Query 009071
Match_columns 544
No_of_seqs 371 out of 1484
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 20:03:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009071.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009071hhsearch_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 9E-130 2E-134 1016.2 36.8 520 17-539 8-534 (541)
2 KOG2443 Uncharacterized conser 100.0 7.4E-67 1.6E-71 527.2 20.7 305 191-530 22-348 (362)
3 PF04258 Peptidase_A22B: Signa 100.0 7E-68 1.5E-72 544.4 -0.0 274 244-521 2-298 (298)
4 smart00730 PSN Presenilin, sig 100.0 2.7E-50 5.9E-55 403.8 20.7 242 248-513 3-249 (249)
5 cd02132 PA_GO-like PA_GO-like: 100.0 7.9E-29 1.7E-33 228.5 16.6 139 46-184 1-139 (139)
6 cd02129 PA_hSPPL_like PA_hSPPL 99.9 3.4E-23 7.3E-28 186.0 11.7 116 47-183 1-119 (120)
7 cd02126 PA_EDEM3_like PA_EDEM3 99.9 5.8E-22 1.3E-26 180.0 12.8 116 66-184 2-126 (126)
8 cd02127 PA_hPAP21_like PA_hPAP 99.9 5.4E-21 1.2E-25 171.8 13.1 110 70-184 1-116 (118)
9 cd02123 PA_C_RZF_like PA_C-RZF 99.8 2.3E-20 4.9E-25 175.0 14.8 116 60-179 20-142 (153)
10 cd02125 PA_VSR PA_VSR: Proteas 99.8 1.7E-20 3.7E-25 170.6 13.2 102 83-184 11-127 (127)
11 cd02122 PA_GRAIL_like PA _GRAI 99.8 2.3E-20 4.9E-25 172.1 13.1 110 67-184 18-138 (138)
12 cd04818 PA_subtilisin_1 PA_sub 99.8 6.9E-19 1.5E-23 157.4 13.0 114 67-184 1-118 (118)
13 cd04813 PA_1 PA_1: Protease-as 99.8 6.6E-19 1.4E-23 158.1 11.1 103 66-175 5-110 (117)
14 cd04816 PA_SaNapH_like PA_SaNa 99.7 1.6E-17 3.5E-22 149.7 13.3 112 68-184 5-122 (122)
15 KOG3920 Uncharacterized conser 99.7 6.5E-18 1.4E-22 155.2 6.9 164 4-187 2-174 (193)
16 PF06550 DUF1119: Protein of u 99.7 3.2E-16 7E-21 157.2 19.1 173 328-514 95-282 (283)
17 cd02130 PA_ScAPY_like PA_ScAPY 99.7 1.1E-16 2.4E-21 144.2 13.6 98 83-184 22-122 (122)
18 cd02124 PA_PoS1_like PA_PoS1_l 99.7 3.4E-16 7.5E-21 142.8 11.6 89 90-184 38-129 (129)
19 cd04817 PA_VapT_like PA_VapT_l 99.6 2.1E-15 4.5E-20 139.2 13.0 95 82-180 35-137 (139)
20 KOG4628 Predicted E3 ubiquitin 99.6 6.3E-15 1.4E-19 152.9 16.2 108 63-177 35-150 (348)
21 PF02225 PA: PA domain; Inter 99.5 4.1E-14 8.8E-19 121.8 6.5 72 101-174 30-101 (101)
22 cd00538 PA PA: Protease-associ 99.5 1.4E-13 3E-18 122.8 10.2 94 90-184 27-126 (126)
23 COG3389 Uncharacterized protei 99.5 2.5E-13 5.3E-18 132.0 9.7 161 332-510 97-271 (277)
24 cd02133 PA_C5a_like PA_C5a_lik 99.4 5.5E-12 1.2E-16 116.7 12.7 94 82-185 25-121 (143)
25 cd04819 PA_2 PA_2: Protease-as 99.3 2E-11 4.3E-16 111.1 12.1 99 83-183 23-126 (127)
26 cd04815 PA_M28_2 PA_M28_2: Pro 99.2 1.8E-11 3.8E-16 112.5 8.2 104 81-184 15-134 (134)
27 cd02120 PA_subtilisin_like PA_ 99.1 1.8E-10 4E-15 103.4 9.4 83 92-180 36-122 (126)
28 cd02128 PA_TfR PA_TfR: Proteas 98.7 6.9E-08 1.5E-12 93.1 10.6 90 83-175 29-154 (183)
29 cd04822 PA_M28_1_3 PA_M28_1_3: 98.2 9.2E-06 2E-10 76.3 10.7 89 83-174 20-132 (151)
30 cd04814 PA_M28_1 PA_M28_1: Pro 98.1 7.8E-06 1.7E-10 76.0 7.7 89 83-172 20-133 (142)
31 cd02121 PA_GCPII_like PA_GCPII 98.1 8.2E-06 1.8E-10 81.2 7.5 90 83-175 45-188 (220)
32 cd04820 PA_M28_1_1 PA_M28_1_1: 98.1 1.1E-05 2.3E-10 74.7 7.5 59 82-140 21-97 (137)
33 cd02131 PA_hNAALADL2_like PA_h 97.9 3.1E-05 6.7E-10 72.4 6.8 75 101-175 37-138 (153)
34 cd04821 PA_M28_1_2 PA_M28_1_2: 94.3 0.054 1.2E-06 51.4 4.4 39 101-139 46-103 (157)
35 KOG2736 Presenilin [Signal tra 94.3 1.7 3.6E-05 46.5 15.5 68 433-510 320-387 (406)
36 PF01080 Presenilin: Presenili 92.5 0.21 4.5E-06 54.1 5.7 64 433-507 326-390 (403)
37 KOG2195 Transferrin receptor a 62.2 8.6 0.00019 44.9 4.2 39 101-139 181-219 (702)
38 PRK11588 hypothetical protein; 50.3 1.1E+02 0.0023 34.7 10.1 43 248-290 280-323 (506)
39 KOG2927 Membrane component of 42.6 20 0.00043 38.3 2.8 26 332-357 240-265 (372)
40 PF06305 DUF1049: Protein of u 36.8 96 0.0021 24.5 5.4 55 175-230 2-58 (68)
41 PF06541 DUF1113: Protein of u 36.2 3E+02 0.0064 25.9 9.5 26 364-389 129-154 (157)
42 COG1786 Swiveling domain assoc 33.1 1.4E+02 0.003 27.7 6.3 73 101-183 47-122 (131)
43 PF03606 DcuC: C4-dicarboxylat 31.5 1.2E+02 0.0026 33.6 6.9 15 435-449 414-430 (465)
44 PF07895 DUF1673: Protein of u 22.8 6.5E+02 0.014 24.9 9.6 13 378-390 168-180 (205)
45 PF01080 Presenilin: Presenili 21.8 30 0.00066 37.8 0.0 42 350-392 151-194 (403)
46 COG4882 Predicted aminopeptida 21.5 3.5E+02 0.0075 29.6 7.6 89 102-195 87-180 (486)
47 PF06624 RAMP4: Ribosome assoc 20.3 63 0.0014 26.2 1.5 14 253-266 42-55 (63)
48 PRK03955 hypothetical protein; 20.0 3.5E+02 0.0075 25.1 6.5 70 102-183 48-120 (131)
No 1
>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=100.00 E-value=8.6e-130 Score=1016.16 Aligned_cols=520 Identities=50% Similarity=0.856 Sum_probs=492.5
Q ss_pred HHHhccccccCCCccccCCCCCCCCCCCcceEEEEEEeeeCCccceeEEecccCcCCcccccccCcceEEEeecCCCCCC
Q 009071 17 SLVCYPASVTAGDIVHDDDLAPKKPGCENDFVLVKVQTWIDGIENEEFVGVGARFGTTIVSKEKNANQIHLTLSHPRDCC 96 (544)
Q Consensus 17 ~~~~~~~~~~~~~~~~~d~~~p~~p~c~~~f~lv~v~~~~~G~e~~~~~~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC 96 (544)
+++-.....+++|..|+++..|++|||+|+||++|+++|+||++..++.+..++||..++...+++...++..++|.|.|
T Consensus 8 ~l~g~~~~v~a~~~~~~~~~~~~s~gc~nd~~~l~~~~w~~~~~~~~~a~~~~~~~~t~~~~~~~a~~~~~a~~~pld~c 87 (541)
T KOG2442|consen 8 LLLGLGSFVTAGDGGHTGNSHPKSPGCSNDFQMLKVPTWVNGVEYLEFAGMLARFGITLPSKCKAADIPHLAQVDPLDSC 87 (541)
T ss_pred hhhhhhheEeecccccccccccCCCCCcCceEEEeccccccccchhhhhhhhhhcCCcCCCCccccccchhhhcCCcccc
Confidence 33333566788999999999999999999999999999999999999999999999999988877777788889999999
Q ss_pred CCCCCCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhhHHHHHHHhc
Q 009071 97 SMPKHKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLN 176 (544)
Q Consensus 97 ~~~~~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~ 176 (544)
+++++.++|+++++.||+|+|++|+++||++||+|++|+||.+++..|.|++.++..+++||++||++++|+++.+....
T Consensus 88 s~~~~kl~~~~~~v~RGnC~Ft~Ka~~Aq~aGAsaLliin~~~d~~~~~~~~~~~~~dv~IPv~mi~~~~~~~l~~~~~~ 167 (541)
T KOG2442|consen 88 STLQSKLSGKVALVFRGNCSFTEKAKLAQAAGASALLIINNKKDLLFMPCGNKETSLDVTIPVAMISYSDGRDLNKSTRS 167 (541)
T ss_pred CCCCccccceeEEEecccceeehhhhhhhhcCceEEEEEcCchhhccCCCCCCCccccccceEEEEEhhhHHHHHhhhcc
Confidence 99999999999999999999999999999999999999999999999999988888999999999999999999999999
Q ss_pred cceEEEEeecCCCcccchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhccccCCCccccccCCCCeeeeccccch
Q 009071 177 TSSVSVQLYSPRRPVVDVAEVFLWLMAVGTILCASYWSAWSARETAIEQEKLLKDAVDEIPDAKAVGVSGVVDINTASAV 256 (544)
Q Consensus 177 G~~V~V~l~~p~~p~vD~s~~~L~l~Av~tV~~gs~ws~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~a~ 256 (544)
+++|++++|+|++|.+|++++++|+|||+||.+|+|||++++||+..|+++.++|..+++.+.+|++|++..++|+..|+
T Consensus 168 ~~~V~~~lYaPk~P~vD~~~v~iwlmAVgTVa~ggyWs~~t~~~~~~~a~~~~~d~~s~~~~~~~~~e~~~vd~s~i~~~ 247 (541)
T KOG2442|consen 168 NDNVELALYAPKRPAVDYAMVFIWLMAVGTVACGGYWSGLTEREKAIEADRLLDDDSSSEGNTKETKEEEVVDISPITAV 247 (541)
T ss_pred CCeEEEEEECCCCCCccHHHHHHHHHHHhHhhccchhhhccChhhhhhhhhhcccccccccccccCCccccEEeeeeEEE
Confidence 99999999999999999999999999999999999999999999999999988887777778888889999999999999
Q ss_pred hhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhcCCceeeeccccccccchhhhhhhHHHhh
Q 009071 257 LFVLVASCFLVMLYKLMSNWFLELLVILFCIGGVEGLQTCLVALLSRWFRRAGESFIKVPFFGAVSHLTLAVTPFCIAFA 336 (544)
Q Consensus 257 ~f~v~as~~L~~ly~f~~~~~~~~l~~~f~i~g~~~l~~~l~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~~~~ 336 (544)
.|++++|.+|++||||++ |++++++++|||+|+.+|++|+.+++.|++.+..+.....|..|..++..+++.++|++++
T Consensus 248 ~fvv~~c~~LvLlyfF~~-~~V~v~iiif~i~g~~gLy~Cl~~lv~r~~~~~~~~~~~~~~l~~~~~~~l~l~~~Cia~a 326 (541)
T KOG2442|consen 248 FFVVTACGFLVLLYFFYS-YLVYVLIIIFCIGGAQGLYNCLAALVHRLPYGAARFPTLAPRLGNMSYRLLFLSILCIAVA 326 (541)
T ss_pred EehhhhHHHHHHHHHHHH-HHHHHHhhheeecccchHHHHHHHHHhhhhhhcccccccccccCChhHHHHHHHHhhhhee
Confidence 999999999999999996 5999999999999999999999999999987665566677888999999999999999999
Q ss_pred hhhheeecCccchhHHHHHHHHHHHHHHHhcccCchhHHHHHHHHHHHhhhheeeecccccc--ceeEEEecccCCCCCC
Q 009071 337 VVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFMYDIFWVFVSKKLFH--ESVMIVVARGDKSGED 414 (544)
Q Consensus 337 ~~w~~~~~~~~~W~~~nilgi~~~~~~i~~~~l~s~k~~~ilL~~lf~YDif~Vf~sp~~~~--~sVMv~VA~~~~~~~~ 414 (544)
++|+++||++|+|++||++|||+|++++|.+|+||+|++++||+++|+|||||||+||++|+ ||||++||+|.++++|
T Consensus 327 V~W~v~R~e~~AwilqDvLGIalci~vLk~vRLPnlK~~tiLL~c~f~YDiF~VFitp~~t~~geSVMieVA~G~~s~~E 406 (541)
T KOG2442|consen 327 VVWAVFRNEDWAWILQDVLGIALCITVLKTVRLPNLKVCTILLLCLFLYDIFFVFITPFITKNGESVMIEVARGPSSTEE 406 (541)
T ss_pred EEEEEeecCchHHHHHhhHhHHHHHHHHHHhcCCchhHHHHHHHHHHHHhhheeeeehhhccCCceEEEEEecCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999998 9999999999999999
Q ss_pred CCCEEEEecccc-----CCCCCeeeecCCCchhhHHHHHHHHhhcccccccccchhHHHHHHHHHHHHHHHHHHHHhhcC
Q 009071 415 GIPMLLKIPRMF-----DPWGGYSIIGFGDILLPGLIIAFSLRYDWLANKSLQAGYFLWAMLAYGLGLLITYVALNLMDG 489 (544)
Q Consensus 415 ~~P~~l~~P~~~-----~~~~~~s~LGlGDIviPGl~ia~~~rfD~~~~~~~~~~YF~~~~igY~~GL~~t~~~~~~~~~ 489 (544)
++||++++||++ ++|++|||||||||++||++|+||+|||...++. ++.||.++++||++||++||+|+++| +
T Consensus 407 kiPMlLkVPrl~~s~~~~~~~~~silGFGDIl~PGlLVa~c~RfD~~~~~~-~~iYfv~~tvaYgiGLlvTfvaL~LM-~ 484 (541)
T KOG2442|consen 407 KIPMLLKVPRLFFSVLSDPWGGYSILGFGDILVPGLLVAFCLRFDVQVNSV-SNIYFVWSTVAYGIGLLVTFVALVLM-K 484 (541)
T ss_pred CcceEEEcchhccccccccCCCeeEeeecccccchHHHHHHHHhhhhcccc-ceeEEehhHHHHHHHHHHHHHHHHHh-c
Confidence 999999999999 8899999999999999999999999999988875 68999999999999999999999999 6
Q ss_pred CCcceecccchhhhHHHHHHHhhccchhhhccccCCCCCCCCCCcCCccc
Q 009071 490 HGQPALLYIVPFTLGTFLALGKKRGDLRVLWTRGEPERPCPHVHLQHSHE 539 (544)
Q Consensus 490 ~~QPALlYlvP~~l~~~~~~a~~rgel~~lw~~~~~~~~~~~~~~~~~~~ 539 (544)
.|||||||||||||++.+++|++|||++++|+|..++..++|.+.++++.
T Consensus 485 ~GQPALLYLVP~TL~t~~~lal~R~El~~fWtg~~~~~~~~~~~~~p~~~ 534 (541)
T KOG2442|consen 485 GGQPALLYLVPCTLGTAVVLALCRGELKKFWTGGSYQKMPAPNDLNPKPI 534 (541)
T ss_pred CCCceEEEEechHHHHHHHHHHHHHHHHHHhccCCcccCCCCCcCCCCcC
Confidence 69999999999999999999999999999999999999888877777643
No 2
>KOG2443 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7.4e-67 Score=527.18 Aligned_cols=305 Identities=31% Similarity=0.543 Sum_probs=257.8
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhccccCCCccccccCCCCeeeeccccchh-hhHHHHHHHHHH
Q 009071 191 VVDVAEVFLWLMAVGTILCASYWSAWSARETAIEQEKLLKDAVDEIPDAKAVGVSGVVDINTASAVL-FVLVASCFLVML 269 (544)
Q Consensus 191 ~vD~s~~~L~l~Av~tV~~gs~ws~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~a~~-f~v~as~~L~~l 269 (544)
..+.+.+.+.+||+.+|++|++||....+|. +++++..+.++.++|.. ||++|||+|++|
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 5678899999999999999999998765431 11124455677888887 999999999999
Q ss_pred HHHhHHH---HHHHHHHHHHHHhHHHHHHHHHHHHHHh----hh---------hcCCceeeeccccccccchhhhhhhHH
Q 009071 270 YKLMSNW---FLELLVILFCIGGVEGLQTCLVALLSRW----FR---------RAGESFIKVPFFGAVSHLTLAVTPFCI 333 (544)
Q Consensus 270 y~f~~~~---~~~~l~~~f~i~g~~~l~~~l~~~~~~~----~~---------~~~~~~~~~p~~~~~~~~~l~~~~~~~ 333 (544)
|++++.. ...+++.||++.|+.++.+.+.++++.. .+ +....+...-+.++++..+++.+..|.
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 9987643 2347899999999999999999988721 11 111111112234678888999999999
Q ss_pred HhhhhhheeecCccchhHHHHHHHHHHHHHHHhcccCchhHHHHHHHHHHHhhhheeeeccccccceeEEEecccCCCCC
Q 009071 334 AFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVARGDKSGE 413 (544)
Q Consensus 334 ~~~~~w~~~~~~~~~W~~~nilgi~~~~~~i~~~~l~s~k~~~ilL~~lf~YDif~Vf~sp~~~~~sVMv~VA~~~~~~~ 413 (544)
.+++.|+.++| |++||++|+++|++.|+.+||||+|+|++||.++|+|||||||+| +||++|||+.+
T Consensus 163 ~i~v~~ll~~H----Wl~nN~lgms~~I~~I~~lrL~s~ktgalLL~gLffYDIfwVFgT------nVMVtVAt~~D--- 229 (362)
T KOG2443|consen 163 MIVVWYLLTKH----WLANNLLGMSFCIAGIEFLRLPSLKTGALLLGGLFFYDIFWVFGT------NVMVTVATSLD--- 229 (362)
T ss_pred HHHHHHHhhhH----HHHHhHHHHHHHHHHHHHhcccchhhhHHHHHHHHHHheEEEecC------ceEEEeecccC---
Confidence 99999999885 999999999999999999999999999999999999999999975 69999999964
Q ss_pred CCCCEEEEeccccCCC----CCeeeecCCCchhhHHHHHHHHhhcccccc-cccchhHHHHHHHHHHHHHHHHHHHHhhc
Q 009071 414 DGIPMLLKIPRMFDPW----GGYSIIGFGDILLPGLIIAFSLRYDWLANK-SLQAGYFLWAMLAYGLGLLITYVALNLMD 488 (544)
Q Consensus 414 ~~~P~~l~~P~~~~~~----~~~s~LGlGDIviPGl~ia~~~rfD~~~~~-~~~~~YF~~~~igY~~GL~~t~~~~~~~~ 488 (544)
+|+|+++|+..... .+|||||||||||||+|+|+++|||.++++ +..+.||..+++||.+||..|+++|+++
T Consensus 230 --~PikL~fP~~l~~~~~~as~fsMLGLGDIviPGiflAl~lRfD~~k~~~s~~~~YF~~t~i~Y~~gL~~ti~~~~~F- 306 (362)
T KOG2443|consen 230 --APIKLVFPQKLLFPGLTASNFSMLGLGDIVIPGIFLALVLRFDIRKKRNSKVRTYFHNTFIAYFLGLLTTIVVLHIF- 306 (362)
T ss_pred --CceEEecchhhccCCCccccceeccccchhhHHHHHHHHHHhhHHHHhcccCceEEEEeHHHHHhhhHHHhhhhhhh-
Confidence 89999999976543 359999999999999999999999987653 2457899999999999999999999999
Q ss_pred CCCcceecccchhhhHHHHHHHhhccchhhhccccCCCCCCC
Q 009071 489 GHGQPALLYIVPFTLGTFLALGKKRGDLRVLWTRGEPERPCP 530 (544)
Q Consensus 489 ~~~QPALlYlvP~~l~~~~~~a~~rgel~~lw~~~~~~~~~~ 530 (544)
+++||||||+||+|+++.+++|++|||++.+|+++++...++
T Consensus 307 kaAQPALLYlVP~~l~~~ll~A~~~gdlk~l~s~~~~~~~~~ 348 (362)
T KOG2443|consen 307 KAAQPALLYLVPACLGPLLLMAYWRGDLKVLWSFDESTKEES 348 (362)
T ss_pred hccchhhhhhhHHHHhHHHHHHHHccchHhhhCccccCCCCc
Confidence 999999999999999999999999999999999998654444
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=7e-68 Score=544.39 Aligned_cols=274 Identities=41% Similarity=0.752 Sum_probs=1.0
Q ss_pred CCCeeeeccccchhhhHHHHHHHHHHHHHhHHHH------HHHHHHHHHHHhHHHHHHHHHHHHHHhhhh-----cCCce
Q 009071 244 VSGVVDINTASAVLFVLVASCFLVMLYKLMSNWF------LELLVILFCIGGVEGLQTCLVALLSRWFRR-----AGESF 312 (544)
Q Consensus 244 ~~~~~~i~~~~a~~f~v~as~~L~~ly~f~~~~~------~~~l~~~f~i~g~~~l~~~l~~~~~~~~~~-----~~~~~ 312 (544)
|++.+++|.+||++||++||++|++||++++++. +++++.||+++|+.++..++.+.+.+.++. ..+.+
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 4567789999999999999999999999987654 468999999999999877777666553321 12222
Q ss_pred eee--------ccccccccchhhhhhhHHHhhhhhheeecCccchhHHHHHHHHHHHHHHHhcccCchhHHHHHHHHHHH
Q 009071 313 IKV--------PFFGAVSHLTLAVTPFCIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFM 384 (544)
Q Consensus 313 ~~~--------p~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~W~~~nilgi~~~~~~i~~~~l~s~k~~~ilL~~lf~ 384 (544)
.++ ++.++++..++++.++|+++++.|+++|++ +|++||++|+|+|+++++.+|+||+|++++||+++|+
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 455678888999999999999999998876 5999999999999999999999999999999999999
Q ss_pred hhhheeeeccccccceeEEEecccCCCCCCCCCEEEEeccccC----CCCCeeeecCCCchhhHHHHHHHHhhccccccc
Q 009071 385 YDIFWVFVSKKLFHESVMIVVARGDKSGEDGIPMLLKIPRMFD----PWGGYSIIGFGDILLPGLIIAFSLRYDWLANKS 460 (544)
Q Consensus 385 YDif~Vf~sp~~~~~sVMv~VA~~~~~~~~~~P~~l~~P~~~~----~~~~~s~LGlGDIviPGl~ia~~~rfD~~~~~~ 460 (544)
|||||||+||++||+|||++|||+..++++++|+|+++|+..+ ..++|||||+||||+||+|+++|+|||..++++
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 9999999999999999999999995445678899999999863 467899999999999999999999999988432
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHhhcCCCcceecccchhhhHHHHHHHhhccchhhhcc
Q 009071 461 LQAGYFLWAMLAYGLGLLITYVALNLMDGHGQPALLYIVPFTLGTFLALGKKRGDLRVLWT 521 (544)
Q Consensus 461 ~~~~YF~~~~igY~~GL~~t~~~~~~~~~~~QPALlYlvP~~l~~~~~~a~~rgel~~lw~ 521 (544)
++.||.++++||++||++|+++++++ ++||||||||||+|+++++++|++|||++++||
T Consensus 240 -~~~Yf~~~~~~Y~~Gl~~t~~~~~~~-~~~QPALlylvP~~l~~~~~~a~~r~el~~~w~ 298 (298)
T PF04258_consen 240 -RKPYFIASLIGYALGLLLTFVALHLF-KHGQPALLYLVPCTLGSVLLVAWIRGELKDFWN 298 (298)
T ss_dssp -------------------------------------------------------------
T ss_pred -cchHHHHHHHHHHHHHHHHHHHHHHh-CCCCCeehHHHHHHHHHHHHHHHHhhHHHHhhC
Confidence 36799999999999999999999999 899999999999999999999999999999997
No 4
>smart00730 PSN Presenilin, signal peptide peptidase, family. Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. Distant homologues, present in eukaryotes and archaea, also contain conserved aspartic acid residues which are predicted to contribute to catalysis. At least one member of this family has been shown to possess signal peptide peptidase activity.
Probab=100.00 E-value=2.7e-50 Score=403.79 Aligned_cols=242 Identities=38% Similarity=0.605 Sum_probs=213.6
Q ss_pred eeeccccchhhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhcCCceeeeccccccccchhh
Q 009071 248 VDINTASAVLFVLVASCFLVMLYKLMSNWFLELLVILFCIGGVEGLQTCLVALLSRWFRRAGESFIKVPFFGAVSHLTLA 327 (544)
Q Consensus 248 ~~i~~~~a~~f~v~as~~L~~ly~f~~~~~~~~l~~~f~i~g~~~l~~~l~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~ 327 (544)
+.+|+++++.||+++|++|++||++++.+ +..+.++|++.|+.+++.++.+..... .+..+..
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 45799999999999999999999999876 788899999999999988887654322 2334556
Q ss_pred hhhhHHHhhhhhheeecCccchhHHHHHHHHHHHHHHHhcccCchhHHHHHHHHHHHhhhheeeeccccccceeEEEecc
Q 009071 328 VTPFCIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIPNLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVAR 407 (544)
Q Consensus 328 ~~~~~~~~~~~w~~~~~~~~~W~~~nilgi~~~~~~i~~~~l~s~k~~~ilL~~lf~YDif~Vf~sp~~~~~sVMv~VA~ 407 (544)
...+++++...|.++++ ++|+.||++|+++++.+++.+++||+|++.+||+++++||+||||+||. +++||++||+
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 67788888889988876 6899999999999999999999999999999999999999999999987 8999999999
Q ss_pred cCCCCCCCCCEEEEeccc-----cCCCCCeeeecCCCchhhHHHHHHHHhhcccccccccchhHHHHHHHHHHHHHHHHH
Q 009071 408 GDKSGEDGIPMLLKIPRM-----FDPWGGYSIIGFGDILLPGLIIAFSLRYDWLANKSLQAGYFLWAMLAYGLGLLITYV 482 (544)
Q Consensus 408 ~~~~~~~~~P~~l~~P~~-----~~~~~~~s~LGlGDIviPGl~ia~~~rfD~~~~~~~~~~YF~~~~igY~~GL~~t~~ 482 (544)
+.++..|.+|+++..||. .+..+++++||+||||+||+++++|+|||..+++ ++.||..+++||++||++|++
T Consensus 142 ~~~~~~~~~P~ll~~p~~~~~~~~~~~~~~~~LGLGDiv~Pgilv~~a~~fd~~~~~--~~~yf~~~~~ay~~GL~~t~~ 219 (249)
T smart00730 142 GRDEPIKVFPALLYVPRLVVSFEDDEEGRFSMLGLGDIVFPGILVASAARFDVSVRS--DSNYFLACFVAYGIGLILTLV 219 (249)
T ss_pred cCCCCcccCChhhcccccccccccCCCCccceecCCCeeeHHHHHHHHHHhhhcccC--CcccHHHHHHHHHHHHHHHHH
Confidence 976433468999999984 2235689999999999999999999999987543 368999999999999999999
Q ss_pred HHHhhcCCCcceecccchhhhHHHHHHHhhc
Q 009071 483 ALNLMDGHGQPALLYIVPFTLGTFLALGKKR 513 (544)
Q Consensus 483 ~~~~~~~~~QPALlYlvP~~l~~~~~~a~~r 513 (544)
+++.+ ++|||||+|+||+++++.++.|+.|
T Consensus 220 ~l~~~-~~aqPALlylvp~~l~~~~~~~~~r 249 (249)
T smart00730 220 LLALF-KKAQPALPYLVPFTLVFYLLTALLR 249 (249)
T ss_pred HHHHh-CCCCccHHHHHHHHHHHHHHHHHhC
Confidence 99999 8999999999999999999999876
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=99.96 E-value=7.9e-29 Score=228.50 Aligned_cols=139 Identities=56% Similarity=0.922 Sum_probs=127.0
Q ss_pred ceEEEEEEeeeCCccceeEEecccCcCCcccccccCcceEEEeecCCCCCCCCCCCCCcceEEEEecCCCCHHHHHHHHH
Q 009071 46 DFVLVKVQTWIDGIENEEFVGVGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPKHKYAGDVIMVDRGNCKFTTKANIAE 125 (544)
Q Consensus 46 ~f~lv~v~~~~~G~e~~~~~~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~~~l~g~IaLV~RG~CsF~~Ka~nAq 125 (544)
+|++|+|.+|.+|.+.+++.+.+|+||..+|++..++.+++++.++|.+||++.+++++|+|+||+||+|+|.+|++|||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~a~FG~~~p~~~~~~~~~~lv~~~~~~gC~~~~~~~~g~IvLV~RG~C~F~~K~~nA~ 80 (139)
T cd02132 1 PFQLVKVQNWVDGDEGDELVGVTARFGASLPSKEDNANKTRAVLANPLDCCSPSTSKLSGSIALVERGECAFTEKAKIAE 80 (139)
T ss_pred CceEEEeeeccCCccccEEEeeccccCCCCCCcccCccEEEEEECCcccccCCCCcccCCeEEEEECCCCCHHHHHHHHH
Confidence 58999999999999999999999999999998877788999999999999999998999999999999999999999999
Q ss_pred HcCCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 126 AAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 126 ~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
++||+++||||+.++...|.+.++++..+++||+++|++++|+.|++++++|++|++++
T Consensus 81 ~aGA~avIv~n~~~~~~~~~~~~~~~~~~~~IP~v~Is~~~G~~L~~~l~~g~~Vtv~~ 139 (139)
T cd02132 81 AGGASALLIINDQEELYKMVCEDNDTSLNISIPVVMIPQSAGDALNKSLDQGKKVEVLL 139 (139)
T ss_pred HcCCcEEEEEECCCcccccccCCCCCCCCCcEeEEEecHHHHHHHHHHHHcCCcEEEeC
Confidence 99999999999987777776543444456899999999999999999999999998864
No 6
>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=99.89 E-value=3.4e-23 Score=186.04 Aligned_cols=116 Identities=23% Similarity=0.396 Sum_probs=98.4
Q ss_pred eEEEEEEeeeCCccceeEEecccCcCCcccccccCcceEEEeecCCCCCCCCCC---CCCcceEEEEecCCCCHHHHHHH
Q 009071 47 FVLVKVQTWIDGIENEEFVGVGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPK---HKYAGDVIMVDRGNCKFTTKANI 123 (544)
Q Consensus 47 f~lv~v~~~~~G~e~~~~~~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~---~~l~g~IaLV~RG~CsF~~Ka~n 123 (544)
||++++++|. .+|++.+++...|++.++|..||++.+ .+++|+|+||+||+|+|.+|++|
T Consensus 1 ~~~~~~~~~~-----------------~l~~~~~~~~~~~~~~~~~~~gC~~~~~~~~~l~gkIaLV~RG~CsF~~K~~~ 63 (120)
T cd02129 1 YCILYNSQWA-----------------SLPSDLDKATLLPLRNLTSSVLCSASDVPPGGLKGKAVVVMRGNCTFYEKARL 63 (120)
T ss_pred CcEEECCcce-----------------ECCcchhhCcceeeecCCCcCCCCccccCccccCCeEEEEECCCcCHHHHHHH
Confidence 7999999994 699888899999999999999999877 47899999999999999999999
Q ss_pred HHHcCCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEE
Q 009071 124 AEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQ 183 (544)
Q Consensus 124 Aq~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~ 183 (544)
||++||+|+|||||++.. .+. ++.+...+++||++||++++|++|++.+.+ .|+|+
T Consensus 64 Aq~aGA~aVII~nn~~~~-~~~-~~~~~~~~v~IP~v~Is~~dG~~i~~~l~~--~~~v~ 119 (120)
T cd02129 64 AQSLGAEGLLIVSRERLV-PPS-GNRSEYEKIDIPVALLSYKDMLDIQQTFGD--SVKVA 119 (120)
T ss_pred HHHCCCCEEEEEECCCCC-CCC-CCCCCCcCCcccEEEEeHHHHHHHHHHhcc--CcEEe
Confidence 999999999999997642 121 112223678999999999999999999864 45554
No 7
>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=99.87 E-value=5.8e-22 Score=179.97 Aligned_cols=116 Identities=26% Similarity=0.472 Sum_probs=97.6
Q ss_pred ecccCcCCcccccccCcceEEEeecCCCCCCCCCCC--CCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc---
Q 009071 66 GVGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPKH--KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE--- 140 (544)
Q Consensus 66 ~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~~--~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~--- 140 (544)
+.+|+||.++|+.. ...++|+.++|.+||++.++ +++|||+|++||+|+|.+|+++||++||+|+||+|+.++
T Consensus 2 ~~pa~FG~~~~~~~--~~~g~l~~~~p~~gC~~~~~~~~~~gkIaLv~RG~C~f~~K~~~Aq~aGA~avII~n~~~~~~~ 79 (126)
T cd02126 2 AGPAQFGMDLTGDK--AGVGRVVKAKPYRACSEITNAEEVKGKIAIMERGDCMFVEKARRVQKAGAIGGIVIDNNEGSSS 79 (126)
T ss_pred CCCcccCCcCCCCC--CceEEEEeCCchhcccCCCCccccCceEEEEECCCCcHHHHHHHHHHCCCcEEEEEECCCCccc
Confidence 46899999999742 36789999999999998774 689999999999999999999999999999999998653
Q ss_pred ----ccccccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 141 ----LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 141 ----l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
.+.|.+. .+...+++||+++|++++|+.|++.+++|.+|++++
T Consensus 80 ~~~~~~~m~~~-~~~~~~~~IP~v~I~~~dG~~L~~~l~~~~~~~~~~ 126 (126)
T cd02126 80 DTAPMFAMSGD-GDSTDDVTIPVVFLFSKEGSKLLAAIKEHQNVEVLL 126 (126)
T ss_pred cccceeEeecC-CCCCCCCeEEEEEEEHHHHHHHHHHHHhCCceEEeC
Confidence 3456442 112346899999999999999999999999998864
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=99.85 E-value=5.4e-21 Score=171.78 Aligned_cols=110 Identities=25% Similarity=0.463 Sum_probs=93.7
Q ss_pred CcCCcccccccCcceEEEeecCCCCCCCCCCC--CCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc----ccc
Q 009071 70 RFGTTIVSKEKNANQIHLTLSHPRDCCSMPKH--KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE----LYK 143 (544)
Q Consensus 70 ~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~~--~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~----l~~ 143 (544)
.||..++.+. ..++|+.++|.+||++.++ +++|+|+||+||+|+|.+|+++||++||+|+||||+.++ .+.
T Consensus 1 ~~~~~~~~~~---~~~~lv~~~p~~gC~~~~~~~~~~g~I~Lv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~~~~ 77 (118)
T cd02127 1 DFGTIFNTRY---KHVPLVPADPLEACEELRNIHDINGNIALIERGGCSFLTKAINAQKAGALAVIITDVNNDSDEYYVE 77 (118)
T ss_pred CCCccccccc---cceEEEECCccccCCCCCCccccCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccceE
Confidence 4888888764 5678999999999998764 689999999999999999999999999999999998653 345
Q ss_pred cccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 144 MVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 144 M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
|.++ +...+++||+++|++++|+.|++.+++|..+++.+
T Consensus 78 m~~~--~~~~~i~IP~v~Is~~dG~~L~~~l~~g~~~~~~~ 116 (118)
T cd02127 78 MIQD--DSSRRADIPAAFLLGKNGYMIRKTLERLGLPYAII 116 (118)
T ss_pred ecCC--CCCCCceEEEEEecHHHHHHHHHHHHcCCceEEee
Confidence 7543 23457899999999999999999999999887765
No 9
>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=99.84 E-value=2.3e-20 Score=174.98 Aligned_cols=116 Identities=26% Similarity=0.410 Sum_probs=98.9
Q ss_pred cceeEEecccCcCCcccccccCcceEEEeecCCCCCCCCCC------CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEE
Q 009071 60 ENEEFVGVGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPK------HKYAGDVIMVDRGNCKFTTKANIAEAAGASALL 133 (544)
Q Consensus 60 e~~~~~~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~------~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avI 133 (544)
+...+.+.+|+||...+.. +.+++|+.++|.+||++.+ ++.+|+|+||+||+|+|.+|++|||++||+|+|
T Consensus 20 ~~~~~~~~~A~FG~~~~~~---~~~g~lv~~~p~~gC~~~~~~~~~~~~~~g~IvLV~RG~CtF~~Kv~nAq~aGA~avI 96 (153)
T cd02123 20 LTDEFDDLPANFGPIPPGS---GLKGVLVVAEPLNACSPIENPPLNSNASGSFIVLIRRGNCSFETKVRNAQRAGYKAAI 96 (153)
T ss_pred ccceEeeecccCCCCCCCC---ceEEEEEeCCccccCCCCcccccccccCCCeEEEEECCCCCHHHHHHHHHHCCCCEEE
Confidence 5667889999999887743 4678899999999999876 467899999999999999999999999999999
Q ss_pred EEeCCCc-ccccccCCCCCCCCccceEEEechhhhHHHHHHHhccce
Q 009071 134 IINNQKE-LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSS 179 (544)
Q Consensus 134 V~N~~~~-l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~ 179 (544)
|||++++ ...|.+.+. ...+++||+++|++++|+.|++.+++++.
T Consensus 97 I~n~~~~~~~~m~~~~~-~~~~v~IP~v~Is~~dg~~L~~~l~~~~~ 142 (153)
T cd02123 97 VYNDESNDLISMSGNDQ-EIKGIDIPSVFVGKSTGEILKKYASYEKG 142 (153)
T ss_pred EEECCCCcceeccCCCC-CCcCCEEEEEEeeHHHHHHHHHHHhcCCc
Confidence 9999755 566765322 22578999999999999999999998876
No 10
>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=99.84 E-value=1.7e-20 Score=170.62 Aligned_cols=102 Identities=28% Similarity=0.389 Sum_probs=85.3
Q ss_pred ceEEEeec-CCCCCCCCCCC---------CCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc-ccccccCCC--
Q 009071 83 NQIHLTLS-HPRDCCSMPKH---------KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE-LYKMVCDPD-- 149 (544)
Q Consensus 83 ~~~~Lv~~-~p~dgC~~~~~---------~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~-l~~M~~~~~-- 149 (544)
..+.|+.+ ++.+||++.++ ..+++|+||+||+|+|.+|++|||++||+|+||||+.++ .+.|.++++
T Consensus 11 ~~G~l~~~~~~~~gC~~~~~~~~~~~~~~~~~~~IvLv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~m~~~~~~~ 90 (127)
T cd02125 11 LTGVVVYPKENRTGCKEFDVFFKPKKSEPGRRPVILLLDRGGCFFTLKAWNAQQAGAAAVLVADNVDEPLLTMDTPEESG 90 (127)
T ss_pred eEEEEEecCCccccCCCCcccccccccccCCCceEEEEECCCcCHHHHHHHHHHCCCcEEEEEECCCCccccccCccccc
Confidence 45666655 67899998763 367899999999999999999999999999999999876 567765322
Q ss_pred --CCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 150 --ETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 150 --~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
+...+++||++||++++|++|++.+++|++|+|++
T Consensus 91 ~~~~~~~i~IP~v~Is~~~G~~L~~~l~~g~~V~v~~ 127 (127)
T cd02125 91 SADYIEKITIPSALITKAFGEKLKKAISNGEMVVIKL 127 (127)
T ss_pred ccccCCCceEeEEEECHHHHHHHHHHHhcCCeEEEeC
Confidence 22457899999999999999999999999999875
No 11
>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=99.84 E-value=2.3e-20 Score=172.13 Aligned_cols=110 Identities=24% Similarity=0.328 Sum_probs=91.4
Q ss_pred cccCcCCcccccccCcceEEEee---cCCCCCCCCCCC-----CCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCC
Q 009071 67 VGARFGTTIVSKEKNANQIHLTL---SHPRDCCSMPKH-----KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQ 138 (544)
Q Consensus 67 ~~A~FG~~lp~~~~~~~~~~Lv~---~~p~dgC~~~~~-----~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~ 138 (544)
..|+||.++|..+ ..+.|+. +++.+||+++++ +++|+||||+||+|+|.+|++|||++||+++||||++
T Consensus 18 ~~a~fg~~~~~~~---~~G~l~~~~~~~~~~gC~~~~~~~~~~~~~g~IaLV~RG~C~F~~K~~nA~~aGA~aVIIyn~~ 94 (138)
T cd02122 18 ESGRYGEHSPKEE---AKGLVVVPDPPNDHYGCDPDTRFPIPPNGEPWIALIQRGNCTFEEKIKLAAERNASAVVIYNNP 94 (138)
T ss_pred cccccCCCCCCCc---cEEEEecCCCCCCcCCCCCCccccCCccCCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECC
Confidence 4799999998865 4455543 445899998764 5789999999999999999999999999999999998
Q ss_pred C-c--ccccccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 139 K-E--LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 139 ~-~--l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
+ . .+.|... ...+||+++|++++|++|++.+++|++|++++
T Consensus 95 ~~~~~~~~m~~~-----~~~~ip~v~Is~~~G~~l~~~l~~G~~Vtv~~ 138 (138)
T cd02122 95 GTGNETVKMSHP-----GTGDIVAIMITNPKGMEILELLERGISVTMVI 138 (138)
T ss_pred CCCCceeeccCC-----CCCcceEEEEcHHHHHHHHHHHHcCCcEEEeC
Confidence 6 2 5566532 13478999999999999999999999998863
No 12
>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=99.79 E-value=6.9e-19 Score=157.40 Aligned_cols=114 Identities=34% Similarity=0.515 Sum_probs=98.0
Q ss_pred cccCcCCcccccccCcceEEEeecCCCCCCCCCC--CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc--cc
Q 009071 67 VGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPK--HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE--LY 142 (544)
Q Consensus 67 ~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~--~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~--l~ 142 (544)
++|+||..+++.....+.++++.+++.++|++.+ ++++|||+|++||+|+|.+|+++|+++||+|+|+||+.++ .+
T Consensus 1 ~~a~fg~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~v~GkIvL~~rg~c~f~~k~~~a~~aGA~gvIi~~~~~~~~~~ 80 (118)
T cd04818 1 VSAGFGPALTNVTADVVLAGAAPASNTDGCTAFTNAAAFAGKIALIDRGTCNFTVKVLNAQNAGAIAVIVANNVAGGAPI 80 (118)
T ss_pred CCcccCCcCccccccceeEEEecCCcccccCCCCcCCCCCCEEEEEECCCCCHHHHHHHHHHCCCeEEEEEECCCCCcce
Confidence 4799999998755445889999999999998876 4799999999999999999999999999999999999764 44
Q ss_pred ccccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 143 KMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 143 ~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
.|... .....||+++|++++|++|++.+++|++|++++
T Consensus 81 ~~~~~----~~~~~iP~v~V~~~~g~~l~~~l~~g~~v~v~~ 118 (118)
T cd04818 81 TMGGD----DPDITIPAVMISQADGDALKAALAAGGTVTVTL 118 (118)
T ss_pred eccCC----CCCCEEeEEEecHHHHHHHHHHHhcCCcEEEeC
Confidence 55321 134679999999999999999999999998874
No 13
>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=99.79 E-value=6.6e-19 Score=158.07 Aligned_cols=103 Identities=25% Similarity=0.413 Sum_probs=83.9
Q ss_pred ecccCcCCcccccccCcceEEEeecCCCCCCCCCC-CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc--cc
Q 009071 66 GVGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPK-HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE--LY 142 (544)
Q Consensus 66 ~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~-~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~--l~ 142 (544)
+..|+||+.+....++ . ..++|.+||++.+ ++++|+|+||+||+|+|.+|++|||++||+|+||||+.++ +.
T Consensus 5 ~~~~~~~~~~~~~~~~---~--~~~~p~~gC~~~~~~~l~gkIvLV~RG~CsF~~K~~nAq~aGA~avII~n~~~~~~~~ 79 (117)
T cd04813 5 GRYASFSPILNPHLRG---S--YKVSPTDACSLQEHAEIDGKVALVLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRGLI 79 (117)
T ss_pred ccccccCCccCccccc---c--ccCCCCCCCCCCCcCCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCcccce
Confidence 3678999988765432 1 1378899999876 5799999999999999999999999999999999998763 45
Q ss_pred ccccCCCCCCCCccceEEEechhhhHHHHHHHh
Q 009071 143 KMVCDPDETDLDIHIPAVMMPQDAGASLEKMLL 175 (544)
Q Consensus 143 ~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~ 175 (544)
.|.+. +...+++||+++|++++|+.|++.+.
T Consensus 80 ~m~~~--~~~~~v~IPav~Is~~~g~~L~~l~~ 110 (117)
T cd04813 80 TMFSN--GDTDNVTIPAMFTSRTSYHLLSSLLP 110 (117)
T ss_pred ecccC--CCCCCcEEEEEEEcHHHHHHHHHhcc
Confidence 66543 22457899999999999999988763
No 14
>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=99.75 E-value=1.6e-17 Score=149.68 Aligned_cols=112 Identities=22% Similarity=0.429 Sum_probs=89.3
Q ss_pred ccCcCCcccccccCcceEEEeecCC--CCCCCCCC---CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcc-
Q 009071 68 GARFGTTIVSKEKNANQIHLTLSHP--RDCCSMPK---HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKEL- 141 (544)
Q Consensus 68 ~A~FG~~lp~~~~~~~~~~Lv~~~p--~dgC~~~~---~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l- 141 (544)
...|++..|. ++.+++++..++ .++|++.+ .+++|||+|++||+|+|.+|++|||++||+|+|+||+.++.
T Consensus 5 ~~~~~~~~~~---~gi~~~lv~~~~~~~~gC~~~~~~~~~~~GkIvLv~rg~c~f~~K~~~A~~aGA~avIi~n~~~~~~ 81 (122)
T cd04816 5 SLSYSPSTPP---GGVTAPLVPLDPERPAGCDASDYDGLDVKGAIVLVDRGGCPFADKQKVAAARGAVAVIVVNNSDGGG 81 (122)
T ss_pred EEeccCCCCC---CCcEEEEEEcCCCCccCCCccccCCCCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEeCCCCcc
Confidence 4567766664 357888887665 59999765 47899999999999999999999999999999999987642
Q ss_pred cccccCCCCCCCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 142 YKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 142 ~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
..+.-. +.....+||+++|++++|++|++.+++|.+|++++
T Consensus 82 ~~~~~~--~~~~~~~iP~~~Is~~~G~~l~~~l~~g~~v~~~~ 122 (122)
T cd04816 82 TAGTLG--APNIDLKVPVGVITKAAGAALRRRLGAGETLELDA 122 (122)
T ss_pred cccccc--CCCCCCeeeEEEEcHHHHHHHHHHHcCCCEEEEeC
Confidence 111111 11245789999999999999999999999998874
No 15
>KOG3920 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=99.72 E-value=6.5e-18 Score=155.18 Aligned_cols=164 Identities=23% Similarity=0.329 Sum_probs=127.4
Q ss_pred ccchhhHHHHHHHHHHhccccccCCCccccCCCCCCCCCCCcceEEEEEEeeeCCccceeEEecccC-cCCcccccccCc
Q 009071 4 KRLSWVLFPVAVVSLVCYPASVTAGDIVHDDDLAPKKPGCENDFVLVKVQTWIDGIENEEFVGVGAR-FGTTIVSKEKNA 82 (544)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~p~~p~c~~~f~lv~v~~~~~G~e~~~~~~~~A~-FG~~lp~~~~~~ 82 (544)
+|++|++|.+.|...+.++..- +..+..+| +.+-. -...+....+|+..+|. ||...|++-+
T Consensus 2 ~p~gWl~l~~~L~~~vaa~~~~--~~~v~~qD-----------~~~F~--vlsP~~l~Yty~~~pAkdfG~~F~~r~e-- 64 (193)
T KOG3920|consen 2 KPRGWLLLSFLLIIQVAAAKIP--YEEVENQD-----------NMLFT--VLSPYTLAYTYQMKPAKDFGVHFPDRFE-- 64 (193)
T ss_pred CcceehHHHHHHHHHHHHccCC--cceeeecc-----------eEEEE--ecCcccEEEEEEecchhhhccccchhhc--
Confidence 6899999999999888777533 33333333 33333 34456677888888885 9999998763
Q ss_pred ceEEEeecCCCCCCCCCCC--CCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc------ccccccCCCCCCCC
Q 009071 83 NQIHLTLSHPRDCCSMPKH--KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE------LYKMVCDPDETDLD 154 (544)
Q Consensus 83 ~~~~Lv~~~p~dgC~~~~~--~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~------l~~M~~~~~~~~~~ 154 (544)
..+++.++|+.||+.+.| ...|.|+|++||+|+|..|.+|+|++||.++||-++... .++|.. +++.++
T Consensus 65 -~~~lV~adPp~aC~elrN~~f~~d~vaL~eRGeCSFl~Ktl~~e~aGa~aiiitd~~~~~~sf~~YveMI~--D~sq~~ 141 (193)
T KOG3920|consen 65 -NLELVLADPPHACEELRNEIFAPDSVALMERGECSFLVKTLNGEKAGATAIIITDSQNYEYSFHQYVEMIP--DESQDR 141 (193)
T ss_pred -CcceeecCChhHHHHHhhcccCCCcEEEEecCCceeeehhhhhhhcCceEEEEecCCCCchhHHHHHHhcC--cccccc
Confidence 578999999999999885 578999999999999999999999999999999987543 357875 345567
Q ss_pred ccceEEEechhhhHHHHHHHhccceEEEEeecC
Q 009071 155 IHIPAVMMPQDAGASLEKMLLNTSSVSVQLYSP 187 (544)
Q Consensus 155 i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l~~p 187 (544)
.+||++++-..+|-.++..|++-..+...+.-|
T Consensus 142 AniPa~fllg~~Gy~ir~sL~r~~r~ha~i~IP 174 (193)
T KOG3920|consen 142 ANIPAVFLLGVTGYYIRVSLKRYFRDHAKIDIP 174 (193)
T ss_pred cCCceEEEeccceEEEehhHHHhCCccEEEecc
Confidence 899999999999999988887765555554433
No 16
>PF06550 DUF1119: Protein of unknown function (DUF1119); InterPro: IPR010545 This family consists of several hypothetical archaeal proteins of unknown function.
Probab=99.72 E-value=3.2e-16 Score=157.23 Aligned_cols=173 Identities=24% Similarity=0.282 Sum_probs=131.4
Q ss_pred hhhhHHHhhhhhheeecCccchhHHHHHHHHHHHHHHHhcccC-chhHHHHHHHHHHHhhhheeeeccccccceeEEEec
Q 009071 328 VTPFCIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIP-NLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVA 406 (544)
Q Consensus 328 ~~~~~~~~~~~w~~~~~~~~~W~~~nilgi~~~~~~i~~~~l~-s~k~~~ilL~~lf~YDif~Vf~sp~~~~~sVMv~VA 406 (544)
....++.+....+.|. .|+..|+.|+.++..+...+.+. ++-.+.+||..+-+||..-||.|+ +|++.|
T Consensus 95 a~~~ai~~~~~L~~yp----EWYviD~~Gil~~aG~aaiFGISl~~lpaiiLL~iLAVYDaISVYkTk------HMltLA 164 (283)
T PF06550_consen 95 ALILAIALTALLYKYP----EWYVIDIAGILMGAGAAAIFGISLGILPAIILLAILAVYDAISVYKTK------HMLTLA 164 (283)
T ss_pred HHHHHHHHHHHHHhcc----hHHHHHHHHHHHHhHHHHHHhhhccHHHHHHHHHHHHHhhhhheecch------HHHHHH
Confidence 3344444444444444 49999999999998877766665 666789999999999999999775 899999
Q ss_pred ccCCCCCCCCCEEEEeccccCC--------------CCCeeeecCCCchhhHHHHHHHHhhcccccccccchhHHHHHHH
Q 009071 407 RGDKSGEDGIPMLLKIPRMFDP--------------WGGYSIIGFGDILLPGLIIAFSLRYDWLANKSLQAGYFLWAMLA 472 (544)
Q Consensus 407 ~~~~~~~~~~P~~l~~P~~~~~--------------~~~~s~LGlGDIviPGl~ia~~~rfD~~~~~~~~~~YF~~~~ig 472 (544)
+|.. +.++|+++++|+..+. .++-.++|+||.++|.++++.+..|.....-...+..-+.+++|
T Consensus 165 egv~--d~klPilfViP~~~~ySf~~~~~~~~~~~~~r~a~fiGlGD~vmPtILVvSa~~f~~~~~~~~~~lpalga~~G 242 (283)
T PF06550_consen 165 EGVM--DLKLPILFVIPKKRGYSFLKDGFDNREEKEERDAFFIGLGDAVMPTILVVSAAFFLSAPILGGLNLPALGAMLG 242 (283)
T ss_pred HHHh--ccCCceEEEEecccCccccccccccccccccccceEeccchhhhHHHHHHHHHHhccccchhhhhHHHHHHHHH
Confidence 9975 3689999999986432 13456999999999999999999997654321111223567888
Q ss_pred HHHHHHHHHHHHHhhcCCCcceecccchhhhHHHHHHHhhcc
Q 009071 473 YGLGLLITYVALNLMDGHGQPALLYIVPFTLGTFLALGKKRG 514 (544)
Q Consensus 473 Y~~GL~~t~~~~~~~~~~~QPALlYlvP~~l~~~~~~a~~rg 514 (544)
-.+|+.+-+.. .+.+++||+|.||.-..++..++-++..|
T Consensus 243 tl~gl~vL~~~--v~kgrp~aGLP~LN~GaI~Gflig~l~sg 282 (283)
T PF06550_consen 243 TLAGLAVLLRF--VMKGRPQAGLPFLNGGAIAGFLIGALASG 282 (283)
T ss_pred HHHHHHHHHHH--HHcCCCCCCCCccchhHHHHHHHHHHHcC
Confidence 88888776553 24589999999999999999888776554
No 17
>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=99.71 E-value=1.1e-16 Score=144.17 Aligned_cols=98 Identities=30% Similarity=0.416 Sum_probs=80.4
Q ss_pred ceEEEeecCCCCCCCCCC--CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCC-CcccccccCCCCCCCCccceE
Q 009071 83 NQIHLTLSHPRDCCSMPK--HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQ-KELYKMVCDPDETDLDIHIPA 159 (544)
Q Consensus 83 ~~~~Lv~~~p~dgC~~~~--~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~-~~l~~M~~~~~~~~~~i~IPv 159 (544)
.+++++.. +.++|++.+ .+++|||+||+||+|+|.+|++|||++||+++||||+. ++...... ....+..||+
T Consensus 22 ~~g~lv~~-~~~gC~~~~~~~~~~gkIvlv~rg~c~f~~K~~~A~~aGA~~vIv~n~~~~~~~~~~~---~~~~~~~Ip~ 97 (122)
T cd02130 22 VTGPLVVV-PNLGCDAADYPASVAGNIALIERGECPFGDKSALAGAAGAAAAIIYNNVPAGGLSGTL---GEPSGPYVPT 97 (122)
T ss_pred cEEEEEEe-CCCCCCcccCCcCCCCEEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccccc---CCCCCCEeeE
Confidence 46788765 467999755 47999999999999999999999999999999999997 33322111 1123578999
Q ss_pred EEechhhhHHHHHHHhccceEEEEe
Q 009071 160 VMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 160 v~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
++|++++|+.|++.+++|++|++++
T Consensus 98 v~Is~~~G~~L~~~l~~g~~v~~~~ 122 (122)
T cd02130 98 VGISQEDGKALVAALANGGEVSANL 122 (122)
T ss_pred EEecHHHHHHHHHHHhcCCcEEEeC
Confidence 9999999999999999999998874
No 18
>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=99.67 E-value=3.4e-16 Score=142.81 Aligned_cols=89 Identities=31% Similarity=0.399 Sum_probs=73.3
Q ss_pred cCCCCCCCCCC---CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhh
Q 009071 90 SHPRDCCSMPK---HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDA 166 (544)
Q Consensus 90 ~~p~dgC~~~~---~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~ 166 (544)
+++.+||++++ .+++|+|+||+||+|+|.+|++|||++||+++||||+.++...+... ....+|.+++ +++
T Consensus 38 ~~~~~gC~~~~~~~~~~~g~IaLv~rg~c~f~~K~~nA~~aGA~aviiyn~~~~~~~~~~~-----~~~~~~~~~~-~~~ 111 (129)
T cd02124 38 SVADDACQPLPDDTPDLSGYIVLVRRGTCTFATKAANAAAKGAKYVLIYNNGSGPTDQVGS-----DADSIIAAVT-PED 111 (129)
T ss_pred CCCcccCcCCCcccccccCeEEEEECCCCCHHHHHHHHHHcCCcEEEEEECCCCcccccCC-----CCcceeeEEe-HHH
Confidence 45789999875 36799999999999999999999999999999999998765444321 2234565555 999
Q ss_pred hHHHHHHHhccceEEEEe
Q 009071 167 GASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 167 G~~L~~~L~~G~~V~V~l 184 (544)
|++|++++++|++|+++|
T Consensus 112 G~~l~~~l~~G~~vtv~f 129 (129)
T cd02124 112 GEAWIDALAAGSNVTVDF 129 (129)
T ss_pred HHHHHHHHhcCCeEEEeC
Confidence 999999999999999875
No 19
>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=99.64 E-value=2.1e-15 Score=139.17 Aligned_cols=95 Identities=24% Similarity=0.305 Sum_probs=74.4
Q ss_pred cceEEEeecCCCCCCCCCCCCCcceEEEEecCCCC-----HHHHHHHHHHcCCcEEEEEeCC--Ccccc-cccCCCCCCC
Q 009071 82 ANQIHLTLSHPRDCCSMPKHKYAGDVIMVDRGNCK-----FTTKANIAEAAGASALLIINNQ--KELYK-MVCDPDETDL 153 (544)
Q Consensus 82 ~~~~~Lv~~~p~dgC~~~~~~l~g~IaLV~RG~Cs-----F~~Ka~nAq~aGA~avIV~N~~--~~l~~-M~~~~~~~~~ 153 (544)
..+++++.... .+|+-...+.+|||+||+||+|+ |.+|++|||++||+|+|||||. ++.+. +-+. ...
T Consensus 35 ~~tg~lv~~g~-~g~d~~~~d~~GkIaLI~RG~c~~~~~~f~~Kv~~A~~aGA~avIIyNn~~~~g~~~~~lg~---~~~ 110 (139)
T cd04817 35 SATGSLYYCGT-SGGSYICGGMAGKICLIERGGNSKSVYPEIDKVKACQNAGAIAAIVYSNAALAGLQNPFLVD---TNN 110 (139)
T ss_pred cceEEEEEccC-CCccccCCCcCccEEEEECCCCCCCcccHHHHHHHHHHCCCeEEEEEeCCCCCCcccccccC---CCC
Confidence 46778877664 34754445799999999999999 9999999999999999999998 44332 2221 123
Q ss_pred CccceEEEechhhhHHHHHHHhccceE
Q 009071 154 DIHIPAVMMPQDAGASLEKMLLNTSSV 180 (544)
Q Consensus 154 ~i~IPvv~Is~~~G~~L~~~L~~G~~V 180 (544)
+++||+++|++++|++|++.+.++.+|
T Consensus 111 ~~~IP~v~is~~dG~~L~~~l~~~~tv 137 (139)
T cd04817 111 DTTIPSVSVDRADGQALLAALGQSTTV 137 (139)
T ss_pred CceEeEEEeeHHHHHHHHHHhcCCCee
Confidence 679999999999999999998655443
No 20
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.62 E-value=6.3e-15 Score=152.90 Aligned_cols=108 Identities=25% Similarity=0.373 Sum_probs=89.8
Q ss_pred eEEecccCcCCcccccccCcceEEEeecCCCCCCCCCCC------CCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEe
Q 009071 63 EFVGVGARFGTTIVSKEKNANQIHLTLSHPRDCCSMPKH------KYAGDVIMVDRGNCKFTTKANIAEAAGASALLIIN 136 (544)
Q Consensus 63 ~~~~~~A~FG~~lp~~~~~~~~~~Lv~~~p~dgC~~~~~------~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N 136 (544)
+|.+.+|.||+.++.++ ..+-++.++|.+||++..+ .-..+++|++||+|+|.+|+++||++|++|+||||
T Consensus 35 sf~d~~a~f~~s~~~e~---~~G~l~~~ep~~aC~~i~~~p~~~~~~~~~laLI~Rg~CsFe~Kv~~AQ~aGfkaaIVyn 111 (348)
T KOG4628|consen 35 SFADLPALFGPSLPSEG---NLGVLVVAEPLNACNPITNFPEHSTRSTSFLALIRRGGCSFEDKVLNAQRAGFKAAIVYN 111 (348)
T ss_pred cccCCccccCCcccccc---ceeeeecCCCccccCccccCccCCCCCcceEEEEEccCCchHHHHhhcccccCceEEEec
Confidence 78889999999998764 5677888999999998763 34578999999999999999999999999999999
Q ss_pred CCCc--ccccccCCCCCCCCccceEEEechhhhHHHHHHHhcc
Q 009071 137 NQKE--LYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNT 177 (544)
Q Consensus 137 ~~~~--l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G 177 (544)
|.+. +..|.. + ..++.|+++|++...|+.|.+....+
T Consensus 112 n~~~~~lv~~~~--~--~~~v~i~~~~vs~~~ge~l~~~~~~~ 150 (348)
T KOG4628|consen 112 NVGSEDLVAMAS--N--PSKVDIHIVFVSVFSGELLSSYAGRT 150 (348)
T ss_pred CCCCchheeecc--C--CccceeEEEEEeeehHHHHHHhhccc
Confidence 8653 455532 1 24789999999999999999854433
No 21
>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=99.49 E-value=4.1e-14 Score=121.84 Aligned_cols=72 Identities=29% Similarity=0.526 Sum_probs=56.2
Q ss_pred CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhhHHHHHHH
Q 009071 101 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKML 174 (544)
Q Consensus 101 ~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L 174 (544)
.+++|||+|++||+|+|.+|+++||++||+|+||+|+.+....+. ......+.+||+++|++++|++|++++
T Consensus 30 ~~~~gkIvlv~rg~~~~~~k~~~a~~~GA~gvIi~~~~~~~~~~~--~~~~~~~~~iP~v~I~~~~g~~L~~~i 101 (101)
T PF02225_consen 30 SDVKGKIVLVERGSCSFDDKVRNAQKAGAKGVIIYNPPPNNGSMI--DSEDPDPIDIPVVFISYEDGEALLAYI 101 (101)
T ss_dssp STCTTSEEEEESTSSCHHHHHHHHHHTTESEEEEE-TSCSCTTTT--CEBTTTSTBSEEEEE-HHHHHHHHHHH
T ss_pred ccccceEEEEecCCCCHHHHHHHHHHcCCEEEEEEeCCccccCcc--cccCCCCcEEEEEEeCHHHHhhhhccC
Confidence 579999999999999999999999999999999999322221211 112235689999999999999999864
No 22
>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=99.49 E-value=1.4e-13 Score=122.84 Aligned_cols=94 Identities=30% Similarity=0.447 Sum_probs=75.2
Q ss_pred cCCCCCCCCCC-----CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCc-ccccccCCCCCCCCccceEEEec
Q 009071 90 SHPRDCCSMPK-----HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKE-LYKMVCDPDETDLDIHIPAVMMP 163 (544)
Q Consensus 90 ~~p~dgC~~~~-----~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~-l~~M~~~~~~~~~~i~IPvv~Is 163 (544)
..+.++|++.+ .+++|||+|++||+|+|.+|+++||++||+|+|++|+.+. ...+... .+...+..||+++|+
T Consensus 27 ~~~~~~C~~~~~~~~~~~~~GkIvl~~~g~~~~~~k~~~a~~~GA~gvii~~~~~~~~~~~~~~-~~~~~~~~iP~~~is 105 (126)
T cd00538 27 AGPLVGCGYGTTDDSGADVKGKIVLVRRGGCSFSEKVKNAQKAGAKAVIIYNNGDDPGPQMGSV-GLESTDPSIPTVGIS 105 (126)
T ss_pred ccceEEEecCcccccCCCccceEEEEECCCcCHHHHHHHHHHCCCEEEEEEECCCCcccccccc-cCCCCCCcEeEEEeC
Confidence 34667887753 4689999999999999999999999999999999999763 2222211 111235689999999
Q ss_pred hhhhHHHHHHHhccceEEEEe
Q 009071 164 QDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 164 ~~~G~~L~~~L~~G~~V~V~l 184 (544)
+++|++|++.+++|+++++++
T Consensus 106 ~~~g~~l~~~~~~~~~v~~~~ 126 (126)
T cd00538 106 YADGEALLSLLEAGKTVTVDL 126 (126)
T ss_pred HHHHHHHHHHHhcCCceEEeC
Confidence 999999999999999888763
No 23
>COG3389 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.45 E-value=2.5e-13 Score=132.05 Aligned_cols=161 Identities=25% Similarity=0.401 Sum_probs=123.8
Q ss_pred HHHhhhhhheeecCccchhHHHHHHHHHHHHHHHhcccC-chhHHHHHHHHHHHhhhheeeeccccccceeEEEecccCC
Q 009071 332 CIAFAVVWAIYRKVSFAWIGQDILGIALIITVLQIVHIP-NLKVGTVLLSCAFMYDIFWVFVSKKLFHESVMIVVARGDK 410 (544)
Q Consensus 332 ~~~~~~~w~~~~~~~~~W~~~nilgi~~~~~~i~~~~l~-s~k~~~ilL~~lf~YDif~Vf~sp~~~~~sVMv~VA~~~~ 410 (544)
.++++.++.++++. .|+..|..|.+++..+-..+.+. ..-.+.+||..+-+||..-||.|. +|++.|++..
T Consensus 97 ~~aI~~~~lL~~~p--eWyVid~ag~~la~Giaai~GIsfgv~pavvlL~~lavYDaIsVYkT~------HMIslA~~v~ 168 (277)
T COG3389 97 GLAIGLVYLLYKYP--EWYVIDLAGFFLAVGIAAIFGISFGVLPAVVLLIALAVYDAISVYKTR------HMISLAEGVM 168 (277)
T ss_pred HHHHHHHHhhhhcc--ceEEeehHHHHHHhhHHHhheeecchHHHHHHHHHHHHHHHHHHHhHH------HHHHHHHHHH
Confidence 34444555444432 49999999999999877765554 455578999999999999999664 8999999964
Q ss_pred CCCCCCCEEEEeccccC-----------CCCCeeeecCCCchhhHHHHHHHHhhcccccccccchhH--HHHHHHHHHHH
Q 009071 411 SGEDGIPMLLKIPRMFD-----------PWGGYSIIGFGDILLPGLIIAFSLRYDWLANKSLQAGYF--LWAMLAYGLGL 477 (544)
Q Consensus 411 ~~~~~~P~~l~~P~~~~-----------~~~~~s~LGlGDIviPGl~ia~~~rfD~~~~~~~~~~YF--~~~~igY~~GL 477 (544)
+.++||++++|...+ .+++--|+|+||+++|-++++.+.-|-.+.- .+| +.++.|-.+|+
T Consensus 169 --d~~lPmlfviP~~l~ysf~~~~fe~r~dgna~miG~GDavmPsIlVvSaa~f~~s~~-----l~f~~Lpal~GglvGl 241 (277)
T COG3389 169 --DLDLPMLFVIPENLAYSFVEDAFENRGDGNAYMIGLGDAVMPSILVVSAAFFLISPI-----LAFIVLPALAGGLVGL 241 (277)
T ss_pred --hcCCceEEEeecccccceeehhhhcCCCCceEEEeechhhcccceeeehHHhccCCc-----hhhhhHHHHhccHHHH
Confidence 368999999996422 1356789999999999999999998865542 334 34689999999
Q ss_pred HHHHHHHHhhcCCCcceecccchhhhHHHHHHH
Q 009071 478 LITYVALNLMDGHGQPALLYIVPFTLGTFLALG 510 (544)
Q Consensus 478 ~~t~~~~~~~~~~~QPALlYlvP~~l~~~~~~a 510 (544)
++-+. ++.+++||.|.|+.-.++...++-+
T Consensus 242 ~vL~~---v~r~Rp~pGLP~lN~GaIaGflig~ 271 (277)
T COG3389 242 AVLYF---VNRGRPHPGLPFLNTGAIAGFLIGF 271 (277)
T ss_pred HHHHH---HhcCCCCCCCceeccchHHHHHHHH
Confidence 88854 3448899999999998888776654
No 24
>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=99.37 E-value=5.5e-12 Score=116.72 Aligned_cols=94 Identities=23% Similarity=0.338 Sum_probs=72.4
Q ss_pred cceEEEeecCCCCCCCC--CC-CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcccccccCCCCCCCCccce
Q 009071 82 ANQIHLTLSHPRDCCSM--PK-HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIP 158 (544)
Q Consensus 82 ~~~~~Lv~~~p~dgC~~--~~-~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IP 158 (544)
...++++.... |++ .. .+++|||+|++||+|+|.+|+++||++||+|+|++|+.+....+... ....||
T Consensus 25 ~~~~~lv~~g~---g~~~d~~~~dv~GkIvL~~rg~c~~~~K~~~a~~aGA~gvIi~n~~~~~~~~~~~-----~~~~iP 96 (143)
T cd02133 25 GKTYELVDAGL---GTPEDFEGKDVKGKIALIQRGEITFVEKIANAKAAGAVGVIIYNNVDGLIPGTLG-----EAVFIP 96 (143)
T ss_pred CcEEEEEEccC---CchhccCCCCccceEEEEECCCCCHHHHHHHHHHCCCeEEEEeecCCCcccccCC-----CCCeEe
Confidence 35677776532 222 22 46999999999999999999999999999999999998665444221 135799
Q ss_pred EEEechhhhHHHHHHHhccceEEEEee
Q 009071 159 AVMMPQDAGASLEKMLLNTSSVSVQLY 185 (544)
Q Consensus 159 vv~Is~~~G~~L~~~L~~G~~V~V~l~ 185 (544)
+++|++++|++|++.+++ ++++++.
T Consensus 97 ~v~Is~~dG~~L~~~l~~--~~~i~~~ 121 (143)
T cd02133 97 VVFISKEDGEALKAALES--SKKLTFN 121 (143)
T ss_pred EEEecHHHHHHHHHHHhC--CCeEEEE
Confidence 999999999999999987 4455543
No 25
>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=99.31 E-value=2e-11 Score=111.05 Aligned_cols=99 Identities=17% Similarity=0.153 Sum_probs=74.2
Q ss_pred ceEEEeecCCCCCCC-CC-CCCCcceEEEEecCCC--CHHHHHHHHHHcCCcEEEEEeCCCcccc-cccCCCCCCCCccc
Q 009071 83 NQIHLTLSHPRDCCS-MP-KHKYAGDVIMVDRGNC--KFTTKANIAEAAGASALLIINNQKELYK-MVCDPDETDLDIHI 157 (544)
Q Consensus 83 ~~~~Lv~~~p~dgC~-~~-~~~l~g~IaLV~RG~C--sF~~Ka~nAq~aGA~avIV~N~~~~l~~-M~~~~~~~~~~i~I 157 (544)
.+++++.+. .|.. +. ..+++|||+|++||.| +|.+|+++|+++||+|+|++|+.++... +............|
T Consensus 23 ~~~~lV~~g--~G~~~d~~~~~v~GkIvlv~~g~~~~~~~~k~~~A~~~GA~avi~~~~~~g~~~~~~~~~~~~~~~~~I 100 (127)
T cd04819 23 AKGEPVDAG--YGLPKDFDGLDLEGKIAVVKRDDPDVDRKEKYAKAVAAGAAAFVVVNTVPGVLPATGDEGTEDGPPSPI 100 (127)
T ss_pred eeEEEEEeC--CCCHHHcCCCCCCCeEEEEEcCCCchhHHHHHHHHHHCCCEEEEEEeCCCCcCcccccccccCCCCCCC
Confidence 567777654 2211 11 2369999999999999 9999999999999999999998765432 11111111234689
Q ss_pred eEEEechhhhHHHHHHHhccceEEEE
Q 009071 158 PAVMMPQDAGASLEKMLLNTSSVSVQ 183 (544)
Q Consensus 158 Pvv~Is~~~G~~L~~~L~~G~~V~V~ 183 (544)
|++.|+++||+.|++++++|+++.++
T Consensus 101 P~v~Is~edg~~L~~~l~~g~~~~~~ 126 (127)
T cd04819 101 PAASVSGEDGLRLARVAERNDTLVLR 126 (127)
T ss_pred CEEEEeHHHHHHHHHHHhcCCceEee
Confidence 99999999999999999999887664
No 26
>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=99.25 E-value=1.8e-11 Score=112.54 Aligned_cols=104 Identities=16% Similarity=0.162 Sum_probs=75.9
Q ss_pred CcceEEEeecCCCCCCCCC-CCCCcceEEEEecCCC------CHHHH-------HHHHHHcCCcEEEEEeCCCccccccc
Q 009071 81 NANQIHLTLSHPRDCCSMP-KHKYAGDVIMVDRGNC------KFTTK-------ANIAEAAGASALLIINNQKELYKMVC 146 (544)
Q Consensus 81 ~~~~~~Lv~~~p~dgC~~~-~~~l~g~IaLV~RG~C------sF~~K-------a~nAq~aGA~avIV~N~~~~l~~M~~ 146 (544)
.+++++++.....+.=+.. ..+++|||||++||.| +|..| +++|+++||.|+|++|+.+....+.+
T Consensus 15 ~gvta~vv~v~~~~~~~~~~~~~v~GKIvlv~~~~~~~~~~~~~~~k~~~r~~~~~~A~~~GA~avIv~s~~~~~~~~~~ 94 (134)
T cd04815 15 EGITAEVVVVKSFDELKAAPAGAVKGKIVFFNQPMVRTQTGSGYGPTVAYRRRGAVEAAKKGAVAVLIRSIGTDSHRSPH 94 (134)
T ss_pred CCcEEEEEEECCHHHHHhcchhhcCCeEEEecCCccccCchhhcCchhhhhhHHHHHHHhCCCEEEEEEecCcccCCCCc
Confidence 4577888765522211111 2479999999999999 99999 79999999999999997543211111
Q ss_pred CC-CCC-CCCccceEEEechhhhHHHHHHHhccceEEEEe
Q 009071 147 DP-DET-DLDIHIPAVMMPQDAGASLEKMLLNTSSVSVQL 184 (544)
Q Consensus 147 ~~-~~~-~~~i~IPvv~Is~~~G~~L~~~L~~G~~V~V~l 184 (544)
.. ... .....||++.|++++|+.|.+++++|.+|++++
T Consensus 95 ~G~~~~~~~~~~IP~v~is~ed~~~L~r~l~~g~~v~~~l 134 (134)
T cd04815 95 TGMMSYDDGVPKIPAAAISVEDADMLERLAARGKPIRVNL 134 (134)
T ss_pred CCccccCCCCCCCCEEEechhcHHHHHHHHhCCCCeEEeC
Confidence 10 111 224679999999999999999999999998864
No 27
>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=99.14 E-value=1.8e-10 Score=103.44 Aligned_cols=83 Identities=22% Similarity=0.368 Sum_probs=69.0
Q ss_pred CCCCCCCCC---CCCcceEEEEecCCC-CHHHHHHHHHHcCCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhh
Q 009071 92 PRDCCSMPK---HKYAGDVIMVDRGNC-KFTTKANIAEAAGASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAG 167 (544)
Q Consensus 92 p~dgC~~~~---~~l~g~IaLV~RG~C-sF~~Ka~nAq~aGA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G 167 (544)
....|++.. .+.+|||+|++||+| +|.+|+++||++||.|+|++|+.++...+.. ....||+++|++++|
T Consensus 36 ~~~~C~~~~~~~~~v~GkIVlc~~~~~~~~~~k~~~~~~~GA~gvI~~~~~~~~~~~~~------~~~~iP~v~I~~~~g 109 (126)
T cd02120 36 DASLCLPGSLDPSKVKGKIVLCDRGGNTSRVAKGDAVKAAGGAGMILANDPTDGLDVVA------DAHVLPAVHVDYEDG 109 (126)
T ss_pred ccccCCCCCCChhhccccEEEEeCCCCccHHHHHHHHHHcCCcEEEEEecCCCCceecc------cccccceEEECHHHH
Confidence 346898764 368999999999999 9999999999999999999999765433321 245799999999999
Q ss_pred HHHHHHHhccceE
Q 009071 168 ASLEKMLLNTSSV 180 (544)
Q Consensus 168 ~~L~~~L~~G~~V 180 (544)
+.|++.++++..-
T Consensus 110 ~~l~~y~~~~~~~ 122 (126)
T cd02120 110 TAILSYINSTSNP 122 (126)
T ss_pred HHHHHHHHcCCCc
Confidence 9999999877543
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=98.73 E-value=6.9e-08 Score=93.13 Aligned_cols=90 Identities=21% Similarity=0.207 Sum_probs=65.5
Q ss_pred ceEEEeecCCCCCCCCCC--------CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcccc-----------
Q 009071 83 NQIHLTLSHPRDCCSMPK--------HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELYK----------- 143 (544)
Q Consensus 83 ~~~~Lv~~~p~dgC~~~~--------~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l~~----------- 143 (544)
++++++.++ .| +..+ .+++|||+|++||+|++.+|+++||++||+|+|+|||..+...
T Consensus 29 v~g~lVyvn--~G-~~~Df~~L~~~gv~v~GkIvLvr~G~~~~~~Kv~~A~~~GA~gvIiy~Dp~d~~~~~~~~~~~g~~ 105 (183)
T cd02128 29 VTGKLVYAN--YG-RKKDFEDLQSVGVSVNGSVVLVRAGKISFAEKVANAEKLGAVGVLIYPDPADFPIDPSETALFGHV 105 (183)
T ss_pred eEEEEEEcC--CC-CHHHHHHHHhcCCCCCCeEEEEECCCCCHHHHHHHHHHCCCEEEEEecCHHHcCcccCcceeecce
Confidence 577887764 23 3222 3789999999999999999999999999999999998532110
Q ss_pred -cccCC---------CC----C---CCCccceEEEechhhhHHHHHHHh
Q 009071 144 -MVCDP---------DE----T---DLDIHIPAVMMPQDAGASLEKMLL 175 (544)
Q Consensus 144 -M~~~~---------~~----~---~~~i~IPvv~Is~~~G~~L~~~L~ 175 (544)
+..+| .+ . ..-.+||+.=|++++++.|++.|.
T Consensus 106 ~~~~GDplTPG~ps~~~~~~~~~~~~~lP~IPs~PIS~~da~~lL~~l~ 154 (183)
T cd02128 106 HLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPAQTISAAAAAKLLSKMG 154 (183)
T ss_pred eccCCCcCCCCCccccccccCcccccCCCCCCEeccCHHHHHHHHHHcC
Confidence 00000 00 0 012479999999999999999886
No 29
>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=98.23 E-value=9.2e-06 Score=76.34 Aligned_cols=89 Identities=12% Similarity=0.079 Sum_probs=62.4
Q ss_pred ceEEEeecC---CCCCCCCCC---CCCcceEEEEecCC------------------CCHHHHHHHHHHcCCcEEEEEeCC
Q 009071 83 NQIHLTLSH---PRDCCSMPK---HKYAGDVIMVDRGN------------------CKFTTKANIAEAAGASALLIINNQ 138 (544)
Q Consensus 83 ~~~~Lv~~~---p~dgC~~~~---~~l~g~IaLV~RG~------------------CsF~~Ka~nAq~aGA~avIV~N~~ 138 (544)
.+++++.+. ..++|...+ .+++||||||.||+ |++..|+++|+++||+|+|+||+.
T Consensus 20 vtg~lVfvGyGi~~~~~~~~Dy~giDVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~aVIv~~d~ 99 (151)
T cd04822 20 VTAPVVFAGYGITAPELGYDDYAGLDVKGKIVLVLRHEPQEDDANSRFNGPGLTRHAGLRYKATNARRHGAAAVIVVNGP 99 (151)
T ss_pred ceEeEEEecCCcCccccchhhccCCCCCCeEEEEEcCCcccccccccccccccccccCHHHHHHHHHHCCCeEEEEEeCC
Confidence 567888765 346786544 47999999999985 999999999999999999999997
Q ss_pred CcccccccCCCCCCCCccceEEEechhhhHHHHHHH
Q 009071 139 KELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKML 174 (544)
Q Consensus 139 ~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L 174 (544)
++.-. ..+..+..+.. .++.++.+..+.+.+++
T Consensus 100 ~~~~~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 132 (151)
T cd04822 100 NSHSG--DADRLPRFGGT-APQRVDIAAADPWFTAA 132 (151)
T ss_pred cccCc--ccccccccCcc-ceEEechHHHHHHhhhh
Confidence 54211 01001100111 27888888877777653
No 30
>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=98.12 E-value=7.8e-06 Score=76.04 Aligned_cols=89 Identities=17% Similarity=0.168 Sum_probs=58.8
Q ss_pred ceEEEeecC---CCCCCCCCC---CCCcceEEEEecCCC------------------CHHHHHHHHHHcCCcEEEEEeCC
Q 009071 83 NQIHLTLSH---PRDCCSMPK---HKYAGDVIMVDRGNC------------------KFTTKANIAEAAGASALLIINNQ 138 (544)
Q Consensus 83 ~~~~Lv~~~---p~dgC~~~~---~~l~g~IaLV~RG~C------------------sF~~Ka~nAq~aGA~avIV~N~~ 138 (544)
..++++.+. ...+|.-.+ .+++||||||.||+| ++..|+++|+++||.|+|++|+.
T Consensus 20 ~~aelVfvGyGi~a~~~~~dDYag~DVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~gvIii~~~ 99 (142)
T cd04814 20 KDAPLVFVGYGIKAPELSWDDYAGLDVKGKVVVVLRNDPQGEPGAGDFGGKAMTYYGRWTYKYEEAARHGAAGVLIVHEL 99 (142)
T ss_pred cceeeEEecCCcCCCCCChhhcCCCCCCCcEEEEEcCCCCcccccccccccccccccCHHHHHHHHHHCCCcEEEEEeCC
Confidence 467777653 345676544 389999999999999 69999999999999999999996
Q ss_pred CcccccccCCCCCCCCccce-EEEechhhhHHHHH
Q 009071 139 KELYKMVCDPDETDLDIHIP-AVMMPQDAGASLEK 172 (544)
Q Consensus 139 ~~l~~M~~~~~~~~~~i~IP-vv~Is~~~G~~L~~ 172 (544)
+.. .+.....-......++ ...|+...+.+|.+
T Consensus 100 ~~~-~~p~~~~~~~~~~~~~~~~~i~~~~a~~l~~ 133 (142)
T cd04814 100 APA-SYGWATWKNPAKVHPNLEAAIQRAVAVDLFE 133 (142)
T ss_pred Ccc-cCChhhhhcccccCCceeeEecHHHHHHHHh
Confidence 531 1111000000111223 44577777776654
No 31
>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=98.08 E-value=8.2e-06 Score=81.16 Aligned_cols=90 Identities=19% Similarity=0.169 Sum_probs=65.5
Q ss_pred ceEEEeecCCCCCCCCCC--------CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCcc----------c--
Q 009071 83 NQIHLTLSHPRDCCSMPK--------HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKEL----------Y-- 142 (544)
Q Consensus 83 ~~~~Lv~~~p~dgC~~~~--------~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l----------~-- 142 (544)
++++++.++ .|...+ .+++|||+|+++|+|.+.+|+++||++||+|+|+|++..+. +
T Consensus 45 v~g~lVyvn---yG~~~D~~~L~~~gvdv~GKIvLvr~G~~~~~~Kv~~A~~~GA~gVIiy~Dp~d~~~~~~~~~~~yP~ 121 (220)
T cd02121 45 VTAELVYAN---YGSPEDFEYLEDLGIDVKGKIVIARYGGIFRGLKVKNAQLAGAVGVIIYSDPADDGYITGENGKTYPD 121 (220)
T ss_pred ceEEEEEcC---CCcHHHHHHHhhcCCCCCCeEEEEECCCccHHHHHHHHHHcCCEEEEEEeCchhcccccccccccCCC
Confidence 567777665 454322 37899999999999999999999999999999999974221 0
Q ss_pred --------------c---cccCCC-----------------CCCCCccceEEEechhhhHHHHHHHh
Q 009071 143 --------------K---MVCDPD-----------------ETDLDIHIPAVMMPQDAGASLEKMLL 175 (544)
Q Consensus 143 --------------~---M~~~~~-----------------~~~~~i~IPvv~Is~~~G~~L~~~L~ 175 (544)
. ...+|. +...-.+||+.=|++.|++.|++.|.
T Consensus 122 g~~~~~~~vqRgsv~~~~~~~GDplTPG~ps~~~~~r~~~~~~~~lP~IPs~PIS~~da~~lL~~L~ 188 (220)
T cd02121 122 GPARPPSGVQRGSVLFMSIGPGDPLTPGYPSKPGAERRDKEESKGLPKIPSLPISYRDAQPLLKALG 188 (220)
T ss_pred CCCCCCCcceecceeccccCCCCCCCCCCCCCCCCcccCcccccCCCCCCcccCCHHHHHHHHHHcC
Confidence 0 000000 00012469999999999999999997
No 32
>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=98.07 E-value=1.1e-05 Score=74.73 Aligned_cols=59 Identities=17% Similarity=0.198 Sum_probs=48.1
Q ss_pred cceEEEeecC---CCCCCCCCC---CCCcceEEEEecCCCC------------HHHHHHHHHHcCCcEEEEEeCCCc
Q 009071 82 ANQIHLTLSH---PRDCCSMPK---HKYAGDVIMVDRGNCK------------FTTKANIAEAAGASALLIINNQKE 140 (544)
Q Consensus 82 ~~~~~Lv~~~---p~dgC~~~~---~~l~g~IaLV~RG~Cs------------F~~Ka~nAq~aGA~avIV~N~~~~ 140 (544)
..+++++.+. ..++|...+ .+++|||||++||+|+ +.+|.++|+++||+|+|+||+..+
T Consensus 21 ~v~gelVfvGyG~~~~~~~~~Dy~~iDVkGKIVlv~~g~p~~~~~~~~~~~~~~~~K~~~A~~~GA~aVIi~~d~~~ 97 (137)
T cd04820 21 SVEAPLVFVGYGLVAPELGHDDYAGLDVKGKIVVVLSGGPAGIPSEEGAHAHSSNEKARYAAKAGAIGMITLTTPRS 97 (137)
T ss_pred CceEeEEEecCCcCccCcCHhhccCCCCCCeEEEEEcCCCCccccccccccccHHHHHHHHHHCCCeEEEEEeCCcc
Confidence 3567887654 346776444 4899999999999995 889999999999999999999653
No 33
>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=97.87 E-value=3.1e-05 Score=72.45 Aligned_cols=75 Identities=11% Similarity=0.049 Sum_probs=55.9
Q ss_pred CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCCccc---------c--ccc--CCC--------------CCCC
Q 009071 101 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQKELY---------K--MVC--DPD--------------ETDL 153 (544)
Q Consensus 101 ~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~~l~---------~--M~~--~~~--------------~~~~ 153 (544)
-+++|||+|++.|......|++|||++||.|+|||.|..+.- . +.+ +|. +...
T Consensus 37 V~v~GkIvi~RyG~~~RG~Kv~~A~~~GA~GviIYsDP~d~~~~~~~~~~v~~v~~~~~GDP~TPG~PS~~~~~R~~~~~ 116 (153)
T cd02131 37 MNVTNQIALLKLGQAPLLYKLSLLEEAGFGGVLLYVDPCDLPKTRHTWHQAFMVSLNPGGDPSTPGYPSADQSCRQCRGN 116 (153)
T ss_pred CCccceEEEEeccCcchHHHHHHHHHCCCeEEEEecChhhccCcCCCccceEEEecCCCCCCCCCCCccccCcccCCcCC
Confidence 368999999999999999999999999999999999853210 0 000 110 0111
Q ss_pred CccceEEEechhhhHHHHHHHh
Q 009071 154 DIHIPAVMMPQDAGASLEKMLL 175 (544)
Q Consensus 154 ~i~IPvv~Is~~~G~~L~~~L~ 175 (544)
-.+||+.=|+..|++.|+++-.
T Consensus 117 lP~IPs~PIS~~dA~~lL~~~~ 138 (153)
T cd02131 117 LTSLLVQPISAYLAKKLLSAPP 138 (153)
T ss_pred CCCCcccccCHHHHHHHHhCCc
Confidence 2479999999999999877543
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=94.31 E-value=0.054 Score=51.43 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=32.9
Q ss_pred CCCcceEEEEecCCCCH-------------------HHHHHHHHHcCCcEEEEEeCCC
Q 009071 101 HKYAGDVIMVDRGNCKF-------------------TTKANIAEAAGASALLIINNQK 139 (544)
Q Consensus 101 ~~l~g~IaLV~RG~CsF-------------------~~Ka~nAq~aGA~avIV~N~~~ 139 (544)
.+++||||++.+|+=.| ..|.+.|+++||.|+|++++..
T Consensus 46 ~DVkGKiVvvl~~~P~~~~~~~~~f~~~~~~~~~~~~~K~~~A~~~GA~gvi~v~~~~ 103 (157)
T cd04821 46 LDVKGKTVVILVNDPGFATPDSGLFNGKAMTYYGRWTYKYEEAARQGAAGALIVHETE 103 (157)
T ss_pred CCcCCcEEEEEcCCCCcccccccccCcccccccccHHHHHHHHHHCCCeEEEEEeCCC
Confidence 48999999999886533 3599999999999999998754
No 35
>KOG2736 consensus Presenilin [Signal transduction mechanisms]
Probab=94.26 E-value=1.7 Score=46.49 Aligned_cols=68 Identities=22% Similarity=0.410 Sum_probs=52.9
Q ss_pred eeecCCCchhhHHHHHHHHhhcccccccccchhHHHHHHHHHHHHHHHHHHHHhhcCCCcceecccchhhhHHHHHHH
Q 009071 433 SIIGFGDILLPGLIIAFSLRYDWLANKSLQAGYFLWAMLAYGLGLLITYVALNLMDGHGQPALLYIVPFTLGTFLALG 510 (544)
Q Consensus 433 s~LGlGDIviPGl~ia~~~rfD~~~~~~~~~~YF~~~~igY~~GL~~t~~~~~~~~~~~QPALlYlvP~~l~~~~~~a 510 (544)
--||+||-|+=-+++.-+.-+|-.. . -++|++|-.+||.+|...+.++ +++-|||.. |.++|.+.-.+
T Consensus 320 ikLGlGDFIFYSvLvGkAa~~~d~~-----T--viAC~vaIL~GL~~TL~llsv~-~kALPALPi--sI~~G~iFYF~ 387 (406)
T KOG2736|consen 320 IKLGLGDFIFYSVLVGKAAAYGDLN-----T--VIACFVAILIGLCLTLLLLSVF-KKALPALPI--SITFGLIFYFS 387 (406)
T ss_pred eeeccCceEEEEeeccchhhcCChH-----H--HHHHHHHHHHHHHHHHHHHHHH-hhcCcCCch--HHHHHHHHHHH
Confidence 4699999998888877776665111 1 2489999999999999999999 899999974 66777665544
No 36
>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=92.50 E-value=0.21 Score=54.12 Aligned_cols=64 Identities=25% Similarity=0.501 Sum_probs=46.4
Q ss_pred eeecCCCchhhHHHHHHHHhh-cccccccccchhHHHHHHHHHHHHHHHHHHHHhhcCCCcceecccchhhhHHHH
Q 009071 433 SIIGFGDILLPGLIIAFSLRY-DWLANKSLQAGYFLWAMLAYGLGLLITYVALNLMDGHGQPALLYIVPFTLGTFL 507 (544)
Q Consensus 433 s~LGlGDIviPGl~ia~~~rf-D~~~~~~~~~~YF~~~~igY~~GL~~t~~~~~~~~~~~QPALlYlvP~~l~~~~ 507 (544)
--|||||-|+=+++++-+.++ |.. -...|++|-.+||.+|.+.+.++ +++-|||.- +.++|.+.
T Consensus 326 ~klGlGDFiFYs~Lvg~aa~~~~~~--------~~~~~~~ail~Gl~~Tl~~l~~~-~~alPALPi--si~~g~~~ 390 (403)
T PF01080_consen 326 IKLGLGDFIFYSVLVGRAAMYGDWN--------TVVACFVAILIGLCLTLLLLAIF-RKALPALPI--SIALGLIF 390 (403)
T ss_dssp -SS-TTTHHHHHHHHHHHHHH-TTT--------THHHHHHHHHHHHHHHHHHHHHH-T-S-SSSSS------HHHH
T ss_pred eeecchhHHHHHHHHhHHHhcCCHH--------HHHHHHHHHHHHHHHHHHHHHhc-CCCCCCCcH--HHHHHHHH
Confidence 359999999999999998876 432 24578999999999999999988 899999963 44554443
No 37
>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=62.19 E-value=8.6 Score=44.86 Aligned_cols=39 Identities=26% Similarity=0.377 Sum_probs=35.9
Q ss_pred CCCcceEEEEecCCCCHHHHHHHHHHcCCcEEEEEeCCC
Q 009071 101 HKYAGDVIMVDRGNCKFTTKANIAEAAGASALLIINNQK 139 (544)
Q Consensus 101 ~~l~g~IaLV~RG~CsF~~Ka~nAq~aGA~avIV~N~~~ 139 (544)
-+++|+|+|++=|.-.+.+|++||+++||.|+++|.+..
T Consensus 181 i~~~g~i~l~r~~~i~~g~~~~na~~~~a~gviiy~d~~ 219 (702)
T KOG2195|consen 181 INLSGKIVLARVGKIYRGKKVKNAEAAGADGVIIYTDPY 219 (702)
T ss_pred ccccCceEEEEccccchhhhHhhHHHhhcCcEEEeeccc
Confidence 368899999999999999999999999999999999754
No 38
>PRK11588 hypothetical protein; Provisional
Probab=50.28 E-value=1.1e+02 Score=34.70 Aligned_cols=43 Identities=9% Similarity=0.371 Sum_probs=26.5
Q ss_pred eeeccccchhhhHHHHHHHHHHHHHhH-HHHHHHHHHHHHHHhH
Q 009071 248 VDINTASAVLFVLVASCFLVMLYKLMS-NWFLELLVILFCIGGV 290 (544)
Q Consensus 248 ~~i~~~~a~~f~v~as~~L~~ly~f~~-~~~~~~l~~~f~i~g~ 290 (544)
.++|.+|-+...++...+..+.|=..+ .|...=+..+|.+.|+
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 478999988877777777777774432 3433334455555543
No 39
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.59 E-value=20 Score=38.31 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=19.4
Q ss_pred HHHhhhhhheeecCccchhHHHHHHH
Q 009071 332 CIAFAVVWAIYRKVSFAWIGQDILGI 357 (544)
Q Consensus 332 ~~~~~~~w~~~~~~~~~W~~~nilgi 357 (544)
+++|++.|++++-..--|++-|++.=
T Consensus 240 lILF~I~~il~~g~~g~W~FPNL~eD 265 (372)
T KOG2927|consen 240 LILFGITWILTGGKHGFWLFPNLTED 265 (372)
T ss_pred HHHHHHHHHHhCCCCceEeccchhhh
Confidence 56788899998833346998888763
No 40
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=36.78 E-value=96 Score=24.50 Aligned_cols=55 Identities=22% Similarity=0.106 Sum_probs=25.3
Q ss_pred hccceEEEEeecCCCcccchhHHHHHH--HHHHHHHHHHHHhhhhhHHHHHHHHHhhc
Q 009071 175 LNTSSVSVQLYSPRRPVVDVAEVFLWL--MAVGTILCASYWSAWSARETAIEQEKLLK 230 (544)
Q Consensus 175 ~~G~~V~V~l~~p~~p~vD~s~~~L~l--~Av~tV~~gs~ws~~~~~~~~~~~~~~~~ 230 (544)
++...|++.+..-..+ .-.+.+.+.. +++...++.+++..++.+.+.++..|+++
T Consensus 2 qN~~~V~v~~~~~~~~-~pl~l~il~~f~~G~llg~l~~~~~~~~~r~~~~~~~k~l~ 58 (68)
T PF06305_consen 2 QNTQPVTVNFLFGQFP-LPLGLLILIAFLLGALLGWLLSLPSRLRLRRRIRRLRKELK 58 (68)
T ss_pred CCCceEEEEEEeeecc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788887655444 3333333333 33333344444444444443433333333
No 41
>PF06541 DUF1113: Protein of unknown function (DUF1113); InterPro: IPR010540 This family consists of several bacterial proteins of unknown function.
Probab=36.20 E-value=3e+02 Score=25.94 Aligned_cols=26 Identities=15% Similarity=0.223 Sum_probs=18.6
Q ss_pred HHhcccCchhHHHHHHHHHHHhhhhe
Q 009071 364 LQIVHIPNLKVGTVLLSCAFMYDIFW 389 (544)
Q Consensus 364 i~~~~l~s~k~~~ilL~~lf~YDif~ 389 (544)
++.+.-...+..++.+..+++.|...
T Consensus 129 ~~~i~~~~~~~~~~~l~~~~~~D~~~ 154 (157)
T PF06541_consen 129 LSKIPPIIRNILALVLLALFLIDFVF 154 (157)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34444556677788889999999764
No 42
>COG1786 Swiveling domain associated with predicted aconitase [Energy production and conversion]
Probab=33.12 E-value=1.4e+02 Score=27.69 Aligned_cols=73 Identities=16% Similarity=0.172 Sum_probs=46.0
Q ss_pred CCCcceEEEEe--cCCCCHHHHHHHHHHcC-CcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhhHHHHHHHhcc
Q 009071 101 HKYAGDVIMVD--RGNCKFTTKANIAEAAG-ASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNT 177 (544)
Q Consensus 101 ~~l~g~IaLV~--RG~CsF~~Ka~nAq~aG-A~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G 177 (544)
.+++|||.+.. ||.|.=.-=...+.+.| |-+.||.-+.+......+ ---.||.+-... ...+.++.|
T Consensus 47 ~~l~Gkilv~P~grGStvGSyVl~~l~~~G~AP~aIv~~e~EpIla~Ga------i~a~iPlv~~~~----e~~~~l~~g 116 (131)
T COG1786 47 ESLTGKILVFPGGRGSTVGSYVLYELAKNGRAPAAIVNEEAEPILAVGA------ILAGIPLVDGVD----EFFEELKTG 116 (131)
T ss_pred ccccceEEEeeCCCCccccHHHHHHHHHcCCCchhhhhcCCcceeeehh------hhcCCceEeccH----HHHHHhccC
Confidence 47899998886 88998777777788888 545555444333333222 112678765544 355667778
Q ss_pred ceEEEE
Q 009071 178 SSVSVQ 183 (544)
Q Consensus 178 ~~V~V~ 183 (544)
..|.+.
T Consensus 117 ~~v~v~ 122 (131)
T COG1786 117 DRVRVN 122 (131)
T ss_pred CEEEEc
Confidence 776654
No 43
>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=31.47 E-value=1.2e+02 Score=33.62 Aligned_cols=15 Identities=27% Similarity=0.636 Sum_probs=10.2
Q ss_pred ecCCCchhhH--HHHHH
Q 009071 435 IGFGDILLPG--LIIAF 449 (544)
Q Consensus 435 LGlGDIviPG--l~ia~ 449 (544)
=|+|+.+-|- .+++.
T Consensus 414 ~gl~n~isPtsg~~m~~ 430 (465)
T PF03606_consen 414 DGLGNSISPTSGVLMAV 430 (465)
T ss_pred HHHHhhccchHHHHHHH
Confidence 4888888885 44443
No 44
>PF07895 DUF1673: Protein of unknown function (DUF1673); InterPro: IPR012874 This family contains hypothetical proteins of unknown function found in Methanosarcina acetivorans and Methanosarcina mazei.
Probab=22.82 E-value=6.5e+02 Score=24.86 Aligned_cols=13 Identities=23% Similarity=0.633 Sum_probs=7.7
Q ss_pred HHHHHHHhhhhee
Q 009071 378 LLSCAFMYDIFWV 390 (544)
Q Consensus 378 lL~~lf~YDif~V 390 (544)
++.+-.++++.|=
T Consensus 168 ~~wl~y~q~iywe 180 (205)
T PF07895_consen 168 LMWLVYFQIIYWE 180 (205)
T ss_pred HHHHHHHHHheee
Confidence 3455556666664
No 45
>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=21.80 E-value=30 Score=37.79 Aligned_cols=42 Identities=21% Similarity=0.306 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHH-Hhcc-cCchhHHHHHHHHHHHhhhheeee
Q 009071 350 IGQDILGIALIITVL-QIVH-IPNLKVGTVLLSCAFMYDIFWVFV 392 (544)
Q Consensus 350 ~~~nilgi~~~~~~i-~~~~-l~s~k~~~ilL~~lf~YDif~Vf~ 392 (544)
.+|-.-=+++++.+. -.++ +|. .+.-++|+++-+||+|-|-.
T Consensus 151 ~l~Q~YLI~is~l~A~~~l~~lPe-WTtW~lL~~iaiyDl~AVL~ 194 (403)
T PF01080_consen 151 LLQQAYLIMISVLMALFFLKYLPE-WTTWFLLVAIAIYDLFAVLC 194 (403)
T ss_dssp ---------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCc-hHHHHHHHHHHHHHHeeEeC
Confidence 344433344443322 2344 777 45678999999999999983
No 46
>COG4882 Predicted aminopeptidase, Iap family [General function prediction only]
Probab=21.48 E-value=3.5e+02 Score=29.61 Aligned_cols=89 Identities=19% Similarity=0.147 Sum_probs=56.6
Q ss_pred CCcceEEEEecCCCCHHHHH--HHHHHcCCcEEEEEeCCCcccccccCCCCC---CCCccceEEEechhhhHHHHHHHhc
Q 009071 102 KYAGDVIMVDRGNCKFTTKA--NIAEAAGASALLIINNQKELYKMVCDPDET---DLDIHIPAVMMPQDAGASLEKMLLN 176 (544)
Q Consensus 102 ~l~g~IaLV~RG~CsF~~Ka--~nAq~aGA~avIV~N~~~~l~~M~~~~~~~---~~~i~IPvv~Is~~~G~~L~~~L~~ 176 (544)
+..|++++-+|-.--...|. ..|.++||.|+|+-.+++..+.- .+|.+. .....||+..++..++...+.+
T Consensus 87 D~~Gr~~Va~~pq~vdd~k~~~i~Aae~ga~a~~f~~~~~rriV~-~Gd~gy~~~s~PtPIPva~v~en~~~y~~~~--- 162 (486)
T COG4882 87 DAGGRVVVARAPQVVDDLKAAAILAAEAGAEALLFESRDPRRIVT-GGDWGYSVSSSPTPIPVAVVPENYSRYAEEA--- 162 (486)
T ss_pred CCCCeEEeeeccccHHHHHHHHHHHHHcCCeEEEEecCCceeEEe-cccccccCCCCCCCcceEEeccCcchhhccc---
Confidence 66789888887665555554 36778999999998876543211 122221 2346799999999998877642
Q ss_pred cceEEEEeecCCCcccchh
Q 009071 177 TSSVSVQLYSPRRPVVDVA 195 (544)
Q Consensus 177 G~~V~V~l~~p~~p~vD~s 195 (544)
..+++..+.-++...|++
T Consensus 163 -~rvrl~vD~~~~~ty~y~ 180 (486)
T COG4882 163 -GRVRLWVDACVERTYDYN 180 (486)
T ss_pred -eeEEEEEecccceeEEEE
Confidence 345555554444444443
No 47
>PF06624 RAMP4: Ribosome associated membrane protein RAMP4; InterPro: IPR010580 This entry contains Serp1/Ramp4, which has been shown to interacts with target proteins during their translocation into the lumen of the endoplasmic reticulum. It has also been shown to protect unfolded target proteins against degradation during ER stress. It may facilitate glycosylation of target proteins after termination of ER stress and may modulate the use of N-glycosylation sites on target proteins [, ].
Probab=20.27 E-value=63 Score=26.19 Aligned_cols=14 Identities=21% Similarity=0.460 Sum_probs=8.4
Q ss_pred ccchhhhHHHHHHH
Q 009071 253 ASAVLFVLVASCFL 266 (544)
Q Consensus 253 ~~a~~f~v~as~~L 266 (544)
..-++|+|+||..+
T Consensus 42 L~l~iFVV~Gs~if 55 (63)
T PF06624_consen 42 LGLFIFVVCGSAIF 55 (63)
T ss_pred HhhhheeeEcHHHH
Confidence 34566677776554
No 48
>PRK03955 hypothetical protein; Reviewed
Probab=20.03 E-value=3.5e+02 Score=25.12 Aligned_cols=70 Identities=14% Similarity=0.097 Sum_probs=43.1
Q ss_pred CCcceEEEEe--cCCCCHHHHHHHHHHc-CCcEEEEEeCCCcccccccCCCCCCCCccceEEEechhhhHHHHHHHhccc
Q 009071 102 KYAGDVIMVD--RGNCKFTTKANIAEAA-GASALLIINNQKELYKMVCDPDETDLDIHIPAVMMPQDAGASLEKMLLNTS 178 (544)
Q Consensus 102 ~l~g~IaLV~--RG~CsF~~Ka~nAq~a-GA~avIV~N~~~~l~~M~~~~~~~~~~i~IPvv~Is~~~G~~L~~~L~~G~ 178 (544)
+++|||.+.. ||.|+=.--...+... -|-+.||..+.+......+ ---.||++.- .. .+.++.|.
T Consensus 48 si~gkIlv~p~~kGSt~gs~vl~~l~~~g~aP~aiI~~~~~~ils~Ga------IvAgIP~V~~-----~~-~~~l~~G~ 115 (131)
T PRK03955 48 SIKGKILVFPHGKGSTVGSYVIYQLAKNGTAPKAIINLEAEPIVATGA------IISGIPLVDK-----VD-ISKLKDGD 115 (131)
T ss_pred ccCCEEEEEeCCCcccchHHHHHHHHHcCCCceEEEEecCCceeEeee------eecCCceEcc-----cc-ceecCCCC
Confidence 6899998876 8899854444444444 3446666666554433321 1126888762 22 55688898
Q ss_pred eEEEE
Q 009071 179 SVSVQ 183 (544)
Q Consensus 179 ~V~V~ 183 (544)
.|++.
T Consensus 116 ~V~Vd 120 (131)
T PRK03955 116 RVVVD 120 (131)
T ss_pred EEEEe
Confidence 88775
Done!