.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhccceeeeccCCCCcceeecCCChhhhhHHHHHHHHHHHHHHHHHHhhccccCCCCC
Q 032884 4 KLLIATVFVFDLIAFGLAVAAEQRRSTATIQTDSEKNYNYCIYDSDISTGMGVGAFLFLLASQVLIMLASRCFCCGKPLS 83 (131)
Q Consensus 4 ~~v~~vv~~LgliAfiLgi~AE~~r~~~~~~~~~~~~~~~C~Yps~~A~~LGv~A~v~Ll~aqvv~~~~~~C~Ccg~~~~ 83 (131)
-...++.++++..++++|+..=-.. +..+-+...|.+.+.+.+.+.=++....=.=..|+ +.+
T Consensus 66 ~afaIisi~~~~~a~v~g~~~l~~~----------------~~~r~v~l~L~~~~~~~~~v~wa~~v~~Y~~~~C~-~~~ 128 (155)
T PF07344_consen 66 QAFAIISIFVYGAAFVLGVLLLCCC----------------SCLRWVCLVLNIVGIVTLLVVWALMVVVYYGGFCG-ALK 128 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh----------------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCc-Ccc
Confidence 3456788889999999999855443 22233557788888877766655433322223444 333
Q ss_pred CCccH-HHHHHHHHHHHHHHHHHHHHH
Q 032884 84 PGGSR-AWAVILFIICWYVRISSDWIA 109 (131)
Q Consensus 84 ~~~~r-~~av~~~v~SWi~f~iA~~lL 109 (131)
+...+ ..+-.+++.+|...+++.+.|
T Consensus 129 ~~~~~yg~GF~L~v~aw~l~~i~ii~L 155 (155)
T PF07344_consen 129 SRGYKYGAGFALFVAAWCLDIINIIFL 155 (155)
T ss_pred CCCcccCccHHHHHHHHHHHHHHHHhC
Confidence 33323 468888999999999987654
No 6
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=76.91 E-value=5.9 Score=32.59 Aligned_cols=60 Identities=23% Similarity=0.351 Sum_probs=42.8
Q ss_pred HHHHHHhhccccCCCCCCC--ccHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhcchhHHHHHH
Q 032884 67 VLIMLASRCFCCGKPLSPG--GSRAWAVILFIICWYVRISSDWIAF-YWTLLDRFGQILYIYM 126 (131)
Q Consensus 67 vv~~~~~~C~Ccg~~~~~~--~~r~~av~~~v~SWi~f~iA~~lLl-~gt~~~~~~~~~~~~~ 126 (131)
-.-|...+|+-|++-.+-+ -.|.-++.||++.-...+.|.++-+ .+....|||.+.+.|-
T Consensus 184 t~tnaLArCPHCrKvSsvGsrfar~Ra~~ffilal~~avta~~lt~gT~s~a~~~gg~yf~~~ 246 (275)
T KOG4684|consen 184 TLTNALARCPHCRKVSSVGSRFARRRALLFFILALTVAVTAVILTMGTASVAPVFGGSYFFNN 246 (275)
T ss_pred hHHHHHhcCCcccchhhhhhHHhhhhhHHHHHHHHHHHHHHHHHHhhhhhhccccchhHHHHH
Confidence 3456778999998755444 2566788889888888777776543 3448889998876554
No 7
>PF04906 Tweety: Tweety; InterPro: IPR006990 None of the members of the tweety (tty) family have been functionally characterised. However, they are considered to be transmembrane proteins with five potential membrane-spanning regions. A number of potential functions have been suggested on the basis of homology to the yeast FTR1 and FTH1 iron transporter proteins and the mammalian neurotensin receptors 1 and 2 in that they have a similar hydrophobicity profiles although there is no detectable sequence homology to the tweety-related proteins. It has been proposed that the tweety-related proteins could be involved in transport of iron or other divalent cations or alternatively that they may be membrane-bound receptors [].
Probab=74.57 E-value=7.6 Score=33.65 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHHHHHHHhhccccCCCCCC
Q 032884 54 MGVGAFLFLLASQVLIMLASRCFCCGKPLSP 84 (131)
Q Consensus 54 LGv~A~v~Ll~aqvv~~~~~~C~Ccg~~~~~ 84 (131)
+|..+++.|.+.-+...+-.-|.||+++.++
T Consensus 22 la~v~~~~l~l~Ll~ll~yl~~~CC~r~~~~ 52 (406)
T PF04906_consen 22 LASVAAACLALSLLFLLIYLICRCCCRRPRE 52 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCc
Confidence 3556666777777666666777777776433
No 8
>KOG4433 consensus Tweety transmembrane/cell surface protein [General function prediction only]
Probab=65.55 E-value=9.9 Score=34.36 Aligned_cols=63 Identities=19% Similarity=0.174 Sum_probs=37.5
Q ss_pred CcceeecCCC--hhhhh-HHHHHHHHHHHHHHHHHHhhccccCCCCCCC----ccHHHHHHHHHHHHHHHH
Q 032884 40 NYNYCIYDSD--ISTGM-GVGAFLFLLASQVLIMLASRCFCCGKPLSPG----GSRAWAVILFIICWYVRI 103 (131)
Q Consensus 40 ~~~~C~Yps~--~A~~L-Gv~A~v~Ll~aqvv~~~~~~C~Ccg~~~~~~----~~r~~av~~~v~SWi~f~ 103 (131)
+...|. +++ +|..+ |..++..|.++-+..-+..-|.||.|+..++ +.|-.+..++|++-+++.
T Consensus 30 s~F~pe-~~~Y~QaL~lla~l~aa~l~l~Ll~ll~yli~~cC~Rr~~~~~~~~~~~c~s~~l~I~tl~cca 99 (526)
T KOG4433|consen 30 SVFRPE-DSEYQQALLLLAALAAACLGLSLLFLLFYLICRCCCRRETTGRKRRRVRCLSWSLIIATLMCCA 99 (526)
T ss_pred ccCCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCCCcceeeehHHHHHHHHHH
Confidence 345555 222 34433 5667777777777777778888777765322 333455556666666553
No 9
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=57.03 E-value=70 Score=30.07 Aligned_cols=24 Identities=4% Similarity=0.052 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 032884 89 AWAVILFIICWYVRISSDWIAFYW 112 (131)
Q Consensus 89 ~~av~~~v~SWi~f~iA~~lLl~g 112 (131)
.+++.+++++.+..+-...+|+.-
T Consensus 141 ~l~~~L~~~~~~il~g~i~aF~~n 164 (806)
T PF05478_consen 141 CLGILLLLLTLIILFGVICAFVAN 164 (806)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577777777766655555555543
No 10
>PF05360 YiaAB: yiaA/B two helix domain; InterPro: IPR008024 This domain consists of two transmembrane helices and a conserved linking section.
Probab=54.74 E-value=14 Score=23.23 Aligned_cols=20 Identities=10% Similarity=-0.164 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 032884 95 FIICWYVRISSDWIAFYWTL 114 (131)
Q Consensus 95 ~v~SWi~f~iA~~lLl~gt~ 114 (131)
...+|+.|+++..++.+|--
T Consensus 2 ~~~~~~~f~i~~~~~~iGl~ 21 (53)
T PF05360_consen 2 VGQSWISFGISIVLMLIGLW 21 (53)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 46799999999999998863
No 11
>PF13903 Claudin_2: PMP-22/EMP/MP20/Claudin tight junction
Probab=47.23 E-value=1e+02 Score=21.88 Aligned_cols=27 Identities=19% Similarity=0.091 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032884 89 AWAVILFIICWYVRISSDWIAFYWTLL 115 (131)
Q Consensus 89 ~~av~~~v~SWi~f~iA~~lLl~gt~~ 115 (131)
..+.+++++|.++.+++...+...-..
T Consensus 102 ~~~~~~~~~ag~~~l~~l~~~~~~~~~ 128 (172)
T PF13903_consen 102 LFAGILFILAGLCILIALIVFVVSVNY 128 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 347778889999988888877766543
No 12
>PF11169 DUF2956: Protein of unknown function (DUF2956); InterPro: IPR021339 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=46.44 E-value=17 Score=26.32 Aligned_cols=18 Identities=17% Similarity=0.270 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 032884 90 WAVILFIICWYVRISSDW 107 (131)
Q Consensus 90 ~av~~~v~SWi~f~iA~~ 107 (131)
+.-.++++||+-|++-+.
T Consensus 85 LPW~LL~lSW~gF~~Y~~ 102 (103)
T PF11169_consen 85 LPWGLLVLSWIGFIAYIF 102 (103)
T ss_pred hhHHHHHHHHHHHHHHHH
Confidence 444589999999987654
No 13
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=44.09 E-value=48 Score=23.28 Aligned_cols=15 Identities=27% Similarity=0.317 Sum_probs=9.1
Q ss_pred CcchhHHHHHHHHHH
Q 032884 1 MASKLLIATVFVFDL 15 (131)
Q Consensus 1 ~~s~~v~~vv~~Lgl 15 (131)
|+|..+.++.++|-+
T Consensus 1 MaSK~~llL~l~LA~ 15 (95)
T PF07172_consen 1 MASKAFLLLGLLLAA 15 (95)
T ss_pred CchhHHHHHHHHHHH
Confidence 888875555554433
No 14
>PF14798 Ca_hom_mod: Calcium homeostasis modulator
Probab=43.94 E-value=60 Score=26.60 Aligned_cols=61 Identities=21% Similarity=0.320 Sum_probs=43.5
Q ss_pred CCChhhhhHHHHHHHHHHHHHHHHHHhhccccCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 032884 47 DSDISTGMGVGAFLFLLASQVLIMLASRCFCCGKPLSPGGSRAWAVILFIICWYVRISSDWIAFYWTLLDRF 118 (131)
Q Consensus 47 ps~~A~~LGv~A~v~Ll~aqvv~~~~~~C~Ccg~~~~~~~~r~~av~~~v~SWi~f~iA~~lLl~gt~~~~~ 118 (131)
.++.+++.|+.+++-+.--|+.-++.=.|||- |+.|..-+..|+ ++=|.+||+.|-+.||+
T Consensus 13 ~~~~~~~ngi~~llt~g~e~lfs~~~F~CPC~-----~~~N~~YGl~fL------lvPAl~LfllG~~ln~~ 73 (251)
T PF14798_consen 13 SHSESLGNGICALLTAGGEQLFSSFVFSCPCS-----PGWNFLYGLVFL------LVPALVLFLLGYLLNRR 73 (251)
T ss_pred hcchhHHHHHHHHHHHHHHhhhheeeeecCCC-----CcccchhHhHHH------HHHHHHHHHHHHHHhcc
Confidence 46778899999999999999999999999985 333444333332 34566777777766664
No 15
>PF13903 Claudin_2: PMP-22/EMP/MP20/Claudin tight junction
Probab=33.97 E-value=1.7e+02 Score=20.67 Aligned_cols=25 Identities=28% Similarity=0.341 Sum_probs=18.8
Q ss_pred ecCCChhhhhHHHHHHHHHHHHHHH
Q 032884 45 IYDSDISTGMGVGAFLFLLASQVLI 69 (131)
Q Consensus 45 ~Yps~~A~~LGv~A~v~Ll~aqvv~ 69 (131)
.+.=+-++.++.+|+++.+++-++.
T Consensus 146 ~~~~gwSf~la~~a~~~~l~a~~l~ 170 (172)
T PF13903_consen 146 SYSYGWSFWLAWVAFILLLLAGILF 170 (172)
T ss_pred eEEECHHHHHHHHHHHHHHHHHHHH
Confidence 3344778999999999988876653
No 16
>PF10320 7TM_GPCR_Srsx: Serpentine type 7TM GPCR chemoreceptor Srsx; InterPro: IPR019424 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 sx (Srsx), which is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' [].
Probab=33.39 E-value=1.3e+02 Score=23.89 Aligned_cols=88 Identities=15% Similarity=0.173 Sum_probs=49.6
Q ss_pred cceeecCC---ChhhhhHHHHHHHHHHHHHHHHHHhhccccCCCC--CCC--c--cH-HHHHHHHHHHHHHHHHHHHHHH
Q 032884 41 YNYCIYDS---DISTGMGVGAFLFLLASQVLIMLASRCFCCGKPL--SPG--G--SR-AWAVILFIICWYVRISSDWIAF 110 (131)
Q Consensus 41 ~~~C~Yps---~~A~~LGv~A~v~Ll~aqvv~~~~~~C~Ccg~~~--~~~--~--~r-~~av~~~v~SWi~f~iA~~lLl 110 (131)
...|.-|. +++...=..+.+.+-+.-++.....-....+++. ++. + +| ...+.+++.+|....+.....+
T Consensus 132 ~~~C~pp~a~~~~~~~~~~~~~~~inv~tvivY~i~~~~~~~k~~~~~~~~~kv~ksL~v~v~i~i~~w~~s~~~~~v~~ 211 (257)
T PF10320_consen 132 IVICNPPLAFHGTASQIWSYSNIIINVITVIVYIITIIIFKRKSRSNSSRSKKVFKSLKVTVIIFIFSWFLSQIINTVSL 211 (257)
T ss_pred cccCCCccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccchhHHHHHHHhhhheeeeeHHHHHHHHHHHHHH
Confidence 56788776 2333332333334444445555555443322222 222 1 22 5788899999999988888877
Q ss_pred HHHhhhcchhHHHHHHHH
Q 032884 111 YWTLLDRFGQILYIYMLI 128 (131)
Q Consensus 111 ~gt~~~~~~~~~~~~~~~ 128 (131)
.-...+-.-+++..|+-+
T Consensus 212 ~~~~~~~~~~~i~~~~~i 229 (257)
T PF10320_consen 212 ALGLDGETIAIIQMYAGI 229 (257)
T ss_pred HhCCcHHHHHHHHHHHHH
Confidence 666555555556666544
No 17
>PF10624 TraS: Plasmid conjugative transfer entry exclusion protein TraS; InterPro: IPR018898 Entry exclusion (Eex) is a process which prevents redundant transfer of DNA between donor cells. TraS is a protein involved in Eex. It blocks redundant conjugative DNA synthesis and transport between donor cells, and it is suggested that TraS interferes with a signalling pathway that is required to trigger DNA transfer []. TraS on the recipient cell is known to form an interaction with TraG on the donor cell [].
Probab=26.24 E-value=68 Score=24.61 Aligned_cols=26 Identities=19% Similarity=0.195 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccce
Q 032884 6 LIATVFVFDLIAFGLAVAAEQRRSTA 31 (131)
Q Consensus 6 v~~vv~~LgliAfiLgi~AE~~r~~~ 31 (131)
-+++.=++.+..|++|=.-|.+|...
T Consensus 73 csllsPllsLM~fI~gtL~~lrrvsg 98 (164)
T PF10624_consen 73 CSLLSPLLSLMVFIIGTLYELRRVSG 98 (164)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHhhc
Confidence 35566788999999999999998544
No 18
>PRK05113 electron transport complex protein RnfB; Provisional
Probab=26.16 E-value=1.6e+02 Score=22.73 Aligned_cols=46 Identities=13% Similarity=0.149 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccceeeecc----------CCCCcceeecCCChhh
Q 032884 7 IATVFVFDLIAFGLAVAAEQRRSTATIQTD----------SEKNYNYCIYDSDIST 52 (131)
Q Consensus 7 ~~vv~~LgliAfiLgi~AE~~r~~~~~~~~----------~~~~~~~C~Yps~~A~ 52 (131)
...+++++++.++||+.-.....+-+..+| +..+=..|.||+-..+
T Consensus 5 ~~~~~~~~~lg~~~g~~l~~a~~~~~ve~dp~~~~l~~~lP~~nCg~Cg~~~c~~~ 60 (191)
T PRK05113 5 WIAVAALSLLALVFGAILGFASRRFKVEGDPIVEKIDAILPQSQCGQCGYPGCRPY 60 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCccccCCChHHHHHHhCCcCCccccCCCCcHHH
Confidence 344556666666666654443322211111 3344567888866443
No 19
>PRK11383 hypothetical protein; Provisional
Probab=25.70 E-value=1.8e+02 Score=22.23 Aligned_cols=35 Identities=14% Similarity=0.219 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----hhhcchhHHHHHHH
Q 032884 93 ILFIICWYVRISSDWIAFYWT-----LLDRFGQILYIYML 127 (131)
Q Consensus 93 ~~~v~SWi~f~iA~~lLl~gt-----~~~~~~~~~~~~~~ 127 (131)
.|.-+||+.++++..++++|- ..|-.|+-+-++|+
T Consensus 11 af~~~sw~al~~g~~~y~iGLwnA~~~LsEKGyY~~vl~l 50 (145)
T PRK11383 11 AFSIVSWIALVGGIVTYLLGLWNAEMQLNEKGYYFAVLVL 50 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccCcccHHHHHHHH
Confidence 467889999999999999885 44556666555554
No 20
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=24.37 E-value=1.6e+02 Score=17.93 Aligned_cols=27 Identities=11% Similarity=0.094 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcch
Q 032884 93 ILFIICWYVRISSDWIAFYWTLLDRFG 119 (131)
Q Consensus 93 ~~~v~SWi~f~iA~~lLl~gt~~~~~~ 119 (131)
++.-+|-+..+++...|+|+.-++||-
T Consensus 5 ~lip~sl~l~~~~l~~f~Wavk~GQfd 31 (45)
T PF03597_consen 5 ILIPVSLILGLIALAAFLWAVKSGQFD 31 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence 455678888899999999999888774
No 21
>KOG4112 consensus Signal peptidase subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.11 E-value=1.3e+02 Score=21.67 Aligned_cols=25 Identities=12% Similarity=-0.076 Sum_probs=20.7
Q ss_pred HHHHHHHHHHhhhcchhHHHHHHHH
Q 032884 104 SSDWIAFYWTLLDRFGQILYIYMLI 128 (131)
Q Consensus 104 iA~~lLl~gt~~~~~~~~~~~~~~~ 128 (131)
-|..-+++|...+++++-+|+|+.-
T Consensus 35 ~aiVg~i~Gf~~Qqls~tvy~vg~~ 59 (101)
T KOG4112|consen 35 GAIVGFIYGFAQQQLSVTVYIVGAG 59 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555678999999999999999854
No 22
>COG4682 Predicted membrane protein [Function unknown]
Probab=22.44 E-value=1.3e+02 Score=22.50 Aligned_cols=26 Identities=8% Similarity=0.146 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032884 88 RAWAVILFIICWYVRISSDWIAFYWT 113 (131)
Q Consensus 88 r~~av~~~v~SWi~f~iA~~lLl~gt 113 (131)
+..+..|-++||..|.+++...++|-
T Consensus 6 ~~~s~af~~va~~~lv~G~vvyLiGL 31 (128)
T COG4682 6 EIVSKAFTIVAWLALVVGAVVYLVGL 31 (128)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34566778899999999999999985
No 23
>PF15048 OSTbeta: Organic solute transporter subunit beta protein
Probab=22.36 E-value=1.3e+02 Score=22.53 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcchhH
Q 032884 90 WAVILFIICWYVRISSDWIAFYWTLLDRFGQI 121 (131)
Q Consensus 90 ~av~~~v~SWi~f~iA~~lLl~gt~~~~~~~~ 121 (131)
|-...+++|-++.++++.+|--....||--.+
T Consensus 35 WNysiL~Ls~vvlvi~~~LLgrsi~ANRnrK~ 66 (125)
T PF15048_consen 35 WNYSILALSFVVLVISFFLLGRSIQANRNRKM 66 (125)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHhHhcccccc
Confidence 33455788899999999999999999996543
No 24
>PF13623 SurA_N_2: SurA N-terminal domain
Probab=22.10 E-value=92 Score=23.26 Aligned_cols=18 Identities=28% Similarity=0.283 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 032884 6 LIATVFVFDLIAFGLAVA 23 (131)
Q Consensus 6 v~~vv~~LgliAfiLgi~ 23 (131)
+.++|+.++++||+++=.
T Consensus 10 lLi~vIglAL~aFIv~d~ 27 (145)
T PF13623_consen 10 LLIIVIGLALFAFIVGDF 27 (145)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 566888999999999744
No 25
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=20.70 E-value=91 Score=21.52 Aligned_cols=14 Identities=43% Similarity=1.127 Sum_probs=10.7
Q ss_pred HhhccccCCCCCCC
Q 032884 72 ASRCFCCGKPLSPG 85 (131)
Q Consensus 72 ~~~C~Ccg~~~~~~ 85 (131)
=++|-||+.+.++.
T Consensus 58 rGrCr~C~~~I~~~ 71 (92)
T PF06750_consen 58 RGRCRYCGAPIPPR 71 (92)
T ss_pred CCCCcccCCCCChH
Confidence 47899998887654
No 26
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=20.48 E-value=2.5e+02 Score=24.63 Aligned_cols=46 Identities=24% Similarity=0.300 Sum_probs=29.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhhccccCCCCCCCccHHHHHHHHHH
Q 032884 52 TGMGVGAFLFLLASQVLIMLASRCFCCGKPLSPGGSRAWAVILFII 97 (131)
Q Consensus 52 ~~LGv~A~v~Ll~aqvv~~~~~~C~Ccg~~~~~~~~r~~av~~~v~ 97 (131)
..++-.-=++|.+.+++...++.+..|..|.-.++.|++..++++.
T Consensus 338 ~~l~k~inllL~l~~vlLv~vSt~~~~~~Pl~~tR~r~~~t~~~v~ 383 (395)
T PF10267_consen 338 ALLGKLINLLLTLLTVLLVFVSTVANCPLPLTRTRLRTLTTLLLVG 383 (395)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCcHHhhccHHHHHHHHHHH
Confidence 4455554566677788877777776666666556677766655543
Done!