Query 020166
Match_columns 330
No_of_seqs 153 out of 452
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:33:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020166hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2443 Uncharacterized conser 100.0 2.4E-76 5.1E-81 563.6 17.9 316 10-327 10-360 (362)
2 KOG2442 Uncharacterized conser 100.0 6.1E-65 1.3E-69 501.8 16.3 287 14-312 173-522 (541)
3 PF04258 Peptidase_A22B: Signa 100.0 7.9E-65 1.7E-69 486.5 0.0 258 49-306 2-298 (298)
4 smart00730 PSN Presenilin, sig 100.0 3.6E-46 7.8E-51 349.7 21.5 219 52-298 2-249 (249)
5 PF06550 DUF1119: Protein of u 99.0 7.9E-08 1.7E-12 91.6 21.9 156 142-299 93-282 (283)
6 COG3389 Uncharacterized protei 97.9 6.2E-05 1.3E-09 70.3 8.5 146 144-295 95-271 (277)
7 PF01080 Presenilin: Presenili 94.3 0.08 1.7E-06 53.6 5.8 63 222-292 327-390 (403)
8 KOG2736 Presenilin [Signal tra 92.9 0.12 2.6E-06 51.7 4.3 66 222-294 321-386 (406)
9 PF06027 DUF914: Eukaryotic pr 71.9 15 0.00032 36.6 7.5 52 152-203 122-186 (334)
10 PF12606 RELT: Tumour necrosis 51.7 25 0.00054 25.6 3.7 12 281-292 4-15 (50)
11 KOG3455 Predicted membrane pro 50.1 47 0.001 29.1 5.7 52 248-299 72-123 (139)
12 KOG1607 Protein transporter of 49.2 89 0.0019 31.1 8.3 67 231-307 218-292 (318)
13 PF07698 7TM-7TMR_HD: 7TM rece 48.1 80 0.0017 28.0 7.3 72 233-305 17-88 (194)
14 PF03596 Cad: Cadmium resistan 44.7 64 0.0014 29.6 6.1 12 255-266 28-39 (191)
15 KOG0569 Permease of the major 44.1 30 0.00065 36.2 4.4 18 296-313 220-237 (485)
16 PRK13743 conjugal transfer pro 42.1 48 0.001 28.9 4.6 63 247-309 36-117 (141)
17 KOG2466 Uridine permease/thiam 39.4 25 0.00055 37.0 2.9 76 228-314 471-546 (572)
18 TIGR02587 putative integral me 37.9 49 0.0011 32.1 4.4 48 252-299 69-126 (271)
19 PRK14397 membrane protein; Pro 37.7 1.4E+02 0.003 28.2 7.3 29 287-315 166-194 (222)
20 COG4300 CadD Predicted permeas 35.5 48 0.001 30.6 3.8 66 239-315 28-96 (205)
21 PRK14412 membrane protein; Pro 29.2 2.2E+02 0.0048 26.2 7.1 30 283-312 162-191 (198)
22 PF03606 DcuC: C4-dicarboxylat 27.1 52 0.0011 33.9 2.9 9 235-243 149-157 (465)
23 PF14181 YqfQ: YqfQ-like prote 27.1 34 0.00074 30.7 1.4 8 300-307 84-91 (161)
24 PF09622 DUF2391: Putative int 25.9 1.5E+02 0.0033 28.7 5.6 44 253-296 66-119 (267)
25 PRK14409 membrane protein; Pro 24.9 3E+02 0.0065 25.6 7.2 32 285-316 173-204 (205)
26 PF14248 DUF4345: Domain of un 23.8 4.2E+02 0.0091 21.9 8.2 85 27-112 5-97 (124)
27 KOG2881 Predicted membrane pro 23.7 1.3E+02 0.0027 29.5 4.5 17 296-312 143-159 (294)
28 COG4956 Integral membrane prot 23.6 2.8E+02 0.0061 27.8 7.0 75 233-307 61-143 (356)
29 PRK10921 twin-arginine protein 23.5 69 0.0015 30.6 2.8 13 318-330 246-258 (258)
30 PF14851 FAM176: FAM176 family 23.2 83 0.0018 28.0 3.0 17 256-272 27-43 (153)
31 PF02487 CLN3: CLN3 protein; 21.7 1.2E+02 0.0025 31.1 4.2 16 224-243 127-142 (402)
32 COG5058 LAG1 Protein transport 20.5 61 0.0013 32.5 1.8 39 286-326 357-395 (395)
33 PRK14402 membrane protein; Pro 20.5 4.2E+02 0.0092 24.4 7.2 30 283-312 164-193 (198)
34 PRK03625 tatE twin arginine tr 20.5 2.2E+02 0.0048 21.9 4.5 14 263-276 10-23 (67)
35 KOG1134 Uncharacterized conser 20.5 3.2E+02 0.007 30.1 7.5 78 228-306 574-666 (728)
36 PF12821 DUF3815: Protein of u 20.3 3.5E+02 0.0076 22.6 6.2 52 253-305 51-107 (130)
37 PRK13755 putative mercury tran 20.1 5.9E+02 0.013 22.2 9.7 45 59-107 23-68 (139)
No 1
>KOG2443 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.4e-76 Score=563.64 Aligned_cols=316 Identities=46% Similarity=0.773 Sum_probs=273.8
Q ss_pred HHHHHHhhcCCccccCcchhhHHHHHHHHHHhcccccCC------C-CCCCCCCccccch-hhhHHHHHHHHHHHHHhhc
Q 020166 10 LALAGLTLAPLLVKVDPNLNVILTACLTVYVGCYRSVKP------T-PPSETMSNEHAMR-FPFVGSAMLLSLFLLFKFL 81 (330)
Q Consensus 10 ~~l~~~~~~~~~~~~~~~~~ii~~Av~~V~iGs~~sl~~------~-~~~e~~s~~~A~~-fPv~aS~~L~~LY~l~k~~ 81 (330)
.+....+.+++.-..+.++.++++|+++|++||.||++. + +..|+++.+||.. ||++|||+|++||+++|.+
T Consensus 10 ~~~~~~~~~~~~~~~~~~~sl~l~A~l~i~~GsfRS~~~~~~~~d~~~~~es~t~~~a~~~fPi~~s~tLl~lyl~fk~l 89 (362)
T KOG2443|consen 10 PAAAGTHWTTSELLASAYVSLILIALLLIVIGSFRSLNYIKENEDKKDKSESITKRDAGKMFPIIGSCTLLLLYLLFKPL 89 (362)
T ss_pred ccccCCcccchhhhcccchHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhhhhhhhcccCCcccchHHHHHHHHHHHH
Confidence 334446677777778889999999999999999999962 2 2366899999998 9999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----hhCCCCCCCCceeeeeccc---cceeeeeehhhHHhhhhHHHHHHH
Q 020166 82 SKDLVNAVLTCYFFVLGIIALSATILPAVK----RFLPNHWNEDLIIWHFPYF---RSLEIEFTRSQIIAAIPGTFFCAW 154 (330)
Q Consensus 82 ~~~~v~~ll~~yf~~~g~~~l~~~l~~~~~----~~~p~~~~~~~~~~~~p~~---~~~~~~~~~~~l~~~~~~~~~~~~ 154 (330)
.++++| +++.||++.|+.++.+.+.|++. .+.|..+.+- ...+-|+. ...+.++|..|+++...|..+++|
T Consensus 90 s~~~~~-ll~~~ff~~g~~al~~~~~p~~~~~~~~l~p~~~~~~-~~~~~~~~~~~~~~~~~Ft~~~iv~~vls~~i~v~ 167 (362)
T KOG2443|consen 90 SKELIN-LLTMYFFFLGVIALLSLLDPFINAFKFLLLPMCQYHL-LFPRGPGEKKEFICNGKFTRAQIVALVLSSMIVVW 167 (362)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHhhHHHHhhhhhhcCccchhhe-eeeccCCcccceeecccccHHHHHHHHHHHHHHHH
Confidence 999998 67899999999999999999988 3445443321 10111222 124789999999999999999999
Q ss_pred hhccchhhhhhHHHHHHHHHhhhhcccCchhHHHHHHHHHHHHHhhhhhccceE------------EEecCCCC-----C
Q 020166 155 YASQKHWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFTPVM------------LLFPTRDT-----A 217 (330)
Q Consensus 155 ~~~~~~W~l~nilgi~~~~~~i~~l~l~sfk~~~ilL~~lf~YDIf~VF~Tpvm------------l~~P~~~~-----~ 217 (330)
|+.++||++||++|+++|+++|+.+|++|+|+|++||.|||+|||||||+|+|| +++|+... .
T Consensus 168 ~ll~~HWl~nN~lgms~~I~~I~~lrL~s~ktgalLL~gLffYDIfwVFgTnVMVtVAt~~D~PikL~fP~~l~~~~~~a 247 (362)
T KOG2443|consen 168 YLLTKHWLANNLLGMSFCIAGIEFLRLPSLKTGALLLGGLFFYDIFWVFGTNVMVTVATSLDAPIKLVFPQKLLFPGLTA 247 (362)
T ss_pred HHhhhHHHHHhHHHHHHHHHHHHHhcccchhhhHHHHHHHHHHheEEEecCceEEEeecccCCceEEecchhhccCCCcc
Confidence 999999999999999999999999999999999999999999999999999999 88998421 4
Q ss_pred CCcccccCCCcchhhHHHHHHHhhhhccCCC---cchhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHH
Q 020166 218 RPFSMLGLGDIVIPGIFVALALRFDVSRGKG---SRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAH 294 (330)
Q Consensus 218 ~~~s~LGlGDIviPGl~ia~~lRfD~~~~~~---~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~ 294 (330)
.+||||||||||+||+|+|+++|||.+++.. ++||+.+++||++|+..|+++|+++|++||||||+||+|+++.+++
T Consensus 248 s~fsMLGLGDIviPGiflAl~lRfD~~k~~~s~~~~YF~~t~i~Y~~gL~~ti~~~~~FkaAQPALLYlVP~~l~~~ll~ 327 (362)
T KOG2443|consen 248 SNFSMLGLGDIVIPGIFLALVLRFDIRKKRNSKVRTYFHNTFIAYFLGLLTTIVVLHIFKAAQPALLYLVPACLGPLLLM 327 (362)
T ss_pred ccceeccccchhhHHHHHHHHHHhhHHHHhcccCceEEEEeHHHHHhhhHHHhhhhhhhhccchhhhhhhHHHHhHHHHH
Confidence 5799999999999999999999999986543 7899999999999999999999999999999999999999999999
Q ss_pred HHHhhHHHHhhcccccccccccccccccccccc
Q 020166 295 CIWNGEVKQLLEFDESKTAAVVSQESGDAKTSK 327 (330)
Q Consensus 295 A~~rgEl~~~w~~~~~~~~~~~~~~~~~~~~~~ 327 (330)
|+.|||++++|+|+|+.+||++++.|.++++|+
T Consensus 328 A~~~gdlk~l~s~~~~~~~~~~~~~e~k~~~e~ 360 (362)
T KOG2443|consen 328 AYWRGDLKVLWSFDESTKEESAEQDEVKEKKEN 360 (362)
T ss_pred HHHccchHhhhCccccCCCCcHHHHhhhhcccc
Confidence 999999999999999888777766666555554
No 2
>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=100.00 E-value=6.1e-65 Score=501.79 Aligned_cols=287 Identities=30% Similarity=0.492 Sum_probs=237.2
Q ss_pred HHhhcCCccccCcchhhH-HHHHHHHHHhcccccCCCCC--------------CC------------CCCccccchhhhH
Q 020166 14 GLTLAPLLVKVDPNLNVI-LTACLTVYVGCYRSVKPTPP--------------SE------------TMSNEHAMRFPFV 66 (330)
Q Consensus 14 ~~~~~~~~~~~~~~~~ii-~~Av~~V~iGs~~sl~~~~~--------------~e------------~~s~~~A~~fPv~ 66 (330)
+.+|+|+.|.+|+++++| ++|++||..|||||..++++ +| .++.-.|..|-+.
T Consensus 173 ~~lYaPk~P~vD~~~v~iwlmAVgTVa~ggyWs~~t~~~~~~~a~~~~~d~~s~~~~~~~~~e~~~vd~s~i~~~~fvv~ 252 (541)
T KOG2442|consen 173 LALYAPKRPAVDYAMVFIWLMAVGTVACGGYWSGLTEREKAIEADRLLDDDSSSEGNTKETKEEEVVDISPITAVFFVVT 252 (541)
T ss_pred EEEECCCCCCccHHHHHHHHHHHhHhhccchhhhccChhhhhhhhhhcccccccccccccCCccccEEeeeeEEEEehhh
Confidence 468999999999999999 99999999999999732110 11 1333345566677
Q ss_pred HHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCCceeeeeccccceeeeeehhhHHhhh
Q 020166 67 GSAMLLSLFLLFKFLSKDLVNAVLTCYFFVLGIIALSATILPAVKRFLPNHWNEDLIIWHFPYFRSLEIEFTRSQIIAAI 146 (330)
Q Consensus 67 aS~~L~~LY~l~k~~~~~~v~~ll~~yf~~~g~~~l~~~l~~~~~~~~p~~~~~~~~~~~~p~~~~~~~~~~~~~l~~~~ 146 (330)
+|.+|+.+|+++++ +++. ++++|++.|..++++|+.+.++|..-+..+. +-.-|..+..+ ...++...
T Consensus 253 ~c~~LvLlyfF~~~----~V~v-~iiif~i~g~~gLy~Cl~~lv~r~~~~~~~~---~~~~~~l~~~~----~~~l~l~~ 320 (541)
T KOG2442|consen 253 ACGFLVLLYFFYSY----LVYV-LIIIFCIGGAQGLYNCLAALVHRLPYGAARF---PTLAPRLGNMS----YRLLFLSI 320 (541)
T ss_pred hHHHHHHHHHHHHH----HHHH-HhhheeecccchHHHHHHHHHhhhhhhcccc---cccccccCChh----HHHHHHHH
Confidence 88888888877765 4555 4688999999999999999999865443221 11112223222 23455555
Q ss_pred hHHHHH-HHhhccc---hhhhhhHHHHHHHHHhhhhcccCchhHHHHHHHHHHHHHhhhhhccceE--------------
Q 020166 147 PGTFFC-AWYASQK---HWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFTPVM-------------- 208 (330)
Q Consensus 147 ~~~~~~-~~~~~~~---~W~l~nilgi~~~~~~i~~l~l~sfk~~~ilL~~lf~YDIf~VF~Tpvm-------------- 208 (330)
+|++++ .|..+|+ +|++||++|||+|++.+|.+|+||+|+|++||..+|+|||||||+||+|
T Consensus 321 ~Cia~aV~W~v~R~e~~AwilqDvLGIalci~vLk~vRLPnlK~~tiLL~c~f~YDiF~VFitp~~t~~geSVMieVA~G 400 (541)
T KOG2442|consen 321 LCIAVAVVWAVFRNEDWAWILQDVLGIALCITVLKTVRLPNLKVCTILLLCLFLYDIFFVFITPFITKNGESVMIEVARG 400 (541)
T ss_pred hhhheeEEEEEeecCchHHHHHhhHhHHHHHHHHHHhcCCchhHHHHHHHHHHHHhhheeeeehhhccCCceEEEEEecC
Confidence 666654 5777775 7999999999999999999999999999999999999999999999965
Q ss_pred -----------EEecC-C-----CCCCCcccccCCCcchhhHHHHHHHhhhhccCC-CcchhHHHHHHHHHHHHHHHHHH
Q 020166 209 -----------LLFPT-R-----DTARPFSMLGLGDIVIPGIFVALALRFDVSRGK-GSRYFKSAFLGYTVGLVLTIIVM 270 (330)
Q Consensus 209 -----------l~~P~-~-----~~~~~~s~LGlGDIviPGl~ia~~lRfD~~~~~-~~~YF~~s~igY~~GL~~t~~~~ 270 (330)
+++|| + ++.++|||||+|||++||++||+|+|||.+.++ +..||.++++||.+||++|++++
T Consensus 401 ~~s~~EkiPMlLkVPrl~~s~~~~~~~~~silGFGDIl~PGlLVa~c~RfD~~~~~~~~iYfv~~tvaYgiGLlvTfvaL 480 (541)
T KOG2442|consen 401 PSSTEEKIPMLLKVPRLFFSVLSDPWGGYSILGFGDILVPGLLVAFCLRFDVQVNSVSNIYFVWSTVAYGIGLLVTFVAL 480 (541)
T ss_pred CCCCCCCcceEEEcchhccccccccCCCeeEeeecccccchHHHHHHHHhhhhccccceeEEehhHHHHHHHHHHHHHHH
Confidence 78898 3 788999999999999999999999999998776 88999999999999999999999
Q ss_pred hhhCCCccchhhhhhHHHHHHHHHHHHhhHHHHhhccccccc
Q 020166 271 NWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLEFDESKT 312 (330)
Q Consensus 271 ~~~~~~QPALLYLVP~~l~~~~~~A~~rgEl~~~w~~~~~~~ 312 (330)
.++|.|||||||||||+|++....|++|||++++|++...+.
T Consensus 481 ~LM~~GQPALLYLVP~TL~t~~~lal~R~El~~fWtg~~~~~ 522 (541)
T KOG2442|consen 481 VLMKGGQPALLYLVPCTLGTAVVLALCRGELKKFWTGGSYQK 522 (541)
T ss_pred HHhcCCCceEEEEechHHHHHHHHHHHHHHHHHHhccCCccc
Confidence 999999999999999999999999999999999999988663
No 3
>PF04258 Peptidase_A22B: Signal peptide peptidase; InterPro: IPR007369 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 group of sequences contain aspartic endopeptidases belong to MEROPS peptidase family A22 (presenilin family, clan AD): subfamily A22B. The peptidases were originally classified by hierarchical homology to the most conserved member - IMPAS 1. They are also known as signal peptide peptidase (SPP) []. They belong to the I-CliP family of peptidases. SPP cleaves cleaves remnant signal peptides left behind in the membrane by the action of signal peptidase and also plays key roles in immune surveillance and the maturation of certain viral proteins []. SPPs do not require cofactors as demonstrated by expression in bacteria and purification of a proteolytically active form. The C-terminal region defines the functional domain, which is in itself sufficient for proteolytic activity []. ; GO: 0004190 aspartic-type endopeptidase activity, 0016021 integral to membrane; PDB: 1JUF_C 1INQ_C.
Probab=100.00 E-value=7.9e-65 Score=486.45 Aligned_cols=258 Identities=45% Similarity=0.818 Sum_probs=0.0
Q ss_pred CCCCCCCCccccchhhhHHHHHHHHHHHHHhhccHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhhCCC----CCCCCc
Q 020166 49 TPPSETMSNEHAMRFPFVGSAMLLSLFLLFKFLSKDLVNA--VLTCYFFVLGIIALSATILPAVKRFLPN----HWNEDL 122 (330)
Q Consensus 49 ~~~~e~~s~~~A~~fPv~aS~~L~~LY~l~k~~~~~~v~~--ll~~yf~~~g~~~l~~~l~~~~~~~~p~----~~~~~~ 122 (330)
+++.|++|.+||+.||++||++|++||+++|+++++++|. +++.||+++|+.++...+.+.+.+..+. ....++
T Consensus 2 ~~~~~~is~~~A~~fpv~~S~~L~gLY~~~k~l~~~~i~~~~vl~~~f~~~gv~a~~~~i~~~l~~~~~~~~~~~~~~~~ 81 (298)
T PF04258_consen 2 EEEEETISSKDALIFPVVASCVLLGLYFFFKYLDKDLINIIYVLTVYFCLAGVIALSFLILPFLTYIFPFFPCRSFPWKK 81 (298)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CccccccCHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccce
Confidence 3568899999999999999999999999999999999986 8999999999999988888877764331 111111
Q ss_pred eeeeeccc--cceeeeeehhhHHhhhhHHHHHH-Hhhccc-hhhhhhHHHHHHHHHhhhhcccCchhHHHHHHHHHHHHH
Q 020166 123 IIWHFPYF--RSLEIEFTRSQIIAAIPGTFFCA-WYASQK-HWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYD 198 (330)
Q Consensus 123 ~~~~~p~~--~~~~~~~~~~~l~~~~~~~~~~~-~~~~~~-~W~l~nilgi~~~~~~i~~l~l~sfk~~~ilL~~lf~YD 198 (330)
.+...+.. +..+.+++..++++..+++.+++ |++.++ ||++||++|+|+|+++++.+|+||+|+++++|+++|+||
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~l~~~~~s~~~~~~w~~~~~~~W~l~nilgi~~~i~~i~~i~l~s~k~~~ilL~~lf~YD 161 (298)
T PF04258_consen 82 WKLSFPRRDIKPFSGSFTLSDLLSFLISLAIAVVWYVYRNEHWILQNILGICFCINIISLIRLPSFKTATILLIGLFLYD 161 (298)
T ss_dssp ---------------------------------S----------------------------------------------
T ss_pred EEEEEEcccccceeeeeeHHHHHHHHHHHHHHHHHHHhccchHHHHhHHHHHHHHHHHHheeccchHHHHHHHHHHHHHH
Confidence 11111111 23456778888999888888865 566677 999999999999999999999999999999999999999
Q ss_pred hhhhh------ccceE-----------------EEecCC-----CCCCCcccccCCCcchhhHHHHHHHhhhhcc-CCCc
Q 020166 199 IFWVF------FTPVM-----------------LLFPTR-----DTARPFSMLGLGDIVIPGIFVALALRFDVSR-GKGS 249 (330)
Q Consensus 199 If~VF------~Tpvm-----------------l~~P~~-----~~~~~~s~LGlGDIviPGl~ia~~lRfD~~~-~~~~ 249 (330)
||||| ++++| +++|+. .+++++||||+||||+||+++++|+|||.++ ++++
T Consensus 162 if~VF~s~~~~g~svM~~VA~~~~~~~~~~P~~l~~P~~~~~~~~~~~~~s~LGlGDIviPGl~i~~~~rfD~~~~~~~~ 241 (298)
T PF04258_consen 162 IFWVFISPYFFGTSVMVTVATGGFDAPEKLPIKLQFPRFFDSNSSCPKPFSMLGLGDIVIPGLFIAFCLRFDKSRNKSRK 241 (298)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHhccccCCCchhhhhhccccccccCCCeEEEEeccccccccCCCCeeEeccchHHHHHHHHHHHHHhhHhhccccc
Confidence 99999 76777 677875 4688999999999999999999999999998 3467
Q ss_pred chhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHHHHHhhHHHHhhc
Q 020166 250 RYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLE 306 (330)
Q Consensus 250 ~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~A~~rgEl~~~w~ 306 (330)
+||.++++||++||++|+++++++|+|||||||+||+|+++++++|++|||++++||
T Consensus 242 ~Yf~~~~~~Y~~Gl~~t~~~~~~~~~~QPALlylvP~~l~~~~~~a~~r~el~~~w~ 298 (298)
T PF04258_consen 242 PYFIASLIGYALGLLLTFVALHLFKHGQPALLYLVPCTLGSVLLVAWIRGELKDFWN 298 (298)
T ss_dssp ---------------------------------------------------------
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCCCeehHHHHHHHHHHHHHHHHhhHHHHhhC
Confidence 899999999999999999999999999999999999999999999999999999997
No 4
>smart00730 PSN Presenilin, signal peptide peptidase, family. Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. Distant homologues, present in eukaryotes and archaea, also contain conserved aspartic acid residues which are predicted to contribute to catalysis. At least one member of this family has been shown to possess signal peptide peptidase activity.
Probab=100.00 E-value=3.6e-46 Score=349.74 Aligned_cols=219 Identities=37% Similarity=0.654 Sum_probs=189.2
Q ss_pred CCCCCccccchhhhHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCCceeeeecccc
Q 020166 52 SETMSNEHAMRFPFVGSAMLLSLFLLFKFLSKDLVNAVLTCYFFVLGIIALSATILPAVKRFLPNHWNEDLIIWHFPYFR 131 (330)
Q Consensus 52 ~e~~s~~~A~~fPv~aS~~L~~LY~l~k~~~~~~v~~ll~~yf~~~g~~~l~~~l~~~~~~~~p~~~~~~~~~~~~p~~~ 131 (330)
.|.+++.+++.||+++|++|+++|...|+ .+..+.+||+..|+.++..++.+......
T Consensus 2 ~~~~n~~~~i~fii~~s~~Ll~Ly~~~~~-----~~i~~~~~f~~~~~~~~~~~~~~~~~~~~----------------- 59 (249)
T smart00730 2 YSLLNSLVAIVFPIVATFVLVLLYKFFKY-----LVIVLVIYFSSLGVLFLYSLLYPLEVFRV----------------- 59 (249)
T ss_pred cccccHHHHhhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------
Confidence 46789999999999999999999998876 26667899999999999999988765420
Q ss_pred ceeeeeehhhHHhhhhH-HHHHHHhhccc-hhhhhhHHHHHHHHHhhhhcccCchhHHHHHHHHHHHHHhhhhhcc----
Q 020166 132 SLEIEFTRSQIIAAIPG-TFFCAWYASQK-HWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFT---- 205 (330)
Q Consensus 132 ~~~~~~~~~~l~~~~~~-~~~~~~~~~~~-~W~l~nilgi~~~~~~i~~l~l~sfk~~~ilL~~lf~YDIf~VF~T---- 205 (330)
+.........+ .+.+.|+.++| +|+.||++|+++|+++++.+++||+|+++++|+++++||+||||+|
T Consensus 60 ------~~~~~~~~~~~~~v~~~~~~~~~~~w~~~~~lgi~~~~~~~~~~~l~~~~~~~iLL~~l~iYDif~Vf~t~~~~ 133 (249)
T smart00730 60 ------DYPTLLILLLNFAVVGFWCIHRKGAWIQQDLIGISLCMAILFILRLPSEWTAWILLGALFIYDIFAVFGTPGPL 133 (249)
T ss_pred ------hHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHheeecCCCCc
Confidence 01122333333 33457887786 9999999999999999999999999999999999999999999999
Q ss_pred ceE-----------EEecC------------CCCCCCcccccCCCcchhhHHHHHHHhhhhccCCCcchhHHHHHHHHHH
Q 020166 206 PVM-----------LLFPT------------RDTARPFSMLGLGDIVIPGIFVALALRFDVSRGKGSRYFKSAFLGYTVG 262 (330)
Q Consensus 206 pvm-----------l~~P~------------~~~~~~~s~LGlGDIviPGl~ia~~lRfD~~~~~~~~YF~~s~igY~~G 262 (330)
++| +++|. +++.+++|+||+||||+||+++++|+|||.+++.+++||.+|++||.+|
T Consensus 134 ~vMv~vA~~~~~~~~~~P~ll~~p~~~~~~~~~~~~~~~~LGLGDiv~Pgilv~~a~~fd~~~~~~~~yf~~~~~ay~~G 213 (249)
T smart00730 134 RVMVEVATGRDEPIKVFPALLYVPRLVVSFEDDEEGRFSMLGLGDIVFPGILVASAARFDVSVRSDSNYFLACFVAYGIG 213 (249)
T ss_pred hHHhhHhccCCCCcccCChhhcccccccccccCCCCccceecCCCeeeHHHHHHHHHHhhhcccCCcccHHHHHHHHHHH
Confidence 788 14554 2346789999999999999999999999998777889999999999999
Q ss_pred HHHHHHHHhhhCCCccchhhhhhHHHHHHHHHHHHh
Q 020166 263 LVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWN 298 (330)
Q Consensus 263 L~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~A~~r 298 (330)
|+.|+++++.+|+|||||+|+||+++++.+++|+.|
T Consensus 214 L~~t~~~l~~~~~aqPALlylvp~~l~~~~~~~~~r 249 (249)
T smart00730 214 LILTLVLLALFKKAQPALPYLVPFTLVFYLLTALLR 249 (249)
T ss_pred HHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999976
No 5
>PF06550 DUF1119: Protein of unknown function (DUF1119); InterPro: IPR010545 This family consists of several hypothetical archaeal proteins of unknown function.
Probab=99.02 E-value=7.9e-08 Score=91.61 Aligned_cols=156 Identities=26% Similarity=0.340 Sum_probs=108.6
Q ss_pred HHhhhhHHHHHHHhhccchhhhhhHHHHHHHHHhhhh--cccCchhHHHHHHHHHHHHHhhhhhccc-------------
Q 020166 142 IIAAIPGTFFCAWYASQKHWLANNTLGLAFCIQGIEM--LSLGSFKTGAILLAGLFVYDIFWVFFTP------------- 206 (330)
Q Consensus 142 l~~~~~~~~~~~~~~~~~~W~l~nilgi~~~~~~i~~--l~l~sfk~~~ilL~~lf~YDIf~VF~Tp------------- 206 (330)
..+.+.+..+..+.+....|+..|+.|+..+...-.. +++ +.-.+.+||..+=+||-.=||.|.
T Consensus 93 ~~a~~~ai~~~~~L~~ypEWYviD~~Gil~~aG~aaiFGISl-~~lpaiiLL~iLAVYDaISVYkTkHMltLAegv~d~k 171 (283)
T PF06550_consen 93 IIALILAIALTALLYKYPEWYVIDIAGILMGAGAAAIFGISL-GILPAIILLAILAVYDAISVYKTKHMLTLAEGVMDLK 171 (283)
T ss_pred HHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhHHHHHHhhhc-cHHHHHHHHHHHHHhhhhheecchHHHHHHHHHhccC
Confidence 4556666666777777889999999999998764333 333 456788999999999999999995
Q ss_pred --eEEEecCC-------------C--CCCCcccccCCCcchhhHHHHHHHhhhhccCC-Ccchh-HHHHHHHHHHHHHHH
Q 020166 207 --VMLLFPTR-------------D--TARPFSMLGLGDIVIPGIFVALALRFDVSRGK-GSRYF-KSAFLGYTVGLVLTI 267 (330)
Q Consensus 207 --vml~~P~~-------------~--~~~~~s~LGlGDIviPGl~ia~~lRfD~~~~~-~~~YF-~~s~igY~~GL~~t~ 267 (330)
+++++|+. + ++|.--++|+||.++|.+++.-+..|...... .-.++ ..+++|=.+|+.+=.
T Consensus 172 lPilfViP~~~~ySf~~~~~~~~~~~~~r~a~fiGlGD~vmPtILVvSa~~f~~~~~~~~~~lpalga~~Gtl~gl~vL~ 251 (283)
T PF06550_consen 172 LPILFVIPKKRGYSFLKDGFDNREEKEERDAFFIGLGDAVMPTILVVSAAFFLSAPILGGLNLPALGAMLGTLAGLAVLL 251 (283)
T ss_pred CceEEEEecccCccccccccccccccccccceEeccchhhhHHHHHHHHHHhccccchhhhhHHHHHHHHHHHHHHHHHH
Confidence 44888972 0 11233488999999999999988888765321 11122 334444444443322
Q ss_pred HHHhhhCCCccchhhhhhHHHHHHHHHHHHhh
Q 020166 268 IVMNWFQAAQPALLYIVPAVIGFLAAHCIWNG 299 (330)
Q Consensus 268 ~~~~~~~~~QPALLYLVP~~l~~~~~~A~~rg 299 (330)
.. ...+++||.|-||--+.++..++-++..|
T Consensus 252 ~~-v~kgrp~aGLP~LN~GaI~Gflig~l~sg 282 (283)
T PF06550_consen 252 RF-VMKGRPQAGLPFLNGGAIAGFLIGALASG 282 (283)
T ss_pred HH-HHcCCCCCCCCccchhHHHHHHHHHHHcC
Confidence 21 23578999999998888888777776544
No 6
>COG3389 Uncharacterized protein conserved in archaea [Function unknown]
Probab=97.86 E-value=6.2e-05 Score=70.28 Aligned_cols=146 Identities=24% Similarity=0.303 Sum_probs=101.7
Q ss_pred hhhhHHHHHHHhhccchhhhhhHHHHHHHHHhhhh--cccCchhHHHHHHHHHHHHHhhhhhccceE-------------
Q 020166 144 AAIPGTFFCAWYASQKHWLANNTLGLAFCIQGIEM--LSLGSFKTGAILLAGLFVYDIFWVFFTPVM------------- 208 (330)
Q Consensus 144 ~~~~~~~~~~~~~~~~~W~l~nilgi~~~~~~i~~--l~l~sfk~~~ilL~~lf~YDIf~VF~Tpvm------------- 208 (330)
+..+++.+....+.++.|+..|..|.+++...-.. +++. ...+..+|..+=+||-.=|+.|.-|
T Consensus 95 si~~aI~~~~lL~~~peWyVid~ag~~la~Giaai~GIsfg-v~pavvlL~~lavYDaIsVYkT~HMIslA~~v~d~~lP 173 (277)
T COG3389 95 SIGLAIGLVYLLYKYPEWYVIDLAGFFLAVGIAAIFGISFG-VLPAVVLLIALAVYDAISVYKTRHMISLAEGVMDLDLP 173 (277)
T ss_pred HHHHHHHHHHhhhhccceEEeehHHHHHHhhHHHhheeecc-hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCCc
Confidence 33344444444456778999999999887765433 3333 3567889999999999999999644
Q ss_pred --EEecCC------------CCCCCcccccCCCcchhhHHHHHHHhhhhccCCCcchh--HHHHHHHHHHHHHHHHHHhh
Q 020166 209 --LLFPTR------------DTARPFSMLGLGDIVIPGIFVALALRFDVSRGKGSRYF--KSAFLGYTVGLVLTIIVMNW 272 (330)
Q Consensus 209 --l~~P~~------------~~~~~~s~LGlGDIviPGl~ia~~lRfD~~~~~~~~YF--~~s~igY~~GL~~t~~~~~~ 272 (330)
.++|.+ ..+++-=|.|+||+++|-+++.=+.-|-.+. .-+| ..++.|=.+|+..- -+..
T Consensus 174 mlfviP~~l~ysf~~~~fe~r~dgna~miG~GDavmPsIlVvSaa~f~~s~---~l~f~~Lpal~GglvGl~vL--~~v~ 248 (277)
T COG3389 174 MLFVIPENLAYSFVEDAFENRGDGNAYMIGLGDAVMPSILVVSAAFFLISP---ILAFIVLPALAGGLVGLAVL--YFVN 248 (277)
T ss_pred eEEEeecccccceeehhhhcCCCCceEEEeechhhcccceeeehHHhccCC---chhhhhHHHHhccHHHHHHH--HHHh
Confidence 677851 2344555899999999999988776664432 3334 33577777777655 3444
Q ss_pred hCCCccchhhhhhHHHHHHHHHH
Q 020166 273 FQAAQPALLYIVPAVIGFLAAHC 295 (330)
Q Consensus 273 ~~~~QPALLYLVP~~l~~~~~~A 295 (330)
-+++||-|-|+--..+.+.++-+
T Consensus 249 r~Rp~pGLP~lN~GaIaGflig~ 271 (277)
T COG3389 249 RGRPHPGLPFLNTGAIAGFLIGF 271 (277)
T ss_pred cCCCCCCCceeccchHHHHHHHH
Confidence 57899999999877776665544
No 7
>PF01080 Presenilin: Presenilin Alzheimer disease; InterPro: IPR001108 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 group of aspartic peptidases belong to MEROPS peptidase family A22 (presenilin family, clan AD): subfamily A22A, the type example being presenilin 1 from Homo sapiens (Human). Presenilins are polytopic transmembrane (TM) proteins, mutations in which are associated with the occurrence of early-onset familial Alzheimer's disease, a rare form of the disease that results from a single-gene mutation [, ]. The physiological functions of presenilins are unknown, but they may be related to developmental signalling, apoptotic signal transduction, or processing of selected proteins, such as the beta-amyloid precursor protein(beta-APP). There are a number of subtypes which belong to this presenilin family. That presenilin homologues have been identified in species that do not have an Alzhemier's disease correlate suggests that they may have functions unrelated to the disease, homologues having been identified in mouse, Drosophila melanogaster, Caenorhabditis elegans [] and other members of the eukarya including plants. ; GO: 0004190 aspartic-type endopeptidase activity, 0016021 integral to membrane; PDB: 2KR6_A.
Probab=94.32 E-value=0.08 Score=53.61 Aligned_cols=63 Identities=30% Similarity=0.581 Sum_probs=47.0
Q ss_pred cccCCCcchhhHHHHHHHhh-hhccCCCcchhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHH
Q 020166 222 MLGLGDIVIPGIFVALALRF-DVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLA 292 (330)
Q Consensus 222 ~LGlGDIviPGl~ia~~lRf-D~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~ 292 (330)
-|||||-|+=+++++-+.++ |. .-..+|++|-.+||++|...+.++|++-|||- ++..+|.+.
T Consensus 327 klGlGDFiFYs~Lvg~aa~~~~~------~~~~~~~~ail~Gl~~Tl~~l~~~~~alPALP--isi~~g~~~ 390 (403)
T PF01080_consen 327 KLGLGDFIFYSVLVGRAAMYGDW------NTVVACFVAILIGLCLTLLLLAIFRKALPALP--ISIALGLIF 390 (403)
T ss_dssp SS-TTTHHHHHHHHHHHHHH-TT------TTHHHHHHHHHHHHHHHHHHHHHHT-S-SSSS--S----HHHH
T ss_pred eecchhHHHHHHHHhHHHhcCCH------HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCc--HHHHHHHHH
Confidence 58999999999999988876 33 33578999999999999999999999999995 555555443
No 8
>KOG2736 consensus Presenilin [Signal transduction mechanisms]
Probab=92.93 E-value=0.12 Score=51.69 Aligned_cols=66 Identities=27% Similarity=0.504 Sum_probs=52.9
Q ss_pred cccCCCcchhhHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHH
Q 020166 222 MLGLGDIVIPGIFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAH 294 (330)
Q Consensus 222 ~LGlGDIviPGl~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~ 294 (330)
-||+||-|+=-++++-+.-+|-+ .=-++|.+|-.+||++|.....++|++-|||- .|.++|.+.-.
T Consensus 321 kLGlGDFIFYSvLvGkAa~~~d~-----~TviAC~vaIL~GL~~TL~llsv~~kALPALP--isI~~G~iFYF 386 (406)
T KOG2736|consen 321 KLGLGDFIFYSVLVGKAAAYGDL-----NTVIACFVAILIGLCLTLLLLSVFKKALPALP--ISITFGLIFYF 386 (406)
T ss_pred eeccCceEEEEeeccchhhcCCh-----HHHHHHHHHHHHHHHHHHHHHHHHhhcCcCCc--hHHHHHHHHHH
Confidence 59999999887777766666521 12378999999999999999999999999996 77777766543
No 9
>PF06027 DUF914: Eukaryotic protein of unknown function (DUF914); InterPro: IPR009262 This family consists of several hypothetical proteins of unknown function. Some of the sequences in this family are annotated as putative membrane proteins.
Probab=71.89 E-value=15 Score=36.56 Aligned_cols=52 Identities=17% Similarity=0.392 Sum_probs=35.9
Q ss_pred HHHhhccchhhhhhHHHHHHHHHhhhhcccCchhH-------------HHHHHHHHHHHHhhhhh
Q 020166 152 CAWYASQKHWLANNTLGLAFCIQGIEMLSLGSFKT-------------GAILLAGLFVYDIFWVF 203 (330)
Q Consensus 152 ~~~~~~~~~W~l~nilgi~~~~~~i~~l~l~sfk~-------------~~ilL~~lf~YDIf~VF 203 (330)
..|.+.+.......++|+.+|+.++-.+...+... =.+.+.+.++|=+.-|.
T Consensus 122 LS~~fL~~ry~~~~~~gv~i~i~Gv~lv~~sD~~~~~~~~~~~~~i~GDll~l~~a~lya~~nV~ 186 (334)
T PF06027_consen 122 LSFIFLKRRYSWFHILGVLICIAGVVLVVVSDVLSGSDSSSGSNPILGDLLALLGAILYAVSNVL 186 (334)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHhhhhheeeecccccccCCCCCccchhHHHHHHHHHHHHHHHHH
Confidence 34555566666678889999988877665554332 35677888888887776
No 10
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=51.74 E-value=25 Score=25.60 Aligned_cols=12 Identities=25% Similarity=0.163 Sum_probs=5.9
Q ss_pred hhhhhHHHHHHH
Q 020166 281 LYIVPAVIGFLA 292 (330)
Q Consensus 281 LYLVP~~l~~~~ 292 (330)
+.+||..++..+
T Consensus 4 ~~iV~i~iv~~l 15 (50)
T PF12606_consen 4 FLIVSIFIVMGL 15 (50)
T ss_pred hHHHHHHHHHHH
Confidence 345665544433
No 11
>KOG3455 consensus Predicted membrane protein [Function unknown]
Probab=50.11 E-value=47 Score=29.13 Aligned_cols=52 Identities=10% Similarity=0.215 Sum_probs=45.8
Q ss_pred CcchhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHHHHHhh
Q 020166 248 GSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNG 299 (330)
Q Consensus 248 ~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~A~~rg 299 (330)
.++-+.++...|++.++=...=..+++...+.-..+.|+++.++.++...++
T Consensus 72 nk~i~~~~~~s~~lal~HflTE~l~yrT~tig~~~~~p~vv~s~Sl~~M~~~ 123 (139)
T KOG3455|consen 72 NKPIYIATFLSFILALGHFLTELLFYRTMTIGIGVLTPLVVNSISLVGMLKF 123 (139)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHhhccccceEEeeeeehhhhHHHHHHH
Confidence 4677888999999999988888899999999999999999999988887654
No 12
>KOG1607 consensus Protein transporter of the TRAM (translocating chain-associating membrane) superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.24 E-value=89 Score=31.05 Aligned_cols=67 Identities=13% Similarity=0.096 Sum_probs=33.3
Q ss_pred hhHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHHHH--HHhhhCCCccchhhhhhHHHHHHHHH------HHHhhHHH
Q 020166 231 PGIFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTII--VMNWFQAAQPALLYIVPAVIGFLAAH------CIWNGEVK 302 (330)
Q Consensus 231 PGl~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~--~~~~~~~~QPALLYLVP~~l~~~~~~------A~~rgEl~ 302 (330)
.-+|+.++.-++..| ++=|..-.+-|.. -...-+.++|-..|+.=++++.+.+. =..|=+-+
T Consensus 218 ~~~F~~F~~~wi~~R----------L~~~p~wil~st~~~~~~~~~~~~~~~~~~~~~lL~~Lqll~i~W~~lI~rm~~r 287 (318)
T KOG1607|consen 218 DFVFVLFAFSWIYTR----------LIYYPFWILRSTSREDFSLRQYQPKPSYYFFNCLLLALQLLHIYWFYLILRMAYR 287 (318)
T ss_pred HHHHHHHHHHHHHHH----------HHHHHHHHHHHhHHHHHHhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555433 3334444444443 23334445555566666666655433 23466667
Q ss_pred Hhhcc
Q 020166 303 QLLEF 307 (330)
Q Consensus 303 ~~w~~ 307 (330)
.+++.
T Consensus 288 ~~~~g 292 (318)
T KOG1607|consen 288 VIKRG 292 (318)
T ss_pred HHhcC
Confidence 77744
No 13
>PF07698 7TM-7TMR_HD: 7TM receptor with intracellular HD hydrolase; InterPro: IPR011621 These bacterial 7TM receptor proteins have an intracellular domain IPR006674 from INTERPRO. This entry corresponds to the 7 helix transmembrane domain. These proteins also contain an N-terminal extracellular domain.
Probab=48.12 E-value=80 Score=27.96 Aligned_cols=72 Identities=15% Similarity=0.231 Sum_probs=47.1
Q ss_pred HHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHHHHHhhHHHHhh
Q 020166 233 IFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLL 305 (330)
Q Consensus 233 l~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~A~~rgEl~~~w 305 (330)
.+.-+.+|+.+....+++++..-..-+.+++.++-.+....+ .++...|++|....+.+++.+...+..-+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~l~l~~~l~~l~l~l~~~~~~~~~-~~~~~~~~~P~a~~~~l~~~l~~~~~ai~~ 88 (194)
T PF07698_consen 17 ILYLYLRRFRPRILRSNKYLLLLSLLLLLSLLLAKIILFFIS-DISYFPYLIPVAAAAMLLTILIDPRLAILA 88 (194)
T ss_pred HHHHHHHHHCcHhhhchhHHHHHHHHHHHHHHHHHHHHHhcc-cchhhhhhhHHHHHHHHHHHHhcchHHHHH
Confidence 344556666443333445555555666777777666544333 678889999999999999988777765443
No 14
>PF03596 Cad: Cadmium resistance transporter; InterPro: IPR004676 These proteins are members of the Cadmium Resistance (CadD) Family. To date, this family of proteins has only been found in Gram-positive bacteria. The CadD family includes two close orthologues in two Staphylococcus species that have been reported to function in cadmium resistance, and another staphylococcal protein that has been reported to possibly function in quaternary ammonium ion export.
Probab=44.71 E-value=64 Score=29.65 Aligned_cols=12 Identities=17% Similarity=0.473 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHH
Q 020166 255 AFLGYTVGLVLT 266 (330)
Q Consensus 255 s~igY~~GL~~t 266 (330)
-++|+.+|..+=
T Consensus 28 I~~GqylG~~~L 39 (191)
T PF03596_consen 28 IVIGQYLGFTIL 39 (191)
T ss_pred hhhhHHHHHHHH
Confidence 455666664433
No 15
>KOG0569 consensus Permease of the major facilitator superfamily [Carbohydrate transport and metabolism]
Probab=44.09 E-value=30 Score=36.16 Aligned_cols=18 Identities=6% Similarity=-0.086 Sum_probs=11.1
Q ss_pred HHhhHHHHhhcccccccc
Q 020166 296 IWNGEVKQLLEFDESKTA 313 (330)
Q Consensus 296 ~~rgEl~~~w~~~~~~~~ 313 (330)
-+|+.++.+...+|++++
T Consensus 220 ~A~~sl~~y~G~~~~~~~ 237 (485)
T KOG0569|consen 220 EARKALKFYRGKEDVEAE 237 (485)
T ss_pred HHHHHHHHHhCCCcchhH
Confidence 346677777776654444
No 16
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=42.08 E-value=48 Score=28.86 Aligned_cols=63 Identities=27% Similarity=0.366 Sum_probs=48.2
Q ss_pred CCcchhHHHHHHHHHHHHHHHHHHhhhCC------Cccch----------hhhhhHHHHHHH---HHHHHhhHHHHhhcc
Q 020166 247 KGSRYFKSAFLGYTVGLVLTIIVMNWFQA------AQPAL----------LYIVPAVIGFLA---AHCIWNGEVKQLLEF 307 (330)
Q Consensus 247 ~~~~YF~~s~igY~~GL~~t~~~~~~~~~------~QPAL----------LYLVP~~l~~~~---~~A~~rgEl~~~w~~ 307 (330)
....||-..++-...|.++..++-.+|+. +-|-| .|..|++|.++. ++|..+.-+.++.++
T Consensus 36 ~~~~Y~~LfiVFl~AG~vLw~vM~~iFd~CIDsWkAdpeLnn~rymWNilMYaIPy~L~Ala~GFlv~~~~~p~~~~i~~ 115 (141)
T PRK13743 36 VSDIYFDLFIVFLTAGIVLWVIMHSIFDACIDSWKADPELNNFRYMWNILMYVIPYTLWALAAGFLVAGVRNPLCELING 115 (141)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhcChhhhhHHHHHHHHHHHHHHHHHHHHhchhhhhhhhHHHHHHhc
Confidence 46789999999999999999988877764 66776 899999997763 555556556666655
Q ss_pred cc
Q 020166 308 DE 309 (330)
Q Consensus 308 ~~ 309 (330)
.-
T Consensus 116 ~~ 117 (141)
T PRK13743 116 GI 117 (141)
T ss_pred ce
Confidence 43
No 17
>KOG2466 consensus Uridine permease/thiamine transporter/allantoin transport [Nucleotide transport and metabolism; Coenzyme transport and metabolism]
Probab=39.35 E-value=25 Score=36.99 Aligned_cols=76 Identities=14% Similarity=0.232 Sum_probs=38.7
Q ss_pred cchhhHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHHHHHhhHHHHhhcc
Q 020166 228 IVIPGIFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLEF 307 (330)
Q Consensus 228 IviPGl~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~A~~rgEl~~~w~~ 307 (330)
..+||+.-..--..-...+.-+-|+...+.||.+.-..--..+.+|-..|--| .--...+. .-+++|.+
T Consensus 471 P~lpG~a~~V~~~~~v~~G~~~~yy~~yf~sf~isf~vYwiLc~~fP~k~t~~--------~~~~~~~~---~~~~~~~~ 539 (572)
T KOG2466|consen 471 PNLPGFAGSVGADIKVPDGAVKLYYLDYFFSFLISFLVYWILCLFFPVKGTPL--------GEAYYPEK---RWLGMWAY 539 (572)
T ss_pred cCCcchhhhcCcccccccceEEEEechHHHHHHHHHHHHHHHHhhcCcccccc--------cccccchh---hhhccccc
Confidence 46888876655422222233456666666666655444444444443222110 11111111 45688999
Q ss_pred ccccccc
Q 020166 308 DESKTAA 314 (330)
Q Consensus 308 ~~~~~~~ 314 (330)
.||-|||
T Consensus 540 ve~s~~e 546 (572)
T KOG2466|consen 540 VEDSEEE 546 (572)
T ss_pred ccchhhh
Confidence 8887776
No 18
>TIGR02587 putative integral membrane protein TIGR02587. Members of this family are found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighborhood. This family, as defined, includes some members of COG4711 but is narrower and strictly bacterial. Members appear to span the membrane seven times.
Probab=37.89 E-value=49 Score=32.12 Aligned_cols=48 Identities=15% Similarity=0.140 Sum_probs=34.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhCC---Cccch-------hhhhhHHHHHHHHHHHHhh
Q 020166 252 FKSAFLGYTVGLVLTIIVMNWFQA---AQPAL-------LYIVPAVIGFLAAHCIWNG 299 (330)
Q Consensus 252 F~~s~igY~~GL~~t~~~~~~~~~---~QPAL-------LYLVP~~l~~~~~~A~~rg 299 (330)
..=++.+|++|++++.+++..++. ++|.= +=-+|+.+|..+.-...++
T Consensus 69 i~eti~ay~Iglv~S~~~L~lfgri~~~~pl~e~Lg~vivl~vP~sIGaAlaR~~L~~ 126 (271)
T TIGR02587 69 VIDTVEAMAIGFVCSAAMLWLFGIITPETSLKEIVGKVAFQGVPFSLGAALARQQLGD 126 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHHhCcHHHHHHHHHHHhCC
Confidence 345889999999999999999988 55632 2237877777666555433
No 19
>PRK14397 membrane protein; Provisional
Probab=37.68 E-value=1.4e+02 Score=28.18 Aligned_cols=29 Identities=7% Similarity=-0.032 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhhHHHHhhcccccccccc
Q 020166 287 VIGFLAAHCIWNGEVKQLLEFDESKTAAV 315 (330)
Q Consensus 287 ~l~~~~~~A~~rgEl~~~w~~~~~~~~~~ 315 (330)
.+++.++.--.|.+++++++.+|..-.++
T Consensus 166 ~~~a~lvi~rHr~NI~RL~~G~E~k~~~k 194 (222)
T PRK14397 166 LVVMALVYWSHRENIGRLARGEEKPWQKK 194 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcchhhcc
Confidence 34555555667899999999999885433
No 20
>COG4300 CadD Predicted permease, cadmium resistance protein [Inorganic ion transport and metabolism]
Probab=35.48 E-value=48 Score=30.60 Aligned_cols=66 Identities=15% Similarity=0.179 Sum_probs=35.7
Q ss_pred HhhhhccCCCcch---hHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHHHHHHHhhHHHHhhcccccccccc
Q 020166 239 LRFDVSRGKGSRY---FKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLEFDESKTAAV 315 (330)
Q Consensus 239 lRfD~~~~~~~~Y---F~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~~~A~~rgEl~~~w~~~~~~~~~~ 315 (330)
.|.|..++..+.| |.-+++=-...+..+++...+-..--|-||=+.|.-+| +|..|..++|+||+.
T Consensus 28 ar~~~~k~~~~I~~GQyLGs~~lilaSL~~a~v~~fvp~e~I~glLGLIPi~LG-----------ik~l~~~d~d~e~~~ 96 (205)
T COG4300 28 ARRKSRKDILHIYLGQYLGSVILILASLLFAFVLNFVPEEWILGLLGLIPIYLG-----------IKVLILGDDDGEEEA 96 (205)
T ss_pred HHhcccCcEEEEeHHHHHhHHHHHHHHHHHHHHHhhCcHHHHHHHHhHHHHHHh-----------hHHhhcccCcCchhh
Confidence 4666533223333 33333333455666665555555566667777777665 466676666444433
No 21
>PRK14412 membrane protein; Provisional
Probab=29.22 E-value=2.2e+02 Score=26.24 Aligned_cols=30 Identities=30% Similarity=0.159 Sum_probs=22.0
Q ss_pred hhhHHHHHHHHHHHHhhHHHHhhccccccc
Q 020166 283 IVPAVIGFLAAHCIWNGEVKQLLEFDESKT 312 (330)
Q Consensus 283 LVP~~l~~~~~~A~~rgEl~~~w~~~~~~~ 312 (330)
.++..+++.++.--.|.+++++++.+|..-
T Consensus 162 ~~~~~~~~~lii~rHr~NI~Rl~~g~E~k~ 191 (198)
T PRK14412 162 FVFSLILASLAIFQHRSNIKRLLAGTESKL 191 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 344555666666677899999999988654
No 22
>PF03606 DcuC: C4-dicarboxylate anaerobic carrier; InterPro: IPR018385 Escherichia coli contains four different secondary carriers (DcuA, DcuB, DcuC, and DctA) for C4-dicarboxylates [, , , ] DcuA is used for aerobic growth on C4-dicarboxylates [, ], whereas the Dcu carriers (encoded by the dcuA, dcuB, and dcuC genes) are used under anaerobic conditions and form a distinct family of carriers [, , , , , ]. Each of the Dcu carriers is able to catalyze the uptake, antiport, and possibly also efflux of C4-dicarboxylates. DcuB is the major C4-dicarboxylate carrier for fumarate respiration with high fumarate-succinate exchange activity. It is synthesized only in the absence of oxygen and nitrate and in the presence of C4-dicarboxylates [, , , ]. DcuA is expressed constitutively in aerobic and anaerobic growth and can substitute for DcuB [, ]. These proteins are members of the C4-dicarboxylate Uptake C (DcuC) family. DcuC has 12 GES predicted transmembrane regions, is induced only under anaerobic conditions, and is not repressed by glucose. DcuC may therefore function as a succinate efflux system during anaerobic glucose fermentation. However, when overexpressed, it can replace either DcuA or DcuB in catalyzing fumarate-succinate exchange and fumarate uptake [, ]. DcuC shows the same transport modes as DcuA and DcuB (exchange, uptake, and presumably efflux of C4-dicarboxylates) [].; GO: 0016021 integral to membrane
Probab=27.13 E-value=52 Score=33.87 Aligned_cols=9 Identities=33% Similarity=0.671 Sum_probs=4.4
Q ss_pred HHHHHhhhh
Q 020166 235 VALALRFDV 243 (330)
Q Consensus 235 ia~~lRfD~ 243 (330)
+...+.+|.
T Consensus 149 i~~alG~d~ 157 (465)
T PF03606_consen 149 ILIALGYDP 157 (465)
T ss_pred HHHHcCCCH
Confidence 444455553
No 23
>PF14181 YqfQ: YqfQ-like protein
Probab=27.11 E-value=34 Score=30.70 Aligned_cols=8 Identities=0% Similarity=0.260 Sum_probs=4.5
Q ss_pred HHHHhhcc
Q 020166 300 EVKQLLEF 307 (330)
Q Consensus 300 El~~~w~~ 307 (330)
.+-.||+.
T Consensus 84 NLPam~ki 91 (161)
T PF14181_consen 84 NLPAMWKI 91 (161)
T ss_pred hhHHHHHH
Confidence 45566654
No 24
>PF09622 DUF2391: Putative integral membrane protein (DUF2391); InterPro: IPR024464 Members of this protein family are found in archaea and bacteria. Their function is unknown.
Probab=25.86 E-value=1.5e+02 Score=28.74 Aligned_cols=44 Identities=25% Similarity=0.315 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCC---Cccchhh-------hhhHHHHHHHHHHH
Q 020166 253 KSAFLGYTVGLVLTIIVMNWFQA---AQPALLY-------IVPAVIGFLAAHCI 296 (330)
Q Consensus 253 ~~s~igY~~GL~~t~~~~~~~~~---~QPALLY-------LVP~~l~~~~~~A~ 296 (330)
.=+..+|.+|.+++.+++..++. ..|.--. -+|+-+|..+..+.
T Consensus 66 ~d~v~A~~ig~v~a~~~L~~l~~l~~~~~~~e~lgkiiv~~vP~siGa~la~~~ 119 (267)
T PF09622_consen 66 RDAVEALAIGAVVAAAVLTLLGKLTLDTPPREALGKIIVQSVPASIGAALARSQ 119 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHhHhheeeEecHHHHHHHHHHH
Confidence 34788999999999999998875 3342222 25666665555444
No 25
>PRK14409 membrane protein; Provisional
Probab=24.89 E-value=3e+02 Score=25.57 Aligned_cols=32 Identities=9% Similarity=-0.003 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHHhhHHHHhhccccccccccc
Q 020166 285 PAVIGFLAAHCIWNGEVKQLLEFDESKTAAVV 316 (330)
Q Consensus 285 P~~l~~~~~~A~~rgEl~~~w~~~~~~~~~~~ 316 (330)
+..+++.++.--.|.+++++++.+|....+||
T Consensus 173 ~~~~~a~lvi~rHr~NI~Rll~GtE~k~~~~~ 204 (205)
T PRK14409 173 TMVFISFGIILTHRENIRRILNRSELFAVKDE 204 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Confidence 45556666777789999999998886655444
No 26
>PF14248 DUF4345: Domain of unknown function (DUF4345)
Probab=23.77 E-value=4.2e+02 Score=21.89 Aligned_cols=85 Identities=19% Similarity=0.240 Sum_probs=55.3
Q ss_pred chhhHHHHHHHHHHhcccccCCCC--------CCCCCCccccchhhhHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHH
Q 020166 27 NLNVILTACLTVYVGCYRSVKPTP--------PSETMSNEHAMRFPFVGSAMLLSLFLLFKFLSKDLVNAVLTCYFFVLG 98 (330)
Q Consensus 27 ~~~ii~~Av~~V~iGs~~sl~~~~--------~~e~~s~~~A~~fPv~aS~~L~~LY~l~k~~~~~~v~~ll~~yf~~~g 98 (330)
+..+.+.++.++.+|...-+.+.+ ..++.+.++...+ ..|...-+|++++.-..+++.....+..-..+++
T Consensus 5 ~~~l~~~~l~~~~~Gl~~~~~p~~~~~~~~~~~~~~~~~~s~~R~-~~G~~~g~Gl~~l~~~~~~~~~~~al~~l~~~~~ 83 (124)
T PF14248_consen 5 RIFLILSALVFIGIGLAYFLAPSSTAPWFGGVLANAAALDSEFRA-YGGLYLGLGLLLLWAAFKPEYRRPALRLLALFIG 83 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcHHHHhhcccccCCchhHHHHHHH-HHHHHHHHHHHHHHHHccHhHHHHHHHHHHHHHH
Confidence 456678899999999988776532 1222233455555 4565577777777766666666655545455667
Q ss_pred HHHHHHHHHHHHHh
Q 020166 99 IIALSATILPAVKR 112 (330)
Q Consensus 99 ~~~l~~~l~~~~~~ 112 (330)
..++...++-..+.
T Consensus 84 ~~~lgRlis~~~dG 97 (124)
T PF14248_consen 84 GGGLGRLISLALDG 97 (124)
T ss_pred HHHHHHHHHHHHcC
Confidence 77888888777654
No 27
>KOG2881 consensus Predicted membrane protein [Function unknown]
Probab=23.73 E-value=1.3e+02 Score=29.48 Aligned_cols=17 Identities=18% Similarity=0.003 Sum_probs=12.2
Q ss_pred HHhhHHHHhhccccccc
Q 020166 296 IWNGEVKQLLEFDESKT 312 (330)
Q Consensus 296 ~~rgEl~~~w~~~~~~~ 312 (330)
.--+-+++=|+.++++.
T Consensus 143 FGlkmL~eg~~~~~~~~ 159 (294)
T KOG2881|consen 143 FGLKMLKEGWEMSPSEG 159 (294)
T ss_pred HHHHHHHHhhcCCCccc
Confidence 34466788888888775
No 28
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=23.59 E-value=2.8e+02 Score=27.79 Aligned_cols=75 Identities=16% Similarity=0.241 Sum_probs=46.6
Q ss_pred HHHHHHHhhhhccC-CCcchhHHHHHHHHHHHHHHHHHHh-hhCCCccchhhhhhHHHHHHHHH-----HH-HhhHHHHh
Q 020166 233 IFVALALRFDVSRG-KGSRYFKSAFLGYTVGLVLTIIVMN-WFQAAQPALLYIVPAVIGFLAAH-----CI-WNGEVKQL 304 (330)
Q Consensus 233 l~ia~~lRfD~~~~-~~~~YF~~s~igY~~GL~~t~~~~~-~~~~~QPALLYLVP~~l~~~~~~-----A~-~rgEl~~~ 304 (330)
.......|++.+.. .+-.=-..+.+|-++||++++.+.. ++..+-|-+--++|..+-.++.+ |. +|.|+-.+
T Consensus 61 ~~~~~~~~le~~i~k~~~~~ilf~tiGLiiGLlia~l~~~pL~~~~ip~~~~ii~vi~t~il~y~G~~~~~k~~de~~~l 140 (356)
T COG4956 61 YVLNWLKRLEEQIRKLPVTTILFGTIGLIIGLLIAVLLSSPLFLLPIPFISTIIPVILTIILAYFGFQLADKKRDEFLRL 140 (356)
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHhhHHhhCCccHHHhHHHHHHHHHHHHHhhHHhhhhhHHHHHh
Confidence 44566777776533 2334456688899999999987766 45678886655666554333322 33 35667666
Q ss_pred hcc
Q 020166 305 LEF 307 (330)
Q Consensus 305 w~~ 307 (330)
.+-
T Consensus 141 ~~~ 143 (356)
T COG4956 141 LNP 143 (356)
T ss_pred cch
Confidence 654
No 29
>PRK10921 twin-arginine protein translocation system subunit TatC; Provisional
Probab=23.46 E-value=69 Score=30.58 Aligned_cols=13 Identities=23% Similarity=0.427 Sum_probs=7.0
Q ss_pred ccccccccccccC
Q 020166 318 QESGDAKTSKKVE 330 (330)
Q Consensus 318 ~~~~~~~~~~~~~ 330 (330)
++|.|+|+||.+|
T Consensus 246 ~~~~~~~~~~~~~ 258 (258)
T PRK10921 246 ENDAEAESEKTEE 258 (258)
T ss_pred cchhhhcccccCC
Confidence 3455566665544
No 30
>PF14851 FAM176: FAM176 family
Probab=23.19 E-value=83 Score=28.03 Aligned_cols=17 Identities=29% Similarity=0.477 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHhh
Q 020166 256 FLGYTVGLVLTIIVMNW 272 (330)
Q Consensus 256 ~igY~~GL~~t~~~~~~ 272 (330)
+.|-++||++|.+++..
T Consensus 27 v~gVC~GLlLtLcllV~ 43 (153)
T PF14851_consen 27 VSGVCAGLLLTLCLLVI 43 (153)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 34556777777766443
No 31
>PF02487 CLN3: CLN3 protein; InterPro: IPR003492 Batten's disease, the juvenile variant of neuronal ceroid lipofuscionosis (NCL), is a recessively inherited disorder affecting children of 5-10 years of age. The disease is characterised by progressive loss of vision, seizures and psychomotor disturbances. Biochemically, the disease is characterised by lysosomal accumulation of hydrophobic material, mainly ATP synthase subunit C, largely in the brain but also in other tissues. The disease is fatal within a decade []. Mutations in the CLN3 gene are believed to cause Batten's disease []. The CLN3 gene, with a predicted 438-residue product, maps to chromosome p16p12.1. The gene contains at least 15 exons spanning 15kb and is highly conserved in mammals []. A 1.02kb deletion in the CLN3 gene, occurring in either one or both alleles, is found in 85% of Batten disease chromosomes causing a frameshift generating a predicted translated product of 181 amino acid residues [, ]. 22 other mutations, including deletions, insertions and point mutations, have been reported. It has been suggested that such mutations result in severely truncated CLN3 proteins, or affect its structure/conformation [, ]. CLN3 proteins, which are believed to associate in complexes, are heavily glycosylated lysosomal membrane proteins [], containing complex Asn-linked oligosaccharides []. Extensive glycosylation is important for the stability of these lysosomal proteins in the highly hydrolytic lysosomal lumen. Lysosomal sequestration of active lysosomal enzymes, transport of degraded molecules from the lysosomes, and fusion and fission between lysosomes and other organelles. The CLN3 protein is a 43kDa, highly hydrophobic, multi-transmembrane (TM), phosphorylated protein []. Hydrophobicity analysis predicts 6-9 TM segments, suggesting that CLN3 is a TM protein that may function as a chaperone or signal transducer. The majority of putative phosphorylation sites are found in the N-terminal domain, encompassing 150 residues []. Phosphorylation is believed to be important for membrane compartment interaction, in the formation of functional complexes, and in regulation and interactions with other proteins []. CLN3 contains several motifs that may undergo lipid post-translational modifications (PTMs). PTMs contribute to targeting and anchoring of modified proteins to distinct biological membranes []. There are three general classes of lipid modification: N-terminal myristoylation, C-terminal prenylation, and palmitoylation of cysteine residues. Such modifications are believed to be a common form of PTM occurring in 0.5% of all cellular proteins, including brain tissue []. The C terminus of the CLN3 contains various lipid modification sites: C435, target for prenylation; G419, target for myristoylation; and C414, target for palmitoylation []. Prenylation results in protein hydrophobicity, influences interaction with upstream regulatory proteins and downstream effectors, facilitates protein-protein interaction (multisubunit assembly) and promotes anchoring to membrane lipids. The prenylation motif, Cys-A-A-X, is highly conserved within CLN3 protein sequences of different species []. Species with known CLN3 protein homologues include: Homo sapiens, Canis familiaris, Mus musculus, Saccharomyces cerevisiae and Drosophila melanogaster.; GO: 0016020 membrane
Probab=21.72 E-value=1.2e+02 Score=31.08 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=12.1
Q ss_pred cCCCcchhhHHHHHHHhhhh
Q 020166 224 GLGDIVIPGIFVALALRFDV 243 (330)
Q Consensus 224 GlGDIviPGl~ia~~lRfD~ 243 (330)
|+|.+. |+++..||+.
T Consensus 127 g~GE~t----fL~lt~~y~~ 142 (402)
T PF02487_consen 127 GLGEVT----FLSLTHFYGK 142 (402)
T ss_pred hhhHHH----HHHHHHhcCc
Confidence 777764 6778889876
No 32
>COG5058 LAG1 Protein transporter of the TRAM (translocating chain-associating membrane) superfamily, longevity assurance factor [Intracellular trafficking and secretion]
Probab=20.55 E-value=61 Score=32.50 Aligned_cols=39 Identities=28% Similarity=0.432 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhhHHHHhhccccccccccccccccccccc
Q 020166 286 AVIGFLAAHCIWNGEVKQLLEFDESKTAAVVSQESGDAKTS 326 (330)
Q Consensus 286 ~~l~~~~~~A~~rgEl~~~w~~~~~~~~~~~~~~~~~~~~~ 326 (330)
.++.-+.--+..+||+++ .-||+++||+++.++++.|.+
T Consensus 357 ~lIvRvayRv~~~~e~~D--~RSd~e~ee~s~~~~s~~k~d 395 (395)
T COG5058 357 FLIVRVAYRVIWEGELKD--ERSDDESEEESDLESSEDKND 395 (395)
T ss_pred HHHHHHHHHHhccccccc--cccccccCChhhhhccccCCC
No 33
>PRK14402 membrane protein; Provisional
Probab=20.52 E-value=4.2e+02 Score=24.43 Aligned_cols=30 Identities=10% Similarity=0.074 Sum_probs=22.0
Q ss_pred hhhHHHHHHHHHHHHhhHHHHhhccccccc
Q 020166 283 IVPAVIGFLAAHCIWNGEVKQLLEFDESKT 312 (330)
Q Consensus 283 LVP~~l~~~~~~A~~rgEl~~~w~~~~~~~ 312 (330)
.....+++.++.--.|.+++++++.+|..-
T Consensus 164 ~~~~~~la~lii~rHr~NI~Rl~~g~E~k~ 193 (198)
T PRK14402 164 VATVVLLAALLFWTHRENIRRLQAGTERRL 193 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCcc
Confidence 455566666777777899999999877543
No 34
>PRK03625 tatE twin arginine translocase protein E; Validated
Probab=20.51 E-value=2.2e+02 Score=21.92 Aligned_cols=14 Identities=29% Similarity=0.460 Sum_probs=7.3
Q ss_pred HHHHHHHHhhhCCC
Q 020166 263 LVLTIIVMNWFQAA 276 (330)
Q Consensus 263 L~~t~~~~~~~~~~ 276 (330)
+++.++++.+|...
T Consensus 10 liIlvI~lllFGpk 23 (67)
T PRK03625 10 LVVAALVVLLFGTK 23 (67)
T ss_pred HHHHHHHHHHcCcc
Confidence 34455555566543
No 35
>KOG1134 consensus Uncharacterized conserved protein [General function prediction only]
Probab=20.50 E-value=3.2e+02 Score=30.13 Aligned_cols=78 Identities=15% Similarity=0.254 Sum_probs=45.2
Q ss_pred cchhhHHHHHHHhhhhccC-----CCcch----------hHHHHHHHHHHHHHHHHHHhhhCCCccchhhhhhHHHHHHH
Q 020166 228 IVIPGIFVALALRFDVSRG-----KGSRY----------FKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLA 292 (330)
Q Consensus 228 IviPGl~ia~~lRfD~~~~-----~~~~Y----------F~~s~igY~~GL~~t~~~~~~~~~~QPALLYLVP~~l~~~~ 292 (330)
+++|=..+.+|++|=.+++ +...| ....+.|-.+.=++ ++...-.+++-++...++|..++++.
T Consensus 574 lILpF~lvyF~l~y~vyr~ql~yvy~~~yes~g~~wp~ih~~ii~~l~l~ql~-l~gl~~~k~~~~~s~~~~~l~~lTi~ 652 (728)
T KOG1134|consen 574 LILPFGLVYFCLAYLVYRYQLIYVYNQKYESGGRFWPDIHRRIIFGLILFQLI-LFGLFSLKKGAVASVLLFPLIVLTIL 652 (728)
T ss_pred HHHHHHHHHHHHHHHHHhhhhheeecccccccccchHHHHHHHHHHHHHHHHH-HHHHHHhccccccchHHHHHHHHHHH
Confidence 4666666777777744332 11222 22223333332222 22345568888888889999999988
Q ss_pred HHHHHhhHHHHhhc
Q 020166 293 AHCIWNGEVKQLLE 306 (330)
Q Consensus 293 ~~A~~rgEl~~~w~ 306 (330)
..=.+++-++-...
T Consensus 653 ~~~~c~~rf~p~f~ 666 (728)
T KOG1134|consen 653 FHIYCKGRFLPLFI 666 (728)
T ss_pred HHHHHhhhcccccc
Confidence 66677776654443
No 36
>PF12821 DUF3815: Protein of unknown function (DUF3815); InterPro: IPR024528 This domain is found in uncharacterised predicted membrane proteins.
Probab=20.29 E-value=3.5e+02 Score=22.62 Aligned_cols=52 Identities=17% Similarity=0.407 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCC-----ccchhhhhhHHHHHHHHHHHHhhHHHHhh
Q 020166 253 KSAFLGYTVGLVLTIIVMNWFQAA-----QPALLYIVPAVIGFLAAHCIWNGEVKQLL 305 (330)
Q Consensus 253 ~~s~igY~~GL~~t~~~~~~~~~~-----QPALLYLVP~~l~~~~~~A~~rgEl~~~w 305 (330)
-+-+.+..+|+.....+-. .|.+ -|++..+||...+--...++.++|..+-+
T Consensus 51 a~f~aa~~vg~~~~~~ar~-~~~P~~v~~vpgiipLVPG~~~y~~~~~~~~~~~~~~~ 107 (130)
T PF12821_consen 51 ATFVAAFVVGLLAELFARR-LKAPATVFIVPGIIPLVPGSLAYRGMYSLVSGNYSSAL 107 (130)
T ss_pred HHHHHHHHHHHHHHHHHHh-ccCchHHhhccchheeCCcHHHHHHHHHHHHhhHHHHH
Confidence 3334445556665555543 3332 26777777777777777777777755544
No 37
>PRK13755 putative mercury transport protein MerC; Provisional
Probab=20.15 E-value=5.9e+02 Score=22.23 Aligned_cols=45 Identities=20% Similarity=0.298 Sum_probs=26.7
Q ss_pred ccchhhhHHHH-HHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020166 59 HAMRFPFVGSA-MLLSLFLLFKFLSKDLVNAVLTCYFFVLGIIALSATIL 107 (330)
Q Consensus 59 ~A~~fPv~aS~-~L~~LY~l~k~~~~~~v~~ll~~yf~~~g~~~l~~~l~ 107 (330)
=|+.||-++|. .-+||=++-+| .--+++.++-.| +++.-+.+.+.
T Consensus 23 CA~CFPAlASLGAAIGLGFLsq~-EGLFi~~LlPlF---A~iALlanalg 68 (139)
T PRK13755 23 CAACFPALASLGAAIGLGFLSQY-EGLFISTLLPLF---AAIALLANALG 68 (139)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHH-HHHHHHHHHHHH---HHHHHHHHHHH
Confidence 47789998887 66677676665 223466665443 33434444443
Done!