Query 030503
Match_columns 176
No_of_seqs 167 out of 1036
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 14:42:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030503.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030503hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0193 Pth Peptidyl-tRNA hydr 100.0 2.6E-43 5.5E-48 291.4 10.5 100 75-174 2-102 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 4.1E-43 8.8E-48 290.5 11.2 101 74-174 1-101 (191)
3 cd00462 PTH Peptidyl-tRNA hydr 100.0 5.6E-42 1.2E-46 279.1 11.0 98 77-174 1-98 (171)
4 TIGR00447 pth peptidyl-tRNA hy 100.0 9E-42 1.9E-46 281.5 11.5 100 75-174 1-101 (188)
5 PRK05426 peptidyl-tRNA hydrola 100.0 7.6E-41 1.6E-45 276.1 11.3 100 75-174 2-102 (189)
6 PF01195 Pept_tRNA_hydro: Pept 100.0 2.5E-39 5.5E-44 265.1 11.3 98 77-174 1-99 (184)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 1.8E-32 3.9E-37 228.7 8.1 101 74-174 38-138 (224)
8 PRK10466 hybD hydrogenase 2 ma 76.9 3.4 7.3E-05 33.0 3.7 30 75-108 2-31 (164)
9 cd06062 H2MP_MemB-H2up Endopep 75.0 3.8 8.2E-05 32.0 3.4 28 76-107 1-28 (146)
10 TIGR00130 frhD coenzyme F420-r 74.3 3.8 8.2E-05 32.3 3.3 29 74-106 3-31 (153)
11 KOG2380 Prephenate dehydrogena 73.0 1.7 3.7E-05 40.5 1.2 47 64-110 41-96 (480)
12 COG0680 HyaD Ni,Fe-hydrogenase 71.3 4.3 9.4E-05 32.9 3.0 31 74-108 2-32 (160)
13 TIGR00072 hydrog_prot hydrogen 69.8 4.3 9.3E-05 31.6 2.6 28 77-108 1-28 (145)
14 PRK10264 hydrogenase 1 maturat 69.3 7.4 0.00016 32.4 4.1 31 74-108 4-34 (195)
15 cd06064 H2MP_F420-Reduc Endope 68.2 4.5 9.8E-05 31.7 2.5 27 77-107 1-27 (150)
16 cd00518 H2MP Hydrogenase speci 65.4 5.9 0.00013 30.4 2.6 27 77-107 1-27 (139)
17 cd06066 H2MP_NAD-link-bidir En 63.8 6.9 0.00015 30.3 2.7 27 77-107 1-27 (139)
18 cd06067 H2MP_MemB-H2evol Endop 62.3 6.9 0.00015 30.2 2.5 27 77-107 1-27 (136)
19 cd06063 H2MP_Cyano-H2up This g 61.7 8.1 0.00018 30.2 2.8 28 76-107 1-28 (146)
20 TIGR00142 hycI hydrogenase mat 61.1 8 0.00017 30.2 2.6 28 76-107 1-28 (146)
21 cd06070 H2MP_like-2 Putative [ 59.1 8.6 0.00019 29.8 2.5 25 77-105 1-25 (140)
22 cd06068 H2MP_like-1 Putative [ 57.7 8.4 0.00018 29.9 2.2 27 77-107 1-27 (144)
23 PRK11544 hycI hydrogenase 3 ma 57.2 11 0.00024 29.9 2.9 28 76-107 3-30 (156)
24 PF03418 Peptidase_A25: Germin 49.2 15 0.00032 33.8 2.7 27 74-104 96-122 (354)
25 COG2179 Predicted hydrolase of 42.8 21 0.00046 29.9 2.4 26 142-167 95-120 (175)
26 COG2897 SseA Rhodanese-related 41.8 30 0.00066 30.7 3.4 32 137-168 69-100 (285)
27 PF08282 Hydrolase_3: haloacid 38.5 29 0.00062 27.2 2.5 25 143-167 188-212 (254)
28 COG0056 AtpA F0F1-type ATP syn 35.0 35 0.00076 32.8 2.9 24 142-168 241-264 (504)
29 KOG1486 GTP-binding protein DR 34.5 1.8E+02 0.0039 26.5 7.1 75 89-165 148-222 (364)
30 PF07431 DUF1512: Protein of u 32.8 2.1E+02 0.0046 26.5 7.4 67 95-163 185-254 (355)
31 PF02789 Peptidase_M17_N: Cyto 32.6 40 0.00086 24.6 2.3 33 73-105 52-84 (126)
32 PF13443 HTH_26: Cro/C1-type H 30.6 11 0.00025 24.5 -0.8 27 140-166 37-63 (63)
33 TIGR01441 GPR GPR endopeptidas 30.6 22 0.00049 32.8 0.8 27 74-104 101-127 (358)
34 PRK12362 germination protease; 30.1 39 0.00084 30.8 2.2 79 74-167 99-182 (318)
35 PRK10513 sugar phosphate phosp 30.1 35 0.00076 28.2 1.9 25 143-167 198-222 (270)
36 PTZ00397 macrophage migration 30.0 69 0.0015 23.8 3.3 29 141-169 77-105 (116)
37 PRK10976 putative hydrolase; P 29.9 38 0.00082 28.0 2.0 25 143-167 192-216 (266)
38 PRK02858 germination protease; 29.8 24 0.00051 32.7 0.8 27 74-104 111-137 (369)
39 PRK07571 bidirectional hydroge 27.5 1.5E+02 0.0032 24.4 5.0 59 96-154 104-168 (169)
40 TIGR01485 SPP_plant-cyano sucr 26.7 71 0.0015 26.4 3.1 27 141-167 167-193 (249)
41 COG5381 Uncharacterized protei 26.3 1.2E+02 0.0025 25.4 4.2 21 87-107 56-76 (184)
42 PRK15126 thiamin pyrimidine py 25.8 41 0.00089 28.0 1.5 26 142-167 189-214 (272)
43 cd01896 DRG The developmentall 25.6 3.1E+02 0.0067 22.7 6.8 82 75-168 81-162 (233)
44 PF11242 DUF2774: Protein of u 25.4 23 0.00049 25.1 -0.1 23 137-159 7-29 (63)
45 TIGR02463 MPGP_rel mannosyl-3- 24.8 75 0.0016 25.4 2.9 26 142-167 180-205 (221)
46 PRK05988 formate dehydrogenase 24.1 2.1E+02 0.0046 22.9 5.3 60 95-154 90-155 (156)
47 PRK01158 phosphoglycolate phos 24.0 51 0.0011 26.4 1.7 25 143-167 159-183 (230)
48 cd06392 PBP1_iGluR_delta_1 N-t 24.0 92 0.002 28.5 3.6 32 130-166 116-147 (400)
49 PF13242 Hydrolase_like: HAD-h 23.5 89 0.0019 21.1 2.6 23 146-168 10-32 (75)
50 TIGR02471 sucr_syn_bact_C sucr 23.2 63 0.0014 26.3 2.1 27 141-167 159-185 (236)
51 COG4046 Uncharacterized protei 22.5 3.8E+02 0.0082 24.9 7.1 68 94-163 197-267 (368)
52 PF01187 MIF: Macrophage migra 21.2 81 0.0018 23.5 2.2 19 151-169 85-103 (114)
53 cd01445 TST_Repeats Thiosulfat 21.1 1.2E+02 0.0027 23.2 3.3 23 144-166 81-103 (138)
54 PF14490 HHH_4: Helix-hairpin- 21.1 51 0.0011 23.9 1.1 20 93-112 52-71 (94)
55 TIGR01482 SPP-subfamily Sucros 21.0 73 0.0016 25.3 2.1 26 141-166 149-174 (225)
56 PRK06437 hypothetical protein; 20.9 85 0.0019 21.5 2.1 29 142-170 19-47 (67)
57 COG2607 Predicted ATPase (AAA+ 20.7 1E+02 0.0022 27.7 3.1 27 147-173 128-154 (287)
58 KOG2882 p-Nitrophenyl phosphat 20.0 83 0.0018 28.6 2.4 37 128-170 218-254 (306)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-43 Score=291.44 Aligned_cols=100 Identities=44% Similarity=0.666 Sum_probs=95.9
Q ss_pred ceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCC-cccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHc
Q 030503 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (176)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~-~~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~y 153 (176)
++|||||||||++|+.||||||||++|.||++++.++ .+++|.+.++++.+.+++|+|+||+||||+||++|.++++||
T Consensus 2 ~kLIVGLGNPG~~Y~~TRHNvGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~l~kP~TyMNlSG~~V~~~~~fy 81 (190)
T COG0193 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASFY 81 (190)
T ss_pred cEEEEECCCCchhhcccchhHHHHHHHHHHHHhCCCCccccccCceeEEEEeCCcEEEEecCccceeCcHHHHHHHHHHh
Confidence 6899999999999999999999999999999999998 456899999999999999999999999999999999999999
Q ss_pred CCCCCcEEEEEecCCCCcccC
Q 030503 154 KIPLKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 154 ki~pe~ILVIHDDLDLplGk~ 174 (176)
++++++|||||||||||+|+.
T Consensus 82 ~i~~~~ilVvhDdLdl~~G~v 102 (190)
T COG0193 82 KIKPEDILVVHDELDLPLGKV 102 (190)
T ss_pred CCCHHHEEEEeeccCCCCceE
Confidence 999999999999999999974
No 2
>cd02406 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH).
Probab=100.00 E-value=4.1e-43 Score=290.50 Aligned_cols=101 Identities=59% Similarity=1.037 Sum_probs=96.0
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHc
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~y 153 (176)
+++|||||||||++|++|||||||+++|.||++++.++++.++++.++++.+++++|+|+||+||||+||++|.++++||
T Consensus 1 ~~~LIvGLGNPG~~Y~~TRHNiGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~y 80 (191)
T cd02406 1 TPWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYY 80 (191)
T ss_pred CcEEEEEcCCCchhhCcCchhHHHHHHHHHHHHcCCCccccccceEEEEEEECCeEEEEEeCCCchhcCHHHHHHHHHHh
Confidence 46899999999999999999999999999999999887666788999999999999999999999999999999999999
Q ss_pred CCCCCcEEEEEecCCCCcccC
Q 030503 154 KIPLKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 154 ki~pe~ILVIHDDLDLplGk~ 174 (176)
+++++++||||||||||+|+.
T Consensus 81 ki~~~~ilVihDdldl~~G~i 101 (191)
T cd02406 81 KVPLRHILVIYDDMSLPNGVL 101 (191)
T ss_pred CCCHHHEEEEEECCCCCCCeE
Confidence 999999999999999999974
No 3
>cd00462 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts.
Probab=100.00 E-value=5.6e-42 Score=279.13 Aligned_cols=98 Identities=47% Similarity=0.749 Sum_probs=93.8
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHcCCC
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKIP 156 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~yki~ 156 (176)
|||||||||++|++|||||||+++|.||++++..+++.++++.++++.+.+++++|+||+||||+||++|.+++++|+++
T Consensus 1 LIvGLGNPG~~Y~~TRHNvGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~~i~ 80 (171)
T cd00462 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYKIP 80 (171)
T ss_pred CEEEECCCCcccCcCchHHHHHHHHHHHHHcCCCCCccccCEEEEEEEECCEEEEEEeCCcccccccHHHHHHHHhcCCC
Confidence 69999999999999999999999999999999888776778999999999999999999999999999999999999999
Q ss_pred CCcEEEEEecCCCCcccC
Q 030503 157 LKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 157 pe~ILVIHDDLDLplGk~ 174 (176)
++++||||||||||+|+.
T Consensus 81 ~~~ilVihDdldl~~G~v 98 (171)
T cd00462 81 PEDILVIHDDLDLPLGKI 98 (171)
T ss_pred hhHEEEEEecCCCCCceE
Confidence 999999999999999974
No 4
>TIGR00447 pth peptidyl-tRNA hydrolase. The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function.
Probab=100.00 E-value=9e-42 Score=281.51 Aligned_cols=100 Identities=40% Similarity=0.639 Sum_probs=94.1
Q ss_pred ceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCc-ccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHc
Q 030503 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVS-SVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (176)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~-~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~y 153 (176)
++|||||||||++|++|||||||+++|.||++++.+++ ..++.+.++++.+++++|+|+||+||||+||++|++++++|
T Consensus 1 ~~LIvGLGNPG~~Y~~TRHNiGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~ 80 (188)
T TIGR00447 1 IKLIVGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKPLTYMNLSGEAVRALASFY 80 (188)
T ss_pred CEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCcCCcccccceEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHHh
Confidence 58999999999999999999999999999999998876 34677888999999999999999999999999999999999
Q ss_pred CCCCCcEEEEEecCCCCcccC
Q 030503 154 KIPLKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 154 ki~pe~ILVIHDDLDLplGk~ 174 (176)
+++++++||||||||||+|+.
T Consensus 81 ~i~~~~ilVihDdldl~~G~i 101 (188)
T TIGR00447 81 RIKPAELLVVHDELDLPLGKV 101 (188)
T ss_pred CCChHHEEEEEecCCCCCceE
Confidence 999999999999999999974
No 5
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=7.6e-41 Score=276.07 Aligned_cols=100 Identities=43% Similarity=0.662 Sum_probs=93.9
Q ss_pred ceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCc-ccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHc
Q 030503 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVS-SVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (176)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~-~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~y 153 (176)
++|||||||||++|++|||||||+++|.||++++..+. ..++++.++++.+++++++|+||+||||+||++|++++++|
T Consensus 2 ~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~ 81 (189)
T PRK05426 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANFY 81 (189)
T ss_pred cEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCCCCcccccccEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHHh
Confidence 68999999999999999999999999999999877654 45678999999998899999999999999999999999999
Q ss_pred CCCCCcEEEEEecCCCCcccC
Q 030503 154 KIPLKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 154 ki~pe~ILVIHDDLDLplGk~ 174 (176)
++++++++|||||||||+|+.
T Consensus 82 ~i~~~~ilVihDdldl~~G~~ 102 (189)
T PRK05426 82 KIPPEDILVIHDDLDLPPGKI 102 (189)
T ss_pred CCCHHHEEEEEecCCCCCceE
Confidence 999999999999999999974
No 6
>PF01195 Pept_tRNA_hydro: Peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis [, ]. Bacterial PTH has been found to be evolutionary related to a yeast protein [].; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 3KJZ_A 3KK0_A 3P2J_A 3V2I_A 3TCN_A 3TD6_A 2Z2K_A 3TD2_A 2Z2J_B 2JRC_A ....
Probab=100.00 E-value=2.5e-39 Score=265.07 Aligned_cols=98 Identities=46% Similarity=0.715 Sum_probs=85.5
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCcccc-eeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHcCC
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVN-FKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKI 155 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~~~k-~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~yki 155 (176)
|||||||||++|++|||||||+++|.|+++++..+++.+ +++.++.+.+.+.+++|+||+||||+||++|++++++|++
T Consensus 1 LivGLGNPG~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~KP~TyMN~SG~~V~~~~~~~~i 80 (184)
T PF01195_consen 1 LIVGLGNPGPKYENTRHNVGFMVLDRLASRLGLSWKQKKKFKSLISEGSIKGEKVILLKPQTYMNLSGKAVKKILSFYKI 80 (184)
T ss_dssp EEEE---SSTTTTTSGGGHHHHHHHHHHHHTT---EEEGGGTEEEEEEEETTEEEEEEEESSTGGGHHHHHHHHHHHTT-
T ss_pred CEEEcCCCChhhcCCCcCchHHHHHHHHHHhCCCccccccceeEEEEEEEeeeeEEEEcCCCeEeCccHhHHHHHHHhCC
Confidence 799999999999999999999999999999998886554 7889999999999999999999999999999999999999
Q ss_pred CCCcEEEEEecCCCCcccC
Q 030503 156 PLKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 156 ~pe~ILVIHDDLDLplGk~ 174 (176)
+++++||||||+|+|+|+.
T Consensus 81 ~~~~ilVihDdldl~~G~i 99 (184)
T PF01195_consen 81 PPENILVIHDDLDLPLGKI 99 (184)
T ss_dssp -GGGEEEEEEETTSSTTEE
T ss_pred CcceEEEEEeccCCCCCeE
Confidence 9999999999999999974
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.8e-32 Score=228.71 Aligned_cols=101 Identities=49% Similarity=0.907 Sum_probs=93.6
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHc
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~y 153 (176)
++|+|+||||||++|.+|||||||.|+|.||++.+++..+.+-++..+-+.+++..+++++|++|||.||++|.++|..|
T Consensus 38 k~wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y 117 (224)
T KOG2255|consen 38 KPWLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALY 117 (224)
T ss_pred CceEEEecCCCcccccccchhhHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhh
Confidence 47999999999999999999999999999999999886655545666777888999999999999999999999999999
Q ss_pred CCCCCcEEEEEecCCCCcccC
Q 030503 154 KIPLKQVLVRQNIFILFYRYS 174 (176)
Q Consensus 154 ki~pe~ILVIHDDLDLplGk~ 174 (176)
+++.++++||||||++|+|++
T Consensus 118 ~i~~~~ivvIhDEl~l~~Gkl 138 (224)
T KOG2255|consen 118 KIPLRHIVVIHDELELPLGKL 138 (224)
T ss_pred cchheeEEEEeccccCcCceE
Confidence 999999999999999999985
No 8
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=76.89 E-value=3.4 Score=33.03 Aligned_cols=30 Identities=27% Similarity=0.377 Sum_probs=23.9
Q ss_pred ceEEEEccCcccccCcCcchHHHHHHHHHHHHhC
Q 030503 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (176)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~ 108 (176)
+.+|+|+|||- .+-==+|..+++.|.+.+.
T Consensus 2 ~ilVlGiGN~l----~gDDGvG~~va~~L~~~~~ 31 (164)
T PRK10466 2 RILVLGVGNIL----LTDEAIGVRIVEALEQRYI 31 (164)
T ss_pred ceEEEEECchh----hccCcHHHHHHHHHHHhcC
Confidence 47999999994 3444599999999988764
No 9
>cd06062 H2MP_MemB-H2up Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.
Probab=74.97 E-value=3.8 Score=31.97 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=22.4
Q ss_pred eEEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
.+|+|+|||- ..-==+|..+++.|++++
T Consensus 1 ilV~GiGN~l----~gDDG~G~~va~~L~~~~ 28 (146)
T cd06062 1 ILVLGIGNIL----LADEGIGVHAVERLEENY 28 (146)
T ss_pred CEEEEECccc----cccCcHHHHHHHHHHHhc
Confidence 3799999994 233459999999999874
No 10
>TIGR00130 frhD coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit). FrhD is not part of the active FRH heterotrimer, but is probably a protease required for maturation. Alternative name: 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) subunit delta.
Probab=74.28 E-value=3.8 Score=32.34 Aligned_cols=29 Identities=28% Similarity=0.354 Sum_probs=22.9
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHHHH
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEA 106 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~ 106 (176)
.+.+|+|+|||- ..-==+|..++++|+++
T Consensus 3 ~~ilVlGiGN~l----~gDDGvG~~v~~~L~~~ 31 (153)
T TIGR00130 3 HEILVVGCGNIL----FGDDGFGPAVIEYLKEN 31 (153)
T ss_pred ceEEEEEeCccc----cccCcHhHHHHHHHHHh
Confidence 568999999993 23345999999999864
No 11
>KOG2380 consensus Prephenate dehydrogenase (NADP+) [Amino acid transport and metabolism]
Probab=73.04 E-value=1.7 Score=40.52 Aligned_cols=47 Identities=28% Similarity=0.346 Sum_probs=35.3
Q ss_pred CCCCCcCCC--CCceEEEEccCcccccCcCcchHHHHHH-------HHHHHHhCCC
Q 030503 64 VSPKPKQQQ--QHPWLIVGLGNPGKQYNGTRHNVGFEMV-------DAIAEAEGIS 110 (176)
Q Consensus 64 ~sp~~~~~~--~~~~LIVGLGNPG~kY~~TRHNVGf~vL-------D~La~~~~~~ 110 (176)
+++....+. ...+-|+|+||.|.-|++|--.+||.++ +.+++++|..
T Consensus 41 ~~~~s~~~~k~tl~IaIIGfGnmGqflAetli~aGh~li~hsRsdyssaa~~yg~~ 96 (480)
T KOG2380|consen 41 VSEDSIEQWKATLVIAIIGFGNMGQFLAETLIDAGHGLICHSRSDYSSAAEKYGSA 96 (480)
T ss_pred cCcchhhhcccceEEEEEecCcHHHHHHHHHHhcCceeEecCcchhHHHHHHhccc
Confidence 445444432 2346799999999999999999999886 6677887764
No 12
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=71.31 E-value=4.3 Score=32.90 Aligned_cols=31 Identities=19% Similarity=0.274 Sum_probs=25.5
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHHHHhC
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~ 108 (176)
.+.+|+|+||+ -..-==+|-.+++.|.+++.
T Consensus 2 ~~ilIlG~GN~----L~~DDG~Gv~vae~L~~~~~ 32 (160)
T COG0680 2 MRILILGVGNI----LMGDDGFGVRVAEKLKKRYK 32 (160)
T ss_pred CeEEEEeeCCc----ccccCcccHHHHHHHHHhcC
Confidence 46899999999 34556799999999999874
No 13
>TIGR00072 hydrog_prot hydrogenase maturation protease. HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase.
Probab=69.78 E-value=4.3 Score=31.56 Aligned_cols=28 Identities=21% Similarity=0.353 Sum_probs=22.3
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHhC
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~ 108 (176)
+|+|+|||- ..-==+|..++++|++++.
T Consensus 1 lViGiGN~l----~~DDg~G~~v~~~L~~~~~ 28 (145)
T TIGR00072 1 LVLGIGNIL----RGDDGFGPRVAERLEERYE 28 (145)
T ss_pred CEEEECchh----cccCcHHHHHHHHHHHhcC
Confidence 699999994 2334599999999998763
No 14
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=69.29 E-value=7.4 Score=32.42 Aligned_cols=31 Identities=16% Similarity=0.242 Sum_probs=24.2
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHHHHhC
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~ 108 (176)
.+.+|+|+|||= ..-==+|..+++.|.+++.
T Consensus 4 ~rilVlGiGN~L----~gDDGvG~~va~~L~~~~~ 34 (195)
T PRK10264 4 QRVVVMGLGNLL----WADEGFGVRVAERLYAHYH 34 (195)
T ss_pred CCEEEEEeCccc----cccCcHHHHHHHHHHhhcC
Confidence 457999999992 3334599999999988754
No 15
>cd06064 H2MP_F420-Reduc Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to the gene cluster of 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum delta H. FrhD subunit is putatively involved in the processing of the coenzyme F420 hydrogenase-processing. It is similar to those frhD genes found in Methanomicrobia and Methanobacteria. It is different from the FrhD conserved domain found in methyl viologen-reducing hydrogenase and F420-non-reducing hydrogenase iron-sulfur subunit D.
Probab=68.25 E-value=4.5 Score=31.66 Aligned_cols=27 Identities=26% Similarity=0.370 Sum_probs=22.0
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
||+|+|||- ..-==+|+.++++|++++
T Consensus 1 lViGiGN~l----~gDDgvG~~va~~l~~~~ 27 (150)
T cd06064 1 LVVGCGNIL----FGDDGFGPAVIEELEKLE 27 (150)
T ss_pred CEEEECCcc----cccCcHHHHHHHHHHhcc
Confidence 689999994 344459999999998875
No 16
>cd00518 H2MP Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.
Probab=65.37 E-value=5.9 Score=30.41 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=21.9
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
+|+|+||+= ..-==+|..+++.|.+++
T Consensus 1 lViGiGN~l----~~DDGvG~~v~~~L~~~~ 27 (139)
T cd00518 1 LVLGIGNPL----RGDDGFGPAVAERLEERY 27 (139)
T ss_pred CEEEECCcc----cccCcHHHHHHHHHHhcC
Confidence 589999993 344459999999999875
No 17
>cd06066 H2MP_NAD-link-bidir Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the NiFe-hydrogenase.
Probab=63.77 E-value=6.9 Score=30.30 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=21.9
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
+|+|+|||= ..-==+|..++++|++++
T Consensus 1 lVlGvGN~l----~~DDGvG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPL----RGDDGLGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCcc----ccccchhHHHHHHHHhhC
Confidence 689999993 344459999999999885
No 18
>cd06067 H2MP_MemB-H2evol Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases. Such hydrogenases as those from Methanosarcina barkeri (EchCE) and Rhodospirillum rubrum (CooLH) also belong to this group of membrane-bound hydrogen evolving hydrogenase. Sequence comparison of the large subunits from related hydrogenase indicates that in contrast to EchE (358 amino acids) and CooH (361 amino acids), the large subunit HycE (569 amino acids) contains an extra carboxy-terminal stretch of 32 amino acids that is cleaved during the maturation process. In
Probab=62.34 E-value=6.9 Score=30.18 Aligned_cols=27 Identities=15% Similarity=0.345 Sum_probs=21.6
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
+|+|+|||- ..-==+|..++++|.++.
T Consensus 1 ~VlGiGN~L----~~DDgvG~~v~~~L~~~~ 27 (136)
T cd06067 1 VLLGVGNEL----RGDDGAGPLLAEKLEDLP 27 (136)
T ss_pred CEEEeCccc----cccCcHHHHHHHHHHhcC
Confidence 589999994 344459999999998764
No 19
>cd06063 H2MP_Cyano-H2up This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial hydrogenase and are involved in the C-terminal cleavage of the hydrogenase large subunit precursor protein. Cyanobacterial nickel-iron (NiFe)-hydrogenases are found exclusively in the N2-fixing strains and are encoded by hup (hydrogen uptake) genes. These uptake hydrogenases are heterodimers with a large (hupL) and small subunit (hupS) and catalyze the consumption of the H2 produced during N2 fixation. Sequence similarity shows that the putative metal-binding resides are well conserved in this group of hydrogen maturation proteases. This group also includes such proteins as the hydrogenase III from Aquifex aeolicus.
Probab=61.67 E-value=8.1 Score=30.16 Aligned_cols=28 Identities=21% Similarity=0.278 Sum_probs=21.8
Q ss_pred eEEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
.+|+|+|||- ..-==+|..++++|++..
T Consensus 1 ~lVlGiGN~L----~~DDG~G~~v~~~L~~~~ 28 (146)
T cd06063 1 LTIIGCGNLN----RGDDGVGPILIRRLQAYL 28 (146)
T ss_pred CEEEEECCcc----cccCcHHHHHHHHHhhcC
Confidence 3799999994 233459999999998753
No 20
>TIGR00142 hycI hydrogenase maturation protease HycI. Hydrogenase maturation protease is a protease that is involved in the C-terminal processing of HycE,the large subunit of hydrogenase 3 from E.Coli. This protein seems to be found in E.Coli and in Archaea.
Probab=61.11 E-value=8 Score=30.18 Aligned_cols=28 Identities=18% Similarity=0.187 Sum_probs=22.0
Q ss_pred eEEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
.+|+|+|||- ..-==+|..++++|.+.+
T Consensus 1 ~lVlGiGN~l----~~DDG~G~~v~~~L~~~~ 28 (146)
T TIGR00142 1 LVLLCVGNEL----MGDDGAGPYLAEKCAAAP 28 (146)
T ss_pred CEEEEeCccc----cccCcHHHHHHHHHHhcc
Confidence 4799999995 233459999999998764
No 21
>cd06070 H2MP_like-2 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=59.14 E-value=8.6 Score=29.80 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=20.1
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHH
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAE 105 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~ 105 (176)
||+|+|||- ..-==+|..+++.|++
T Consensus 1 lVlGiGN~l----~~DDg~G~~v~~~L~~ 25 (140)
T cd06070 1 LIIGVGNRL----YGDDGFGSCLAEALEQ 25 (140)
T ss_pred CEEEECchh----cccCcHHHHHHHHHhh
Confidence 689999994 2344599999999987
No 22
>cd06068 H2MP_like-1 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=57.73 E-value=8.4 Score=29.93 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=21.2
Q ss_pred EEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 77 LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
||+|+|||- ..-==+|..+++.|.++.
T Consensus 1 lViGiGN~l----~~DDGvG~~v~~~L~~~~ 27 (144)
T cd06068 1 LVAGVGNIF----LGDDGFGVEVARRLRPRQ 27 (144)
T ss_pred CEEEECccc----cccCcHHHHHHHHHhccC
Confidence 699999994 233349999999998764
No 23
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=57.20 E-value=11 Score=29.88 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=22.1
Q ss_pred eEEEEccCcccccCcCcchHHHHHHHHHHHHh
Q 030503 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~ 107 (176)
.+|+|+|||- ..-==+|..++++|.+..
T Consensus 3 ~lVlGiGN~L----~gDDGvG~~v~~~L~~~~ 30 (156)
T PRK11544 3 DVVLTVGNSM----MGDDGAGPLLAEKLAAAP 30 (156)
T ss_pred EEEEEeCccc----cccCcHHHHHHHHHhccC
Confidence 5899999994 234459999999998753
No 24
>PF03418 Peptidase_A25: Germination protease This family belongs to family A25 of the peptidase classification.; InterPro: IPR005080 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. Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date []. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family A25 (gpr protease family, clan AE). These are tetrameric proteases that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species during spore germination. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0009847 spore germination; PDB: 1C8B_A.
Probab=49.19 E-value=15 Score=33.84 Aligned_cols=27 Identities=37% Similarity=0.501 Sum_probs=18.1
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHH
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIA 104 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La 104 (176)
...|||||||. .-|--..|-.++|.+.
T Consensus 96 ~~iLVVGLGN~----~vTPDALGP~vv~~l~ 122 (354)
T PF03418_consen 96 ASILVVGLGNW----NVTPDALGPRVVENLL 122 (354)
T ss_dssp --EEEEE-S-S----SSGGG-HHHHHHHT--
T ss_pred CeEEEEeCCCc----CCCccccchhhhhhhh
Confidence 55899999998 4699999999999764
No 25
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=42.78 E-value=21 Score=29.88 Aligned_cols=26 Identities=12% Similarity=0.276 Sum_probs=23.9
Q ss_pred chHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 142 SGQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 142 SG~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
+|.++.++++.++++++++++|-|.|
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL 120 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQL 120 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchh
Confidence 57899999999999999999999986
No 26
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=41.75 E-value=30 Score=30.68 Aligned_cols=32 Identities=13% Similarity=-0.021 Sum_probs=28.3
Q ss_pred cccccchHHHHHHHHHcCCCCCcEEEEEecCC
Q 030503 137 TFMNASGQSVGSIVSYYKIPLKQVLVRQNIFI 168 (176)
Q Consensus 137 TYMNlSG~aV~~l~~~yki~pe~ILVIHDDLD 168 (176)
.=|=-+.+.+.+++...+|..++.||||||-.
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd~~ 100 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDDGG 100 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECCCC
Confidence 56777889999999999999999999999943
No 27
>PF08282 Hydrolase_3: haloacid dehalogenase-like hydrolase; InterPro: IPR013200 The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification []. This HAD domain is found in several distinct enzymes including: Phospholipid-transporting ATPase 1 (3.6.3.1 from EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [] 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (3.1.3.45 from EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [] Mannosyl-3-phosphoglycerate phosphatase (3.1.3.70 from EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [] Phosphoglycolate phopshatase (3.1.3.18 from EC), which catalyses the dephosphorylation of 2-phosphoglycolate [] ; PDB: 2B30_B 3R4C_A 1XVI_B 3IJ5_B 3MMZ_C 3L7Y_A 1XPJ_C 1RLT_B 1RLM_B 2HF2_A ....
Probab=38.48 E-value=29 Score=27.21 Aligned_cols=25 Identities=12% Similarity=0.295 Sum_probs=22.9
Q ss_pred hHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 143 GQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 143 G~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
|.++..+++++++++++++++=|+.
T Consensus 188 ~~ai~~l~~~~~i~~~~~~~~GD~~ 212 (254)
T PF08282_consen 188 GSAIKYLLEYLGISPEDIIAFGDSE 212 (254)
T ss_dssp HHHHHHHHHHHTTSGGGEEEEESSG
T ss_pred HHHHHHHhhhcccccceeEEeeccc
Confidence 6889999999999999999999975
No 28
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=35.05 E-value=35 Score=32.80 Aligned_cols=24 Identities=17% Similarity=0.131 Sum_probs=17.8
Q ss_pred chHHHHHHHHHcCCCCCcEEEEEecCC
Q 030503 142 SGQSVGSIVSYYKIPLKQVLVRQNIFI 168 (176)
Q Consensus 142 SG~aV~~l~~~yki~pe~ILVIHDDLD 168 (176)
+|-++.+.+.+ .-++.|||+|||.
T Consensus 241 ~g~a~aE~f~~---~G~dvLIVyDDLs 264 (504)
T COG0056 241 AGCAMAEYFRD---NGKDVLIVYDDLS 264 (504)
T ss_pred hhhHHHHHHHh---cCCeEEEEecCch
Confidence 56666665554 4489999999985
No 29
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=34.48 E-value=1.8e+02 Score=26.55 Aligned_cols=75 Identities=24% Similarity=0.308 Sum_probs=57.2
Q ss_pred CcCcchHHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHcCCCCCcEEEEEe
Q 030503 89 NGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVRQN 165 (176)
Q Consensus 89 ~~TRHNVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~yki~pe~ILVIHD 165 (176)
..|+|+.-...++.=.+..|+.+.+.+.+-.+.....+|.++-.--|.|-||. +.+..++..|+|-..++++--|
T Consensus 148 Datk~e~qr~~le~ELe~vGiRLNk~~Pniy~k~kk~gGi~f~~T~~lT~~~e--k~i~~ILheykI~Naevl~ReD 222 (364)
T KOG1486|consen 148 DATKSEDQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPLTHCDE--KLIYTILHEYKIHNAEVLFRED 222 (364)
T ss_pred cCCcchhHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeeccccccH--HHHHHHHHHHeeccceEEEecC
Confidence 45889988888888888889888776655555556666777777788886664 7889999999998777766443
No 30
>PF07431 DUF1512: Protein of unknown function (DUF1512); InterPro: IPR009995 This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown.
Probab=32.81 E-value=2.1e+02 Score=26.49 Aligned_cols=67 Identities=12% Similarity=0.071 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEec---CcccccchHHHHHHHHHcCCCCCcEEEE
Q 030503 95 VGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKP---QTFMNASGQSVGSIVSYYKIPLKQVLVR 163 (176)
Q Consensus 95 VGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP---~TYMNlSG~aV~~l~~~yki~pe~ILVI 163 (176)
+|=+++-.|...... ...-++-.+++..+.|.+++++|. .+=.=.=|++|..+.+.++-.++.|+-|
T Consensus 185 aGPLVA~~l~~~~~~--~~~~~dtv~~e~~~egRrv~viKA~GPGstVGrpgeave~i~~~~~~k~~~IITV 254 (355)
T PF07431_consen 185 AGPLVAGRLMENCSK--WEIAKDTVIAECEFEGRRVYVIKAEGPGSTVGRPGEAVEYIVEKLGGKVDLIITV 254 (355)
T ss_pred cchHHHHHHHhcCcc--cccccccEEEEEEECCcEEEEEeccCCCccCCChHHHHHHHHHHhcCCccEEEEe
Confidence 455666666654332 222345667888999999999995 5555566799999999886677665543
No 31
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=32.62 E-value=40 Score=24.59 Aligned_cols=33 Identities=24% Similarity=0.330 Sum_probs=20.1
Q ss_pred CCceEEEEccCcccccCcCcchHHHHHHHHHHH
Q 030503 73 QHPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAE 105 (176)
Q Consensus 73 ~~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~ 105 (176)
..++++||||+...-=..+--.+|--++..+.+
T Consensus 52 ~~~v~lvGlG~~~~~~~~~~r~a~~~~~~~l~~ 84 (126)
T PF02789_consen 52 AKRVLLVGLGKKEKLTAESLRKAGAAAARALKK 84 (126)
T ss_dssp CSEEEEEEEESCTGBCHHHHHHHHHHHHHHHHH
T ss_pred ccEEEEEECCCcCcCCHHHHHHHHHHHHHHHhh
Confidence 456899999999752223333455555555554
No 32
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.61 E-value=11 Score=24.53 Aligned_cols=27 Identities=11% Similarity=0.067 Sum_probs=18.4
Q ss_pred ccchHHHHHHHHHcCCCCCcEEEEEec
Q 030503 140 NASGQSVGSIVSYYKIPLKQVLVRQNI 166 (176)
Q Consensus 140 NlSG~aV~~l~~~yki~pe~ILVIHDD 166 (176)
+.|-..+.++++++++++++++...+|
T Consensus 37 ~~~~~~l~~ia~~l~~~~~el~~~~~d 63 (63)
T PF13443_consen 37 NPSLDTLEKIAKALNCSPEELFEYEPD 63 (63)
T ss_dssp ---HHHHHHHHHHHT--HHHCTECCE-
T ss_pred cccHHHHHHHHHHcCCCHHHHhhcCCC
Confidence 556788999999999999998877665
No 33
>TIGR01441 GPR GPR endopeptidase. This model describes a tetrameric protease that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs.
Probab=30.59 E-value=22 Score=32.77 Aligned_cols=27 Identities=37% Similarity=0.511 Sum_probs=22.6
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHH
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIA 104 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La 104 (176)
...|||||||- .-|--..|-.+++.+.
T Consensus 101 ~~iLVVGLGN~----~VTPDALGP~vv~~l~ 127 (358)
T TIGR01441 101 MTCLVVGLGNW----NVTPDALGPKVVENLL 127 (358)
T ss_pred CcEEEEeCCCc----CCCccccChheeccee
Confidence 56899999997 4688889999888775
No 34
>PRK12362 germination protease; Provisional
Probab=30.14 E-value=39 Score=30.76 Aligned_cols=79 Identities=20% Similarity=0.241 Sum_probs=46.4
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCcccceeeEEEEEEECC-eeEEEEec----CcccccchHHHHH
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGN-VPVMLAKP----QTFMNASGQSVGS 148 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~-~~ViLlKP----~TYMNlSG~aV~~ 148 (176)
...|||||||- +-|--..|-.+++.|.-.... + ..+++....+ .+|.-+-| +|=||. ++-++.
T Consensus 99 ~~iLVvGLGN~----~vTpDaLGP~Vv~~l~vTrhl-~------~~~~~~~~~~~~pV~AiaPGVmg~TGiet-~Eii~g 166 (318)
T PRK12362 99 MTVLVVGLGNW----NVTPDALGPKVVSKLMVTRHL-K------EYAPEEIDEGIRPVCAIAPGVLGITGIET-AEIIKG 166 (318)
T ss_pred CcEEEEEcCCC----CcCccccchhhhhhhhhhhhh-h------hhcCchhcCCCCcceEecCCcccccchhH-HHHHHH
Confidence 55899999998 469999999999998743111 0 0011000011 23443334 566664 466777
Q ss_pred HHHHcCCCCCcEEEEEecC
Q 030503 149 IVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 149 l~~~yki~pe~ILVIHDDL 167 (176)
+.++++ | +++|.-|-|
T Consensus 167 Iv~k~k--p-d~IIAIDAL 182 (318)
T PRK12362 167 VVEKIK--P-DLVIAIDAL 182 (318)
T ss_pred HHHhcC--C-CEEEEEecc
Confidence 777544 4 566666654
No 35
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=30.09 E-value=35 Score=28.17 Aligned_cols=25 Identities=20% Similarity=0.197 Sum_probs=23.0
Q ss_pred hHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 143 GQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 143 G~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
|.++..+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 7899999999999999999999864
No 36
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=30.01 E-value=69 Score=23.76 Aligned_cols=29 Identities=10% Similarity=0.032 Sum_probs=20.6
Q ss_pred cchHHHHHHHHHcCCCCCcEEEEEecCCC
Q 030503 141 ASGQSVGSIVSYYKIPLKQVLVRQNIFIL 169 (176)
Q Consensus 141 lSG~aV~~l~~~yki~pe~ILVIHDDLDL 169 (176)
++..-...+.+..+++++++.|+..|++-
T Consensus 77 l~~~i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 77 IAAAITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred HHHHHHHHHHHHhCcCcccEEEEEEECCh
Confidence 33333344455689999999999999864
No 37
>PRK10976 putative hydrolase; Provisional
Probab=29.92 E-value=38 Score=27.98 Aligned_cols=25 Identities=12% Similarity=0.227 Sum_probs=23.1
Q ss_pred hHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 143 GQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 143 G~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
|.++..+++++++++++++++=|..
T Consensus 192 g~al~~l~~~lgi~~~~viafGD~~ 216 (266)
T PRK10976 192 GHALEAVAKKLGYSLKDCIAFGDGM 216 (266)
T ss_pred HHHHHHHHHHcCCCHHHeEEEcCCc
Confidence 8999999999999999999998864
No 38
>PRK02858 germination protease; Provisional
Probab=29.82 E-value=24 Score=32.74 Aligned_cols=27 Identities=41% Similarity=0.486 Sum_probs=22.4
Q ss_pred CceEEEEccCcccccCcCcchHHHHHHHHHH
Q 030503 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIA 104 (176)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNVGf~vLD~La 104 (176)
...|||||||- .-|--..|-.+++.|.
T Consensus 111 ~~vLVVGLGN~----~VTPDALGP~vv~~l~ 137 (369)
T PRK02858 111 ASCLIVGLGNW----NVTPDALGPLVVENVL 137 (369)
T ss_pred CcEEEEeCCCc----CCCccccChheeccee
Confidence 55899999998 4688889999988664
No 39
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=27.48 E-value=1.5e+02 Score=24.35 Aligned_cols=59 Identities=14% Similarity=0.176 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHhCCCCcccceeeEEE------EEEECCeeEEEEecCcccccchHHHHHHHHHcC
Q 030503 96 GFEMVDAIAEAEGISVSSVNFKAHFG------KGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYK 154 (176)
Q Consensus 96 Gf~vLD~La~~~~~~~~~~k~~g~~a------~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~yk 154 (176)
|-.+++.|.+++|+......-+|.+. -+..+.-+++++.-..|-|++-+.|.++++.|+
T Consensus 104 ~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~ClG~C~~AP~~~Vn~~~~~~lt~e~v~~il~~~~ 168 (169)
T PRK07571 104 SAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDGKVAGKQTPESVLEKVQGWL 168 (169)
T ss_pred cHHHHHHHHHHhCCCCCCcCCCCeEEEEEecccCccCCCCeEEECCEEeCCCCHHHHHHHHHHHh
Confidence 56789999999998765433333332 233445678889889999999999999998774
No 40
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=26.73 E-value=71 Score=26.39 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=23.8
Q ss_pred cchHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 141 ASGQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 141 lSG~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
--|.++..+++.|++++++++++=|..
T Consensus 167 ~K~~al~~l~~~~~i~~~~~i~~GD~~ 193 (249)
T TIGR01485 167 GKGQALQYLLQKLAMEPSQTLVCGDSG 193 (249)
T ss_pred ChHHHHHHHHHHcCCCccCEEEEECCh
Confidence 357899999999999999999999864
No 41
>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.29 E-value=1.2e+02 Score=25.39 Aligned_cols=21 Identities=33% Similarity=0.604 Sum_probs=17.3
Q ss_pred ccCcCcchHHHHHHHHHHHHh
Q 030503 87 QYNGTRHNVGFEMVDAIAEAE 107 (176)
Q Consensus 87 kY~~TRHNVGf~vLD~La~~~ 107 (176)
.|..-|||||+++-+.+.+.-
T Consensus 56 dy~evrhsvgYl~NELiENAV 76 (184)
T COG5381 56 DYDEVRHSVGYLANELIENAV 76 (184)
T ss_pred cHHHHhhhHHHHHHHHHHhhh
Confidence 389999999999888776654
No 42
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=25.79 E-value=41 Score=28.02 Aligned_cols=26 Identities=8% Similarity=0.220 Sum_probs=23.5
Q ss_pred chHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 142 SGQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 142 SG~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
-|.++..+++.+++++++++++=|..
T Consensus 189 Kg~al~~l~~~~gi~~~~v~afGD~~ 214 (272)
T PRK15126 189 KGAALAVLSQHLGLSLADCMAFGDAM 214 (272)
T ss_pred hHHHHHHHHHHhCCCHHHeEEecCCH
Confidence 58999999999999999999998864
No 43
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=25.61 E-value=3.1e+02 Score=22.74 Aligned_cols=82 Identities=15% Similarity=0.193 Sum_probs=43.8
Q ss_pred ceEEEEccCcccccCcCcchHHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEecCcccccchHHHHHHHHHcC
Q 030503 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYK 154 (176)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~yk 154 (176)
.++++..-++.. ....+....++.|+.+.+.+..-.+.....+|-.+.-- .--.+..-+.|+++++.|+
T Consensus 81 il~V~D~t~~~~---------~~~~~~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~--~~~~~~~~~~v~~~l~~~~ 149 (233)
T cd01896 81 ILMVLDATKPEG---------HREILERELEGVGIRLNKRPPNITIKKKKKGGINITST--VPLTKLDEKTIKAILREYK 149 (233)
T ss_pred EEEEecCCcchh---------HHHHHHHHHHHcCceecCCCCeEEEEEEecCCEEEecc--CCCCCCCHHHHHHHHHHhC
Confidence 345666655543 22334555666777544332222233333334333322 3334457789999999999
Q ss_pred CCCCcEEEEEecCC
Q 030503 155 IPLKQVLVRQNIFI 168 (176)
Q Consensus 155 i~pe~ILVIHDDLD 168 (176)
|...++ .+.+|..
T Consensus 150 i~~~~v-~~~~~~~ 162 (233)
T cd01896 150 IHNADV-LIREDIT 162 (233)
T ss_pred eeeEEE-EEccCCC
Confidence 975444 4444444
No 44
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=25.42 E-value=23 Score=25.11 Aligned_cols=23 Identities=30% Similarity=0.362 Sum_probs=20.2
Q ss_pred cccccchHHHHHHHHHcCCCCCc
Q 030503 137 TFMNASGQSVGSIVSYYKIPLKQ 159 (176)
Q Consensus 137 TYMNlSG~aV~~l~~~yki~pe~ 159 (176)
-||..||....++++.+++.+.+
T Consensus 7 hflhE~g~~FveIAr~~~i~a~e 29 (63)
T PF11242_consen 7 HFLHESGLSFVEIARKIGITAKE 29 (63)
T ss_pred hhHHHcCCcHHHHHHHhCCCHHH
Confidence 47899999999999999998765
No 45
>TIGR02463 MPGP_rel mannosyl-3-phosphoglycerate phosphatase-related protein. This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbor-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (TIGR02460). Members of this family are like to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate.
Probab=24.85 E-value=75 Score=25.41 Aligned_cols=26 Identities=15% Similarity=0.109 Sum_probs=23.3
Q ss_pred chHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 142 SGQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 142 SG~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
-|.++..+++.+++++++++.+=|..
T Consensus 180 Kg~al~~l~~~lgi~~~~vi~~GD~~ 205 (221)
T TIGR02463 180 KGKAANWLKATYNQPDVKTLGLGDGP 205 (221)
T ss_pred HHHHHHHHHHHhCCCCCcEEEECCCH
Confidence 68899999999999999999998853
No 46
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=24.08 E-value=2.1e+02 Score=22.91 Aligned_cols=60 Identities=10% Similarity=0.115 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhCCCCcccceeeEEE------EEEECCeeEEEEecCcccccchHHHHHHHHHcC
Q 030503 95 VGFEMVDAIAEAEGISVSSVNFKAHFG------KGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYK 154 (176)
Q Consensus 95 VGf~vLD~La~~~~~~~~~~k~~g~~a------~~~i~~~~ViLlKP~TYMNlSG~aV~~l~~~yk 154 (176)
=|..+++.|.+.+|+.......+|.+. -+..+..+++++.-..|-|++-+.+.++++.++
T Consensus 90 G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~ClG~C~~aP~~~in~~~~~~lt~~~~~~il~~~~ 155 (156)
T PRK05988 90 GGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDGEVHGRLDPQRLDALLAEAR 155 (156)
T ss_pred CHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECCEEeCCCCHHHHHHHHHHhh
Confidence 457899999999998765433334332 233444578888889999999999998887653
No 47
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=24.04 E-value=51 Score=26.39 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=23.1
Q ss_pred hHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 143 GQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 143 G~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
|.++..+++++++++++++++=|..
T Consensus 159 g~al~~l~~~~~i~~~~~i~~GD~~ 183 (230)
T PRK01158 159 GTGLKKLAELMGIDPEEVAAIGDSE 183 (230)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 8999999999999999999998864
No 48
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=23.97 E-value=92 Score=28.53 Aligned_cols=32 Identities=13% Similarity=0.180 Sum_probs=25.1
Q ss_pred EEEEecCcccccchHHHHHHHHHcCCCCCcEEEEEec
Q 030503 130 VMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVRQNI 166 (176)
Q Consensus 130 ViLlKP~TYMNlSG~aV~~l~~~yki~pe~ILVIHDD 166 (176)
.++++|..+ -..|+..+..+|++ .++++||||
T Consensus 116 ~~~lrp~~~---~~~Ai~dlV~~~~W--~~v~~iYD~ 147 (400)
T cd06392 116 TLAARPPVR---LNDVMLKLVTELRW--QKFIVFYDS 147 (400)
T ss_pred eEEecCchH---HHHHHHHHHHhCCC--cEEEEEEEC
Confidence 467788533 34499999999998 589999975
No 49
>PF13242 Hydrolase_like: HAD-hyrolase-like; PDB: 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A 2HX1_D 2X4D_A 3HLT_C 3L1U_B ....
Probab=23.52 E-value=89 Score=21.09 Aligned_cols=23 Identities=0% Similarity=0.020 Sum_probs=19.5
Q ss_pred HHHHHHHcCCCCCcEEEEEecCC
Q 030503 146 VGSIVSYYKIPLKQVLVRQNIFI 168 (176)
Q Consensus 146 V~~l~~~yki~pe~ILVIHDDLD 168 (176)
+..+++.++++++++++|=|.+.
T Consensus 10 ~~~a~~~~~~~~~~~~~VGD~~~ 32 (75)
T PF13242_consen 10 LEQALKRLGVDPSRCVMVGDSLE 32 (75)
T ss_dssp HHHHHHHHTSGGGGEEEEESSTT
T ss_pred HHHHHHHcCCCHHHEEEEcCCcH
Confidence 56777888999999999999844
No 50
>TIGR02471 sucr_syn_bact_C sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial. Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by TIGR02472.
Probab=23.16 E-value=63 Score=26.34 Aligned_cols=27 Identities=22% Similarity=0.368 Sum_probs=24.0
Q ss_pred cchHHHHHHHHHcCCCCCcEEEEEecC
Q 030503 141 ASGQSVGSIVSYYKIPLKQVLVRQNIF 167 (176)
Q Consensus 141 lSG~aV~~l~~~yki~pe~ILVIHDDL 167 (176)
.-|.++..+++.+++++++++++=|+.
T Consensus 159 ~K~~al~~l~~~~g~~~~~~i~~GD~~ 185 (236)
T TIGR02471 159 SKGLALRYLSYRWGLPLEQILVAGDSG 185 (236)
T ss_pred ChHHHHHHHHHHhCCCHHHEEEEcCCc
Confidence 458999999999999999999999875
No 51
>COG4046 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.52 E-value=3.8e+02 Score=24.91 Aligned_cols=68 Identities=10% Similarity=0.158 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHhCCCCcccceeeEEEEEEECCeeEEEEecC---cccccchHHHHHHHHHcCCCCCcEEEE
Q 030503 94 NVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQ---TFMNASGQSVGSIVSYYKIPLKQVLVR 163 (176)
Q Consensus 94 NVGf~vLD~La~~~~~~~~~~k~~g~~a~~~i~~~~ViLlKP~---TYMNlSG~aV~~l~~~yki~pe~ILVI 163 (176)
++|=+++-.|..+- ..+.......+++..+.|.+++.+|+. +=.-.=|++|..+...|+-.+..|+-|
T Consensus 197 saGPlvA~~L~~~~--~~~e~~~etV~~e~e~eGRkl~IvKa~GpgstvGr~g~AvE~vv~~~g~~~k~IItI 267 (368)
T COG4046 197 SAGPLVAARLIGNR--DVREHEKETVYAEKELEGRKLYIVKAEGPGSTVGRLGEAVEEVVERLGAVPKEIITI 267 (368)
T ss_pred CcchHHHHHHHhcc--ccccccccceEEEEeecCcEEEEEecCCCCcccCChHHHHHHHHHHhccCcceEEEe
Confidence 45666666666543 112222345677888999999999974 444455789999999887766656554
No 52
>PF01187 MIF: Macrophage migration inhibitory factor (MIF); InterPro: IPR001398 Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response []. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis []. The MIF homologue D-dopachrome tautomerase (4.1.1.84 from EC) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [, ].; PDB: 1UIZ_C 3FWT_A 1HFO_F 2WKB_D 3RF4_B 2OS5_A 3RF5_A 2XCZ_A 3FWU_A 3B64_A ....
Probab=21.16 E-value=81 Score=23.48 Aligned_cols=19 Identities=11% Similarity=0.128 Sum_probs=14.4
Q ss_pred HHcCCCCCcEEEEEecCCC
Q 030503 151 SYYKIPLKQVLVRQNIFIL 169 (176)
Q Consensus 151 ~~yki~pe~ILVIHDDLDL 169 (176)
+.++++++++.|.++|++-
T Consensus 85 ~~LgIp~~Riyi~f~d~~~ 103 (114)
T PF01187_consen 85 EELGIPPDRIYINFHDLPA 103 (114)
T ss_dssp HHHT--GGGEEEEEEEETG
T ss_pred HHhCCCcCceEEEEEECCH
Confidence 4679999999999999874
No 53
>cd01445 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.
Probab=21.14 E-value=1.2e+02 Score=23.23 Aligned_cols=23 Identities=13% Similarity=0.156 Sum_probs=19.8
Q ss_pred HHHHHHHHHcCCCCCcEEEEEec
Q 030503 144 QSVGSIVSYYKIPLKQVLVRQNI 166 (176)
Q Consensus 144 ~aV~~l~~~yki~pe~ILVIHDD 166 (176)
+-+.+++...+|.++.-+|+||+
T Consensus 81 ~~~~~~~~~~GI~~~~~vVvY~~ 103 (138)
T cd01445 81 AEFAAMFEAKGIDLDKHLIATDG 103 (138)
T ss_pred HHHHHHHHHcCCCCCCeEEEECC
Confidence 45778888889999999999996
No 54
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=21.05 E-value=51 Score=23.86 Aligned_cols=20 Identities=35% Similarity=0.541 Sum_probs=15.3
Q ss_pred chHHHHHHHHHHHHhCCCCc
Q 030503 93 HNVGFEMVDAIAEAEGISVS 112 (176)
Q Consensus 93 HNVGf~vLD~La~~~~~~~~ 112 (176)
--+||..+|.+|.++|....
T Consensus 52 ~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 52 DGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp SSSBHHHHHHHHHTTT--TT
T ss_pred cCCCHHHHHHHHHHcCCCCC
Confidence 46789999999999987654
No 55
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=21.02 E-value=73 Score=25.29 Aligned_cols=26 Identities=19% Similarity=0.166 Sum_probs=23.2
Q ss_pred cchHHHHHHHHHcCCCCCcEEEEEec
Q 030503 141 ASGQSVGSIVSYYKIPLKQVLVRQNI 166 (176)
Q Consensus 141 lSG~aV~~l~~~yki~pe~ILVIHDD 166 (176)
.-|.++..+++.++++++++++|=|.
T Consensus 149 ~K~~~i~~l~~~~~i~~~~~i~~GD~ 174 (225)
T TIGR01482 149 NKGVAVKKLKEKLGIKPGETLVCGDS 174 (225)
T ss_pred CHHHHHHHHHHHhCCCHHHEEEECCC
Confidence 46789999999999999999999885
No 56
>PRK06437 hypothetical protein; Provisional
Probab=20.90 E-value=85 Score=21.52 Aligned_cols=29 Identities=14% Similarity=0.078 Sum_probs=23.2
Q ss_pred chHHHHHHHHHcCCCCCcEEEEEecCCCC
Q 030503 142 SGQSVGSIVSYYKIPLKQVLVRQNIFILF 170 (176)
Q Consensus 142 SG~aV~~l~~~yki~pe~ILVIHDDLDLp 170 (176)
.|..|.++++.++++++.+.|++|.--+|
T Consensus 19 ~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 19 HELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 34568999999999999998888765544
No 57
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=20.66 E-value=1e+02 Score=27.67 Aligned_cols=27 Identities=4% Similarity=-0.047 Sum_probs=21.6
Q ss_pred HHHHHHcCCCCCcEEEEEecCCCCccc
Q 030503 147 GSIVSYYKIPLKQVLVRQNIFILFYRY 173 (176)
Q Consensus 147 ~~l~~~yki~pe~ILVIHDDLDLplGk 173 (176)
..+++..+..+++.||++|||..+-|.
T Consensus 128 p~l~~~Lr~~~~kFIlFcDDLSFe~gd 154 (287)
T COG2607 128 PDLVELLRARPEKFILFCDDLSFEEGD 154 (287)
T ss_pred HHHHHHHhcCCceEEEEecCCCCCCCc
Confidence 455666677889999999999987664
No 58
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=20.01 E-value=83 Score=28.55 Aligned_cols=37 Identities=22% Similarity=0.315 Sum_probs=30.4
Q ss_pred eeEEEEecCcccccchHHHHHHHHHcCCCCCcEEEEEecCCCC
Q 030503 128 VPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVRQNIFILF 170 (176)
Q Consensus 128 ~~ViLlKP~TYMNlSG~aV~~l~~~yki~pe~ILVIHDDLDLp 170 (176)
+.+++=||.++|= ..+.+.|+|.|++.+.|-|-||-+
T Consensus 218 ~P~v~GKP~~~m~------~~l~~~~~i~psRt~mvGDRL~TD 254 (306)
T KOG2882|consen 218 QPIVLGKPSTFMF------EYLLEKFNIDPSRTCMVGDRLDTD 254 (306)
T ss_pred CCeecCCCCHHHH------HHHHHHcCCCcceEEEEcccchhh
Confidence 5688999999983 356678999999999999988644
Done!