Query 009302
Match_columns 538
No_of_seqs 250 out of 1271
Neff 5.6
Searched_HMMs 46136
Date Thu Mar 28 22:54:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1400 Predicted ATP-dependen 100.0 7E-44 1.5E-48 361.0 4.8 334 49-480 28-367 (371)
2 PF02190 LON: ATP-dependent pr 99.9 3.3E-22 7.1E-27 190.6 20.7 109 86-197 1-116 (205)
3 PRK10787 DNA-binding ATP-depen 99.9 3.2E-21 6.8E-26 220.5 22.0 114 80-198 4-120 (784)
4 TIGR00763 lon ATP-dependent pr 99.8 2.2E-19 4.7E-24 205.9 19.9 106 88-198 1-113 (775)
5 COG2802 Uncharacterized protei 99.8 2.5E-17 5.5E-22 160.8 18.3 115 81-198 6-123 (221)
6 COG0466 Lon ATP-dependent Lon 99.7 2.6E-17 5.5E-22 182.0 18.1 127 86-216 9-147 (782)
7 smart00464 LON Found in ATP-de 98.6 2E-07 4.4E-12 79.7 9.1 37 87-123 2-38 (92)
8 PF03226 Yippee-Mis18: Yippee 98.5 1.1E-07 2.5E-12 82.3 4.8 91 432-534 2-93 (96)
9 KOG4159 Predicted E3 ubiquitin 98.1 2.2E-06 4.8E-11 91.8 3.4 111 82-198 172-282 (398)
10 KOG2004 Mitochondrial ATP-depe 97.3 0.00072 1.6E-08 76.6 9.0 54 81-137 63-116 (906)
11 KOG3399 Predicted Yippee-type 86.3 0.16 3.4E-06 46.3 -0.9 75 431-516 14-88 (122)
12 TIGR00357 methionine-R-sulfoxi 85.6 1.1 2.3E-05 41.8 4.1 66 430-515 38-105 (134)
13 KOG1400 Predicted ATP-dependen 84.9 0.12 2.5E-06 54.5 -2.8 49 484-532 304-357 (371)
14 PRK05508 methionine sulfoxide 84.5 1.4 3E-05 40.2 4.2 65 429-514 30-94 (119)
15 PRK00222 methionine sulfoxide 82.6 1.7 3.7E-05 40.8 4.2 68 430-515 41-108 (142)
16 PF01641 SelR: SelR domain; I 78.8 1.5 3.3E-05 40.2 2.5 64 431-514 36-101 (124)
17 PRK05550 bifunctional methioni 76.4 3.3 7.1E-05 43.1 4.4 64 430-514 34-97 (283)
18 PF11648 RIG-I_C-RD: C-termina 70.1 2.5 5.4E-05 38.6 1.5 72 432-515 4-76 (123)
19 COG0229 Conserved domain frequ 62.7 12 0.00027 35.0 4.5 69 430-516 40-108 (140)
20 PRK14018 trifunctional thiored 53.2 17 0.00038 41.0 4.6 65 431-515 417-483 (521)
21 KOG3507 DNA-directed RNA polym 50.6 5.9 0.00013 31.8 0.3 18 426-443 31-48 (62)
22 PRK05417 glutathione-dependent 48.7 21 0.00045 35.3 3.8 52 462-514 56-108 (191)
23 COG3791 Uncharacterized conser 41.3 37 0.0008 31.2 4.1 35 493-534 64-98 (133)
24 PF04828 GFA: Glutathione-depe 35.9 51 0.0011 27.0 3.8 38 493-536 42-79 (92)
25 PF09814 HECT_2: HECT-like Ubi 30.4 55 0.0012 34.5 3.9 13 498-510 192-204 (354)
26 PF03604 DNA_RNApol_7kD: DNA d 26.8 26 0.00057 24.8 0.4 16 427-442 12-27 (32)
27 PF02202 Tachykinin: Tachykini 25.1 7.7 0.00017 21.2 -1.9 8 521-528 3-10 (11)
28 cd00246 RabGEF Nucleotide exch 23.6 2.1E+02 0.0046 25.6 5.6 68 432-517 2-90 (103)
29 COG1996 RPC10 DNA-directed RNA 21.1 30 0.00065 26.9 -0.2 19 424-442 16-34 (49)
No 1
>KOG1400 consensus Predicted ATP-dependent protease PIL, contains LON domain [General function prediction only]
Probab=100.00 E-value=7e-44 Score=360.99 Aligned_cols=334 Identities=27% Similarity=0.324 Sum_probs=249.2
Q ss_pred CCCCccccccccccccccCC-CccccCcccccCCCeeeeEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCc
Q 009302 49 SSNQLTFDTCLASLHTYLGD-VEDTHNRMAFLEGGAILTLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPY 127 (538)
Q Consensus 49 ~~~~~~fd~sl~s~H~YLG~-~ed~~gr~~~le~g~~~~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~ 127 (538)
-.++..|||+||..|+|||+ .|+..+ .+++++|.+..+|+++...+|+|||++||+.+..|+.+.+++...... ..+
T Consensus 28 l~de~~~n~al~d~~~~~ged~ee~~~-~~~ldd~t~~~~p~~~~~~~v~~PgqtLPl~~i~~~~~s~~r~lvs~a-r~~ 105 (371)
T KOG1400|consen 28 LEDENVFNTALPDYHLYLGEDREEYEN-EARLDDDTTNWIPICGQVMAVLFPGQTLPLKFIDPQERSIVRRLVSSA-RDN 105 (371)
T ss_pred ccchhcccccCcccccccccchhhhhc-eeeecCCceeeecccCceeeEecCcccCcchhcCHHHHHHHHHHHHhh-cCC
Confidence 34488999999999999998 455554 599999999999999999999999999999999998888887766552 125
Q ss_pred EEEEEEeecCCCCCCcccccceeEEEEEEEEECCC--Cc--EEEEEEEeEEEEEeeeeeccCCcceEEEEEecCCCcccC
Q 009302 128 TIGVVRVFREPDNGRITFATIGTTAEIRQYRRLED--GS--LNVVTRGQQRFRLRRRWIDVEGVPCGEIQIIQEDLPLRT 203 (538)
Q Consensus 128 ~IgVv~~~k~~~~~~~~l~~IGT~AeI~~v~~l~D--Gs--l~V~v~G~qRfrI~~~~~~~dg~l~AeVeiL~E~~~~r~ 203 (538)
.|.|+.. .. -......-+|+++|...+.-.| |. ..+++.|+.|+++.+..++..|.-.|+|+++|+...-.
T Consensus 106 ~F~vl~r-~~---v~~re~~r~tt~evd~~R~p~d~Fgn~l~~~~~~G~y~~~vl~lR~qs~g~~e~~~qL~P~~~i~~- 180 (371)
T KOG1400|consen 106 GFVVLFR-SD---VPERESLRYTTTEVDAYRVPQDNFGNALSMVKAMGRYRCKVLKLRTQSLGRGEAEVQLLPDVEIPC- 180 (371)
T ss_pred ceEEEec-cc---chHHhhccccceeccccccchhhhhhhhhhhhhhcccccceeeecccCCCcccceEEecccccccc-
Confidence 6777664 11 1233446788899875443334 43 46677899999999866778888899999888533100
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCcCCCCCCCcccccccccCChhhhhhcccccccccccCccCCCCCCCcc
Q 009302 204 PRDVFETLGCVSNLSQSLSHTLPSNSSSRGYGIRDNDSDATSEESFESELSPTERRIHQSVIDFAYGCDIMDESTSSDDD 283 (538)
Q Consensus 204 l~d~f~~la~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~s~~~~~~~~~~~~~~~~~~~~d~~~~~~~~ 283 (538)
+ .+++.|.. .+|..++.-|.
T Consensus 181 ----------~------~~Sf~~~~------------------------------avq~~~~n~~~-------------- 200 (371)
T KOG1400|consen 181 ----------L------LPSFIPKS------------------------------AVQLPAHNKCS-------------- 200 (371)
T ss_pred ----------c------cccccchh------------------------------hheecccCcce--------------
Confidence 0 11111100 01110000000
Q ss_pred cccccccccccCCCCCCCCCCCCcccccccccccccccccCCCCcCCCCccchhhh-hhhhhcccCCCCChhHHHhhcCH
Q 009302 284 KSAFQSDIQSRRPHLNDSDSIGNWKQSENVGLRIGKSSALGRQSHRGEGSKMCWRN-ELSQFRRTSRAFLPHWVYRMYDS 362 (538)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~wp~wvy~~yd~ 362 (538)
+-++.+. ..| +..+ .-...+..|.. .++.++++.+.+||.|.|.+|++
T Consensus 201 ----------ia~~~n~--------------~p~-----s~e~--dm~sla~f~~i~sls~~h~~~ll~~~~was~tyqS 249 (371)
T KOG1400|consen 201 ----------IATRING--------------YPF-----SAER--DMTSLAVFRQIGSLSGFHGDDLLSWPKWASLTYQS 249 (371)
T ss_pred ----------eccCCCC--------------Ccc-----cccc--chhhhhhheehhhhhhhcccccccccccchHHHHH
Confidence 0000000 000 0000 00011112233 56677889999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCcCCCCcchhhhhhhcCCCCHHHhhhhhccCChhHHHHHHHHHHhcCCceecccccccc
Q 009302 363 YCLAQRAADKWKQIVGTPNMDGLVKKPDLLSFYIASKIPVSESTRQELLEIDGVSYRLRREIELLESFDLVRCKTCKTAI 442 (538)
Q Consensus 363 ~~L~~r~~~~~~~~~~~~~~~~~~~~P~~~Sywva~~lpl~~~~r~~LL~~d~~~~RL~~el~~l~~~~~l~C~~C~~~I 442 (538)
|.||.||.+..+++.+..+.|.++.+|+.||||+|++||+++..|.+||.++++.+|||+|+..++++++++|++|++.|
T Consensus 250 y~la~rivenarl~yE~lk~ds~~~kpivlSf~~a~kihv~e~~~~hL~~~g~v~tRlq~e~~~~~k~ti~fCk~Cqt~i 329 (371)
T KOG1400|consen 250 YFLAKRIVENARLWYELLKEDSAPGKPIVLSFKYAWKIHVCERCREHLLWEGSVMTRLQREFFGIQKETITFCKECQTDI 329 (371)
T ss_pred HHHHHHHHHHHHHHHHhccccccCCCceEeehhhhhhhhhhHHHHHHHHhhcccccchheeeecccchhhhhhHhhchhh
Confidence 99999998877777777777999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCce
Q 009302 443 AKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLA 480 (538)
Q Consensus 443 a~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~ 480 (538)
+.++|+|.|+..|++..|+||+||+||++|++++.-+.
T Consensus 330 a~~~d~f~msk~g~qee~~np~gyIhei~t~y~~v~i~ 367 (371)
T KOG1400|consen 330 AENWDHFPMSKNGPQEEYDNPMGYIHEILTRYDYVLIK 367 (371)
T ss_pred hhhhcccccccCCchHhhcChhhHHHHHHhhhhheeec
Confidence 99999999999999999999999999999999987333
No 2
>PF02190 LON: ATP-dependent protease La (LON) domain; InterPro: IPR003111 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature defines the N-terminal domain of the archael, bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). In the eukaryotes the majority of the proteins are located in the mitochondrial matrix [, ]. In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response [].; GO: 0004176 ATP-dependent peptidase activity, 0006508 proteolysis; PDB: 3LJC_A 2ANE_G 1ZBO_A 3M65_A.
Probab=99.90 E-value=3.3e-22 Score=190.65 Aligned_cols=109 Identities=30% Similarity=0.526 Sum_probs=86.3
Q ss_pred eEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEEEEEe-ecCCC---CCCcccccceeEEEEEEEEECC
Q 009302 86 TLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIGVVRV-FREPD---NGRITFATIGTTAEIRQYRRLE 161 (538)
Q Consensus 86 ~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~IgVv~~-~k~~~---~~~~~l~~IGT~AeI~~v~~l~ 161 (538)
+||+||+++.|+|||+++||+|+++++++|+++++.++. ..||+++. ..... +...++|.+||+|+|.++.+.+
T Consensus 1 ~lPv~pl~~~vlfPg~~~~i~i~~~~~~~~l~~~~~~~~--~~~~i~~~~~~~~~~~~~~~~~~~~~G~~~~I~~~~~~~ 78 (205)
T PF02190_consen 1 ELPVFPLRNQVLFPGQTLPIHIFEPRYIALLKRALDNNN--PYFGIFLVKSNKDDSDEPSIDDLYSVGTLARIIRVEELP 78 (205)
T ss_dssp EEEEEEESSS---TTBEEEEEE-SHHHHHHHHHHHTTTS--E-EEEEEE-EBSSTSSSS-GGGB-SEEEEEEEEEEEEST
T ss_pred CEEEEEeCCcccCCCeeEEEEECCHHHHHHHHHHHhcCC--CceeEEeecccCCcccCCcccccccceEEEEEEEEEecC
Confidence 589999999999999999999999999999999998751 25888876 22111 4457899999999999999999
Q ss_pred CCcEEEEEEEeEEEEEeeee---eccCCcceEEEEEecC
Q 009302 162 DGSLNVVTRGQQRFRLRRRW---IDVEGVPCGEIQIIQE 197 (538)
Q Consensus 162 DGsl~V~v~G~qRfrI~~~~---~~~dg~l~AeVeiL~E 197 (538)
||++.|+++|++||+|.+ + .+.+|++.|+|++++|
T Consensus 79 dg~~~v~~~g~~R~ki~~-~~~~~~~~~~~~a~v~~l~d 116 (205)
T PF02190_consen 79 DGTYKVLVQGLQRFKILK-INNETQEDPYLVAEVEPLED 116 (205)
T ss_dssp TS-EEEEEEEEEEEEEEE-EEE--ECSSCEEEEEEEE--
T ss_pred CCCEEEEEEEEEEEEEEE-EecccccCCceEEEEEEecc
Confidence 999999999999999998 6 5589999999999977
No 3
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=99.87 E-value=3.2e-21 Score=220.53 Aligned_cols=114 Identities=27% Similarity=0.383 Sum_probs=101.2
Q ss_pred CCCeeeeEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEEEEEeecCCC---CCCcccccceeEEEEEE
Q 009302 80 EGGAILTLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIGVVRVFREPD---NGRITFATIGTTAEIRQ 156 (538)
Q Consensus 80 e~g~~~~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~IgVv~~~k~~~---~~~~~l~~IGT~AeI~~ 156 (538)
++....+||||||+++|||||+.+||+|+++++++||++|+.++ +.|||+.+ ++.. +..+++|.|||+|+|.+
T Consensus 4 ~~~~~~~LPLfPLr~~VLFPg~~lPL~Ife~R~i~~Ve~al~~~---~~~gvv~~-k~~~~~~p~~~dLy~VGtla~I~~ 79 (784)
T PRK10787 4 ERSERIEIPVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHD---KKIMLVAQ-KEASTDEPGVNDLFTVGTVASILQ 79 (784)
T ss_pred ccCCCceEEEEECCCceeCCCceeeeecCCHHHHHHHHHHHhcC---CEEEEEEe-cCCCCCCCCcccccCccEEEEEEE
Confidence 33445689999999999999999999999999999999999875 78999987 4332 34468999999999999
Q ss_pred EEECCCCcEEEEEEEeEEEEEeeeeeccCCcceEEEEEecCC
Q 009302 157 YRRLEDGSLNVVTRGQQRFRLRRRWIDVEGVPCGEIQIIQED 198 (538)
Q Consensus 157 v~~l~DGsl~V~v~G~qRfrI~~~~~~~dg~l~AeVeiL~E~ 198 (538)
+.+.+||.++|+++|++||+|.+ +.+.+||+.|+|++++++
T Consensus 80 ~~~l~DG~~~Ilv~Gl~RfrI~~-~~~~~py~~A~Ve~l~~~ 120 (784)
T PRK10787 80 MLKLPDGTVKVLVEGLQRARISA-LSDNGEHFSAKAEYLESP 120 (784)
T ss_pred eeECCCCeEEEEEEEEEEEEEEE-EEcCCCCEEEEEEEecCC
Confidence 99999999999999999999998 688999999999999764
No 4
>TIGR00763 lon ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
Probab=99.82 E-value=2.2e-19 Score=205.88 Aligned_cols=106 Identities=23% Similarity=0.307 Sum_probs=93.1
Q ss_pred EEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEE-EEEeecCCC---CCCcccccceeEEEEEEEEECC--
Q 009302 88 PLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIG-VVRVFREPD---NGRITFATIGTTAEIRQYRRLE-- 161 (538)
Q Consensus 88 PVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~Ig-Vv~~~k~~~---~~~~~l~~IGT~AeI~~v~~l~-- 161 (538)
|||||+++|||||+.+||+|++|++++||++|+.++ +.|+ ++.+ ++.. +...++|.|||+|+|.++.+.+
T Consensus 1 Pl~PLr~~VLfPg~~lpL~Ife~r~i~mV~~al~~~---~~~~~vv~~-k~~~~~~p~~~~ly~VGt~a~I~~~~~~~d~ 76 (775)
T TIGR00763 1 PLLPLRRRPLFPGMIKPIDVGREKSIKLIKEALRLK---QPYLGLFLQ-KDDDNEEPEEDDIYSVGVVAQILEMLPLPSS 76 (775)
T ss_pred CeEcCCCCccCCCcceeEecCCHHHHHHHHHHHhcC---CcEEEEEEe-cCcccCCCCcccccCCceEEEEEEeccCCCC
Confidence 899999999999999999999999999999999875 5666 6665 4432 3456899999999999999954
Q ss_pred -CCcEEEEEEEeEEEEEeeeeeccCCcceEEEEEecCC
Q 009302 162 -DGSLNVVTRGQQRFRLRRRWIDVEGVPCGEIQIIQED 198 (538)
Q Consensus 162 -DGsl~V~v~G~qRfrI~~~~~~~dg~l~AeVeiL~E~ 198 (538)
||.++|+++|.+||+|.+ +.+.+||+.|+|+.++++
T Consensus 77 ~dG~~~Ilv~G~~R~rI~~-~~~~~p~~~A~V~~l~~~ 113 (775)
T TIGR00763 77 GTATYKVVVEGLRRIRIKE-LSDKGGYLVVRVDNLKEE 113 (775)
T ss_pred CCCeEEEEEEEEEEEEEEE-EecCCCcEEEEEEEecCc
Confidence 499999999999999997 788999999999999764
No 5
>COG2802 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]
Probab=99.76 E-value=2.5e-17 Score=160.78 Aligned_cols=115 Identities=29% Similarity=0.479 Sum_probs=100.6
Q ss_pred CCeeeeEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEEEEEeecCCC---CCCcccccceeEEEEEEE
Q 009302 81 GGAILTLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIGVVRVFREPD---NGRITFATIGTTAEIRQY 157 (538)
Q Consensus 81 ~g~~~~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~IgVv~~~k~~~---~~~~~l~~IGT~AeI~~v 157 (538)
...+..||||||++.|||||..+||+||+++|..||+.+++++ +.|||+...++.+ +....+..|||+|+|+++
T Consensus 6 ~~~p~~LplFPL~~~vLlPg~~LpL~IFEpRY~~Mv~~~~~~~---r~fGvv~i~~~~~~~~~~~~~ls~VGcla~I~~~ 82 (221)
T COG2802 6 DDLPLELPLFPLPGAVLLPGGLLPLNIFEPRYLAMVRTCLAEG---RRFGVVLIDRGREVGGGLPPELSDVGCLARITEF 82 (221)
T ss_pred CCccceeeccccccccccCCCCCchhhccHHHHHHHHHHHhcC---CceeEEEecccccccCCCcchhhccceeEEEeEe
Confidence 3457789999999999999999999999999999999999975 8999998744332 233568899999999999
Q ss_pred EECCCCcEEEEEEEeEEEEEeeeeeccCCcceEEEEEecCC
Q 009302 158 RRLEDGSLNVVTRGQQRFRLRRRWIDVEGVPCGEIQIIQED 198 (538)
Q Consensus 158 ~~l~DGsl~V~v~G~qRfrI~~~~~~~dg~l~AeVeiL~E~ 198 (538)
...+||.+.|.++|.+||||.+...+.+||..|+++.++|.
T Consensus 83 ~~~~DGr~~I~~~G~~RFRv~~~~~~~~pyr~~~~~~~~D~ 123 (221)
T COG2802 83 EELGDGRYLILVRGGQRFRVLEELADDDPYRRARVPFWPDL 123 (221)
T ss_pred eEcCCCcEEEEEEeEEEEEEEEEecccCcceeeccccCCCC
Confidence 99999999999999999999996666899999998888774
No 6
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=99.75 E-value=2.6e-17 Score=182.00 Aligned_cols=127 Identities=28% Similarity=0.398 Sum_probs=108.1
Q ss_pred eEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEEEEEeecCCC---CCCcccccceeEEEEEEEEECCC
Q 009302 86 TLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIGVVRVFREPD---NGRITFATIGTTAEIRQYRRLED 162 (538)
Q Consensus 86 ~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~IgVv~~~k~~~---~~~~~l~~IGT~AeI~~v~~l~D 162 (538)
.||++|++++|+||++++||.|.++.++++++.++..+ .+.|++++| ++.. +..+++|.+||+|+|.++.++||
T Consensus 9 ~lpvlplr~~vvfP~m~~pl~vgr~~si~ale~a~~~~--~k~i~l~~q-k~~~~d~p~~~dly~vGt~a~I~q~~~lpd 85 (782)
T COG0466 9 ELPVLPLRDVVVFPGMVIPLFVGREKSIKALEEAMKND--QKYILLVTQ-KDASTDEPTEDDLYEVGTLAKILQILKLPD 85 (782)
T ss_pred cceeEEecCceeCCCceeeEEcCChhHHHHHHHHHhCC--CCEEEEEEe-cccccCCCChhhhhhcchheeeeeeeeCCC
Confidence 79999999999999999999999999999999999875 378999988 5332 56679999999999999999999
Q ss_pred CcEEEEEEEeEEEEEeeeeeccCCcceEEEEEecCCC---------cccCHHHHHHHHHhhcC
Q 009302 163 GSLNVVTRGQQRFRLRRRWIDVEGVPCGEIQIIQEDL---------PLRTPRDVFETLGCVSN 216 (538)
Q Consensus 163 Gsl~V~v~G~qRfrI~~~~~~~dg~l~AeVeiL~E~~---------~~r~l~d~f~~la~l~~ 216 (538)
|+++|+++|++|++|.+ +...++++.|+++.+++.. +.+.+...|.+|+.+++
T Consensus 86 g~~kvlveg~~R~~I~~-~~~~~~~~~a~~~~i~~~~~~~~~~~~al~~~i~~~~~~~~~l~~ 147 (782)
T COG0466 86 GTVKVLVEGLQRVRISK-LSDEEEFFEAEIELLPDEPIDEEREIEALVRSILSEFEEYAKLNK 147 (782)
T ss_pred CcEEEEEEeeeeEEEEe-eccCCCceEEEEEecCCCcccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999998 7888899999999998754 23444455555555544
No 7
>smart00464 LON Found in ATP-dependent protease La (LON). N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs.
Probab=98.61 E-value=2e-07 Score=79.69 Aligned_cols=37 Identities=38% Similarity=0.597 Sum_probs=34.8
Q ss_pred EEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcC
Q 009302 87 LPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQV 123 (538)
Q Consensus 87 LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~ 123 (538)
+|++|++++|+|||+++||.+.+++.+++++++++++
T Consensus 2 lpviPl~~~vlfP~~~~pl~v~~~~~i~~i~~~~~~~ 38 (92)
T smart00464 2 LPLLPIRRRPLFPGFVLPIPVKRPKSVAAIKEALRRS 38 (92)
T ss_pred ceEEEcCCCccCCCceEEEEeCCHHHHHHHHHHHhcC
Confidence 7999999999999999999999999999999988764
No 8
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=98.51 E-value=1.1e-07 Score=82.27 Aligned_cols=91 Identities=18% Similarity=0.285 Sum_probs=66.3
Q ss_pred ceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCCcce
Q 009302 432 LVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETHMGW 511 (538)
Q Consensus 432 ~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~HlGW 511 (538)
+|.|++|.+.|+...++++ .+|.....++|.++.+-...+..-.--.+...|.|+.+.|..|+++|||
T Consensus 2 vf~C~~C~t~l~ds~~lvs------------~~g~~~~a~l~~~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGw 69 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVS------------FHGREGKAYLFNNVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGW 69 (96)
T ss_pred EEECCCCCCCcCCHHHhee------------cCCCCccEEEEeeeeecccccceEEEeeCCCCEEEEEeEcccCChhHCc
Confidence 5899999999999999887 3444446666666544333444444444444499999999999999999
Q ss_pred eEEecCCCCCc-ceeEEEeccccc
Q 009302 512 LFTATKKKLKP-KSFWGIRSSQVA 534 (538)
Q Consensus 512 ~F~a~~~~~~p-~~F~Gl~~~~l~ 534 (538)
+|..+....+. .+.|-|-.+.|.
T Consensus 70 kY~~a~~~~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 70 KYESAPEEQKYKEGKFILEKASIS 93 (96)
T ss_pred EEEEcCHhHhhhCCEEEEEhhHEE
Confidence 99988765544 577887776653
No 9
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=2.2e-06 Score=91.79 Aligned_cols=111 Identities=28% Similarity=0.480 Sum_probs=94.3
Q ss_pred CeeeeEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEEEEEeecCCCCCCcccccceeEEEEEEEEECC
Q 009302 82 GAILTLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIGVVRVFREPDNGRITFATIGTTAEIRQYRRLE 161 (538)
Q Consensus 82 g~~~~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~IgVv~~~k~~~~~~~~l~~IGT~AeI~~v~~l~ 161 (538)
+.....|+|++ .+..||+...|++++++++..|+++++..++ ..+|++.. +...+....+.||++.+|..+..+.
T Consensus 172 ~~e~~~p~f~v-~~~~~p~v~cpl~vfe~~y~lm~~r~~~~~~--~rf~i~~s--d~~~~~~~~~e~g~i~ei~~v~~l~ 246 (398)
T KOG4159|consen 172 SRECESPLFPV-CTLAFPEVPCPLQVFEPRYRLMIRRLLETGD--KRFGICLS--DSSKGSGQAAEIGCILEIRKVESLG 246 (398)
T ss_pred cccccCCcccc-cccccccccCcHHHccchHHHHHHHHHhhcc--eeeeeecc--cccCCcchhhhccchhhhccccccc
Confidence 34567899987 5789999999999999999999999998753 68998764 2222222467899999999999999
Q ss_pred CCcEEEEEEEeEEEEEeeeeeccCCcceEEEEEecCC
Q 009302 162 DGSLNVVTRGQQRFRLRRRWIDVEGVPCGEIQIIQED 198 (538)
Q Consensus 162 DGsl~V~v~G~qRfrI~~~~~~~dg~l~AeVeiL~E~ 198 (538)
||...+...|..||++.. ..+.++|..|+|+.+++.
T Consensus 247 dgrsv~~~~gk~r~r~~~-~~~~d~y~~~~ve~l~d~ 282 (398)
T KOG4159|consen 247 DGRSVVDSIGKSRFRVLL-FSQTDGYPVADVEYLEDR 282 (398)
T ss_pred ccchhhhhhcCcceeeee-ecCCCcceeeeeeeeeCc
Confidence 999999999999999997 789999999999999884
No 10
>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]
Probab=97.32 E-value=0.00072 Score=76.62 Aligned_cols=54 Identities=20% Similarity=0.256 Sum_probs=46.8
Q ss_pred CCeeeeEEEEeeCCceecCCCceeEEecChhHHHHHHHHHhcCCCCcEEEEEEeecC
Q 009302 81 GGAILTLPLFYLDGVVLFPEATLPLRVIKPNFIAAAERALSQVDVPYTIGVVRVFRE 137 (538)
Q Consensus 81 ~g~~~~LPVlpL~~vVLFPG~tlPL~V~~p~~i~aV~~a~~~~da~~~IgVv~~~k~ 137 (538)
.....+||++|++.-+||||..+++.|.+++.+++|++-+... ..++|++.. ++
T Consensus 63 ~~~~~~l~~Lpi~~~pL~PGf~~~i~v~~~~~~~~i~~~l~~~--qpyiG~fl~-kd 116 (906)
T KOG2004|consen 63 PDVPPRLPALPITRGPLFPGFYKRIEVKSPKVLALIREKLRRQ--QPYIGAFLL-KD 116 (906)
T ss_pred cccCcccceeeccCCCcCCCceeEEEecCHHHHHHHHHHHHhc--Ccccceeee-cc
Confidence 3445789999999999999999999999999999999998775 358999987 54
No 11
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=86.29 E-value=0.16 Score=46.26 Aligned_cols=75 Identities=24% Similarity=0.457 Sum_probs=43.8
Q ss_pred CceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCCcc
Q 009302 431 DLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETHMG 510 (538)
Q Consensus 431 ~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~HlG 510 (538)
....|++|.+-+++..|+++-+-.| -+|-. -.|.++.|+. .|+....+=-===++=+-+.|..|++-+|
T Consensus 14 ~~y~C~~C~thla~~~dliSksf~g-------r~G~A---yLf~~vvNv~-~ge~e~R~mlTG~h~V~di~C~~C~~~~G 82 (122)
T KOG3399|consen 14 RLYSCAHCKTHLARHDDLISKSFRG-------RTGRA---YLFNRVVNVI-IGETEQRVMLTGLHTVADIFCVLCGTGLG 82 (122)
T ss_pred ceEeccCCcccccchhhcccccccc-------CCCcc---hhhhhhhhhe-echHHHHHHHHhHHhhcchhhhhcCCCcc
Confidence 3689999999999999988765443 22221 1233333322 12221111100012223478999999999
Q ss_pred eeEEec
Q 009302 511 WLFTAT 516 (538)
Q Consensus 511 W~F~a~ 516 (538)
|+|.-.
T Consensus 83 WkYe~a 88 (122)
T KOG3399|consen 83 WKYEHA 88 (122)
T ss_pred eeeeec
Confidence 999754
No 12
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=85.58 E-value=1.1 Score=41.75 Aligned_cols=66 Identities=20% Similarity=0.301 Sum_probs=42.2
Q ss_pred CCceecccccccccCCCceeeeccCCceeEEeCCC--CceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCC
Q 009302 430 FDLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPH--GCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICET 507 (538)
Q Consensus 430 ~~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~--G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~ 507 (538)
..+..|+.|+.++....+-|.-. ...-+|..|- +.|-+. .+.| -|+.=+-+.|++|++
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~KfdSg--~GWPSF~~~i~~~~V~~~----------------~D~s--~gm~RtEv~C~~Cg~ 97 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSEDKFDSG--CGWPSFYKPISEEVVAYE----------------RDES--HGMIRTEVRCRNCDA 97 (134)
T ss_pred CeEEEccCCCCccccccchhcCC--CCCcCcCcccCCCceEEe----------------ecCC--CCcEEEEEEecCCCC
Confidence 34789999999999988855422 2233454442 111110 1112 256667799999999
Q ss_pred CcceeEEe
Q 009302 508 HMGWLFTA 515 (538)
Q Consensus 508 HlGW~F~a 515 (538)
|||=-|.-
T Consensus 98 HLGHVF~D 105 (134)
T TIGR00357 98 HLGHVFDD 105 (134)
T ss_pred ccCcccCC
Confidence 99999974
No 13
>KOG1400 consensus Predicted ATP-dependent protease PIL, contains LON domain [General function prediction only]
Probab=84.85 E-value=0.12 Score=54.53 Aligned_cols=49 Identities=14% Similarity=0.096 Sum_probs=38.2
Q ss_pred CCCcccccCCCCceEEEeCccCC---CCcceeEEecCCCCC--cceeEEEeccc
Q 009302 484 PAETEYSWFPGYAWTVASCSICE---THMGWLFTATKKKLK--PKSFWGIRSSQ 532 (538)
Q Consensus 484 ~ps~e~SWFpGYaW~ia~C~~C~---~HlGW~F~a~~~~~~--p~~F~Gl~~~~ 532 (538)
.+-..-.||++|.|||+.|..|. .|.+|+|...+.+-. -..|-|++++.
T Consensus 304 ~tRlq~e~~~~~k~ti~fCk~Cqt~ia~~~d~f~msk~g~qee~~np~gyIhei 357 (371)
T KOG1400|consen 304 MTRLQREFFGIQKETITFCKECQTDIAENWDHFPMSKNGPQEEYDNPMGYIHEI 357 (371)
T ss_pred ccchheeeecccchhhhhhHhhchhhhhhhcccccccCCchHhhcChhhHHHHH
Confidence 45667789999999999999999 999999987664321 25677776554
No 14
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=84.45 E-value=1.4 Score=40.20 Aligned_cols=65 Identities=18% Similarity=0.316 Sum_probs=41.5
Q ss_pred cCCceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCC
Q 009302 429 SFDLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETH 508 (538)
Q Consensus 429 ~~~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~H 508 (538)
...+.+|+.|+.++.+..+-|. | ..-.-+|..|-. +.+....- .+ | .=+-+.|++|++|
T Consensus 30 ~~G~Y~C~~Cg~pLF~S~~Kfd-S-g~GWPSF~~~i~---~~v~~~~D------------~~---~-~RtEv~C~~C~~H 88 (119)
T PRK05508 30 EKGTYVCKQCGAPLYRSEDKFK-S-GCGWPSFDDEIK---GAVKRIPD------------AD---G-RRTEIVCANCGGH 88 (119)
T ss_pred CCeEEEecCCCCcccccccccc-C-CCCCcccCcccc---cceEEEec------------CC---C-cEEEEEeCCCCCc
Confidence 3457899999999999888554 2 222455655531 12221111 11 2 1255999999999
Q ss_pred cceeEE
Q 009302 509 MGWLFT 514 (538)
Q Consensus 509 lGW~F~ 514 (538)
||=-|.
T Consensus 89 LGHVF~ 94 (119)
T PRK05508 89 LGHVFE 94 (119)
T ss_pred cCcccC
Confidence 999997
No 15
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=82.60 E-value=1.7 Score=40.78 Aligned_cols=68 Identities=18% Similarity=0.376 Sum_probs=40.8
Q ss_pred CCceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCCc
Q 009302 430 FDLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETHM 509 (538)
Q Consensus 430 ~~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~Hl 509 (538)
..+..|+.|++++....+-|.-. ...-+|..|-- -+.|....- +| .|+.=+-+.|++|++||
T Consensus 41 ~G~Y~C~~Cg~pLF~S~~Kf~Sg--~GWPSF~~~i~--~~~V~~~~D------------~s--~gm~RtEv~C~~Cg~HL 102 (142)
T PRK00222 41 KGIYVCIVCGEPLFSSDTKFDSG--CGWPSFTKPID--EEAIRELRD------------TS--HGMVRTEVRCANCDSHL 102 (142)
T ss_pred CeEEEecCCCchhcCCcccccCC--CCCcCcCcccC--CCceEEeec------------cC--CCceEEEEEeCCCCCcc
Confidence 34789999999999988866422 22334544421 001111110 11 13444669999999999
Q ss_pred ceeEEe
Q 009302 510 GWLFTA 515 (538)
Q Consensus 510 GW~F~a 515 (538)
|=-|.-
T Consensus 103 GHVF~D 108 (142)
T PRK00222 103 GHVFPD 108 (142)
T ss_pred CcccCC
Confidence 999964
No 16
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=78.81 E-value=1.5 Score=40.22 Aligned_cols=64 Identities=23% Similarity=0.469 Sum_probs=41.9
Q ss_pred CceecccccccccCCCceeeeccCCceeEEeCCCCc--eEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCC
Q 009302 431 DLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGC--VHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETH 508 (538)
Q Consensus 431 ~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~--v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~H 508 (538)
.+..|+.|+.++....+-|. +..-.-+|..|.-. |-.. .++|+ |..=+-+.|++|+.|
T Consensus 36 G~Y~C~~Cg~pLF~S~~Kf~--Sg~GWPSF~~~i~~~~v~~~----------------~D~s~--g~~R~Ev~C~~Cg~H 95 (124)
T PF01641_consen 36 GIYVCAVCGTPLFSSDTKFD--SGCGWPSFWQPIPGDAVKER----------------EDFSH--GMVRTEVRCARCGSH 95 (124)
T ss_dssp EEEEETTTS-EEEEGGGEET--SSSSSSEESSCSSTTSEEEE----------------EEECT--SSEEEEEEETTTCCE
T ss_pred EEEEcCCCCCccccCccccc--CCcCCccccCcCChHHEEEe----------------ccccC--CceEEEEEecCCCCc
Confidence 47899999999998887554 22224456665321 1111 12232 566677999999999
Q ss_pred cceeEE
Q 009302 509 MGWLFT 514 (538)
Q Consensus 509 lGW~F~ 514 (538)
||=-|.
T Consensus 96 LGHVF~ 101 (124)
T PF01641_consen 96 LGHVFD 101 (124)
T ss_dssp EEEEES
T ss_pred cccEeC
Confidence 999998
No 17
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=76.41 E-value=3.3 Score=43.15 Aligned_cols=64 Identities=17% Similarity=0.360 Sum_probs=41.0
Q ss_pred CCceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCCc
Q 009302 430 FDLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETHM 509 (538)
Q Consensus 430 ~~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~Hl 509 (538)
..+..|+.|+.++...++-|.-. ...-+|..|-- -.+++... .+ |. =+-+.|++|++||
T Consensus 34 ~G~y~c~~c~~~LF~s~~Kf~sg--~GWPsF~~~~~--~~~~~~~d-------------~~---~~-R~Ev~c~~c~~HL 92 (283)
T PRK05550 34 KGVYLCRRCGAPLFRSEDKFNSG--CGWPSFDDEIP--GAVKRLPD-------------AD---GR-RTEIVCANCGAHL 92 (283)
T ss_pred CcEEEcCCCCchhcCChhhccCC--CCCcCcCcccC--CccEEEEc-------------CC---Cc-eEEEEecCCCCcc
Confidence 35789999999999988855422 22445655531 11221111 11 33 2559999999999
Q ss_pred ceeEE
Q 009302 510 GWLFT 514 (538)
Q Consensus 510 GW~F~ 514 (538)
|--|.
T Consensus 93 GHvF~ 97 (283)
T PRK05550 93 GHVFE 97 (283)
T ss_pred CcccC
Confidence 99997
No 18
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=70.12 E-value=2.5 Score=38.63 Aligned_cols=72 Identities=18% Similarity=0.295 Sum_probs=46.2
Q ss_pred ceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCce-EEEeCccCCCCcc
Q 009302 432 LVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAW-TVASCSICETHMG 510 (538)
Q Consensus 432 ~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW-~ia~C~~C~~HlG 510 (538)
.|+|+.|...++..+||..+ ++..|+.+||. +. +...++.. |....-.|.+|.= ..+.|..|++-.|
T Consensus 4 ~llC~kC~~~~C~~~DIr~i--e~~hhv~v~p~-F~-~~~~~~~~--------~~~~~~~~~d~~~~~~I~C~~C~~~wG 71 (123)
T PF11648_consen 4 KLLCRKCKKFACSGSDIRKI--ENSHHVVVDPE-FW-ERYIVRPH--------PKPLQKSFGDWEPNGKIHCKNCGQDWG 71 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEE--TTTEEEE-SHH-HH-CTEEEEEC--------SSCTSEEESSSEEEEEEEETSTSBEEE
T ss_pred EEECCCCCceeEchhheEEe--cCCcEEEcCcc-ce-eeEEeccC--------CccccceecceEeCCEEEcCCCChHhh
Confidence 58999999999999999887 35678888886 33 22222221 1111122333321 3489999999998
Q ss_pred eeEEe
Q 009302 511 WLFTA 515 (538)
Q Consensus 511 W~F~a 515 (538)
-...-
T Consensus 72 ~~m~y 76 (123)
T PF11648_consen 72 IMMKY 76 (123)
T ss_dssp EEEEE
T ss_pred hheEE
Confidence 87654
No 19
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=62.75 E-value=12 Score=34.95 Aligned_cols=69 Identities=20% Similarity=0.427 Sum_probs=44.8
Q ss_pred CCceecccccccccCCCceeeeccCCceeEEeCCCCceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCCc
Q 009302 430 FDLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPHGCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETHM 509 (538)
Q Consensus 430 ~~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~Hl 509 (538)
..+.+|..|+.++....+-|- +..-.-+|..|-- .+.|+-..- +|- |..=+-+.|++|.+||
T Consensus 40 ~GiY~c~~cg~pLF~S~~Kfd--SgcGWPSF~~pi~--~~~I~~~~D------------~S~--gM~RtEVrc~~c~sHL 101 (140)
T COG0229 40 KGIYVCIVCGEPLFSSEDKFD--SGCGWPSFTKPIS--PDAITYKED------------RSH--GMVRTEVRCANCDSHL 101 (140)
T ss_pred CceEEeecCCCcccccccccc--CCCCCccccccCC--cccceEeec------------cCC--CcEEEEEEecCCCCcc
Confidence 357899999999999888654 2223556666631 122222211 111 4455679999999999
Q ss_pred ceeEEec
Q 009302 510 GWLFTAT 516 (538)
Q Consensus 510 GW~F~a~ 516 (538)
|--|.-.
T Consensus 102 GHVF~DG 108 (140)
T COG0229 102 GHVFPDG 108 (140)
T ss_pred ccccCCC
Confidence 9999754
No 20
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=53.17 E-value=17 Score=41.00 Aligned_cols=65 Identities=15% Similarity=0.253 Sum_probs=41.2
Q ss_pred CceecccccccccCCCceeeeccCCceeEEeCCC--CceEEEEEEeeecCceecCCCCcccccCCCCceEEEeCccCCCC
Q 009302 431 DLVRCKTCKTAIAKRSDMLVMSSEGPLGAYVNPH--GCVHEILTLNKANGLALYGPAETEYSWFPGYAWTVASCSICETH 508 (538)
Q Consensus 431 ~~l~C~~C~~~Ia~~~~~~~ms~~g~~~~~vNP~--G~v~ei~t~~~a~~~~~~G~ps~e~SWFpGYaW~ia~C~~C~~H 508 (538)
.+.+|+.||.++....+-|. | ....-+|.-|. +.+-+ ..++|. |+.=+-+.|+.|++|
T Consensus 417 G~y~c~~c~~pLf~s~~Kf~-s-g~GWPsF~~~i~~~~v~~----------------~~d~s~--g~~R~Ev~c~~c~~H 476 (521)
T PRK14018 417 GIYVDVVSGEPLFSSADKYD-S-GCGWPSFTRPIDAKVVTE----------------HDDFSY--NMRRTEVRSRAADSH 476 (521)
T ss_pred EEEEecCCCCccccCccccc-C-CCCCcccCcccCcCceEE----------------eeccCC--CceEEEEEECCCCCc
Confidence 47899999999999888655 2 22244554442 11100 111222 344467999999999
Q ss_pred cceeEEe
Q 009302 509 MGWLFTA 515 (538)
Q Consensus 509 lGW~F~a 515 (538)
||--|.-
T Consensus 477 LGHvf~d 483 (521)
T PRK14018 477 LGHVFPD 483 (521)
T ss_pred CCcccCC
Confidence 9999964
No 21
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=50.63 E-value=5.9 Score=31.83 Aligned_cols=18 Identities=33% Similarity=0.696 Sum_probs=14.3
Q ss_pred HHhcCCceeccccccccc
Q 009302 426 LLESFDLVRCKTCKTAIA 443 (538)
Q Consensus 426 ~l~~~~~l~C~~C~~~Ia 443 (538)
.|++.|++.|+.||..|-
T Consensus 31 ~lk~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 31 TLKRGDVIRCRECGYRIL 48 (62)
T ss_pred cccCCCcEehhhcchHHH
Confidence 356778999999998873
No 22
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=48.70 E-value=21 Score=35.27 Aligned_cols=52 Identities=12% Similarity=0.186 Sum_probs=32.2
Q ss_pred CCCCceEEEEEEeeecCceec-CCCCcccccCCCCceEEEeCccCCCCcceeEE
Q 009302 462 NPHGCVHEILTLNKANGLALY-GPAETEYSWFPGYAWTVASCSICETHMGWLFT 514 (538)
Q Consensus 462 NP~G~v~ei~t~~~a~~~~~~-G~ps~e~SWFpGYaW~ia~C~~C~~HlGW~F~ 514 (538)
-++|-.|-+..+-....+.+. |.+. -..|-.|-.-+-..|+.|++||-++..
T Consensus 56 K~sGs~fs~~a~vp~d~~~it~g~~~-l~~y~ss~~i~R~FC~~CGS~L~~~~e 108 (191)
T PRK05417 56 KPEGALFSVVAVVPRDNVTVTANGDK-LKVVDESATIQRHACKECGVHMYGRIE 108 (191)
T ss_pred ccccCcceEEEEEEhhheEEEeCCcc-eEEEeCCCCeEeeeCCCCCCccccccc
Confidence 355666666666566566654 5443 222333444456799999999977665
No 23
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=41.31 E-value=37 Score=31.24 Aligned_cols=35 Identities=20% Similarity=0.399 Sum_probs=24.7
Q ss_pred CCCceEEEeCccCCCCcceeEEecCCCCCcceeEEEeccccc
Q 009302 493 PGYAWTVASCSICETHMGWLFTATKKKLKPKSFWGIRSSQVA 534 (538)
Q Consensus 493 pGYaW~ia~C~~C~~HlGW~F~a~~~~~~p~~F~Gl~~~~l~ 534 (538)
.+.+.+. .|+.|++||-|+....+ .|+|+....+.
T Consensus 64 s~~~~r~-FC~~CGs~l~~~~~~~~------~~~~v~~~~ld 98 (133)
T COG3791 64 SGSAGRG-FCPTCGSPLFWRGPDED------PFVGVNAGALD 98 (133)
T ss_pred cCCCCCe-ecccCCCceEEecCCCC------ceEEEEEeeec
Confidence 3444444 89999999999876643 47777766655
No 24
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=35.90 E-value=51 Score=27.04 Aligned_cols=38 Identities=11% Similarity=0.158 Sum_probs=25.6
Q ss_pred CCCceEEEeCccCCCCcceeEEecCCCCCcceeEEEeccccccC
Q 009302 493 PGYAWTVASCSICETHMGWLFTATKKKLKPKSFWGIRSSQVAEG 536 (538)
Q Consensus 493 pGYaW~ia~C~~C~~HlGW~F~a~~~~~~p~~F~Gl~~~~l~~~ 536 (538)
.|-.-+...|+.|+++|.+..... ...++|....|.+.
T Consensus 42 s~~~~~r~FC~~CGs~l~~~~~~~------~~~~~V~~g~ld~~ 79 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSEDERD------PDLVGVNAGTLDDP 79 (92)
T ss_dssp TTSSCEEEEETTT--EEEEEESST------TTEEEEEGGGBTT-
T ss_pred CCCcCcCcccCCCCCeeecccCCC------CCEEEEEeEeeCCC
Confidence 566777899999999999883222 24888887777653
No 25
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=30.43 E-value=55 Score=34.47 Aligned_cols=13 Identities=23% Similarity=0.917 Sum_probs=12.7
Q ss_pred EEEeCccCCCCcc
Q 009302 498 TVASCSICETHMG 510 (538)
Q Consensus 498 ~ia~C~~C~~HlG 510 (538)
..+.|.+|.+.||
T Consensus 192 ~~v~C~~C~~~LG 204 (354)
T PF09814_consen 192 RIVRCKRCSSQLG 204 (354)
T ss_pred cEEEeCCCCceeC
Confidence 8999999999999
No 26
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=26.82 E-value=26 Score=24.76 Aligned_cols=16 Identities=38% Similarity=0.727 Sum_probs=11.8
Q ss_pred HhcCCceecccccccc
Q 009302 427 LESFDLVRCKTCKTAI 442 (538)
Q Consensus 427 l~~~~~l~C~~C~~~I 442 (538)
|+..+.+.|..||..|
T Consensus 12 ~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRI 27 (32)
T ss_dssp BSTSSTSSBSSSS-SE
T ss_pred cCCCCcEECCcCCCeE
Confidence 4556788999999876
No 27
>PF02202 Tachykinin: Tachykinin family; InterPro: IPR002040 This family includes peptides, which belong to the tachykinin family. Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. Tachykinins, like most other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Tachykinins are from ten to twelve residues long.; GO: 0007217 tachykinin receptor signaling pathway, 0007268 synaptic transmission; PDB: 1MYU_A 1N6T_A 2GFR_A.
Probab=25.08 E-value=7.7 Score=21.24 Aligned_cols=8 Identities=50% Similarity=1.331 Sum_probs=6.4
Q ss_pred CcceeEEE
Q 009302 521 KPKSFWGI 528 (538)
Q Consensus 521 ~p~~F~Gl 528 (538)
.|..||||
T Consensus 3 ~pd~F~GL 10 (11)
T PF02202_consen 3 KPDQFYGL 10 (11)
T ss_dssp CHHHHCCC
T ss_pred Ccccceec
Confidence 47789997
No 28
>cd00246 RabGEF Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport;
Probab=23.59 E-value=2.1e+02 Score=25.62 Aligned_cols=68 Identities=21% Similarity=0.366 Sum_probs=39.5
Q ss_pred ceeccccccccc--CCCceeeeccC------------C----ce--eEEeCCCCceEEEEEEeeecCceecCCCCccccc
Q 009302 432 LVRCKTCKTAIA--KRSDMLVMSSE------------G----PL--GAYVNPHGCVHEILTLNKANGLALYGPAETEYSW 491 (538)
Q Consensus 432 ~l~C~~C~~~Ia--~~~~~~~ms~~------------g----~~--~~~vNP~G~v~ei~t~~~a~~~~~~G~ps~e~SW 491 (538)
.++|.+|++.|- .....+....+ . +. .-+|| -=+.||-+.|++..+
T Consensus 2 ~v~C~~C~S~VL~~~~~~~~~~~~e~~lp~~~~k~~~~~~~e~~~~~~~v~-Dm~~FeNigfs~~~~------------- 67 (103)
T cd00246 2 AVLCQRCGSRVLTIQPGTVLFLPRQLFLPSMRKKPGSNPDGDLLEDHWLVV-DMFTFENVGFSKDVG------------- 67 (103)
T ss_pred ceECCCCCCEEEecCCCccEechhhhcchhhhhccCCCCCcceeeeeEEec-ccceeeeeeeccCCC-------------
Confidence 478999999876 44433322111 0 11 12333 344566666655543
Q ss_pred CCCCceEEEeCccCC-CCcceeEEecC
Q 009302 492 FPGYAWTVASCSICE-THMGWLFTATK 517 (538)
Q Consensus 492 FpGYaW~ia~C~~C~-~HlGW~F~a~~ 517 (538)
++ ....|+.|. ..|||+...++
T Consensus 68 --~~--k~L~CadCe~GPiG~~~~~~~ 90 (103)
T cd00246 68 --NL--KYLVCADCEKGPIGYHCLDDK 90 (103)
T ss_pred --Ce--eEEEeccCCCCceEeEeeccc
Confidence 22 678899995 46999997644
No 29
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.09 E-value=30 Score=26.92 Aligned_cols=19 Identities=32% Similarity=0.593 Sum_probs=12.1
Q ss_pred HHHHhcCCceecccccccc
Q 009302 424 IELLESFDLVRCKTCKTAI 442 (538)
Q Consensus 424 l~~l~~~~~l~C~~C~~~I 442 (538)
+++++....+.|..||+.|
T Consensus 16 ~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 16 VELDQETRGIRCPYCGSRI 34 (49)
T ss_pred eehhhccCceeCCCCCcEE
Confidence 3455555667777777665
Done!