Query 019365
Match_columns 342
No_of_seqs 174 out of 496
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:52:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019365.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019365hhsearch_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 9.3E-82 2E-86 603.6 17.9 328 10-339 10-360 (362)
2 PF04258 Peptidase_A22B: Signa 100.0 1.1E-68 2.4E-73 515.8 -0.2 270 49-318 2-298 (298)
3 KOG2442 Uncharacterized conser 100.0 4.9E-65 1.1E-69 504.9 17.0 299 14-324 173-522 (541)
4 smart00730 PSN Presenilin, sig 100.0 2.9E-50 6.3E-55 379.3 22.5 231 52-310 2-249 (249)
5 PF06550 DUF1119: Protein of u 99.8 6.4E-19 1.4E-23 167.3 21.6 169 141-311 92-282 (283)
6 COG3389 Uncharacterized protei 99.7 8.4E-17 1.8E-21 148.7 9.4 159 144-308 95-272 (277)
7 PF01080 Presenilin: Presenili 95.3 0.037 8.1E-07 56.3 6.3 66 233-306 326-392 (403)
8 KOG2736 Presenilin [Signal tra 95.2 0.018 3.9E-07 57.7 3.8 68 232-306 319-386 (406)
9 PF06027 DUF914: Eukaryotic pr 70.2 14 0.0003 37.0 6.9 52 152-203 122-186 (334)
10 PF03596 Cad: Cadmium resistan 53.4 40 0.00087 31.1 6.3 12 267-278 28-39 (191)
11 PF12606 RELT: Tumour necrosis 52.6 24 0.00052 25.8 3.7 9 317-325 27-35 (50)
12 COG4300 CadD Predicted permeas 47.9 21 0.00046 33.1 3.5 65 249-324 26-93 (205)
13 PF07698 7TM-7TMR_HD: 7TM rece 46.8 81 0.0018 28.1 7.1 71 246-317 18-88 (194)
14 KOG1607 Protein transporter of 46.3 78 0.0017 31.6 7.4 39 286-324 253-297 (318)
15 KOG3455 Predicted membrane pro 44.0 56 0.0012 28.8 5.3 51 261-311 73-123 (139)
16 KOG0569 Permease of the major 42.2 32 0.0007 36.1 4.3 17 309-325 221-237 (485)
17 TIGR02587 putative integral me 41.7 44 0.00094 32.6 4.7 48 264-311 69-126 (271)
18 KOG2466 Uridine permease/thiam 37.3 31 0.00067 36.5 3.2 76 240-326 471-546 (572)
19 PRK13743 conjugal transfer pro 36.5 60 0.0013 28.5 4.3 64 259-322 36-118 (141)
20 PF14181 YqfQ: YqfQ-like prote 35.9 20 0.00043 32.4 1.4 8 312-319 84-91 (161)
21 PRK14397 membrane protein; Pro 33.9 1.5E+02 0.0032 28.2 6.9 25 300-324 167-191 (222)
22 PF13038 DUF3899: Domain of un 30.1 76 0.0017 25.2 3.8 20 262-281 4-23 (92)
23 PF14248 DUF4345: Domain of un 30.0 2.4E+02 0.0052 23.5 7.0 85 27-112 5-97 (124)
24 PF11368 DUF3169: Protein of u 29.4 53 0.0012 31.0 3.2 15 267-281 19-33 (248)
25 PRK13755 putative mercury tran 28.7 4E+02 0.0088 23.3 9.3 45 59-107 23-68 (139)
26 PRK14409 membrane protein; Pro 27.2 2.6E+02 0.0055 26.2 7.2 32 297-328 173-204 (205)
27 PF09622 DUF2391: Putative int 27.2 1.5E+02 0.0034 28.8 5.9 22 266-287 67-88 (267)
28 PF12821 DUF3815: Protein of u 26.2 2.2E+02 0.0047 24.0 6.1 48 269-317 55-107 (130)
29 PF01080 Presenilin: Presenili 25.4 23 0.00051 36.3 0.0 61 158-219 147-213 (403)
30 PF03606 DcuC: C4-dicarboxylat 23.7 66 0.0014 33.3 2.9 10 296-305 206-215 (465)
31 PRK14412 membrane protein; Pro 23.5 3.3E+02 0.0072 25.2 7.2 29 296-324 163-191 (198)
32 KOG2736 Presenilin [Signal tra 23.0 3.7E+02 0.008 27.7 7.8 59 158-217 153-217 (406)
33 PRK10995 inner membrane protei 22.0 1.7E+02 0.0036 27.3 5.0 48 245-293 27-77 (221)
34 COG1298 FlhA Flagellar biosynt 22.0 1.7E+02 0.0037 32.2 5.6 27 177-203 112-138 (696)
35 PRK14859 tatA twin arginine tr 21.2 53 0.0011 25.1 1.2 11 276-286 11-21 (63)
36 PF02939 UcrQ: UcrQ family; I 21.1 1.5E+02 0.0032 23.7 3.8 34 284-317 37-70 (80)
37 PF01914 MarC: MarC family int 20.9 1.4E+02 0.003 27.5 4.2 60 245-306 23-85 (203)
38 KOG2881 Predicted membrane pro 20.8 1.5E+02 0.0033 29.1 4.4 15 310-324 145-159 (294)
No 1
>KOG2443 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=9.3e-82 Score=603.64 Aligned_cols=328 Identities=47% Similarity=0.782 Sum_probs=286.5
Q ss_pred HHHHHHhhcCCccccCcchhhHHHHHHHHhHhcccccCC------C-CCCCCCCccccch-hhhHHHHHHHHHHHHHHhc
Q 019365 10 LALAGLTLAPLLVKVDPNLNVILTACLTVYVGCYRSVKP------T-PPSETMSNEHAMR-FPFVGSAMLLSLFLLFKFL 81 (342)
Q Consensus 10 ~~~~~~~~~~~~~~v~~~~~~i~~Av~~I~iGs~~s~~~------~-~~~e~i~~~~A~~-fPv~aS~~L~~LY~l~k~~ 81 (342)
.+....+.++.....+.++.++++|+++|++||.||++. + +..|+++.+||.. ||++|||+|++||+++|.+
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 344446677777788889999999999999999999962 1 2467899999998 9999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----hhCCCCCCcCceeeeeccc---cceeeeeehhhHHhhhhhHHHHHH
Q 019365 82 SKDLVNAVLTCYFFVLGIIALSATILPAVK----RFLPNHWNEDLIIWHFPYF---RSLEIEFTRSQIIAAIPGTFFCAW 154 (342)
Q Consensus 82 ~~~~i~~ll~~yf~~~g~~~l~~~l~~~~~----~~~p~~~~~~~~~~~~p~~---~~~~~~~~~~~l~~~~~~~~~~~~ 154 (342)
+++++| +++.||++.|+.++.+.+.|++. .++|..+.+- ...+-|.. ...+.+||..++++...|..+++|
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 3455444321 00011111 124789999999999999999999
Q ss_pred hhccchhhHhhHHHHHHHHHhhhhcccCchhhHHHHHHHHHHhhhheeeccchhhhhhccCCCCEEEEeeccCC-----C
Q 019365 155 YASQKHWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFTPVMVSVAKSFDAPIKLLFPTRDT-----A 229 (342)
Q Consensus 155 ~~~~~~W~l~nilgi~~~~~~i~~i~l~s~k~~~iLL~~lf~YDif~VF~T~vMvtVA~~~~~Pikl~~P~~~~-----~ 229 (342)
|+.++||++||++|+++|+++|+.+|++|+|+|++||.|||+|||||||+|+|||||||++|.|+|+++|++.. .
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 99999999999999999999999999999999999999999999999999999999999999999999999622 4
Q ss_pred CCceeccCCCccchhHHhhhHhhhcccCCCC---cchHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHH
Q 019365 230 RPFSMLGLGDIVIPGIFVALALRFDVSRGKG---SRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAH 306 (342)
Q Consensus 230 ~~~s~LGlGDIviPGi~ia~~lRfD~~~~~~---~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~ 306 (342)
.+||||||||||+||+|+|+++|||.+++.. +.||+.+++||.+|+..|+++|+++|++||||||+||+|+++.+++
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 4699999999999999999999999886543 7899999999999999999999999999999999999999999999
Q ss_pred HHHhhhHHHhhcccccccccccccccccccccc
Q 019365 307 CIWNGEVKQLLEFDESKTAAVVSQESGDAKTSK 339 (342)
Q Consensus 307 A~~rgEl~~lw~~~~~~~~~~~~~~~~~~~~~~ 339 (342)
|++|||++++|+|+++.+||++++.|.|+++|+
T Consensus 328 A~~~gdlk~l~s~~~~~~~~~~~~~e~k~~~e~ 360 (362)
T KOG2443|consen 328 AYWRGDLKVLWSFDESTKEESAEQDEVKEKKEN 360 (362)
T ss_pred HHHccchHhhhCccccCCCCcHHHHhhhhcccc
Confidence 999999999999999887777656666655554
No 2
>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=1.1e-68 Score=515.83 Aligned_cols=270 Identities=46% Similarity=0.831 Sum_probs=0.0
Q ss_pred CCCCCCCCccccchhhhHHHHHHHHHHHHHHhccHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhhCCC----CCCcCc
Q 019365 49 TPPSETMSNEHAMRFPFVGSAMLLSLFLLFKFLSKDLVNA--VLTCYFFVLGIIALSATILPAVKRFLPN----HWNEDL 122 (342)
Q Consensus 49 ~~~~e~i~~~~A~~fPv~aS~~L~~LY~l~k~~~~~~i~~--ll~~yf~~~g~~~l~~~l~~~~~~~~p~----~~~~~~ 122 (342)
+++.|++|.+||+.||++||++|+++|+++|+++++++|. +++.||++.|+.++..++.+.+.+..+. ....++
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 3578899999999999999999999999999999999986 8999999999999988888877764331 111111
Q ss_pred eeeeeccc--cceeeeeehhhHHhhhhhHHHHH-Hhhccc-hhhHhhHHHHHHHHHhhhhcccCchhhHHHHHHHHHHhh
Q 019365 123 IIWHFPYF--RSLEIEFTRSQIIAAIPGTFFCA-WYASQK-HWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYD 198 (342)
Q Consensus 123 ~~~~~p~~--~~~~~~~~~~~l~~~~~~~~~~~-~~~~~~-~W~l~nilgi~~~~~~i~~i~l~s~k~~~iLL~~lf~YD 198 (342)
.+...+.. +..+.+++..++++..+|+.+++ |++.++ ||++||++|+|+|+++++.+|++|+|+++++|+++|+||
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 23557788889999999888865 566677 999999999999999999999999999999999999999
Q ss_pred hheee------ccchhhhhhcc-CCC----CEEEEeecc-----CCCCCceeccCCCccchhHHhhhHhhhcccC-CCCc
Q 019365 199 IFWVF------FTPVMVSVAKS-FDA----PIKLLFPTR-----DTARPFSMLGLGDIVIPGIFVALALRFDVSR-GKGS 261 (342)
Q Consensus 199 if~VF------~T~vMvtVA~~-~~~----Pikl~~P~~-----~~~~~~s~LGlGDIviPGi~ia~~lRfD~~~-~~~~ 261 (342)
||||| +++||++|||+ .|. |+|+++|+. ++++++||||+||||+||+++++|+|||.++ +.++
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 88899999999 888 999999997 4678999999999999999999999999988 3467
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHHHHHhhhHHHhhc
Q 019365 262 RYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLE 318 (342)
Q Consensus 262 ~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~rgEl~~lw~ 318 (342)
+||.++++||++||++|+++++++|+|||||||+||+|+++++++|++|||++++||
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 3
>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=100.00 E-value=4.9e-65 Score=504.86 Aligned_cols=299 Identities=31% Similarity=0.503 Sum_probs=249.3
Q ss_pred HHhhcCCccccCcchhhH-HHHHHHHhHhcccccCCCCC--------------CC------------CCCccccchhhhH
Q 019365 14 GLTLAPLLVKVDPNLNVI-LTACLTVYVGCYRSVKPTPP--------------SE------------TMSNEHAMRFPFV 66 (342)
Q Consensus 14 ~~~~~~~~~~v~~~~~~i-~~Av~~I~iGs~~s~~~~~~--------------~e------------~i~~~~A~~fPv~ 66 (342)
++.|+|.+|.+|+++++| +||++||..|||||..++++ .| .+|.-.|..|.+.
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 467999999999999999 99999999999999732110 11 1344456667778
Q ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCcCceeeeeccccceeeeeehhhHHhhh
Q 019365 67 GSAMLLSLFLLFKFLSKDLVNAVLTCYFFVLGIIALSATILPAVKRFLPNHWNEDLIIWHFPYFRSLEIEFTRSQIIAAI 146 (342)
Q Consensus 67 aS~~L~~LY~l~k~~~~~~i~~ll~~yf~~~g~~~l~~~l~~~~~~~~p~~~~~~~~~~~~p~~~~~~~~~~~~~l~~~~ 146 (342)
++.+|+.+|+++++ +++. ++++|++.|..++++|+.+.++|..-+..+ .+-.-|..+..+ ...++..+
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-LIIIFCIGGAQGLYNCLAALVHRLPYGAAR---FPTLAPRLGNMS----YRLLFLSI 320 (541)
T ss_pred hHHHHHHHHHHHHH----HHHH-HhhheeecccchHHHHHHHHHhhhhhhccc---ccccccccCChh----HHHHHHHH
Confidence 88888888887765 3554 568899999999999999999885433321 111112222222 23455556
Q ss_pred hhHHHH-HHhhccc---hhhHhhHHHHHHHHHhhhhcccCchhhHHHHHHHHHHhhhheeeccc--------hhhhhhcc
Q 019365 147 PGTFFC-AWYASQK---HWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFTP--------VMVSVAKS 214 (342)
Q Consensus 147 ~~~~~~-~~~~~~~---~W~l~nilgi~~~~~~i~~i~l~s~k~~~iLL~~lf~YDif~VF~T~--------vMvtVA~~ 214 (342)
++++++ .|.++|+ .|++||++|||+|++.+|.+|+||+|++++||..+|+|||||||+|| ||++||+|
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 666664 5777776 69999999999999999999999999999999999999999999997 78999998
Q ss_pred C-----CCCEEEEeecc------CCCCCceeccCCCccchhHHhhhHhhhcccCCC-CcchHHHHHHHHHHHHHHHHHHH
Q 019365 215 F-----DAPIKLLFPTR------DTARPFSMLGLGDIVIPGIFVALALRFDVSRGK-GSRYFKSAFLGYTVGLVLTIIVM 282 (342)
Q Consensus 215 ~-----~~Pikl~~P~~------~~~~~~s~LGlGDIviPGi~ia~~lRfD~~~~~-~~~YF~~s~igY~~GL~~t~~~~ 282 (342)
. ..||.+++||. ++.++|||||+|||++||+++|+|+|||...++ +..||.++++||.+||++|++++
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 4 58999999993 678999999999999999999999999998776 88999999999999999999999
Q ss_pred HHhCCCccchhhhhhHHHHHHHHHHHHhhhHHHhhccccccc
Q 019365 283 NWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLEFDESKT 324 (342)
Q Consensus 283 ~~~~~~QPALLYLvP~~l~~~~~~A~~rgEl~~lw~~~~~~~ 324 (342)
..+|.|||||||||||+|++....|++|||++++|++...+.
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 999999999999999999999999999999999999988664
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=2.9e-50 Score=379.32 Aligned_cols=231 Identities=38% Similarity=0.631 Sum_probs=201.8
Q ss_pred CCCCCccccchhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCcCceeeeecccc
Q 019365 52 SETMSNEHAMRFPFVGSAMLLSLFLLFKFLSKDLVNAVLTCYFFVLGIIALSATILPAVKRFLPNHWNEDLIIWHFPYFR 131 (342)
Q Consensus 52 ~e~i~~~~A~~fPv~aS~~L~~LY~l~k~~~~~~i~~ll~~yf~~~g~~~l~~~l~~~~~~~~p~~~~~~~~~~~~p~~~ 131 (342)
.|.+++++++.||+++|++|+++|...|+ .+..+.+||+..|+.++..++.+......
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 46789999999999999999999988876 26677899999999999999888765420
Q ss_pred ceeeeeehhhHHhhhhhH-HHHHHhhccc-hhhHhhHHHHHHHHHhhhhcccCchhhHHHHHHHHHHhhhheeecc----
Q 019365 132 SLEIEFTRSQIIAAIPGT-FFCAWYASQK-HWLANNTLGLAFCIQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFT---- 205 (342)
Q Consensus 132 ~~~~~~~~~~l~~~~~~~-~~~~~~~~~~-~W~l~nilgi~~~~~~i~~i~l~s~k~~~iLL~~lf~YDif~VF~T---- 205 (342)
+....+....+. +.+.|+.++| +|+.||++|+++|+++++.+++||+|++.++|+++++||+||||+|
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 011223333333 3467887786 9999999999999999999999999999999999999999999999
Q ss_pred chhhhhhccCC-----CCEEEEeec------cCCCCCceeccCCCccchhHHhhhHhhhcccCCCCcchHHHHHHHHHHH
Q 019365 206 PVMVSVAKSFD-----APIKLLFPT------RDTARPFSMLGLGDIVIPGIFVALALRFDVSRGKGSRYFKSAFLGYTVG 274 (342)
Q Consensus 206 ~vMvtVA~~~~-----~Pikl~~P~------~~~~~~~s~LGlGDIviPGi~ia~~lRfD~~~~~~~~YF~~s~igY~~G 274 (342)
+||++|||+.| .|+++..|| +++++++++||+||||+||+++++|+|||.+++.++.||..|++||++|
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 89999999976 467778887 3456789999999999999999999999988777889999999999999
Q ss_pred HHHHHHHHHHhCCCccchhhhhhHHHHHHHHHHHHh
Q 019365 275 LVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWN 310 (342)
Q Consensus 275 L~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~r 310 (342)
|+.|+++++.+|+|||||+|+||+++++.+++|+.|
T Consensus 214 L~~t~~~l~~~~~aqPALlylvp~~l~~~~~~~~~r 249 (249)
T smart00730 214 LILTLVLLALFKKAQPALPYLVPFTLVFYLLTALLR 249 (249)
T ss_pred HHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999876
No 5
>PF06550 DUF1119: Protein of unknown function (DUF1119); InterPro: IPR010545 This family consists of several hypothetical archaeal proteins of unknown function.
Probab=99.83 E-value=6.4e-19 Score=167.27 Aligned_cols=169 Identities=28% Similarity=0.348 Sum_probs=137.5
Q ss_pred hHHhhhhhHHHHHHhhccchhhHhhHHHHHHHH--HhhhhcccCchhhHHHHHHHHHHhhhheeeccchhhhhhcc---C
Q 019365 141 QIIAAIPGTFFCAWYASQKHWLANNTLGLAFCI--QGIEMLSLGSFKTGAILLAGLFVYDIFWVFFTPVMVSVAKS---F 215 (342)
Q Consensus 141 ~l~~~~~~~~~~~~~~~~~~W~l~nilgi~~~~--~~i~~i~l~s~k~~~iLL~~lf~YDif~VF~T~vMvtVA~~---~ 215 (342)
...+.+.+..+..+++.+++|+..|+.|+.++. .++..++++-+. +.+||+.|-+||..-||+|+||++.|++ .
T Consensus 92 ~~~a~~~ai~~~~~L~~ypEWYviD~~Gil~~aG~aaiFGISl~~lp-aiiLL~iLAVYDaISVYkTkHMltLAegv~d~ 170 (283)
T PF06550_consen 92 NIIALILAIALTALLYKYPEWYVIDIAGILMGAGAAAIFGISLGILP-AIILLAILAVYDAISVYKTKHMLTLAEGVMDL 170 (283)
T ss_pred HHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhHHHHHHhhhccHHH-HHHHHHHHHHhhhhheecchHHHHHHHHHhcc
Confidence 345666777778888889999999999999985 578999998876 9999999999999999999999999998 4
Q ss_pred CCCEEEEeecc---------------CCCCCceeccCCCccchhHHhhhHhhhcccCCCC-cchH-HHHHHHHHHHHHHH
Q 019365 216 DAPIKLLFPTR---------------DTARPFSMLGLGDIVIPGIFVALALRFDVSRGKG-SRYF-KSAFLGYTVGLVLT 278 (342)
Q Consensus 216 ~~Pikl~~P~~---------------~~~~~~s~LGlGDIviPGi~ia~~lRfD~~~~~~-~~YF-~~s~igY~~GL~~t 278 (342)
+.|+.+++|+. +++|+..++|+||.++|.++++.+..|....... -.++ ..+++|-.+|+.+-
T Consensus 171 klPilfViP~~~~ySf~~~~~~~~~~~~~r~a~fiGlGD~vmPtILVvSa~~f~~~~~~~~~~lpalga~~Gtl~gl~vL 250 (283)
T PF06550_consen 171 KLPILFVIPKKRGYSFLKDGFDNREEKEERDAFFIGLGDAVMPTILVVSAAFFLSAPILGGLNLPALGAMLGTLAGLAVL 250 (283)
T ss_pred CCceEEEEecccCccccccccccccccccccceEeccchhhhHHHHHHHHHHhccccchhhhhHHHHHHHHHHHHHHHHH
Confidence 79999999983 1124556899999999999999999997653321 1222 45777777777665
Q ss_pred HHHHHHhCCCccchhhhhhHHHHHHHHHHHHhh
Q 019365 279 IIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNG 311 (342)
Q Consensus 279 ~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~rg 311 (342)
... ...+++||+|.||.-+.+++.++.++..|
T Consensus 251 ~~~-v~kgrp~aGLP~LN~GaI~Gflig~l~sg 282 (283)
T PF06550_consen 251 LRF-VMKGRPQAGLPFLNGGAIAGFLIGALASG 282 (283)
T ss_pred HHH-HHcCCCCCCCCccchhHHHHHHHHHHHcC
Confidence 543 24689999999999999999998887655
No 6
>COG3389 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.69 E-value=8.4e-17 Score=148.66 Aligned_cols=159 Identities=26% Similarity=0.355 Sum_probs=130.9
Q ss_pred hhhhhHHHHHHhhccchhhHhhHHHHHHH--HHhhhhcccCchhhHHHHHHHHHHhhhheeeccchhhhhhcc---CCCC
Q 019365 144 AAIPGTFFCAWYASQKHWLANNTLGLAFC--IQGIEMLSLGSFKTGAILLAGLFVYDIFWVFFTPVMVSVAKS---FDAP 218 (342)
Q Consensus 144 ~~~~~~~~~~~~~~~~~W~l~nilgi~~~--~~~i~~i~l~s~k~~~iLL~~lf~YDif~VF~T~vMvtVA~~---~~~P 218 (342)
+..+++.+....+.++.|+..|..|.+++ +.++..++++-.. +..+|..+-+||..-||+|.+|++.|++ .|+|
T Consensus 95 si~~aI~~~~lL~~~peWyVid~ag~~la~Giaai~GIsfgv~p-avvlL~~lavYDaIsVYkT~HMIslA~~v~d~~lP 173 (277)
T COG3389 95 SIGLAIGLVYLLYKYPEWYVIDLAGFFLAVGIAAIFGISFGVLP-AVVLLIALAVYDAISVYKTRHMISLAEGVMDLDLP 173 (277)
T ss_pred HHHHHHHHHHhhhhccceEEeehHHHHHHhhHHHhheeecchHH-HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCCc
Confidence 34445555555567889999999999988 5778899998876 8899999999999999999999999998 5999
Q ss_pred EEEEeecc------------CCCCCceeccCCCccchhHHhhhHhhhcccCCCCcchH--HHHHHHHHHHHHHHHHHHHH
Q 019365 219 IKLLFPTR------------DTARPFSMLGLGDIVIPGIFVALALRFDVSRGKGSRYF--KSAFLGYTVGLVLTIIVMNW 284 (342)
Q Consensus 219 ikl~~P~~------------~~~~~~s~LGlGDIviPGi~ia~~lRfD~~~~~~~~YF--~~s~igY~~GL~~t~~~~~~ 284 (342)
|.+++|.+ ..+++.-|.|+||+++|.+++..+.-|-.+. ..+| ..++.|-.+|+.+-.++ .
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---ILAFIVLPALAGGLVGLAVLYFV--N 248 (277)
T ss_pred eEEEeecccccceeehhhhcCCCCceEEEeechhhcccceeeehHHhccCC---chhhhhHHHHhccHHHHHHHHHH--h
Confidence 99999962 3466778999999999999999998886543 3455 33799999999776443 5
Q ss_pred hCCCccchhhhhhHHHHHHHHHHH
Q 019365 285 FQAAQPALLYIVPAVIGFLAAHCI 308 (342)
Q Consensus 285 ~~~~QPALLYLvP~~l~~~~~~A~ 308 (342)
.+++||.|.|+.-+.+.+.++.+.
T Consensus 249 r~Rp~pGLP~lN~GaIaGflig~V 272 (277)
T COG3389 249 RGRPHPGLPFLNTGAIAGFLIGFV 272 (277)
T ss_pred cCCCCCCCceeccchHHHHHHHHH
Confidence 689999999999999888777654
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=95.26 E-value=0.037 Score=56.26 Aligned_cols=66 Identities=29% Similarity=0.534 Sum_probs=48.6
Q ss_pred eeccCCCccchhHHhhhHhhh-cccCCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHH
Q 019365 233 SMLGLGDIVIPGIFVALALRF-DVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAH 306 (342)
Q Consensus 233 s~LGlGDIviPGi~ia~~lRf-D~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~ 306 (342)
--|||||-|+=+++++-+.++ |. .-..+|++|-.+||.+|...+.+++++-|||. ++..+|.+.-.
T Consensus 326 ~klGlGDFiFYs~Lvg~aa~~~~~------~~~~~~~~ail~Gl~~Tl~~l~~~~~alPALP--isi~~g~~~yf 392 (403)
T PF01080_consen 326 IKLGLGDFIFYSVLVGRAAMYGDW------NTVVACFVAILIGLCLTLLLLAIFRKALPALP--ISIALGLIFYF 392 (403)
T ss_dssp -SS-TTTHHHHHHHHHHHHHH-TT------TTHHHHHHHHHHHHHHHHHHHHHHT-S-SSSS--S----HHHHHH
T ss_pred eeecchhHHHHHHHHhHHHhcCCH------HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCc--HHHHHHHHHHH
Confidence 358999999999999988875 43 33578999999999999999999999999998 66666655443
No 8
>KOG2736 consensus Presenilin [Signal transduction mechanisms]
Probab=95.23 E-value=0.018 Score=57.67 Aligned_cols=68 Identities=26% Similarity=0.455 Sum_probs=54.7
Q ss_pred ceeccCCCccchhHHhhhHhhhcccCCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHH
Q 019365 232 FSMLGLGDIVIPGIFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAH 306 (342)
Q Consensus 232 ~s~LGlGDIviPGi~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~ 306 (342)
---||+||-++=.++++=+.-+|-+ .=-++|.+|-.+||.+|.....++|++-|||. .|.++|.+.-.
T Consensus 319 ~ikLGlGDFIFYSvLvGkAa~~~d~-----~TviAC~vaIL~GL~~TL~llsv~~kALPALP--isI~~G~iFYF 386 (406)
T KOG2736|consen 319 GIKLGLGDFIFYSVLVGKAAAYGDL-----NTVIACFVAILIGLCLTLLLLSVFKKALPALP--ISITFGLIFYF 386 (406)
T ss_pred ceeeccCceEEEEeeccchhhcCCh-----HHHHHHHHHHHHHHHHHHHHHHHHhhcCcCCc--hHHHHHHHHHH
Confidence 3469999999988887776666521 12278999999999999999999999999999 78887777654
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=70.19 E-value=14 Score=36.98 Aligned_cols=52 Identities=17% Similarity=0.381 Sum_probs=32.9
Q ss_pred HHHhhccchhhHhhHHHHHHHHHhhhhcccCc-------------hhhHHHHHHHHHHhhhheee
Q 019365 152 CAWYASQKHWLANNTLGLAFCIQGIEMLSLGS-------------FKTGAILLAGLFVYDIFWVF 203 (342)
Q Consensus 152 ~~~~~~~~~W~l~nilgi~~~~~~i~~i~l~s-------------~k~~~iLL~~lf~YDif~VF 203 (342)
..|.+.+...-...++|+.+|+.++-.+...+ .+-=.+.+.+.++|=+.-|.
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 34555566666678889999988776654443 23234667777777766444
No 10
>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=53.36 E-value=40 Score=31.13 Aligned_cols=12 Identities=17% Similarity=0.473 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHH
Q 019365 267 AFLGYTVGLVLT 278 (342)
Q Consensus 267 s~igY~~GL~~t 278 (342)
-++|+.+|..+-
T Consensus 28 I~~GqylG~~~L 39 (191)
T PF03596_consen 28 IVIGQYLGFTIL 39 (191)
T ss_pred hhhhHHHHHHHH
Confidence 445555554333
No 11
>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=52.64 E-value=24 Score=25.85 Aligned_cols=9 Identities=0% Similarity=0.198 Sum_probs=4.2
Q ss_pred hcccccccc
Q 019365 317 LEFDESKTA 325 (342)
Q Consensus 317 w~~~~~~~~ 325 (342)
..|.-..|+
T Consensus 27 ygYkht~d~ 35 (50)
T PF12606_consen 27 YGYKHTVDP 35 (50)
T ss_pred cccccccCC
Confidence 445444444
No 12
>COG4300 CadD Predicted permease, cadmium resistance protein [Inorganic ion transport and metabolism]
Probab=47.91 E-value=21 Score=33.06 Aligned_cols=65 Identities=15% Similarity=0.179 Sum_probs=35.4
Q ss_pred hHhhhcccCCCCcch---HHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHHHHHhhhHHHhhccccccc
Q 019365 249 LALRFDVSRGKGSRY---FKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLEFDESKT 324 (342)
Q Consensus 249 ~~lRfD~~~~~~~~Y---F~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~rgEl~~lw~~~~~~~ 324 (342)
+-.|.|..++..+.| |..+++=-.+.+..+++...+-..--|.|+=+.|.-+| +|..|..++|+|
T Consensus 26 ~Far~~~~k~~~~I~~GQyLGs~~lilaSL~~a~v~~fvp~e~I~glLGLIPi~LG-----------ik~l~~~d~d~e 93 (205)
T COG4300 26 FFARRKSRKDILHIYLGQYLGSVILILASLLFAFVLNFVPEEWILGLLGLIPIYLG-----------IKVLILGDDDGE 93 (205)
T ss_pred HHHHhcccCcEEEEeHHHHHhHHHHHHHHHHHHHHHhhCcHHHHHHHHhHHHHHHh-----------hHHhhcccCcCc
Confidence 344666533323333 33344444456666665555555666777777777665 455566555333
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=46.79 E-value=81 Score=28.07 Aligned_cols=71 Identities=14% Similarity=0.215 Sum_probs=44.8
Q ss_pred HhhhHhhhcccCCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHHHHHhhhHHHhh
Q 019365 246 FVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLL 317 (342)
Q Consensus 246 ~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~rgEl~~lw 317 (342)
+.-+.+|+.+....++.++..-..-+.+++.++-......+ .++...|++|....+.+++.+...+..-+.
T Consensus 18 ~~~~~~~~~~~~~~~~~~l~l~~~l~~l~l~l~~~~~~~~~-~~~~~~~~~P~a~~~~l~~~l~~~~~ai~~ 88 (194)
T PF07698_consen 18 LYLYLRRFRPRILRSNKYLLLLSLLLLLSLLLAKIILFFIS-DISYFPYLIPVAAAAMLLTILIDPRLAILA 88 (194)
T ss_pred HHHHHHHHCcHhhhchhHHHHHHHHHHHHHHHHHHHHHhcc-cchhhhhhhHHHHHHHHHHHHhcchHHHHH
Confidence 44556666433323334444444556666666666543333 678899999999999998888776665433
No 14
>KOG1607 consensus Protein transporter of the TRAM (translocating chain-associating membrane) superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.27 E-value=78 Score=31.61 Aligned_cols=39 Identities=10% Similarity=-0.000 Sum_probs=20.5
Q ss_pred CCCccchhhhhhHHHHHHHHH------HHHhhhHHHhhccccccc
Q 019365 286 QAAQPALLYIVPAVIGFLAAH------CIWNGEVKQLLEFDESKT 324 (342)
Q Consensus 286 ~~~QPALLYLvP~~l~~~~~~------A~~rgEl~~lw~~~~~~~ 324 (342)
+.++|-..|+.=+.++.+.+. =..|=+-+.+++..+.+|
T Consensus 253 ~~~~~~~~~~~~~lL~~Lqll~i~W~~lI~rm~~r~~~~g~~~eD 297 (318)
T KOG1607|consen 253 QYQPKPSYYFFNCLLLALQLLHIYWFYLILRMAYRVIKRGMQGED 297 (318)
T ss_pred ccCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccc
Confidence 444555555566666555432 234556677774534443
No 15
>KOG3455 consensus Predicted membrane protein [Function unknown]
Probab=44.02 E-value=56 Score=28.82 Aligned_cols=51 Identities=10% Similarity=0.216 Sum_probs=42.3
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHHHHHhh
Q 019365 261 SRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNG 311 (342)
Q Consensus 261 ~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~rg 311 (342)
++-+.+++..|++.+.-..-=..+++...++-..+.|+++.++.++....+
T Consensus 73 k~i~~~~~~s~~lal~HflTE~l~yrT~tig~~~~~p~vv~s~Sl~~M~~~ 123 (139)
T KOG3455|consen 73 KPIYIATFLSFILALGHFLTELLFYRTMTIGIGVLTPLVVNSISLVGMLKF 123 (139)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhhccccceEEeeeeehhhhHHHHHHH
Confidence 466778888888888777777778999999999999999999988876553
No 16
>KOG0569 consensus Permease of the major facilitator superfamily [Carbohydrate transport and metabolism]
Probab=42.22 E-value=32 Score=36.11 Aligned_cols=17 Identities=6% Similarity=-0.038 Sum_probs=10.1
Q ss_pred HhhhHHHhhcccccccc
Q 019365 309 WNGEVKQLLEFDESKTA 325 (342)
Q Consensus 309 ~rgEl~~lw~~~~~~~~ 325 (342)
+|+.++.+...+|++++
T Consensus 221 A~~sl~~y~G~~~~~~~ 237 (485)
T KOG0569|consen 221 ARKALKFYRGKEDVEAE 237 (485)
T ss_pred HHHHHHHHhCCCcchhH
Confidence 45567777666654443
No 17
>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=41.71 E-value=44 Score=32.63 Aligned_cols=48 Identities=15% Similarity=0.210 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCC---Cccc------hhhh-hhHHHHHHHHHHHHhh
Q 019365 264 FKSAFLGYTVGLVLTIIVMNWFQA---AQPA------LLYI-VPAVIGFLAAHCIWNG 311 (342)
Q Consensus 264 F~~s~igY~~GL~~t~~~~~~~~~---~QPA------LLYL-vP~~l~~~~~~A~~rg 311 (342)
..=++.+|++|++++.+++..+++ ++|- ...+ +|+.+|+.+.-...++
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 344899999999999999999987 5553 1222 7887777665554433
No 18
>KOG2466 consensus Uridine permease/thiamine transporter/allantoin transport [Nucleotide transport and metabolism; Coenzyme transport and metabolism]
Probab=37.29 E-value=31 Score=36.55 Aligned_cols=76 Identities=14% Similarity=0.232 Sum_probs=37.4
Q ss_pred ccchhHHhhhHhhhcccCCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCccchhhhhhHHHHHHHHHHHHhhhHHHhhcc
Q 019365 240 IVIPGIFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTIIVMNWFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLLEF 319 (342)
Q Consensus 240 IviPGi~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~~~~~~~~~~QPALLYLvP~~l~~~~~~A~~rgEl~~lw~~ 319 (342)
..+||+.-..-...-.....-+.|+...+.|+.+.-..--..+.++-..|--| .--...+. .-+++|.+
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 56788776554322222223456666666666665444444443443222110 11111111 45688999
Q ss_pred ccccccc
Q 019365 320 DESKTAA 326 (342)
Q Consensus 320 ~~~~~~~ 326 (342)
.||-|||
T Consensus 540 ve~s~~e 546 (572)
T KOG2466|consen 540 VEDSEEE 546 (572)
T ss_pred ccchhhh
Confidence 8887766
No 19
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=36.49 E-value=60 Score=28.45 Aligned_cols=64 Identities=23% Similarity=0.321 Sum_probs=48.6
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHhC------CCccch----------hhhhhHHHHHH---HHHHHHhhhHHHhhcc
Q 019365 259 KGSRYFKSAFLGYTVGLVLTIIVMNWFQ------AAQPAL----------LYIVPAVIGFL---AAHCIWNGEVKQLLEF 319 (342)
Q Consensus 259 ~~~~YF~~s~igY~~GL~~t~~~~~~~~------~~QPAL----------LYLvP~~l~~~---~~~A~~rgEl~~lw~~ 319 (342)
....||-..++-...|.+++.++-.+|+ ++-|-| .|..|++|.++ +++|..+.-+.++.++
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 3568999999999999999988877764 577776 89999998766 4556666666666665
Q ss_pred ccc
Q 019365 320 DES 322 (342)
Q Consensus 320 ~~~ 322 (342)
.-.
T Consensus 116 ~~~ 118 (141)
T PRK13743 116 GIR 118 (141)
T ss_pred cee
Confidence 443
No 20
>PF14181 YqfQ: YqfQ-like protein
Probab=35.93 E-value=20 Score=32.36 Aligned_cols=8 Identities=0% Similarity=0.260 Sum_probs=4.7
Q ss_pred hHHHhhcc
Q 019365 312 EVKQLLEF 319 (342)
Q Consensus 312 El~~lw~~ 319 (342)
.+-.||+.
T Consensus 84 NLPam~ki 91 (161)
T PF14181_consen 84 NLPAMWKI 91 (161)
T ss_pred hhHHHHHH
Confidence 46666654
No 21
>PRK14397 membrane protein; Provisional
Probab=33.91 E-value=1.5e+02 Score=28.16 Aligned_cols=25 Identities=8% Similarity=-0.031 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhhhHHHhhccccccc
Q 019365 300 IGFLAAHCIWNGEVKQLLEFDESKT 324 (342)
Q Consensus 300 l~~~~~~A~~rgEl~~lw~~~~~~~ 324 (342)
+++.++.--.|.+++++++.+|..-
T Consensus 167 ~~a~lvi~rHr~NI~RL~~G~E~k~ 191 (222)
T PRK14397 167 VVMALVYWSHRENIGRLARGEEKPW 191 (222)
T ss_pred HHHHHHHHHHHHHHHHHHcCCcchh
Confidence 4444454456889999999999875
No 22
>PF13038 DUF3899: Domain of unknown function (DUF3899)
Probab=30.12 E-value=76 Score=25.16 Aligned_cols=20 Identities=15% Similarity=0.195 Sum_probs=11.2
Q ss_pred chHHHHHHHHHHHHHHHHHH
Q 019365 262 RYFKSAFLGYTVGLVLTIIV 281 (342)
Q Consensus 262 ~YF~~s~igY~~GL~~t~~~ 281 (342)
..|+.+++--++|....+.-
T Consensus 4 ~~Fl~~l~lliig~~~~v~~ 23 (92)
T PF13038_consen 4 ILFLVGLILLIIGGFLFVFQ 23 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 45666666666665554433
No 23
>PF14248 DUF4345: Domain of unknown function (DUF4345)
Probab=30.02 E-value=2.4e+02 Score=23.51 Aligned_cols=85 Identities=19% Similarity=0.240 Sum_probs=55.7
Q ss_pred chhhHHHHHHHHhHhcccccCCCC--------CCCCCCccccchhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHH
Q 019365 27 NLNVILTACLTVYVGCYRSVKPTP--------PSETMSNEHAMRFPFVGSAMLLSLFLLFKFLSKDLVNAVLTCYFFVLG 98 (342)
Q Consensus 27 ~~~~i~~Av~~I~iGs~~s~~~~~--------~~e~i~~~~A~~fPv~aS~~L~~LY~l~k~~~~~~i~~ll~~yf~~~g 98 (342)
+..+.+.++.++.+|...-+.+.+ ..++.+.++...+ ..|...-+|+++++-..+++.....+..-..+++
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 456668899999999988776532 1222333555666 5566677777777776776666655545455667
Q ss_pred HHHHHHHHHHHHHh
Q 019365 99 IIALSATILPAVKR 112 (342)
Q Consensus 99 ~~~l~~~l~~~~~~ 112 (342)
..++...++-..+.
T Consensus 84 ~~~lgRlis~~~dG 97 (124)
T PF14248_consen 84 GGGLGRLISLALDG 97 (124)
T ss_pred HHHHHHHHHHHHcC
Confidence 77788887776653
No 24
>PF11368 DUF3169: Protein of unknown function (DUF3169); InterPro: IPR021509 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=29.41 E-value=53 Score=30.95 Aligned_cols=15 Identities=20% Similarity=0.390 Sum_probs=7.5
Q ss_pred HHHHHHHHHHHHHHH
Q 019365 267 AFLGYTVGLVLTIIV 281 (342)
Q Consensus 267 s~igY~~GL~~t~~~ 281 (342)
+++|.++|.......
T Consensus 19 ~~iGg~~G~~~~~~~ 33 (248)
T PF11368_consen 19 GLIGGFIGFFIGRIG 33 (248)
T ss_pred HHHHHHHHHHHHHHH
Confidence 455555555444444
No 25
>PRK13755 putative mercury transport protein MerC; Provisional
Probab=28.66 E-value=4e+02 Score=23.35 Aligned_cols=45 Identities=20% Similarity=0.298 Sum_probs=26.9
Q ss_pred ccchhhhHHHH-HHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 019365 59 HAMRFPFVGSA-MLLSLFLLFKFLSKDLVNAVLTCYFFVLGIIALSATIL 107 (342)
Q Consensus 59 ~A~~fPv~aS~-~L~~LY~l~k~~~~~~i~~ll~~yf~~~g~~~l~~~l~ 107 (342)
=|..||-++|. .-.||=++-+| .--+++.++-.| +++.-+.+.+.
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 46789998887 66677676665 223466666553 33333444443
No 26
>PRK14409 membrane protein; Provisional
Probab=27.24 E-value=2.6e+02 Score=26.17 Aligned_cols=32 Identities=9% Similarity=-0.003 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHHhhhHHHhhccccccccccc
Q 019365 297 PAVIGFLAAHCIWNGEVKQLLEFDESKTAAVV 328 (342)
Q Consensus 297 P~~l~~~~~~A~~rgEl~~lw~~~~~~~~~~~ 328 (342)
+..+++.++.--.|.+++++++.+|....+||
T Consensus 173 ~~~~~a~lvi~rHr~NI~Rll~GtE~k~~~~~ 204 (205)
T PRK14409 173 TMVFISFGIILTHRENIRRILNRSELFAVKDE 204 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Confidence 44555556666678999999998886665544
No 27
>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=27.21 E-value=1.5e+02 Score=28.82 Aligned_cols=22 Identities=18% Similarity=0.314 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhCC
Q 019365 266 SAFLGYTVGLVLTIIVMNWFQA 287 (342)
Q Consensus 266 ~s~igY~~GL~~t~~~~~~~~~ 287 (342)
=+..+|.+|.+++.+++..+++
T Consensus 67 d~v~A~~ig~v~a~~~L~~l~~ 88 (267)
T PF09622_consen 67 DAVEALAIGAVVAAAVLTLLGK 88 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh
Confidence 3889999999999999888865
No 28
>PF12821 DUF3815: Protein of unknown function (DUF3815); InterPro: IPR024528 This domain is found in uncharacterised predicted membrane proteins.
Probab=26.16 E-value=2.2e+02 Score=24.05 Aligned_cols=48 Identities=19% Similarity=0.445 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHhCCCc-----cchhhhhhHHHHHHHHHHHHhhhHHHhh
Q 019365 269 LGYTVGLVLTIIVMNWFQAAQ-----PALLYIVPAVIGFLAAHCIWNGEVKQLL 317 (342)
Q Consensus 269 igY~~GL~~t~~~~~~~~~~Q-----PALLYLvP~~l~~~~~~A~~rgEl~~lw 317 (342)
.+..+|+.....+- ..|.+. |++..+||+..+--....+..+|..+-+
T Consensus 55 aa~~vg~~~~~~ar-~~~~P~~v~~vpgiipLVPG~~~y~~~~~~~~~~~~~~~ 107 (130)
T PF12821_consen 55 AAFVVGLLAELFAR-RLKAPATVFIVPGIIPLVPGSLAYRGMYSLVSGNYSSAL 107 (130)
T ss_pred HHHHHHHHHHHHHH-hccCchHHhhccchheeCCcHHHHHHHHHHHHhhHHHHH
Confidence 33445655555543 334333 6677777777666666677766654443
No 29
>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=25.40 E-value=23 Score=36.35 Aligned_cols=61 Identities=25% Similarity=0.411 Sum_probs=0.0
Q ss_pred cchhhHhhHHHHHHHH-Hhhhhcc-cCchhhHHHHHHHHHHhhhheeecc--c--hhhhhhccCCCCE
Q 019365 158 QKHWLANNTLGLAFCI-QGIEMLS-LGSFKTGAILLAGLFVYDIFWVFFT--P--VMVSVAKSFDAPI 219 (342)
Q Consensus 158 ~~~W~l~nilgi~~~~-~~i~~i~-l~s~k~~~iLL~~lf~YDif~VF~T--~--vMvtVA~~~~~Pi 219 (342)
+++=.++-.-=++.|. .++..++ +|. +|.-.+|+.+.+||+|-|-.+ | ..|+.|+.-|.|+
T Consensus 147 ~~Pl~l~Q~YLI~is~l~A~~~l~~lPe-WTtW~lL~~iaiyDl~AVL~P~GPLr~Lve~a~er~e~i 213 (403)
T PF01080_consen 147 KGPLLLQQAYLIMISVLMALFFLKYLPE-WTTWFLLVAIAIYDLFAVLCPCGPLRMLVELAQERNEPI 213 (403)
T ss_dssp --------------------------------------------------------------------
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHcCCc-hHHHHHHHHHHHHHHeeEeCCCCcHHHHHHHHHHcCCcc
Confidence 4566666655555553 3334554 777 789999999999999999865 2 6788888777664
No 30
>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=23.73 E-value=66 Score=33.32 Aligned_cols=10 Identities=10% Similarity=0.132 Sum_probs=3.7
Q ss_pred hhHHHHHHHH
Q 019365 296 VPAVIGFLAA 305 (342)
Q Consensus 296 vP~~l~~~~~ 305 (342)
++..+.....
T Consensus 206 i~~~i~~~~~ 215 (465)
T PF03606_consen 206 IFTLIAIAYV 215 (465)
T ss_pred HHHHHHHHHH
Confidence 3433333333
No 31
>PRK14412 membrane protein; Provisional
Probab=23.52 E-value=3.3e+02 Score=25.25 Aligned_cols=29 Identities=31% Similarity=0.153 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHHHhhhHHHhhccccccc
Q 019365 296 VPAVIGFLAAHCIWNGEVKQLLEFDESKT 324 (342)
Q Consensus 296 vP~~l~~~~~~A~~rgEl~~lw~~~~~~~ 324 (342)
++..+++.+..--.|.+++++++.+|..-
T Consensus 163 ~~~~~~~~lii~rHr~NI~Rl~~g~E~k~ 191 (198)
T PRK14412 163 VFSLILASLAIFQHRSNIKRLLAGTESKL 191 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 44455555666567889999999877553
No 32
>KOG2736 consensus Presenilin [Signal transduction mechanisms]
Probab=22.97 E-value=3.7e+02 Score=27.72 Aligned_cols=59 Identities=15% Similarity=0.193 Sum_probs=38.6
Q ss_pred cchhhHhhHHHHHHH-HHhhhhc-ccCchhhHHHHHHHHHHhhhheeeccc----hhhhhhccCCC
Q 019365 158 QKHWLANNTLGLAFC-IQGIEML-SLGSFKTGAILLAGLFVYDIFWVFFTP----VMVSVAKSFDA 217 (342)
Q Consensus 158 ~~~W~l~nilgi~~~-~~~i~~i-~l~s~k~~~iLL~~lf~YDif~VF~T~----vMvtVA~~~~~ 217 (342)
+++=.+|-.-=+.+| ..++..+ -+|. ||.-..|...-+||++-|--+. ..|+-|+.-|.
T Consensus 153 kgpl~L~Q~YlI~~~aLmAl~fik~LPe-WTtW~iL~ais~~DLvAVL~P~GPLr~LVEtA~~R~e 217 (406)
T KOG2736|consen 153 KGPLRLQQAYLIMISALMALFFIKYLPE-WTTWFILVAISVYDLVAVLAPKGPLRMLVETAQERNE 217 (406)
T ss_pred CCceeehhHHHHHHHHHHHHHHHHHCcc-HHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHhcCc
Confidence 344445554434444 2344555 3566 7888999999999999998652 56788876543
No 33
>PRK10995 inner membrane protein; Provisional
Probab=22.01 E-value=1.7e+02 Score=27.28 Aligned_cols=48 Identities=17% Similarity=0.288 Sum_probs=29.6
Q ss_pred HHhhhHhhhcccCCCCcchHHHHHHHHHHHHHHHH---HHHHHhCCCccchh
Q 019365 245 IFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTI---IVMNWFQAAQPALL 293 (342)
Q Consensus 245 i~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~---~~~~~~~~~QPALL 293 (342)
+|+++..++|...+ ++.-..+++.+.++.++..+ .++..++..+|++=
T Consensus 27 if~~lt~~~~~~~r-~~ia~~~~~~a~~ill~f~~~G~~il~~fgIs~~a~r 77 (221)
T PRK10995 27 LFLGLSGNMTPEER-NRQALMASVYVFAIMMVAFYAGQLVMSTFGISIPGLR 77 (221)
T ss_pred HHHHHhCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Confidence 67888888877543 23334555555555554444 34556788998885
No 34
>COG1298 FlhA Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=21.97 E-value=1.7e+02 Score=32.20 Aligned_cols=27 Identities=19% Similarity=0.348 Sum_probs=20.6
Q ss_pred hhcccCchhhHHHHHHHHHHhhhheee
Q 019365 177 EMLSLGSFKTGAILLAGLFVYDIFWVF 203 (342)
Q Consensus 177 ~~i~l~s~k~~~iLL~~lf~YDif~VF 203 (342)
+++--+||.+|.+....|++....=+-
T Consensus 112 ~fvvgGn~viG~iVFlILiivnFiVIT 138 (696)
T COG1298 112 NFVVGGNFVIGLIVFLILIIVNFIVIT 138 (696)
T ss_pred ceeecCceehHHHHHHHHHHhheeEEc
Confidence 566788999999998888887654433
No 35
>PRK14859 tatA twin arginine translocase protein A; Provisional
Probab=21.23 E-value=53 Score=25.15 Aligned_cols=11 Identities=36% Similarity=0.570 Sum_probs=5.1
Q ss_pred HHHHHHHHHhC
Q 019365 276 VLTIIVMNWFQ 286 (342)
Q Consensus 276 ~~t~~~~~~~~ 286 (342)
++.++++.+|+
T Consensus 11 iIlvv~LlvfG 21 (63)
T PRK14859 11 VILVIVLIVFG 21 (63)
T ss_pred HHHHHHHHHhC
Confidence 33444444554
No 36
>PF02939 UcrQ: UcrQ family; InterPro: IPR004205 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multi-enzyme complex [], which recognises a mitochondrial targeting presequence. The bc1 complex contains 11 subunits: 3 respiratory subunits (cytochrome b, cytochrome c1 and Rieske protein), 2 core proteins and 6 low molecular weight proteins. This family represents the 9.5 kDa subunit of the complex. This subunit together with cytochrome B binds to ubiquinone.; GO: 0008121 ubiquinol-cytochrome-c reductase activity; PDB: 1L0N_G 1SQQ_G 1PP9_G 1PPJ_T 2FYU_G 2BCC_G 1BCC_G 2A06_G 1NTZ_G 2YBB_g ....
Probab=21.11 E-value=1.5e+02 Score=23.71 Aligned_cols=34 Identities=24% Similarity=0.161 Sum_probs=27.2
Q ss_pred HhCCCccchhhhhhHHHHHHHHHHHHhhhHHHhh
Q 019365 284 WFQAAQPALLYIVPAVIGFLAAHCIWNGEVKQLL 317 (342)
Q Consensus 284 ~~~~~QPALLYLvP~~l~~~~~~A~~rgEl~~lw 317 (342)
.+++-+-.++|++|..+++-.+..|.+.+-..+=
T Consensus 37 ~~RR~~~q~~~v~ppfi~~y~i~~Wa~~~~~~~~ 70 (80)
T PF02939_consen 37 TFRRFRSQVLYVAPPFIVGYLIYDWANEENEYLN 70 (80)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHc
Confidence 4455566789999999999999999888776654
No 37
>PF01914 MarC: MarC family integral membrane protein; InterPro: IPR002771 Members of this family are integral membrane proteins that includes the antibiotic resistance protein MarC. These proteins may be transporters. ; GO: 0016021 integral to membrane
Probab=20.90 E-value=1.4e+02 Score=27.55 Aligned_cols=60 Identities=22% Similarity=0.425 Sum_probs=34.9
Q ss_pred HHhhhHhhhcccCCCCcchHHHHHHHHHHHHHHHH---HHHHHhCCCccchhhhhhHHHHHHHHH
Q 019365 245 IFVALALRFDVSRGKGSRYFKSAFLGYTVGLVLTI---IVMNWFQAAQPALLYIVPAVIGFLAAH 306 (342)
Q Consensus 245 i~ia~~lRfD~~~~~~~~YF~~s~igY~~GL~~t~---~~~~~~~~~QPALLYLvP~~l~~~~~~ 306 (342)
+|+++..++|...+ ++.-..+++.+.++.+...+ ..+..++-..||+= +--+.++.....
T Consensus 23 ~f~~lt~~~~~~~r-~~ia~~a~~~a~~ill~f~~~G~~iL~~fgIsl~af~-IaGGiiL~~ia~ 85 (203)
T PF01914_consen 23 IFLSLTKGMSPKER-RRIARRASIIAFIILLIFAFFGQLILNFFGISLPAFR-IAGGIILFLIAL 85 (203)
T ss_pred HHHHHhCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHH-HHHHHHHHHHHH
Confidence 57788888876543 23444555555555544444 34556788988875 444444444443
No 38
>KOG2881 consensus Predicted membrane protein [Function unknown]
Probab=20.82 E-value=1.5e+02 Score=29.12 Aligned_cols=15 Identities=20% Similarity=0.069 Sum_probs=10.7
Q ss_pred hhhHHHhhccccccc
Q 019365 310 NGEVKQLLEFDESKT 324 (342)
Q Consensus 310 rgEl~~lw~~~~~~~ 324 (342)
-+-+++=|+.++++.
T Consensus 145 lkmL~eg~~~~~~~~ 159 (294)
T KOG2881|consen 145 LKMLKEGWEMSPSEG 159 (294)
T ss_pred HHHHHHhhcCCCccc
Confidence 356777788887775
Done!