Query 030210
Match_columns 181
No_of_seqs 174 out of 1077
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 10:14:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030210hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0793 Prc Periplasmic protea 100.0 2.7E-37 5.9E-42 267.7 18.2 163 2-175 233-395 (406)
2 cd07560 Peptidase_S41_CPP C-te 100.0 1.5E-34 3.2E-39 231.3 17.5 133 3-137 79-211 (211)
3 smart00245 TSPc tail specific 100.0 2.3E-34 5.1E-39 226.9 17.3 133 3-137 59-192 (192)
4 cd06567 Peptidase_S41 C-termin 100.0 1.1E-33 2.3E-38 227.2 17.3 135 3-137 90-224 (224)
5 TIGR00225 prc C-terminal pepti 100.0 3.7E-33 7.9E-38 236.9 18.4 137 3-141 182-318 (334)
6 cd07561 Peptidase_S41_CPP_like 100.0 5.8E-33 1.3E-37 227.9 16.8 138 3-140 95-245 (256)
7 PLN00049 carboxyl-terminal pro 100.0 6.2E-33 1.3E-37 239.8 17.4 137 3-140 225-362 (389)
8 cd07562 Peptidase_S41_TRI Tric 100.0 8.1E-33 1.8E-37 228.0 15.9 150 3-173 116-266 (266)
9 cd07563 Peptidase_S41_IRBP Int 100.0 2E-32 4.3E-37 223.7 15.3 138 3-140 96-241 (250)
10 PRK11186 carboxy-terminal prot 100.0 5E-32 1.1E-36 245.7 15.7 137 3-140 384-528 (667)
11 PF03572 Peptidase_S41: Peptid 100.0 4.2E-30 9E-35 196.8 12.7 133 3-136 33-169 (169)
12 cd07021 Clp_protease_NfeD_like 82.4 3.1 6.8E-05 32.3 5.0 25 56-80 57-81 (178)
13 PF01972 SDH_sah: Serine dehyd 60.2 30 0.00065 29.1 5.9 31 56-90 117-147 (285)
14 cd07016 S14_ClpP_1 Caseinolyti 42.5 47 0.001 24.7 4.2 25 56-80 57-81 (160)
15 cd00394 Clp_protease_like Case 42.1 53 0.0012 24.3 4.4 23 56-78 56-78 (161)
16 cd07020 Clp_protease_NfeD_1 No 41.6 59 0.0013 25.1 4.7 25 56-80 57-84 (187)
17 COG0616 SppA Periplasmic serin 40.2 25 0.00055 29.8 2.6 23 58-80 129-151 (317)
18 TIGR03121 one_C_dehyd_A formyl 37.5 29 0.00062 32.0 2.6 69 67-136 282-352 (556)
19 PRK14512 ATP-dependent Clp pro 35.6 56 0.0012 25.7 3.8 27 55-81 79-105 (197)
20 PF04028 DUF374: Domain of unk 27.0 1.4E+02 0.0031 19.6 4.1 52 57-110 9-62 (74)
21 MTH00261 ATP8 ATP synthase F0 23.7 39 0.00085 21.4 0.8 15 3-17 34-48 (68)
22 TIGR03000 plancto_dom_1 Planct 22.9 2.3E+02 0.0049 19.0 4.4 42 84-125 14-57 (75)
23 PRK00277 clpP ATP-dependent Cl 22.5 1.9E+02 0.0041 22.7 4.7 24 55-78 87-110 (200)
24 PF12854 PPR_1: PPR repeat 21.4 7.4 0.00016 21.4 -2.6 32 128-173 1-32 (34)
25 smart00726 UIM Ubiquitin-inter 20.8 87 0.0019 16.4 1.7 16 160-175 2-17 (26)
26 cd01785 PDZ_GEF_RA Ubiquitin-l 20.7 1.6E+02 0.0035 20.0 3.3 45 61-106 16-65 (85)
27 PLN02994 1-aminocyclopropane-1 20.6 1.3E+02 0.0029 22.6 3.3 34 62-95 120-153 (153)
28 smart00843 Ftsk_gamma This dom 20.6 1E+02 0.0022 19.8 2.3 20 159-178 2-21 (63)
29 COG1030 NfeD Membrane-bound se 20.0 1.7E+02 0.0038 26.2 4.3 31 5-36 60-90 (436)
No 1
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=100.00 E-value=2.7e-37 Score=267.70 Aligned_cols=163 Identities=40% Similarity=0.533 Sum_probs=145.6
Q ss_pred ceEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210 2 VFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHD 81 (181)
Q Consensus 2 ~~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~ 81 (181)
+.-||||||+|+||.+.++..++++|++++ ++++++.|+|+..++....+...+++|++||||++||||+|+||.+||+
T Consensus 233 ~~GlIlDLR~N~GG~L~~av~i~~~f~~~g-~iv~~~~r~g~~~~~~~~~~~~~~~~PlvvLvn~~SASAsEI~agalqd 311 (406)
T COG0793 233 AKGLILDLRNNPGGLLSQAVKLAGLFLPSG-PIVSTRGRNGKVNVYFSASGEALYDGPLVVLVNEGSASASEIFAGALQD 311 (406)
T ss_pred CcEEEEEeCCCCCccHHHHHHHHHcccCCC-cEEEEecCCCceeeccccccccCCCCCEEEEECCCCccHHHHHHHHHHH
Confidence 356999999999999999999999999984 8899999999887776555555789999999999999999999999999
Q ss_pred CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCCCC
Q 030210 82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEAD 161 (181)
Q Consensus 82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~D 161 (181)
+++++|||++|+|++++|+.++|++|+.+++++++||+|+|+++++.||.|||+|+..... +.. ...++|
T Consensus 312 ~~ra~lVG~~TfGkg~vQ~~~~L~dg~~lklT~a~yytp~G~~i~~~GI~PDI~v~~~~~~-~~e---------~~~~~~ 381 (406)
T COG0793 312 YGRATLVGETTFGKGTVQTLRPLSDGSALKLTIAKYYTPSGRSIEGKGITPDIEVPQADDE-PGE---------YAAGRD 381 (406)
T ss_pred cCCcEEEecccccceEEEeeEEcCCCCeEEEEEEEEECCCCccccccCcCCCEeccCCccc-chh---------hhcccc
Confidence 9999999999999999999999999999999999999999999999999999999987531 111 122789
Q ss_pred HHHHHHHHHHhhhc
Q 030210 162 SCIMVAEHELDVQE 175 (181)
Q Consensus 162 ~~l~~Ai~~L~~~~ 175 (181)
++++.|++.+....
T Consensus 382 ~~~~~~~~~~~~~~ 395 (406)
T COG0793 382 PQLEAALEALLKGL 395 (406)
T ss_pred hHhhhhhhhhhhhh
Confidence 99999999887665
No 2
>cd07560 Peptidase_S41_CPP C-terminal processing peptidase; serine protease family S41. The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectl
Probab=100.00 E-value=1.5e-34 Score=231.28 Aligned_cols=133 Identities=46% Similarity=0.689 Sum_probs=121.1
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN 82 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~ 82 (181)
..||||||+|+||++..+..++++|+++. .+++++.|+|+...+.. .....+.+|++||||+.|+||||+||++||++
T Consensus 79 ~~lIlDLR~N~GG~~~~~~~i~~~f~~~~-~~~~~~~~~g~~~~~~~-~~~~~~~~pvvVLvn~~TaSaaE~~a~~lk~~ 156 (211)
T cd07560 79 KGLILDLRNNPGGLLDEAVEIADLFLPGG-PIVSTKGRNGKREAYAS-DDGGLYDGPLVVLVNGGSASASEIVAGALQDN 156 (211)
T ss_pred ceEEEEcCCCCCCCHHHHHHHHHHhcCCC-eEEEEEecCCceEEEec-CCCccCCCCEEEEeCCCcccHHHHHHHHHhhc
Confidence 57999999999999999999999999965 67788888887654433 33457899999999999999999999999999
Q ss_pred CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEec
Q 030210 83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCT 137 (181)
Q Consensus 83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~ 137 (181)
+++++||++|+|++..+..+.|++|+.+++++.++++++|+.+|+.||+|||+|+
T Consensus 157 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~G~~~e~~GV~PDi~V~ 211 (211)
T cd07560 157 GRAVLVGERTFGKGSVQTVFPLSDGSALKLTTAKYYTPSGRSIQKKGIEPDIEVP 211 (211)
T ss_pred CCEEEEecCCCCCCeeeEEEEcCCCCEEEEEEEEEECCCCCCccCCCcCCCEECC
Confidence 9999999999999999999999999999999999999999999999999999985
No 3
>smart00245 TSPc tail specific protease. tail specific protease
Probab=100.00 E-value=2.3e-34 Score=226.92 Aligned_cols=133 Identities=44% Similarity=0.628 Sum_probs=116.9
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCC-CceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDRE-GHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHD 81 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~-g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~ 81 (181)
..||||||+|+||.+..+..++++|++++. +.....+. ++...+.. .....+++|++||||+.|+||||+||++||+
T Consensus 59 ~~lIiDLR~N~GG~~~~~~~~~~~f~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~pv~vL~~~~TaSaaE~~a~~lk~ 136 (192)
T smart00245 59 EGLILDLRNNPGGLLSAAIDVSSLFLDKGV-IVYTIYRRTGELETYPA-NLGRKYSKPLVVLVNEGTASASEIFAGALKD 136 (192)
T ss_pred cEEEEEecCCCCCCHHHHHHHHHHhcCCCc-EEEEEecCCCceEEEec-CCCcccCCCEEEEECCCCeeHHHHHHHHHhh
Confidence 579999999999999999999999999874 44444444 54433332 3334679999999999999999999999999
Q ss_pred CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEec
Q 030210 82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCT 137 (181)
Q Consensus 82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~ 137 (181)
++++++||++|+|++..+..+.|++|+.+++++.++++++|+++|+.||+|||+|+
T Consensus 137 ~~~a~viG~~T~G~~~~~~~~~l~~g~~l~it~~~~~~~~g~~~e~~Gv~PDi~v~ 192 (192)
T smart00245 137 LGRALIVGERTFGKGLVQQTVPLGDGSGLKLTVAKYYTPSGKSIEKKGVEPDIQVP 192 (192)
T ss_pred CCCEEEEecCCcCCcceeeEEEeCCCCEEEEEEEEEECCCCCEecCCCcCCCEECc
Confidence 99999999999999999999999999999999999999999999999999999985
No 4
>cd06567 Peptidase_S41 C-terminal processing peptidase family S41. Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn pr
Probab=100.00 E-value=1.1e-33 Score=227.21 Aligned_cols=135 Identities=44% Similarity=0.633 Sum_probs=118.2
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN 82 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~ 82 (181)
..||||||+|+||++..+..++++|+++...+.....+.+....+........+.+|++||||+.|+||||+|+.+||++
T Consensus 90 ~~lIiDLR~N~GG~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~vL~~~~taSaaE~~a~~lk~~ 169 (224)
T cd06567 90 KGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDL 169 (224)
T ss_pred CEEEEEcCCCCCccHHHHHHHHHHhcCCCcEEEEEecCCCceeEEecCCCCcccCCCEEEEECCCCccHHHHHHHHHHhC
Confidence 57999999999999999999999999987554444433332233333455678999999999999999999999999999
Q ss_pred CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEec
Q 030210 83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCT 137 (181)
Q Consensus 83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~ 137 (181)
+++++||++|+|+++.+..+.|++|+.+.+|+.++++|+|..+|+.||+|||+|+
T Consensus 170 ~~~~vvG~~T~G~~~~~~~~~l~~g~~~~~~~~~~~~~~g~~~~~~Gv~PDi~v~ 224 (224)
T cd06567 170 GRATLVGERTFGKGSVQTVFPLLDGSALKLTTAKYYTPSGRSIEGKGVEPDIEVP 224 (224)
T ss_pred CCeEEEeeCCCCCCcceEEEEcCCCCEEEEEEEEEECCCCCCccCCccCCCEECC
Confidence 9999999999999998899999999999999999999999999999999999874
No 5
>TIGR00225 prc C-terminal peptidase (prc). A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database.
Probab=100.00 E-value=3.7e-33 Score=236.87 Aligned_cols=137 Identities=43% Similarity=0.622 Sum_probs=124.9
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN 82 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~ 82 (181)
..||||||+|+||++..+..++++|++++ .++++++++|+...+. .++...+++|++||||+.||||||+||++||++
T Consensus 182 ~~lIiDLR~N~GG~~~~a~~~a~~f~~~~-~~~~~~~~~g~~~~~~-~~~~~~~~~pv~vLvn~~TaSaaE~~a~~l~~~ 259 (334)
T TIGR00225 182 KGYILDLRGNPGGLLQSAVDISRLFITKG-PIVQTKDRNGSKRHYK-ANGRQPYNLPLVVLVNRGSASASEIFAGALQDN 259 (334)
T ss_pred ceEEEEcCCCCCCCHHHHHHHHHHhcCCC-cEEEEEcCCCcceEEe-cCCCccCCCCEEEEECCCCCcHHHHHHHHHHhC
Confidence 46999999999999999999999999987 6778888888765443 344567899999999999999999999999999
Q ss_pred CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCC
Q 030210 83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDML 141 (181)
Q Consensus 83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~ 141 (181)
+++++||++|+|++..+..+.|++|+.+.+++.++++|+|+++|+.||+|||+|+.++.
T Consensus 260 ~~a~viG~~T~G~~~~~~~~~l~~g~~l~~~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~ 318 (334)
T TIGR00225 260 GRATIVGEKTFGKGTVQQVRPLNDGSGIKVTIAKYYTPNGGSIHKKGIEPDIVIEQPDD 318 (334)
T ss_pred CCeEEEeeCCccCceeeeEEEcCCCCEEEEEEEEEECCCCCCccCcCcCCCEEecCccc
Confidence 99999999999999989999999999999999999999999999999999999997764
No 6
>cd07561 Peptidase_S41_CPP_like C-terminal processing peptidase-like; serine protease family S41. Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.
Probab=100.00 E-value=5.8e-33 Score=227.91 Aligned_cols=138 Identities=22% Similarity=0.233 Sum_probs=118.7
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCC---CceeEEEEcCCCc-----eeEEEccC---CCccCCCcEEEEEcCCCccH
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDG---DETLVNAVDREGH-----TLPINMVD---GHAITHDPLVVLVNEGSASA 71 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~---~~~~~~~~~r~g~-----~~~~~~~~---~~~~~~~pv~VL~~~~TaSa 71 (181)
..||||||+|+||.+..|..+|++|+++ +.++.++.++++. ...+.... ......+||+||||+.||||
T Consensus 95 ~~LIlDLR~N~GG~~~~a~~las~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~VL~~~~TASA 174 (256)
T cd07561 95 TELVLDLRYNGGGLVSSANLLASLLAPAVALGQVFATLEYNDKRSANNEDLLFSSKTLAGGNSLNLSKVYVLTSGSTASA 174 (256)
T ss_pred CeEEEEeCCCCCccHHHHHHHHHHhcCcccCCCeEEEEEecCCccCCCceeecccccccccCcCCcccEEEEECCCcccH
Confidence 5799999999999999999999999994 4456666666652 12232221 23456789999999999999
Q ss_pred HHHHHHHHhcCCCeEEEcccCCCCceeceEEEcc--CCceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210 72 SEILAGALHDNGRAILVGHKTFGKGKIQSVTELH--DGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM 140 (181)
Q Consensus 72 aE~fa~~l~~~~~~~vIG~~T~G~~~~~~~~~L~--~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~ 140 (181)
||+||.+||+++++++||++|+|++..+..+.++ +|+.++++++++++|+|+.+++.||+||++|+.+.
T Consensus 175 aE~~a~~Lk~~~~a~vIGe~T~Gk~~~~~~~~l~~~~g~~l~~t~~~~~~~~G~~~~~~Gi~PDi~v~~~~ 245 (256)
T cd07561 175 SELVINSLKPYMDVVLIGETTYGKNVGSLTFEDDRKHKWALQPVVFKVVNADGQGDYSNGLTPDIEVNEDS 245 (256)
T ss_pred HHHHHHHhhccCCEEEEeCCCCCCCccceEEEccCCCCeEEEEEEEEEECCCCCCccCCCcCCceEeCccc
Confidence 9999999999999999999999999999999998 89999999999999999999999999999998764
No 7
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=100.00 E-value=6.2e-33 Score=239.82 Aligned_cols=137 Identities=50% Similarity=0.685 Sum_probs=120.2
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCC-CccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDG-HAITHDPLVVLVNEGSASASEILAGALHD 81 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~-~~~~~~pv~VL~~~~TaSaaE~fa~~l~~ 81 (181)
..||||||+|+||.+..+..++++|++++ .+++...+++....+..... ...+.+|++||||+.||||||+||.+||+
T Consensus 225 ~glIlDLR~N~GG~~~~a~~ia~~f~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~PvvVLvn~~TaSasEi~a~alk~ 303 (389)
T PLN00049 225 DAFVLDLRDNSGGLFPAGIEIAKLWLDKG-VIVYIADSRGVRDIYDADGSSAIATSEPLAVLVNKGTASASEILAGALKD 303 (389)
T ss_pred CEEEEEcCCCCCCCHHHHHHHHHHhcCCC-cEEEEecCCCceeEEecCCCccccCCCCEEEEECCCCccHHHHHHHHHhh
Confidence 46999999999999999999999999987 45565555665444443222 23578999999999999999999999999
Q ss_pred CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210 82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM 140 (181)
Q Consensus 82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~ 140 (181)
++++++||++|+|+++.+..+.|+||+.+++++++|++|+|+++|+.||+||++|+...
T Consensus 304 ~~~~~vvG~~T~Gkg~~q~~~~L~dG~~l~lt~~~~~~p~G~~ie~~Gi~PDi~v~~~~ 362 (389)
T PLN00049 304 NKRAVVLGEPTFGKGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGITPDHPLPESL 362 (389)
T ss_pred CCCeEEEecCCcCCcccceeEEeCCCCEEEEEEEEEECCCCCCcCCCCcCCCeECCCCC
Confidence 99999999999999999999999999999999999999999999999999999998654
No 8
>cd07562 Peptidase_S41_TRI Tricorn protease; serine protease family S41. The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active sit
Probab=100.00 E-value=8.1e-33 Score=228.04 Aligned_cols=150 Identities=25% Similarity=0.235 Sum_probs=126.6
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCC-CceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDRE-GHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHD 81 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~-g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~ 81 (181)
..||||||+|+||++ +..++++|.+. .+.+...|+ +.... .+...|++|++||||+.|+||||+|+.+||+
T Consensus 116 ~glIiDlR~N~GG~~--~~~l~~~~~~~--~~~~~~~r~~~~~~~----~p~~~~~~pv~vL~~~~t~SaaE~~a~~lk~ 187 (266)
T cd07562 116 DGLIIDVRFNGGGNV--ADLLLDFLSRR--RYGYDIPRGGGKPVT----YPSGRWRGPVVVLVNEGSASDAEIFAYGFRA 187 (266)
T ss_pred ceEEEEecCCCCCcH--HHHHHHHhCCC--ceEEEccCCCCCCCC----CcccccCCCEEEEECCCCCchHHHHHHHHHH
Confidence 469999999999994 44678888765 455666666 33221 1122389999999999999999999999999
Q ss_pred CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCCCC
Q 030210 82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEAD 161 (181)
Q Consensus 82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~D 161 (181)
++++++||++|+|++..+..+.||+|+.+.++...+++++|+.+|+.||.|||+|+.++... .. ++|
T Consensus 188 ~~~~~vvG~~T~G~~~~~~~~~L~~g~~~~~~~~~~~~~~g~~~e~~Gi~PDi~v~~~~~~~------------~~-g~D 254 (266)
T cd07562 188 LGLGPVVGTRTAGGVIISGRYRLPDGGSLTVPEFGVYLPDGGPLENRGVAPDIEVENTPEDV------------AA-GRD 254 (266)
T ss_pred cCCeeEEeeccCCceeecCceecCCCCEEEeeceeEEcCCCCccccCCCCCCEEecCCHhHh------------hc-CCC
Confidence 99999999999999998888999999999999999999999999999999999999876542 12 899
Q ss_pred HHHHHHHHHHhh
Q 030210 162 SCIMVAEHELDV 173 (181)
Q Consensus 162 ~~l~~Ai~~L~~ 173 (181)
|+|++|+++|.+
T Consensus 255 ~~L~~Al~~l~~ 266 (266)
T cd07562 255 PQLEAAIEELLK 266 (266)
T ss_pred HHHHHHHHHHhC
Confidence 999999999863
No 9
>cd07563 Peptidase_S41_IRBP Interphotoreceptor retinoid-binding protein; serine protease family S41. Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors
Probab=100.00 E-value=2e-32 Score=223.66 Aligned_cols=138 Identities=25% Similarity=0.230 Sum_probs=117.2
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCcee--EEEEcCCCceeE-----EEccCCCccCCCcEEEEEcCCCccHHHHH
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETL--VNAVDREGHTLP-----INMVDGHAITHDPLVVLVNEGSASASEIL 75 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~--~~~~~r~g~~~~-----~~~~~~~~~~~~pv~VL~~~~TaSaaE~f 75 (181)
..||||||+|+||+...+..++++|+++...+ .....|++.... +..+.....+++||+||||+.|+||||+|
T Consensus 96 ~~LIIDLR~N~GG~~~~~~~l~s~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~vL~~~~T~SaaE~~ 175 (250)
T cd07563 96 DALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEF 175 (250)
T ss_pred CeEEEEECCCCCCCHHHHHHHHHHcCCCCCcEEEEEEEECCCCCCcccceeeecCCCcccCCCCEEEEeCCCcCcHHHHH
Confidence 36999999999999999999999999644333 333444443221 22234456799999999999999999999
Q ss_pred HHHHhcCCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCC-CCcccCCCcccceEecCCC
Q 030210 76 AGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPA-LHDIDHVGITPDVQCTTDM 140 (181)
Q Consensus 76 a~~l~~~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~-g~~~e~~Gv~PDi~v~~~~ 140 (181)
+++||+++++++||++|+|++..+..+.||+|+.+.+++.++++++ |..+|+.||.|||.|+.++
T Consensus 176 a~~lk~~~~~~viGe~T~G~~~~~~~~~Lp~g~~~~~~~~~~~~~~~g~~~e~~Gv~PDi~v~~~~ 241 (250)
T cd07563 176 AYALKQLKRATVVGETTAGGASPVLPFPLPNGLYLTVPTSRSVDPITGTNWEGVGVPPDIEVPATP 241 (250)
T ss_pred HHHHHhCCCcEEEeecCCCCCCCceEEEcCCCeEEEEecceeEeCCCCCcccccCcCCCeeecCCC
Confidence 9999999999999999999999889999999999999999999998 9999999999999998753
No 10
>PRK11186 carboxy-terminal protease; Provisional
Probab=99.98 E-value=5e-32 Score=245.73 Aligned_cols=137 Identities=31% Similarity=0.427 Sum_probs=121.7
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN 82 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~ 82 (181)
..||||||+|+||.+..|..++++|++++ ++++.++++|+...+....+...|.+|++||||++||||||+||++||++
T Consensus 384 ~gLIlDLR~NgGG~l~~a~~la~lFi~~g-~vv~~~~~~g~~~~~~~~~~~~~~~gPlvVLVN~~SASASEIfA~alqd~ 462 (667)
T PRK11186 384 SGIIIDLRGNGGGALTEAVSLSGLFIPSG-PVVQVRDNNGRVRVDSDTDGVVYYKGPLVVLVDRYSASASEIFAAAMQDY 462 (667)
T ss_pred CEEEEEcCCCCCCcHHHHHHHHHHHhcCC-ceEEEecCCCceeccccCCcccccCCCEEEEeCCCCccHHHHHHHHHHhc
Confidence 57999999999999999999999999986 67788888887655444455568999999999999999999999999999
Q ss_pred CCeEEEcccCCCCceeceEEEccC--------CceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210 83 GRAILVGHKTFGKGKIQSVTELHD--------GSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM 140 (181)
Q Consensus 83 ~~~~vIG~~T~G~~~~~~~~~L~~--------g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~ 140 (181)
+++++||++|+|+|++|..++|++ +..+++|+++|++|+|.++++.||+|||.|+...
T Consensus 463 ~ra~vVG~~T~GKGtvQ~~~~L~~~~~~~~~~~G~lk~Tiak~y~p~G~s~q~~GV~PDi~vp~~~ 528 (667)
T PRK11186 463 GRALIVGEPTFGKGTVQQHRSLNRIYDQMLRPLGSVQYTIQKFYRINGGSTQRKGVTPDIIFPTGI 528 (667)
T ss_pred CCEEEEeccCCCccccccccccccccccccCCCCeeEEEEeEEECCCCCcccCCCCCCCeEcCCCc
Confidence 999999999999999998777653 3469999999999999999999999999998643
No 11
>PF03572 Peptidase_S41: Peptidase family S41; InterPro: IPR005151 This group of putative serine peptidases belong to the MEROPS peptidase family S41 (C-terminal processing peptidase family, clan SM). The members of this group include: the tricorn protease of bacteria and archaea, C-terminal peptidases with different substrates specificities in different species including processing of D1 protein of the photosystem II reaction centre in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and some appear to be responsible for degrading oligopeptides, probably derived from the proteasome. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A 3K50_A 3DJA_B 3DPM_B 3DPN_A 3DOR_B 1J7X_A ....
Probab=99.97 E-value=4.2e-30 Score=196.84 Aligned_cols=133 Identities=30% Similarity=0.379 Sum_probs=99.5
Q ss_pred eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCcee----EEEccCCCccCCCcEEEEEcCCCccHHHHHHHH
Q 030210 3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTL----PINMVDGHAITHDPLVVLVNEGSASASEILAGA 78 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~----~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~ 78 (181)
..||||||+|+||+...+..++++|.++. ..+....+.+... ..........+.+|++||||+.|+||||.|+.+
T Consensus 33 ~~lIIDlR~N~GG~~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vL~~~~t~Saae~fa~~ 111 (169)
T PF03572_consen 33 DGLIIDLRGNGGGSDEYAIELLSYLIPKP-IIFYYRDRIGSNKKWVSTIKWSTPKNRFNGPVYVLTDENTASAAEIFASA 111 (169)
T ss_dssp SEEEEE-TTB--BSHHHHHHHHHCHSSSS-EEEEEEEEEEEETTCCHEEEECSSTT-SSSEEEEEE-TTBBTHHHHHHHH
T ss_pred CEEEEEcccCCCcchHHHHHHHhcccCCC-cEEEEecccccccccccCCCCccccccCCCCEEEEeCCCCCChhHHHHHH
Confidence 57999999999999999999999999975 3333222211111 000111156799999999999999999999999
Q ss_pred HhcCCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEe
Q 030210 79 LHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQC 136 (181)
Q Consensus 79 l~~~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v 136 (181)
||+++++++||++|+|.+..+..+.|++|+.++++...+++++|..+|+.||.|||+|
T Consensus 112 lk~~~~~~ivGe~T~G~~~~~~~~~l~~g~~~~i~~~~~~~~~g~~~~~~Gi~PDi~V 169 (169)
T PF03572_consen 112 LKDNKRATIVGEPTAGAGGGQTGFSLPSGSILSIPTSRYYNPDGQKIEGIGIEPDIEV 169 (169)
T ss_dssp HHHTTSEEEEES--SB-EEEEEEEE-TTSEEEEEEEEEEEETTSBBTTTTS---SEE-
T ss_pred HHhcCCCeEEeecCCCCCEEeeEEEECCCcEEEeEeEEEEeCCCCEEcCCcEEccEEC
Confidence 9999999999999999998888999999999999999999999999999999999987
No 12
>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentiall
Probab=82.41 E-value=3.1 Score=32.33 Aligned_cols=25 Identities=32% Similarity=0.384 Sum_probs=21.3
Q ss_pred CCCcEEEEEcCCCccHHHHHHHHHh
Q 030210 56 THDPLVVLVNEGSASASEILAGALH 80 (181)
Q Consensus 56 ~~~pv~VL~~~~TaSaaE~fa~~l~ 80 (181)
..+|+++.+++..+|++-+++.+-.
T Consensus 57 ~~~pvva~V~g~AaSaG~~ia~a~d 81 (178)
T cd07021 57 SPIPTIAYVNDRAASAGALIALAAD 81 (178)
T ss_pred CCCCEEEEECCchHHHHHHHHHhCC
Confidence 3479999999999999999988654
No 13
>PF01972 SDH_sah: Serine dehydrogenase proteinase; InterPro: IPR002825 This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family belong to MEROPS peptidase family S49; they are mostly unassigned peptidases but include the archaean signal peptide peptidase 1 []. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan []. ; GO: 0016021 integral to membrane
Probab=60.17 E-value=30 Score=29.06 Aligned_cols=31 Identities=26% Similarity=0.332 Sum_probs=23.4
Q ss_pred CCCcEEEEEcCCCccHHHHHHHHHhcCCCeEEEcc
Q 030210 56 THDPLVVLVNEGSASASEILAGALHDNGRAILVGH 90 (181)
Q Consensus 56 ~~~pv~VL~~~~TaSaaE~fa~~l~~~~~~~vIG~ 90 (181)
+..|+.|+|..+..||+-++|.+-.+ .++|.
T Consensus 117 ~~~~v~v~VP~~A~SAGTlIALaADe----IvM~p 147 (285)
T PF01972_consen 117 HPAKVTVIVPHYAMSAGTLIALAADE----IVMGP 147 (285)
T ss_pred CCCCEEEEECcccccHHHHHHHhCCe----EEECC
Confidence 34688899999999999999877443 45554
No 14
>cd07016 S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which a
Probab=42.48 E-value=47 Score=24.70 Aligned_cols=25 Identities=24% Similarity=0.210 Sum_probs=20.8
Q ss_pred CCCcEEEEEcCCCccHHHHHHHHHh
Q 030210 56 THDPLVVLVNEGSASASEILAGALH 80 (181)
Q Consensus 56 ~~~pv~VL~~~~TaSaaE~fa~~l~ 80 (181)
..+|+++.+++..+|+|=.++.+-.
T Consensus 57 ~~~pvi~~v~g~a~s~g~~ia~a~d 81 (160)
T cd07016 57 HKGKVTVKIDGLAASAASVIAMAGD 81 (160)
T ss_pred cCCCEEEEEcchHHhHHHHHHhcCC
Confidence 4689999999999999988776644
No 15
>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradec
Probab=42.09 E-value=53 Score=24.30 Aligned_cols=23 Identities=30% Similarity=0.419 Sum_probs=16.7
Q ss_pred CCCcEEEEEcCCCccHHHHHHHH
Q 030210 56 THDPLVVLVNEGSASASEILAGA 78 (181)
Q Consensus 56 ~~~pv~VL~~~~TaSaaE~fa~~ 78 (181)
+++|++..+++..+|++=.++.+
T Consensus 56 ~~kpvva~~~g~~~s~g~~la~~ 78 (161)
T cd00394 56 SRKPVIAYVGGQAASAGYYIATA 78 (161)
T ss_pred hCCCEEEEECChhHHHHHHHHhC
Confidence 34788888888888777666554
No 16
>cd07020 Clp_protease_NfeD_1 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially c
Probab=41.57 E-value=59 Score=25.09 Aligned_cols=25 Identities=36% Similarity=0.359 Sum_probs=20.8
Q ss_pred CCCcEEEEEc---CCCccHHHHHHHHHh
Q 030210 56 THDPLVVLVN---EGSASASEILAGALH 80 (181)
Q Consensus 56 ~~~pv~VL~~---~~TaSaaE~fa~~l~ 80 (181)
..+|++..++ +..+|++=.++.+-.
T Consensus 57 ~~kPvia~v~~~~G~AasgG~~iala~D 84 (187)
T cd07020 57 SPVPVVVYVYPSGARAASAGTYILLAAH 84 (187)
T ss_pred CCCCEEEEEecCCCCchhHHHHHHHhCC
Confidence 5689999998 899999988877644
No 17
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=40.24 E-value=25 Score=29.77 Aligned_cols=23 Identities=35% Similarity=0.280 Sum_probs=20.1
Q ss_pred CcEEEEEcCCCccHHHHHHHHHh
Q 030210 58 DPLVVLVNEGSASASEILAGALH 80 (181)
Q Consensus 58 ~pv~VL~~~~TaSaaE~fa~~l~ 80 (181)
+||+|.++...||++=++|.+-.
T Consensus 129 ~PV~v~v~~~AASGGY~IA~aAd 151 (317)
T COG0616 129 KPVVVSVGGYAASGGYYIALAAD 151 (317)
T ss_pred CCEEEEECCeecchhhhhhccCC
Confidence 39999999999999999887744
No 18
>TIGR03121 one_C_dehyd_A formylmethanofuran dehydrogenase subunit A. Members of this largely archaeal protein family are subunit A of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit A. Note that this model does not distinguish tungsten (FwdA) from molybdenum-containing (FmdA) forms of this enzyme; a single gene from this family is expressed constitutively in Methanobacterium thermoautotrophicum, which has both tungsten and molybdenum forms and may work interchangeably.
Probab=37.47 E-value=29 Score=32.00 Aligned_cols=69 Identities=19% Similarity=0.146 Sum_probs=41.7
Q ss_pred CCccHHHHHHHHHhcCCCeEE-EcccCCCCceeceEEEccCCc-eEEEEEEEEECCCCCcccCCCcccceEe
Q 030210 67 GSASASEILAGALHDNGRAIL-VGHKTFGKGKIQSVTELHDGS-ALFVTVAKYLSPALHDIDHVGITPDVQC 136 (181)
Q Consensus 67 ~TaSaaE~fa~~l~~~~~~~v-IG~~T~G~~~~~~~~~L~~g~-~l~i~~~~~~~~~g~~~e~~Gv~PDi~v 136 (181)
.-.|+|+-+|.++..++++++ ||+-++|..+..+.- -|-.. .-.++..+|.+.|-+.--+.||.|=+.-
T Consensus 282 ~f~s~a~~~a~~vn~~~~~t~d~Gqv~fg~t~tmt~d-~~~~~~~~~~~~~kw~~~d~e~e~g~gvvp~~y~ 352 (556)
T TIGR03121 282 DFESGAEKIADYVNANPNVTIDVGQVTFGETTTMTAD-GPMEYDLHKLTGLKWANKDVELETGSGVVPFKYS 352 (556)
T ss_pred CcchhHHHHHHHHhcCCCEEEEeCceecCCceEEecc-chhhhhcccCCCCceeeeeeecccCCceEEeeec
Confidence 446889999999999998765 899999985432110 00000 1122334565555544346688876543
No 19
>PRK14512 ATP-dependent Clp protease proteolytic subunit; Provisional
Probab=35.63 E-value=56 Score=25.71 Aligned_cols=27 Identities=15% Similarity=0.035 Sum_probs=22.5
Q ss_pred cCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210 55 ITHDPLVVLVNEGSASASEILAGALHD 81 (181)
Q Consensus 55 ~~~~pv~VL~~~~TaSaaE~fa~~l~~ 81 (181)
..+.||++++++..+|+|-+++.+=..
T Consensus 79 ~~~~~V~t~v~G~AaSaaslIl~ag~~ 105 (197)
T PRK14512 79 FVKPKVFTIGVGLVASAAALIFLAAKK 105 (197)
T ss_pred hCCCCEEEEEEeeeHhHHHHHHhcCCc
Confidence 456799999999999999998877543
No 20
>PF04028 DUF374: Domain of unknown function (DUF374); InterPro: IPR007172 This is a bacterial domain of unknown function.
Probab=27.00 E-value=1.4e+02 Score=19.64 Aligned_cols=52 Identities=19% Similarity=0.345 Sum_probs=38.6
Q ss_pred CCcEEEEEcCCCccHHHHHHHHHhcCCCeEEEcccCCCCceec--eEEEccCCceE
Q 030210 57 HDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQ--SVTELHDGSAL 110 (181)
Q Consensus 57 ~~pv~VL~~~~TaSaaE~fa~~l~~~~~~~vIG~~T~G~~~~~--~~~~L~~g~~l 110 (181)
..++++|+++.- .+|+++..++.++--+|=|..+-|..... ....|.+|..+
T Consensus 9 ~~~~~~lvS~s~--DGe~ia~~~~~~G~~~iRGSs~rgg~~Alr~~~~~lk~G~~~ 62 (74)
T PF04028_consen 9 RRKIAALVSRSR--DGELIARVLERFGFRTIRGSSSRGGARALREMLRALKEGYSI 62 (74)
T ss_pred CCCEEEEEccCc--CHHHHHHHHHHcCCCeEEeCCCCcHHHHHHHHHHHHHCCCeE
Confidence 478999998754 78999999999999999999888764322 12235555443
No 21
>MTH00261 ATP8 ATP synthase F0 subunit 8; Provisional
Probab=23.71 E-value=39 Score=21.35 Aligned_cols=15 Identities=13% Similarity=-0.168 Sum_probs=11.9
Q ss_pred eEEEeecCCCCCCCH
Q 030210 3 FFSPPSLSIFQGGLV 17 (181)
Q Consensus 3 ~~lIiDLR~N~GG~~ 17 (181)
|++|+.+|+|---+.
T Consensus 34 fflvlnirnn~~~~s 48 (68)
T MTH00261 34 FFLVLNIRNNFICNS 48 (68)
T ss_pred hheeEecccceecch
Confidence 789999999975543
No 22
>TIGR03000 plancto_dom_1 Planctomycetes uncharacterized domain TIGR03000. Domains described by this model are found, so far, only in the Planctomycetes (Pirellula sp. strain 1 and Gemmata obscuriglobus), in up to six proteins per genome, and may be duplicated within a protein. The function is unknown.
Probab=22.89 E-value=2.3e+02 Score=18.96 Aligned_cols=42 Identities=21% Similarity=0.251 Sum_probs=30.4
Q ss_pred CeEEEcccCCCCceeceEE--EccCCceEEEEEEEEECCCCCcc
Q 030210 84 RAILVGHKTFGKGKIQSVT--ELHDGSALFVTVAKYLSPALHDI 125 (181)
Q Consensus 84 ~~~vIG~~T~G~~~~~~~~--~L~~g~~l~i~~~~~~~~~g~~~ 125 (181)
+..+=|.+|.|.|...+.. .|+.|..+.+.+.--+.+||+.+
T Consensus 14 kl~v~G~~t~~~G~~R~F~T~~L~~G~~y~Y~v~a~~~~dG~~~ 57 (75)
T TIGR03000 14 KLKVDGKETNGTGTVRTFTTPPLEAGKEYEYTVTAEYDRDGRIL 57 (75)
T ss_pred EEEECCeEcccCccEEEEECCCCCCCCEEEEEEEEEEecCCcEE
Confidence 4566699999987654433 58889887787777778888643
No 23
>PRK00277 clpP ATP-dependent Clp protease proteolytic subunit; Reviewed
Probab=22.51 E-value=1.9e+02 Score=22.67 Aligned_cols=24 Identities=17% Similarity=0.151 Sum_probs=19.8
Q ss_pred cCCCcEEEEEcCCCccHHHHHHHH
Q 030210 55 ITHDPLVVLVNEGSASASEILAGA 78 (181)
Q Consensus 55 ~~~~pv~VL~~~~TaSaaE~fa~~ 78 (181)
....|++.++++..+|+|-+++.+
T Consensus 87 ~~~~~v~t~~~G~aaS~a~~I~~a 110 (200)
T PRK00277 87 FIKPDVSTICIGQAASMGAFLLAA 110 (200)
T ss_pred hcCCCEEEEEEeEeccHHHHHHhc
Confidence 345689999999999999888777
No 24
>PF12854 PPR_1: PPR repeat
Probab=21.40 E-value=7.4 Score=21.45 Aligned_cols=32 Identities=19% Similarity=0.167 Sum_probs=19.2
Q ss_pred CCcccceEecCCCCCCchhhhhccccCCCCCCCCHHHHHHHHHHhh
Q 030210 128 VGITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDV 173 (181)
Q Consensus 128 ~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~D~~l~~Ai~~L~~ 173 (181)
+|+.||...-.... ...-+--.++.|++++.+
T Consensus 1 ~G~~Pd~~ty~~lI--------------~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 1 RGCEPDVVTYNTLI--------------DGYCKAGRVDEAFELFDE 32 (34)
T ss_pred CCCCCcHhHHHHHH--------------HHHHHCCCHHHHHHHHHh
Confidence 47778876544322 112355678888888754
No 25
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=20.81 E-value=87 Score=16.38 Aligned_cols=16 Identities=13% Similarity=-0.068 Sum_probs=12.8
Q ss_pred CCHHHHHHHHHHhhhc
Q 030210 160 ADSCIMVAEHELDVQE 175 (181)
Q Consensus 160 ~D~~l~~Ai~~L~~~~ 175 (181)
+|.+|+.||++-....
T Consensus 2 EDe~Lq~Ai~lSl~e~ 17 (26)
T smart00726 2 EDEDLQLALELSLQEA 17 (26)
T ss_pred hHHHHHHHHHHhHHHh
Confidence 6899999999866554
No 26
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=20.70 E-value=1.6e+02 Score=20.03 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=30.4
Q ss_pred EEEEcCCCccHHHHHHHHHhcCCCe-----EEEcccCCCCceeceEEEccC
Q 030210 61 VVLVNEGSASASEILAGALHDNGRA-----ILVGHKTFGKGKIQSVTELHD 106 (181)
Q Consensus 61 ~VL~~~~TaSaaE~fa~~l~~~~~~-----~vIG~~T~G~~~~~~~~~L~~ 106 (181)
++|++..| +|.|.+..+|++++.- --+-|-|.+.+.......|||
T Consensus 16 yili~K~T-ta~evv~lal~eFgi~~~s~~~sLceVtV~~~g~IKQrRLPd 65 (85)
T cd01785 16 YLLIYKET-TAHEVVMLALQEFGITAPSSNFSLCEVSVTPGGVIKQRRLPD 65 (85)
T ss_pred EEEEeccc-cHHHHHHHHHHHhCCCCCccceEEEEEEecCCceeeeccCCH
Confidence 56777775 6899999999998632 223444555555666666776
No 27
>PLN02994 1-aminocyclopropane-1-carboxylate synthase
Probab=20.61 E-value=1.3e+02 Score=22.57 Aligned_cols=34 Identities=26% Similarity=0.481 Sum_probs=27.5
Q ss_pred EEEcCCCccHHHHHHHHHhcCCCeEEEcccCCCC
Q 030210 62 VLVNEGSASASEILAGALHDNGRAILVGHKTFGK 95 (181)
Q Consensus 62 VL~~~~TaSaaE~fa~~l~~~~~~~vIG~~T~G~ 95 (181)
|++..++.++-++++.+|.+-+.+++|-+++|.+
T Consensus 120 Ivvt~Ga~~al~~l~~~l~dpGD~VlVp~P~Y~~ 153 (153)
T PLN02994 120 IVLSAGATAANEIIMFCIADPGDAFLVPTPYYAA 153 (153)
T ss_pred eEEcCCHHHHHHHHHHHHcCCCCEEEEeCCCCCC
Confidence 5555666777888999999989999999998863
No 28
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=20.58 E-value=1e+02 Score=19.84 Aligned_cols=20 Identities=15% Similarity=-0.044 Sum_probs=16.5
Q ss_pred CCCHHHHHHHHHHhhhcccC
Q 030210 159 EADSCIMVAEHELDVQESRG 178 (181)
Q Consensus 159 ~~D~~l~~Ai~~L~~~~~~~ 178 (181)
+.|+.++.|+++..+..+..
T Consensus 2 ~~D~ly~~a~~~V~~~~~~S 21 (63)
T smart00843 2 EEDELYDEAVELVIETQKAS 21 (63)
T ss_pred cccHHHHHHHHHHHHhCCCC
Confidence 57999999999998876554
No 29
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=20.01 E-value=1.7e+02 Score=26.15 Aligned_cols=31 Identities=16% Similarity=0.219 Sum_probs=23.8
Q ss_pred EEeecCCCCCCCHHHHHHHHhhccCCCceeEE
Q 030210 5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVN 36 (181)
Q Consensus 5 lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~ 36 (181)
+||+| +-|||.++++.++.+.|.....++..
T Consensus 60 vvl~l-dTPGGl~~sm~~iv~~i~~s~vPV~~ 90 (436)
T COG1030 60 VVLEL-DTPGGLLDSMRQIVRAILNSPVPVIG 90 (436)
T ss_pred EEEEe-cCCCchHHHHHHHHHHHHcCCCCEEE
Confidence 45555 57899999999999999887666433
Done!