Query 026114
Match_columns 243
No_of_seqs 129 out of 1098
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 03:57:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026114.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026114hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02406 CRS2 Chloroplast RNA s 100.0 3.5E-74 7.6E-79 498.5 22.2 189 49-237 2-191 (191)
2 COG0193 Pth Peptidyl-tRNA hydr 100.0 4.9E-74 1.1E-78 495.4 20.7 187 48-235 1-189 (190)
3 TIGR00447 pth peptidyl-tRNA hy 100.0 8.8E-72 1.9E-76 482.5 22.2 185 49-234 1-188 (188)
4 PRK05426 peptidyl-tRNA hydrola 100.0 1E-70 2.2E-75 476.1 22.4 186 48-235 1-188 (189)
5 PF01195 Pept_tRNA_hydro: Pept 100.0 6.5E-70 1.4E-74 468.5 18.4 182 51-233 1-184 (184)
6 cd00462 PTH Peptidyl-tRNA hydr 100.0 5.9E-69 1.3E-73 458.8 19.6 170 51-221 1-171 (171)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 9E-62 2E-66 420.1 17.8 222 1-236 1-224 (224)
8 PRK11544 hycI hydrogenase 3 ma 93.9 2.2 4.7E-05 35.8 12.8 135 49-224 2-146 (156)
9 TIGR00142 hycI hydrogenase mat 90.0 9.7 0.00021 31.3 14.4 133 50-221 1-142 (146)
10 cd06070 H2MP_like-2 Putative [ 88.5 12 0.00026 30.5 11.8 84 51-168 1-96 (140)
11 COG0680 HyaD Ni,Fe-hydrogenase 86.4 20 0.00042 30.6 12.1 140 48-220 2-154 (160)
12 PRK10264 hydrogenase 1 maturat 84.7 27 0.00058 30.6 14.2 138 48-221 4-157 (195)
13 TIGR00072 hydrog_prot hydrogen 84.0 22 0.00047 29.1 12.7 126 51-211 1-139 (145)
14 cd06062 H2MP_MemB-H2up Endopep 83.3 24 0.00051 28.9 12.3 129 50-213 1-142 (146)
15 cd06064 H2MP_F420-Reduc Endope 82.4 26 0.00057 28.8 11.8 128 51-212 1-145 (150)
16 PRK12362 germination protease; 77.4 38 0.00081 32.3 11.2 162 48-229 99-312 (318)
17 TIGR00130 frhD coenzyme F420-r 75.2 46 0.001 27.5 13.4 130 49-211 4-145 (153)
18 cd06068 H2MP_like-1 Putative [ 72.7 51 0.0011 26.9 12.3 130 51-220 1-143 (144)
19 PRK10466 hybD hydrogenase 2 ma 61.7 11 0.00024 31.7 3.8 135 48-221 1-149 (164)
20 PF06154 YagB_YeeU_YfjZ: YagB/ 56.2 21 0.00045 28.7 4.2 31 194-224 35-65 (103)
21 PF11775 CobT_C: Cobalamin bio 48.9 39 0.00085 30.6 5.3 89 113-208 115-207 (219)
22 KOG2380 Prephenate dehydrogena 39.8 3.1 6.8E-05 40.5 -3.3 48 37-85 43-97 (480)
23 PF11458 Mistic: Membrane-inte 38.9 57 0.0012 25.1 4.0 26 197-222 2-27 (84)
24 KOG1486 GTP-binding protein DR 38.8 1.2E+02 0.0025 28.9 6.8 76 64-141 149-224 (364)
25 PF03418 Peptidase_A25: Germin 33.5 36 0.00079 32.8 2.8 77 49-140 97-179 (354)
26 PF11463 R-HINP1I: R.HinP1I re 32.3 23 0.00049 31.5 1.1 38 120-159 153-190 (205)
27 cd06067 H2MP_MemB-H2evol Endop 30.8 46 0.00099 27.0 2.6 124 51-210 1-133 (136)
28 cd06063 H2MP_Cyano-H2up This g 30.5 56 0.0012 26.7 3.2 87 51-167 2-99 (146)
29 cd00518 H2MP Hydrogenase speci 29.7 52 0.0011 26.5 2.8 125 51-211 1-137 (139)
30 TIGR01441 GPR GPR endopeptidas 29.4 23 0.00049 34.3 0.7 80 48-141 101-185 (358)
31 PRK10870 transcriptional repre 29.4 51 0.0011 28.0 2.8 39 191-229 136-175 (176)
32 PF14490 HHH_4: Helix-hairpin- 29.1 33 0.00071 26.2 1.4 26 62-87 45-72 (94)
33 PRK09256 hypothetical protein; 28.4 26 0.00056 29.3 0.8 24 136-159 4-29 (138)
34 PRK02858 germination protease; 28.2 25 0.00053 34.2 0.7 80 48-141 111-195 (369)
35 cd01896 DRG The developmentall 26.4 2.3E+02 0.005 24.8 6.5 92 71-184 94-185 (233)
36 TIGR01651 CobT cobaltochelatas 26.2 1.3E+02 0.0028 31.2 5.4 88 114-208 496-587 (600)
37 PF12896 Apc4: Anaphase-promot 25.1 96 0.0021 26.5 3.8 44 188-231 89-132 (210)
38 PF02318 FYVE_2: FYVE-type zin 21.7 1.8E+02 0.0039 23.1 4.5 20 196-215 1-20 (118)
39 PF06466 PCAF_N: PCAF (P300/CB 20.6 64 0.0014 29.8 1.8 47 190-236 150-199 (252)
40 cd06066 H2MP_NAD-link-bidir En 20.1 4.7E+02 0.01 21.1 12.5 86 51-167 1-93 (139)
No 1
>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=3.5e-74 Score=498.50 Aligned_cols=189 Identities=78% Similarity=1.267 Sum_probs=181.1
Q ss_pred CeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcC
Q 026114 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQ 128 (243)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~k 128 (243)
+||||||||||++|++|||||||+++|.||+++++++++.++++.++++.+++++++|+||+||||+||++|+++++||+
T Consensus 2 ~~LIvGLGNPG~~Y~~TRHNiGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~yk 81 (191)
T cd02406 2 PWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYYK 81 (191)
T ss_pred cEEEEEcCCCchhhCcCchhHHHHHHHHHHHHcCCCccccccceEEEEEEECCeEEEEEeCCCchhcCHHHHHHHHHHhC
Confidence 58999999999999999999999999999999998876667889999999999999999999999999999999999999
Q ss_pred CCCccEE-EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHHHH
Q 026114 129 VPLRHIL-IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQID 207 (243)
Q Consensus 129 i~~~~il-IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~l~ 207 (243)
+++++|| ||||||||+|++|+|.+||++||||||||+++|+++++|+|||||||||+...++++|||++|+++|++.|+
T Consensus 82 i~~~~ilVihDdldl~~G~irlk~gGs~gGHNGlkSI~~~Lggt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~l~ 161 (191)
T cd02406 82 VPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEHLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQID 161 (191)
T ss_pred CCHHHEEEEEECCCCCCCeEEEcCCCCCCCcCCHHHHHHHhCCCCCeEEEEEEeCCCCCCCchhhhhcCCCCHHHHHHHH
Confidence 9999999 999999999999999999999999999999999657899999999999987678999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhCHHHHHHhhhCCCC
Q 026114 208 AALEQGVEAVRTLVLNGFDQNISRFNMGQK 237 (243)
Q Consensus 208 ~~l~~a~~al~~li~~g~~~~mn~~n~~~~ 237 (243)
++++.|+++++.|+.++++++||+||+.+|
T Consensus 162 ~~~~~a~~~~~~~~~~~~~~~~n~~n~~~~ 191 (191)
T cd02406 162 TALEQGVDAVRTLVLKGFNGSAERFNLVQK 191 (191)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHhCCCC
Confidence 999999999999999999999999998775
No 2
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-74 Score=495.41 Aligned_cols=187 Identities=42% Similarity=0.716 Sum_probs=180.2
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCc-cccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHH
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAM-NTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAH 126 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~-~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~ 126 (243)
+++|||||||||++|+.|||||||+++|.||+++++++ ...++.+.++++.+.+++|+|+||+||||+||++|.++++|
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 46899999999999999999999999999999999998 55678899999999999999999999999999999999999
Q ss_pred cCCCCccEE-EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHH
Q 026114 127 YQVPLRHIL-IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQ 205 (243)
Q Consensus 127 ~ki~~~~il-IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~ 205 (243)
|++++++|| ||||||||+|++|||.+||+|||||||||+++| ||++|+|||||||||+..+++++|||++|+++|++.
T Consensus 81 y~i~~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGlKSi~~~l-Gt~~f~RlRiGIGrP~~~~~v~~~VL~~f~~~E~~~ 159 (190)
T COG0193 81 YKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHL-GTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEEREL 159 (190)
T ss_pred hCCCHHHEEEEeeccCCCCceEEEEcCCCCCCcccHHHHHHHh-CCCccceEEEEcCCCCCCCchhHhhcCCCCHHHHHH
Confidence 999999999 999999999999999999999999999999999 599999999999999888899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhCHHHHHHhhhCC
Q 026114 206 IDAALEQGVEAVRTLVLNGFDQNISRFNMG 235 (243)
Q Consensus 206 l~~~l~~a~~al~~li~~g~~~~mn~~n~~ 235 (243)
|+++++.++++++.++..+++++||+||+.
T Consensus 160 l~~~~~~a~~~~~~~~~~~~~~~mn~~~~~ 189 (190)
T COG0193 160 LDKAIDKAADALELLLEGDFEKAMNKLNAL 189 (190)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHhcc
Confidence 999999999999999999999999999975
No 3
>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=8.8e-72 Score=482.46 Aligned_cols=185 Identities=42% Similarity=0.686 Sum_probs=176.5
Q ss_pred CeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccc-cccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 026114 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 127 (243)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~-~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ 127 (243)
+||||||||||++|++|||||||+++|.||++++.++.+ .++.+.+++..+++.+++|+||+||||+||++|++++++|
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 489999999999999999999999999999999988763 4567888888899999999999999999999999999999
Q ss_pred CCCCccEE-EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHHH
Q 026114 128 QVPLRHIL-IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQI 206 (243)
Q Consensus 128 ki~~~~il-IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~l 206 (243)
+++++++| ||||||||+|++|+|++||++||||||||+++| ++++|+|||||||||+.+.++++|||++|+++|++.|
T Consensus 81 ~i~~~~ilVihDdldl~~G~irlk~~G~~gGHNGlkSI~~~l-gt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~e~~~l 159 (188)
T TIGR00447 81 RIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL-GTNNFNRLRIGIGSPGGSNKVVEFVLSKFTKSELPLL 159 (188)
T ss_pred CCChHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHh-CCCCcceEEEEeCCCCCCCchhhhccCCCCHHHHHHH
Confidence 99999999 999999999999999999999999999999999 6899999999999998777899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhC-HHHHHHhhhC
Q 026114 207 DAALEQGVEAVRTLVLNG-FDQNISRFNM 234 (243)
Q Consensus 207 ~~~l~~a~~al~~li~~g-~~~~mn~~n~ 234 (243)
+++++.++++++.|+.++ ++++||+||+
T Consensus 160 ~~~i~~~~~~~~~~~~~~~~~~~~n~~n~ 188 (188)
T TIGR00447 160 EKALDKAVEALEMSFSEGAFLKAMNRFNS 188 (188)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHhhC
Confidence 999999999999999999 9999999995
No 4
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=1e-70 Score=476.11 Aligned_cols=186 Identities=44% Similarity=0.751 Sum_probs=176.2
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCcc-ccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHH
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMN-TIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAH 126 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~-~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~ 126 (243)
++||||||||||++|++|||||||+++|.||++++..+. ..++++.++++.+++.+++|+||+||||+||++|++++++
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 368999999999999999999999999999999887654 3466789999999989999999999999999999999999
Q ss_pred cCCCCccEE-EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHH
Q 026114 127 YQVPLRHIL-IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQ 205 (243)
Q Consensus 127 ~ki~~~~il-IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~ 205 (243)
|+++++++| ||||||+|+|++|+|++||++||||||||+++| ++++|+|||||||||+ ..++++|||++|+++|++.
T Consensus 81 ~~i~~~~ilVihDdldl~~G~~r~k~gGs~~GHNGlkSI~~~l-gt~~f~RlriGIGrP~-~~~v~~yVL~~f~~~E~~~ 158 (189)
T PRK05426 81 YKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHL-GTQDFWRLRIGIGRPD-KKKVVDYVLGKFSKEEQEL 158 (189)
T ss_pred hCCCHHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHh-CCCCeeEEEEEeCCCC-CCCcchhhcCCCCHHHHHH
Confidence 999999999 999999999999999999999999999999999 5889999999999997 5689999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhCHHHHHHhhhCC
Q 026114 206 IDAALEQGVEAVRTLVLNGFDQNISRFNMG 235 (243)
Q Consensus 206 l~~~l~~a~~al~~li~~g~~~~mn~~n~~ 235 (243)
|++++++|+++++.|+.++++++||+||+.
T Consensus 159 l~~~~~~a~~~v~~~~~~~~~~~~~~~n~~ 188 (189)
T PRK05426 159 LDKAIDKAADAIELLLEGGFEKAMNKFNSK 188 (189)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHhCC
Confidence 999999999999999999999999999964
No 5
>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=6.5e-70 Score=468.50 Aligned_cols=182 Identities=47% Similarity=0.838 Sum_probs=162.4
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccc-cceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQ-SKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQV 129 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~-~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki 129 (243)
|||||||||++|++|||||||+++|.||+.++.+|.+.+ +++.++.+.+.+.+++|+||+||||+||++|++++++|++
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 799999999999999999999999999999999886654 7788888899999999999999999999999999999999
Q ss_pred CCccEE-EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHHHHH
Q 026114 130 PLRHIL-IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDA 208 (243)
Q Consensus 130 ~~~~il-IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~l~~ 208 (243)
+++++| ||||+|+|+|++|+|++||++||||||||+++| +|++|+|||||||||+...++++|||++|+++|++.|++
T Consensus 81 ~~~~ilVihDdldl~~G~irlk~~Gs~~GHNGlkSI~~~L-gt~~f~RlrIGIGrp~~~~~v~~yVL~~f~~~E~~~l~~ 159 (184)
T PF01195_consen 81 PPENILVIHDDLDLPLGKIRLKKGGSSGGHNGLKSIIQHL-GTEDFPRLRIGIGRPPSKEDVADYVLSKFSPEERELLDK 159 (184)
T ss_dssp -GGGEEEEEEETTSSTTEEEEEESS--TT-HHHHHHHHHC-TSSGSEEEEEEE--TSTTSGHHHHHTSB-HHHHHHHHHH
T ss_pred CcceEEEEEeccCCCCCeEEEccCCCCCCCCCHHHHHHHh-ccccceeEEEecCCCCCcchHHHHHhcCCCHHHHHHHHH
Confidence 999999 999999999999999999999999999999999 589999999999999877899999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCHHHHHHhhh
Q 026114 209 ALEQGVEAVRTLVLNGFDQNISRFN 233 (243)
Q Consensus 209 ~l~~a~~al~~li~~g~~~~mn~~n 233 (243)
++++|+++++.|++++++++||+||
T Consensus 160 ~~~~a~~~l~~~i~~~~~~~mn~~n 184 (184)
T PF01195_consen 160 VIPQAAEALEQIIEGGFEKAMNKFN 184 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHhC
Confidence 9999999999999999999999998
No 6
>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=5.9e-69 Score=458.79 Aligned_cols=170 Identities=51% Similarity=0.892 Sum_probs=163.3
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
|||||||||++|++|||||||+++|.||++++.++.+.++++.++++.+++++++|+||+||||+||++|++++++|+++
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 69999999999999999999999999999999988777778999999999999999999999999999999999999999
Q ss_pred CccEE-EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHHHHHH
Q 026114 131 LRHIL-IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAA 209 (243)
Q Consensus 131 ~~~il-IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~l~~~ 209 (243)
++++| ||||||||+|++|+|++||++||||||||+++| +|++|+|||||||||+.+.++++|||++|+++|++.|+++
T Consensus 81 ~~~ilVihDdldl~~G~vrlk~~G~~gGHNGlkSI~~~l-gt~~f~RlriGIGrP~~~~~v~~yVL~~f~~~E~~~l~~~ 159 (171)
T cd00462 81 PEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL-GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEA 159 (171)
T ss_pred hhHEEEEEecCCCCCceEEEeCCCCCCCCCCHHHHHHHh-CCCCeeEEEEEeCCCCCCCChhhhhcCCCCHHHHHHHHHH
Confidence 99999 999999999999999999999999999999999 5899999999999998778999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 026114 210 LEQGVEAVRTLV 221 (243)
Q Consensus 210 l~~a~~al~~li 221 (243)
++.|+++++.++
T Consensus 160 ~~~~~~~~~~~~ 171 (171)
T cd00462 160 IEKAADALEDIL 171 (171)
T ss_pred HHHHHHHHHHhC
Confidence 999999998763
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9e-62 Score=420.13 Aligned_cols=222 Identities=56% Similarity=0.916 Sum_probs=197.6
Q ss_pred CccccCCCcccccCCCCCCCCCCccccceeEEEec-CCCCCCCccccccCeEEEeecCCCCCcCcccchHHHHHHHHHHH
Q 026114 1 MLYALSAPKTCISCPRGPPFPQKRQVSTRLCVHAS-LPADNGGFKVEYTPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQ 79 (243)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~ 79 (243)
|+|++++|...-.-|+..-++ +.||++.|+ .|..... +|+|+||||||++|.+|||||||.|+|.||+
T Consensus 1 m~~~~~~~~~~~~~p~~~i~~-----~qr~~~~c~l~~~~~~k------~wli~GLGNPg~~y~gTRHnvG~~Ml~~lar 69 (224)
T KOG2255|consen 1 MTCGGGVPMAYKFLPKKLIAR-----KQRFSVHCDLKPRVSIK------PWLIVGLGNPGSKYVGTRHNVGFEMLDMLAR 69 (224)
T ss_pred CcCCCCCcceeeecccccccc-----ccchheeeecccCCCCC------ceEEEecCCCcccccccchhhHHHHHHHHHH
Confidence 899999988776666654443 455654444 3443222 7999999999999999999999999999999
Q ss_pred HcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCCCccEE-EEecCCCCCceEEEccCCCCCCC
Q 026114 80 AQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVPLRHIL-IYDEMSLMNGVLRLQPKGGHGHH 158 (243)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~~~~il-IhDDldl~~G~irlk~~Gs~gGH 158 (243)
+++++.++.+.++..+.+.+++.++++++|++|||.||++|.+++..|+++.++++ |||||++|+|+++|+++||++||
T Consensus 70 rlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y~i~~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgH 149 (224)
T KOG2255|consen 70 RLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALYKIPLRHIVVIHDELELPLGKLRLRPGGSHRGH 149 (224)
T ss_pred HhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhhcchheeEEEEeccccCcCceEEeccCCCcccc
Confidence 99999888887888888999999999999999999999999999999999999999 99999999999999999999999
Q ss_pred CcHHHHHHhhcCCCCccEEEEcccCCCCCCccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhCCC
Q 026114 159 NGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFNMGQ 236 (243)
Q Consensus 159 NGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yVLs~Fs~~E~~~l~~~l~~a~~al~~li~~g~~~~mn~~n~~~ 236 (243)
||+||++.+++++..|+||+||||||++++|+++|||++|++.|++ +.+++..+.++.++.+++..-+++||..|
T Consensus 150 NGvrs~~~~l~g~~~fpRL~iGIGrppg~~d~~a~vLskfsp~e~k---e~Let~l~~~~~lil~~l~~~is~~~lg~ 224 (224)
T KOG2255|consen 150 NGVRSVFNCLNGRRSFPRLSIGIGRPPGNEDVKAFVLSKFSPAEQK---ELLETLLEHVKTLILQGLQQSISRFNLGQ 224 (224)
T ss_pred ccHHHHHhhccCCcccceeeeecCCCCCchhhhHHHHHhcChhhhH---HHHHHHHhhhHHHHHHHHHHhcccCcCCC
Confidence 9999999999888899999999999999999999999999999998 44666777788888889999999999764
No 8
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=93.88 E-value=2.2 Score=35.82 Aligned_cols=135 Identities=18% Similarity=0.234 Sum_probs=75.6
Q ss_pred CeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcC
Q 026114 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQ 128 (243)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~k 128 (243)
..+|+|+|||-.. -==+|..++++|++.. . . . +.++.-.| .|.-+-.++..
T Consensus 2 ~~lVlGiGN~L~g----DDGvG~~v~~~L~~~~-~--~-----~-----------v~vid~gt----~~~~~~~~i~~-- 52 (156)
T PRK11544 2 TDVVLTVGNSMMG----DDGAGPLLAEKLAAAP-K--G-----G-----------WVVIDGGS----APENDIVAIRE-- 52 (156)
T ss_pred cEEEEEeCccccc----cCcHHHHHHHHHhccC-C--C-----C-----------eEEEECCC----CHHHHHHHHHh--
Confidence 4699999999643 2349999999997642 1 0 0 11221112 12222222332
Q ss_pred CCCccEEEEec--CCCCCceEEEccC-------CCCCCCCcHHHHHHhhcCCCCccEEEE-cccCCCCCCccccccccCC
Q 026114 129 VPLRHILIYDE--MSLMNGVLRLQPK-------GGHGHHNGLKSVMNHLDGCREFPRLCI-GIGNPPGKMDMKAYLLQKF 198 (243)
Q Consensus 129 i~~~~ilIhDD--ldl~~G~irlk~~-------Gs~gGHNGLKSIi~~L~gt~~f~RLrI-GIGrP~~~~~v~~yVLs~F 198 (243)
..++.+||.|= .+.++|.++.-.. ..+.+.-||..++..+.+ ..+++.| ||= |. ++ +| =..+
T Consensus 53 ~~~d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~~--~~p~v~iigI~-~~---~~-~~-g~~L 124 (156)
T PRK11544 53 LRPERLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKE--DVPEVIFLGIQ-PD---IV-GF-YYPM 124 (156)
T ss_pred cCCCEEEEEECCccCcCCCEEEEEchhhcccccCCCCCcCCHHHHHHHHhc--CCCcEEEEEEE-ee---ec-cC-CCCC
Confidence 23577778784 5678999987311 124445589999988853 3456554 443 32 22 22 2355
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhC
Q 026114 199 SPIEREQIDAALEQGVEAVRTLVLNG 224 (243)
Q Consensus 199 s~~E~~~l~~~l~~a~~al~~li~~g 224 (243)
|++= .+.++++++.++.|...+
T Consensus 125 S~~v----~~av~~~~~~l~~~~~~~ 146 (156)
T PRK11544 125 TQPV----KDAVETVYQRLEGWEGNG 146 (156)
T ss_pred CHHH----HHHHHHHHHHHHHhhccC
Confidence 5554 444566667777776544
No 9
>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=89.99 E-value=9.7 Score=31.32 Aligned_cols=133 Identities=16% Similarity=0.177 Sum_probs=72.9
Q ss_pred eEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 026114 50 WLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQV 129 (243)
Q Consensus 50 ~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki 129 (243)
.||+|+|||-.. -==+|..++++|.+.+.- . .+.++.-.| .|.-.-.+++.+
T Consensus 1 ~lVlGiGN~l~~----DDG~G~~v~~~L~~~~~~-------~-----------~v~v~d~gt----~~~~~~~~~~~~-- 52 (146)
T TIGR00142 1 LVLLCVGNELMG----DDGAGPYLAEKCAAAPKE-------E-----------NWVVINAGT----VPENFTVAIREL-- 52 (146)
T ss_pred CEEEEeCccccc----cCcHHHHHHHHHHhccCC-------C-----------CEEEEECCC----ChHHHHHHHHhc--
Confidence 379999999743 234999999999865321 0 022222222 122222233322
Q ss_pred CCccEEEEecC--CCCCceEEEccC-----C-CCCCCCcHHHHHHhhcCCCCccEEEE-cccCCCCCCccccccccCCCH
Q 026114 130 PLRHILIYDEM--SLMNGVLRLQPK-----G-GHGHHNGLKSVMNHLDGCREFPRLCI-GIGNPPGKMDMKAYLLQKFSP 200 (243)
Q Consensus 130 ~~~~ilIhDDl--dl~~G~irlk~~-----G-s~gGHNGLKSIi~~L~gt~~f~RLrI-GIGrP~~~~~v~~yVLs~Fs~ 200 (243)
.++.+||-|-+ +.++|.++.... . .+-+..|+..+++.+.+ .--.++.| ||- |. ++ +|- ..+|+
T Consensus 53 ~~d~viivDA~~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~ll~~~~~-~~~~~~~ligi~-~~---~~-~~g-~~LS~ 125 (146)
T TIGR00142 53 RPTHILIVDATDMGLNPGEVRIIDDDIIEMYSMSTHNMPLSYLVDYLKE-DINGEIIFLGIQ-PD---IV-GFY-YPMSQ 125 (146)
T ss_pred CCCEEEEEECcccCCCCCeEEEEChhhccccccCcCcCCHHHHHHHHHh-cCCCeEEEEEEe-ee---ee-ecC-CCCCH
Confidence 25777788865 569999887331 1 24444599999888742 22245555 543 32 22 333 46666
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 026114 201 IEREQIDAALEQGVEAVRTLV 221 (243)
Q Consensus 201 ~E~~~l~~~l~~a~~al~~li 221 (243)
+=++.++ ++++.+..++
T Consensus 126 ~v~~a~~----~~~~~i~~~i 142 (146)
T TIGR00142 126 PVKDAVE----TLYQRLIGWE 142 (146)
T ss_pred HHHHHHH----HHHHHHHHHH
Confidence 6555554 4444454444
No 10
>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=88.51 E-value=12 Score=30.50 Aligned_cols=84 Identities=20% Similarity=0.237 Sum_probs=50.6
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
||+|+|||-.. -==+|+.+++.|++ .++ -++.- |...-.++..+. .
T Consensus 1 lVlGiGN~l~~----DDg~G~~v~~~L~~-~~v---------------------~vi~~-------g~~~~~ll~~i~-~ 46 (140)
T cd06070 1 LIIGVGNRLYG----DDGFGSCLAEALEQ-CGA---------------------PVFDG-------GLDGFGLLSHLE-N 46 (140)
T ss_pred CEEEECchhcc----cCcHHHHHHHHHhh-CCC---------------------EEEEC-------CCcHHHHHHHHc-C
Confidence 68999998632 23499999999986 111 11111 112223344432 4
Q ss_pred CccEEEEecCC--CCCceEEEccC---------CC-CCCCCcHHHHHHhh
Q 026114 131 LRHILIYDEMS--LMNGVLRLQPK---------GG-HGHHNGLKSVMNHL 168 (243)
Q Consensus 131 ~~~ilIhDDld--l~~G~irlk~~---------Gs-~gGHNGLKSIi~~L 168 (243)
.+.+||.|=++ .++|.+++... .+ +.++-|+..+++-+
T Consensus 47 ~d~viiVDA~~~~~~pG~~~~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~ 96 (140)
T cd06070 47 YDIVIFIDVAVIDEDVGVFKITPEPASVAEQISFETDAHRLGPAHLLLLL 96 (140)
T ss_pred CCEEEEEEeecCCCCCeEEEEecCchhccccccCCCCCCcCCHHHHHHHH
Confidence 56777777654 68898888543 12 34444999997766
No 11
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=86.37 E-value=20 Score=30.56 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=83.0
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeC-CCcccccchhHHHHHHH
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKP-QAYMNFSGESVGPLAAH 126 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP-~TyMN~SG~aV~~i~~~ 126 (243)
|+++|+|+|||=. .-==+|-.+++.|.+.+--.. .+-++.- +--+|+.+. +
T Consensus 2 ~~ilIlG~GN~L~----~DDG~Gv~vae~L~~~~~~~~-----------------~v~vid~Gt~~~~l~~~-----l-- 53 (160)
T COG0680 2 MRILILGVGNILM----GDDGFGVRVAEKLKKRYKPPE-----------------NVEVIDGGTAGPNLLGL-----L-- 53 (160)
T ss_pred CeEEEEeeCCccc----ccCcccHHHHHHHHHhcCCCC-----------------CeEEEEcCCCcHHHHHH-----h--
Confidence 4689999999853 334589999999988763211 0111111 111232221 1
Q ss_pred cCCCCccEEEEecCC--CCCceEEEccC------CCC----CCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCcccccc
Q 026114 127 YQVPLRHILIYDEMS--LMNGVLRLQPK------GGH----GHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYL 194 (243)
Q Consensus 127 ~ki~~~~ilIhDDld--l~~G~irlk~~------Gs~----gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~v~~yV 194 (243)
...+.+||.|=++ ..+|++++-+. ..+ .+-.++..++..+.-..++...-+|+.-++. ...+ +
T Consensus 54 --~~~d~vIIVDav~~g~epG~v~~i~~e~i~~~~~~~~~s~H~~~~~~~L~~~~~~~~~~~~~~~~~v~~~--~~~~-~ 128 (160)
T COG0680 54 --AGYDPVIIVDAVLFGLEPGEVRIIDPEEIPAYSSASKDSAHELPLSELLALLKELGGLPVLILGVQVPIV--SLPE-F 128 (160)
T ss_pred --cCCCcEEEEEeeecCCCCceEEEechhhcccccccCCCccccCCHHHHHHHHHHhcCCceEEEEEeecee--cccc-c
Confidence 1234466888555 45999987322 233 3445788888888544556788888885542 1111 3
Q ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHH
Q 026114 195 LQKFSPIEREQIDAALEQGVEAVRTL 220 (243)
Q Consensus 195 Ls~Fs~~E~~~l~~~l~~a~~al~~l 220 (243)
-..+|++=++.++.+++++.+.++.+
T Consensus 129 ~~~lS~ev~~a~~~av~~i~~~l~~~ 154 (160)
T COG0680 129 GGGLSPEVEEAVDKAVERILEELREW 154 (160)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHhh
Confidence 35667776667777777666665544
No 12
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=84.70 E-value=27 Score=30.62 Aligned_cols=138 Identities=20% Similarity=0.312 Sum_probs=79.2
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 127 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ 127 (243)
++.+|+|+|||=.. -==+|..+++.|++.+..+.. +.++--.| .|. .++...
T Consensus 4 ~rilVlGiGN~L~g----DDGvG~~va~~L~~~~~~~~~-----------------V~vid~Gt----~g~---~ll~~i 55 (195)
T PRK10264 4 QRVVVMGLGNLLWA----DEGFGVRVAERLYAHYHWPEY-----------------VEIVDGGT----QGL---NLLGYV 55 (195)
T ss_pred CCEEEEEeCccccc----cCcHHHHHHHHHHhhcCCCCC-----------------eEEEECCC----CHH---HHHHHH
Confidence 45799999998422 224999999999877543210 11111111 122 333333
Q ss_pred CCCCccEEEEecC--CCCCceEEEccC----------CCCCCCCcHHHHHHh--hcCCCCcc-EEE-EcccCCCCCCccc
Q 026114 128 QVPLRHILIYDEM--SLMNGVLRLQPK----------GGHGHHNGLKSVMNH--LDGCREFP-RLC-IGIGNPPGKMDMK 191 (243)
Q Consensus 128 ki~~~~ilIhDDl--dl~~G~irlk~~----------Gs~gGHNGLKSIi~~--L~gt~~f~-RLr-IGIGrP~~~~~v~ 191 (243)
. ..+.+||-|=+ +.++|.++.-.. +-+-++-|+..+++. +.+ +.+ ++. |||= |.. +.
T Consensus 56 ~-~~d~vIiVDAv~~g~~PGtv~~~~~~~~~~~~~~~~~S~H~~~l~~~L~l~~l~g--~~P~~v~iiGie-p~~---~~ 128 (195)
T PRK10264 56 E-SASHLLILDAIDYGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSEVLALADIRG--HLPAHIALVGLQ-PAM---LD 128 (195)
T ss_pred c-CCCEEEEEECCccCCCCCeEEEEehhhcccccccCCcCcccCCHHHHHHHHHHcC--CCCCeEEEEEEE-EeE---ec
Confidence 2 35677788854 558999887321 113455799999863 322 344 566 4764 321 11
Q ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHHHH
Q 026114 192 AYLLQKFSPIEREQIDAALEQGVEAVRTLV 221 (243)
Q Consensus 192 ~yVLs~Fs~~E~~~l~~~l~~a~~al~~li 221 (243)
..=-.+|++=++.++++++.+.+.++.|.
T Consensus 129 -~~g~~LSp~V~~av~~~v~~i~~~l~~~~ 157 (195)
T PRK10264 129 -DYGGSLSELAREQLPAAEQAALAQLAAWG 157 (195)
T ss_pred -CCCCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 12246777777777777777776666554
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=84.02 E-value=22 Score=29.07 Aligned_cols=126 Identities=20% Similarity=0.322 Sum_probs=67.4
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
||+|+|||-.. -==+|..+++.|++.+.... . +-++.-.| .|. .++..+. .
T Consensus 1 lViGiGN~l~~----DDg~G~~v~~~L~~~~~~~~------~-----------v~~id~g~----~~~---~l~~~l~-~ 51 (145)
T TIGR00072 1 LVLGIGNILRG----DDGFGPRVAERLEERYEFPP------G-----------VEVLDGGT----LGL---ELLDAIE-G 51 (145)
T ss_pred CEEEECchhcc----cCcHHHHHHHHHHHhcCCCC------C-----------eEEEECCC----CHH---HHHHHHh-C
Confidence 69999999532 23599999999988753210 0 11111100 122 2333332 3
Q ss_pred CccEEEEecC--CCCCceEEEcc-C--------CCCCCCCcHHHHHHhhcCCCCcc-EEEE-cccCCCCCCccccccccC
Q 026114 131 LRHILIYDEM--SLMNGVLRLQP-K--------GGHGHHNGLKSVMNHLDGCREFP-RLCI-GIGNPPGKMDMKAYLLQK 197 (243)
Q Consensus 131 ~~~ilIhDDl--dl~~G~irlk~-~--------Gs~gGHNGLKSIi~~L~gt~~f~-RLrI-GIGrP~~~~~v~~yVLs~ 197 (243)
.+.+||-|=. +.++|.++.-. . ..+.++-|+..+++.+.-....+ ++.| ||= |. ++ +| =..
T Consensus 52 ~d~viiVDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~g~~p~~~~lvgi~-~~---~~-~~-g~~ 125 (145)
T TIGR00072 52 ADRVIVVDAVDSGAEPGTVRRLPGEDLPAFLGGKLSTHQLGLSEVLALLELLGALPPEVVLLGIQ-PE---SL-EF-GLG 125 (145)
T ss_pred CCEEEEEEccCCCcCCceEEEEchhhccccccCCCCcCcCCHHHHHHHHHHcCCCCCeEEEEEEE-ee---ec-cc-CCC
Confidence 5677777865 55899988621 1 22455569999988773222344 4444 543 21 12 22 135
Q ss_pred CCHHHHHHHHHHHH
Q 026114 198 FSPIEREQIDAALE 211 (243)
Q Consensus 198 Fs~~E~~~l~~~l~ 211 (243)
+|++=++.++++++
T Consensus 126 LS~~v~~~~~~~~~ 139 (145)
T TIGR00072 126 LSPEVAAAVPAAVE 139 (145)
T ss_pred CCHHHHHHHHHHHH
Confidence 56654444444433
No 14
>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=83.28 E-value=24 Score=28.94 Aligned_cols=129 Identities=18% Similarity=0.258 Sum_probs=69.4
Q ss_pred eEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 026114 50 WLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQV 129 (243)
Q Consensus 50 ~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki 129 (243)
.+|+|+|||-.. -==+|+.+++.|++.++.... +.++. .|...-.++..+.
T Consensus 1 ilV~GiGN~l~g----DDG~G~~va~~L~~~~~~~~~-----------------v~vi~-------~~~~~~~l~~~l~- 51 (146)
T cd06062 1 ILVLGIGNILLA----DEGIGVHAVERLEENYSFPEN-----------------VELID-------GGTLGLELLPYIE- 51 (146)
T ss_pred CEEEEECccccc----cCcHHHHHHHHHHHhcCCCCC-----------------eEEEE-------CCCCHHHHHHHHh-
Confidence 379999999632 235999999999887543211 11111 1111122333322
Q ss_pred CCccEEEEec--CCCCCceEEEc-cC--------CCCCCCCcHHHHHHhhcCC-CCccEEEE-cccCCCCCCcccccccc
Q 026114 130 PLRHILIYDE--MSLMNGVLRLQ-PK--------GGHGHHNGLKSVMNHLDGC-REFPRLCI-GIGNPPGKMDMKAYLLQ 196 (243)
Q Consensus 130 ~~~~ilIhDD--ldl~~G~irlk-~~--------Gs~gGHNGLKSIi~~L~gt-~~f~RLrI-GIGrP~~~~~v~~yVLs 196 (243)
..+.+||.|= .+.++|+++.- .. ..+.++-|+..+++.+.-. ..-+++.| ||= |. ++ +| =.
T Consensus 52 ~~d~viiVDA~~~g~~pG~i~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~~~~~~~v~ivgie-~~---~~-~~-g~ 125 (146)
T cd06062 52 EADRLIIVDAVDAGGPPGTVYRFEGEDVPAFLSAKLSAHQVGLLEVLALAELLGDLPPEIVLIGVQ-PE---SI-EW-GL 125 (146)
T ss_pred cCCEEEEEEcccCCCCCCeEEEEechhccccccCCcCcccCCHHHHHHHHHHcCCCCCeEEEEEEE-Ee---ec-cC-CC
Confidence 2366668886 46799998763 21 2355677788888765211 11234444 443 21 22 12 23
Q ss_pred CCCHHHHHHHHHHHHHH
Q 026114 197 KFSPIEREQIDAALEQG 213 (243)
Q Consensus 197 ~Fs~~E~~~l~~~l~~a 213 (243)
.+|++=++.++++++.+
T Consensus 126 ~LS~~v~~av~~~~~~i 142 (146)
T cd06062 126 ELSPEVAAALPTAIEAV 142 (146)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 66776566665555443
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=82.36 E-value=26 Score=28.80 Aligned_cols=128 Identities=18% Similarity=0.278 Sum_probs=69.4
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhH-H---HHHHH
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESV-G---PLAAH 126 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV-~---~i~~~ 126 (243)
||+|+|||-.. -==+|+.+++.|++....+ . .+.++. .|... . .+...
T Consensus 1 lViGiGN~l~g----DDgvG~~va~~l~~~~~~~------~-----------~v~vid-------~g~~~~~~~~~~~~~ 52 (150)
T cd06064 1 LVVGCGNILFG----DDGFGPAVIEELEKLELLP------D-----------NVQVID-------AGTGAPHLLFTLLDE 52 (150)
T ss_pred CEEEECCcccc----cCcHHHHHHHHHHhccCCC------C-----------CEEEEE-------CCCcHHHHHHHHHhc
Confidence 68999999642 3349999999998764211 0 012222 22211 1 11222
Q ss_pred cCCCCccEEEEecC--CCCCceEEEccC---------CCCCCCCcHHHHHHhhcCCCCcc-EEEE-cccCCCCCCccccc
Q 026114 127 YQVPLRHILIYDEM--SLMNGVLRLQPK---------GGHGHHNGLKSVMNHLDGCREFP-RLCI-GIGNPPGKMDMKAY 193 (243)
Q Consensus 127 ~ki~~~~ilIhDDl--dl~~G~irlk~~---------Gs~gGHNGLKSIi~~L~gt~~f~-RLrI-GIGrP~~~~~v~~y 193 (243)
+ -.++.+||-|=+ +.++|.++.... ..+.++-|+..+++.+.+ ..+ ++.| ||- |. ..+..+|
T Consensus 53 ~-~~~d~viivDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~--~~~~~~~iigi~-p~-~~~~~~~ 127 (150)
T cd06064 53 E-SKPKKIIIVDAIDFGLEPGTLKKISVDELPPGKYYDFDAHSWPLADPLHELKD--KYGIEIVVIGCQ-PK-RVPEPDV 127 (150)
T ss_pred c-CCCCEEEEEEecCCCCCCCeEEEEehhhcccccCCCcCCCcCCHHHHHHHHHh--cCCCeEEEEEEE-Ee-eecCCCC
Confidence 2 125677788874 779999887321 135678899999987742 232 4443 443 22 1110111
Q ss_pred cccCCCHHHHHHHHHHHHH
Q 026114 194 LLQKFSPIEREQIDAALEQ 212 (243)
Q Consensus 194 VLs~Fs~~E~~~l~~~l~~ 212 (243)
= ..+|++=++.++++++.
T Consensus 128 ~-~~LS~~v~~a~~~~~~~ 145 (150)
T cd06064 128 E-PGLSEEVEKAVPKAVEI 145 (150)
T ss_pred C-CCCCHHHHHHHHHHHHH
Confidence 1 35666655555544443
No 16
>PRK12362 germination protease; Provisional
Probab=77.43 E-value=38 Score=32.32 Aligned_cols=162 Identities=18% Similarity=0.335 Sum_probs=88.9
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEE-ECCeeEEEEeC----CCcccccchhHHH
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGS-IGEVPILLAKP----QAYMNFSGESVGP 122 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~-i~~~~v~L~KP----~TyMN~SG~aV~~ 122 (243)
.+.|||||||.- -|--..|-.+++.|.-.... . ..+++.. -+-.+|.-+-| +|=||. ++.++.
T Consensus 99 ~~iLVvGLGN~~----vTpDaLGP~Vv~~l~vTrhl--~-----~~~~~~~~~~~~pV~AiaPGVmg~TGiet-~Eii~g 166 (318)
T PRK12362 99 MTVLVVGLGNWN----VTPDALGPKVVSKLMVTRHL--K-----EYAPEEIDEGIRPVCAIAPGVLGITGIET-AEIIKG 166 (318)
T ss_pred CcEEEEEcCCCC----cCccccchhhhhhhhhhhhh--h-----hhcCchhcCCCCcceEecCCcccccchhH-HHHHHH
Confidence 458999999964 59999999999998764221 0 0111000 11234555555 555664 355666
Q ss_pred HHHHcCCCCccEEEEecCC----CCCc-eEEEccCC---CCCCCCcHHHHH-HhhcCCCCccEEEEcccCCCC-C-----
Q 026114 123 LAAHYQVPLRHILIYDEMS----LMNG-VLRLQPKG---GHGHHNGLKSVM-NHLDGCREFPRLCIGIGNPPG-K----- 187 (243)
Q Consensus 123 i~~~~ki~~~~ilIhDDld----l~~G-~irlk~~G---s~gGHNGLKSIi-~~L~gt~~f~RLrIGIGrP~~-~----- 187 (243)
+..+++ |+-||.-|-+- =-+| .|.+.-.| |+|=.|==+.|. +.| | .+=|.||| |-- .
T Consensus 167 Iv~k~k--pd~IIAIDALaar~~~Rl~~tIQisdtGI~PGSGVGN~R~~l~~etL-G---VPVIAIGV--PTVVdAatI~ 238 (318)
T PRK12362 167 VVEKIK--PDLVIAIDALAARSVERVNTTIQISDTGISPGSGVGNKRMGINEETL-G---VPVIAIGV--PTVVDAATIA 238 (318)
T ss_pred HHHhcC--CCEEEEEeccccCCHHHccCeEEECCCCCCCCccCCCcccccCHHHc-C---CCEEEEcC--CeeechHHHH
Confidence 666544 56666778765 2356 77776555 232223222222 233 2 45566665 421 0
Q ss_pred Cccccc-----------------cccCCCHHHHHHH-HHH--------------HHHHHHHHHHHHHhCHHHHH
Q 026114 188 MDMKAY-----------------LLQKFSPIEREQI-DAA--------------LEQGVEAVRTLVLNGFDQNI 229 (243)
Q Consensus 188 ~~v~~y-----------------VLs~Fs~~E~~~l-~~~--------------l~~a~~al~~li~~g~~~~m 229 (243)
.|.-++ +|..++++|+.++ .++ +|..++-+-.++++|++.+.
T Consensus 239 ~D~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ek~~li~evl~p~~~~l~VTPKeID~~i~~~s~iIa~giN~al 312 (318)
T PRK12362 239 NDTIDLVLDELINQSEEGSEFYNMLKSLNQEEKQQLIKEVLSPYVGNLIVTPKEIDELIENLSKIIAGGINMAL 312 (318)
T ss_pred HHHHHHHHHHHhhhcccccchhhhhhccCHHHHHHHHHHHhCccCCcceECcHhHHHHHHHHHHHHHHHHHHHh
Confidence 122233 4566778887655 333 44455555556666766654
No 17
>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=75.25 E-value=46 Score=27.55 Aligned_cols=130 Identities=18% Similarity=0.192 Sum_probs=68.8
Q ss_pred CeEEEeecCCCCCcCcccchHHHHHHHHHHHH-cCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 026114 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQA-QRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 127 (243)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~-~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ 127 (243)
+.+|+|+|||-.. -==+|..++++|++. +..+. .+.+ ++-.......+....
T Consensus 4 ~ilVlGiGN~l~g----DDGvG~~v~~~L~~~~~~~~~-----------------~v~v------id~gt~~~~~l~~~~ 56 (153)
T TIGR00130 4 EILVVGCGNILFG----DDGFGPAVIEYLKENGVEKPD-----------------NVCL------IDAGTGAPHFVFTLI 56 (153)
T ss_pred eEEEEEeCccccc----cCcHhHHHHHHHHHhCCCCCC-----------------CeEE------EECCCcHHHHHHHHh
Confidence 4699999998632 234999999999863 22110 0111 111111111111111
Q ss_pred C-CCCccEEEEec--CCCCCceEEEccC-----C-C-CCCCCcHHHHHHhhcCCCCccEEEE-cccCCCCCCcccccccc
Q 026114 128 Q-VPLRHILIYDE--MSLMNGVLRLQPK-----G-G-HGHHNGLKSVMNHLDGCREFPRLCI-GIGNPPGKMDMKAYLLQ 196 (243)
Q Consensus 128 k-i~~~~ilIhDD--ldl~~G~irlk~~-----G-s-~gGHNGLKSIi~~L~gt~~f~RLrI-GIGrP~~~~~v~~yVLs 196 (243)
. -..+.+||-|= ++.++|.++.-.. + . +.++-|+..+++.+.. . .++.| ||- |.. -+..+|= -
T Consensus 57 ~~~~~d~vIivDA~~~~~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~~-~--~~~~iiGi~-p~~-~~~~~~~-~ 130 (153)
T TIGR00130 57 PQSKWKKIIVVDIADFGAEPGTLRVLNVDELPNGRYMDAHGWSLAYPLHDLEE-R--IDIRVVGCQ-PKY-VSQPDVD-I 130 (153)
T ss_pred hhcCCCEEEEEEccCCCcCCCEEEEEchHHcCCCCCCCCccCCHHHHHHHhcC-C--CCEEEEEEE-EeE-ecCCCCC-C
Confidence 1 23567778885 5789999887321 2 2 5566699999988742 2 56555 553 321 1111222 2
Q ss_pred CCCHHHHHHHHHHHH
Q 026114 197 KFSPIEREQIDAALE 211 (243)
Q Consensus 197 ~Fs~~E~~~l~~~l~ 211 (243)
.+|++=++.++++++
T Consensus 131 ~LS~~v~~a~~~~~~ 145 (153)
T TIGR00130 131 GLTEEVNKAIPRAVE 145 (153)
T ss_pred CCCHHHHHHHHHHHH
Confidence 566664555444443
No 18
>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=72.67 E-value=51 Score=26.90 Aligned_cols=130 Identities=22% Similarity=0.245 Sum_probs=66.9
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHH-HHcCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLA-AHYQV 129 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~-~~~ki 129 (243)
||+|+|||-.. -==+|..+++.|+++.. + . .+.++-..| .|. .++ ....
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~~~-~------~-----------~v~~~d~g~----~~~---~l~~~~~~- 50 (144)
T cd06068 1 LVAGVGNIFLG----DDGFGVEVARRLRPRQL-P------P-----------GVRVADFGI----RGI---HLAYELLD- 50 (144)
T ss_pred CEEEECccccc----cCcHHHHHHHHHhccCC-C------C-----------CeEEEECCC----CHH---HHHHHHHh-
Confidence 68999999643 22499999999986531 0 0 022221111 122 222 2222
Q ss_pred CCccEEEEecC--CCCCceEEEccC------C--CCCCCCcHHHHHHhhcCC-CCccEEEE-cccCCCCCCccccccccC
Q 026114 130 PLRHILIYDEM--SLMNGVLRLQPK------G--GHGHHNGLKSVMNHLDGC-REFPRLCI-GIGNPPGKMDMKAYLLQK 197 (243)
Q Consensus 130 ~~~~ilIhDDl--dl~~G~irlk~~------G--s~gGHNGLKSIi~~L~gt-~~f~RLrI-GIGrP~~~~~v~~yVLs~ 197 (243)
..+.+||.|=. +.++|+++.... . .+.++-|+..+++.+.-. ..-+++.| ||= |. ++ +| =..
T Consensus 51 ~~d~viiVDA~~~g~~PG~v~~~~~~~~~~~~~~~s~H~~~~~~~l~~~~~l~~~~~~~~lvgi~-~~---~~-~~-g~~ 124 (144)
T cd06068 51 GYDTLILVDAVPRGGEPGTLYVIELEDVDAAPELLDAHGMNPDAVLALLRALGGTPPRVVVVGCE-PA---DV-DE-GIG 124 (144)
T ss_pred cCCEEEEEEeccCCcCCCEEEEEechhcccccCCCCCCCCCHHHHHHHHHHhCCCCCeEEEEEEE-ec---cc-CC-CCC
Confidence 35677777754 669999887321 1 235555888885554211 12234554 554 32 11 23 235
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q 026114 198 FSPIEREQIDAALEQGVEAVRTL 220 (243)
Q Consensus 198 Fs~~E~~~l~~~l~~a~~al~~l 220 (243)
+|++= +++++++++.++.|
T Consensus 125 LS~~v----~~a~~~~~~~i~~~ 143 (144)
T cd06068 125 LSEPV----AAAVPEAVRLVRDV 143 (144)
T ss_pred cCHHH----HHHHHHHHHHHHHh
Confidence 55554 44455555555544
No 19
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=61.73 E-value=11 Score=31.65 Aligned_cols=135 Identities=21% Similarity=0.352 Sum_probs=69.8
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 127 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ 127 (243)
|+.+|+|+|||-. +-==+|..+++.|.+.+..+.. +.+ ++ -|...-.++..+
T Consensus 1 m~ilVlGiGN~l~----gDDGvG~~va~~L~~~~~~~~~-----------------v~v------id-~gt~~~~ll~~l 52 (164)
T PRK10466 1 MRILVLGVGNILL----TDEAIGVRIVEALEQRYILPDY-----------------VEI------LD-GGTAGMELLGDM 52 (164)
T ss_pred CceEEEEECchhh----ccCcHHHHHHHHHHHhcCCCCC-----------------eEE------Ee-ccccHHHHHHHH
Confidence 4579999999863 2334999999999876543110 111 11 011122333333
Q ss_pred CCCCccEEEEecC--CCC-CceEEEccC----C-----CCCCCCcHHHHHHhhcCCCCcc-EEEE-cccCCCCCCccccc
Q 026114 128 QVPLRHILIYDEM--SLM-NGVLRLQPK----G-----GHGHHNGLKSVMNHLDGCREFP-RLCI-GIGNPPGKMDMKAY 193 (243)
Q Consensus 128 ki~~~~ilIhDDl--dl~-~G~irlk~~----G-----s~gGHNGLKSIi~~L~gt~~f~-RLrI-GIGrP~~~~~v~~y 193 (243)
. ..+.+||.|=+ +.+ +|+++.-.. + -+.+.-|+..++..+.-..+.+ ++.| ||- |. ++ +|
T Consensus 53 ~-~~d~vIiVDA~~~g~~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~L~~~~~~g~~p~~v~lvgie-p~---~~-~~ 126 (164)
T PRK10466 53 A-NRDHLIIADAIVSKKNAPGTIMVLRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVI-PE---SL-EP 126 (164)
T ss_pred h-CCCEEEEEEecCCCCCCCCEEEEEchhhccccccCCCCcccCCHHHHHHHHHHcCCCCCeEEEEEEE-Ee---ec-cC
Confidence 2 34666688865 434 999876221 1 1334457777776542112343 4444 765 32 11 22
Q ss_pred cccCCCHHHHHHHHHHHHHHHHHHHHHH
Q 026114 194 LLQKFSPIEREQIDAALEQGVEAVRTLV 221 (243)
Q Consensus 194 VLs~Fs~~E~~~l~~~l~~a~~al~~li 221 (243)
-..+|++=++.+ +.+++.+..++
T Consensus 127 -g~~LS~~V~~av----~~~~~~i~~~l 149 (164)
T PRK10466 127 -HIGLTPTVEAMI----EPALEQVLAAL 149 (164)
T ss_pred -CCCCCHHHHHHH----HHHHHHHHHHH
Confidence 125666544444 44444454444
No 20
>PF06154 YagB_YeeU_YfjZ: YagB/YeeU/YfjZ family; InterPro: IPR009320 This family of proteins includes three proteins from Escherichia coli proteins YagB, YeeU and YfjZ. The function of these proteins is unknown. They are about 120 amino acids in length.; PDB: 2H28_A 2INW_B 2JN7_A 2EA9_A.
Probab=56.22 E-value=21 Score=28.69 Aligned_cols=31 Identities=19% Similarity=0.353 Sum_probs=24.5
Q ss_pred cccCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Q 026114 194 LLQKFSPIEREQIDAALEQGVEAVRTLVLNG 224 (243)
Q Consensus 194 VLs~Fs~~E~~~l~~~l~~a~~al~~li~~g 224 (243)
+-+.|+++|...||++++...+-++.++..|
T Consensus 35 i~G~Fs~~~~~~Ld~aFP~~ikqlE~ml~sG 65 (103)
T PF06154_consen 35 ITGTFSEEEAQHLDQAFPLFIKQLELMLTSG 65 (103)
T ss_dssp EES---HHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred eEEEcCHHHHHHHHhHhHHHHHHHHHHHhcC
Confidence 5689999999999999999999998887654
No 21
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=48.94 E-value=39 Score=30.56 Aligned_cols=89 Identities=22% Similarity=0.304 Sum_probs=52.1
Q ss_pred ccccchhHHHHHHHcCCCC--ccEE--EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCC
Q 026114 113 MNFSGESVGPLAAHYQVPL--RHIL--IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKM 188 (243)
Q Consensus 113 MN~SG~aV~~i~~~~ki~~--~~il--IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~ 188 (243)
=|..|+|+..+.+.+.-.+ .+|| |.|= -|...--+...+++-=.+=||.+++......+.-=+.||||.
T Consensus 115 eniDGeAl~~a~~rL~~r~e~rkiLiViSDG--~P~d~st~~~n~~~~L~~HLr~vi~~ie~~~~Vel~aiGIg~----- 187 (219)
T PF11775_consen 115 ENIDGEALRWAAERLLARPEQRKILIVISDG--APADDSTLSANDGDYLDAHLRQVIAEIETRSDVELIAIGIGH----- 187 (219)
T ss_pred cCCcHHHHHHHHHHHHcCCccceEEEEEeCC--CcCcccccccCChHHHHHHHHHHHHHHhccCCcEEEEEEcCC-----
Confidence 4899999998887764333 3466 6663 233222222223333334588999988433456668999985
Q ss_pred ccccccccCCCHHHHHHHHH
Q 026114 189 DMKAYLLQKFSPIEREQIDA 208 (243)
Q Consensus 189 ~v~~yVLs~Fs~~E~~~l~~ 208 (243)
|+..|=-....-...+.|..
T Consensus 188 D~~~yY~~~~~i~~~e~l~~ 207 (219)
T PF11775_consen 188 DVSRYYRRAVTIDDVEELGG 207 (219)
T ss_pred CchhhcccceecCCHHHHHH
Confidence 44456555555555555644
No 22
>KOG2380 consensus Prephenate dehydrogenase (NADP+) [Amino acid transport and metabolism]
Probab=39.81 E-value=3.1 Score=40.49 Aligned_cols=48 Identities=23% Similarity=0.223 Sum_probs=35.8
Q ss_pred CCCCCCccccccCeEEEeecCCCCCcCcccchHHHHHH-------HHHHHHcCCCc
Q 026114 37 PADNGGFKVEYTPWLIVGLGNPGIKYHGTRHNVGFEMI-------DHIAQAQRIAM 85 (243)
Q Consensus 37 ~~~~~~~~~~~~~~LIVGLGNPG~~Y~~TRHNvGf~vl-------d~La~~~~~~~ 85 (243)
+++++..|.. -.+-|+|+||-|.-|+.|--.+||.++ +.+|+++|...
T Consensus 43 ~~s~~~~k~t-l~IaIIGfGnmGqflAetli~aGh~li~hsRsdyssaa~~yg~~~ 97 (480)
T KOG2380|consen 43 EDSIEQWKAT-LVIAIIGFGNMGQFLAETLIDAGHGLICHSRSDYSSAAEKYGSAK 97 (480)
T ss_pred cchhhhcccc-eEEEEEecCcHHHHHHHHHHhcCceeEecCcchhHHHHHHhcccc
Confidence 4555555542 235799999999999999999999876 56788887653
No 23
>PF11458 Mistic: Membrane-integrating protein Mistic; InterPro: IPR021078 Mistic is an integral membrane protein that folds autonomously into the membrane []. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
Probab=38.89 E-value=57 Score=25.09 Aligned_cols=26 Identities=27% Similarity=0.437 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Q 026114 197 KFSPIEREQIDAALEQGVEAVRTLVL 222 (243)
Q Consensus 197 ~Fs~~E~~~l~~~l~~a~~al~~li~ 222 (243)
+.+.+|+++|..++++..+.+..+|.
T Consensus 2 KVt~~EkeQLS~AID~mnEGLD~fI~ 27 (84)
T PF11458_consen 2 KVTDQEKEQLSTAIDRMNEGLDTFIQ 27 (84)
T ss_pred CCchHHHHHHHHHHHHHHhhHHHHHH
Confidence 46789999999999988776655553
No 24
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=38.78 E-value=1.2e+02 Score=28.94 Aligned_cols=76 Identities=12% Similarity=0.184 Sum_probs=59.6
Q ss_pred cccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCCCccEEEEecCC
Q 026114 64 GTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVPLRHILIYDEMS 141 (243)
Q Consensus 64 ~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~~~~ilIhDDld 141 (243)
.|+|+.--.+++.=.+..|+.+++.+.+-.+..-.-+|-++-.--|.|-||. +.+..++..|+|--.++++-+|..
T Consensus 149 atk~e~qr~~le~ELe~vGiRLNk~~Pniy~k~kk~gGi~f~~T~~lT~~~e--k~i~~ILheykI~Naevl~ReD~t 224 (364)
T KOG1486|consen 149 ATKSEDQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPLTHCDE--KLIYTILHEYKIHNAEVLFREDCT 224 (364)
T ss_pred CCcchhHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeeccccccH--HHHHHHHHHHeeccceEEEecCCC
Confidence 4788888888888888899999887776666666667888888889887765 678889999999766666665543
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=33.52 E-value=36 Score=32.85 Aligned_cols=77 Identities=18% Similarity=0.311 Sum_probs=34.9
Q ss_pred CeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCC-CccccccceEEEEEEECC-eeEEEEeCCCcccccc----hhHHH
Q 026114 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRI-AMNTIQSKALIGIGSIGE-VPILLAKPQAYMNFSG----ESVGP 122 (243)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~-~~~~~~~~~~~~~~~i~~-~~v~L~KP~TyMN~SG----~aV~~ 122 (243)
..|||||||.. -|.-..|-.+++.+--...+ .+..... .++ .+|..+-| --|=..| +.|+-
T Consensus 97 ~iLVVGLGN~~----vTPDALGP~vv~~l~VTRHL~~~~pe~~--------~~g~r~VsaiaP-GVmg~TGiET~eIi~g 163 (354)
T PF03418_consen 97 SILVVGLGNWN----VTPDALGPRVVENLLVTRHLFELQPEEV--------DEGYRPVSAIAP-GVMGQTGIETAEIIKG 163 (354)
T ss_dssp -EEEEE-S-SS----SGGG-HHHHHHHT----HHHHHHS--SS---------SS---EEEE-S-GGG---SS-HHHHHHH
T ss_pred eEEEEeCCCcC----CCccccchhhhhhhhhhhhhhhhCchhh--------ccCcceeeEEcC-CccccccccHHHHHHH
Confidence 47999999964 59999999999976443221 1111011 011 23555555 3344444 55666
Q ss_pred HHHHcCCCCccEEEEecC
Q 026114 123 LAAHYQVPLRHILIYDEM 140 (243)
Q Consensus 123 i~~~~ki~~~~ilIhDDl 140 (243)
+++.. .|+-||.-|-|
T Consensus 164 vv~~~--kPd~VIaIDAL 179 (354)
T PF03418_consen 164 VVEKI--KPDLVIAIDAL 179 (354)
T ss_dssp HHHHH----SEEEEEEEE
T ss_pred HHHhh--CCCEEEEehhh
Confidence 66654 46666666654
No 26
>PF11463 R-HINP1I: R.HinP1I restriction endonuclease; InterPro: IPR021107 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Hinp1I is a type II restriction endonuclease that recognises and cleaves a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends []. Structurally HinP1I consists of a conserved catalytic core domain, containing an active site motif SDC18QXK, and a DNA-binding domain []. ; PDB: 1YNM_A 2FKC_A 2FLC_A 2FL3_A 2FKH_B.
Probab=32.33 E-value=23 Score=31.45 Aligned_cols=38 Identities=24% Similarity=0.377 Sum_probs=25.2
Q ss_pred HHHHHHHcCCCCccEEEEecCCCCCceEEEccCCCCCCCC
Q 026114 120 VGPLAAHYQVPLRHILIYDEMSLMNGVLRLQPKGGHGHHN 159 (243)
Q Consensus 120 V~~i~~~~ki~~~~ilIhDDldl~~G~irlk~~Gs~gGHN 159 (243)
+-.++++| ..-++.|..-=.+.+|++.+.++||++||-
T Consensus 153 IneVi~~y--~~g~v~iS~rGsik~GkiTiQRKGGDngr~ 190 (205)
T PF11463_consen 153 INEVIQHY--GSGDVSISPRGSIKIGKITIQRKGGDNGRE 190 (205)
T ss_dssp HHHHHHHH--T-S-EEE-TTSSEEETTEEEEE---GGG-G
T ss_pred HHHHHHhh--cCCcEEEcCCccEEeeeEEEEeccCCCccc
Confidence 44678888 345666888888999999999999999984
No 27
>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=30.82 E-value=46 Score=26.95 Aligned_cols=124 Identities=16% Similarity=0.195 Sum_probs=66.4
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
+|+|+|||-.. -==+|..++++|.+.. .. . +.++.-.| .|..+...+.. ..
T Consensus 1 ~VlGiGN~L~~----DDgvG~~v~~~L~~~~---~~-----~-----------v~vid~gt----~~~~~~~~l~~--~~ 51 (136)
T cd06067 1 VLLGVGNELRG----DDGAGPLLAEKLEDLP---NP-----N-----------WLVIDGGT----VPENFTGKIRE--EK 51 (136)
T ss_pred CEEEeCccccc----cCcHHHHHHHHHHhcC---CC-----C-----------EEEEECCC----CHHHHHHHHHh--cC
Confidence 58999998643 2359999999998753 11 0 11111111 22222122221 24
Q ss_pred CccEEEEecC--CCCCceEEEccC----C--CCCCCCcHHHHHHhhcCCCCccEEEE-cccCCCCCCccccccccCCCHH
Q 026114 131 LRHILIYDEM--SLMNGVLRLQPK----G--GHGHHNGLKSVMNHLDGCREFPRLCI-GIGNPPGKMDMKAYLLQKFSPI 201 (243)
Q Consensus 131 ~~~ilIhDDl--dl~~G~irlk~~----G--s~gGHNGLKSIi~~L~gt~~f~RLrI-GIGrP~~~~~v~~yVLs~Fs~~ 201 (243)
.+.+||.|=+ +.++|+++.-.. . .+.++-|+..+.+.+. ...-+++.+ ||- |. ++ +|- ..+|++
T Consensus 52 ~d~vIiVDAv~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~~L~~~~-~~~~~~~~~vgi~-~~---~~-~~g-~~LS~~ 124 (136)
T cd06067 52 PDLIVIVDAADMGLEPGEIRIIDPEEIAEYFFSTHTLPLSILIDYLR-ESTGAEVIFLGIQ-PE---NL-EFG-EPLSPE 124 (136)
T ss_pred CCEEEEEECCccCcCCCEEEEEchhhcccccCCCCcCCHHHHHHHHH-hcCCCcEEEEEee-ee---ee-ecC-CCCCHH
Confidence 5677788876 459999987321 1 3456669999998774 221234444 332 22 22 222 356666
Q ss_pred HHHHHHHHH
Q 026114 202 EREQIDAAL 210 (243)
Q Consensus 202 E~~~l~~~l 210 (243)
=++.+++++
T Consensus 125 v~~a~~~~~ 133 (136)
T cd06067 125 VKDAAEELA 133 (136)
T ss_pred HHHHHHHHH
Confidence 555554443
No 28
>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=30.54 E-value=56 Score=26.75 Aligned_cols=87 Identities=15% Similarity=0.127 Sum_probs=49.8
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
||+|+|||-.. -==+|..++++|++. ..+. . +.++-- |.....++.... .
T Consensus 2 lVlGiGN~L~~----DDG~G~~v~~~L~~~-~~~~------~-----------v~~id~-------gt~~~~l~~~l~-~ 51 (146)
T cd06063 2 TIIGCGNLNRG----DDGVGPILIRRLQAY-LLPP------H-----------VRLVDC-------GTAGMEVMFRAR-G 51 (146)
T ss_pred EEEEECCcccc----cCcHHHHHHHHHhhc-CCCC------C-----------eEEEEC-------CCCHHHHHHHhc-C
Confidence 79999999643 234999999999864 2110 0 111111 111122333322 3
Q ss_pred CccEEEEecC--CCCCceEEEc------c---CCCCCCCCcHHHHHHh
Q 026114 131 LRHILIYDEM--SLMNGVLRLQ------P---KGGHGHHNGLKSVMNH 167 (243)
Q Consensus 131 ~~~ilIhDDl--dl~~G~irlk------~---~Gs~gGHNGLKSIi~~ 167 (243)
.+.+||.|=. +.++|+++.- . ...+.++=|+..+++.
T Consensus 52 ~d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~ 99 (146)
T cd06063 52 AKQLIIIDASSTGSEPGAVFEVPGEELEALPEPSYNLHDFRWDHALAA 99 (146)
T ss_pred CCEEEEEEeCCCCCCCCeEEEEcchhccccccCCcCcccCCHHHHHHH
Confidence 4666687865 5699998752 1 1335567789988764
No 29
>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=29.75 E-value=52 Score=26.49 Aligned_cols=125 Identities=19% Similarity=0.259 Sum_probs=66.8
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
+|+|+|||=.. -==+|..+++.|+++.. . . .+.++.-.| .|. .++.... .
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~~~-~-~----------------~v~~id~gt----~~~---~l~~~l~-~ 50 (139)
T cd00518 1 LVLGIGNPLRG----DDGFGPAVAERLEERYL-P-P----------------GVEVIDGGT----LGL---ELLDLLE-G 50 (139)
T ss_pred CEEEECCcccc----cCcHHHHHHHHHHhcCC-C-C----------------CeEEEECCC----CHH---HHHHHHh-c
Confidence 58999998632 23499999999988642 0 0 011111111 122 2333322 2
Q ss_pred CccEEEEecCC--CCCceEEEcc------CCC--CCCCCcHHHHHHhhcCCC-CccEEEE-cccCCCCCCccccccccCC
Q 026114 131 LRHILIYDEMS--LMNGVLRLQP------KGG--HGHHNGLKSVMNHLDGCR-EFPRLCI-GIGNPPGKMDMKAYLLQKF 198 (243)
Q Consensus 131 ~~~ilIhDDld--l~~G~irlk~------~Gs--~gGHNGLKSIi~~L~gt~-~f~RLrI-GIGrP~~~~~v~~yVLs~F 198 (243)
.+.+||.|=++ .++|+++.-. ... +.++-|+..+++.+.... .-+++.| ||= |. ++ +|= ..+
T Consensus 51 ~d~viiVDA~~~~~~pG~i~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~~~~~~~~~lvgi~-~~---~~-~~g-~~L 124 (139)
T cd00518 51 ADRVIIVDAVDSGGEPGTVRRLEPEELPAYLSALSTHQLGLAELLALLRLLGGLPPEVVLIGIQ-PE---SL-ELG-EGL 124 (139)
T ss_pred CCeEEEEECccCCCCCCeEEEEchhhcccccCCCCCccCCHHHHHHHHHHhCCCCCeEEEEEEE-ee---ec-CCC-CCC
Confidence 56666888764 6999988722 122 345559999998884111 1234443 443 22 11 111 566
Q ss_pred CHHHHHHHHHHHH
Q 026114 199 SPIEREQIDAALE 211 (243)
Q Consensus 199 s~~E~~~l~~~l~ 211 (243)
|++=++.++++++
T Consensus 125 S~~v~~a~~~~~~ 137 (139)
T cd00518 125 SPEVAAAVPKAVE 137 (139)
T ss_pred CHHHHHHHHHHHH
Confidence 7665555554443
No 30
>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=29.45 E-value=23 Score=34.27 Aligned_cols=80 Identities=16% Similarity=0.331 Sum_probs=44.9
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCC-CccccccceEEEEEEECCeeEEEEeCCCcccc----cchhHHH
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRI-AMNTIQSKALIGIGSIGEVPILLAKPQAYMNF----SGESVGP 122 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~-~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~----SG~aV~~ 122 (243)
...|||||||- .-|.-..|-.+++.|.-...+ .+..... .. +=.+|.-+-| --|=. +++.|+.
T Consensus 101 ~~iLVVGLGN~----~VTPDALGP~vv~~l~VTRHL~~~~p~~~----~~---g~r~VsaiaP-GVmg~TGiET~EIIkg 168 (358)
T TIGR01441 101 MTCLVVGLGNW----NVTPDALGPKVVENLLVTRHLFKLIPESV----DE---GIRPVSAVAP-GVMGITGIETSDIIRG 168 (358)
T ss_pred CcEEEEeCCCc----CCCccccChheecceeeehhhhhhcchhh----cc---CCceeeEEcC-CccccccccHHHHHHH
Confidence 45899999995 359999999999877533221 1111011 00 1123444555 22333 4456666
Q ss_pred HHHHcCCCCccEEEEecCC
Q 026114 123 LAAHYQVPLRHILIYDEMS 141 (243)
Q Consensus 123 i~~~~ki~~~~ilIhDDld 141 (243)
+..+ +.|+-||.-|-|.
T Consensus 169 iVek--~kPD~VIaIDALA 185 (358)
T TIGR01441 169 IIEQ--IKPDFVIAIDALA 185 (358)
T ss_pred HHHh--hCCCEEEEechhh
Confidence 7774 4566666667553
No 31
>PRK10870 transcriptional repressor MprA; Provisional
Probab=29.38 E-value=51 Score=27.98 Aligned_cols=39 Identities=13% Similarity=0.221 Sum_probs=31.3
Q ss_pred ccccccCCCHHHHHHHHHHHHHHHHHHHHHHHhC-HHHHH
Q 026114 191 KAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNG-FDQNI 229 (243)
Q Consensus 191 ~~yVLs~Fs~~E~~~l~~~l~~a~~al~~li~~g-~~~~m 229 (243)
.+-+++.|+++|++.+...+.+..+.++.+-.+| +-++|
T Consensus 136 ~~~~~~~ls~~e~~~l~~~L~kl~~~l~~~~~~~~~~~~~ 175 (176)
T PRK10870 136 LHQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAM 175 (176)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHHHHhhCCCchhhhhc
Confidence 3567899999999999999999888888776655 65655
No 32
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=29.05 E-value=33 Score=26.21 Aligned_cols=26 Identities=27% Similarity=0.411 Sum_probs=18.1
Q ss_pred cCccc--chHHHHHHHHHHHHcCCCccc
Q 026114 62 YHGTR--HNVGFEMIDHIAQAQRIAMNT 87 (243)
Q Consensus 62 Y~~TR--HNvGf~vld~La~~~~~~~~~ 87 (243)
|.-.. --+||..+|.+|.++|+....
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~d 72 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPDD 72 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT-
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCCC
Confidence 44444 568999999999999987654
No 33
>PRK09256 hypothetical protein; Provisional
Probab=28.37 E-value=26 Score=29.33 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=20.0
Q ss_pred EEecCCCCCceEEE--ccCCCCCCCC
Q 026114 136 IYDEMSLMNGVLRL--QPKGGHGHHN 159 (243)
Q Consensus 136 IhDDldl~~G~irl--k~~Gs~gGHN 159 (243)
|.+++++|...+++ ..++|.||.|
T Consensus 4 ~~~~~~i~~~~l~~~~~RSSGPGGQ~ 29 (138)
T PRK09256 4 ITRRLVIPENELEWRFIRASGPGGQN 29 (138)
T ss_pred cCccCccCHHHeEEEEEEcCCCCccc
Confidence 78899999888877 4678999976
No 34
>PRK02858 germination protease; Provisional
Probab=28.24 E-value=25 Score=34.15 Aligned_cols=80 Identities=18% Similarity=0.301 Sum_probs=44.0
Q ss_pred cCeEEEeecCCCCCcCcccchHHHHHHHHHHHHcCC-CccccccceEEEEEEECCeeEEEEeCCCcccc----cchhHHH
Q 026114 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRI-AMNTIQSKALIGIGSIGEVPILLAKPQAYMNF----SGESVGP 122 (243)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~-~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~----SG~aV~~ 122 (243)
...|||||||- .-|.-..|-.+++.|.-...+ .+..... .. +=.+|.-+-| --|=. +++.|+-
T Consensus 111 ~~vLVVGLGN~----~VTPDALGP~vv~~l~VTRHL~~~~p~~~----~~---g~r~VsAiaP-GVmg~TGiET~EIIkg 178 (369)
T PRK02858 111 ASCLIVGLGNW----NVTPDALGPLVVENVLVTRHLFQLQPESV----EE---GFRPVSAIAP-GVMGITGIETSDIIYG 178 (369)
T ss_pred CcEEEEeCCCc----CCCccccChheecceeeehhhhhhcchhh----cc---CCceeeEEcC-CcccccchhHHHHHHH
Confidence 35899999995 459999999999866432221 1100000 00 0123444444 22333 4455666
Q ss_pred HHHHcCCCCccEEEEecCC
Q 026114 123 LAAHYQVPLRHILIYDEMS 141 (243)
Q Consensus 123 i~~~~ki~~~~ilIhDDld 141 (243)
+..+ +.|+-||.-|-|.
T Consensus 179 IVek--~KPD~VIaIDALA 195 (369)
T PRK02858 179 IIEK--TKPDFVIAIDALA 195 (369)
T ss_pred HHHh--hCCCEEEEechhh
Confidence 6664 4566666667553
No 35
>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=26.39 E-value=2.3e+02 Score=24.83 Aligned_cols=92 Identities=14% Similarity=0.285 Sum_probs=56.3
Q ss_pred HHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCCCccEEEEecCCCCCceEEEc
Q 026114 71 FEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVPLRHILIYDEMSLMNGVLRLQ 150 (243)
Q Consensus 71 f~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~~~~ilIhDDldl~~G~irlk 150 (243)
...+....+..|+.+.+....-.+.....++-.+.-.-+. .+.+-+.|+.+++.|++.-..+.+.+|..
T Consensus 94 ~~~~~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~~~~--~~~~~~~v~~~l~~~~i~~~~v~~~~~~~--------- 162 (233)
T cd01896 94 REILERELEGVGIRLNKRPPNITIKKKKKGGINITSTVPL--TKLDEKTIKAILREYKIHNADVLIREDIT--------- 162 (233)
T ss_pred HHHHHHHHHHcCceecCCCCeEEEEEEecCCEEEeccCCC--CCCCHHHHHHHHHHhCeeeEEEEEccCCC---------
Confidence 3445666667888655433333333334445444333333 44567899999999999766666877765
Q ss_pred cCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCC
Q 026114 151 PKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNP 184 (243)
Q Consensus 151 ~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP 184 (243)
+.++++.+.|+..|...=+ |++.
T Consensus 163 ----------~~~~~~~~~~~~~y~p~ii-V~NK 185 (233)
T cd01896 163 ----------VDDLIDVIEGNRVYIPCLY-VYNK 185 (233)
T ss_pred ----------HHHHHHHHhCCceEeeEEE-EEEC
Confidence 6788888866555555333 5643
No 36
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=26.18 E-value=1.3e+02 Score=31.17 Aligned_cols=88 Identities=22% Similarity=0.335 Sum_probs=54.2
Q ss_pred cccchhHHHHHHHcCCCCc--cEE--EEecCCCCCceEEEccCCCCCCCCcHHHHHHhhcCCCCccEEEEcccCCCCCCc
Q 026114 114 NFSGESVGPLAAHYQVPLR--HIL--IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMD 189 (243)
Q Consensus 114 N~SG~aV~~i~~~~ki~~~--~il--IhDDldl~~G~irlk~~Gs~gGHNGLKSIi~~L~gt~~f~RLrIGIGrP~~~~~ 189 (243)
|..|++|..++..+.-.++ .|| |.|=-=.+-++ +.-..+.-=++=||.+|+........-=+.||||. |
T Consensus 496 N~DGeAl~wa~~rL~~R~e~rKiL~ViSDG~P~D~~T--lsvN~~~~l~~hLr~vi~~~e~~~~vel~aigIg~-----D 568 (600)
T TIGR01651 496 NIDGEALMWAHQRLIARPEQRRILMMISDGAPVDDST--LSVNPGNYLERHLRAVIEEIETRSPVELLAIGIGH-----D 568 (600)
T ss_pred CCchHHHHHHHHHHhcCcccceEEEEEeCCCcCCccc--cccCchhHHHHHHHHHHHHHhccCCceEEEeeccc-----c
Confidence 8889999998887654443 455 77743332222 22222333345599999999422356669999995 3
Q ss_pred cccccccCCCHHHHHHHHH
Q 026114 190 MKAYLLQKFSPIEREQIDA 208 (243)
Q Consensus 190 v~~yVLs~Fs~~E~~~l~~ 208 (243)
|..|-=.-++-.+.+.|..
T Consensus 569 v~r~Y~~~v~i~~~~eL~~ 587 (600)
T TIGR01651 569 VTRYYRRAVTIVDAEELAG 587 (600)
T ss_pred HHHHccccceecCHHHHHH
Confidence 6666555555556666644
No 37
>PF12896 Apc4: Anaphase-promoting complex, cyclosome, subunit 4; InterPro: IPR024790 Apc4 is one of the larger of the subunits of the anaphase-promoting complex (APC) or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [, ]. Results in Caenorhabditis elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle. The APC is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism []. This entry represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits.
Probab=25.11 E-value=96 Score=26.49 Aligned_cols=44 Identities=14% Similarity=0.337 Sum_probs=37.1
Q ss_pred CccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHh
Q 026114 188 MDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISR 231 (243)
Q Consensus 188 ~~v~~yVLs~Fs~~E~~~l~~~l~~a~~al~~li~~g~~~~mn~ 231 (243)
+++.+|....+++.-.++++++++.+.+.++.++.+.+.-++.+
T Consensus 89 ~~l~~fL~~~l~erglKr~~k~~~~~y~~i~~l~~~~l~pa~er 132 (210)
T PF12896_consen 89 PALKQFLVNQLGERGLKRWEKAVDSAYSSIRKLLFEHLIPALER 132 (210)
T ss_pred HHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999999999998887666555544
No 38
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=21.68 E-value=1.8e+02 Score=23.11 Aligned_cols=20 Identities=30% Similarity=0.335 Sum_probs=16.1
Q ss_pred cCCCHHHHHHHHHHHHHHHH
Q 026114 196 QKFSPIEREQIDAALEQGVE 215 (243)
Q Consensus 196 s~Fs~~E~~~l~~~l~~a~~ 215 (243)
|.+|++|++.|.+++.++.+
T Consensus 1 s~Lt~eE~~~I~~Vl~R~~~ 20 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQRDEE 20 (118)
T ss_dssp TTS-CHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhHHH
Confidence 46789999999999988665
No 39
>PF06466 PCAF_N: PCAF (P300/CBP-associated factor) N-terminal domain; InterPro: IPR009464 This region is spliced out of Q92830 from SWISSPROT isoform 2. It is predicted to be of a mixed alpha/beta fold - though predominantly helical.; GO: 0004402 histone acetyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.56 E-value=64 Score=29.81 Aligned_cols=47 Identities=19% Similarity=0.192 Sum_probs=30.9
Q ss_pred cccccccCCC---HHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhCCC
Q 026114 190 MKAYLLQKFS---PIEREQIDAALEQGVEAVRTLVLNGFDQNISRFNMGQ 236 (243)
Q Consensus 190 v~~yVLs~Fs---~~E~~~l~~~l~~a~~al~~li~~g~~~~mn~~n~~~ 236 (243)
|..||+.+|+ +.|.+.+-++-....-.+..|-.+....-.+..|..+
T Consensus 150 V~nfv~~kf~~l~~~E~q~m~elakmFL~~lN~W~le~ps~~~~~~~~~d 199 (252)
T PF06466_consen 150 VTNFVLYKFSHLPQKEWQTMYELAKMFLHCLNHWKLEAPSQRRQRSNAED 199 (252)
T ss_pred HHHHHHHHccCCCcHHHHHHHHHHHHHHHHHhhccCCChHHHHhhcCcch
Confidence 4689999995 5677777555555555666666667766666665443
No 40
>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=20.14 E-value=4.7e+02 Score=21.06 Aligned_cols=86 Identities=13% Similarity=0.150 Sum_probs=48.4
Q ss_pred EEEeecCCCCCcCcccchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 026114 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQVP 130 (243)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~~~~~~~~~~~i~~~~v~L~KP~TyMN~SG~aV~~i~~~~ki~ 130 (243)
||+|+|||=.. -==+|..++++|++++ . . .+.++.-.| .|..+ +..+. .
T Consensus 1 lVlGvGN~l~~----DDGvG~~v~~~L~~~~-~--~----------------~v~~id~g~----~g~~l---~~~l~-~ 49 (139)
T cd06066 1 LVIGYGNPLRG----DDGLGPAVAERIEEWL-L--P----------------GVEVLAVHQ----LTPEL---AEDLA-G 49 (139)
T ss_pred CEEEeCCcccc----ccchhHHHHHHHHhhC-C--C----------------CeEEEEcCC----CCHHH---HHHhc-C
Confidence 58999998532 2349999999998774 1 0 012222111 12222 22222 4
Q ss_pred CccEEEEecCCCC-CceEEEcc------CCCCCCCCcHHHHHHh
Q 026114 131 LRHILIYDEMSLM-NGVLRLQP------KGGHGHHNGLKSVMNH 167 (243)
Q Consensus 131 ~~~ilIhDDldl~-~G~irlk~------~Gs~gGHNGLKSIi~~ 167 (243)
++.+||.|=++.. +|.+++.. ...+.++=|+.++...
T Consensus 50 ~d~vIivDA~~~~~~g~~~~~~~~~~~~~~~s~H~~~l~~~l~~ 93 (139)
T cd06066 50 ADRVIFIDASLGGSPAPFRIVRLEPRRDSSFTSHALSPAALLAL 93 (139)
T ss_pred CCEEEEEEccCCCCCCceEEEEecCCCCCCcCCCCCCHHHHHHH
Confidence 5677788865555 78777631 1223455587777663
Done!