Query 017077
Match_columns 378
No_of_seqs 270 out of 1384
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 05:24:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017077.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017077hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2442 Uncharacterized conser 100.0 2.9E-91 6.2E-96 692.5 27.1 365 3-368 91-462 (541)
2 KOG2443 Uncharacterized conser 100.0 5E-51 1.1E-55 392.0 19.0 236 94-363 22-278 (362)
3 PF04258 Peptidase_A22B: Signa 100.0 8.7E-52 1.9E-56 403.3 -0.1 217 147-365 2-241 (298)
4 smart00730 PSN Presenilin, sig 100.0 4E-39 8.7E-44 306.5 16.8 199 151-370 3-206 (249)
5 cd02132 PA_GO-like PA_GO-like: 99.8 2.6E-18 5.7E-23 150.3 10.2 84 4-87 56-139 (139)
6 cd02125 PA_VSR PA_VSR: Proteas 99.8 2.5E-18 5.3E-23 148.3 9.9 83 5-87 40-127 (127)
7 cd02129 PA_hSPPL_like PA_hSPPL 99.7 4.8E-18 1E-22 144.8 9.6 80 3-86 40-119 (120)
8 cd02127 PA_hPAP21_like PA_hPAP 99.7 7.9E-18 1.7E-22 143.4 10.1 82 4-87 31-116 (118)
9 cd02126 PA_EDEM3_like PA_EDEM3 99.7 2.8E-17 6E-22 141.5 9.8 83 4-87 37-126 (126)
10 cd02122 PA_GRAIL_like PA _GRAI 99.7 4.2E-17 9.1E-22 142.5 9.6 79 4-87 57-138 (138)
11 cd04813 PA_1 PA_1: Protease-as 99.7 2.9E-16 6.3E-21 133.6 8.5 73 3-77 35-109 (117)
12 cd04817 PA_VapT_like PA_VapT_l 99.7 3.9E-16 8.4E-21 136.4 9.5 77 3-81 52-135 (139)
13 cd02123 PA_C_RZF_like PA_C-RZF 99.7 6.4E-16 1.4E-20 137.3 10.9 78 4-82 64-142 (153)
14 cd02130 PA_ScAPY_like PA_ScAPY 99.7 5.4E-16 1.2E-20 132.4 9.8 81 4-87 41-122 (122)
15 cd04816 PA_SaNapH_like PA_SaNa 99.6 8.8E-16 1.9E-20 131.1 10.2 83 4-87 40-122 (122)
16 cd02124 PA_PoS1_like PA_PoS1_l 99.6 3.1E-15 6.7E-20 129.4 9.4 77 5-87 53-129 (129)
17 PF02225 PA: PA domain; Inter 99.5 2.8E-14 6E-19 116.5 8.7 74 2-77 28-101 (101)
18 cd04818 PA_subtilisin_1 PA_sub 99.5 5.6E-14 1.2E-18 119.1 9.6 80 4-87 37-118 (118)
19 cd00538 PA PA: Protease-associ 99.5 9.6E-14 2.1E-18 117.4 10.1 84 3-87 42-126 (126)
20 cd02133 PA_C5a_like PA_C5a_lik 99.4 8.8E-13 1.9E-17 115.6 9.6 79 3-88 43-121 (143)
21 PF06550 DUF1119: Protein of u 99.4 4.3E-12 9.3E-17 121.2 13.8 101 251-359 111-226 (283)
22 cd04819 PA_2 PA_2: Protease-as 99.4 2.3E-12 5E-17 111.0 9.8 83 4-86 41-126 (127)
23 cd04815 PA_M28_2 PA_M28_2: Pro 99.3 1.3E-11 2.7E-16 107.5 7.5 86 2-87 34-134 (134)
24 KOG4628 Predicted E3 ubiquitin 99.2 1.4E-10 3.1E-15 114.5 12.4 70 5-78 77-148 (348)
25 COG3389 Uncharacterized protei 99.2 1.6E-11 3.4E-16 113.6 5.2 114 235-358 97-222 (277)
26 cd02120 PA_subtilisin_like PA_ 99.1 1.9E-10 4.1E-15 97.9 8.1 73 4-82 48-121 (126)
27 KOG3920 Uncharacterized conser 98.9 1.2E-09 2.5E-14 96.1 3.8 82 5-88 85-172 (193)
28 cd02128 PA_TfR PA_TfR: Proteas 98.9 3.9E-09 8.4E-14 96.3 6.9 75 4-78 52-154 (183)
29 cd02121 PA_GCPII_like PA_GCPII 98.3 9.1E-07 2E-11 83.2 6.8 75 4-78 68-188 (220)
30 cd02131 PA_hNAALADL2_like PA_h 98.2 3E-06 6.5E-11 74.9 5.9 73 5-77 38-137 (153)
31 cd04822 PA_M28_1_3 PA_M28_1_3: 98.2 7.5E-06 1.6E-10 72.8 8.2 70 4-76 44-131 (151)
32 cd04814 PA_M28_1 PA_M28_1: Pro 98.1 3.2E-06 7E-11 74.4 5.6 39 4-42 44-100 (142)
33 cd04820 PA_M28_1_1 PA_M28_1_1: 98.1 6.6E-06 1.4E-10 72.0 5.5 40 4-43 46-97 (137)
34 cd04821 PA_M28_1_2 PA_M28_1_2: 96.0 0.008 1.7E-07 53.9 4.4 39 4-42 46-103 (157)
35 KOG2195 Transferrin receptor a 80.4 1.9 4.2E-05 47.4 4.2 38 5-42 182-219 (702)
36 COG4882 Predicted aminopeptida 62.0 34 0.00074 35.0 7.8 90 4-98 86-180 (486)
37 COG5540 RING-finger-containing 56.3 1.8 3.8E-05 42.7 -2.2 32 12-43 151-182 (374)
38 PF06305 DUF1049: Protein of u 48.9 50 0.0011 24.5 5.3 16 78-93 2-17 (68)
39 PRK11588 hypothetical protein; 48.8 2.9E+02 0.0062 29.6 12.5 43 151-193 280-323 (506)
40 KOG2927 Membrane component of 47.3 19 0.00042 36.3 3.4 26 234-259 239-264 (372)
41 PF06541 DUF1113: Protein of u 40.8 2.4E+02 0.0051 25.0 9.1 26 267-292 129-154 (157)
42 PRK03955 hypothetical protein; 31.6 1.7E+02 0.0038 25.4 6.5 71 4-86 47-120 (131)
43 COG1786 Swiveling domain assoc 31.3 1E+02 0.0022 26.8 4.9 73 4-86 47-122 (131)
44 PRK03427 cell division protein 30.5 40 0.00086 33.9 2.6 26 98-123 8-33 (333)
45 PF03606 DcuC: C4-dicarboxylat 29.8 1.7E+02 0.0036 30.7 7.2 14 338-351 414-429 (465)
46 cd00860 ThrRS_anticodon ThrRS 20.9 2.3E+02 0.005 21.4 5.0 34 8-41 28-61 (91)
47 cd03028 GRX_PICOT_like Glutare 20.7 1.9E+02 0.0041 22.8 4.4 69 7-80 7-87 (90)
48 PF01080 Presenilin: Presenili 20.5 33 0.00072 35.4 0.0 57 252-312 150-209 (403)
No 1
>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=100.00 E-value=2.9e-91 Score=692.50 Aligned_cols=365 Identities=52% Similarity=0.878 Sum_probs=339.2
Q ss_pred CCCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccce
Q 017077 3 KHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 82 (378)
Q Consensus 3 ~~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~ 82 (378)
...+++++++|.||||+|.+|+++||++||.|+++.||.+++..|++.+.++..+++||+++|++++|+.+.+....+++
T Consensus 91 ~~kl~~~~~~v~RGnC~Ft~Ka~~Aq~aGAsaLliin~~~d~~~~~~~~~~~~~dv~IPv~mi~~~~~~~l~~~~~~~~~ 170 (541)
T KOG2442|consen 91 QSKLSGKVALVFRGNCSFTEKAKLAQAAGASALLIINNKKDLLFMPCGNKETSLDVTIPVAMISYSDGRDLNKSTRSNDN 170 (541)
T ss_pred CccccceeEEEecccceeehhhhhhhhcCceEEEEEcCchhhccCCCCCCCccccccceEEEEEhhhHHHHHhhhccCCe
Confidence 45789999999999999999999999999999999999988888998877778899999999999999999988888999
Q ss_pred EEEEEecCCCCccchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhcccCCCCccccccCCCCeeeecccchhhHH
Q 017077 83 VSVQLYSPRRPVVDVAEVFLWLMAVGTILCASYWSAWSARETAIEQEKLLKDAVDEIPDAKAVGVSGVVDINTASAVLFV 162 (378)
Q Consensus 83 V~v~l~~p~~~~~D~s~~~l~l~Av~tv~~gs~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~a~~fp 162 (378)
|++.+|+|++|.+|++.+++|+||++||.+|+|||.+++||+..|+++.++|..+++.+.+|.+|++..++|+..|+.|+
T Consensus 171 V~~~lYaPk~P~vD~~~v~iwlmAVgTVa~ggyWs~~t~~~~~~~a~~~~~d~~s~~~~~~~~~e~~~vd~s~i~~~~fv 250 (541)
T KOG2442|consen 171 VELALYAPKRPAVDYAMVFIWLMAVGTVACGGYWSGLTEREKAIEADRLLDDDSSSEGNTKETKEEEVVDISPITAVFFV 250 (541)
T ss_pred EEEEEECCCCCCccHHHHHHHHHHHhHhhccchhhhccChhhhhhhhhhcccccccccccccCCccccEEeeeeEEEEeh
Confidence 99999999999999999999999999999999999999999877777766666665556677788899999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhccCCCceeeeccccccccchhhhhhhHHHHHhhh
Q 017077 163 LVASCFLVMLYKLMSNWFLELLVILFCIGGVEGLQTCLVALLSRWFRRAGESFIKVPFFGAVSHLTLAVTPFCIAFAVVW 242 (378)
Q Consensus 163 v~~s~~Ll~ly~f~~~~~~~~l~~~f~~~g~~~l~~~l~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~~~~~~w 242 (378)
+++|.+|++||||+++ ++++++++||++|..++++|+.++++|++.+..+.....|..|+.++..+++.++|++++++|
T Consensus 251 v~~c~~LvLlyfF~~~-~V~v~iiif~i~g~~gLy~Cl~~lv~r~~~~~~~~~~~~~~l~~~~~~~l~l~~~Cia~aV~W 329 (541)
T KOG2442|consen 251 VTACGFLVLLYFFYSY-LVYVLIIIFCIGGAQGLYNCLAALVHRLPYGAARFPTLAPRLGNMSYRLLFLSILCIAVAVVW 329 (541)
T ss_pred hhhHHHHHHHHHHHHH-HHHHHhhheeecccchHHHHHHHHHhhhhhhcccccccccccCChhHHHHHHHHhhhheeEEE
Confidence 9999999999999975 999999999999999999999999998865543344456777889999999999999999999
Q ss_pred hhhhcCccchhHHhHHHHHHHHHHHHhcccCchhHHHHHHHHHHHhhhhheeecccccc--ceeEEEeecCCCCCCCCCC
Q 017077 243 AIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFMYDIFWVFVSKKLFH--ESVMIVVARGDKSGEDGIP 320 (378)
Q Consensus 243 ~~~~~~~~~W~l~ni~g~~~~~~~i~~~~l~~~k~~~~lL~~lf~YDif~Vf~tp~~~~--~svMv~VA~~~~~~~~~~P 320 (378)
+++|||+|+|++||++|||+|+++++.+||||+|+|++||.++|+|||||||+||++|+ +|||++||+|.++++|++|
T Consensus 330 ~v~R~e~~AwilqDvLGIalci~vLk~vRLPnlK~~tiLL~c~f~YDiF~VFitp~~t~~geSVMieVA~G~~s~~EkiP 409 (541)
T KOG2442|consen 330 AVFRNEDWAWILQDVLGIALCITVLKTVRLPNLKVCTILLLCLFLYDIFFVFITPFITKNGESVMIEVARGPSSTEEKIP 409 (541)
T ss_pred EEeecCchHHHHHhhHhHHHHHHHHHHhcCCchhHHHHHHHHHHHHhhheeeeehhhccCCceEEEEEecCCCCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999998 9999999999999999999
Q ss_pred EEEEccccc-----CCCCcccccccchhhhHHHHHHHHHHhhcccCCCCccch
Q 017077 321 MLLKIPRMF-----DPWGGYSIIGFGDILLPGLIIAFSLRFKLSDLSSHHIPI 368 (378)
Q Consensus 321 ~~l~~P~~~-----~~~~~~s~LGlGDiviPGl~i~~~~rfD~~~~~~~~~~~ 368 (378)
|++++||++ +++++|||||+|||++||++||||+|||...++.|++++
T Consensus 410 MlLkVPrl~~s~~~~~~~~~silGFGDIl~PGlLVa~c~RfD~~~~~~~~iYf 462 (541)
T KOG2442|consen 410 MLLKVPRLFFSVLSDPWGGYSILGFGDILVPGLLVAFCLRFDVQVNSVSNIYF 462 (541)
T ss_pred eEEEcchhccccccccCCCeeEeeecccccchHHHHHHHHhhhhccccceeEE
Confidence 999999998 788999999999999999999999999999988666543
No 2
>KOG2443 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5e-51 Score=392.03 Aligned_cols=236 Identities=27% Similarity=0.483 Sum_probs=194.6
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhcccCCCCccccccCCCCeeeecccchhh-HHHHHHHHHHHH
Q 017077 94 VVDVAEVFLWLMAVGTILCASYWSAWSARETAIEQEKLLKDAVDEIPDAKAVGVSGVVDINTASAVL-FVLVASCFLVML 172 (378)
Q Consensus 94 ~~D~s~~~l~l~Av~tv~~gs~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~a~~-fpv~~s~~Ll~l 172 (378)
..+.+.+.+.++|+.+|++|++||++..+|. |++++..++++.++|.. ||+++||+|++|
T Consensus 22 ~~~~~~~sl~l~A~l~i~~GsfRS~~~~~~~-------------------~d~~~~~es~t~~~a~~~fPi~~s~tLl~l 82 (362)
T KOG2443|consen 22 LLASAYVSLILIALLLIVIGSFRSLNYIKEN-------------------EDKKDKSESITKRDAGKMFPIIGSCTLLLL 82 (362)
T ss_pred hhcccchHHHHHHHHHHHHHHHHHhhhhhhh-------------------hcccchhhhhhhhhhcccCCcccchHHHHH
Confidence 4677889999999999999999998765431 11124556788888887 999999999999
Q ss_pred HHHHHHH---HHHHHHHHHHHHhHHHHHHHHHHHHHhh----hccC---------CCceeeeccccccccchhhhhhhHH
Q 017077 173 YKLMSNW---FLELLVILFCIGGVEGLQTCLVALLSRW----FRRA---------GESFIKVPFFGAVSHLTLAVTPFCI 236 (378)
Q Consensus 173 y~f~~~~---~~~~l~~~f~~~g~~~l~~~l~~~~~~~----~~~~---------~~~~~~~p~~~~~~~~~l~~~~~~~ 236 (378)
|++++.. ...+++.||++.|+.++.+.+.|+++.. .+.| ...+...-+.++++..++++...|.
T Consensus 83 yl~fk~ls~~~~~ll~~~ff~~g~~al~~~~~p~~~~~~~~l~p~~~~~~~~~~~~~~~~~~~~~~~Ft~~~iv~~vls~ 162 (362)
T KOG2443|consen 83 YLLFKPLSKELINLLTMYFFFLGVIALLSLLDPFINAFKFLLLPMCQYHLLFPRGPGEKKEFICNGKFTRAQIVALVLSS 162 (362)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhhhhhcCccchhheeeeccCCcccceeecccccHHHHHHHHHHH
Confidence 9988643 2337899999999999999999988721 1111 1111112234578888999999999
Q ss_pred HHHhhhhhhhcCccchhHHhHHHHHHHHHHHHhcccCchhHHHHHHHHHHHhhhhheeeccccccceeEEEeecCCCCCC
Q 017077 237 AFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVARGDKSGE 316 (378)
Q Consensus 237 ~~~~~w~~~~~~~~~W~l~ni~g~~~~~~~i~~~~l~~~k~~~~lL~~lf~YDif~Vf~tp~~~~~svMv~VA~~~~~~~ 316 (378)
.+++.|++.+| |++||++|+++|+++|+.+||||+|+|++||.|||+|||||||+ ++|||||||+.|
T Consensus 163 ~i~v~~ll~~H----Wl~nN~lgms~~I~~I~~lrL~s~ktgalLL~gLffYDIfwVFg------TnVMVtVAt~~D--- 229 (362)
T KOG2443|consen 163 MIVVWYLLTKH----WLANNLLGMSFCIAGIEFLRLPSLKTGALLLGGLFFYDIFWVFG------TNVMVTVATSLD--- 229 (362)
T ss_pred HHHHHHHhhhH----HHHHhHHHHHHHHHHHHHhcccchhhhHHHHHHHHHHheEEEec------CceEEEeecccC---
Confidence 99999998884 99999999999999999999999999999999999999999996 569999999976
Q ss_pred CCCCEEEEcccccCCC----CcccccccchhhhHHHHHHHHHHhhcccCCC
Q 017077 317 DGIPMLLKIPRMFDPW----GGYSIIGFGDILLPGLIIAFSLRFKLSDLSS 363 (378)
Q Consensus 317 ~~~P~~l~~P~~~~~~----~~~s~LGlGDiviPGl~i~~~~rfD~~~~~~ 363 (378)
+|+|+++|+..... .+||||||||||+||+|+|+++|||.++...
T Consensus 230 --~PikL~fP~~l~~~~~~as~fsMLGLGDIviPGiflAl~lRfD~~k~~~ 278 (362)
T KOG2443|consen 230 --APIKLVFPQKLLFPGLTASNFSMLGLGDIVIPGIFLALVLRFDIRKKRN 278 (362)
T ss_pred --CceEEecchhhccCCCccccceeccccchhhHHHHHHHHHHhhHHHHhc
Confidence 99999999976532 3599999999999999999999999986443
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=8.7e-52 Score=403.32 Aligned_cols=217 Identities=37% Similarity=0.671 Sum_probs=1.0
Q ss_pred CCCeeeecccchhhHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHHhhhcc-----CCCce
Q 017077 147 VSGVVDINTASAVLFVLVASCFLVMLYKLMSNWF------LELLVILFCIGGVEGLQTCLVALLSRWFRR-----AGESF 215 (378)
Q Consensus 147 ~~~~~~~s~~~a~~fpv~~s~~Ll~ly~f~~~~~------~~~l~~~f~~~g~~~l~~~l~~~~~~~~~~-----~~~~~ 215 (378)
||+.+++|++||++||++||++|++|||+++++. +++++.||+++|+.++..++.+.+.+.++. ..+.+
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 4566789999999999999999999999987654 468999999999999877777776654331 11222
Q ss_pred eee--------ccccccccchhhhhhhHHHHHhhhhhhhcCccchhHHhHHHHHHHHHHHHhcccCchhHHHHHHHHHHH
Q 017077 216 IKV--------PFFGAVSHLTLAVTPFCIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFM 287 (378)
Q Consensus 216 ~~~--------p~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~W~l~ni~g~~~~~~~i~~~~l~~~k~~~~lL~~lf~ 287 (378)
.++ ++.++++..++++.++|+++++.|+++|++ +|++||++|+|+|+++++.+|+||+|++++||+++|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~l~~~~~s~~~~~~w~~~~~~--~W~l~nilgi~~~i~~i~~i~l~s~k~~~ilL~~lf~ 159 (298)
T PF04258_consen 82 WKLSFPRRDIKPFSGSFTLSDLLSFLISLAIAVVWYVYRNE--HWILQNILGICFCINIISLIRLPSFKTATILLIGLFL 159 (298)
T ss_dssp ---------------------------------S----------------------------------------------
T ss_pred EEEEEEcccccceeeeeeHHHHHHHHHHHHHHHHHHHhccc--hHHHHhHHHHHHHHHHHHheeccchHHHHHHHHHHHH
Confidence 222 344567788899999999999999998876 5999999999999999999999999999999999999
Q ss_pred hhhhheeeccccccceeEEEeecCCCCCCCCCCEEEEcccccC----CCCcccccccchhhhHHHHHHHHHHhhcccCCC
Q 017077 288 YDIFWVFVSKKLFHESVMIVVARGDKSGEDGIPMLLKIPRMFD----PWGGYSIIGFGDILLPGLIIAFSLRFKLSDLSS 363 (378)
Q Consensus 288 YDif~Vf~tp~~~~~svMv~VA~~~~~~~~~~P~~l~~P~~~~----~~~~~s~LGlGDiviPGl~i~~~~rfD~~~~~~ 363 (378)
|||||||+||++||+|||++|||+..++++++|+|+++|+..+ ..+++|||||||||+||+|+++|+|||.+++..
T Consensus 160 YDif~VF~s~~~~g~svM~~VA~~~~~~~~~~P~~l~~P~~~~~~~~~~~~~s~LGlGDIviPGl~i~~~~rfD~~~~~~ 239 (298)
T PF04258_consen 160 YDIFWVFISPYFFGTSVMVTVATGGFDAPEKLPIKLQFPRFFDSNSSCPKPFSMLGLGDIVIPGLFIAFCLRFDKSRNKS 239 (298)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHhccccCCCchhhhhhccccccccCCCeEEEEeccccccccCCCCeeEeccchHHHHHHHHHHHHHhhHhhccc
Confidence 9999999999999999999999994445578899999999863 358899999999999999999999999998443
Q ss_pred Cc
Q 017077 364 HH 365 (378)
Q Consensus 364 ~~ 365 (378)
++
T Consensus 240 ~~ 241 (298)
T PF04258_consen 240 RK 241 (298)
T ss_dssp --
T ss_pred cc
Confidence 33
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=4e-39 Score=306.51 Aligned_cols=199 Identities=36% Similarity=0.546 Sum_probs=168.9
Q ss_pred eeecccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhccCCCceeeeccccccccchhh
Q 017077 151 VDINTASAVLFVLVASCFLVMLYKLMSNWFLELLVILFCIGGVEGLQTCLVALLSRWFRRAGESFIKVPFFGAVSHLTLA 230 (378)
Q Consensus 151 ~~~s~~~a~~fpv~~s~~Ll~ly~f~~~~~~~~l~~~f~~~g~~~l~~~l~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~ 230 (378)
+.+++.+++.||+++|++|+++|++++++ +..+..+|++.|+.+++.++.+..... .+.....
T Consensus 3 ~~~n~~~~i~fii~~s~~Ll~Ly~~~~~~-~i~~~~~f~~~~~~~~~~~~~~~~~~~----------------~~~~~~~ 65 (249)
T smart00730 3 SLLNSLVAIVFPIVATFVLVLLYKFFKYL-VIVLVIYFSSLGVLFLYSLLYPLEVFR----------------VDYPTLL 65 (249)
T ss_pred ccccHHHHhhHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HhHHHHH
Confidence 46789999999999999999999999865 778899999999999988887764432 2334456
Q ss_pred hhhhHHHHHhhhhhhhcCccchhHHhHHHHHHHHHHHHhcccCchhHHHHHHHHHHHhhhhheeeccccccceeEEEeec
Q 017077 231 VTPFCIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVAR 310 (378)
Q Consensus 231 ~~~~~~~~~~~w~~~~~~~~~W~l~ni~g~~~~~~~i~~~~l~~~k~~~~lL~~lf~YDif~Vf~tp~~~~~svMv~VA~ 310 (378)
...++++++.+|+++++ ++|++||++|+|+|+.+++.+|+||+|++++||+++++||+||||+||. +++||++|||
T Consensus 66 ~~~~~~~v~~~~~~~~~--~~w~~~~~lgi~~~~~~~~~~~l~~~~~~~iLL~~l~iYDif~Vf~t~~--~~~vMv~vA~ 141 (249)
T smart00730 66 ILLLNFAVVGFWCIHRK--GAWIQQDLIGISLCMAILFILRLPSEWTAWILLGALFIYDIFAVFGTPG--PLRVMVEVAT 141 (249)
T ss_pred HHHHHHHHHHHHHHHhh--hHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHheeecCCC--CchHHhhHhc
Confidence 67778888899998886 6899999999999999999999999999999999999999999999997 8999999999
Q ss_pred CCCCCCCCCCEEEEccccc-----CCCCcccccccchhhhHHHHHHHHHHhhcccCCCCccchhh
Q 017077 311 GDKSGEDGIPMLLKIPRMF-----DPWGGYSIIGFGDILLPGLIIAFSLRFKLSDLSSHHIPISA 370 (378)
Q Consensus 311 ~~~~~~~~~P~~l~~P~~~-----~~~~~~s~LGlGDiviPGl~i~~~~rfD~~~~~~~~~~~~~ 370 (378)
+.++..|++|+++..||.. +..+++++|||||||+||+++++|+|||..++..+.-..++
T Consensus 142 ~~~~~~~~~P~ll~~p~~~~~~~~~~~~~~~~LGLGDiv~Pgilv~~a~~fd~~~~~~~~yf~~~ 206 (249)
T smart00730 142 GRDEPIKVFPALLYVPRLVVSFEDDEEGRFSMLGLGDIVFPGILVASAARFDVSVRSDSNYFLAC 206 (249)
T ss_pred cCCCCcccCChhhcccccccccccCCCCccceecCCCeeeHHHHHHHHHHhhhcccCCcccHHHH
Confidence 9874334689999999842 23468999999999999999999999998765544434433
No 5
>cd02132 PA_GO-like PA_GO-like: Protease-associated domain containing proteins like Arabidopsis thaliana growth-on protein GRO10. This group contains various PA domain-containing proteins similar to the functionally uncharacterized Arabidopsis GRO10. The PA domain may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=99.76 E-value=2.6e-18 Score=150.28 Aligned_cols=84 Identities=57% Similarity=0.912 Sum_probs=72.7
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccceE
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSV 83 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~V 83 (378)
.+++|+|+||+||+|+|.+|++|||++||+++||||+.++...|.+..++...+.+||+++|++++|+.|++.+++|.+|
T Consensus 56 ~~~~g~IvLV~RG~C~F~~K~~nA~~aGA~avIv~n~~~~~~~~~~~~~~~~~~~~IP~v~Is~~~G~~L~~~l~~g~~V 135 (139)
T cd02132 56 SKLSGSIALVERGECAFTEKAKIAEAGGASALLIINDQEELYKMVCEDNDTSLNISIPVVMIPQSAGDALNKSLDQGKKV 135 (139)
T ss_pred cccCCeEEEEECCCCCHHHHHHHHHHcCCcEEEEEECCCcccccccCCCCCCCCCcEeEEEecHHHHHHHHHHHHcCCcE
Confidence 47899999999999999999999999999999999998776666543233334579999999999999999999999999
Q ss_pred EEEE
Q 017077 84 SVQL 87 (378)
Q Consensus 84 ~v~l 87 (378)
++++
T Consensus 136 tv~~ 139 (139)
T cd02132 136 EVLL 139 (139)
T ss_pred EEeC
Confidence 8863
No 6
>cd02125 PA_VSR PA_VSR: Protease-associated (PA) domain-containing plant vacuolar sorting receptor (VSR). This group includes various PA domain-containing VSRs such as garden pea BP-80, pumpkin PV72, and various Arabidopsis VSRs including AtVSR1. In contrast to most eukaryotes, which only have one or two VSRs, plants have several. This may in part be a reflection of having a more complex vacuolar system with both lytic vacuoles and storage vacuoles. The lytic vacuole is thought to be equivalent to the mammalian lysosome and the yeast vacuole. Pea BP-80 is a type 1 transmembrane protein, involved in the targeting of proteins to the lytic vacuole; it has been suggested that this protein also mediates targeting to the storage vacuole. PV72 and AtVSR1 may mediate transport of seed storage proteins to protein storage vacuoles. The significance of the PA domain to VSRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may partic
Probab=99.76 E-value=2.5e-18 Score=148.30 Aligned_cols=83 Identities=33% Similarity=0.481 Sum_probs=70.7
Q ss_pred CCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc-ccccccCCC----CCCCCcceeEEEEehhchHhHHHHhhc
Q 017077 5 KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE-LYKMVCDPD----ETDLDIHIPAVMMPQDAGASLEKMLLN 79 (378)
Q Consensus 5 ~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~-~~~m~~~~~----~~~~~i~IPvv~Is~~~G~~L~~~l~~ 79 (378)
...++|+||+||+|+|.+|++|||++||+++||||+.++ ...|.+..+ ....+++||+++|++++|++|++.+++
T Consensus 40 ~~~~~IvLv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~m~~~~~~~~~~~~~~i~IP~v~Is~~~G~~L~~~l~~ 119 (127)
T cd02125 40 GRRPVILLLDRGGCFFTLKAWNAQQAGAAAVLVADNVDEPLLTMDTPEESGSADYIEKITIPSALITKAFGEKLKKAISN 119 (127)
T ss_pred CCCceEEEEECCCcCHHHHHHHHHHCCCcEEEEEECCCCccccccCcccccccccCCCceEeEEEECHHHHHHHHHHHhc
Confidence 477899999999999999999999999999999999876 455643221 123467899999999999999999999
Q ss_pred cceEEEEE
Q 017077 80 TSSVSVQL 87 (378)
Q Consensus 80 G~~V~v~l 87 (378)
|.+|+|++
T Consensus 120 g~~V~v~~ 127 (127)
T cd02125 120 GEMVVIKL 127 (127)
T ss_pred CCeEEEeC
Confidence 99999875
No 7
>cd02129 PA_hSPPL_like PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like. This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha triggering IL-12 production. hSPPL2a and 2b may have a broad substrate spectrum. The significance of the PA domain to these SPPLs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=99.75 E-value=4.8e-18 Score=144.78 Aligned_cols=80 Identities=26% Similarity=0.428 Sum_probs=64.8
Q ss_pred CCCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccce
Q 017077 3 KHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 82 (378)
Q Consensus 3 ~~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~ 82 (378)
+.+++|+|+||+||+|+|.+|++|||++||+|||||||++.. .+... .....+++||+++|++++|++|++.+. ..
T Consensus 40 ~~~l~gkIaLV~RG~CsF~~K~~~Aq~aGA~aVII~nn~~~~-~~~~~-~~~~~~v~IP~v~Is~~dG~~i~~~l~--~~ 115 (120)
T cd02129 40 PGGLKGKAVVVMRGNCTFYEKARLAQSLGAEGLLIVSRERLV-PPSGN-RSEYEKIDIPVALLSYKDMLDIQQTFG--DS 115 (120)
T ss_pred ccccCCeEEEEECCCcCHHHHHHHHHHCCCCEEEEEECCCCC-CCCCC-CCCCcCCcccEEEEeHHHHHHHHHHhc--cC
Confidence 357899999999999999999999999999999999997642 12111 122356799999999999999999994 55
Q ss_pred EEEE
Q 017077 83 VSVQ 86 (378)
Q Consensus 83 V~v~ 86 (378)
++|.
T Consensus 116 ~~v~ 119 (120)
T cd02129 116 VKVA 119 (120)
T ss_pred cEEe
Confidence 6654
No 8
>cd02127 PA_hPAP21_like PA_hPAP21_like: Protease-associated domain containing proteins like the human secreted glycoprotein hPAP21 (human protease-associated domain-containing protein, 21kDa). This group contains various PA domain-containing proteins similar to hPAP21. Complex N-glycosylation may be required for the secretion of hPAP21. The significance of the PA domain to hPAP21 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=99.74 E-value=7.9e-18 Score=143.38 Aligned_cols=82 Identities=28% Similarity=0.472 Sum_probs=69.6
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc----ccccccCCCCCCCCcceeEEEEehhchHhHHHHhhc
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE----LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLN 79 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~----~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~ 79 (378)
.+++|+|+||+||+|+|.+|++|||++||+|+||||+.++ .+.|.+. ....+++||+++|++++|+.|++.+++
T Consensus 31 ~~~~g~I~Lv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~~~~m~~~--~~~~~i~IP~v~Is~~dG~~L~~~l~~ 108 (118)
T cd02127 31 HDINGNIALIERGGCSFLTKAINAQKAGALAVIITDVNNDSDEYYVEMIQD--DSSRRADIPAAFLLGKNGYMIRKTLER 108 (118)
T ss_pred cccCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccceEecCC--CCCCCceEEEEEecHHHHHHHHHHHHc
Confidence 4689999999999999999999999999999999998653 2345432 223567999999999999999999999
Q ss_pred cceEEEEE
Q 017077 80 TSSVSVQL 87 (378)
Q Consensus 80 G~~V~v~l 87 (378)
|..+++.+
T Consensus 109 g~~~~~~~ 116 (118)
T cd02127 109 LGLPYAII 116 (118)
T ss_pred CCceEEee
Confidence 99888765
No 9
>cd02126 PA_EDEM3_like PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I alpha-mannosidases (gylcosyl hydrolase family 47), N-terminal to the PA domain. EDEM3 accelerates glycoprotein ERAD (ER-associated degradation). In transfected mammalian cells, overexpression of EDEM3 enhances the mannose trimming from the N-glycans, of a model misfolded protein [alpha1-antitrypsin null (Hong Kong)] as well as, from total glycoproteins. Mannose trimming appears to be involved in the selection of ERAD substrates. EDEM3 has a different specificity of trimming than ER alpha-mannosidase 1. The significance of the PA domain to EDEM3 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or pr
Probab=99.72 E-value=2.8e-17 Score=141.52 Aligned_cols=83 Identities=28% Similarity=0.530 Sum_probs=69.1
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc-------ccccccCCCCCCCCcceeEEEEehhchHhHHHH
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE-------LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKM 76 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~-------~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~ 76 (378)
.+++|||+||+||+|+|.+|+++||++||+|+||+||.++ .+.|.+. .....+++||+++|+++||+.|++.
T Consensus 37 ~~~~gkIaLv~RG~C~f~~K~~~Aq~aGA~avII~n~~~~~~~~~~~~~~m~~~-~~~~~~~~IP~v~I~~~dG~~L~~~ 115 (126)
T cd02126 37 EEVKGKIAIMERGDCMFVEKARRVQKAGAIGGIVIDNNEGSSSDTAPMFAMSGD-GDSTDDVTIPVVFLFSKEGSKLLAA 115 (126)
T ss_pred cccCceEEEEECCCCcHHHHHHHHHHCCCcEEEEEECCCCccccccceeEeecC-CCCCCCCeEEEEEEEHHHHHHHHHH
Confidence 4689999999999999999999999999999999997654 2345332 1112357999999999999999999
Q ss_pred hhccceEEEEE
Q 017077 77 LLNTSSVSVQL 87 (378)
Q Consensus 77 l~~G~~V~v~l 87 (378)
+++|.+|++.+
T Consensus 116 l~~~~~~~~~~ 126 (126)
T cd02126 116 IKEHQNVEVLL 126 (126)
T ss_pred HHhCCceEEeC
Confidence 99999998864
No 10
>cd02122 PA_GRAIL_like PA _GRAIL_like: Protease-associated (PA) domain GRAIL-like. This group includes PA domain containing E3 (ubiquitin ligases) similar to human GRAIL (gene related to anergy in lymphocytes) protein. Proteins in this group contain a C3H2C3 RING finger. E3 ubiquitin ligase is part of an enzymic cascade, the end result of which is the ubiquitination of proteins. In this cascade, E1 activates the ubiquitin, the activated ubiquitin is carried by E2, and E3 recognizes the acceptor protein as well as catalyzes the transfer of the activated ubiquitin from E2 to this acceptor. GRAIL, a transmembrane protein localized in the endosomes, controls the development of T cell clonal anergy, and may ubiquitinate membrane-associated targets for T cell activation. GRAIL1 is associated with, and regulated by, two isoforms of otubain 1 (the ubiquitin-specific protease). Additional E3s belonging to this group include human (h)Goliath and Xenopus GREUL1 (Goliath Related E3 Ubiquitin Ligase
Probab=99.70 E-value=4.2e-17 Score=142.54 Aligned_cols=79 Identities=28% Similarity=0.363 Sum_probs=68.2
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccc-c--ccccccCCCCCCCCcceeEEEEehhchHhHHHHhhcc
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQK-E--LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNT 80 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~-~--~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G 80 (378)
.+++|+||||+||+|+|.+|++|||++||+++||||+.+ . .+.|... ...+||+++|++++|+.|++.+++|
T Consensus 57 ~~~~g~IaLV~RG~C~F~~K~~nA~~aGA~aVIIyn~~~~~~~~~~m~~~-----~~~~ip~v~Is~~~G~~l~~~l~~G 131 (138)
T cd02122 57 PNGEPWIALIQRGNCTFEEKIKLAAERNASAVVIYNNPGTGNETVKMSHP-----GTGDIVAIMITNPKGMEILELLERG 131 (138)
T ss_pred ccCCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCCCceeeccCC-----CCCcceEEEEcHHHHHHHHHHHHcC
Confidence 568999999999999999999999999999999999986 2 4445331 1247999999999999999999999
Q ss_pred ceEEEEE
Q 017077 81 SSVSVQL 87 (378)
Q Consensus 81 ~~V~v~l 87 (378)
++|++++
T Consensus 132 ~~Vtv~~ 138 (138)
T cd02122 132 ISVTMVI 138 (138)
T ss_pred CcEEEeC
Confidence 9998863
No 11
>cd04813 PA_1 PA_1: Protease-associated (PA) domain subgroup 1. A subgroup of PA-domain containing proteins. Proteins in this subgroup contain a RING-finger (Really Interesting New Gene) domain C-terminal to this PA domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabid
Probab=99.66 E-value=2.9e-16 Score=133.60 Aligned_cols=73 Identities=26% Similarity=0.437 Sum_probs=61.8
Q ss_pred CCCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc--ccccccCCCCCCCCcceeEEEEehhchHhHHHHh
Q 017077 3 KHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE--LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKML 77 (378)
Q Consensus 3 ~~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~--~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l 77 (378)
.++++||||||+||+|+|.+|++|||++||+++||||+.++ ...|.+. +...+++||+++|++++|+.|++.+
T Consensus 35 ~~~l~gkIvLV~RG~CsF~~K~~nAq~aGA~avII~n~~~~~~~~~m~~~--~~~~~v~IPav~Is~~~g~~L~~l~ 109 (117)
T cd04813 35 HAEIDGKVALVLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRGLITMFSN--GDTDNVTIPAMFTSRTSYHLLSSLL 109 (117)
T ss_pred cCCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCcccceecccC--CCCCCcEEEEEEEcHHHHHHHHHhc
Confidence 35789999999999999999999999999999999998764 3445432 2235679999999999999999876
No 12
>cd04817 PA_VapT_like PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from the psychotroph Shewanella strain Ac10 and the Apa1 protease from the psychrotroph Pseudoalteromonas Sp. As-11. VapT is a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease showing high activity over a broad pH range and temperature. SapSh has a high level of protease activity at low temperatures. Apa1 is also cold-adapted. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=99.65 E-value=3.9e-16 Score=136.43 Aligned_cols=77 Identities=25% Similarity=0.333 Sum_probs=62.1
Q ss_pred CCCCCCcEEEEEcCCCC-----HHHHHHHHHHcCCcEEEEEecc--ccccccccCCCCCCCCcceeEEEEehhchHhHHH
Q 017077 3 KHKYAGDVIMVDRGNCK-----FTTKANIAEAAGASALLIINNQ--KELYKMVCDPDETDLDIHIPAVMMPQDAGASLEK 75 (378)
Q Consensus 3 ~~~l~g~IaLV~RG~Ct-----F~~K~~nAq~aGA~avIV~n~~--~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~ 75 (378)
..+++|||+||+||+|+ |.+|++|||++||+|+|||||+ ++...+.. .+...+.+||+++|++++|++|++
T Consensus 52 ~~d~~GkIaLI~RG~c~~~~~~f~~Kv~~A~~aGA~avIIyNn~~~~g~~~~~l--g~~~~~~~IP~v~is~~dG~~L~~ 129 (139)
T cd04817 52 CGGMAGKICLIERGGNSKSVYPEIDKVKACQNAGAIAAIVYSNAALAGLQNPFL--VDTNNDTTIPSVSVDRADGQALLA 129 (139)
T ss_pred CCCcCccEEEEECCCCCCCcccHHHHHHHHHHCCCeEEEEEeCCCCCCcccccc--cCCCCCceEeEEEeeHHHHHHHHH
Confidence 34789999999999999 9999999999999999999998 44322211 112235799999999999999999
Q ss_pred Hhhccc
Q 017077 76 MLLNTS 81 (378)
Q Consensus 76 ~l~~G~ 81 (378)
.+.++.
T Consensus 130 ~l~~~~ 135 (139)
T cd04817 130 ALGQST 135 (139)
T ss_pred HhcCCC
Confidence 984443
No 13
>cd02123 PA_C_RZF_like PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and acce
Probab=99.65 E-value=6.4e-16 Score=137.35 Aligned_cols=78 Identities=28% Similarity=0.472 Sum_probs=66.2
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc-ccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccce
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE-LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 82 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~-~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~ 82 (378)
.+..|+|+||+||+|+|.+|++|||++||+|+||||++++ ...|.+. +....+++||+++|++++|+.|++.+++++.
T Consensus 64 ~~~~g~IvLV~RG~CtF~~Kv~nAq~aGA~avII~n~~~~~~~~m~~~-~~~~~~v~IP~v~Is~~dg~~L~~~l~~~~~ 142 (153)
T cd02123 64 NASGSFIVLIRRGNCSFETKVRNAQRAGYKAAIVYNDESNDLISMSGN-DQEIKGIDIPSVFVGKSTGEILKKYASYEKG 142 (153)
T ss_pred ccCCCeEEEEECCCCCHHHHHHHHHHCCCCEEEEEECCCCcceeccCC-CCCCcCCEEEEEEeeHHHHHHHHHHHhcCCc
Confidence 5788999999999999999999999999999999998765 4455432 2112468999999999999999999988776
No 14
>cd02130 PA_ScAPY_like PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY). This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stab
Probab=99.65 E-value=5.4e-16 Score=132.37 Aligned_cols=81 Identities=32% Similarity=0.462 Sum_probs=67.8
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecc-ccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccce
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQ-KELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 82 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~-~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~ 82 (378)
.+++||||||+||+|+|.+|++|||++||+|+||||+. ++...... . ...+..||+++|++++|+.|++.+++|++
T Consensus 41 ~~~~gkIvlv~rg~c~f~~K~~~A~~aGA~~vIv~n~~~~~~~~~~~--~-~~~~~~Ip~v~Is~~~G~~L~~~l~~g~~ 117 (122)
T cd02130 41 ASVAGNIALIERGECPFGDKSALAGAAGAAAAIIYNNVPAGGLSGTL--G-EPSGPYVPTVGISQEDGKALVAALANGGE 117 (122)
T ss_pred cCCCCEEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccccc--C-CCCCCEeeEEEecHHHHHHHHHHHhcCCc
Confidence 46999999999999999999999999999999999987 33322111 1 12356899999999999999999999999
Q ss_pred EEEEE
Q 017077 83 VSVQL 87 (378)
Q Consensus 83 V~v~l 87 (378)
|++++
T Consensus 118 v~~~~ 122 (122)
T cd02130 118 VSANL 122 (122)
T ss_pred EEEeC
Confidence 98874
No 15
>cd04816 PA_SaNapH_like PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH).This group contains various PA domain-containing proteins similar SaNapH. Proteins in this group belong to the peptidase M28 family. NapH is a terminal enzyme in the puromycin biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin to the active antibiotic. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=99.64 E-value=8.8e-16 Score=131.13 Aligned_cols=83 Identities=27% Similarity=0.505 Sum_probs=68.1
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccceE
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSV 83 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~V 83 (378)
.+++|||+|++||+|+|.+|++|||++||+|+|+||+.++... ...........+||+++|++++|++|++.+++|.+|
T Consensus 40 ~~~~GkIvLv~rg~c~f~~K~~~A~~aGA~avIi~n~~~~~~~-~~~~~~~~~~~~iP~~~Is~~~G~~l~~~l~~g~~v 118 (122)
T cd04816 40 LDVKGAIVLVDRGGCPFADKQKVAAARGAVAVIVVNNSDGGGT-AGTLGAPNIDLKVPVGVITKAAGAALRRRLGAGETL 118 (122)
T ss_pred CCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEeCCCCccc-cccccCCCCCCeeeEEEEcHHHHHHHHHHHcCCCEE
Confidence 4689999999999999999999999999999999998764211 111111123568999999999999999999999999
Q ss_pred EEEE
Q 017077 84 SVQL 87 (378)
Q Consensus 84 ~v~l 87 (378)
++++
T Consensus 119 ~~~~ 122 (122)
T cd04816 119 ELDA 122 (122)
T ss_pred EEeC
Confidence 8874
No 16
>cd02124 PA_PoS1_like PA_PoS1_like: Protease-associated (PA) domain PoS1-like. This group includes various PA domain-containing proteins similar to Pleurotus ostreatus (Po)S1. PoSl, the main extracellular protease in P. ostreatus is a subtilisin-like serine protease belonging to the peptidase S8 family. Ca2+ and Mn2+ both stimulate the protease activity of (Po)S1. Ca2+ protects PoS1 from autolysis. PoS1 is a monomeric glycoprotein, which may play a role in the regulation of laccases in lignin formation. (Po)S1 participates in the degradation of POXA1b, and in the activation of POXA3, (POXA1b and POXA3 are laccase isoenzymes), but its effect may be indirect. The significance of the PA domain to PoS1 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=99.60 E-value=3.1e-15 Score=129.38 Aligned_cols=77 Identities=32% Similarity=0.415 Sum_probs=64.1
Q ss_pred CCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccceEE
Q 017077 5 KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVS 84 (378)
Q Consensus 5 ~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~V~ 84 (378)
+++|||+||+||+|+|.+|++|||++||+++||||++++...+.. + ....+|.+.+ +++|++|++.+++|++++
T Consensus 53 ~~~g~IaLv~rg~c~f~~K~~nA~~aGA~aviiyn~~~~~~~~~~--~---~~~~~~~~~~-~~~G~~l~~~l~~G~~vt 126 (129)
T cd02124 53 DLSGYIVLVRRGTCTFATKAANAAAKGAKYVLIYNNGSGPTDQVG--S---DADSIIAAVT-PEDGEAWIDALAAGSNVT 126 (129)
T ss_pred cccCeEEEEECCCCCHHHHHHHHHHcCCcEEEEEECCCCcccccC--C---CCcceeeEEe-HHHHHHHHHHHhcCCeEE
Confidence 689999999999999999999999999999999999876544321 1 2234566666 999999999999999999
Q ss_pred EEE
Q 017077 85 VQL 87 (378)
Q Consensus 85 v~l 87 (378)
++|
T Consensus 127 v~f 129 (129)
T cd02124 127 VDF 129 (129)
T ss_pred EeC
Confidence 875
No 17
>PF02225 PA: PA domain; InterPro: IPR003137 The PA (Protease associated) domain is found as an insert domain in diverse proteases, which include the MEROPS peptidase families A22B, M28, and S8A []. The PA domain is also found in a plant vacuolar sorting receptor O22925 from SWISSPROT and members of the RZF family, e.g. O43567 from SWISSPROT.; PDB: 3EIF_A 1XF1_B 3BXM_A 2C6P_A 1Z8L_C 3SJF_A 3BHX_A 2C6G_A 3D7F_A 2XEG_A ....
Probab=99.53 E-value=2.8e-14 Score=116.48 Aligned_cols=74 Identities=28% Similarity=0.492 Sum_probs=56.6
Q ss_pred CCCCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHh
Q 017077 2 PKHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKML 77 (378)
Q Consensus 2 p~~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l 77 (378)
...+++|||||++||+|+|.+|++|||++||+|+||+|+.+....+.. .....+.+||+++|++++|++|++.+
T Consensus 28 ~~~~~~gkIvlv~rg~~~~~~k~~~a~~~GA~gvIi~~~~~~~~~~~~--~~~~~~~~iP~v~I~~~~g~~L~~~i 101 (101)
T PF02225_consen 28 NGSDVKGKIVLVERGSCSFDDKVRNAQKAGAKGVIIYNPPPNNGSMID--SEDPDPIDIPVVFISYEDGEALLAYI 101 (101)
T ss_dssp STSTCTTSEEEEESTSSCHHHHHHHHHHTTESEEEEE-TSCSCTTTTC--EBTTTSTBSEEEEE-HHHHHHHHHHH
T ss_pred CCccccceEEEEecCCCCHHHHHHHHHHcCCEEEEEEeCCccccCccc--ccCCCCcEEEEEEeCHHHHhhhhccC
Confidence 346899999999999999999999999999999999993222211111 11234578999999999999999864
No 18
>cd04818 PA_subtilisin_1 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following subtilisin-like proteases: i) melon cucumisin, ii) Arabidopsis thaliana Ara12, iii) Alnus glutinosa ag12, iv) members of the tomato P69 family, and v) tomato LeSBT2. However, these proteins belong to other subtilisin-like subgroups. Relatively little is known about proteins in this subgroup.
Probab=99.52 E-value=5.6e-14 Score=119.10 Aligned_cols=80 Identities=41% Similarity=0.627 Sum_probs=68.4
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc--ccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccc
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE--LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTS 81 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~--~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~ 81 (378)
.+++|||+|++||+|+|.+|+++|+++||+|+|+||+.++ .+.|... .....||+++|++++|+.|++.+++|+
T Consensus 37 ~~v~GkIvL~~rg~c~f~~k~~~a~~aGA~gvIi~~~~~~~~~~~~~~~----~~~~~iP~v~V~~~~g~~l~~~l~~g~ 112 (118)
T cd04818 37 AAFAGKIALIDRGTCNFTVKVLNAQNAGAIAVIVANNVAGGAPITMGGD----DPDITIPAVMISQADGDALKAALAAGG 112 (118)
T ss_pred CCCCCEEEEEECCCCCHHHHHHHHHHCCCeEEEEEECCCCCcceeccCC----CCCCEEeEEEecHHHHHHHHHHHhcCC
Confidence 4699999999999999999999999999999999998764 3334221 134579999999999999999999999
Q ss_pred eEEEEE
Q 017077 82 SVSVQL 87 (378)
Q Consensus 82 ~V~v~l 87 (378)
+|++++
T Consensus 113 ~v~v~~ 118 (118)
T cd04818 113 TVTVTL 118 (118)
T ss_pred cEEEeC
Confidence 998874
No 19
>cd00538 PA PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) g
Probab=99.51 E-value=9.6e-14 Score=117.44 Aligned_cols=84 Identities=31% Similarity=0.462 Sum_probs=68.0
Q ss_pred CCCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccc-cccccCCCCCCCCcceeEEEEehhchHhHHHHhhccc
Q 017077 3 KHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKEL-YKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTS 81 (378)
Q Consensus 3 ~~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~-~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~ 81 (378)
..+++|||+|++||+|+|.+|+++||++||+|+|++|+.+.. ..+... +.......||+++|++++|++|++.+++|.
T Consensus 42 ~~~~~GkIvl~~~g~~~~~~k~~~a~~~GA~gvii~~~~~~~~~~~~~~-~~~~~~~~iP~~~is~~~g~~l~~~~~~~~ 120 (126)
T cd00538 42 GADVKGKIVLVRRGGCSFSEKVKNAQKAGAKAVIIYNNGDDPGPQMGSV-GLESTDPSIPTVGISYADGEALLSLLEAGK 120 (126)
T ss_pred CCCccceEEEEECCCcCHHHHHHHHHHCCCEEEEEEECCCCcccccccc-cCCCCCCcEeEEEeCHHHHHHHHHHHhcCC
Confidence 457999999999999999999999999999999999987632 222111 111234679999999999999999999998
Q ss_pred eEEEEE
Q 017077 82 SVSVQL 87 (378)
Q Consensus 82 ~V~v~l 87 (378)
++++++
T Consensus 121 ~v~~~~ 126 (126)
T cd00538 121 TVTVDL 126 (126)
T ss_pred ceEEeC
Confidence 888753
No 20
>cd02133 PA_C5a_like PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase. This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from Bacillus subtilis, ii) a large molecular mass collagenolytic protease from Geobacillus collagenovorans MO-1, and iii) PrtS, a cell envelope protease from Streptococcus thermophilus CNRZ 385. Proteins in this group belong to the peptidase S8 family. C5a peptidase is a cell surface serine protease which specifically inactivates C5a [a chemotactic peptide, which attracts polymorphonuclear leukocytes (PMNs)], by cleaving it to release a 7-residue carboxy-terminal fragment which contains the PMN binding site. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promotin
Probab=99.41 E-value=8.8e-13 Score=115.61 Aligned_cols=79 Identities=27% Similarity=0.426 Sum_probs=64.7
Q ss_pred CCCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccce
Q 017077 3 KHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 82 (378)
Q Consensus 3 ~~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~ 82 (378)
..+++|||+|++||+|+|.+|++|||++||+|+|+||+.++...+.. + ....||+++|++++|++|++.+++ +
T Consensus 43 ~~dv~GkIvL~~rg~c~~~~K~~~a~~aGA~gvIi~n~~~~~~~~~~--~---~~~~iP~v~Is~~dG~~L~~~l~~--~ 115 (143)
T cd02133 43 GKDVKGKIALIQRGEITFVEKIANAKAAGAVGVIIYNNVDGLIPGTL--G---EAVFIPVVFISKEDGEALKAALES--S 115 (143)
T ss_pred CCCccceEEEEECCCCCHHHHHHHHHHCCCeEEEEeecCCCcccccC--C---CCCeEeEEEecHHHHHHHHHHHhC--C
Confidence 35799999999999999999999999999999999999866543321 1 134799999999999999999976 4
Q ss_pred EEEEEe
Q 017077 83 VSVQLY 88 (378)
Q Consensus 83 V~v~l~ 88 (378)
+++++.
T Consensus 116 ~~i~~~ 121 (143)
T cd02133 116 KKLTFN 121 (143)
T ss_pred CeEEEE
Confidence 555544
No 21
>PF06550 DUF1119: Protein of unknown function (DUF1119); InterPro: IPR010545 This family consists of several hypothetical archaeal proteins of unknown function.
Probab=99.40 E-value=4.3e-12 Score=121.18 Aligned_cols=101 Identities=25% Similarity=0.388 Sum_probs=84.8
Q ss_pred chhHHhHHHHHHHHHHHHhcccC-chhHHHHHHHHHHHhhhhheeeccccccceeEEEeecCCCCCCCCCCEEEEccccc
Q 017077 251 AWIGQDILGIALIITVLQIVHIP-NLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVARGDKSGEDGIPMLLKIPRMF 329 (378)
Q Consensus 251 ~W~l~ni~g~~~~~~~i~~~~l~-~~k~~~~lL~~lf~YDif~Vf~tp~~~~~svMv~VA~~~~~~~~~~P~~l~~P~~~ 329 (378)
.|+..|+.|+.++...-..+.+. +.-.+.+||..+-+||..-||. |.+|++.|.|.- +.|+|+.+++|+..
T Consensus 111 EWYviD~~Gil~~aG~aaiFGISl~~lpaiiLL~iLAVYDaISVYk------TkHMltLAegv~--d~klPilfViP~~~ 182 (283)
T PF06550_consen 111 EWYVIDIAGILMGAGAAAIFGISLGILPAIILLAILAVYDAISVYK------TKHMLTLAEGVM--DLKLPILFVIPKKR 182 (283)
T ss_pred hHHHHHHHHHHHHhHHHHHHhhhccHHHHHHHHHHHHHhhhhheec------chHHHHHHHHHh--ccCCceEEEEeccc
Confidence 59999999999998877765555 6667999999999999999995 558999999975 26899999999864
Q ss_pred CC--------------CCcccccccchhhhHHHHHHHHHHhhcc
Q 017077 330 DP--------------WGGYSIIGFGDILLPGLIIAFSLRFKLS 359 (378)
Q Consensus 330 ~~--------------~~~~s~LGlGDiviPGl~i~~~~rfD~~ 359 (378)
+. .++-.++|+||.++|.++++-...|...
T Consensus 183 ~ySf~~~~~~~~~~~~~r~a~fiGlGD~vmPtILVvSa~~f~~~ 226 (283)
T PF06550_consen 183 GYSFLKDGFDNREEKEERDAFFIGLGDAVMPTILVVSAAFFLSA 226 (283)
T ss_pred CccccccccccccccccccceEeccchhhhHHHHHHHHHHhccc
Confidence 31 1345689999999999999999998655
No 22
>cd04819 PA_2 PA_2: Protease-associated (PA) domain subgroup 2. A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuola
Probab=99.38 E-value=2.3e-12 Score=110.96 Aligned_cols=83 Identities=22% Similarity=0.305 Sum_probs=66.4
Q ss_pred CCCCCcEEEEEcCCC--CHHHHHHHHHHcCCcEEEEEeccccccccccCCC-CCCCCcceeEEEEehhchHhHHHHhhcc
Q 017077 4 HKYAGDVIMVDRGNC--KFTTKANIAEAAGASALLIINNQKELYKMVCDPD-ETDLDIHIPAVMMPQDAGASLEKMLLNT 80 (378)
Q Consensus 4 ~~l~g~IaLV~RG~C--tF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~-~~~~~i~IPvv~Is~~~G~~L~~~l~~G 80 (378)
.+++|||||++||.| +|.+|+++|+++||+|+|++|+.++......... .......||++.|+++||+.|++++++|
T Consensus 41 ~~v~GkIvlv~~g~~~~~~~~k~~~A~~~GA~avi~~~~~~g~~~~~~~~~~~~~~~~~IP~v~Is~edg~~L~~~l~~g 120 (127)
T cd04819 41 LDLEGKIAVVKRDDPDVDRKEKYAKAVAAGAAAFVVVNTVPGVLPATGDEGTEDGPPSPIPAASVSGEDGLRLARVAERN 120 (127)
T ss_pred CCCCCeEEEEEcCCCchhHHHHHHHHHHCCCEEEEEEeCCCCcCcccccccccCCCCCCCCEEEEeHHHHHHHHHHHhcC
Confidence 479999999999999 9999999999999999999998765432111111 1122457999999999999999999988
Q ss_pred ceEEEE
Q 017077 81 SSVSVQ 86 (378)
Q Consensus 81 ~~V~v~ 86 (378)
.++.++
T Consensus 121 ~~~~~~ 126 (127)
T cd04819 121 DTLVLR 126 (127)
T ss_pred CceEee
Confidence 877653
No 23
>cd04815 PA_M28_2 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies; relatively little is known a
Probab=99.26 E-value=1.3e-11 Score=107.48 Aligned_cols=86 Identities=20% Similarity=0.223 Sum_probs=67.7
Q ss_pred CCCCCCCcEEEEEcCCC------CHHHH-------HHHHHHcCCcEEEEEeccccccccc--cCCCCCCCCcceeEEEEe
Q 017077 2 PKHKYAGDVIMVDRGNC------KFTTK-------ANIAEAAGASALLIINNQKELYKMV--CDPDETDLDIHIPAVMMP 66 (378)
Q Consensus 2 p~~~l~g~IaLV~RG~C------tF~~K-------~~nAq~aGA~avIV~n~~~~~~~m~--~~~~~~~~~i~IPvv~Is 66 (378)
|..+++|||||++||.| +|.+| .++|+++||.|+|++|+.+....+. +..........||++.|+
T Consensus 34 ~~~~v~GKIvlv~~~~~~~~~~~~~~~k~~~r~~~~~~A~~~GA~avIv~s~~~~~~~~~~~G~~~~~~~~~~IP~v~is 113 (134)
T cd04815 34 PAGAVKGKIVFFNQPMVRTQTGSGYGPTVAYRRRGAVEAAKKGAVAVLIRSIGTDSHRSPHTGMMSYDDGVPKIPAAAIS 113 (134)
T ss_pred chhhcCCeEEEecCCccccCchhhcCchhhhhhHHHHHHHhCCCEEEEEEecCcccCCCCcCCccccCCCCCCCCEEEec
Confidence 45689999999999999 99999 7999999999999999754321111 111111223579999999
Q ss_pred hhchHhHHHHhhccceEEEEE
Q 017077 67 QDAGASLEKMLLNTSSVSVQL 87 (378)
Q Consensus 67 ~~~G~~L~~~l~~G~~V~v~l 87 (378)
++||+.|.+.+++|.+|++++
T Consensus 114 ~ed~~~L~r~l~~g~~v~~~l 134 (134)
T cd04815 114 VEDADMLERLAARGKPIRVNL 134 (134)
T ss_pred hhcHHHHHHHHhCCCCeEEeC
Confidence 999999999999999998864
No 24
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=1.4e-10 Score=114.51 Aligned_cols=70 Identities=24% Similarity=0.340 Sum_probs=58.5
Q ss_pred CCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc--ccccccCCCCCCCCcceeEEEEehhchHhHHHHhh
Q 017077 5 KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE--LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLL 78 (378)
Q Consensus 5 ~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~--~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~ 78 (378)
.-..+++||+||+|+|.+|++|||++|++|+|||||.+. +..|.. + ..+++|++++++...|+.|.+...
T Consensus 77 ~~~~~laLI~Rg~CsFe~Kv~~AQ~aGfkaaIVynn~~~~~lv~~~~--~--~~~v~i~~~~vs~~~ge~l~~~~~ 148 (348)
T KOG4628|consen 77 RSTSFLALIRRGGCSFEDKVLNAQRAGFKAAIVYNNVGSEDLVAMAS--N--PSKVDIHIVFVSVFSGELLSSYAG 148 (348)
T ss_pred CCcceEEEEEccCCchHHHHhhcccccCceEEEecCCCCchheeecc--C--CccceeEEEEEeeehHHHHHHhhc
Confidence 456789999999999999999999999999999998653 444522 2 246899999999999999998643
No 25
>COG3389 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.19 E-value=1.6e-11 Score=113.57 Aligned_cols=114 Identities=27% Similarity=0.486 Sum_probs=90.6
Q ss_pred HHHHHhhhhhhhcCccchhHHhHHHHHHHHHHHHhcccC-chhHHHHHHHHHHHhhhhheeeccccccceeEEEeecCCC
Q 017077 235 CIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIP-NLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVARGDK 313 (378)
Q Consensus 235 ~~~~~~~w~~~~~~~~~W~l~ni~g~~~~~~~i~~~~l~-~~k~~~~lL~~lf~YDif~Vf~tp~~~~~svMv~VA~~~~ 313 (378)
..+++.++.++++. .|+..|..|.+++..+-..+.+. ....+.+||+.+-+||..-|| ||.+|++.|.+.-
T Consensus 97 ~~aI~~~~lL~~~p--eWyVid~ag~~la~Giaai~GIsfgv~pavvlL~~lavYDaIsVY------kT~HMIslA~~v~ 168 (277)
T COG3389 97 GLAIGLVYLLYKYP--EWYVIDLAGFFLAVGIAAIFGISFGVLPAVVLLIALAVYDAISVY------KTRHMISLAEGVM 168 (277)
T ss_pred HHHHHHHHhhhhcc--ceEEeehHHHHHHhhHHHhheeecchHHHHHHHHHHHHHHHHHHH------hHHHHHHHHHHHH
Confidence 44555666555543 59999999999998887776655 566689999999999999999 4668999999964
Q ss_pred CCCCCCCEEEEcccccCC-----------CCcccccccchhhhHHHHHHHHHHhhc
Q 017077 314 SGEDGIPMLLKIPRMFDP-----------WGGYSIIGFGDILLPGLIIAFSLRFKL 358 (378)
Q Consensus 314 ~~~~~~P~~l~~P~~~~~-----------~~~~s~LGlGDiviPGl~i~~~~rfD~ 358 (378)
..++||.+++|...+. +++--|+|+||+++|.++++-+.-|-.
T Consensus 169 --d~~lPmlfviP~~l~ysf~~~~fe~r~dgna~miG~GDavmPsIlVvSaa~f~~ 222 (277)
T COG3389 169 --DLDLPMLFVIPENLAYSFVEDAFENRGDGNAYMIGLGDAVMPSILVVSAAFFLI 222 (277)
T ss_pred --hcCCceEEEeecccccceeehhhhcCCCCceEEEeechhhcccceeeehHHhcc
Confidence 2679999999975431 466779999999999999988777644
No 26
>cd02120 PA_subtilisin_like PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from Alnus glutinosa ag12, members of the tomato P69 family, and tomato LeSBT2. These proteins belong to the peptidase S8 family. Cucumisin from the juice of melon fruits is a thermostable serine peptidase, with a broad substrate specificity for oligopeptides and proteins. A. thaliana Ara12 is a thermostable, extracellular serine protease, found chiefly in silique tissue and stem tissue. Ara12 is stimulated by Ca2+ ions. A. glutinosa ag12 is expressed at high levels in the nodules, and at low levels in the shoot tips; it is implicated in both symbiotic and non-symbiotic processes in plant development. The tomato P69 protease family is comprised of various protein isoforms of approximately 69KDa. These isoforms accu
Probab=99.12 E-value=1.9e-10 Score=97.89 Aligned_cols=73 Identities=23% Similarity=0.408 Sum_probs=62.1
Q ss_pred CCCCCcEEEEEcCCC-CHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhccce
Q 017077 4 HKYAGDVIMVDRGNC-KFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 82 (378)
Q Consensus 4 ~~l~g~IaLV~RG~C-tF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G~~ 82 (378)
.+++|||+|++||+| +|.+|+++|+++||.|+|++|+.++...+. .....||++.|++++|+.|++.++++..
T Consensus 48 ~~v~GkIVlc~~~~~~~~~~k~~~~~~~GA~gvI~~~~~~~~~~~~------~~~~~iP~v~I~~~~g~~l~~y~~~~~~ 121 (126)
T cd02120 48 SKVKGKIVLCDRGGNTSRVAKGDAVKAAGGAGMILANDPTDGLDVV------ADAHVLPAVHVDYEDGTAILSYINSTSN 121 (126)
T ss_pred hhccccEEEEeCCCCccHHHHHHHHHHcCCcEEEEEecCCCCceec------ccccccceEEECHHHHHHHHHHHHcCCC
Confidence 469999999999999 999999999999999999999876543221 1135799999999999999999987654
No 27
>KOG3920 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=98.89 E-value=1.2e-09 Score=96.07 Aligned_cols=82 Identities=27% Similarity=0.368 Sum_probs=65.4
Q ss_pred CCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccc------ccccccCCCCCCCCcceeEEEEehhchHhHHHHhh
Q 017077 5 KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE------LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLL 78 (378)
Q Consensus 5 ~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~------~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~ 78 (378)
...|.|+|++||+|+|..|.+|+|++||.++||-++... .++|-. +++.++.+||++++-..+|-.++..++
T Consensus 85 f~~d~vaL~eRGeCSFl~Ktl~~e~aGa~aiiitd~~~~~~sf~~YveMI~--D~sq~~AniPa~fllg~~Gy~ir~sL~ 162 (193)
T KOG3920|consen 85 FAPDSVALMERGECSFLVKTLNGEKAGATAIIITDSQNYEYSFHQYVEMIP--DESQDRANIPAVFLLGVTGYYIRVSLK 162 (193)
T ss_pred cCCCcEEEEecCCceeeehhhhhhhcCceEEEEecCCCCchhHHHHHHhcC--cccccccCCceEEEeccceEEEehhHH
Confidence 467899999999999999999999999999999986542 356754 344567899999999999988888777
Q ss_pred ccceEEEEEe
Q 017077 79 NTSSVSVQLY 88 (378)
Q Consensus 79 ~G~~V~v~l~ 88 (378)
+-......++
T Consensus 163 r~~r~ha~i~ 172 (193)
T KOG3920|consen 163 RYFRDHAKID 172 (193)
T ss_pred HhCCccEEEe
Confidence 6544444443
No 28
>cd02128 PA_TfR PA_TfR: Protease-associated domain containing proteins like transferrin receptor (TfR). This group contains various PA domain-containing proteins similar to human TfR1 and TfR2. TfR1 and TfR2 are type II membrane proteins, belonging to the peptidase M28 family. TfR1 is homodimeric, widely expressed, and a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and this complex is internalized. In addition to its role in iron uptake, TfR1 may participate in cell growth and proliferation. TfR2 also binds Tf but with a significantly lower affinity than does TfR1. TfR2 is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis. HFE and TfR2 interact in cells. By one model for serum iron sensing, at low or basal iron concentrations, HFE and TFR1 form a complex at the plasma membra
Probab=98.87 E-value=3.9e-09 Score=96.31 Aligned_cols=75 Identities=24% Similarity=0.233 Sum_probs=57.2
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccccccc------------cc----------CCC------CCC
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKM------------VC----------DPD------ETD 55 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~~m------------~~----------~~~------~~~ 55 (378)
.+++|||||++||+|++.+|+++||++||+|+|+|||..+...+ .. .+. +..
T Consensus 52 v~v~GkIvLvr~G~~~~~~Kv~~A~~~GA~gvIiy~Dp~d~~~~~~~~~~~g~~~~~~GDplTPG~ps~~~~~~~~~~~~ 131 (183)
T cd02128 52 VSVNGSVVLVRAGKISFAEKVANAEKLGAVGVLIYPDPADFPIDPSETALFGHVHLGTGDPYTPGFPSFNHTQFPPSQSS 131 (183)
T ss_pred CCCCCeEEEEECCCCCHHHHHHHHHHCCCEEEEEecCHHHcCcccCcceeecceeccCCCcCCCCCccccccccCccccc
Confidence 37899999999999999999999999999999999985221100 00 000 000
Q ss_pred CCcceeEEEEehhchHhHHHHhh
Q 017077 56 LDIHIPAVMMPQDAGASLEKMLL 78 (378)
Q Consensus 56 ~~i~IPvv~Is~~~G~~L~~~l~ 78 (378)
.-.+||+.-||.++++.|++.+.
T Consensus 132 ~lP~IPs~PIS~~da~~lL~~l~ 154 (183)
T cd02128 132 GLPNIPAQTISAAAAAKLLSKMG 154 (183)
T ss_pred CCCCCCEeccCHHHHHHHHHHcC
Confidence 12479999999999999999885
No 29
>cd02121 PA_GCPII_like PA_GCPII_like: Protease-associated domain containing protein, glutamate carboxypeptidase II (GCPII)-like. This group contains various PA domain-containing proteins similar to GCPII including, GCPIII (NAALADase2) and NAALADase L. These proteins belong to the peptidase M28 family. GCPII is also known N-acetylated-alpha-linked acidic dipeptidase (NAALDase1), folate hydrolase or prostate-specific membrane antigen (PSMA). GCPII is found in various human tissues including prostate, small intestine, and the central nervous system. In the brain, GCPII is known as NAALDase1, it functions as a NAALDase hydrolyzing the neuropeptide N-acetyl-L-aspartyl-L-glutamate (alpha-NAAG), to release free glutamate. In the small intestine, GCPII releases the terminal glutamate from poly-gamma-glutamated folates. GCPII (PSMA) is a useful cancer marker; its expression is markedly increased in prostate cancer and in tumor-associated neovasculature. GCPIII hydrolyzes alpha-NAAG with a lower
Probab=98.34 E-value=9.1e-07 Score=83.20 Aligned_cols=75 Identities=20% Similarity=0.206 Sum_probs=56.9
Q ss_pred CCCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccccc---------------------ccc-------ccCCC---
Q 017077 4 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKEL---------------------YKM-------VCDPD--- 52 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~---------------------~~m-------~~~~~--- 52 (378)
-+++|||||+++|.|.+.+|+++|+++||+|||+|++..+. +.. ....+
T Consensus 68 vdv~GKIvLvr~G~~~~~~Kv~~A~~~GA~gVIiy~Dp~d~~~~~~~~~~~yP~g~~~~~~~vqRgsv~~~~~~~GDplT 147 (220)
T cd02121 68 IDVKGKIVIARYGGIFRGLKVKNAQLAGAVGVIIYSDPADDGYITGENGKTYPDGPARPPSGVQRGSVLFMSIGPGDPLT 147 (220)
T ss_pred CCCCCeEEEEECCCccHHHHHHHHHHcCCEEEEEEeCchhcccccccccccCCCCCCCCCCcceecceeccccCCCCCCC
Confidence 37899999999999999999999999999999999974221 000 00000
Q ss_pred ---------------CCCCCcceeEEEEehhchHhHHHHhh
Q 017077 53 ---------------ETDLDIHIPAVMMPQDAGASLEKMLL 78 (378)
Q Consensus 53 ---------------~~~~~i~IPvv~Is~~~G~~L~~~l~ 78 (378)
+...-.+||+.=||..|++.|++.|.
T Consensus 148 PG~ps~~~~~r~~~~~~~~lP~IPs~PIS~~da~~lL~~L~ 188 (220)
T cd02121 148 PGYPSKPGAERRDKEESKGLPKIPSLPISYRDAQPLLKALG 188 (220)
T ss_pred CCCCCCCCCcccCcccccCCCCCCcccCCHHHHHHHHHHcC
Confidence 00012369999999999999999996
No 30
>cd02131 PA_hNAALADL2_like PA_hNAALADL2_like: Protease-associated domain containing proteins like human N-acetylated alpha-linked acidic dipeptidase-like 2 protein (hNAALADL2). This group contains various PA domain-containing proteins similar to hNAALADL2. The function of hNAALADL2 is unknown. This gene has been mapped to a chromosomal region associated with Cornelia de Lange syndrome. The significance of the PA domain to hNAALADL2 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=98.18 E-value=3e-06 Score=74.94 Aligned_cols=73 Identities=12% Similarity=0.097 Sum_probs=54.8
Q ss_pred CCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecccccc------------ccccCCC---------------CCCCC
Q 017077 5 KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELY------------KMVCDPD---------------ETDLD 57 (378)
Q Consensus 5 ~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~~~------------~m~~~~~---------------~~~~~ 57 (378)
+++|||+|++.|+....+|++|||++||.|+|+|.|..+.. ......+ +...-
T Consensus 38 ~v~GkIvi~RyG~~~RG~Kv~~A~~~GA~GviIYsDP~d~~~~~~~~~~v~~v~~~~~GDP~TPG~PS~~~~~R~~~~~l 117 (153)
T cd02131 38 NVTNQIALLKLGQAPLLYKLSLLEEAGFGGVLLYVDPCDLPKTRHTWHQAFMVSLNPGGDPSTPGYPSADQSCRQCRGNL 117 (153)
T ss_pred CccceEEEEeccCcchHHHHHHHHHCCCeEEEEecChhhccCcCCCccceEEEecCCCCCCCCCCCccccCcccCCcCCC
Confidence 68999999999999999999999999999999999753210 0000000 01122
Q ss_pred cceeEEEEehhchHhHHHHh
Q 017077 58 IHIPAVMMPQDAGASLEKML 77 (378)
Q Consensus 58 i~IPvv~Is~~~G~~L~~~l 77 (378)
.+||+.-||..|++.|+++-
T Consensus 118 P~IPs~PIS~~dA~~lL~~~ 137 (153)
T cd02131 118 TSLLVQPISAYLAKKLLSAP 137 (153)
T ss_pred CCCcccccCHHHHHHHHhCC
Confidence 46999999999999988754
No 31
>cd04822 PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt
Probab=98.16 E-value=7.5e-06 Score=72.76 Aligned_cols=70 Identities=16% Similarity=0.134 Sum_probs=49.6
Q ss_pred CCCCCcEEEEEcCC------------------CCHHHHHHHHHHcCCcEEEEEeccccccccccCCCCCCCCcceeEEEE
Q 017077 4 HKYAGDVIMVDRGN------------------CKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMM 65 (378)
Q Consensus 4 ~~l~g~IaLV~RG~------------------CtF~~K~~nAq~aGA~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~I 65 (378)
.|++||||||.||+ |++.+|+++|+++||+|||+||+.++... ..+....... -.++.+
T Consensus 44 iDVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~aVIv~~d~~~~~~--~~~~~~~~~~-~~~~~~ 120 (151)
T cd04822 44 LDVKGKIVLVLRHEPQEDDANSRFNGPGLTRHAGLRYKATNARRHGAAAVIVVNGPNSHSG--DADRLPRFGG-TAPQRV 120 (151)
T ss_pred CCCCCeEEEEEcCCcccccccccccccccccccCHHHHHHHHHHCCCeEEEEEeCCcccCc--ccccccccCc-cceEEe
Confidence 47999999999985 99999999999999999999998654311 0000000011 127778
Q ss_pred ehhchHhHHHH
Q 017077 66 PQDAGASLEKM 76 (378)
Q Consensus 66 s~~~G~~L~~~ 76 (378)
+....+.+..+
T Consensus 121 ~~~~~~~~~~~ 131 (151)
T cd04822 121 DIAAADPWFTA 131 (151)
T ss_pred chHHHHHHhhh
Confidence 87777777664
No 32
>cd04814 PA_M28_1 PA_M28_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies, relatively little is known a
Probab=98.15 E-value=3.2e-06 Score=74.35 Aligned_cols=39 Identities=28% Similarity=0.399 Sum_probs=36.5
Q ss_pred CCCCCcEEEEEcCCC------------------CHHHHHHHHHHcCCcEEEEEeccc
Q 017077 4 HKYAGDVIMVDRGNC------------------KFTTKANIAEAAGASALLIINNQK 42 (378)
Q Consensus 4 ~~l~g~IaLV~RG~C------------------tF~~K~~nAq~aGA~avIV~n~~~ 42 (378)
.|++||||||.||+| ++.+|.++|+++||+|+|++|+.+
T Consensus 44 ~DVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~gvIii~~~~ 100 (142)
T cd04814 44 LDVKGKVVVVLRNDPQGEPGAGDFGGKAMTYYGRWTYKYEEAARHGAAGVLIVHELA 100 (142)
T ss_pred CCCCCcEEEEEcCCCCcccccccccccccccccCHHHHHHHHHHCCCcEEEEEeCCC
Confidence 489999999999999 689999999999999999999865
No 33
>cd04820 PA_M28_1_1 PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt
Probab=98.05 E-value=6.6e-06 Score=72.00 Aligned_cols=40 Identities=23% Similarity=0.344 Sum_probs=36.5
Q ss_pred CCCCCcEEEEEcCCCC------------HHHHHHHHHHcCCcEEEEEecccc
Q 017077 4 HKYAGDVIMVDRGNCK------------FTTKANIAEAAGASALLIINNQKE 43 (378)
Q Consensus 4 ~~l~g~IaLV~RG~Ct------------F~~K~~nAq~aGA~avIV~n~~~~ 43 (378)
.|++|||||++||+|. +.+|.++|+++||+|+|++|+...
T Consensus 46 iDVkGKIVlv~~g~p~~~~~~~~~~~~~~~~K~~~A~~~GA~aVIi~~d~~~ 97 (137)
T cd04820 46 LDVKGKIVVVLSGGPAGIPSEEGAHAHSSNEKARYAAKAGAIGMITLTTPRS 97 (137)
T ss_pred CCCCCeEEEEEcCCCCccccccccccccHHHHHHHHHHCCCeEEEEEeCCcc
Confidence 4899999999999994 889999999999999999998653
No 34
>cd04821 PA_M28_1_2 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt
Probab=96.05 E-value=0.008 Score=53.87 Aligned_cols=39 Identities=21% Similarity=0.298 Sum_probs=32.9
Q ss_pred CCCCCcEEEEEcCCCCHH-------------------HHHHHHHHcCCcEEEEEeccc
Q 017077 4 HKYAGDVIMVDRGNCKFT-------------------TKANIAEAAGASALLIINNQK 42 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~-------------------~K~~nAq~aGA~avIV~n~~~ 42 (378)
-|++||||++.+|+=.+. .|.+.|+++||+|+|++++..
T Consensus 46 ~DVkGKiVvvl~~~P~~~~~~~~~f~~~~~~~~~~~~~K~~~A~~~GA~gvi~v~~~~ 103 (157)
T cd04821 46 LDVKGKTVVILVNDPGFATPDSGLFNGKAMTYYGRWTYKYEEAARQGAAGALIVHETE 103 (157)
T ss_pred CCcCCcEEEEEcCCCCcccccccccCcccccccccHHHHHHHHHHCCCeEEEEEeCCC
Confidence 489999999998865433 499999999999999998753
No 35
>KOG2195 consensus Transferrin receptor and related proteins containing the protease-associated (PA) domain [Posttranslational modification, protein turnover, chaperones; Inorganic ion transport and metabolism; General function prediction only]
Probab=80.41 E-value=1.9 Score=47.35 Aligned_cols=38 Identities=26% Similarity=0.406 Sum_probs=35.0
Q ss_pred CCCCcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEeccc
Q 017077 5 KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQK 42 (378)
Q Consensus 5 ~l~g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~~ 42 (378)
+++|+|++++-|.-...+|++||+++||.|+++|.+..
T Consensus 182 ~~~g~i~l~r~~~i~~g~~~~na~~~~a~gviiy~d~~ 219 (702)
T KOG2195|consen 182 NLSGKIVLARVGKIYRGKKVKNAEAAGADGVIIYTDPY 219 (702)
T ss_pred cccCceEEEEccccchhhhHhhHHHhhcCcEEEeeccc
Confidence 47899999999999999999999999999999998643
No 36
>COG4882 Predicted aminopeptidase, Iap family [General function prediction only]
Probab=61.95 E-value=34 Score=34.98 Aligned_cols=90 Identities=19% Similarity=0.158 Sum_probs=56.4
Q ss_pred CCCCCcEEEEEcCCCCHHHHH--HHHHHcCCcEEEEEeccccccccccCCCC---CCCCcceeEEEEehhchHhHHHHhh
Q 017077 4 HKYAGDVIMVDRGNCKFTTKA--NIAEAAGASALLIINNQKELYKMVCDPDE---TDLDIHIPAVMMPQDAGASLEKMLL 78 (378)
Q Consensus 4 ~~l~g~IaLV~RG~CtF~~K~--~nAq~aGA~avIV~n~~~~~~~m~~~~~~---~~~~i~IPvv~Is~~~G~~L~~~l~ 78 (378)
.|..|++++-+|-.--...|. ..|.++||.|+|+-.+.+....- ..+-. ......||++.+...++....+
T Consensus 86 gD~~Gr~~Va~~pq~vdd~k~~~i~Aae~ga~a~~f~~~~~rriV~-~Gd~gy~~~s~PtPIPva~v~en~~~y~~~--- 161 (486)
T COG4882 86 GDAGGRVVVARAPQVVDDLKAAAILAAEAGAEALLFESRDPRRIVT-GGDWGYSVSSSPTPIPVAVVPENYSRYAEE--- 161 (486)
T ss_pred CCCCCeEEeeeccccHHHHHHHHHHHHHcCCeEEEEecCCceeEEe-cccccccCCCCCCCcceEEeccCcchhhcc---
Confidence 467788887777555555554 37899999999998876543111 11111 1123479999999999987754
Q ss_pred ccceEEEEEecCCCCccchh
Q 017077 79 NTSSVSVQLYSPRRPVVDVA 98 (378)
Q Consensus 79 ~G~~V~v~l~~p~~~~~D~s 98 (378)
.+.+++..+.......||+
T Consensus 162 -~~rvrl~vD~~~~~ty~y~ 180 (486)
T COG4882 162 -AGRVRLWVDACVERTYDYN 180 (486)
T ss_pred -ceeEEEEEecccceeEEEE
Confidence 2456666665544444443
No 37
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.34 E-value=1.8 Score=42.74 Aligned_cols=32 Identities=9% Similarity=0.008 Sum_probs=28.8
Q ss_pred EEEcCCCCHHHHHHHHHHcCCcEEEEEecccc
Q 017077 12 MVDRGNCKFTTKANIAEAAGASALLIINNQKE 43 (378)
Q Consensus 12 LV~RG~CtF~~K~~nAq~aGA~avIV~n~~~~ 43 (378)
.++||||+..+|.+.+|+.|-+|+|..++.+.
T Consensus 151 ~~~rgn~t~~d~~rer~r~~fkgvi~Gs~r~~ 182 (374)
T COG5540 151 CNRRGNETEEDPTRERRRTRFKGVIRGSERNG 182 (374)
T ss_pred HHHccCccccCccccchhccccceeeccccCC
Confidence 45799999999999999999999999998654
No 38
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=48.91 E-value=50 Score=24.53 Aligned_cols=16 Identities=31% Similarity=0.372 Sum_probs=10.0
Q ss_pred hccceEEEEEecCCCC
Q 017077 78 LNTSSVSVQLYSPRRP 93 (378)
Q Consensus 78 ~~G~~V~v~l~~p~~~ 93 (378)
++...|++++..-..+
T Consensus 2 qN~~~V~v~~~~~~~~ 17 (68)
T PF06305_consen 2 QNTQPVTVNFLFGQFP 17 (68)
T ss_pred CCCceEEEEEEeeecc
Confidence 4556788887654433
No 39
>PRK11588 hypothetical protein; Provisional
Probab=48.79 E-value=2.9e+02 Score=29.57 Aligned_cols=43 Identities=9% Similarity=0.371 Sum_probs=25.9
Q ss_pred eeecccchhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhH
Q 017077 151 VDINTASAVLFVLVASCFLVMLYKLMS-NWFLELLVILFCIGGV 193 (378)
Q Consensus 151 ~~~s~~~a~~fpv~~s~~Ll~ly~f~~-~~~~~~l~~~f~~~g~ 193 (378)
.++|.+|-+..-++........|=..+ .|...=+..+|.+.|+
T Consensus 280 ~~~t~r~klvL~~f~~~~~~~i~Gv~~~gW~~~Eia~~Fl~~gi 323 (506)
T PRK11588 280 RPFTFGDWLVLLVLTAVMVWVIWGVVVNAWFIPEIASQFFTMGL 323 (506)
T ss_pred cCcChhhHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence 479999988877776666666664332 2322234555655554
No 40
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.31 E-value=19 Score=36.31 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=18.6
Q ss_pred hHHHHHhhhhhhhcCccchhHHhHHH
Q 017077 234 FCIAFAVVWAIYRKVSFAWIGQDILG 259 (378)
Q Consensus 234 ~~~~~~~~w~~~~~~~~~W~l~ni~g 259 (378)
=+++++++|++++-..--|++-|++.
T Consensus 239 RlILF~I~~il~~g~~g~W~FPNL~e 264 (372)
T KOG2927|consen 239 RLILFGITWILTGGKHGFWLFPNLTE 264 (372)
T ss_pred HHHHHHHHHHHhCCCCceEeccchhh
Confidence 35677889999883233688888876
No 41
>PF06541 DUF1113: Protein of unknown function (DUF1113); InterPro: IPR010540 This family consists of several bacterial proteins of unknown function.
Probab=40.84 E-value=2.4e+02 Score=24.99 Aligned_cols=26 Identities=15% Similarity=0.223 Sum_probs=18.5
Q ss_pred HHhcccCchhHHHHHHHHHHHhhhhh
Q 017077 267 LQIVHIPNLKVGTVLLSCAFMYDIFW 292 (378)
Q Consensus 267 i~~~~l~~~k~~~~lL~~lf~YDif~ 292 (378)
++.+.-...+..+.++.++++.|...
T Consensus 129 ~~~i~~~~~~~~~~~l~~~~~~D~~~ 154 (157)
T PF06541_consen 129 LSKIPPIIRNILALVLLALFLIDFVF 154 (157)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455677888889999999764
No 42
>PRK03955 hypothetical protein; Reviewed
Probab=31.62 E-value=1.7e+02 Score=25.44 Aligned_cols=71 Identities=14% Similarity=0.085 Sum_probs=43.4
Q ss_pred CCCCCcEEEEE--cCCCCHHHHHHHHHHcCC-cEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhcc
Q 017077 4 HKYAGDVIMVD--RGNCKFTTKANIAEAAGA-SALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNT 80 (378)
Q Consensus 4 ~~l~g~IaLV~--RG~CtF~~K~~nAq~aGA-~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G 80 (378)
++++|||.+.. ||.|.=.-=...+.+.|- =+.||..+.+......+- --.||++.-. . .+.++.|
T Consensus 47 ~si~gkIlv~p~~kGSt~gs~vl~~l~~~g~aP~aiI~~~~~~ils~GaI------vAgIP~V~~~-----~-~~~l~~G 114 (131)
T PRK03955 47 ESIKGKILVFPHGKGSTVGSYVIYQLAKNGTAPKAIINLEAEPIVATGAI------ISGIPLVDKV-----D-ISKLKDG 114 (131)
T ss_pred CccCCEEEEEeCCCcccchHHHHHHHHHcCCCceEEEEecCCceeEeeee------ecCCceEccc-----c-ceecCCC
Confidence 46799999886 788975555555555543 355666655544332211 1168888622 2 4567789
Q ss_pred ceEEEE
Q 017077 81 SSVSVQ 86 (378)
Q Consensus 81 ~~V~v~ 86 (378)
..|++.
T Consensus 115 ~~V~Vd 120 (131)
T PRK03955 115 DRVVVD 120 (131)
T ss_pred CEEEEe
Confidence 888875
No 43
>COG1786 Swiveling domain associated with predicted aconitase [Energy production and conversion]
Probab=31.32 E-value=1e+02 Score=26.81 Aligned_cols=73 Identities=16% Similarity=0.142 Sum_probs=48.2
Q ss_pred CCCCCcEEEEE--cCCCCHHHHHHHHHHcC-CcEEEEEeccccccccccCCCCCCCCcceeEEEEehhchHhHHHHhhcc
Q 017077 4 HKYAGDVIMVD--RGNCKFTTKANIAEAAG-ASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNT 80 (378)
Q Consensus 4 ~~l~g~IaLV~--RG~CtF~~K~~nAq~aG-A~avIV~n~~~~~~~m~~~~~~~~~~i~IPvv~Is~~~G~~L~~~l~~G 80 (378)
++++|||.+.. ||.|.=.-=...+.+.| |-+.|+.-+.+..+...+- --.||.+-... .+.+.++.|
T Consensus 47 ~~l~Gkilv~P~grGStvGSyVl~~l~~~G~AP~aIv~~e~EpIla~Gai------~a~iPlv~~~~----e~~~~l~~g 116 (131)
T COG1786 47 ESLTGKILVFPGGRGSTVGSYVLYELAKNGRAPAAIVNEEAEPILAVGAI------LAGIPLVDGVD----EFFEELKTG 116 (131)
T ss_pred ccccceEEEeeCCCCccccHHHHHHHHHcCCCchhhhhcCCcceeeehhh------hcCCceEeccH----HHHHHhccC
Confidence 47899999986 78898777788888888 4455555544443332221 12688876654 366667778
Q ss_pred ceEEEE
Q 017077 81 SSVSVQ 86 (378)
Q Consensus 81 ~~V~v~ 86 (378)
..|++.
T Consensus 117 ~~v~v~ 122 (131)
T COG1786 117 DRVRVN 122 (131)
T ss_pred CEEEEc
Confidence 777764
No 44
>PRK03427 cell division protein ZipA; Provisional
Probab=30.46 E-value=40 Score=33.91 Aligned_cols=26 Identities=15% Similarity=0.423 Sum_probs=21.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhhhHH
Q 017077 98 AEVFLWLMAVGTILCASYWSAWSARE 123 (378)
Q Consensus 98 s~~~l~l~Av~tv~~gs~~s~~~~~~ 123 (378)
-++++..+|++.+.+-|+|+.|++|.
T Consensus 8 iLivvGAIAIiAlL~HGlWtsRKers 33 (333)
T PRK03427 8 ILIIVGAIAIIALLVHGFWTSRKERS 33 (333)
T ss_pred HHHHHHHHHHHHHHHHhhhhcccccc
Confidence 35677778889999999999887764
No 45
>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=29.76 E-value=1.7e+02 Score=30.70 Aligned_cols=14 Identities=36% Similarity=0.862 Sum_probs=8.8
Q ss_pred cccchhhhH--HHHHH
Q 017077 338 IGFGDILLP--GLIIA 351 (378)
Q Consensus 338 LGlGDiviP--Gl~i~ 351 (378)
=|+|+.+-| |.+++
T Consensus 414 ~gl~n~isPtsg~~m~ 429 (465)
T PF03606_consen 414 DGLGNSISPTSGVLMA 429 (465)
T ss_pred HHHHhhccchHHHHHH
Confidence 467777777 34444
No 46
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=20.89 E-value=2.3e+02 Score=21.44 Aligned_cols=34 Identities=24% Similarity=0.275 Sum_probs=26.6
Q ss_pred CcEEEEEcCCCCHHHHHHHHHHcCCcEEEEEecc
Q 017077 8 GDVIMVDRGNCKFTTKANIAEAAGASALLIINNQ 41 (378)
Q Consensus 8 g~IaLV~RG~CtF~~K~~nAq~aGA~avIV~n~~ 41 (378)
|.-+.++-.+-++..|.+.|++.|+..+++++..
T Consensus 28 g~~v~~d~~~~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 28 GIRVEVDLRNEKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred CCEEEEECCCCCHHHHHHHHHHcCCCEEEEECcc
Confidence 4445554445799999999999999999999854
No 47
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=20.65 E-value=1.9e+02 Score=22.75 Aligned_cols=69 Identities=12% Similarity=0.155 Sum_probs=38.4
Q ss_pred CCcEEEEEcC-----CCCHHHHHHHH-HHcCCcEEEEEeccccc---cccccCCCCCCCCcceeEEEEehh---chHhHH
Q 017077 7 AGDVIMVDRG-----NCKFTTKANIA-EAAGASALLIINNQKEL---YKMVCDPDETDLDIHIPAVMMPQD---AGASLE 74 (378)
Q Consensus 7 ~g~IaLV~RG-----~CtF~~K~~nA-q~aGA~avIV~n~~~~~---~~m~~~~~~~~~~i~IPvv~Is~~---~G~~L~ 74 (378)
+++|++...| .|.+-.|++.. ++.|.. .-.+|-.++. -.+.. .....++|.++|... ..+.+.
T Consensus 7 ~~~vvvf~k~~~~~~~Cp~C~~ak~~L~~~~i~-y~~idv~~~~~~~~~l~~----~~g~~tvP~vfi~g~~iGG~~~l~ 81 (90)
T cd03028 7 ENPVVLFMKGTPEEPRCGFSRKVVQILNQLGVD-FGTFDILEDEEVRQGLKE----YSNWPTFPQLYVNGELVGGCDIVK 81 (90)
T ss_pred cCCEEEEEcCCCCCCCCcHHHHHHHHHHHcCCC-eEEEEcCCCHHHHHHHHH----HhCCCCCCEEEECCEEEeCHHHHH
Confidence 3678888776 89999999976 555654 3333422211 00100 012246899988754 234455
Q ss_pred HHhhcc
Q 017077 75 KMLLNT 80 (378)
Q Consensus 75 ~~l~~G 80 (378)
+..++|
T Consensus 82 ~l~~~g 87 (90)
T cd03028 82 EMHESG 87 (90)
T ss_pred HHHHcC
Confidence 544444
No 48
>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=20.54 E-value=33 Score=35.37 Aligned_cols=57 Identities=18% Similarity=0.242 Sum_probs=0.0
Q ss_pred hhHHhHHHHHHHHHHH-Hhcc-cCchhHHHHHHHHHHHhhhhheeecccccc-ceeEEEeecCC
Q 017077 252 WIGQDILGIALIITVL-QIVH-IPNLKVGTVLLSCAFMYDIFWVFVSKKLFH-ESVMIVVARGD 312 (378)
Q Consensus 252 W~l~ni~g~~~~~~~i-~~~~-l~~~k~~~~lL~~lf~YDif~Vf~tp~~~~-~svMv~VA~~~ 312 (378)
=.+|-..=++++..+- -.++ +|. ++.-.+|+.+-+||+|-|-.. . | -...|+.|+.-
T Consensus 150 l~l~Q~YLI~is~l~A~~~l~~lPe-WTtW~lL~~iaiyDl~AVL~P-~--GPLr~Lve~a~er 209 (403)
T PF01080_consen 150 LLLQQAYLIMISVLMALFFLKYLPE-WTTWFLLVAIAIYDLFAVLCP-C--GPLRMLVELAQER 209 (403)
T ss_dssp ----------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCc-hHHHHHHHHHHHHHHeeEeCC-C--CcHHHHHHHHHHc
Confidence 3444444444444333 2343 676 567889999999999999853 1 2 35566666654
Done!