Query 027267
Match_columns 225
No_of_seqs 97 out of 99
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 07:24:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027267.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027267hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02341 RcbX: RbcX protein; 100.0 1.9E-44 4.2E-49 287.7 12.2 101 110-211 8-109 (111)
2 PF12112 DUF3579: Protein of u 62.6 2.2 4.7E-05 33.9 -0.3 24 130-153 63-86 (92)
3 cd00131 PAX Paired Box domain 59.5 25 0.00054 28.4 5.3 76 98-173 5-99 (128)
4 PF12234 Rav1p_C: RAVE protein 49.5 28 0.00062 35.7 5.0 69 109-177 481-555 (631)
5 PF11985 DUF3486: Protein of u 48.2 1E+02 0.0022 25.9 7.4 45 166-212 60-104 (180)
6 PF00872 Transposase_mut: Tran 45.8 12 0.00027 35.0 1.7 77 13-105 157-240 (381)
7 PF14842 FliG_N: FliG N-termin 43.0 82 0.0018 24.6 5.7 64 111-174 21-96 (108)
8 cd02518 GT2_SpsF SpsF is a gly 42.9 27 0.00058 29.4 3.1 29 123-151 196-225 (233)
9 smart00351 PAX Paired Box doma 42.9 40 0.00088 26.9 4.0 31 123-153 34-64 (125)
10 PRK07417 arogenate dehydrogena 42.8 2E+02 0.0044 25.3 8.7 98 109-211 170-270 (279)
11 TIGR02414 pepN_proteo aminopep 41.7 36 0.00079 35.9 4.5 77 108-188 732-832 (863)
12 smart00674 CENPB Putative DNA- 40.9 98 0.0021 21.3 5.3 26 128-153 37-63 (66)
13 TIGR02865 spore_II_E stage II 38.6 2E+02 0.0042 30.0 9.0 64 119-184 373-443 (764)
14 PF14677 FANCI_S3: FANCI solen 32.1 48 0.001 29.4 3.1 25 138-163 191-215 (219)
15 cd08330 CARD_ASC_NALP1 Caspase 31.1 59 0.0013 24.5 3.0 37 135-171 43-80 (82)
16 PF09268 Clathrin-link: Clathr 30.8 34 0.00075 21.2 1.4 15 158-172 7-21 (24)
17 PF03115 Astro_capsid: Astrovi 30.6 17 0.00036 38.3 0.0 42 1-55 147-188 (787)
18 TIGR01987 HI0074 nucleotidyltr 30.5 90 0.002 25.4 4.2 63 106-174 35-105 (123)
19 PRK14015 pepN aminopeptidase N 30.4 53 0.0011 34.8 3.5 76 109-188 743-842 (875)
20 COG2992 Bax Uncharacterized Fl 27.8 1E+02 0.0022 28.7 4.5 107 47-164 131-249 (262)
21 COG4902 Uncharacterized protei 25.2 4.3E+02 0.0094 23.4 7.6 82 133-222 27-111 (189)
22 PF08740 BCS1_N: BCS1 N termin 24.4 1E+02 0.0023 25.2 3.7 19 136-154 34-52 (187)
23 PRK10356 hypothetical protein; 22.3 1.5E+02 0.0032 27.8 4.5 54 106-164 203-261 (274)
24 cd06258 Peptidase_M3_like The 22.1 1.7E+02 0.0037 26.5 4.8 58 122-180 7-65 (365)
25 COG5183 SSM4 Protein involved 20.6 2E+02 0.0043 31.6 5.5 95 120-224 153-266 (1175)
26 PF10436 BCDHK_Adom3: Mitochon 20.2 2.1E+02 0.0046 24.0 4.7 57 140-197 66-135 (164)
No 1
>PF02341 RcbX: RbcX protein; InterPro: IPR003435 The RbcX protein has been identified as having a possible chaperonin-like function []. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RubisCO in Anabaena sp. (strain CA / ATCC 33047). RbcX has been shown to possess a chaperonin-like function assisting correct folding of RubisCO in Escherichia coli expression studies and is needed for RubisCO to reach its maximal activity [].; PDB: 2PEM_B 2PEI_L 2PEK_A 2Z46_E 2Z44_A 2PEJ_F 2PEN_D 2PEQ_B 2Z45_A 3Q20_A ....
Probab=100.00 E-value=1.9e-44 Score=287.74 Aligned_cols=101 Identities=44% Similarity=0.698 Sum_probs=97.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhchhcCCCCCHHHHHHHHcC-CchhHHHHHHHHHHHHHHHHHhcc
Q 027267 110 EDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK-KQDLAERVMITRLHLYGKWVKKCD 188 (225)
Q Consensus 110 ~DtAk~L~~yFTY~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr-~~eLAlRIMeVRehla~EW~~~l~ 188 (225)
.|||++|+|||||+||||||+||+|||||.|.||+||+++|||+|||+||++||+ +|+||+|||+||+|||+++.++++
T Consensus 8 kdtak~L~~yfTy~Avr~Vl~QL~etnp~~~~wL~~F~~~~~~~DGd~fl~~L~~e~~~LA~RIM~vR~~la~~~~d~l~ 87 (111)
T PF02341_consen 8 KDTAKVLQSYFTYQAVRTVLAQLYETNPPAYIWLYNFLSRNPLQDGDAFLEALMRENQELALRIMEVREHLAEEVFDFLP 87 (111)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHSTCSSHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHGGGHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCccHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHhH
Confidence 5999999999999999999999999999999999999999999999999999999 999999999999999999988887
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhh
Q 027267 189 HAQMYKAISDENLELMRERLIET 211 (225)
Q Consensus 189 ~~m~~~~I~e~N~elmRe~L~eT 211 (225)
+|++++|+++|+++||+||.+.
T Consensus 88 -em~~~~I~~~N~e~~R~~L~r~ 109 (111)
T PF02341_consen 88 -EMVREGIQQANMELMRQYLERM 109 (111)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHH
T ss_pred -HHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999764
No 2
>PF12112 DUF3579: Protein of unknown function (DUF3579); InterPro: IPR021969 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif. ; PDB: 2L9D_A.
Probab=62.57 E-value=2.2 Score=33.92 Aligned_cols=24 Identities=21% Similarity=0.474 Sum_probs=20.8
Q ss_pred HHhhccCcchHHHHHhchhcCCCC
Q 027267 130 HQLYEMNPTQYMWFYNFVATNKPG 153 (225)
Q Consensus 130 ~QL~EtNPp~y~WL~~Fl~~npl~ 153 (225)
.+|++.||.+|..+++|...|.++
T Consensus 63 ~~L~~~~P~af~fvm~FA~dN~L~ 86 (92)
T PF12112_consen 63 ERLRDIEPMAFDFVMNFAKDNDLQ 86 (92)
T ss_dssp THHHHH-HHHHHHHHHHHHHHTEE
T ss_pred cHhhhcChHHHHHHHHHHHHCCCe
Confidence 578999999999999999999875
No 3
>cd00131 PAX Paired Box domain
Probab=59.48 E-value=25 Score=28.37 Aligned_cols=76 Identities=12% Similarity=0.035 Sum_probs=48.0
Q ss_pred ecCCCCCC--cc--cHHHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhchhcCCCCC--------------HHHHH
Q 027267 98 VNEVGGQY--ED--SFEDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGD--------------GKHFI 159 (225)
Q Consensus 98 ~~~~gGq~--ed--~f~DtAk~L~~yFTY~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~D--------------GD~fL 159 (225)
+|.+||.| +- +-+.=++++.-|-.=...+.+..+|.=.-+..+.|+..|-++..+.. -+.||
T Consensus 5 ~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i 84 (128)
T cd00131 5 VNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKI 84 (128)
T ss_pred ccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHH
Confidence 45677776 12 22344555555555556777777777777899999999998765531 24566
Q ss_pred HHHcC-CchhHHHHH
Q 027267 160 RILGK-KQDLAERVM 173 (225)
Q Consensus 160 ~~Lmr-~~eLAlRIM 173 (225)
.++.+ ||++-++=|
T Consensus 85 ~~~v~~~p~~Tl~El 99 (128)
T cd00131 85 EIYKQENPGMFAWEI 99 (128)
T ss_pred HHHHHHCCCCCHHHH
Confidence 66666 776644433
No 4
>PF12234 Rav1p_C: RAVE protein 1 C terminal; InterPro: IPR022033 This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C-terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.
Probab=49.51 E-value=28 Score=35.75 Aligned_cols=69 Identities=14% Similarity=0.166 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccC-cchHHHHH-hchhcCCCCCHHHHHHHHcC----CchhHHHHHHHHH
Q 027267 109 FEDVKKQIQNYFTYKAVRTVLHQLYEMN-PTQYMWFY-NFVATNKPGDGKHFIRILGK----KQDLAERVMITRL 177 (225)
Q Consensus 109 f~DtAk~L~~yFTY~AVRtVL~QL~EtN-Pp~y~WL~-~Fl~~npl~DGD~fL~~Lmr----~~eLAlRIMeVRe 177 (225)
..||..++.+++-=.-+-++++-|+|-+ .|.+.+|. +++--.-+.+||.|++...- +.+.|.|.+....
T Consensus 481 l~dAv~V~~~~l~D~qLAi~i~Rl~e~d~gp~~~~ll~~~vLp~a~~~~d~wl~s~~~W~L~~~~~ai~~Li~~~ 555 (631)
T PF12234_consen 481 LKDAVNVCLRQLNDPQLAIAIARLYEGDNGPVLKKLLEEHVLPEAIKEGDRWLASWAFWMLGDYDEAIRALISPP 555 (631)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHcCCCchHHHHHHHHhhhccccccCCHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence 4689999999888888888888887754 67776665 67666677899999998754 8888988886543
No 5
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=48.22 E-value=1e+02 Score=25.94 Aligned_cols=45 Identities=13% Similarity=0.268 Sum_probs=36.5
Q ss_pred chhHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhhc
Q 027267 166 QDLAERVMITRLHLYGKWVKKCDHAQMYKAISDENLELMRERLIETV 212 (225)
Q Consensus 166 ~eLAlRIMeVRehla~EW~~~l~~~m~~~~I~e~N~elmRe~L~eT~ 212 (225)
.+.+.++-+.|+ +++-|.+.+. ..--..+.+.++++++..+++.+
T Consensus 60 ~~~~~~lr~are-~a~al~~~~~-~~~~~~~~~al~~~~~~~~f~~l 104 (180)
T PF11985_consen 60 EEVLERLREARE-IAEALAEELG-DEPEDDVTEALIEMLQTLLFEAL 104 (180)
T ss_pred HHHHHHHHHHHH-HHHHHHHHhc-CCCcchHHHHHHHHHHHHHHHHH
Confidence 578899999999 8998987765 22345889999999999997765
No 6
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=45.79 E-value=12 Score=35.02 Aligned_cols=77 Identities=17% Similarity=0.235 Sum_probs=46.8
Q ss_pred ccCCCCceeeeccCCCcccCCcce-------EEeecccccchhheecccccccccccccccchhhhhhhhhhceeccccc
Q 027267 13 MDSHAGPCLCLDALPTSVKGGGEL-------VLRRNSSVKRKKVKVAARSLELGSSFVDSWDDWRLSSKVISNMVNRSSR 85 (225)
Q Consensus 13 ~~~~~~~~~~~~a~p~~~~~~~~~-------~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~v~~~~r 85 (225)
.+++.-|++-+|++-..++.+|.+ ++=-+.+|+ |+++ ++......+...|+- +...=.
T Consensus 157 L~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~-r~vL------g~~~~~~Es~~~W~~-------~l~~L~- 221 (381)
T PF00872_consen 157 LESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGR-REVL------GFWVGDRESAASWRE-------FLQDLK- 221 (381)
T ss_pred cccccccceeeeeeecccccccccccchhhhhhhhhcccc-ccee------eeecccCCccCEeee-------cchhhh-
Confidence 345567999999998887654443 344567888 4444 333333445566763 332222
Q ss_pred ccccCCCCccEeecCCCCCC
Q 027267 86 KRKQRRDRRPVIVNEVGGQY 105 (225)
Q Consensus 86 ~~~~~~~~~l~i~~~~gGq~ 105 (225)
.+|=++..|+|.|..-|-.
T Consensus 222 -~RGl~~~~lvv~Dg~~gl~ 240 (381)
T PF00872_consen 222 -ERGLKDILLVVSDGHKGLK 240 (381)
T ss_pred -hccccccceeecccccccc
Confidence 2444678899988876654
No 7
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=43.02 E-value=82 Score=24.56 Aligned_cols=64 Identities=13% Similarity=0.277 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc---cCc----chHHHHHh-ch-hcCCCCCHHHHHHHHcC---CchhHHHHHH
Q 027267 111 DVKKQIQNYFTYKAVRTVLHQLYE---MNP----TQYMWFYN-FV-ATNKPGDGKHFIRILGK---KQDLAERVMI 174 (225)
Q Consensus 111 DtAk~L~~yFTY~AVRtVL~QL~E---tNP----p~y~WL~~-Fl-~~npl~DGD~fL~~Lmr---~~eLAlRIMe 174 (225)
|+|..+..+|+=.-++-|...+.. ..+ .....|++ .. ....+..|..|++.|+. -++-|..||.
T Consensus 21 e~Aa~vlk~l~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~~~~~~~~~~~gg~~~~~~lL~~alg~~~a~~il~ 96 (108)
T PF14842_consen 21 EAAAEVLKHLDEEEIERISREMAKLGSVSPEEVEEVLEEFYDEIRAQGGIVSGGRDFARRLLEKALGEEKAKEILD 96 (108)
T ss_dssp HHHHHHHHHS-HHHHHHHHHHHHT-----HHHHHHHHHHHHHHHHHTT---S-HHHHHHH-HHHHS---HHHHH--
T ss_pred HHHHHHHccCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHccccccChHHHHHHHHHHHCCHHHHHHHHH
Confidence 555556666777777776655444 444 34444444 22 34455789999999887 7888888874
No 8
>cd02518 GT2_SpsF SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration.
Probab=42.93 E-value=27 Score=29.38 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=22.4
Q ss_pred HHHHHHHHHhhccCcc-hHHHHHhchhcCC
Q 027267 123 KAVRTVLHQLYEMNPT-QYMWFYNFVATNK 151 (225)
Q Consensus 123 ~AVRtVL~QL~EtNPp-~y~WL~~Fl~~np 151 (225)
..++.+..+|++.|++ .+.|+.+|+++||
T Consensus 196 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p 225 (233)
T cd02518 196 ELIKEIYEALYPKNPDFSLEDIIELLDKNP 225 (233)
T ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhCh
Confidence 4446666778888775 8899999999887
No 9
>smart00351 PAX Paired Box domain.
Probab=42.87 E-value=40 Score=26.87 Aligned_cols=31 Identities=10% Similarity=-0.079 Sum_probs=22.6
Q ss_pred HHHHHHHHHhhccCcchHHHHHhchhcCCCC
Q 027267 123 KAVRTVLHQLYEMNPTQYMWFYNFVATNKPG 153 (225)
Q Consensus 123 ~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~ 153 (225)
...+.+..+|.=.-+..|.|+..|-++..+.
T Consensus 34 ~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~ 64 (125)
T smart00351 34 VRPCDISRQLCVSHGCVSKILGRYYETGSIR 64 (125)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 3456666666666678999999998776544
No 10
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=42.78 E-value=2e+02 Score=25.31 Aligned_cols=98 Identities=15% Similarity=0.137 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhchhcCCCCCHHHHHHHHcC-CchhHHHHH-HHHHHHHHHHHHh
Q 027267 109 FEDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK-KQDLAERVM-ITRLHLYGKWVKK 186 (225)
Q Consensus 109 f~DtAk~L~~yFTY~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr-~~eLAlRIM-eVRehla~EW~~~ 186 (225)
.+.+.+...++..|.|.-.+...+.+.++..-.....|.. ...+| +..+.. +|+|=.-|+ ..|+.+.+..+++
T Consensus 170 hD~~~a~~shlp~~~a~~l~~~~~~~~~~~~~~~~~~~~~-~gfrd----~tRia~~~p~~w~~i~~~N~~~i~~~l~~~ 244 (279)
T PRK07417 170 HDRAVALISHLPVMVSAALIQTCGTEKDPSVLKLAQNLAS-SGFAD----TSRVGGGNPELGVMMAEYNRAALLRSLASY 244 (279)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHhhcccchhhHHhhhhcc-Ccccc----cccccCCChHHHHHHHHHhHHHHHHHHHHH
Confidence 3455555556666666555544444333332121234443 45554 222222 676643333 5555454433333
Q ss_pred cc-hHHHHHHHHHHHHHHHHHHHHhh
Q 027267 187 CD-HAQMYKAISDENLELMRERLIET 211 (225)
Q Consensus 187 l~-~~m~~~~I~e~N~elmRe~L~eT 211 (225)
.. -..+++.|+++|-+-+++.+.+.
T Consensus 245 ~~~l~~~~~~l~~~d~~~l~~~~~~~ 270 (279)
T PRK07417 245 RQSLDQLEELIEQENWSALEQKLEQT 270 (279)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 21 12466677777777777776554
No 11
>TIGR02414 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile. This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc.
Probab=41.70 E-value=36 Score=35.92 Aligned_cols=77 Identities=18% Similarity=0.247 Sum_probs=51.6
Q ss_pred cHHHHHHHHHHHHHHHHHHH---HHHHhhc---------cCcchHHH-HHhchhcCCC----CC--HHHHHHHHcC----
Q 027267 108 SFEDVKKQIQNYFTYKAVRT---VLHQLYE---------MNPTQYMW-FYNFVATNKP----GD--GKHFIRILGK---- 164 (225)
Q Consensus 108 ~f~DtAk~L~~yFTY~AVRt---VL~QL~E---------tNPp~y~W-L~~Fl~~npl----~D--GD~fL~~Lmr---- 164 (225)
.+.+-+-+|-.+|.-||..- +++++.. .||..-.= +--|...||. .| |=+||+....
T Consensus 732 ~~~~~~lv~~kwf~~qa~~~~~~~~~~v~~l~~h~~f~~~npn~~ral~~~f~~~n~~~fh~~~g~gy~~~~~~i~~ld~ 811 (863)
T TIGR02414 732 KWKDDPLVMDKWFALQATSPRPDTLERVKALLQHPAFDLKNPNRVRALIGAFANNNLVRFHDISGSGYRFLADQIIAIDR 811 (863)
T ss_pred HHCCCchhHHHHHHHHhCCCcccHHHHHHHHhcCCCCCcCCCcHHHHHHHHHHhcCcccccCCCCcHHHHHHHHHHHhcC
Confidence 34566778999999999765 4444444 46654333 4477778887 35 5566655433
Q ss_pred -CchhHHHHHHHHHHHHHHHHHhcc
Q 027267 165 -KQDLAERVMITRLHLYGKWVKKCD 188 (225)
Q Consensus 165 -~~eLAlRIMeVRehla~EW~~~l~ 188 (225)
||.+|-|+++.=. .|.++-+
T Consensus 812 ~Np~~aarl~~~~~----~w~~~~~ 832 (863)
T TIGR02414 812 FNPQVAARLLEPLT----RWRKLDP 832 (863)
T ss_pred cCHHHHHHHHHHhh----hhhcCCH
Confidence 9999999887544 8986643
No 12
>smart00674 CENPB Putative DNA-binding domain in centromere protein B, mouse jerky and transposases.
Probab=40.87 E-value=98 Score=21.26 Aligned_cols=26 Identities=19% Similarity=0.243 Sum_probs=17.4
Q ss_pred HHHHhh-ccCcchHHHHHhchhcCCCC
Q 027267 128 VLHQLY-EMNPTQYMWFYNFVATNKPG 153 (225)
Q Consensus 128 VL~QL~-EtNPp~y~WL~~Fl~~npl~ 153 (225)
++.++. +.-.....||.+|..++++.
T Consensus 37 i~~~~~~~~f~~s~~Wl~rF~~Rh~~~ 63 (66)
T smart00674 37 ILQRLGLENFKASNGWLTRFKKRHNIV 63 (66)
T ss_pred HHHHcCCCCCCCCHHHHHHHHHHcCCc
Confidence 344443 23347888999999988874
No 13
>TIGR02865 spore_II_E stage II sporulation protein E. Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs.
Probab=38.56 E-value=2e+02 Score=30.02 Aligned_cols=64 Identities=14% Similarity=0.098 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHhhccCcchHHHHHhchhcCCCCCHHHHHHHHcC-------CchhHHHHHHHHHHHHHHHH
Q 027267 119 YFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK-------KQDLAERVMITRLHLYGKWV 184 (225)
Q Consensus 119 yFTY~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr-------~~eLAlRIMeVRehla~EW~ 184 (225)
+-||++..-++.++++..... ..+-+.+..+ =.-.++|++++-. |...-.|+.|-|+-+++...
T Consensus 373 ~~Ty~~~~~l~~~~e~~~~~~-~~~p~~~~~~-C~r~~~~~~~~~~~~~~~~~n~~w~~rl~e~R~~va~Ql~ 443 (764)
T TIGR02865 373 DYTYSAMEELIENLEEKKDPN-SKLPDEFERK-CIKRKELINTTEDILNNYIINEMWRKRLEEGRRLVAEQLK 443 (764)
T ss_pred HHHHHHHHHHHHHHHhcCCch-hhhhHHHHHh-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 448999999999999987655 6666666533 3446677777754 66778999999997777544
No 14
>PF14677 FANCI_S3: FANCI solenoid 3; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=32.12 E-value=48 Score=29.40 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=16.7
Q ss_pred chHHHHHhchhcCCCCCHHHHHHHHc
Q 027267 138 TQYMWFYNFVATNKPGDGKHFIRILG 163 (225)
Q Consensus 138 p~y~WL~~Fl~~npl~DGD~fL~~Lm 163 (225)
..|.|+.+|+.++++.|-. |+++|+
T Consensus 191 q~~~W~~~~ck~~~l~d~~-~~k~ll 215 (219)
T PF14677_consen 191 QMLSWTLKFCKENSLEDSS-FCKGLL 215 (219)
T ss_dssp HHHHHHHHHHHS---S-HH-HHHHHH
T ss_pred HHHHHHHHHHHhcCCCcHH-HHHHHH
Confidence 6899999999999998864 666554
No 15
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=31.09 E-value=59 Score=24.48 Aligned_cols=37 Identities=22% Similarity=0.271 Sum_probs=31.5
Q ss_pred cCcchHHHHHhchhcCCCCCHHHHHHHHcC-CchhHHH
Q 027267 135 MNPTQYMWFYNFVATNKPGDGKHFIRILGK-KQDLAER 171 (225)
Q Consensus 135 tNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr-~~eLAlR 171 (225)
|++..+.-|.+++.+-...-=+.|+..|.. +|.|+..
T Consensus 43 T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~p~L~~~ 80 (82)
T cd08330 43 TNQEKMRKLFSFVRSWGASCKDIFYQILREEEPYLVED 80 (82)
T ss_pred CcHHHHHHHHHHHHccCHHHHHHHHHHHHHhChHHHhH
Confidence 778899999999988777777899999976 9998765
No 16
>PF09268 Clathrin-link: Clathrin, heavy-chain linker; InterPro: IPR015348 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the core motif for the alpha-helical zigzag linker region connecting the conserved N-terminal beta-propeller region to the C-terminal alpha-alpha-superhelical region in clathrin heavy chains []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 1C9I_A 1BPO_B 1C9L_A 1UTC_B 3GD1_I 3GC3_B 2XZG_A 2XZH_A.
Probab=30.78 E-value=34 Score=21.25 Aligned_cols=15 Identities=33% Similarity=0.341 Sum_probs=9.5
Q ss_pred HHHHHcCCchhHHHH
Q 027267 158 FIRILGKKQDLAERV 172 (225)
Q Consensus 158 fL~~Lmr~~eLAlRI 172 (225)
|+..=++|++||+|+
T Consensus 7 yi~~~L~N~~LAl~l 21 (24)
T PF09268_consen 7 YILNTLQNPDLALRL 21 (24)
T ss_dssp HHHHTT--HHHHHHH
T ss_pred HHHhccCCHHHHHHH
Confidence 455556689999986
No 17
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=30.59 E-value=17 Score=38.32 Aligned_cols=42 Identities=33% Similarity=0.370 Sum_probs=0.0
Q ss_pred CCcceeeeccccccCCCCceeeeccCCCcccCCcceEEeecccccchhheecccc
Q 027267 1 MVGALSVVGSSVMDSHAGPCLCLDALPTSVKGGGELVLRRNSSVKRKKVKVAARS 55 (225)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~a~p~~~~~~~~~~~~~~~~~~r~~~~~~~~~ 55 (225)
|||+-.|.|+.+. -+|-..+.|+...-+ -.|+|||+-|.||-
T Consensus 147 lvG~saV~Gtv~r-----~sln~~~~p~~tsws--------~lgARkH~dv~~G~ 188 (787)
T PF03115_consen 147 LVGASAVSGTVVR-----VSLNLTGTPSSTSWS--------GLGARKHVDVPVGR 188 (787)
T ss_dssp -------------------------------------------------------
T ss_pred ccCccccCceEEE-----EEecCCCCCCCCCcc--------ccCceeEEEEcCCC
Confidence 7999999999864 345566777765433 47999999986664
No 18
>TIGR01987 HI0074 nucleotidyltransferase substrate binding protein, HI0074 family. The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (pfam01909).
Probab=30.53 E-value=90 Score=25.43 Aligned_cols=63 Identities=17% Similarity=0.207 Sum_probs=35.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhchhcCCCCCHHHHHHHHcC--------CchhHHHHHH
Q 027267 106 EDSFEDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK--------KQDLAERVMI 174 (225)
Q Consensus 106 ed~f~DtAk~L~~yFTY~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr--------~~eLAlRIMe 174 (225)
|=+|+=+=|+|+.||.|+.+. ..+.++|.- =+......+-|.||+.|++-|-. +.+.|..|..
T Consensus 35 E~t~ELaWK~lK~~L~~~G~~-----~~~~~spr~-~ir~A~~~glI~d~~~W~~ml~~RN~tsHtYde~~a~~i~~ 105 (123)
T TIGR01987 35 EFTFELAWKLMKRYLAQEGIN-----DIGAYSPKD-VLKEAFRAGLIGDESLWIAMLDDRNITSHTYDQEKAREIYA 105 (123)
T ss_pred hhHHHHHHHHHHHHHHHcCCc-----ccccCCHHH-HHHHHHHcCCcCCHHHHHHHHHHhCcccccCCHHHHHHHHH
Confidence 434444446666666665431 101222221 14445556777999999998855 4567776664
No 19
>PRK14015 pepN aminopeptidase N; Provisional
Probab=30.40 E-value=53 Score=34.78 Aligned_cols=76 Identities=20% Similarity=0.343 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHHHHHH---HHHHhhc---------cCcchHHHH-HhchhcCCC------CCHHHHHHHHcC-----
Q 027267 109 FEDVKKQIQNYFTYKAVRT---VLHQLYE---------MNPTQYMWF-YNFVATNKP------GDGKHFIRILGK----- 164 (225)
Q Consensus 109 f~DtAk~L~~yFTY~AVRt---VL~QL~E---------tNPp~y~WL-~~Fl~~npl------~DGD~fL~~Lmr----- 164 (225)
+.+-.-+|-.+|..||... +++++.. .||..-.=| .-|...||+ ..|=+||+...-
T Consensus 743 ~~~~~lv~~kwf~~qa~~~~~~~~~~v~~l~~hp~f~~~npn~~ral~~~f~~~n~~~fh~~~g~gy~~~~~~i~~ld~~ 822 (875)
T PRK14015 743 WKDDPLVMDKWFALQATSPAPDTLERVRALMQHPAFDLKNPNRVRSLIGAFAAANPAGFHAADGSGYRFLADQILALDKI 822 (875)
T ss_pred hCCCchhhHHHHHHHhCCCCcCHHHHHHHHhcCCCCCCCCCcHHHHHHHHHhhcCCcccCCCCCcHHHHHHHHHHHhcCc
Confidence 4566778889999998643 2333322 567544444 467788888 246777765543
Q ss_pred CchhHHHHHHHHHHHHHHHHHhcc
Q 027267 165 KQDLAERVMITRLHLYGKWVKKCD 188 (225)
Q Consensus 165 ~~eLAlRIMeVRehla~EW~~~l~ 188 (225)
||.+|-|+.+.=. .|.++-+
T Consensus 823 Np~~aarl~~~~~----~~~~~~~ 842 (875)
T PRK14015 823 NPQVAARLATPLI----RWRRYDP 842 (875)
T ss_pred CHHHHHHHHHHhh----hhhccCH
Confidence 9999999887544 8986643
No 20
>COG2992 Bax Uncharacterized FlgJ-related protein [General function prediction only]
Probab=27.83 E-value=1e+02 Score=28.70 Aligned_cols=107 Identities=20% Similarity=0.242 Sum_probs=68.4
Q ss_pred hhheecccccccccccccccchhhhhhhhhhceecccccccccCCCCccEeecCCCCCCcccHHHHHHHHHHHH------
Q 027267 47 KKVKVAARSLELGSSFVDSWDDWRLSSKVISNMVNRSSRKRKQRRDRRPVIVNEVGGQYEDSFEDVKKQIQNYF------ 120 (225)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~v~~~~r~~~~~~~~~l~i~~~~gGq~ed~f~DtAk~L~~yF------ 120 (225)
+|+-|-|-+|.++-.-+.|++---.-+|-.++++--.| -++ + -++++-|.+-|-. -|+-+.+...+|+
T Consensus 131 ~RvdviPtSmvltqAa~ESgwGTSklAreaNNlFg~~c--~kg-~-c~~vplgk~h~yk--kfdSvqeSV~sYvmnLNrh 204 (262)
T COG2992 131 HRVDVIPTSMVLTQAAAESGWGTSKLAREANNLFGMWC--TKG-R-CGLVPLGKVHGYK--KFDSVQESVSSYVMNLNRH 204 (262)
T ss_pred HHhccCcHHHHHHHHHHHhccchHHHHHhcccceeeee--ccC-C-cccccCCcccchh--hhhhHHHHHHHHHHhcccc
Confidence 66777799999988777775554455788888876665 232 2 2355545555433 3555555566664
Q ss_pred -HHHHHHHHHHHhhccCc-----chHHHHHhchhcCCCCCHHHHHHHHcC
Q 027267 121 -TYKAVRTVLHQLYEMNP-----TQYMWFYNFVATNKPGDGKHFIRILGK 164 (225)
Q Consensus 121 -TY~AVRtVL~QL~EtNP-----p~y~WL~~Fl~~npl~DGD~fL~~Lmr 164 (225)
-|--.|-..+||+.-|. ..-.-|-+|++ -|+.|..-|++
T Consensus 205 pAYs~fRkaraqlr~~~~e~ta~amik~L~~YSe-----rg~~Y~n~Lta 249 (262)
T COG2992 205 PAYSSFRKARAQLRKADQEVTATAMIKKLKGYSE-----RGKSYNNYLTA 249 (262)
T ss_pred hhHHHHHHHHHHhhcCCchhhHHHHHHHhhchhh-----hhHHHHHHHHH
Confidence 58889999999996554 33445566665 36666665544
No 21
>COG4902 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.19 E-value=4.3e+02 Score=23.41 Aligned_cols=82 Identities=21% Similarity=0.181 Sum_probs=58.0
Q ss_pred hccCcchHHHHHhchhcCCCCCHHHHHHHHcC-CchhHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHH--HHH
Q 027267 133 YEMNPTQYMWFYNFVATNKPGDGKHFIRILGK-KQDLAERVMITRLHLYGKWVKKCDHAQMYKAISDENLELMRE--RLI 209 (225)
Q Consensus 133 ~EtNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr-~~eLAlRIMeVRehla~EW~~~l~~~m~~~~I~e~N~elmRe--~L~ 209 (225)
++||.|.-.-+-.-+...|+.|-|.=----|+ ...||.- |=..+|.+|. -.+++.|+++--+||-. .|.
T Consensus 27 ~gt~~~s~~~~~~~l~~~plsdeE~nsLiyMrEEEKLARD---VYL~LYnkw~-----l~IF~nIA~SEQ~HmDAVk~Ll 98 (189)
T COG4902 27 EGTNSESTDTSGVTLQDSPLSDEEINSLIYMREEEKLARD---VYLYLYNKWN-----LPIFRNIAASEQEHMDAVKSLL 98 (189)
T ss_pred cCCCCCCccchhhcccCCCCChHHHhhHHHHHHHHHHHhh---HHhhhhhccC-----cHHHHHHHHhHHHHHHHHHHHH
Confidence 36888877777777888889887654333355 5567754 3456788886 34788999999888875 467
Q ss_pred hhcccCCCCCCCC
Q 027267 210 ETVIWPSDDSNTE 222 (225)
Q Consensus 210 eT~~~psd~~n~~ 222 (225)
|-...|..+++++
T Consensus 99 ekYnv~dP~~~~s 111 (189)
T COG4902 99 EKYNVQDPASTTS 111 (189)
T ss_pred HHcCCCCCCccCc
Confidence 8888877776653
No 22
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=24.35 E-value=1e+02 Score=25.24 Aligned_cols=19 Identities=11% Similarity=0.483 Sum_probs=16.7
Q ss_pred CcchHHHHHhchhcCCCCC
Q 027267 136 NPTQYMWFYNFVATNKPGD 154 (225)
Q Consensus 136 NPp~y~WL~~Fl~~npl~D 154 (225)
+-+.|.||+.+++++|...
T Consensus 34 ~D~~Y~~lm~Wls~q~~~~ 52 (187)
T PF08740_consen 34 DDEAYDWLMRWLSSQPFSK 52 (187)
T ss_pred CCHHHHHHHHHHhhCCccc
Confidence 4579999999999999865
No 23
>PRK10356 hypothetical protein; Provisional
Probab=22.35 E-value=1.5e+02 Score=27.82 Aligned_cols=54 Identities=13% Similarity=0.162 Sum_probs=40.0
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHhhccCc-----chHHHHHhchhcCCCCCHHHHHHHHcC
Q 027267 106 EDSFEDVKKQIQNYFTYKAVRTVLHQLYEMNP-----TQYMWFYNFVATNKPGDGKHFIRILGK 164 (225)
Q Consensus 106 ed~f~DtAk~L~~yFTY~AVRtVL~QL~EtNP-----p~y~WL~~Fl~~npl~DGD~fL~~Lmr 164 (225)
+++|+|=+..|.+--.|.-+|.+-+|+...+. .+..-|.+|++. |++|.+.|..
T Consensus 203 ~~Sv~~Y~~nLn~~~aY~~lR~iRa~lR~~~~~lt~~~La~gL~~YSEr-----G~~Yv~~L~~ 261 (274)
T PRK10356 203 KESVSAYVTNLNTHPAYSSFRKSRAQLRKADQEVTATAMIHKLKGYSTK-----GSSYNNYLFA 261 (274)
T ss_pred HHHHHHHHHHHhcChhHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHh-----HHHHHHHHHH
Confidence 44455666666666689999999999887553 466788888873 9999988855
No 24
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=22.08 E-value=1.7e+02 Score=26.53 Aligned_cols=58 Identities=14% Similarity=0.037 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhhccCcchHHHHHhchhcCCCCCHHHHHHHHcC-CchhHHHHHHHHHHHH
Q 027267 122 YKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK-KQDLAERVMITRLHLY 180 (225)
Q Consensus 122 Y~AVRtVL~QL~EtNPp~y~WL~~Fl~~npl~DGD~fL~~Lmr-~~eLAlRIMeVRehla 180 (225)
++-+|.-++|+-+++-..-.||.++... .+.+=++|++.|-+ =..++.++++.....+
T Consensus 7 lv~lr~e~A~~lGy~~~~d~~l~~~~~~-~~e~v~~f~~~l~~~~~p~~~~~~~~l~~~~ 65 (365)
T cd06258 7 LVSLRNQLARLLGYENFADYKLALQEAK-SPETVEGFFEELKRKLRPLLAKLREEISAAK 65 (365)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888899989977788888888876 78899999999987 5677888887666444
No 25
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=20.63 E-value=2e+02 Score=31.58 Aligned_cols=95 Identities=22% Similarity=0.241 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHhhccCcchHHHHH-----hchhcCCCCCHHHHHHHHcC--Cc-----hhHHHHHHHHHHHHHHHHHhc
Q 027267 120 FTYKAVRTVLHQLYEMNPTQYMWFY-----NFVATNKPGDGKHFIRILGK--KQ-----DLAERVMITRLHLYGKWVKKC 187 (225)
Q Consensus 120 FTY~AVRtVL~QL~EtNPp~y~WL~-----~Fl~~npl~DGD~fL~~Lmr--~~-----eLAlRIMeVRehla~EW~~~l 187 (225)
+|-.|.-+-+.|-.+.- -.++|+- .|++.+-++-.|.++...+. +| +|+-| .|+ ... ..
T Consensus 153 LtT~~~~~q~~q~~~F~-~sfI~I~v~~~~~w~~qd~V~reD~l~~qifek~g~r~s~~~~~~R---~r~----R~~-M~ 223 (1175)
T COG5183 153 LTTRAGFYQLLQNSGFR-NSFIWIGVGIPLTWLAQDMVNREDCLLNQIFEKFGERLSDKDLMRR---LRR----RML-MN 223 (1175)
T ss_pred hhhHHHHHHhhcccceE-eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccChHHHHHH---HHH----hcc-cC
Confidence 34455555555533322 4556653 45666777888998888876 44 44544 233 221 22
Q ss_pred chHHHHHHHHHHHHHHHHH-------HHHhhcccCCCCCCCCCC
Q 027267 188 DHAQMYKAISDENLELMRE-------RLIETVIWPSDDSNTEKI 224 (225)
Q Consensus 188 ~~~m~~~~I~e~N~elmRe-------~L~eT~~~psd~~n~~~~ 224 (225)
+ +-+.+.++++|.+|-|. |+-+-..-|+.|+|.+-|
T Consensus 224 ~-~~~~E~~~re~~~l~rn~arq~~~h~r~n~r~~~~d~Nnnv~ 266 (1175)
T COG5183 224 P-RAILESISRESAQLERNTARQQGEHARENGRDLSSDSNNNVI 266 (1175)
T ss_pred H-HHHHHHHHHHHHHHhhcccccchhhhhhcccccccccccccc
Confidence 2 55778899999988876 566667778888886544
No 26
>PF10436 BCDHK_Adom3: Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase; InterPro: IPR018955 Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. Regulating the activity of the branched-chain alpha-ketoacid dehydrogenase (BCDH) complex is the primary means by which these processes are coordinated. BCDH kinase regulates BCDH by phosphorylation, thereby inactivating it when synthesis is required. Pyruvate dehydrogenase kinase inhibits the pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism. It is also involved in telomere maintenance. This entry is associated with IPR003594 from INTERPRO which is found towards the C terminus. ; PDB: 1GKX_A 1GJV_A 1GKZ_A 1JM6_B 3CRL_B 3CRK_B 1Y8O_A 2PNR_A 1Y8P_A 1Y8N_A ....
Probab=20.20 E-value=2.1e+02 Score=24.01 Aligned_cols=57 Identities=18% Similarity=0.189 Sum_probs=37.5
Q ss_pred HHHHHhchhcCCCCCHHHHHHHHcC----C----chhHHHHHHHHHHH----H-HHHHHhcchHHHHHHHH
Q 027267 140 YMWFYNFVATNKPGDGKHFIRILGK----K----QDLAERVMITRLHL----Y-GKWVKKCDHAQMYKAIS 197 (225)
Q Consensus 140 y~WL~~Fl~~npl~DGD~fL~~Lmr----~----~eLAlRIMeVRehl----a-~EW~~~l~~~m~~~~I~ 197 (225)
+..|.+|-.-....|-++|++.|-+ | +.||.=++|.+.+. . ++...||+ ++....|.
T Consensus 66 F~~L~~~~~~~~~~~~~~F~~~l~~i~~~H~~vv~~lA~G~~E~~~~~~~~~~~~~i~~fLd-~f~~sRIg 135 (164)
T PF10436_consen 66 FEELRSFPPPKTLEDNEKFTELLERILDRHSDVVPTLAQGVLELKKYLQSSESEEQIQSFLD-RFYRSRIG 135 (164)
T ss_dssp HHHHHTTSTTTSCCHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHC--HHHHHHHHHHHH-HHHHHHHH
T ss_pred HHHHHhcCCCCCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcccccHHHHHHHHH-HHHHHhHH
Confidence 3445555444555678899988766 3 46899999999976 2 35666666 55555443
Done!