Query 029635
Match_columns 190
No_of_seqs 138 out of 1135
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 16:04:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029635.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029635hhsearch_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 4.7E-51 1E-55 342.3 11.3 116 74-189 1-117 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 1E-50 2.3E-55 340.1 12.5 116 74-189 1-116 (191)
3 cd00462 PTH Peptidyl-tRNA hydr 100.0 1.1E-49 2.5E-54 328.4 12.3 113 77-189 1-113 (171)
4 TIGR00447 pth peptidyl-tRNA hy 100.0 2.1E-49 4.6E-54 331.0 12.7 115 75-189 1-116 (188)
5 PRK05426 peptidyl-tRNA hydrola 100.0 1.7E-48 3.7E-53 325.5 12.7 116 74-189 1-117 (189)
6 PF01195 Pept_tRNA_hydro: Pept 100.0 4E-47 8.7E-52 314.8 10.9 113 77-189 1-114 (184)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 5.9E-39 1.3E-43 271.8 10.1 116 74-189 38-153 (224)
8 PRK10466 hybD hydrogenase 2 ma 66.4 8.6 0.00019 31.2 3.8 30 75-108 2-31 (164)
9 cd06062 H2MP_MemB-H2up Endopep 62.1 11 0.00023 29.9 3.5 28 76-107 1-28 (146)
10 TIGR00072 hydrog_prot hydrogen 59.2 9.5 0.00021 30.0 2.8 27 77-107 1-27 (145)
11 cd06064 H2MP_F420-Reduc Endope 56.2 11 0.00024 29.9 2.7 27 77-107 1-27 (150)
12 TIGR00130 frhD coenzyme F420-r 55.8 14 0.00031 29.4 3.3 29 74-106 3-31 (153)
13 COG0680 HyaD Ni,Fe-hydrogenase 54.9 14 0.0003 30.5 3.1 31 74-108 2-32 (160)
14 cd00518 H2MP Hydrogenase speci 53.9 13 0.00029 28.9 2.8 27 77-107 1-27 (139)
15 PRK10264 hydrogenase 1 maturat 51.1 23 0.0005 30.0 4.0 31 74-108 4-34 (195)
16 cd06066 H2MP_NAD-link-bidir En 50.6 17 0.00036 28.6 2.9 27 77-107 1-27 (139)
17 cd06067 H2MP_MemB-H2evol Endop 49.4 16 0.00035 28.5 2.6 27 77-107 1-27 (136)
18 cd06070 H2MP_like-2 Putative [ 47.7 18 0.00039 28.4 2.7 25 77-105 1-25 (140)
19 TIGR00142 hycI hydrogenase mat 47.0 19 0.00042 28.4 2.7 28 76-107 1-28 (146)
20 cd06063 H2MP_Cyano-H2up This g 45.2 25 0.00054 27.8 3.1 27 76-106 1-27 (146)
21 cd06068 H2MP_like-1 Putative [ 44.6 19 0.00042 28.3 2.4 27 77-107 1-27 (144)
22 PRK11544 hycI hydrogenase 3 ma 44.3 26 0.00057 28.2 3.2 27 76-106 3-29 (156)
23 COG2897 SseA Rhodanese-related 41.5 30 0.00066 31.2 3.4 32 137-168 69-100 (285)
24 PF08282 Hydrolase_3: haloacid 40.2 29 0.00062 27.5 2.8 26 143-168 188-213 (254)
25 PF03418 Peptidase_A25: Germin 39.8 25 0.00055 32.9 2.7 79 74-167 96-179 (354)
26 KOG2380 Prephenate dehydrogena 39.1 11 0.00024 35.9 0.3 36 75-110 54-96 (480)
27 COG2179 Predicted hydrolase of 38.0 27 0.00059 29.8 2.4 29 142-170 95-123 (175)
28 COG5381 Uncharacterized protei 36.3 59 0.0013 27.7 4.1 20 88-107 57-76 (184)
29 PF13443 HTH_26: Cro/C1-type H 35.2 11 0.00025 24.9 -0.2 27 140-166 37-63 (63)
30 PF14490 HHH_4: Helix-hairpin- 31.8 26 0.00057 25.8 1.3 24 88-111 45-70 (94)
31 PRK10513 sugar phosphate phosp 30.5 36 0.00078 28.5 2.0 25 143-167 198-222 (270)
32 PRK10976 putative hydrolase; P 29.4 40 0.00088 28.2 2.1 25 143-167 192-216 (266)
33 KOG2882 p-Nitrophenyl phosphat 29.3 46 0.001 30.7 2.6 38 127-170 217-254 (306)
34 TIGR01441 GPR GPR endopeptidas 28.2 27 0.00058 32.8 0.9 78 74-167 101-184 (358)
35 PRK02858 germination protease; 27.8 28 0.0006 32.8 0.9 78 74-167 111-194 (369)
36 PF02789 Peptidase_M17_N: Cyto 27.4 57 0.0012 24.1 2.4 33 73-105 52-84 (126)
37 PTZ00397 macrophage migration 27.0 79 0.0017 23.8 3.2 32 138-169 74-105 (116)
38 COG2607 Predicted ATPase (AAA+ 26.6 43 0.00094 30.5 1.9 34 145-178 126-159 (287)
39 PRK15126 thiamin pyrimidine py 26.3 41 0.0009 28.3 1.7 26 142-167 189-214 (272)
40 TIGR01485 SPP_plant-cyano sucr 26.3 74 0.0016 26.6 3.2 28 141-168 167-194 (249)
41 PRK01158 phosphoglycolate phos 25.9 48 0.001 26.9 1.9 26 143-168 159-184 (230)
42 PF13242 Hydrolase_like: HAD-h 25.6 84 0.0018 21.6 2.9 25 145-169 9-33 (75)
43 COG0056 AtpA F0F1-type ATP syn 25.6 60 0.0013 31.8 2.8 25 141-168 240-264 (504)
44 TIGR02463 MPGP_rel mannosyl-3- 24.8 80 0.0017 25.6 3.1 26 142-167 180-205 (221)
45 COG4841 Uncharacterized protei 24.7 49 0.0011 25.7 1.6 25 164-188 14-41 (95)
46 TIGR02471 sucr_syn_bact_C sucr 23.5 62 0.0013 26.7 2.2 28 141-168 159-186 (236)
47 PRK06437 hypothetical protein; 23.0 98 0.0021 21.6 2.8 28 143-170 20-47 (67)
48 cd01445 TST_Repeats Thiosulfat 22.6 1.1E+02 0.0024 23.9 3.4 24 144-167 81-104 (138)
49 PF07431 DUF1512: Protein of u 22.4 3.8E+02 0.0083 25.3 7.2 67 95-163 185-254 (355)
50 COG4128 Zot Zonula occludens t 21.7 79 0.0017 29.8 2.6 38 140-177 36-73 (398)
51 cd01896 DRG The developmentall 21.5 4E+02 0.0087 22.4 6.8 65 100-167 97-161 (233)
52 TIGR01482 SPP-subfamily Sucros 21.4 76 0.0016 25.5 2.2 27 141-167 149-175 (225)
53 smart00852 MoCF_biosynth Proba 21.2 60 0.0013 24.8 1.5 35 134-168 11-45 (135)
54 KOG1486 GTP-binding protein DR 20.5 4.9E+02 0.011 24.3 7.4 73 89-163 148-220 (364)
55 PF01187 MIF: Macrophage migra 20.3 87 0.0019 23.7 2.3 20 150-169 84-103 (114)
56 PF05116 S6PP: Sucrose-6F-phos 20.3 90 0.0019 26.7 2.6 27 142-168 166-192 (247)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-51 Score=342.31 Aligned_cols=116 Identities=51% Similarity=0.838 Sum_probs=111.4
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCC-CccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHH
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSY 152 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~-~~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~ 152 (190)
.++|||||||||++|+.||||||||++|.||++++.++ ..+++.+.++++.+.+++|+|+||+||||+||++|.++++|
T Consensus 1 ~~kLIVGLGNPG~~Y~~TRHNvGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~l~kP~TyMNlSG~~V~~~~~f 80 (190)
T COG0193 1 MMKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASF 80 (190)
T ss_pred CcEEEEECCCCchhhcccchhHHHHHHHHHHHHhCCCCccccccCceeEEEEeCCcEEEEecCccceeCcHHHHHHHHHH
Confidence 36899999999999999999999999999999999988 45688899999999999999999999999999999999999
Q ss_pred cCCCCCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 153 YKIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 153 yki~~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
|+++++++||||||||||+|++|||.+||++||||||
T Consensus 81 y~i~~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGlK 117 (190)
T COG0193 81 YKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLK 117 (190)
T ss_pred hCCCHHHEEEEeeccCCCCceEEEEcCCCCCCcccHH
Confidence 9999999999999999999999999999999999997
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=1e-50 Score=340.15 Aligned_cols=116 Identities=65% Similarity=1.200 Sum_probs=111.0
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHc
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~y 153 (190)
+|+|||||||||++|++|||||||+++|.||++++.++++.++++.++++.+.+++|+|+||+||||+||++|.+++++|
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 47899999999999999999999999999999999887666778888999999999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 154 KIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 154 ki~~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
+++++++||||||||||+|++|+|.+||++||||||
T Consensus 81 ki~~~~ilVihDdldl~~G~irlk~gGs~gGHNGlk 116 (191)
T cd02406 81 KVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQ 116 (191)
T ss_pred CCCHHHEEEEEECCCCCCCeEEEcCCCCCCCcCCHH
Confidence 999999999999999999999999999999999997
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=1.1e-49 Score=328.40 Aligned_cols=113 Identities=56% Similarity=0.949 Sum_probs=108.6
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHcCCC
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKIP 156 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~yki~ 156 (190)
|||||||||++|++|||||||+++|.||++++..+.+.++++.++++.+.+++++|+||+||||+||++|.+++++|+++
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 69999999999999999999999999999999888766667889999999999999999999999999999999999999
Q ss_pred CCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 157 LKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 157 ~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
++++||||||||||+|++|+|.+||++||||||
T Consensus 81 ~~~ilVihDdldl~~G~vrlk~~G~~gGHNGlk 113 (171)
T cd00462 81 PEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLK 113 (171)
T ss_pred hhHEEEEEecCCCCCceEEEeCCCCCCCCCCHH
Confidence 999999999999999999999999999999997
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=2.1e-49 Score=330.97 Aligned_cols=115 Identities=48% Similarity=0.829 Sum_probs=108.9
Q ss_pred CeeEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCCCc-cceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHc
Q 029635 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSS-VNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (190)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~~~-~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~y 153 (190)
|+|||||||||++|++|||||||+++|.||++++.++++ .++.+.+++..+.+++|+|+||+||||+||++|.+++++|
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 689999999999999999999999999999999988753 4567788888888999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 154 KIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 154 ki~~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
+++++++||||||||||+|++|+|.+||++||||||
T Consensus 81 ~i~~~~ilVihDdldl~~G~irlk~~G~~gGHNGlk 116 (188)
T TIGR00447 81 RIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLK 116 (188)
T ss_pred CCChHHEEEEEecCCCCCceEEEecCCCCCCcCCHH
Confidence 999999999999999999999999999999999997
No 5
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=1.7e-48 Score=325.53 Aligned_cols=116 Identities=52% Similarity=0.849 Sum_probs=109.0
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCCC-ccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHH
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVS-SVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSY 152 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~~-~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~ 152 (190)
.++|||||||||++|++|||||||+++|.||++++..+. ..++.+.++++.+.+++++|+||+||||+||++|.+++++
T Consensus 1 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~ 80 (189)
T PRK05426 1 MMKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANF 80 (189)
T ss_pred CcEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCCCCcccccccEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHH
Confidence 368999999999999999999999999999999877654 3466788999999889999999999999999999999999
Q ss_pred cCCCCCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 153 YKIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 153 yki~~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
|+++++++||||||+|+|+|++|+|.+||++||||||
T Consensus 81 ~~i~~~~ilVihDdldl~~G~~r~k~gGs~~GHNGlk 117 (189)
T PRK05426 81 YKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLK 117 (189)
T ss_pred hCCCHHHEEEEEecCCCCCceEEEecCCCCCCcCCHH
Confidence 9999999999999999999999999999999999997
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=4e-47 Score=314.78 Aligned_cols=113 Identities=54% Similarity=0.901 Sum_probs=97.3
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCCCccc-eeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHcCC
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVN-FKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKI 155 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~~~~~-~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~yki 155 (190)
|||||||||++|++|||||||+++|.||+.++.++.+.+ +++.++.+.+.+++++|+||+||||+||.+|++++++|++
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 799999999999999999999999999999998875543 6788888889999999999999999999999999999999
Q ss_pred CCCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 156 PLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 156 ~~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
+++++||||||+|+|+|++|+|.+||++||||||
T Consensus 81 ~~~~ilVihDdldl~~G~irlk~~Gs~~GHNGlk 114 (184)
T PF01195_consen 81 PPENILVIHDDLDLPLGKIRLKKGGSSGGHNGLK 114 (184)
T ss_dssp -GGGEEEEEEETTSSTTEEEEEESS--TT-HHHH
T ss_pred CcceEEEEEeccCCCCCeEEEccCCCCCCCCCHH
Confidence 9999999999999999999999999999999996
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.9e-39 Score=271.75 Aligned_cols=116 Identities=54% Similarity=1.062 Sum_probs=109.0
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHc
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYY 153 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~y 153 (190)
.+|+|+||||||++|.+|||||||.++|.||++++++..+.+.+...+-+.+++.++++++|++|||.||++|.+++..|
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 38999999999999999999999999999999999887665555666777889999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCcceEEEccCCCCCCCCccC
Q 029635 154 KIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189 (190)
Q Consensus 154 ki~~~~iLVIhDDLdLp~GkirlK~gGs~~GHNGLK 189 (190)
+++.++++||||||++|+|+++||.+||++||||+|
T Consensus 118 ~i~~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgHNGvr 153 (224)
T KOG2255|consen 118 KIPLRHIVVIHDELELPLGKLRLRPGGSHRGHNGVR 153 (224)
T ss_pred cchheeEEEEeccccCcCceEEeccCCCccccccHH
Confidence 999999999999999999999999999999999986
No 8
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=66.45 E-value=8.6 Score=31.15 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=23.2
Q ss_pred CeeEEEecCcccCCCcCcchHHHHHHHHHHHHhC
Q 029635 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (190)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~ 108 (190)
+.+|+|+|||-- +-==+|..+++.|.+.+.
T Consensus 2 ~ilVlGiGN~l~----gDDGvG~~va~~L~~~~~ 31 (164)
T PRK10466 2 RILVLGVGNILL----TDEAIGVRIVEALEQRYI 31 (164)
T ss_pred ceEEEEECchhh----ccCcHHHHHHHHHHHhcC
Confidence 468999999942 334599999999987654
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=62.11 E-value=11 Score=29.87 Aligned_cols=28 Identities=25% Similarity=0.445 Sum_probs=21.7
Q ss_pred eeEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
.+|+|+|||-- .-==+|+.+++.|++.+
T Consensus 1 ilV~GiGN~l~----gDDG~G~~va~~L~~~~ 28 (146)
T cd06062 1 ILVLGIGNILL----ADEGIGVHAVERLEENY 28 (146)
T ss_pred CEEEEECcccc----ccCcHHHHHHHHHHHhc
Confidence 37999999942 22349999999999874
No 10
>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=59.16 E-value=9.5 Score=30.01 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=21.3
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
||+|+|||-- .-==+|..+++.|++.+
T Consensus 1 lViGiGN~l~----~DDg~G~~v~~~L~~~~ 27 (145)
T TIGR00072 1 LVLGIGNILR----GDDGFGPRVAERLEERY 27 (145)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHHHhc
Confidence 6899999942 22349999999999875
No 11
>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=56.21 E-value=11 Score=29.92 Aligned_cols=27 Identities=26% Similarity=0.394 Sum_probs=21.2
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
||+|+|||-- .-==+|+.+++.|++.+
T Consensus 1 lViGiGN~l~----gDDgvG~~va~~l~~~~ 27 (150)
T cd06064 1 LVVGCGNILF----GDDGFGPAVIEELEKLE 27 (150)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcc
Confidence 6899999942 33359999999998764
No 12
>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=55.75 E-value=14 Score=29.43 Aligned_cols=29 Identities=28% Similarity=0.376 Sum_probs=22.3
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHH
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEA 106 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~ 106 (190)
.+.+|+|+|||-- .-==+|..++++|++.
T Consensus 3 ~~ilVlGiGN~l~----gDDGvG~~v~~~L~~~ 31 (153)
T TIGR00130 3 HEILVVGCGNILF----GDDGFGPAVIEYLKEN 31 (153)
T ss_pred ceEEEEEeCcccc----ccCcHhHHHHHHHHHh
Confidence 4679999999942 2234999999999863
No 13
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=54.89 E-value=14 Score=30.47 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=24.4
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHHhC
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~ 108 (190)
.+.+|+|+|||=- .-==+|-.+++.|.+.+.
T Consensus 2 ~~ilIlG~GN~L~----~DDG~Gv~vae~L~~~~~ 32 (160)
T COG0680 2 MRILILGVGNILM----GDDGFGVRVAEKLKKRYK 32 (160)
T ss_pred CeEEEEeeCCccc----ccCcccHHHHHHHHHhcC
Confidence 4689999999942 444589999999998763
No 14
>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=53.91 E-value=13 Score=28.85 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=21.2
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
+|+|+|||-- .-==+|..+++.|++.+
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd00518 1 LVLGIGNPLR----GDDGFGPAVAERLEERY 27 (139)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcC
Confidence 5899999932 33359999999998875
No 15
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=51.13 E-value=23 Score=29.95 Aligned_cols=31 Identities=16% Similarity=0.242 Sum_probs=23.5
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHHHhC
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEG 108 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~~ 108 (190)
.+.+|+|+|||= ..-==+|..+++.|.+.+.
T Consensus 4 ~rilVlGiGN~L----~gDDGvG~~va~~L~~~~~ 34 (195)
T PRK10264 4 QRVVVMGLGNLL----WADEGFGVRVAERLYAHYH 34 (195)
T ss_pred CCEEEEEeCccc----cccCcHHHHHHHHHHhhcC
Confidence 457999999993 1223499999999988753
No 16
>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=50.57 E-value=17 Score=28.55 Aligned_cols=27 Identities=30% Similarity=0.521 Sum_probs=21.3
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
||+|+|||=- .-==+|..++++|++++
T Consensus 1 lVlGvGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPLR----GDDGLGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCccc----cccchhHHHHHHHHhhC
Confidence 6899999942 33359999999998875
No 17
>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=49.44 E-value=16 Score=28.52 Aligned_cols=27 Identities=15% Similarity=0.390 Sum_probs=20.8
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
+|+|+|||-- .-==+|..+++.|.+.+
T Consensus 1 ~VlGiGN~L~----~DDgvG~~v~~~L~~~~ 27 (136)
T cd06067 1 VLLGVGNELR----GDDGAGPLLAEKLEDLP 27 (136)
T ss_pred CEEEeCcccc----ccCcHHHHHHHHHHhcC
Confidence 5899999942 33359999999998764
No 18
>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=47.70 E-value=18 Score=28.38 Aligned_cols=25 Identities=28% Similarity=0.472 Sum_probs=19.6
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHH
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAE 105 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~ 105 (190)
||+|+|||-- .-==+|+.+++.|++
T Consensus 1 lVlGiGN~l~----~DDg~G~~v~~~L~~ 25 (140)
T cd06070 1 LIIGVGNRLY----GDDGFGSCLAEALEQ 25 (140)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHhh
Confidence 6899999942 233499999999977
No 19
>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=47.02 E-value=19 Score=28.44 Aligned_cols=28 Identities=18% Similarity=0.211 Sum_probs=21.3
Q ss_pred eeEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
.+|+|+|||-- .-==+|..++++|.+.+
T Consensus 1 ~lVlGiGN~l~----~DDG~G~~v~~~L~~~~ 28 (146)
T TIGR00142 1 LVLLCVGNELM----GDDGAGPYLAEKCAAAP 28 (146)
T ss_pred CEEEEeCcccc----ccCcHHHHHHHHHHhcc
Confidence 47999999952 22349999999998653
No 20
>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=45.22 E-value=25 Score=27.80 Aligned_cols=27 Identities=22% Similarity=0.368 Sum_probs=20.8
Q ss_pred eeEEEecCcccCCCcCcchHHHHHHHHHHHH
Q 029635 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEA 106 (190)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~ 106 (190)
.+|+|+|||-- .-==+|..++++|++.
T Consensus 1 ~lVlGiGN~L~----~DDG~G~~v~~~L~~~ 27 (146)
T cd06063 1 LTIIGCGNLNR----GDDGVGPILIRRLQAY 27 (146)
T ss_pred CEEEEECCccc----ccCcHHHHHHHHHhhc
Confidence 37999999942 2234999999999875
No 21
>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=44.59 E-value=19 Score=28.28 Aligned_cols=27 Identities=22% Similarity=0.366 Sum_probs=20.6
Q ss_pred eEEEecCcccCCCcCcchHHHHHHHHHHHHh
Q 029635 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 77 LIVGLGNPG~kY~~TRHNvGf~vlD~La~~~ 107 (190)
||+|+|||-- .-==+|..+++.|++.+
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~ 27 (144)
T cd06068 1 LVAGVGNIFL----GDDGFGVEVARRLRPRQ 27 (144)
T ss_pred CEEEECcccc----ccCcHHHHHHHHHhccC
Confidence 6899999953 22349999999998753
No 22
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=44.27 E-value=26 Score=28.19 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=21.1
Q ss_pred eeEEEecCcccCCCcCcchHHHHHHHHHHHH
Q 029635 76 WLIVGLGNPGKQYNGTRHNVGFEMVDAIAEA 106 (190)
Q Consensus 76 ~LIVGLGNPG~kY~~TRHNvGf~vlD~La~~ 106 (190)
.+|+|+|||-- .-==+|..++++|++.
T Consensus 3 ~lVlGiGN~L~----gDDGvG~~v~~~L~~~ 29 (156)
T PRK11544 3 DVVLTVGNSMM----GDDGAGPLLAEKLAAA 29 (156)
T ss_pred EEEEEeCcccc----ccCcHHHHHHHHHhcc
Confidence 58999999942 2334999999999765
No 23
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=41.48 E-value=30 Score=31.17 Aligned_cols=32 Identities=19% Similarity=0.272 Sum_probs=28.1
Q ss_pred chhhhchHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 137 TFMNASGQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 137 TyMNlSG~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
.=|=.+.+.+.+++...+|..++.||+|||-+
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd~~ 100 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDDGG 100 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECCCC
Confidence 46667889999999999999999999999933
No 24
>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=40.24 E-value=29 Score=27.51 Aligned_cols=26 Identities=15% Similarity=0.387 Sum_probs=23.5
Q ss_pred hHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 143 GQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 143 G~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
|.++..+++.+++++++++++=|+.+
T Consensus 188 ~~ai~~l~~~~~i~~~~~~~~GD~~N 213 (254)
T PF08282_consen 188 GSAIKYLLEYLGISPEDIIAFGDSEN 213 (254)
T ss_dssp HHHHHHHHHHHTTSGGGEEEEESSGG
T ss_pred HHHHHHHhhhcccccceeEEeecccc
Confidence 67999999999999999999999753
No 25
>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=39.84 E-value=25 Score=32.93 Aligned_cols=79 Identities=24% Similarity=0.359 Sum_probs=36.4
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHHH-HhCCCCCccceeeEEEEEEECCeEEEEEeCCchhhh----chHHHHH
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAE-AEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNA----SGQSVGS 148 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~-~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMNl----SG~aV~~ 148 (190)
...|||||||. .-|--..|-.++|.+.- ++-..+..... .. +-.+|..+-| --|=. +++.|+.
T Consensus 96 ~~iLVVGLGN~----~vTPDALGP~vv~~l~VTRHL~~~~pe~~----~~---g~r~VsaiaP-GVmg~TGiET~eIi~g 163 (354)
T PF03418_consen 96 ASILVVGLGNW----NVTPDALGPRVVENLLVTRHLFELQPEEV----DE---GYRPVSAIAP-GVMGQTGIETAEIIKG 163 (354)
T ss_dssp --EEEEE-S-S----SSGGG-HHHHHHHT----HHHHHHS--SS-----S---S---EEEE-S-GGG---SS-HHHHHHH
T ss_pred CeEEEEeCCCc----CCCccccchhhhhhhhhhhhhhhhCchhh----cc---CcceeeEEcC-CccccccccHHHHHHH
Confidence 56899999997 46999999999997641 11000000000 00 1123555555 34444 4467777
Q ss_pred HHHHcCCCCCcEEEEeccC
Q 029635 149 IVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 149 i~~~yki~~~~iLVIhDDL 167 (190)
+.+..+ | ++||.-|-|
T Consensus 164 vv~~~k--P-d~VIaIDAL 179 (354)
T PF03418_consen 164 VVEKIK--P-DLVIAIDAL 179 (354)
T ss_dssp HHHHH-----SEEEEEEEE
T ss_pred HHHhhC--C-CEEEEehhh
Confidence 777655 3 566666654
No 26
>KOG2380 consensus Prephenate dehydrogenase (NADP+) [Amino acid transport and metabolism]
Probab=39.09 E-value=11 Score=35.92 Aligned_cols=36 Identities=28% Similarity=0.417 Sum_probs=30.0
Q ss_pred CeeEEEecCcccCCCcCcchHHHHHH-------HHHHHHhCCC
Q 029635 75 PWLIVGLGNPGKQYNGTRHNVGFEMV-------DAIAEAEGIS 110 (190)
Q Consensus 75 ~~LIVGLGNPG~kY~~TRHNvGf~vl-------D~La~~~~~~ 110 (190)
..-|+|+||-|.-|++|--.+||.++ +.+|+++|..
T Consensus 54 ~IaIIGfGnmGqflAetli~aGh~li~hsRsdyssaa~~yg~~ 96 (480)
T KOG2380|consen 54 VIAIIGFGNMGQFLAETLIDAGHGLICHSRSDYSSAAEKYGSA 96 (480)
T ss_pred EEEEEecCcHHHHHHHHHHhcCceeEecCcchhHHHHHHhccc
Confidence 35689999999999999999999776 6677888764
No 27
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=38.01 E-value=27 Score=29.77 Aligned_cols=29 Identities=17% Similarity=0.267 Sum_probs=25.6
Q ss_pred chHHHHHHHHHcCCCCCcEEEEeccCCCC
Q 029635 142 SGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170 (190)
Q Consensus 142 SG~aV~~i~~~yki~~~~iLVIhDDLdLp 170 (190)
++.++.++++.++++++++++|-|.|=.+
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL~TD 123 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQLFTD 123 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchhhhh
Confidence 67899999999999999999999987443
No 28
>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.32 E-value=59 Score=27.66 Aligned_cols=20 Identities=35% Similarity=0.619 Sum_probs=17.3
Q ss_pred CCcCcchHHHHHHHHHHHHh
Q 029635 88 YNGTRHNVGFEMVDAIAEAE 107 (190)
Q Consensus 88 Y~~TRHNvGf~vlD~La~~~ 107 (190)
|..-||||||++-+.|-+..
T Consensus 57 y~evrhsvgYl~NELiENAV 76 (184)
T COG5381 57 YDEVRHSVGYLANELIENAV 76 (184)
T ss_pred HHHHhhhHHHHHHHHHHhhh
Confidence 99999999999988876654
No 29
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=35.16 E-value=11 Score=24.92 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=18.6
Q ss_pred hhchHHHHHHHHHcCCCCCcEEEEecc
Q 029635 140 NASGQSVGSIVSYYKIPLKQVLVIFDD 166 (190)
Q Consensus 140 NlSG~aV~~i~~~yki~~~~iLVIhDD 166 (190)
+.+-..+.++++++++++++++...+|
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 556688999999999999999887766
No 30
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=31.81 E-value=26 Score=25.81 Aligned_cols=24 Identities=33% Similarity=0.493 Sum_probs=17.6
Q ss_pred CCcCc--chHHHHHHHHHHHHhCCCC
Q 029635 88 YNGTR--HNVGFEMVDAIAEAEGISV 111 (190)
Q Consensus 88 Y~~TR--HNvGf~vlD~La~~~~~~~ 111 (190)
|.-.. --+||..+|.+|.++|...
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~ 70 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEP 70 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--T
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCC
Confidence 54555 5689999999999998764
No 31
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=30.52 E-value=36 Score=28.47 Aligned_cols=25 Identities=28% Similarity=0.311 Sum_probs=23.2
Q ss_pred hHHHHHHHHHcCCCCCcEEEEeccC
Q 029635 143 GQSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 143 G~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
|.++..+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 7899999999999999999999975
No 32
>PRK10976 putative hydrolase; Provisional
Probab=29.43 E-value=40 Score=28.17 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=23.3
Q ss_pred hHHHHHHHHHcCCCCCcEEEEeccC
Q 029635 143 GQSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 143 G~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
|.++..+++.+++++++++++=|..
T Consensus 192 g~al~~l~~~lgi~~~~viafGD~~ 216 (266)
T PRK10976 192 GHALEAVAKKLGYSLKDCIAFGDGM 216 (266)
T ss_pred HHHHHHHHHHcCCCHHHeEEEcCCc
Confidence 8899999999999999999999865
No 33
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=29.32 E-value=46 Score=30.67 Aligned_cols=38 Identities=29% Similarity=0.482 Sum_probs=31.8
Q ss_pred CeEEEEEeCCchhhhchHHHHHHHHHcCCCCCcEEEEeccCCCC
Q 029635 127 NVPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170 (190)
Q Consensus 127 ~~~v~L~KP~TyMNlSG~aV~~i~~~yki~~~~iLVIhDDLdLp 170 (190)
-+++++=||.++|= ..+.+.|+|+|++.+.|-|-||..
T Consensus 217 R~P~v~GKP~~~m~------~~l~~~~~i~psRt~mvGDRL~TD 254 (306)
T KOG2882|consen 217 RQPIVLGKPSTFMF------EYLLEKFNIDPSRTCMVGDRLDTD 254 (306)
T ss_pred CCCeecCCCCHHHH------HHHHHHcCCCcceEEEEcccchhh
Confidence 35689999999983 357789999999999999988765
No 34
>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=28.15 E-value=27 Score=32.81 Aligned_cols=78 Identities=24% Similarity=0.365 Sum_probs=44.8
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHH--HHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhh----hchHHHH
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIA--EAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMN----ASGQSVG 147 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La--~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN----lSG~aV~ 147 (190)
...|||||||- .-|--..|-.+++.|. +++ ..+.... +.+ +-.+|.-+-| --|= .+++.|+
T Consensus 101 ~~iLVVGLGN~----~VTPDALGP~vv~~l~VTRHL-~~~~p~~----~~~---g~r~VsaiaP-GVmg~TGiET~EIIk 167 (358)
T TIGR01441 101 MTCLVVGLGNW----NVTPDALGPKVVENLLVTRHL-FKLIPES----VDE---GIRPVSAVAP-GVMGITGIETSDIIR 167 (358)
T ss_pred CcEEEEeCCCc----CCCccccChheecceeeehhh-hhhcchh----hcc---CCceeeEEcC-CccccccccHHHHHH
Confidence 56899999996 4688999999998875 221 1110000 111 1123455555 2333 3456777
Q ss_pred HHHHHcCCCCCcEEEEeccC
Q 029635 148 SIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 148 ~i~~~yki~~~~iLVIhDDL 167 (190)
.+.+..| | ++||.-|-|
T Consensus 168 giVek~k--P-D~VIaIDAL 184 (358)
T TIGR01441 168 GIIEQIK--P-DFVIAIDAL 184 (358)
T ss_pred HHHHhhC--C-CEEEEechh
Confidence 7777554 3 566666755
No 35
>PRK02858 germination protease; Provisional
Probab=27.80 E-value=28 Score=32.85 Aligned_cols=78 Identities=26% Similarity=0.336 Sum_probs=44.1
Q ss_pred CCeeEEEecCcccCCCcCcchHHHHHHHHHH--HHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhh----hchHHHH
Q 029635 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIA--EAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMN----ASGQSVG 147 (190)
Q Consensus 74 ~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La--~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN----lSG~aV~ 147 (190)
...|||||||- .-|--..|-.+++.|. +++ ..+.... +.+ +-.+|.-+-| --|= .+++.|+
T Consensus 111 ~~vLVVGLGN~----~VTPDALGP~vv~~l~VTRHL-~~~~p~~----~~~---g~r~VsAiaP-GVmg~TGiET~EIIk 177 (369)
T PRK02858 111 ASCLIVGLGNW----NVTPDALGPLVVENVLVTRHL-FQLQPES----VEE---GFRPVSAIAP-GVMGITGIETSDIIY 177 (369)
T ss_pred CcEEEEeCCCc----CCCccccChheecceeeehhh-hhhcchh----hcc---CCceeeEEcC-CcccccchhHHHHHH
Confidence 56899999996 5699999999998664 211 0100000 011 1123444445 2333 3456677
Q ss_pred HHHHHcCCCCCcEEEEeccC
Q 029635 148 SIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 148 ~i~~~yki~~~~iLVIhDDL 167 (190)
.+.+..| | ++||.-|-|
T Consensus 178 gIVek~K--P-D~VIaIDAL 194 (369)
T PRK02858 178 GIIEKTK--P-DFVIAIDAL 194 (369)
T ss_pred HHHHhhC--C-CEEEEechh
Confidence 7777554 3 566666755
No 36
>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=27.43 E-value=57 Score=24.07 Aligned_cols=33 Identities=24% Similarity=0.330 Sum_probs=20.1
Q ss_pred CCCeeEEEecCcccCCCcCcchHHHHHHHHHHH
Q 029635 73 QHPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAE 105 (190)
Q Consensus 73 ~~~~LIVGLGNPG~kY~~TRHNvGf~vlD~La~ 105 (190)
..+.++||||+..+--..+--.++-.++..+.+
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 457899999999762223333455555555544
No 37
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=26.99 E-value=79 Score=23.83 Aligned_cols=32 Identities=16% Similarity=0.161 Sum_probs=23.2
Q ss_pred hhhhchHHHHHHHHHcCCCCCcEEEEeccCCC
Q 029635 138 FMNASGQSVGSIVSYYKIPLKQVLVIFDDLDL 169 (190)
Q Consensus 138 yMNlSG~aV~~i~~~yki~~~~iLVIhDDLdL 169 (190)
.-.++......+.+..+++++++.|...|++-
T Consensus 74 k~~l~~~i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 74 NSSIAAAITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred HHHHHHHHHHHHHHHhCcCcccEEEEEEECCh
Confidence 44455544455556789999999999998864
No 38
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=26.59 E-value=43 Score=30.53 Aligned_cols=34 Identities=12% Similarity=0.216 Sum_probs=27.4
Q ss_pred HHHHHHHHcCCCCCcEEEEeccCCCCcceEEEcc
Q 029635 145 SVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRLLP 178 (190)
Q Consensus 145 aV~~i~~~yki~~~~iLVIhDDLdLp~GkirlK~ 178 (190)
.+..+++..+..++.+||++|||..+-|.-..|.
T Consensus 126 ~Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~ 159 (287)
T COG2607 126 TLPDLVELLRARPEKFILFCDDLSFEEGDDAYKA 159 (287)
T ss_pred hHHHHHHHHhcCCceEEEEecCCCCCCCchHHHH
Confidence 3446667778889999999999999999877653
No 39
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=26.28 E-value=41 Score=28.34 Aligned_cols=26 Identities=12% Similarity=0.273 Sum_probs=23.7
Q ss_pred chHHHHHHHHHcCCCCCcEEEEeccC
Q 029635 142 SGQSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 142 SG~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
-|.++..+++.++|++++++++=|..
T Consensus 189 Kg~al~~l~~~~gi~~~~v~afGD~~ 214 (272)
T PRK15126 189 KGAALAVLSQHLGLSLADCMAFGDAM 214 (272)
T ss_pred hHHHHHHHHHHhCCCHHHeEEecCCH
Confidence 58899999999999999999999864
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=26.26 E-value=74 Score=26.64 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=24.4
Q ss_pred hchHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 141 ASGQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 141 lSG~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
.-|.++..+++.|++++++++++=|..+
T Consensus 167 ~K~~al~~l~~~~~i~~~~~i~~GD~~N 194 (249)
T TIGR01485 167 GKGQALQYLLQKLAMEPSQTLVCGDSGN 194 (249)
T ss_pred ChHHHHHHHHHHcCCCccCEEEEECChh
Confidence 3578999999999999999999998754
No 41
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=25.92 E-value=48 Score=26.88 Aligned_cols=26 Identities=19% Similarity=0.248 Sum_probs=23.8
Q ss_pred hHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 143 GQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 143 G~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
|.++..+++.+++++++++++=|..+
T Consensus 159 g~al~~l~~~~~i~~~~~i~~GD~~N 184 (230)
T PRK01158 159 GTGLKKLAELMGIDPEEVAAIGDSEN 184 (230)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCchh
Confidence 89999999999999999999998753
No 42
>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=25.63 E-value=84 Score=21.56 Aligned_cols=25 Identities=8% Similarity=0.157 Sum_probs=20.6
Q ss_pred HHHHHHHHcCCCCCcEEEEeccCCC
Q 029635 145 SVGSIVSYYKIPLKQVLVIFDDLDL 169 (190)
Q Consensus 145 aV~~i~~~yki~~~~iLVIhDDLdL 169 (190)
.+..+++.++++++++++|=|.+..
T Consensus 9 ~~~~a~~~~~~~~~~~~~VGD~~~~ 33 (75)
T PF13242_consen 9 MLEQALKRLGVDPSRCVMVGDSLET 33 (75)
T ss_dssp HHHHHHHHHTSGGGGEEEEESSTTT
T ss_pred HHHHHHHHcCCCHHHEEEEcCCcHh
Confidence 3567788899999999999999543
No 43
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=25.56 E-value=60 Score=31.78 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=18.2
Q ss_pred hchHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 141 ASGQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 141 lSG~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
-+|-++++.+.+- -+++|||+|||.
T Consensus 240 y~g~a~aE~f~~~---G~dvLIVyDDLs 264 (504)
T COG0056 240 YAGCAMAEYFRDN---GKDVLIVYDDLS 264 (504)
T ss_pred hhhhHHHHHHHhc---CCeEEEEecCch
Confidence 3577777655543 489999999985
No 44
>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=24.82 E-value=80 Score=25.58 Aligned_cols=26 Identities=19% Similarity=0.229 Sum_probs=23.5
Q ss_pred chHHHHHHHHHcCCCCCcEEEEeccC
Q 029635 142 SGQSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 142 SG~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
-|.++..+++.+++++++++.+=|..
T Consensus 180 Kg~al~~l~~~lgi~~~~vi~~GD~~ 205 (221)
T TIGR02463 180 KGKAANWLKATYNQPDVKTLGLGDGP 205 (221)
T ss_pred HHHHHHHHHHHhCCCCCcEEEECCCH
Confidence 67899999999999999999999864
No 45
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.66 E-value=49 Score=25.66 Aligned_cols=25 Identities=24% Similarity=0.368 Sum_probs=19.8
Q ss_pred eccCCCCcce-EEE--ccCCCCCCCCcc
Q 029635 164 FDDLDLPFSK-MRL--LPKGGHGGHNGY 188 (190)
Q Consensus 164 hDDLdLp~Gk-irl--K~gGs~~GHNGL 188 (190)
+||++|+-|. ||+ |-||...+|-|.
T Consensus 14 k~E~~l~~g~~vrffvRyGG~~~~~~GF 41 (95)
T COG4841 14 KEELDLEEGNKVRFFVRYGGCSSLQQGF 41 (95)
T ss_pred HHhcCCCCCCEEEEEEEEcCcccccCCc
Confidence 4899999884 565 779988888875
No 46
>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=23.53 E-value=62 Score=26.73 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=24.6
Q ss_pred hchHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 141 ASGQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 141 lSG~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
.-|.++..+++.+++++++++.+=|+.+
T Consensus 159 ~K~~al~~l~~~~g~~~~~~i~~GD~~n 186 (236)
T TIGR02471 159 SKGLALRYLSYRWGLPLEQILVAGDSGN 186 (236)
T ss_pred ChHHHHHHHHHHhCCCHHHEEEEcCCcc
Confidence 4578999999999999999999998754
No 47
>PRK06437 hypothetical protein; Provisional
Probab=22.99 E-value=98 Score=21.59 Aligned_cols=28 Identities=14% Similarity=0.194 Sum_probs=23.8
Q ss_pred hHHHHHHHHHcCCCCCcEEEEeccCCCC
Q 029635 143 GQSVGSIVSYYKIPLKQVLVIFDDLDLP 170 (190)
Q Consensus 143 G~aV~~i~~~yki~~~~iLVIhDDLdLp 170 (190)
|..|+++++.++++++.+.|..|.--+|
T Consensus 20 ~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 20 ELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 4579999999999999999988876666
No 48
>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=22.56 E-value=1.1e+02 Score=23.88 Aligned_cols=24 Identities=17% Similarity=0.159 Sum_probs=20.4
Q ss_pred HHHHHHHHHcCCCCCcEEEEeccC
Q 029635 144 QSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 144 ~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
+-+.+++..++|+++.-||+||+-
T Consensus 81 ~~~~~~~~~~GI~~~~~vVvY~~~ 104 (138)
T cd01445 81 AEFAAMFEAKGIDLDKHLIATDGD 104 (138)
T ss_pred HHHHHHHHHcCCCCCCeEEEECCC
Confidence 467788888999999999999963
No 49
>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=22.40 E-value=3.8e+02 Score=25.31 Aligned_cols=67 Identities=12% Similarity=0.096 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHhCCCCCccceeeEEEEEEECCeEEEEEeC---CchhhhchHHHHHHHHHcCCCCCcEEEE
Q 029635 95 VGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKP---QTFMNASGQSVGSIVSYYKIPLKQVLVI 163 (190)
Q Consensus 95 vGf~vlD~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP---~TyMNlSG~aV~~i~~~yki~~~~iLVI 163 (190)
+|=+++-.|...... .....+-.+++..+++++++++|. .+=.=.=|++|.++.+.++-.++.||-|
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 222334566788899999999995 4444556789999999886666655543
No 50
>COG4128 Zot Zonula occludens toxin [General function prediction only]
Probab=21.66 E-value=79 Score=29.84 Aligned_cols=38 Identities=16% Similarity=0.105 Sum_probs=32.8
Q ss_pred hhchHHHHHHHHHcCCCCCcEEEEeccCCCCcceEEEc
Q 029635 140 NASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRLL 177 (190)
Q Consensus 140 NlSG~aV~~i~~~yki~~~~iLVIhDDLdLp~GkirlK 177 (190)
|+-|-....+.+.|+-.+.+++|+.||++-+=|.....
T Consensus 36 NVrGl~ler~~~~~pd~~~~i~I~n~D~~~~d~~~~m~ 73 (398)
T COG4128 36 NVRGLQLERITERYPDATGEIIIVNDDVLKADFFPFMG 73 (398)
T ss_pred ecccccHHHHHHhccCCCCceEEEeccccCcccchhhc
Confidence 77788889999999999999999999999887765544
No 51
>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=21.49 E-value=4e+02 Score=22.43 Aligned_cols=65 Identities=18% Similarity=0.264 Sum_probs=34.8
Q ss_pred HHHHHHHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHcCCCCCcEEEEeccC
Q 029635 100 VDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 100 lD~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
+....+..|+.+.+....-.+.....++-.+.-. ..-.+..-+.|.++++.|+|...++ .+.||+
T Consensus 97 ~~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~--~~~~~~~~~~v~~~l~~~~i~~~~v-~~~~~~ 161 (233)
T cd01896 97 LERELEGVGIRLNKRPPNITIKKKKKGGINITST--VPLTKLDEKTIKAILREYKIHNADV-LIREDI 161 (233)
T ss_pred HHHHHHHcCceecCCCCeEEEEEEecCCEEEecc--CCCCCCCHHHHHHHHHHhCeeeEEE-EEccCC
Confidence 4455566777544333222333333344333322 3344556789999999999865544 333333
No 52
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=21.37 E-value=76 Score=25.54 Aligned_cols=27 Identities=22% Similarity=0.147 Sum_probs=23.7
Q ss_pred hchHHHHHHHHHcCCCCCcEEEEeccC
Q 029635 141 ASGQSVGSIVSYYKIPLKQVLVIFDDL 167 (190)
Q Consensus 141 lSG~aV~~i~~~yki~~~~iLVIhDDL 167 (190)
.-|.++..+++.+++++++++.|=|..
T Consensus 149 ~K~~~i~~l~~~~~i~~~~~i~~GD~~ 175 (225)
T TIGR01482 149 NKGVAVKKLKEKLGIKPGETLVCGDSE 175 (225)
T ss_pred CHHHHHHHHHHHhCCCHHHEEEECCCH
Confidence 457899999999999999999999853
No 53
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=21.16 E-value=60 Score=24.85 Aligned_cols=35 Identities=11% Similarity=0.333 Sum_probs=28.5
Q ss_pred eCCchhhhchHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 134 KPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 134 KP~TyMNlSG~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
.+.+.=|.+|..+.++++.++.......++-||.+
T Consensus 11 ~~~~~~d~~~~~l~~~l~~~G~~~~~~~~v~Dd~~ 45 (135)
T smart00852 11 SGGQIYDSNGPALAELLTELGIEVTRYVIVPDDKE 45 (135)
T ss_pred cCCCcccCcHHHHHHHHHHCCCeEEEEEEeCCCHH
Confidence 34455599999999999999988888888888855
No 54
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=20.49 E-value=4.9e+02 Score=24.33 Aligned_cols=73 Identities=23% Similarity=0.266 Sum_probs=54.8
Q ss_pred CcCcchHHHHHHHHHHHHhCCCCCccceeeEEEEEEECCeEEEEEeCCchhhhchHHHHHHHHHcCCCCCcEEEE
Q 029635 89 NGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVI 163 (190)
Q Consensus 89 ~~TRHNvGf~vlD~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMNlSG~aV~~i~~~yki~~~~iLVI 163 (190)
..|+|+.--.+++.=.+..|+.+.+.+..-.+.....++-++-.--|.|-||. +.+..++..|+|-..++++=
T Consensus 148 Datk~e~qr~~le~ELe~vGiRLNk~~Pniy~k~kk~gGi~f~~T~~lT~~~e--k~i~~ILheykI~Naevl~R 220 (364)
T KOG1486|consen 148 DATKSEDQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPLTHCDE--KLIYTILHEYKIHNAEVLFR 220 (364)
T ss_pred cCCcchhHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeeccccccH--HHHHHHHHHHeeccceEEEe
Confidence 45888888888888888888887766555555555556767777778887665 78899999999987777653
No 55
>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=20.33 E-value=87 Score=23.67 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=14.7
Q ss_pred HHHcCCCCCcEEEEeccCCC
Q 029635 150 VSYYKIPLKQVLVIFDDLDL 169 (190)
Q Consensus 150 ~~~yki~~~~iLVIhDDLdL 169 (190)
.+.++|+++++.|.++|++-
T Consensus 84 ~~~LgIp~~Riyi~f~d~~~ 103 (114)
T PF01187_consen 84 EEELGIPPDRIYINFHDLPA 103 (114)
T ss_dssp HHHHT--GGGEEEEEEEETG
T ss_pred HHHhCCCcCceEEEEEECCH
Confidence 35679999999999998863
No 56
>PF05116 S6PP: Sucrose-6F-phosphate phosphohydrolase; InterPro: IPR006380 This family of sequences represent sucrose phosphate phosphohydrolase (SPP) from plants and cyanobacteria []. SPP is a member of the Class IIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. 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.; PDB: 1TJ5_A 2B1Q_A 1TJ4_A 1S2O_A 1U2T_A 2D2V_A 1TJ3_A 1U2S_A 2B1R_A 3GYG_B ....
Probab=20.33 E-value=90 Score=26.67 Aligned_cols=27 Identities=30% Similarity=0.412 Sum_probs=22.4
Q ss_pred chHHHHHHHHHcCCCCCcEEEEeccCC
Q 029635 142 SGQSVGSIVSYYKIPLKQVLVIFDDLD 168 (190)
Q Consensus 142 SG~aV~~i~~~yki~~~~iLVIhDDLd 168 (190)
-|.+|..+++.++++++++|++-|.-+
T Consensus 166 K~~Al~~L~~~~~~~~~~vl~aGDSgN 192 (247)
T PF05116_consen 166 KGAALRYLMERWGIPPEQVLVAGDSGN 192 (247)
T ss_dssp HHHHHHHHHHHHT--GGGEEEEESSGG
T ss_pred HHHHHHHHHHHhCCCHHHEEEEeCCCC
Confidence 788999999999999999999988643
Done!