Query 027180
Match_columns 227
No_of_seqs 197 out of 1057
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:09:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027180hhsearch_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 6.6E-70 1.4E-74 466.6 18.3 171 48-219 1-189 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 2.7E-69 5.7E-74 464.1 19.7 173 49-221 2-191 (191)
3 TIGR00447 pth peptidyl-tRNA hy 100.0 1.9E-67 4.2E-72 451.2 19.7 169 49-218 1-188 (188)
4 PRK05426 peptidyl-tRNA hydrola 100.0 3.4E-66 7.3E-71 443.8 19.9 170 48-219 1-188 (189)
5 PF01195 Pept_tRNA_hydro: Pept 100.0 2.5E-65 5.4E-70 435.6 15.4 166 51-217 1-184 (184)
6 cd00462 PTH Peptidyl-tRNA hydr 100.0 2.9E-64 6.4E-69 426.1 17.0 154 51-205 1-171 (171)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 8.8E-50 1.9E-54 344.0 15.7 166 49-218 39-222 (224)
8 COG0680 HyaD Ni,Fe-hydrogenase 71.2 35 0.00076 28.8 8.6 134 48-204 2-154 (160)
9 PRK10466 hybD hydrogenase 2 ma 61.4 12 0.00025 31.2 3.8 31 48-82 1-31 (164)
10 COG4841 Uncharacterized protei 52.0 11 0.00023 29.8 1.9 25 120-144 13-40 (95)
11 cd06062 H2MP_MemB-H2up Endopep 49.8 23 0.0005 28.8 3.7 28 51-82 2-29 (146)
12 PF06154 YagB_YeeU_YfjZ: YagB/ 46.4 36 0.00077 27.3 4.1 35 173-208 31-65 (103)
13 PRK11544 hycI hydrogenase 3 ma 46.3 23 0.00049 29.4 3.2 28 49-80 2-29 (156)
14 cd06064 H2MP_F420-Reduc Endope 46.2 19 0.00041 29.4 2.7 27 51-81 1-27 (150)
15 TIGR00072 hydrog_prot hydrogen 45.9 20 0.00043 29.0 2.8 28 51-82 1-28 (145)
16 TIGR00130 frhD coenzyme F420-r 42.2 31 0.00068 28.3 3.4 28 49-80 4-31 (153)
17 PF03418 Peptidase_A25: Germin 37.9 28 0.0006 33.4 2.7 26 49-78 97-122 (354)
18 cd06068 H2MP_like-1 Putative [ 35.3 32 0.0007 27.8 2.4 26 51-80 1-26 (144)
19 cd06067 H2MP_MemB-H2evol Endop 35.0 36 0.00078 27.3 2.6 27 51-81 1-27 (136)
20 cd00518 H2MP Hydrogenase speci 34.8 39 0.00084 27.0 2.8 27 51-81 1-27 (139)
21 cd06063 H2MP_Cyano-H2up This g 34.6 43 0.00093 27.2 3.0 26 51-80 2-27 (146)
22 PF14490 HHH_4: Helix-hairpin- 34.1 25 0.00053 26.7 1.4 25 62-86 45-71 (94)
23 cd06066 H2MP_NAD-link-bidir En 33.9 42 0.00091 27.0 2.9 27 51-81 1-27 (139)
24 PRK10264 hydrogenase 1 maturat 33.7 66 0.0014 27.9 4.2 134 48-205 4-157 (195)
25 cd06070 H2MP_like-2 Putative [ 33.7 38 0.00083 27.3 2.6 25 51-79 1-25 (140)
26 TIGR00142 hycI hydrogenase mat 33.5 44 0.00095 27.1 2.9 27 51-81 2-28 (146)
27 PF11575 FhuF_C: FhuF 2Fe-2S C 32.0 25 0.00055 20.5 0.9 16 1-16 6-21 (22)
28 PRK10870 transcriptional repre 31.3 47 0.001 27.9 2.9 39 175-213 136-175 (176)
29 cd00736 bacteriophage_lambda_l 28.4 92 0.002 26.4 4.1 42 177-218 81-122 (151)
30 TIGR01441 GPR GPR endopeptidas 27.0 27 0.00058 33.6 0.7 27 48-78 101-127 (358)
31 PRK02858 germination protease; 26.5 28 0.00061 33.6 0.7 26 49-78 112-137 (369)
32 PF11458 Mistic: Membrane-inte 26.3 1.1E+02 0.0024 23.5 3.8 25 181-205 2-26 (84)
33 PF02318 FYVE_2: FYVE-type zin 25.8 1.3E+02 0.0028 23.8 4.3 36 180-216 1-36 (118)
34 PF06880 DUF1262: Protein of u 25.7 35 0.00075 27.4 1.0 15 16-30 32-46 (104)
35 PF12896 Apc4: Anaphase-promot 25.0 97 0.0021 26.2 3.7 48 166-215 85-132 (210)
36 PF06466 PCAF_N: PCAF (P300/CB 24.8 49 0.0011 30.4 1.9 47 174-220 150-199 (252)
37 PRK09256 hypothetical protein; 22.9 50 0.0011 27.4 1.5 24 120-143 4-29 (138)
38 PF13873 Myb_DNA-bind_5: Myb/S 22.8 1.8E+02 0.004 20.6 4.4 40 180-219 3-51 (78)
39 COG2248 Predicted hydrolase (m 22.6 1.4E+02 0.0029 28.1 4.3 51 143-199 11-61 (304)
40 PRK12362 germination protease; 21.3 68 0.0015 30.4 2.2 28 49-80 100-127 (318)
41 PF05017 TMP: TMP repeat; Int 20.2 53 0.0012 16.0 0.7 8 143-150 2-9 (11)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.6e-70 Score=466.59 Aligned_cols=171 Identities=42% Similarity=0.701 Sum_probs=164.8
Q ss_pred cCeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCc-cccccceEEEEEEECCeeEEEEecCccccccccc-------
Q 027180 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAM-NTIQSKALIGIGSIGEVPILLAKPQAYMNFSGES------- 119 (227)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~-~~~k~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s------- 119 (227)
+++|||||||||++|+.||||||||++|.||++++.++ +.++|.++++++.+.+++|+|+||+||||+||++
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 5578899999999999999999999999999999
Q ss_pred ----------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHH
Q 027180 120 ----------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQ 189 (227)
Q Consensus 120 ----------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~ 189 (227)
||||||||+|++|||.+||+|||||||||+++|| |++|+|||||||||..+++|++|||++|+++|++.
T Consensus 81 y~i~~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGlKSi~~~lG-t~~f~RlRiGIGrP~~~~~v~~~VL~~f~~~E~~~ 159 (190)
T COG0193 81 YKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHLG-TNNFYRLRIGIGRPGNGEDVADYVLGKFSKEEREL 159 (190)
T ss_pred hCCCHHHEEEEeeccCCCCceEEEEcCCCCCCcccHHHHHHHhC-CCccceEEEEcCCCCCCCchhHhhcCCCCHHHHHH
Confidence 9999999999999999999999999999999995 89999999999999888899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhCHHHHHHhhhcc
Q 027180 190 IDAALEQGVEAVRTLVLNGFDQNISRFNMG 219 (227)
Q Consensus 190 l~~~i~~a~eal~~~i~~g~~~amn~~n~~ 219 (227)
|++++++|+++++.+++.+++++||+||+.
T Consensus 160 l~~~~~~a~~~~~~~~~~~~~~~mn~~~~~ 189 (190)
T COG0193 160 LDKAIDKAADALELLLEGDFEKAMNKLNAL 189 (190)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHhcc
Confidence 999999999999999999999999999975
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=2.7e-69 Score=464.07 Aligned_cols=173 Identities=77% Similarity=1.255 Sum_probs=165.0
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEecCccccccccc---------
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGES--------- 119 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~~k~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s--------- 119 (227)
|+|||||||||++|++|||||||+++|.||++++.++++.++++++++..+++++++|+||+||||+||++
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 68999999999999999999999999999999998876677889999999999999999999999999999
Q ss_pred --------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHHHH
Q 027180 120 --------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQID 191 (227)
Q Consensus 120 --------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~l~ 191 (227)
||||||||+|++|+|.+||++||||||||+++|++|++|+|||||||||+.+.++++|||++|+++|++.|+
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 999999999999999999999999999999999557899999999999987678999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhCHHHHHHhhhccCC
Q 027180 192 AALEQGVEAVRTLVLNGFDQNISRFNMGQK 221 (227)
Q Consensus 192 ~~i~~a~eal~~~i~~g~~~amn~~n~~~~ 221 (227)
++++.|+++++.|+.++++++||+||+.++
T Consensus 162 ~~~~~a~~~~~~~~~~~~~~~~n~~n~~~~ 191 (191)
T cd02406 162 TALEQGVDAVRTLVLKGFNGSAERFNLVQK 191 (191)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHhCCCC
Confidence 999999999999999999999999997654
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=1.9e-67 Score=451.23 Aligned_cols=169 Identities=43% Similarity=0.699 Sum_probs=160.9
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccc-cccceEEEEEEECCeeEEEEecCccccccccc--------
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGES-------- 119 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~-~k~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s-------- 119 (227)
|+|||||||||++|++|||||||+++|.||++++.++.+ .++.+++++..+++++++|+||+||||+||++
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 589999999999999999999999999999999988763 46778899989999999999999999999999
Q ss_pred ---------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHHH
Q 027180 120 ---------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQI 190 (227)
Q Consensus 120 ---------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~l 190 (227)
||||||||+|++|+|++||++||||||||+++| +|++|+|||||||||+.+.++++|||++|+++|++.|
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 999999999999999999999999999999999 5899999999999998777899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhC-HHHHHHhhhc
Q 027180 191 DAALEQGVEAVRTLVLNG-FDQNISRFNM 218 (227)
Q Consensus 191 ~~~i~~a~eal~~~i~~g-~~~amn~~n~ 218 (227)
+++++.++++++.|++++ ++++||+||+
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=3.4e-66 Score=443.76 Aligned_cols=170 Identities=43% Similarity=0.737 Sum_probs=160.6
Q ss_pred cCeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCcc-ccccceEEEEEEECCeeEEEEecCccccccccc-------
Q 027180 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMN-TIQSKALIGIGSIGEVPILLAKPQAYMNFSGES------- 119 (227)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~-~~k~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s------- 119 (227)
+|||||||||||++|++|||||||+++|.||++++..+. ..++.+++++..+++++++|+||+||||+||++
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 369999999999999999999999999999999887664 456789999999998999999999999999999
Q ss_pred ----------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHH
Q 027180 120 ----------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQ 189 (227)
Q Consensus 120 ----------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~ 189 (227)
||||||||+|++|+|.+||++||||||||+++|| |++|+|||||||||+ ..++++|||++|+++|++.
T Consensus 81 ~~i~~~~ilVihDdldl~~G~~r~k~gGs~~GHNGlkSI~~~lg-t~~f~RlriGIGrP~-~~~v~~yVL~~f~~~E~~~ 158 (189)
T PRK05426 81 YKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHLG-TQDFWRLRIGIGRPD-KKKVVDYVLGKFSKEEQEL 158 (189)
T ss_pred hCCCHHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHhC-CCCeeEEEEEeCCCC-CCCcchhhcCCCCHHHHHH
Confidence 9999999999999999999999999999999994 789999999999997 5679999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhCHHHHHHhhhcc
Q 027180 190 IDAALEQGVEAVRTLVLNGFDQNISRFNMG 219 (227)
Q Consensus 190 l~~~i~~a~eal~~~i~~g~~~amn~~n~~ 219 (227)
|+++++.|+++++.|++++++++||+||++
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=2.5e-65 Score=435.56 Aligned_cols=166 Identities=49% Similarity=0.855 Sum_probs=148.3
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccccc-cceEEEEEEECCeeEEEEecCccccccccc----------
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQ-SKALIGIGSIGEVPILLAKPQAYMNFSGES---------- 119 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~~k-~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s---------- 119 (227)
|||||||||++|++|||||||+++|.||++++.+|...+ +.+.++++.+.+++++|+||+||||+||.+
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 799999999999999999999999999999998886654 789999999999999999999999999999
Q ss_pred -------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHHHHH
Q 027180 120 -------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDA 192 (227)
Q Consensus 120 -------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~l~~ 192 (227)
||||||+|+|++|+|.+||++||||||||+++| +|++|+|||||||||+.+.++++|||++|+++|++.|++
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 999999999999999999999999999999999 589999999999999877899999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCHHHHHHhhh
Q 027180 193 ALEQGVEAVRTLVLNGFDQNISRFN 217 (227)
Q Consensus 193 ~i~~a~eal~~~i~~g~~~amn~~n 217 (227)
+++.|+++++.|+++++++|||+||
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=2.9e-64 Score=426.06 Aligned_cols=154 Identities=51% Similarity=0.905 Sum_probs=147.5
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEecCccccccccc-----------
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGES----------- 119 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~~k~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s----------- 119 (227)
|||||||||++|++|||||||+++|.||++++.++.+.++.+++++..+.+++++|+||+||||+||++
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 699999999999999999999999999999999887777789999999999999999999999999999
Q ss_pred ------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHHHHHH
Q 027180 120 ------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAA 193 (227)
Q Consensus 120 ------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~l~~~ 193 (227)
||||||||+|++|+|++||++||||||||+++| +|++|+|||||||||+.+.++++|||++|+++|++.|+++
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 999999999999999999999999999999999 5899999999999998778999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 027180 194 LEQGVEAVRTLV 205 (227)
Q Consensus 194 i~~a~eal~~~i 205 (227)
++.|+++++.|+
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=8.8e-50 Score=344.02 Aligned_cols=166 Identities=62% Similarity=1.070 Sum_probs=148.3
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccccccceEEEEEEECCeeEEEEecCccccccccc---------
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGES--------- 119 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~~k~~~~~~~~~i~~~~v~L~KP~TyMN~SG~s--------- 119 (227)
+|+|+||||||++|..|||||||.++|.||++++++..+.+.++..+...+++..+++++|++|||.||++
T Consensus 39 ~wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y~ 118 (224)
T KOG2255|consen 39 PWLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALYK 118 (224)
T ss_pred ceEEEecCCCcccccccchhhHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhhc
Confidence 69999999999999999999999999999999998766555567777788999999999999999999999
Q ss_pred --------hhcccCCCCccEEEccCCCCCCCCchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHH-HH
Q 027180 120 --------IYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIERE-QI 190 (227)
Q Consensus 120 --------vhDDLdL~~G~irlk~gGs~gGHNGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~-~l 190 (227)
|||||++|+|++|+|++||++||||+||++++|++...|+||+||||||++++|+.+|||++|++.|++ .|
T Consensus 119 i~~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgHNGvrs~~~~l~g~~~fpRL~iGIGrppg~~d~~a~vLskfsp~e~ke~L 198 (224)
T KOG2255|consen 119 IPLRHIVVIHDELELPLGKLRLRPGGSHRGHNGVRSVFNCLNGRRSFPRLSIGIGRPPGNEDVKAFVLSKFSPAEQKELL 198 (224)
T ss_pred chheeEEEEeccccCcCceEEeccCCCccccccHHHHHhhccCCcccceeeeecCCCCCchhhhHHHHHhcChhhhHHHH
Confidence 999999999999999999999999999999999887799999999999999999999999999999998 44
Q ss_pred HHHHHHHHHHHHHHHHhCHHHHHHhhhc
Q 027180 191 DAALEQGVEAVRTLVLNGFDQNISRFNM 218 (227)
Q Consensus 191 ~~~i~~a~eal~~~i~~g~~~amn~~n~ 218 (227)
+.. .+.++.++.++++.-.++||.
T Consensus 199 et~----l~~~~~lil~~l~~~is~~~l 222 (224)
T KOG2255|consen 199 ETL----LEHVKTLILQGLQQSISRFNL 222 (224)
T ss_pred HHH----HhhhHHHHHHHHHHhcccCcC
Confidence 444 445555666667777777774
No 8
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=71.24 E-value=35 Score=28.81 Aligned_cols=134 Identities=21% Similarity=0.330 Sum_probs=73.4
Q ss_pred cCeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccccccceEEEEEE---------ECCeeEEEEecCcccccccc
Q 027180 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGS---------IGEVPILLAKPQAYMNFSGE 118 (227)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~~k~~~~~~~~~---------i~~~~v~L~KP~TyMN~SG~ 118 (227)
++.+|+|+|||=. .-==+|-.++++|.+++--.. .. ..+.-+. .+..+++++--.
T Consensus 2 ~~ilIlG~GN~L~----~DDG~Gv~vae~L~~~~~~~~---~v-~vid~Gt~~~~l~~~l~~~d~vIIVDav-------- 65 (160)
T COG0680 2 MRILILGVGNILM----GDDGFGVRVAEKLKKRYKPPE---NV-EVIDGGTAGPNLLGLLAGYDPVIIVDAV-------- 65 (160)
T ss_pred CeEEEEeeCCccc----ccCcccHHHHHHHHHhcCCCC---Ce-EEEEcCCCcHHHHHHhcCCCcEEEEEee--------
Confidence 4689999999853 344689999999998754221 00 0000000 011223333211
Q ss_pred chhcccCCCCccEEEcc------CCCCC---CCC-chHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHH
Q 027180 119 SIYDEMSLMNGVLRLQP------KGGHG---HHN-GLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIERE 188 (227)
Q Consensus 119 svhDDLdL~~G~irlk~------gGs~g---GHN-GLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~ 188 (227)
+.+..+|++++-. ...+. .|+ ++..+++.+.-..++...-+|+.-+.. ...+ +...+|++=++
T Consensus 66 ----~~g~epG~v~~i~~e~i~~~~~~~~~s~H~~~~~~~L~~~~~~~~~~~~~~~~~v~~~--~~~~-~~~~lS~ev~~ 138 (160)
T COG0680 66 ----LFGLEPGEVRIIDPEEIPAYSSASKDSAHELPLSELLALLKELGGLPVLILGVQVPIV--SLPE-FGGGLSPEVEE 138 (160)
T ss_pred ----ecCCCCceEEEechhhcccccccCCCccccCCHHHHHHHHHHhcCCceEEEEEeecee--cccc-cccccCHHHHH
Confidence 1223466666521 22232 455 688888777433445777788885432 2122 23567777667
Q ss_pred HHHHHHHHHHHHHHHH
Q 027180 189 QIDAALEQGVEAVRTL 204 (227)
Q Consensus 189 ~l~~~i~~a~eal~~~ 204 (227)
.++.+++.+.+.++.+
T Consensus 139 a~~~av~~i~~~l~~~ 154 (160)
T COG0680 139 AVDKAVERILEELREW 154 (160)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 7777777766666554
No 9
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=61.35 E-value=12 Score=31.23 Aligned_cols=31 Identities=23% Similarity=0.442 Sum_probs=24.0
Q ss_pred cCeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcC
Q 027180 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQR 82 (227)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~ 82 (227)
|+.+|+|+|||-. +-==+|..++++|.+.+.
T Consensus 1 m~ilVlGiGN~l~----gDDGvG~~va~~L~~~~~ 31 (164)
T PRK10466 1 MRILVLGVGNILL----TDEAIGVRIVEALEQRYI 31 (164)
T ss_pred CceEEEEECchhh----ccCcHHHHHHHHHHHhcC
Confidence 3579999999853 334599999999987654
No 10
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.98 E-value=11 Score=29.76 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=21.3
Q ss_pred hhcccCCCCc-cEEE--ccCCCCCCCCc
Q 027180 120 IYDEMSLMNG-VLRL--QPKGGHGHHNG 144 (227)
Q Consensus 120 vhDDLdL~~G-~irl--k~gGs~gGHNG 144 (227)
.+||+||+-| +||+ |.||.+.+|-|
T Consensus 13 fk~E~~l~~g~~vrffvRyGG~~~~~~G 40 (95)
T COG4841 13 FKEELDLEEGNKVRFFVRYGGCSSLQQG 40 (95)
T ss_pred HHHhcCCCCCCEEEEEEEEcCcccccCC
Confidence 7899999999 6787 88998877776
No 11
>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=49.80 E-value=23 Score=28.75 Aligned_cols=28 Identities=18% Similarity=0.510 Sum_probs=22.2
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHcC
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQR 82 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~ 82 (227)
+|+|+|||-.. -==+|+.++++|++.+.
T Consensus 2 lV~GiGN~l~g----DDG~G~~va~~L~~~~~ 29 (146)
T cd06062 2 LVLGIGNILLA----DEGIGVHAVERLEENYS 29 (146)
T ss_pred EEEEECccccc----cCcHHHHHHHHHHHhcC
Confidence 79999999632 23599999999988743
No 12
>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=46.40 E-value=36 Score=27.29 Aligned_cols=35 Identities=20% Similarity=0.309 Sum_probs=25.7
Q ss_pred ccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Q 027180 173 DMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNG 208 (227)
Q Consensus 173 ~v~~yVLs~Fs~eE~~~l~~~i~~a~eal~~~i~~g 208 (227)
|-++++ +.|+++|...||++++..++-+|..+..|
T Consensus 31 DRA~i~-G~Fs~~~~~~Ld~aFP~~ikqlE~ml~sG 65 (103)
T PF06154_consen 31 DRAGIT-GTFSEEEAQHLDQAFPLFIKQLELMLTSG 65 (103)
T ss_dssp GGEEEE-S---HHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred ccCCeE-EEcCHHHHHHHHhHhHHHHHHHHHHHhcC
Confidence 334444 89999999999999999999898887643
No 13
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=46.35 E-value=23 Score=29.37 Aligned_cols=28 Identities=18% Similarity=0.291 Sum_probs=22.2
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHHHH
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQA 80 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~ 80 (227)
..+|+|+|||-.. -==+|..++++|++.
T Consensus 2 ~~lVlGiGN~L~g----DDGvG~~v~~~L~~~ 29 (156)
T PRK11544 2 TDVVLTVGNSMMG----DDGAGPLLAEKLAAA 29 (156)
T ss_pred cEEEEEeCccccc----cCcHHHHHHHHHhcc
Confidence 3699999998643 335999999999765
No 14
>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=46.24 E-value=19 Score=29.40 Aligned_cols=27 Identities=26% Similarity=0.443 Sum_probs=21.6
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHc
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQ 81 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~ 81 (227)
||+|+|||-. .-==+|+.++++|++.+
T Consensus 1 lViGiGN~l~----gDDgvG~~va~~l~~~~ 27 (150)
T cd06064 1 LVVGCGNILF----GDDGFGPAVIEELEKLE 27 (150)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcc
Confidence 6999999863 33459999999998764
No 15
>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=45.90 E-value=20 Score=29.00 Aligned_cols=28 Identities=18% Similarity=0.343 Sum_probs=22.0
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHcC
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQR 82 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~ 82 (227)
||+|+|||-.. -==+|..++++|++++.
T Consensus 1 lViGiGN~l~~----DDg~G~~v~~~L~~~~~ 28 (145)
T TIGR00072 1 LVLGIGNILRG----DDGFGPRVAERLEERYE 28 (145)
T ss_pred CEEEECchhcc----cCcHHHHHHHHHHHhcC
Confidence 69999998532 33599999999998753
No 16
>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=42.22 E-value=31 Score=28.27 Aligned_cols=28 Identities=25% Similarity=0.357 Sum_probs=21.9
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHHHH
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQA 80 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~ 80 (227)
+.+|+|+|||-. .-==+|..++++|++.
T Consensus 4 ~ilVlGiGN~l~----gDDGvG~~v~~~L~~~ 31 (153)
T TIGR00130 4 EILVVGCGNILF----GDDGFGPAVIEYLKEN 31 (153)
T ss_pred eEEEEEeCcccc----ccCcHhHHHHHHHHHh
Confidence 469999999853 2335999999999863
No 17
>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=37.95 E-value=28 Score=33.44 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=17.6
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHH
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIA 78 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La 78 (227)
..|||||||. .-|--..|-.++|.|.
T Consensus 97 ~iLVVGLGN~----~vTPDALGP~vv~~l~ 122 (354)
T PF03418_consen 97 SILVVGLGNW----NVTPDALGPRVVENLL 122 (354)
T ss_dssp -EEEEE-S-S----SSGGG-HHHHHHHT--
T ss_pred eEEEEeCCCc----CCCccccchhhhhhhh
Confidence 4799999995 3699999999999763
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=35.34 E-value=32 Score=27.81 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=20.8
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHH
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQA 80 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~ 80 (227)
||+|+|||-.. -==+|..++++|+++
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~ 26 (144)
T cd06068 1 LVAGVGNIFLG----DDGFGVEVARRLRPR 26 (144)
T ss_pred CEEEECccccc----cCcHHHHHHHHHhcc
Confidence 69999998643 234999999999875
No 19
>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=35.05 E-value=36 Score=27.32 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=21.2
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHc
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQ 81 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~ 81 (227)
+|+|+|||-. .-==+|..++++|.+..
T Consensus 1 ~VlGiGN~L~----~DDgvG~~v~~~L~~~~ 27 (136)
T cd06067 1 VLLGVGNELR----GDDGAGPLLAEKLEDLP 27 (136)
T ss_pred CEEEeCcccc----ccCcHHHHHHHHHHhcC
Confidence 5899999863 23459999999998764
No 20
>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=34.85 E-value=39 Score=26.99 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=21.5
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHc
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQ 81 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~ 81 (227)
+|+|+|||=. .-==+|..++++|+++.
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd00518 1 LVLGIGNPLR----GDDGFGPAVAERLEERY 27 (139)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcC
Confidence 5899999853 23359999999998875
No 21
>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=34.58 E-value=43 Score=27.20 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=20.9
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHH
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQA 80 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~ 80 (227)
||+|+|||-.. -==+|..++++|++.
T Consensus 2 lVlGiGN~L~~----DDG~G~~v~~~L~~~ 27 (146)
T cd06063 2 TIIGCGNLNRG----DDGVGPILIRRLQAY 27 (146)
T ss_pred EEEEECCcccc----cCcHHHHHHHHHhhc
Confidence 79999998632 235999999999874
No 22
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=34.05 E-value=25 Score=26.68 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=18.9
Q ss_pred CCcCc--chHHHHHHHHHHHHcCCCcc
Q 027180 62 YHGTR--HNVGFEMIDHIAQAQRIAMN 86 (227)
Q Consensus 62 Y~~TR--HNiGf~vlD~La~~~~~~~~ 86 (227)
|.-.. -.+||..+|.+|.++|+...
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 55555 67999999999999998654
No 23
>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=33.95 E-value=42 Score=27.01 Aligned_cols=27 Identities=26% Similarity=0.453 Sum_probs=21.6
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHc
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQ 81 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~ 81 (227)
||+|+|||=. .-==+|..++++|++++
T Consensus 1 lVlGvGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPLR----GDDGLGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCccc----cccchhHHHHHHHHhhC
Confidence 6899999853 23359999999998875
No 24
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=33.68 E-value=66 Score=27.91 Aligned_cols=134 Identities=19% Similarity=0.282 Sum_probs=69.6
Q ss_pred cCeEEEeecCCCCCCCcCcchHHHHHHHHHHHHcCCCccccccc-e-----EEEEEEECCeeEEEEecCccccccccchh
Q 027180 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSK-A-----LIGIGSIGEVPILLAKPQAYMNFSGESIY 121 (227)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~~~~~~~~k~~-~-----~~~~~~i~~~~v~L~KP~TyMN~SG~svh 121 (227)
++.+|+|+|||=. .-==+|..++++|.+.+..+..-.-.. + ++... .+-..++++--..
T Consensus 4 ~rilVlGiGN~L~----gDDGvG~~va~~L~~~~~~~~~V~vid~Gt~g~~ll~~i-~~~d~vIiVDAv~---------- 68 (195)
T PRK10264 4 QRVVVMGLGNLLW----ADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYV-ESASHLLILDAID---------- 68 (195)
T ss_pred CCEEEEEeCcccc----ccCcHHHHHHHHHHhhcCCCCCeEEEECCCCHHHHHHHH-cCCCEEEEEECCc----------
Confidence 3479999999842 233599999999987754221000000 0 00000 0112334443211
Q ss_pred cccCCCCccEEEccC---------CC-CCCCCchHHHHHh--ccCCCCcc-EEE-EeecCCCCCCccccccccCCCHHHH
Q 027180 122 DEMSLMNGVLRLQPK---------GG-HGHHNGLKSVMNH--LDGCREFP-RLC-IGIGNPPGKMDMKAYLLQKFSPIER 187 (227)
Q Consensus 122 DDLdL~~G~irlk~g---------Gs-~gGHNGLKSI~~~--Lggt~~f~-RLR-IGIGrP~~~~~v~~yVLs~Fs~eE~ 187 (227)
.+.++|+++.-.. .+ +-.+-|+.++.+. +.+ +.+ ++. |||= |. ++.+ .=-.+|++=+
T Consensus 69 --~g~~PGtv~~~~~~~~~~~~~~~~~S~H~~~l~~~L~l~~l~g--~~P~~v~iiGie-p~---~~~~-~g~~LSp~V~ 139 (195)
T PRK10264 69 --YGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSEVLALADIRG--HLPAHIALVGLQ-PA---MLDD-YGGSLSELAR 139 (195)
T ss_pred --cCCCCCeEEEEehhhcccccccCCcCcccCCHHHHHHHHHHcC--CCCCeEEEEEEE-Ee---EecC-CCCCCCHHHH
Confidence 1345666554211 11 2344688888753 322 333 555 4764 32 1211 2247788878
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 027180 188 EQIDAALEQGVEAVRTLV 205 (227)
Q Consensus 188 ~~l~~~i~~a~eal~~~i 205 (227)
+.++++++.+.+.++.|.
T Consensus 140 ~av~~~v~~i~~~l~~~~ 157 (195)
T PRK10264 140 EQLPAAEQAALAQLAAWG 157 (195)
T ss_pred HHHHHHHHHHHHHHHHcC
Confidence 888888887777776654
No 25
>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=33.67 E-value=38 Score=27.28 Aligned_cols=25 Identities=28% Similarity=0.449 Sum_probs=20.2
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHH
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQ 79 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~ 79 (227)
||+|+|||-. .-==+|+.++++|++
T Consensus 1 lVlGiGN~l~----~DDg~G~~v~~~L~~ 25 (140)
T cd06070 1 LIIGVGNRLY----GDDGFGSCLAEALEQ 25 (140)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHhh
Confidence 6999999863 233599999999987
No 26
>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=33.45 E-value=44 Score=27.14 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=21.4
Q ss_pred EEEeecCCCCCCCcCcchHHHHHHHHHHHHc
Q 027180 51 LIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQ 81 (227)
Q Consensus 51 LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~~ 81 (227)
||+|+|||-.. -==+|..++++|.+.+
T Consensus 2 lVlGiGN~l~~----DDG~G~~v~~~L~~~~ 28 (146)
T TIGR00142 2 VLLCVGNELMG----DDGAGPYLAEKCAAAP 28 (146)
T ss_pred EEEEeCccccc----cCcHHHHHHHHHHhcc
Confidence 79999998643 2359999999998653
No 27
>PF11575 FhuF_C: FhuF 2Fe-2S C-terminal domain; InterPro: IPR024726 Ferric iron reductase (FhuF) is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B []. This entry represents the C-terminal domain that contains 4 conserved cysteine residues found to be part of a 2Fe-2S cluster [].; GO: 0051537 2 iron, 2 sulfur cluster binding
Probab=31.96 E-value=25 Score=20.54 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=12.2
Q ss_pred CccccCCCcccccCCC
Q 027180 1 MLYALSAPKTCISCPR 16 (227)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (227)
|.|-+.....|.+||+
T Consensus 6 l~y~~~~~~~C~~CP~ 21 (22)
T PF11575_consen 6 LYYRLPGGGYCGTCPL 21 (22)
T ss_pred eeEEcCCCCccCCCCC
Confidence 3466767788999996
No 28
>PRK10870 transcriptional repressor MprA; Provisional
Probab=31.34 E-value=47 Score=27.92 Aligned_cols=39 Identities=13% Similarity=0.221 Sum_probs=30.3
Q ss_pred ccccccCCCHHHHHHHHHHHHHHHHHHHHHHHhC-HHHHH
Q 027180 175 KAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNG-FDQNI 213 (227)
Q Consensus 175 ~~yVLs~Fs~eE~~~l~~~i~~a~eal~~~i~~g-~~~am 213 (227)
.+-+++.|+++|++.+..++.+..+.++.+-++| +.+||
T Consensus 136 ~~~~~~~ls~~e~~~l~~~L~kl~~~l~~~~~~~~~~~~~ 175 (176)
T PRK10870 136 LHQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAM 175 (176)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHHHHhhCCCchhhhhc
Confidence 3557889999999999999888888887766544 66665
No 29
>cd00736 bacteriophage_lambda_lysozyme The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli. However, they differ structurally.
Probab=28.36 E-value=92 Score=26.43 Aligned_cols=42 Identities=21% Similarity=0.346 Sum_probs=31.6
Q ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhc
Q 027180 177 YLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFNM 218 (227)
Q Consensus 177 yVLs~Fs~eE~~~l~~~i~~a~eal~~~i~~g~~~amn~~n~ 218 (227)
+=|..|+++.++.+.-.+-+...++..+....++.||+++..
T Consensus 81 ~gl~~F~P~~QD~~A~~Li~~~gal~~i~~G~~~~a~~~La~ 122 (151)
T cd00736 81 YGLYDFSPESQDLVAYQLIRERGALPDILAGRIEQAIAKLSN 122 (151)
T ss_pred cCCCCCCHHHHHHHHHHHHHHcCcHHHHHcCCHHHHHHHHHh
Confidence 335899999998886544444557888888889999998763
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=27.03 E-value=27 Score=33.57 Aligned_cols=27 Identities=30% Similarity=0.502 Sum_probs=22.1
Q ss_pred cCeEEEeecCCCCCCCcCcchHHHHHHHHHH
Q 027180 48 TPWLIVGLGNPGIKYHGTRHNVGFEMIDHIA 78 (227)
Q Consensus 48 ~~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La 78 (227)
...|||||||- .-|--..|-++++.|.
T Consensus 101 ~~iLVVGLGN~----~VTPDALGP~vv~~l~ 127 (358)
T TIGR01441 101 MTCLVVGLGNW----NVTPDALGPKVVENLL 127 (358)
T ss_pred CcEEEEeCCCc----CCCccccChheeccee
Confidence 34799999994 4688999999998774
No 31
>PRK02858 germination protease; Provisional
Probab=26.46 E-value=28 Score=33.56 Aligned_cols=26 Identities=35% Similarity=0.497 Sum_probs=21.6
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHH
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIA 78 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La 78 (227)
..|||||||- .-|--..|-++++.|.
T Consensus 112 ~vLVVGLGN~----~VTPDALGP~vv~~l~ 137 (369)
T PRK02858 112 SCLIVGLGNW----NVTPDALGPLVVENVL 137 (369)
T ss_pred cEEEEeCCCc----CCCccccChheeccee
Confidence 4799999994 4688999999998664
No 32
>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=26.31 E-value=1.1e+02 Score=23.52 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Q 027180 181 KFSPIEREQIDAALEQGVEAVRTLV 205 (227)
Q Consensus 181 ~Fs~eE~~~l~~~i~~a~eal~~~i 205 (227)
+.+..|+++|..+|++..+.++.|+
T Consensus 2 KVt~~EkeQLS~AID~mnEGLD~fI 26 (84)
T PF11458_consen 2 KVTDQEKEQLSTAIDRMNEGLDTFI 26 (84)
T ss_pred CCchHHHHHHHHHHHHHHhhHHHHH
Confidence 4578899999999998877766665
No 33
>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=25.76 E-value=1.3e+02 Score=23.78 Aligned_cols=36 Identities=19% Similarity=0.182 Sum_probs=22.4
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHhh
Q 027180 180 QKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRF 216 (227)
Q Consensus 180 s~Fs~eE~~~l~~~i~~a~eal~~~i~~g~~~amn~~ 216 (227)
|.++++|++.|.+++.++.+ ++..-++.+.+..+++
T Consensus 1 s~Lt~eE~~~I~~Vl~R~~~-l~~~E~~Ri~kLk~~L 36 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQRDEE-LRKKEEERIRKLKQEL 36 (118)
T ss_dssp TTS-CHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHHHH
Confidence 46789999999999988655 3333333344444443
No 34
>PF06880 DUF1262: Protein of unknown function (DUF1262); InterPro: IPR010683 This family represents a conserved region within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that some family members contain more than one copy of this region.
Probab=25.68 E-value=35 Score=27.45 Aligned_cols=15 Identities=47% Similarity=1.023 Sum_probs=12.4
Q ss_pred CCCCCCCCcccccee
Q 027180 16 RGPPFPQKRQVSTRL 30 (227)
Q Consensus 16 ~~~~~~~~~~~~~~~ 30 (227)
++-||||.|.+..+-
T Consensus 32 ~~LPFPQN~~Ltv~~ 46 (104)
T PF06880_consen 32 RGLPFPQNKNLTVRY 46 (104)
T ss_pred ccCCCCCCCEEEEEE
Confidence 688999999887664
No 35
>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=24.97 E-value=97 Score=26.18 Aligned_cols=48 Identities=15% Similarity=0.368 Sum_probs=39.0
Q ss_pred cCCCCCCccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHh
Q 027180 166 GNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISR 215 (227)
Q Consensus 166 GrP~~~~~v~~yVLs~Fs~eE~~~l~~~i~~a~eal~~~i~~g~~~amn~ 215 (227)
|.++ ..+.+|....+++.-.+++++.++.+.+.+..++.+.+.-|+.+
T Consensus 85 G~~s--~~l~~fL~~~l~erglKr~~k~~~~~y~~i~~l~~~~l~pa~er 132 (210)
T PF12896_consen 85 GHAS--PALKQFLVNQLGERGLKRWEKAVDSAYSSIRKLLFEHLIPALER 132 (210)
T ss_pred cCCC--HHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5443 36789999999999999999999999999998887766666544
No 36
>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=24.76 E-value=49 Score=30.37 Aligned_cols=47 Identities=19% Similarity=0.192 Sum_probs=31.4
Q ss_pred cccccccCCC---HHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHhhhccC
Q 027180 174 MKAYLLQKFS---PIEREQIDAALEQGVEAVRTLVLNGFDQNISRFNMGQ 220 (227)
Q Consensus 174 v~~yVLs~Fs---~eE~~~l~~~i~~a~eal~~~i~~g~~~amn~~n~~~ 220 (227)
|.+||+.+|+ +.|.+.+-++.....-.+..|--+..+...+.++..+
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 5789999885 6677777666555556666665566666666655443
No 37
>PRK09256 hypothetical protein; Provisional
Probab=22.86 E-value=50 Score=27.43 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=19.2
Q ss_pred hhcccCCCCccEEE--ccCCCCCCCC
Q 027180 120 IYDEMSLMNGVLRL--QPKGGHGHHN 143 (227)
Q Consensus 120 vhDDLdL~~G~irl--k~gGs~gGHN 143 (227)
|.+++++|...+++ ..++|.||+|
T Consensus 4 ~~~~~~i~~~~l~~~~~RSSGPGGQ~ 29 (138)
T PRK09256 4 ITRRLVIPENELEWRFIRASGPGGQN 29 (138)
T ss_pred cCccCccCHHHeEEEEEEcCCCCccc
Confidence 56788888887766 5688999998
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=22.79 E-value=1.8e+02 Score=20.57 Aligned_cols=40 Identities=15% Similarity=0.185 Sum_probs=27.0
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHH---------HHHhCHHHHHHhhhcc
Q 027180 180 QKFSPIEREQIDAALEQGVEAVRT---------LVLNGFDQNISRFNMG 219 (227)
Q Consensus 180 s~Fs~eE~~~l~~~i~~a~eal~~---------~i~~g~~~amn~~n~~ 219 (227)
.+||.+|.+.|-+.+..-.+.++. .-..-++.+.+.||..
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~ 51 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNAL 51 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhc
Confidence 479999999988777665555543 1123467777777763
No 39
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=22.59 E-value=1.4e+02 Score=28.13 Aligned_cols=51 Identities=22% Similarity=0.135 Sum_probs=33.2
Q ss_pred CchHHHHHhccCCCCccEEEEeecCCCCCCccccccccCCCHHHHHHHHHHHHHHHH
Q 027180 143 NGLKSVMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVE 199 (227)
Q Consensus 143 NGLKSI~~~Lggt~~f~RLRIGIGrP~~~~~v~~yVLs~Fs~eE~~~l~~~i~~a~e 199 (227)
-|+||+...+ .| .-++|.|.. .-.-....|=| +..+.|++.|+++.+.+.+
T Consensus 11 LGVRSmAt~v-et---~dv~ILiDp-GVsLaPkRy~L-PPh~~E~erl~~~r~~i~~ 61 (304)
T COG2248 11 LGVRSMATFV-ET---KDVGILIDP-GVSLAPKRYGL-PPHQRELERLRQAREKIQR 61 (304)
T ss_pred cchhhhhhee-ec---CCeeEEECC-ccccCccccCC-CCCHHHHHHHHHHHHHHHH
Confidence 3889998777 34 457888873 22223357766 5577888888776665444
No 40
>PRK12362 germination protease; Provisional
Probab=21.26 E-value=68 Score=30.44 Aligned_cols=28 Identities=29% Similarity=0.434 Sum_probs=23.5
Q ss_pred CeEEEeecCCCCCCCcCcchHHHHHHHHHHHH
Q 027180 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQA 80 (227)
Q Consensus 49 ~~LIVGLGNPG~~Y~~TRHNiGf~vlD~La~~ 80 (227)
..|||||||. .-|--..|-.+++.|.-.
T Consensus 100 ~iLVvGLGN~----~vTpDaLGP~Vv~~l~vT 127 (318)
T PRK12362 100 TVLVVGLGNW----NVTPDALGPKVVSKLMVT 127 (318)
T ss_pred cEEEEEcCCC----CcCccccchhhhhhhhhh
Confidence 4799999995 369999999999988653
No 41
>PF05017 TMP: TMP repeat; InterPro: IPR007713 This short repeat consists of the motif WXXh where X can be any residue and h is a hydrophobic residue. The repeat is named TMP after its occurrence in the tape measure protein (TMP). Tape measure protein is a component of phage tail and probably forms a beta-helix. Truncated forms of TMP lead to shortened tail fibres []. This repeat is also found in non-phage proteins where it may play a structural role.
Probab=20.22 E-value=53 Score=16.01 Aligned_cols=8 Identities=50% Similarity=0.883 Sum_probs=6.1
Q ss_pred CchHHHHH
Q 027180 143 NGLKSVMN 150 (227)
Q Consensus 143 NGLKSI~~ 150 (227)
||+|+++.
T Consensus 2 n~Ik~~~s 9 (11)
T PF05017_consen 2 NGIKSFFS 9 (11)
T ss_pred chHHHHhh
Confidence 78888864
Done!