Query 029820
Match_columns 187
No_of_seqs 126 out of 1060
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:10:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029820.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029820hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05697 Trigger_N: Bacterial 100.0 5.8E-28 1.3E-32 190.6 12.3 124 34-172 1-130 (145)
2 COG0544 Tig FKBP-type peptidyl 99.9 3.6E-25 7.8E-30 204.1 14.9 129 34-177 1-135 (441)
3 PRK01490 tig trigger factor; P 99.9 2.8E-24 6.1E-29 195.3 14.5 127 34-175 1-133 (435)
4 TIGR00115 tig trigger factor. 99.9 2E-21 4.4E-26 175.1 12.8 114 46-174 1-120 (408)
5 PHA00440 host protein H-NS-int 67.1 56 0.0012 25.1 8.9 62 55-124 19-82 (98)
6 PF06857 ACP: Malonate decarbo 48.5 85 0.0018 23.3 6.2 60 33-98 15-78 (87)
7 COG0199 RpsN Ribosomal protein 44.1 14 0.0003 26.0 1.3 18 62-80 41-58 (61)
8 PF10458 Val_tRNA-synt_C: Valy 41.4 24 0.00051 24.4 2.2 33 60-100 15-47 (66)
9 PF11247 DUF2675: Protein of u 36.1 2E+02 0.0043 22.1 9.4 70 46-124 11-82 (98)
10 PF07708 Tash_PEST: Tash prote 33.5 21 0.00046 19.7 0.7 17 164-180 2-18 (19)
11 cd04915 ACT_AK-Ectoine_2 ACT d 25.4 93 0.002 21.0 3.0 58 11-68 5-64 (66)
12 PRK13253 citrate lyase subunit 24.7 3.1E+02 0.0066 20.6 6.1 60 33-98 16-79 (92)
13 PF00344 SecY: SecY translocas 23.6 1.3E+02 0.0028 27.0 4.4 40 63-108 269-308 (346)
14 cd04937 ACT_AKi-DapG-BS_2 ACT 23.4 85 0.0018 20.8 2.5 58 11-68 4-62 (64)
15 PRK10788 periplasmic folding c 23.4 2.7E+02 0.0059 26.8 6.8 64 50-127 48-112 (623)
16 cd04917 ACT_AKiii-LysC-EC_2 AC 23.3 1.6E+02 0.0035 19.2 3.9 57 12-68 5-62 (64)
17 cd04920 ACT_AKiii-DAPDC_2 ACT 21.3 1.5E+02 0.0032 19.8 3.4 58 11-68 3-61 (63)
18 TIGR02920 acc_sec_Y2 accessory 21.1 1E+02 0.0023 28.5 3.3 36 65-106 303-338 (395)
19 COG2036 HHT1 Histones H3 and H 20.9 2.4E+02 0.0052 21.2 4.7 33 88-121 22-54 (91)
No 1
>PF05697 Trigger_N: Bacterial trigger factor protein (TF); InterPro: IPR008881 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This group of sequences contain the ribosomal subunit association domain.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 2D3O_1 1W26_A 1P9Y_A 1OMS_C 1T11_A 3GU0_A 2NSB_A 2NSC_A 3GTY_X.
Probab=99.95 E-value=5.8e-28 Score=190.60 Aligned_cols=124 Identities=24% Similarity=0.498 Sum_probs=107.6
Q ss_pred cEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHH
Q 029820 34 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVR 113 (187)
Q Consensus 34 M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~eai~~li~ 113 (187)
|+++++..+++.+.++|+|++++|+.+++++|++++++++ |||||| | |||+++|+++||.+ |++++++++++
T Consensus 1 M~v~~~~~~~~~~~~~v~v~~~~~~~~~~~~l~~~~k~~~-ipGFRk--G----K~P~~vi~~~~g~~-i~~~~~~~~~~ 72 (145)
T PF05697_consen 1 MKVTVEKIEDSKVKLEVEVPAEEVEKAYEKALKELAKKVK-IPGFRK--G----KAPRNVIEKRYGKE-IREEAIEELLQ 72 (145)
T ss_dssp -EEEEEEESTTEEEEEEEE-HHHHHHHHHHHHHHHHTTTT-BTTS-T--T----SS-HHHHHHHHCHH-HHHHHHHHHHH
T ss_pred CccEEEECCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCC-CCCCCC--C----CCCHHHHHHHHHHH-HHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999 999999 9 99999999999996 99999999999
Q ss_pred HHHHHHHHHcCCccCCCCceeehhhhhhhhccCCCCcEEEEEEEEee------cCCccccccccc
Q 029820 114 STLTDYTKKEGLNVKDKKVTTTQKAEELRKSFYPGNEFGFSAVLELE------KSEVEESETETS 172 (187)
Q Consensus 114 ~~~~eAike~~l~pv~~~P~i~~~fe~l~~~~~~g~~~~ft~~veV~------~~e~~~~~~~~~ 172 (187)
.+|.+|+++++++|++ +|.+. ...+.++++|+|+++|++. +++++..+.+..
T Consensus 73 ~~~~~~~~~~~~~~i~-~p~i~------~~~~~~~~~~~~~~~~~~~Pev~l~~~~~i~v~~~~~ 130 (145)
T PF05697_consen 73 EAYEEAIKEEKIKPIG-DPEIE------EKDFKEGEDFEFEVEFEVFPEVELKDYKGIKVEKPEV 130 (145)
T ss_dssp HHHHHHHHHTTS-ESS-EEEEE------EEEEETTS-EEEEEEEEE--ECEETTCTTSEEEEEEH
T ss_pred HHHHHHHHHcCCCccc-ccccc------ccccccCCCEEEEEEEEecCCcccCCCCCceeeeccc
Confidence 9999999999999999 99986 3678999999999999987 455555544443
No 2
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=3.6e-25 Score=204.14 Aligned_cols=129 Identities=29% Similarity=0.485 Sum_probs=120.7
Q ss_pred cEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHH
Q 029820 34 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVR 113 (187)
Q Consensus 34 M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~eai~~li~ 113 (187)
|++++++++++.+.|+|+||++.|++++++++++++++++ |||||| | |||+.+++++|| .+|++++++++|+
T Consensus 1 M~v~~e~~~~~~~~l~v~vp~~~~~~~~~~~~~~~~k~v~-IpGFRk--G----KvP~~ii~~ryg-~~v~~d~~~~ll~ 72 (441)
T COG0544 1 MKVTVEKLEGLEVRLTVEVPAEEIKKALDKALKKLAKKVK-IPGFRK--G----KVPRKVIEQRYG-EAVRQDVLNELLP 72 (441)
T ss_pred CCeeeeecCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCc-CCCCCC--C----CCCHHHHHHHHh-HHHHHHHHHHHHH
Confidence 8899999999999999999999999999999999999999 999999 9 999999999999 4899999999999
Q ss_pred HHHHHHHHHcCCccCCCCceeehhhhhhhhccCCCCcEEEEEEEEee------cCCcccccccccCCCCC
Q 029820 114 STLTDYTKKEGLNVKDKKVTTTQKAEELRKSFYPGNEFGFSAVLELE------KSEVEESETETSSSSSS 177 (187)
Q Consensus 114 ~~~~eAike~~l~pv~~~P~i~~~fe~l~~~~~~g~~~~ft~~veV~------~~e~~~~~~~~~~~~~~ 177 (187)
.+|.+|+++++++|++ +|.+. ...++.|++|.|+++|+|+ ++..+++++.+.+.++.
T Consensus 73 ~~~~~a~~e~~~~~~~-~p~~~------~~~~e~~~~~~f~~~~ev~Pev~l~d~~~i~v~~~~~ev~d~ 135 (441)
T COG0544 73 EAFEEAIKEEGLKPAG-QPEIE------ITEFEKGEDFEFTAEVEVYPEVELGDYKGIEVEKPVVEVTDE 135 (441)
T ss_pred HHHHHHHHHhCcCcCC-CCCcc------cccccCCCceEEEEEEEEeeceecCccccceeecCCcccCHH
Confidence 9999999999999999 99776 4678999999999999997 67888888888888743
No 3
>PRK01490 tig trigger factor; Provisional
Probab=99.92 E-value=2.8e-24 Score=195.33 Aligned_cols=127 Identities=24% Similarity=0.407 Sum_probs=114.0
Q ss_pred cEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHH
Q 029820 34 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVR 113 (187)
Q Consensus 34 M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~eai~~li~ 113 (187)
|+++++.+++|++.|+|+||+++|+.++++++++++++++ |||||| | |||++||+++||.. |++++++.+|+
T Consensus 1 M~v~~~~~~~~~~~l~v~v~~~~~~~~~~~~~~~~~k~~~-ipGFRk--G----kvP~~ii~k~~g~~-i~~e~~~~li~ 72 (435)
T PRK01490 1 MQVTVEKLEGLERRLTITVPAEEIEKAVDKALKKLAKTVR-IPGFRK--G----KVPRKIVEQRYGES-VRQEALNDLLP 72 (435)
T ss_pred CcceEEEcCCcEEEEEEEEcHHHHHHHHHHHHHHHHhhCc-CCCccC--C----CCCHHHHHHHHhHH-HHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999 999999 9 99999999999985 99999999999
Q ss_pred HHHHHHHHHcCCccCCCCceeehhhhhhhhccCCCCcEEEEEEEEee------cCCcccccccccCCC
Q 029820 114 STLTDYTKKEGLNVKDKKVTTTQKAEELRKSFYPGNEFGFSAVLELE------KSEVEESETETSSSS 175 (187)
Q Consensus 114 ~~~~eAike~~l~pv~~~P~i~~~fe~l~~~~~~g~~~~ft~~veV~------~~e~~~~~~~~~~~~ 175 (187)
.+|.+|+++++++|++ +|.+. ...++++++|+|+++|+|. +|.++........++
T Consensus 73 ~~~~~~i~~~~~~~~~-~p~i~------~~~~~~~~~~~~~~~~~v~Pev~l~~y~~i~v~~~~~~vt 133 (435)
T PRK01490 73 EAYEEAIKEEGIRPAG-QPEIE------PTEEEKGKDLEFTAEVEVYPEVELGDYKGLEVEKPVVEVT 133 (435)
T ss_pred HHHHHHHHHcCCCcCC-CCccc------ccccCCCCcEEEEEEeeecCCcccCCCCceEEEeccCCCC
Confidence 9999999999999999 99997 2467888999999999997 344455544444333
No 4
>TIGR00115 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.
Probab=99.86 E-value=2e-21 Score=175.11 Aligned_cols=114 Identities=25% Similarity=0.421 Sum_probs=101.1
Q ss_pred EEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHcCC
Q 029820 46 IQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVRSTLTDYTKKEGL 125 (187)
Q Consensus 46 ~~l~V~V~~~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~eai~~li~~~~~eAike~~l 125 (187)
+.|+|+||+++|+.++++++++++++++ |||||| | |||++||+++||. .|++++++.+|+.+|.+|++++++
T Consensus 1 ~~l~v~v~~~~~~~~~~k~~~~~~k~~~-ipGFRk--G----KvP~~~i~k~~g~-~i~~e~~~~li~~~~~~~~~~~~~ 72 (408)
T TIGR00115 1 RKLTVEVPAEEVEEEVDKALKELAKKVK-IPGFRK--G----KVPRSVVEKRYGK-EVRQEALNELLQEAFSEAVKEEKI 72 (408)
T ss_pred CeEEEEECHHHHHHHHHHHHHHHHhhCC-CCCccC--C----CCCHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 3689999999999999999999999999 999999 9 9999999999998 599999999999999999999999
Q ss_pred ccCCCCceeehhhhhhhhccCCCCcEEEEEEEEee------cCCcccccccccCC
Q 029820 126 NVKDKKVTTTQKAEELRKSFYPGNEFGFSAVLELE------KSEVEESETETSSS 174 (187)
Q Consensus 126 ~pv~~~P~i~~~fe~l~~~~~~g~~~~ft~~veV~------~~e~~~~~~~~~~~ 174 (187)
+|+| +|.+. ...+.+|++|+|+++|++. .+.+++.......+
T Consensus 73 ~~~~-~p~~~------~~~~~~~~~~~~~~~~~v~Pev~l~~y~~i~v~~~~~~v 120 (408)
T TIGR00115 73 RPIG-QPEIE------VKEIEDGKDLEFTAEFEVYPEVELGDYKGIEVEKPEVEV 120 (408)
T ss_pred CcCC-CCccc------cccccCCCCEEEEEEEEecCceecCCCCceEEEeccCCC
Confidence 9999 99986 2467889999999999997 44555555444433
No 5
>PHA00440 host protein H-NS-interacting protein
Probab=67.08 E-value=56 Score=25.12 Aligned_cols=62 Identities=23% Similarity=0.451 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHh--CHHHHHHHHHHHHHHHHHHHHHHHcC
Q 029820 55 DATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQIL--GEERVTKFVVQEIVRSTLTDYTKKEG 124 (187)
Q Consensus 55 ~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~y--G~e~I~~eai~~li~~~~~eAike~~ 124 (187)
.+.++.+.+.|.+|++.+. . |-+.+.--+.++.+-+ |++.+...++.+=+++.+.+.+.+++
T Consensus 19 se~e~~~~e~l~~Lak~v~------~--GE~~~~~~re~lvqaLT~G~egai~F~~k~giRe~IKe~~~E~~ 82 (98)
T PHA00440 19 SETEAILEEDILDLAKQAG------A--GEEVNPKDKELLVQALTHGPEGAAAFAVRQGIREAIKDMHEEST 82 (98)
T ss_pred hHHHHHHHHHHHHHHhhcC------C--cccCChHHHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHhHhhc
Confidence 5677889999999999996 2 5343334567887765 77767767766666666666666644
No 6
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=48.47 E-value=85 Score=23.31 Aligned_cols=60 Identities=15% Similarity=0.197 Sum_probs=42.6
Q ss_pred CcEEEEEecCCceEEEEEEeC-HHHHHHHHHHHHHHHhhcCCCCCCCCC---CCCCCCCCCcHHHHHHHh
Q 029820 33 DAKIVVESQDEDKIQVRVDLT-GDATQRVFDKVLTNLARSAPPIPGFRR---EKGGKTTKVPRDFLIQIL 98 (187)
Q Consensus 33 ~M~Vtve~l~~~~~~l~V~V~-~~~v~~~~~kal~~lak~ak~IPGFRk---~kG~k~~KvP~~viek~y 98 (187)
|+.|+++..++..+.+.++-+ ...+...+++.+.+..+... |++=+- -|| +=..+|+.+.
T Consensus 15 D~~V~v~p~~~~gi~i~l~S~v~~~fg~~i~~vi~~~l~~~~-i~~~~v~i~D~G-----Ald~vi~aRl 78 (87)
T PF06857_consen 15 DLEVTVEPAESGGIEIELESSVVKQFGDQIRAVIRETLEELG-IEDAKVEINDKG-----ALDCVIRARL 78 (87)
T ss_pred cEEEEEEeCCCCcEEEEEEchHHhhhHHHHHHHHHHHHHhcC-CCceEEEEEeCC-----CCHHHHHHHH
Confidence 478889888778888888888 67777777888888877777 766431 226 4555665555
No 7
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=44.11 E-value=14 Score=26.02 Aligned_cols=18 Identities=28% Similarity=0.576 Sum_probs=15.8
Q ss_pred HHHHHHHhhcCCCCCCCCC
Q 029820 62 DKVLTNLARSAPPIPGFRR 80 (187)
Q Consensus 62 ~kal~~lak~ak~IPGFRk 80 (187)
-.+++++|-+=+ ||||+|
T Consensus 41 R~cfRE~A~~g~-ipGv~K 58 (61)
T COG0199 41 RICFRELAHKGE-IPGVKK 58 (61)
T ss_pred HHHHHHHhhccC-CCCeEe
Confidence 357889999999 999998
No 8
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=41.39 E-value=24 Score=24.38 Aligned_cols=33 Identities=15% Similarity=0.264 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCH
Q 029820 60 VFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGE 100 (187)
Q Consensus 60 ~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~ 100 (187)
.+++-+..+.++++ -|||-. |||..||++.-..
T Consensus 15 kl~~~i~~~~~kL~-n~~F~~-------kAP~eVve~er~k 47 (66)
T PF10458_consen 15 KLEKEIERLEKKLS-NENFVE-------KAPEEVVEKEREK 47 (66)
T ss_dssp HHHHHHHHHHHHHC-STTHHH-------HS-CCHHHHHHHH
T ss_pred HHHHHHHHHHHHHc-Cccccc-------cCCHHHHHHHHHH
Confidence 45666777888888 899999 8999999986643
No 9
>PF11247 DUF2675: Protein of unknown function (DUF2675) ; InterPro: IPR022611 Members in this family of proteins include Bacteriophage T7 gene 5.5; they have no known function.
Probab=36.15 E-value=2e+02 Score=22.10 Aligned_cols=70 Identities=24% Similarity=0.425 Sum_probs=45.8
Q ss_pred EEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHh--CHHHHHHHHHHHHHHHHHHHHHHHc
Q 029820 46 IQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQIL--GEERVTKFVVQEIVRSTLTDYTKKE 123 (187)
Q Consensus 46 ~~l~V~V~~~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~y--G~e~I~~eai~~li~~~~~eAike~ 123 (187)
..++..++.+.+ +.+.+.+..+++.+- . |-|.+.--+.++.+-+ |++.+...++..-+++.+.+.+.++
T Consensus 11 F~vtav~~se~e-~~~~e~ll~Lak~v~------~--GE~~~~~~re~l~qaLT~G~egav~f~~k~g~R~~IKe~~~E~ 81 (98)
T PF11247_consen 11 FDVTAVIDSEQE-EEFEEDLLELAKKVG------A--GEKVSGFQREMLVQALTHGPEGAVAFVVKQGIREAIKEMLSEY 81 (98)
T ss_pred EEEEEEeCHHHH-HHHHHHHHHHHhhcC------C--ccccCHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456666776666 556677778888885 1 3222223456777754 7877777777777777777777766
Q ss_pred C
Q 029820 124 G 124 (187)
Q Consensus 124 ~ 124 (187)
+
T Consensus 82 s 82 (98)
T PF11247_consen 82 S 82 (98)
T ss_pred c
Confidence 5
No 10
>PF07708 Tash_PEST: Tash protein PEST motif; InterPro: IPR011695 The PEST motif is found in one or more copies in Tash AT-hook proteins from Theileria annulata. Tash proteins are transported to the host nucleus and are thought to be involved in pathogenesis []. The PEST motif is often found in conjunction with the (IPR007480 from INTERPRO), whose function is unknown. These repeats may be part of the PEST motif (a signal for rapid proteolytic degradation) [], though this is not proven. This motif is also found in other T. annulata proteins, which have no other known domains.
Probab=33.49 E-value=21 Score=19.70 Aligned_cols=17 Identities=35% Similarity=0.261 Sum_probs=12.1
Q ss_pred cccccccccCCCCCccc
Q 029820 164 VEESETETSSSSSSDEE 180 (187)
Q Consensus 164 ~~~~~~~~~~~~~~~~~ 180 (187)
..+||+=+++.+|++|+
T Consensus 2 ~lePEti~vEi~SDeee 18 (19)
T PF07708_consen 2 ELEPETIPVEIGSDEEE 18 (19)
T ss_pred CcCCceEEEEecccccC
Confidence 45677777777777665
No 11
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=25.38 E-value=93 Score=21.01 Aligned_cols=58 Identities=12% Similarity=0.166 Sum_probs=39.0
Q ss_pred eeeccCCCccccCCccccccc--cCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029820 11 VSAVDSGVEVSITEPEDLITV--KDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 68 (187)
Q Consensus 11 ~~~~~sg~~~~~~~~~~~~~~--~~M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~l 68 (187)
+|.+..|+..++...+=|.-. ...++.....+.+...+.+-|+.++..++++.....+
T Consensus 5 VsvVG~gm~~~gv~~ki~~~L~~~~I~v~~i~~~~s~~~is~~V~~~~~~~av~~Lh~~f 64 (66)
T cd04915 5 VSVIGRDLSTPGVLARGLAALAEAGIEPIAAHQSMRNVDVQFVVDRDDYDNAIKALHAAL 64 (66)
T ss_pred EEEECCCCCcchHHHHHHHHHHHCCCCEEEEEecCCeeEEEEEEEHHHHHHHHHHHHHHH
Confidence 566777776555444322212 2244444667778899999999999999988877654
No 12
>PRK13253 citrate lyase subunit gamma; Provisional
Probab=24.69 E-value=3.1e+02 Score=20.62 Aligned_cols=60 Identities=13% Similarity=0.168 Sum_probs=39.2
Q ss_pred CcEEEEEecCCceEEEEEEeCHH-HHHHHHHHHHHHHhhcCCCCCCCCC---CCCCCCCCCcHHHHHHHh
Q 029820 33 DAKIVVESQDEDKIQVRVDLTGD-ATQRVFDKVLTNLARSAPPIPGFRR---EKGGKTTKVPRDFLIQIL 98 (187)
Q Consensus 33 ~M~Vtve~l~~~~~~l~V~V~~~-~v~~~~~kal~~lak~ak~IPGFRk---~kG~k~~KvP~~viek~y 98 (187)
++.|.++...+..+.+.|+-+.. .+...+++.+.+...... +++=+- -|| +=..+|+.+.
T Consensus 16 Dl~V~veP~~~~~i~i~i~SsV~~~Fg~~i~~vv~~~l~~~~-v~~~~i~i~D~G-----Ald~vI~aRl 79 (92)
T PRK13253 16 DVMIRIAPADTQGIDIQLESSVEKQFGDQIRAVILETLAKLG-VENAQVKVDDKG-----ALDCVIRARL 79 (92)
T ss_pred CEEEEEEeCCCCcEEEEEEeeHHhhhHHHHHHHHHHHHHhcC-CCceEEEEEcCC-----CCHHHHHHHH
Confidence 47788888754567777777776 677777777777777776 655431 226 5556665555
No 13
>PF00344 SecY: SecY translocase; InterPro: IPR002208 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The eubacterial secY protein [] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions. Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export []. Homologs of secY are found in archaebacteria []. SecY is also encoded in the chloroplast genome of some algae [] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0015031 protein transport, 0016020 membrane; PDB: 3J01_A 2ZJS_Y 2ZQP_Y 2WWA_A 2WW9_A 2YXR_A 1RHZ_A 3KCR_A 3DKN_A 2YXQ_A ....
Probab=23.64 E-value=1.3e+02 Score=27.05 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=26.7
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHHHH
Q 029820 63 KVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVV 108 (187)
Q Consensus 63 kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~eai 108 (187)
+.-++++|.=.-|||+|| | |.-.+.+.++.-.-.+.....
T Consensus 269 ~iA~~lkk~g~~I~Girp--G----~~T~~yL~~~i~~~~~~G~~~ 308 (346)
T PF00344_consen 269 DIAENLKKSGDYIPGIRP--G----KPTEKYLNKVIPRLSFLGALF 308 (346)
T ss_dssp HHHHHCHCTTSSSSTCTT--S----CHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCEeCCCCC--C----hhHHHHHHHHHHHHhhhhHHH
Confidence 344566665434999999 9 888888888775544444433
No 14
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=23.41 E-value=85 Score=20.77 Aligned_cols=58 Identities=9% Similarity=0.134 Sum_probs=34.9
Q ss_pred eeeccCCCc-cccCCccccccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029820 11 VSAVDSGVE-VSITEPEDLITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 68 (187)
Q Consensus 11 ~~~~~sg~~-~~~~~~~~~~~~~~M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~l 68 (187)
+|.+.+|+. .++.-.+=|.....-.+.+.....+...+.+-|+.++..++++...+.+
T Consensus 4 isvvG~~~~~~~gi~~~if~aL~~~~I~v~~~~~Se~~is~~v~~~~~~~av~~Lh~~f 62 (64)
T cd04937 4 VTIIGSRIRGVPGVMAKIVGALSKEGIEILQTADSHTTISCLVSEDDVKEAVNALHEAF 62 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHHCCCCEEEEEcCccEEEEEEcHHHHHHHHHHHHHHh
Confidence 455566663 2333333222233333444444458899999999999988887766554
No 15
>PRK10788 periplasmic folding chaperone; Provisional
Probab=23.39 E-value=2.7e+02 Score=26.82 Aligned_cols=64 Identities=11% Similarity=0.229 Sum_probs=41.6
Q ss_pred EEeCHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHHHHH-HHHHHHcCCcc
Q 029820 50 VDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVRSTL-TDYTKKEGLNV 127 (187)
Q Consensus 50 V~V~~~~v~~~~~kal~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~eai~~li~~~~-~eAike~~l~p 127 (187)
-.|+..+++.+++.....+..... + ..+.......+.. .+.+++++.||++.+ .+..++.||.+
T Consensus 48 ~~Is~~e~~~~~~~~~~~~~~~~g---------~----~~~~~~~~~~~~~-~l~~qvl~~LI~~~Ll~q~A~~lgi~v 112 (623)
T PRK10788 48 QEISRAQLEQAFQSERNRLQQQLG---------D----QFSELAANEGYMK-QLRQQVLNRLIDEALLDQYARELGLGI 112 (623)
T ss_pred EEeCHHHHHHHHHHHHHHHHHHhc---------c----ccchhhcChhHHH-HHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 357888898888888777776543 2 2222222222323 578888888888775 67777788765
No 16
>cd04917 ACT_AKiii-LysC-EC_2 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The second ACT domain (ACT2), this CD, is not involved in the binding of heterotrophic effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.33 E-value=1.6e+02 Score=19.21 Aligned_cols=57 Identities=9% Similarity=0.149 Sum_probs=36.3
Q ss_pred eeccCCC-ccccCCccccccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029820 12 SAVDSGV-EVSITEPEDLITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 68 (187)
Q Consensus 12 ~~~~sg~-~~~~~~~~~~~~~~~M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~l 68 (187)
+.+-.|+ ..++...+=|.......+..-..+.+...+++-|+.++.++++....+.+
T Consensus 5 svvG~~~~~~~~v~~~i~~~L~~i~i~~i~~~~s~~~is~~V~~~~~~~a~~~Lh~~f 62 (64)
T cd04917 5 ALIGNDISETAGVEKRIFDALEDINVRMICYGASNHNLCFLVKEEDKDEVVQRLHSRL 62 (64)
T ss_pred EEECCCccCCcCHHHHHHHHHHhCCeEEEEEecCccEEEEEEeHHHHHHHHHHHHHHH
Confidence 4455555 23333333222233455666677788999999999999888887766554
No 17
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.34 E-value=1.5e+02 Score=19.76 Aligned_cols=58 Identities=16% Similarity=0.188 Sum_probs=37.2
Q ss_pred eeeccCCCc-cccCCccccccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029820 11 VSAVDSGVE-VSITEPEDLITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 68 (187)
Q Consensus 11 ~~~~~sg~~-~~~~~~~~~~~~~~M~Vtve~l~~~~~~l~V~V~~~~v~~~~~kal~~l 68 (187)
+|.+-+|+. .++.-.+=|......++.+-....+...+++-|+.++..+++...-..+
T Consensus 3 VsvVG~g~~~~~gv~~~~~~~L~~~~i~~i~~~~s~~~is~vv~~~d~~~av~~LH~~f 61 (63)
T cd04920 3 VSLVGRGIRSLLHKLGPALEVFGKKPVHLVSQAANDLNLTFVVDEDQADGLCARLHFQL 61 (63)
T ss_pred EEEECCCcccCccHHHHHHHHHhcCCceEEEEeCCCCeEEEEEeHHHHHHHHHHHHHHH
Confidence 455666663 2332222121223356677778889999999999999988887765543
No 18
>TIGR02920 acc_sec_Y2 accessory Sec system translocase SecY2. Members of this family are restricted to the Firmicutes lineage (low-GC Gram-positive bacteria) and appear to be paralogous to, and much more divergent than, the preprotein translocase SecY. Members include the SecY2 protein of the accessory Sec system in Streptococcus gordonii, involved in export of the highly glycosylated platelet-binding protein GspB.
Probab=21.09 E-value=1e+02 Score=28.49 Aligned_cols=36 Identities=19% Similarity=0.180 Sum_probs=23.5
Q ss_pred HHHHhhcCCCCCCCCCCCCCCCCCCcHHHHHHHhCHHHHHHH
Q 029820 65 LTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKF 106 (187)
Q Consensus 65 l~~lak~ak~IPGFRk~kG~k~~KvP~~viek~yG~e~I~~e 106 (187)
-++++|+=--|||+|| | |.-.+.+++....-.+..-
T Consensus 303 A~~Lkk~g~~IpGiRp--G----~~T~~yL~~~i~~~t~~Ga 338 (395)
T TIGR02920 303 SKSFRKSGNYIPGIAP--G----KDTQRYLNRLARRFCWFGG 338 (395)
T ss_pred HHHHHHCCCCccCcCC--C----chHHHHHHHHHHHHHHHHH
Confidence 3444444433999999 9 7778888887755434333
No 19
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=20.90 E-value=2.4e+02 Score=21.19 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=21.8
Q ss_pred CCcHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHH
Q 029820 88 KVPRDFLIQILGEERVTKFVVQEIVRSTLTDYTK 121 (187)
Q Consensus 88 KvP~~viek~yG~e~I~~eai~~li~~~~~eAik 121 (187)
++|..=|.+..|.+.|..+|.+.+ ++++.+++.
T Consensus 22 ~apv~Ri~r~~~~~Rvs~~A~~~l-~~~~e~~~~ 54 (91)
T COG2036 22 KAPVRRILRKAGAERVSSSAIEEL-QEALEEYLE 54 (91)
T ss_pred chHHHHHHHHHhHHHhhHHHHHHH-HHHHHHHHH
Confidence 678888888888887777666544 444444443
Done!