Query 031606
Match_columns 156
No_of_seqs 166 out of 1022
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:51:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031606hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0721 GatC Asp-tRNAAsn/Glu-t 99.9 1.2E-21 2.7E-26 144.4 8.2 81 56-137 1-81 (96)
2 PRK00034 gatC aspartyl/glutamy 99.9 4.1E-21 8.8E-26 138.5 9.2 81 56-137 1-81 (95)
3 TIGR00135 gatC glutamyl-tRNA(G 99.9 3.9E-21 8.5E-26 138.7 9.1 78 58-136 1-78 (93)
4 PRK12821 aspartyl/glutamyl-tRN 99.8 5.9E-20 1.3E-24 165.9 9.5 82 55-136 386-467 (477)
5 PRK12820 bifunctional aspartyl 99.6 3.2E-15 6.9E-20 141.2 9.1 81 54-136 608-691 (706)
6 PF02686 Glu-tRNAGln: Glu-tRNA 99.6 3.6E-15 7.8E-20 101.9 4.6 62 74-136 1-62 (72)
7 TIGR01827 gatC_rel Asp-tRNA(As 98.3 1.1E-06 2.4E-11 62.4 4.8 51 83-136 3-56 (73)
8 KOG4247 Mitochondrial DNA poly 96.7 0.0055 1.2E-07 48.8 6.2 80 54-136 44-123 (175)
9 PF13318 DUF4089: Protein of u 78.6 9.2 0.0002 25.3 5.5 41 63-103 2-42 (50)
10 COG3079 Uncharacterized protei 73.4 4.9 0.00011 33.4 3.8 38 59-96 127-165 (186)
11 PRK02166 hypothetical protein; 68.2 5.4 0.00012 32.6 3.0 37 59-95 126-162 (184)
12 PF13833 EF-hand_8: EF-hand do 60.9 12 0.00027 23.2 3.0 31 56-86 3-34 (54)
13 PRK04758 hypothetical protein; 60.1 11 0.00023 30.9 3.2 38 58-95 123-161 (181)
14 PRK01736 hypothetical protein; 58.4 12 0.00026 30.5 3.3 37 59-95 128-165 (190)
15 PF07128 DUF1380: Protein of u 53.3 16 0.00035 29.1 3.2 91 57-151 26-116 (139)
16 PRK07235 amidase; Provisional 50.2 32 0.00069 31.7 5.0 51 56-107 4-54 (502)
17 PF05397 Med15_fungi: Mediator 46.1 14 0.0003 28.0 1.7 38 61-98 14-53 (115)
18 COG4860 Uncharacterized protei 39.2 23 0.00049 29.0 2.0 73 2-91 51-125 (170)
19 PF11181 YflT: Heat induced st 37.4 30 0.00064 25.1 2.3 22 67-88 75-96 (103)
20 PRK01546 hypothetical protein; 30.6 74 0.0016 23.1 3.4 24 58-81 2-29 (79)
21 PRK02539 hypothetical protein; 30.5 72 0.0016 23.6 3.3 23 59-81 2-28 (85)
22 PF02969 TAF: TATA box binding 29.9 1.5E+02 0.0031 20.6 4.6 37 55-91 1-38 (66)
23 cd04766 HTH_HspR Helix-Turn-He 28.6 1.4E+02 0.0031 20.8 4.5 58 36-96 20-81 (91)
24 PF09677 TrbI_Ftype: Type-F co 28.4 1.1E+02 0.0023 23.2 4.0 37 64-102 44-80 (111)
25 TIGR03798 ocin_TIGR03798 bacte 28.2 82 0.0018 21.0 3.1 29 58-86 25-53 (64)
26 PF06580 His_kinase: Histidine 28.2 1.3E+02 0.0029 20.8 4.3 32 61-94 16-47 (82)
27 PF04201 TPD52: Tumour protein 27.4 91 0.002 25.5 3.7 30 70-99 22-51 (162)
28 PRK13717 conjugal transfer pro 27.2 1.1E+02 0.0025 24.1 4.1 29 64-92 58-86 (128)
29 PRK06474 hypothetical protein; 26.6 60 0.0013 25.9 2.6 25 70-94 132-156 (178)
30 PF07308 DUF1456: Protein of u 26.0 91 0.002 21.6 3.1 30 56-85 12-41 (68)
31 TIGR02744 TrbI_Ftype type-F co 24.6 1.3E+02 0.0029 23.0 4.0 28 64-91 45-72 (112)
32 PTZ00373 60S Acidic ribosomal 24.0 1.3E+02 0.0029 23.0 3.9 45 55-99 17-67 (112)
33 cd02062 Nitro_FMN_reductase Pr 23.7 86 0.0019 21.8 2.7 27 45-75 6-32 (122)
34 PF09754 PAC2: PAC2 family; I 22.8 1.4E+02 0.0031 23.5 4.1 41 58-98 179-219 (219)
35 PRK10870 transcriptional repre 22.1 1.4E+02 0.003 23.5 3.9 28 73-100 142-169 (176)
36 cd01279 HTH_HspR-like Helix-Tu 21.9 2.1E+02 0.0046 20.4 4.5 61 36-99 20-84 (98)
37 TIGR00268 conserved hypothetic 21.8 26 0.00057 29.0 -0.4 42 56-97 177-238 (252)
38 PF15036 IL34: Interleukin 34; 21.7 28 0.00061 28.6 -0.2 81 58-139 44-155 (169)
39 cd00051 EFh EF-hand, calcium b 21.3 1.8E+02 0.0038 16.6 4.3 32 54-85 13-44 (63)
40 PF14394 DUF4423: Domain of un 20.7 1.2E+02 0.0027 24.1 3.3 38 43-91 116-153 (171)
41 PF15335 CAAP1: Caspase activi 20.7 59 0.0013 22.8 1.3 16 126-141 9-24 (64)
42 cd04411 Ribosomal_P1_P2_L12p R 20.4 1.7E+02 0.0037 21.9 3.8 31 57-87 16-46 (105)
43 PRK09706 transcriptional repre 20.1 1.4E+02 0.0031 22.1 3.4 39 57-97 84-122 (135)
No 1
>COG0721 GatC Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.2e-21 Score=144.44 Aligned_cols=81 Identities=21% Similarity=0.306 Sum_probs=76.8
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHHHh
Q 031606 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLIIQ 135 (156)
Q Consensus 56 m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL~~ 135 (156)
|+||+++|+|||+||||+++++|++.|..+|++|++||++|++|||+||+|++|+.+.. ..+|+|++..+.+++++|+|
T Consensus 1 ~~i~~e~v~~la~LarL~lseee~e~~~~~l~~Il~~veql~evD~~~vep~~~~~~~~-~~lReD~~~~~~~~~~~l~n 79 (96)
T COG0721 1 MAIDREEVKHLAKLARLELSEEELEKFATQLEDILGYVEQLNEVDTEGVEPTTHPLEVS-NVLREDEVTEGLDREELLAN 79 (96)
T ss_pred CccCHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHHHHHHHHhccccCCCccccccccc-ccccCCCCCCCcCHHHHHhc
Confidence 67999999999999999999999999999999999999999999999999999998865 45999999999999999999
Q ss_pred hh
Q 031606 136 LF 137 (156)
Q Consensus 136 ~f 137 (156)
|=
T Consensus 80 ap 81 (96)
T COG0721 80 AP 81 (96)
T ss_pred CC
Confidence 73
No 2
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=99.85 E-value=4.1e-21 Score=138.50 Aligned_cols=81 Identities=21% Similarity=0.297 Sum_probs=76.5
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHHHh
Q 031606 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLIIQ 135 (156)
Q Consensus 56 m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL~~ 135 (156)
|+|++++|+|||+||||+|+++|++.+.++|++|++||++|+++||+||+|+.|+.+. ...+|+|++.++.+++++|.|
T Consensus 1 M~i~~e~i~~la~La~l~l~~ee~~~~~~~l~~il~~~~~l~~vd~~~vep~~~~~~~-~~~lReD~~~~~~~~e~~l~n 79 (95)
T PRK00034 1 MAITREEVKHLAKLARLELSEEELEKFAGQLNKILDFVEQLNEVDTEGVEPTTHPLDM-KNVLREDVVTESLPREEALKN 79 (95)
T ss_pred CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCcccCcccc-cCCCCCCCCCCCCCHHHHHhc
Confidence 6899999999999999999999999999999999999999999999999999999764 456999999999999999998
Q ss_pred hh
Q 031606 136 LF 137 (156)
Q Consensus 136 ~f 137 (156)
|-
T Consensus 80 ap 81 (95)
T PRK00034 80 AP 81 (95)
T ss_pred Cc
Confidence 84
No 3
>TIGR00135 gatC glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, C subunit. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model.
Probab=99.85 E-value=3.9e-21 Score=138.73 Aligned_cols=78 Identities=22% Similarity=0.325 Sum_probs=73.9
Q ss_pred CChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHHHhh
Q 031606 58 LEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLIIQL 136 (156)
Q Consensus 58 I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL~~~ 136 (156)
||+++|+|||+||||+|+++|++.+.++|++|++||++|+++||+||+||+|+.... ..+|+|++.++.+++.+|.||
T Consensus 1 i~~~~v~~lA~La~L~l~eee~~~~~~~l~~il~~~~~L~~vdt~~v~p~~~~~~~~-~~lReD~~~~~~~~e~~l~na 78 (93)
T TIGR00135 1 ISDEEVKHLAKLARLELSEEEAESFAGDLDKILGFVEQLNEVDTENVEPMTHPLEIS-NVLREDEPEEPLSRDDILKNA 78 (93)
T ss_pred CCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhcCccCCCCcccCccccc-cCCCCCCCCCCCCHHHHHhcC
Confidence 689999999999999999999999999999999999999999999999999997654 469999999999999999987
No 4
>PRK12821 aspartyl/glutamyl-tRNA amidotransferase subunit C-like protein; Provisional
Probab=99.81 E-value=5.9e-20 Score=165.86 Aligned_cols=82 Identities=16% Similarity=0.209 Sum_probs=76.6
Q ss_pred CCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHHH
Q 031606 55 RSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLII 134 (156)
Q Consensus 55 ~m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL~ 134 (156)
++++|+|+|+|+|+||||+++|||+|++.+||++|++|+|+|+||||+|||||.|+.+...+.+|||+|+++.++|++|.
T Consensus 386 k~~ItkEeVkKLAkLARLeLSEEElEkl~~dLn~ILdyVEkLnEVDTegVEPM~hp~e~~~nvLREDeV~~sl~rEeaLs 465 (477)
T PRK12821 386 KQQLNKDELKKLARLVMFDLDDAELEKLQVEFKDITSSFKQVEKIDTTNVKPMYAPFSNSPTPLRKDKDVVQKHQKILLK 465 (477)
T ss_pred cccCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcccCcCCCCCcccCcccccCCCCCCCCCCCCCHHHHHh
Confidence 36899999999999999999999999999999999999999999999999999999643345699999999999999999
Q ss_pred hh
Q 031606 135 QL 136 (156)
Q Consensus 135 ~~ 136 (156)
||
T Consensus 466 NA 467 (477)
T PRK12821 466 NC 467 (477)
T ss_pred cC
Confidence 87
No 5
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=99.59 E-value=3.2e-15 Score=141.17 Aligned_cols=81 Identities=10% Similarity=0.096 Sum_probs=73.3
Q ss_pred CCCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCC---ChH
Q 031606 54 TRSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICA---GGT 130 (156)
Q Consensus 54 ~~m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~---~~~ 130 (156)
..-.=++++|+|||+||||+|+|+|++.+.+||++||+||++|++||| +|+||.|+.+..+ .+|+|+|+++. +++
T Consensus 608 ~~~~~~~~~V~~iA~LARL~l~eeE~~~~~~~L~~IL~~ve~L~evdt-~VeP~~~~~~~~~-~lReD~v~~~~~~~~~e 685 (706)
T PRK12820 608 PGDAEKEDLIDHLSWVSRIGFAEAERAAIESALADAEELAAQLEDIAC-DEEPLFSPAPAAN-RMGEGLEARECSFAATG 685 (706)
T ss_pred cccccchHHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhccC-CCCCCcCcccccc-CCCCCcCCCCCCccCHH
Confidence 334668999999999999999999999999999999999999999999 5999999976644 59999999997 599
Q ss_pred HHHHhh
Q 031606 131 SLIIQL 136 (156)
Q Consensus 131 ~LL~~~ 136 (156)
++|.||
T Consensus 686 ~~L~nA 691 (706)
T PRK12820 686 EILKNA 691 (706)
T ss_pred HHHhcC
Confidence 999986
No 6
>PF02686 Glu-tRNAGln: Glu-tRNAGln amidotransferase C subunit; InterPro: IPR003837 Glu-tRNAGln amidotransferase is a heterotrimeric enzyme that is required for correct decoding of glutamine codons during translation. The Glu-tRNA Gln amidotransferase enzyme is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln []. This activity supplements the lack of glutaminyl-tRNA synthetase activity in Gram-positive eubacteria, cyanobacteria, archaea, and organelles [].; GO: 0006450 regulation of translational fidelity; PDB: 2DQN_C 3IP4_C 2G5I_C 2F2A_C 2G5H_C 2DF4_C 3AL0_C 3KFU_G 3H0R_I 3H0L_U ....
Probab=99.56 E-value=3.6e-15 Score=101.93 Aligned_cols=62 Identities=18% Similarity=0.289 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHHHhh
Q 031606 74 LTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLIIQL 136 (156)
Q Consensus 74 LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL~~~ 136 (156)
|+|+|++.+.++|++|++||++|++|||+||+||+|+.+. ...+|+|++.++.+++++|.||
T Consensus 1 l~eeE~~~~~~~l~~il~~~~~l~~vdt~~v~p~~~~~~~-~~~lReD~~~~~~~~e~iL~nA 62 (72)
T PF02686_consen 1 LTEEELEKLTKQLNDILDYVEKLQEVDTEGVEPMYHPVEM-SNPLREDEVEESLDREEILKNA 62 (72)
T ss_dssp --HHHHHHHHHHHHHHHHHHTTGGGS--TT----S-SS-S-S--EB-S-----CTHHHHHTT-
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCcccccccc-cCCCCCCCCCCCCCHHHHHhcc
Confidence 6899999999999999999999999999999999999764 4569999999999999999987
No 7
>TIGR01827 gatC_rel Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase, subunit C, putative. This model represents a family small family related to GatC, the third subunit of an enzyme for completing the charging of tRNA(Gln) by amidating the Glu-tRNA(Gln). The few known archaea that contain a member of this family appear to produce Asn-tRNA(Asn) by an analogous amidotransferase reaction. This protein is proposed to substitute for GatC in the charging of both tRNAs.
Probab=98.30 E-value=1.1e-06 Score=62.35 Aligned_cols=51 Identities=10% Similarity=0.155 Sum_probs=40.8
Q ss_pred HHHHHHHHH-HHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCC--hHHHHHhh
Q 031606 83 APKIRQVID-WFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAG--GTSLIIQL 136 (156)
Q Consensus 83 ~~qLn~ILe-~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~--~~~LL~~~ 136 (156)
.++-..|++ |-++|++|| ||+||+|+.... +.+|+|+++++.+ ++.+|.||
T Consensus 3 ~~~~~~~~~~~~e~L~evd--~VeP~~~~~~~~-n~lReD~~~~s~~~~re~iL~NA 56 (73)
T TIGR01827 3 LKEAEEILEEFSERLEDVD--EEEETYYISDGS-NKFREDEEPRCDPEFKKKMLENA 56 (73)
T ss_pred HHHHHHHHHHHHHHHHccC--CCCCcccccccc-cCCCCCcCCCCcchhHHHHHHcC
Confidence 344455553 557899999 999999997643 4699999999998 99999987
No 8
>KOG4247 consensus Mitochondrial DNA polymerase accessory subunit [Replication, recombination and repair]
Probab=96.67 E-value=0.0055 Score=48.83 Aligned_cols=80 Identities=13% Similarity=0.118 Sum_probs=66.0
Q ss_pred CCCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHH
Q 031606 54 TRSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLI 133 (156)
Q Consensus 54 ~~m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL 133 (156)
.|.+|+.+.+.|+..|+-..++.|+. ...|..-+.-...|.-||++|||||-...+..+-...+|+-...+.-++..
T Consensus 44 pmpqidaklinhlerlslvrfdseqa---vanlrssirvakrlelvdvegvepmhtvwedqecptfedveedplpieevf 120 (175)
T KOG4247|consen 44 PMPQIDAKLINHLERLSLVRFDSEQA---VANLRSSIRVAKRLELVDVEGVEPMHTVWEDQECPTFEDVEEDPLPIEEVF 120 (175)
T ss_pred CcchhhHHHHHHHHhhhheeecHHHH---HHHHHHHHhHHhheeeeeccCccchhhhcccccCCcccccccCCcCHHHHH
Confidence 56689999999999999999887765 667888888899999999999999966655555557789988888888777
Q ss_pred Hhh
Q 031606 134 IQL 136 (156)
Q Consensus 134 ~~~ 136 (156)
+||
T Consensus 121 rna 123 (175)
T KOG4247|consen 121 RNA 123 (175)
T ss_pred hcc
Confidence 775
No 9
>PF13318 DUF4089: Protein of unknown function (DUF4089)
Probab=78.64 E-value=9.2 Score=25.26 Aligned_cols=41 Identities=10% Similarity=0.101 Sum_probs=37.6
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 031606 63 VPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDS 103 (156)
Q Consensus 63 VkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTeg 103 (156)
|+..+.+--|.|+++-.+....+|..|..+.+.+.+..+.+
T Consensus 2 v~~~a~llgL~l~~~~r~~V~~n~~ri~~mA~~v~~fpL~~ 42 (50)
T PF13318_consen 2 VDQMAALLGLPLDEEWRPGVVANFERIAAMAQLVMEFPLPD 42 (50)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCCc
Confidence 56789999999999999999999999999999999988754
No 10
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.41 E-value=4.9 Score=33.41 Aligned_cols=38 Identities=16% Similarity=0.327 Sum_probs=32.8
Q ss_pred ChhHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHHHh
Q 031606 59 EPPDVPRLAQTARISLTP-HEVEEFAPKIRQVIDWFGQL 96 (156)
Q Consensus 59 ~kEeVkkIA~LARL~LsE-EEle~~~~qLn~ILe~~d~L 96 (156)
..|-++-++++|++..+| ++.|+....+.+|++|+...
T Consensus 127 ~~EaldDL~~iaQlg~Deded~EE~~~~leEiiEyvRva 165 (186)
T COG3079 127 AGEALDDLANIAQLGYDEDEDQEELEESLEEIIEYVRVA 165 (186)
T ss_pred HHHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHHHH
Confidence 356688899999999998 88999999999999999753
No 11
>PRK02166 hypothetical protein; Reviewed
Probab=68.19 E-value=5.4 Score=32.65 Aligned_cols=37 Identities=14% Similarity=0.176 Sum_probs=31.3
Q ss_pred ChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHH
Q 031606 59 EPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQ 95 (156)
Q Consensus 59 ~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~ 95 (156)
.+|-++.++.+|+++.++++-+.-...+.+|++|+..
T Consensus 126 ~~E~l~Dl~~Iaql~~d~dd~ee~E~al~Ei~EyvRv 162 (184)
T PRK02166 126 AKEVLQDLAAISQVQDALEESEDGETDYMEVMEYLRV 162 (184)
T ss_pred HHHHHHHHHHHHccCCCCCCCchHHHHHHHHHHHHHH
Confidence 5677889999999999877777888889999999863
No 12
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=60.90 E-value=12 Score=23.16 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=25.9
Q ss_pred CCCChhHHHHHHHHcCCC-CCHHHHHHHHHHH
Q 031606 56 SSLEPPDVPRLAQTARIS-LTPHEVEEFAPKI 86 (156)
Q Consensus 56 m~I~kEeVkkIA~LARL~-LsEEEle~~~~qL 86 (156)
..|+.++++++...-.+. ++++|++.+...+
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~ 34 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEEVDRLFREF 34 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHHHHHHHHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHHHHHHHHhc
Confidence 468999999999777888 9999998877654
No 13
>PRK04758 hypothetical protein; Validated
Probab=60.13 E-value=11 Score=30.94 Aligned_cols=38 Identities=16% Similarity=0.145 Sum_probs=31.0
Q ss_pred CChhHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHHH
Q 031606 58 LEPPDVPRLAQTARISLTP-HEVEEFAPKIRQVIDWFGQ 95 (156)
Q Consensus 58 I~kEeVkkIA~LARL~LsE-EEle~~~~qLn~ILe~~d~ 95 (156)
=.+|-++.++.+|++++++ ++-+.-...+.+|++|+..
T Consensus 123 e~~E~L~Dl~~Iaql~~d~~ed~ee~E~al~El~EyvRv 161 (181)
T PRK04758 123 EGEEALQDLARLAQASSDDFDAAEEDDTALAEIEEFVRV 161 (181)
T ss_pred HHHHHHHHHHHHHccCCCcccCchHHHHHHHHHHHHHHH
Confidence 3567789999999999884 4567788899999999863
No 14
>PRK01736 hypothetical protein; Reviewed
Probab=58.40 E-value=12 Score=30.53 Aligned_cols=37 Identities=19% Similarity=0.357 Sum_probs=31.0
Q ss_pred ChhHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHHH
Q 031606 59 EPPDVPRLAQTARISLTP-HEVEEFAPKIRQVIDWFGQ 95 (156)
Q Consensus 59 ~kEeVkkIA~LARL~LsE-EEle~~~~qLn~ILe~~d~ 95 (156)
.+|-++.++.+|++++++ ++-+.....+.+|++|+..
T Consensus 128 ~~E~l~Dl~~Ia~~~~d~~ed~ee~e~~~~Ei~EyvR~ 165 (190)
T PRK01736 128 TGEAIDDLRNIAQLGYDEDEDQEELAQSLEEVIEYVRV 165 (190)
T ss_pred HHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHHHHH
Confidence 477899999999999875 4667888999999999864
No 15
>PF07128 DUF1380: Protein of unknown function (DUF1380); InterPro: IPR009811 This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Probab=53.26 E-value=16 Score=29.10 Aligned_cols=91 Identities=16% Similarity=0.090 Sum_probs=53.5
Q ss_pred CCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccccCCCCCCCCCCcccCCCChHHHHHhh
Q 031606 57 SLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPALRAGSKREKNTLCYYPRICAGGTSLIIQL 136 (156)
Q Consensus 57 ~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm~r~dev~~s~~ReDep~~~~~~~~LL~~~ 136 (156)
-.|++||.++|.=.-.++|++|++.+...+.++-..-..=..|....|..+..... ...+.+..|-.--+.+++.+
T Consensus 26 IWT~eDV~~~a~gme~~lTd~E~~aVL~~I~~~~~~~~~~~GVs~~~V~el~~~~r----~~~R~VtVPA~lLe~vl~~A 101 (139)
T PF07128_consen 26 IWTREDVRALADGMEYNLTDDEARAVLARIGDIPEDQRHEEGVSSGTVMELIREVR----RAARQVTVPADLLERVLRLA 101 (139)
T ss_pred EecHHHHHHHHhcCCCCCCHHHHHHHHHHHhcCccccchhccccHHHHHHHHHHHH----hcCCcccccHHHHHHHHHHH
Confidence 46999999999877899999999988877766533211001121222222222110 01134444444455677777
Q ss_pred hhheeeeeeeeecCC
Q 031606 137 FCLLSVRVYCKWNAS 151 (156)
Q Consensus 137 f~~~~~~~~~~~~~~ 151 (156)
=+-|--|-|--|.+.
T Consensus 102 ~~~L~~~~~~a~~~~ 116 (139)
T PF07128_consen 102 EQALWKREWAAWDAG 116 (139)
T ss_pred HHHHhhhhhhhcccC
Confidence 777777777777654
No 16
>PRK07235 amidase; Provisional
Probab=50.23 E-value=32 Score=31.73 Aligned_cols=51 Identities=14% Similarity=0.330 Sum_probs=42.9
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCc
Q 031606 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLDSVDPA 107 (156)
Q Consensus 56 m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTegVEPm 107 (156)
...++++++.+|.--.++|++++++.+..-++.-++-.|.++++ .+-+++.
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 54 (502)
T PRK07235 4 KRPTLEQLREIAAQFGLDLTDEELASYLSLMQASLDAYDRIDEL-PDEIPPV 54 (502)
T ss_pred CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHhccCHHHHHHHH-hhccccc
Confidence 35799999999998899999999999999999888888888877 4455544
No 17
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=46.06 E-value=14 Score=28.03 Aligned_cols=38 Identities=11% Similarity=0.291 Sum_probs=29.3
Q ss_pred hHHHHHHHHcCCC--CCHHHHHHHHHHHHHHHHHHHHhcc
Q 031606 61 PDVPRLAQTARIS--LTPHEVEEFAPKIRQVIDWFGQLQD 98 (156)
Q Consensus 61 EeVkkIA~LARL~--LsEEEle~~~~qLn~ILe~~d~L~e 98 (156)
|..+.--.|.-+. +++||.+.+.+++.++.+++..++.
T Consensus 14 e~~~~~~~l~~v~~~ls~eeK~~i~~~l~~~~~m~~~vd~ 53 (115)
T PF05397_consen 14 EVSRNPVRLSPVTNSLSPEEKAAIRQQLQEIQDMLARVDS 53 (115)
T ss_pred HHHhcCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333334556666 9999999999999999999888765
No 18
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.22 E-value=23 Score=29.01 Aligned_cols=73 Identities=25% Similarity=0.283 Sum_probs=42.4
Q ss_pred CccceeeeecCCCCceeecccCCccCCC--CCCcccccccccccccCCCCccCCCCCCCChhHHHHHHHHcCCCCCHHHH
Q 031606 2 GSRGLLLLKGAAPKHHIFNNTKGSIFSS--KMPTRYYYYDYDYNNRTRNCSTTTTRSSLEPPDVPRLAQTARISLTPHEV 79 (156)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~st~~~~m~I~kEeVkkIA~LARL~LsEEEl 79 (156)
|+|||+.||-+-- +.++-..++. +-.+-||.| ||--.-.-..+-+|+..|-.++- +++||+
T Consensus 51 g~RaL~iLkkagm-----lEtqWr~p~~G~kPeKeYHts----------Yt~VqiNf~~Sl~dL~dii~~~f--~sdeev 113 (170)
T COG4860 51 GRRALLILKKAGM-----LETQWRTPSNGQKPEKEYHTS----------YTNVQINFMGSLSDLADIIYAAF--LSDEEV 113 (170)
T ss_pred hHHHHHHHHhhcc-----hhheeeccCCCCCchhhhhhh----------eeeEEEEEEEeHHHHHHHHHHHh--CCHHHH
Confidence 6889988887653 2222222221 111234332 44433334568888888888775 478888
Q ss_pred HHHHHHHHHHHH
Q 031606 80 EEFAPKIRQVID 91 (156)
Q Consensus 80 e~~~~qLn~ILe 91 (156)
+.+..++...++
T Consensus 114 ~ey~~ei~~l~e 125 (170)
T COG4860 114 KEYEDEIKALME 125 (170)
T ss_pred HHHHHHHHHHHH
Confidence 887777665543
No 19
>PF11181 YflT: Heat induced stress protein YflT
Probab=37.39 E-value=30 Score=25.06 Aligned_cols=22 Identities=18% Similarity=0.431 Sum_probs=20.1
Q ss_pred HHHcCCCCCHHHHHHHHHHHHH
Q 031606 67 AQTARISLTPHEVEEFAPKIRQ 88 (156)
Q Consensus 67 A~LARL~LsEEEle~~~~qLn~ 88 (156)
++|.++.|+++|.+.+.+++.+
T Consensus 75 ~~l~~lGl~~~ea~~y~~~l~~ 96 (103)
T PF11181_consen 75 SKLESLGLSEDEAERYEEELDQ 96 (103)
T ss_pred HHHHHcCCCHHHHHHHHHHHHC
Confidence 8999999999999999998863
No 20
>PRK01546 hypothetical protein; Provisional
Probab=30.58 E-value=74 Score=23.14 Aligned_cols=24 Identities=33% Similarity=0.289 Sum_probs=16.4
Q ss_pred CChhHHHHHHHHcCC----CCCHHHHHH
Q 031606 58 LEPPDVPRLAQTARI----SLTPHEVEE 81 (156)
Q Consensus 58 I~kEeVkkIA~LARL----~LsEEEle~ 81 (156)
++++.+.+|=.||+. .||++|.++
T Consensus 2 ~~~~~i~RINeLakK~K~~gLT~eEk~E 29 (79)
T PRK01546 2 LSHELVERINFLAKKAKAEGLTEEEQRE 29 (79)
T ss_pred CcHHHHHHHHHHHHhhcccCCCHHHHHH
Confidence 466667777666665 588888753
No 21
>PRK02539 hypothetical protein; Provisional
Probab=30.54 E-value=72 Score=23.57 Aligned_cols=23 Identities=30% Similarity=0.486 Sum_probs=15.6
Q ss_pred ChhHHHHHHHHcCC----CCCHHHHHH
Q 031606 59 EPPDVPRLAQTARI----SLTPHEVEE 81 (156)
Q Consensus 59 ~kEeVkkIA~LARL----~LsEEEle~ 81 (156)
+++.+.+|=.||+. .||++|.++
T Consensus 2 ~~~~I~RINeLakK~K~~gLT~eEk~E 28 (85)
T PRK02539 2 DPKKIARINELAKKKKTEGLTGEEKVE 28 (85)
T ss_pred CHHHHHHHHHHHHHhcccCCCHHHHHH
Confidence 56666777666665 588888753
No 22
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=29.92 E-value=1.5e+02 Score=20.61 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=24.4
Q ss_pred CCCCChhHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHH
Q 031606 55 RSSLEPPDVPRLAQTARI-SLTPHEVEEFAPKIRQVID 91 (156)
Q Consensus 55 ~m~I~kEeVkkIA~LARL-~LsEEEle~~~~qLn~ILe 91 (156)
|..+++|.|+-+|.-.-| +|+|+-...++++.+--|.
T Consensus 1 ~s~~~~esvk~iAes~Gi~~l~de~a~~La~dveyrlr 38 (66)
T PF02969_consen 1 MSVFSQESVKDIAESLGISNLSDEAAKALAEDVEYRLR 38 (66)
T ss_dssp -----HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHH
T ss_pred CCcCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 345789999999999999 9999999988888765443
No 23
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.60 E-value=1.4e+02 Score=20.79 Aligned_cols=58 Identities=14% Similarity=0.194 Sum_probs=36.0
Q ss_pred ccccccccccCCCCccCCCCCCCChhHHHHHH---HHcC-CCCCHHHHHHHHHHHHHHHHHHHHh
Q 031606 36 YYYDYDYNNRTRNCSTTTTRSSLEPPDVPRLA---QTAR-ISLTPHEVEEFAPKIRQVIDWFGQL 96 (156)
Q Consensus 36 ~~~~~~~~~~~~~~st~~~~m~I~kEeVkkIA---~LAR-L~LsEEEle~~~~qLn~ILe~~d~L 96 (156)
||-..|+.++.+ +..+....+.++|..+. .|.+ ++++-+++..+..-.+++-..-.+|
T Consensus 20 ~ye~~Gli~p~r---~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~~l 81 (91)
T cd04766 20 LYERLGLLSPSR---TDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAEL 81 (91)
T ss_pred HHHHCCCcCCCc---CCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 455568887643 33455567777776655 4556 8899888887776444444443333
No 24
>PF09677 TrbI_Ftype: Type-F conjugative transfer system protein (TrbI_Ftype); InterPro: IPR014115 This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [, ].
Probab=28.36 E-value=1.1e+02 Score=23.20 Aligned_cols=37 Identities=30% Similarity=0.425 Sum_probs=27.6
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 031606 64 PRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQDVDLD 102 (156)
Q Consensus 64 kkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~eVDTe 102 (156)
..+..+|+-+++|++.+....+|+..|+- .|.+.-.+
T Consensus 44 ~f~~~~a~~~lt~~q~~a~t~~F~~aL~~--~L~~~~~~ 80 (111)
T PF09677_consen 44 EFVQQLARSSLTPEQVEALTQRFMQALEA--SLAEYQAE 80 (111)
T ss_pred HHHHHHhccCCCHHHHHHHHHHHHHHHHH--HHHHHHHc
Confidence 34666899999999999999999888863 34443333
No 25
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=28.23 E-value=82 Score=20.99 Aligned_cols=29 Identities=21% Similarity=0.355 Sum_probs=23.7
Q ss_pred CChhHHHHHHHHcCCCCCHHHHHHHHHHH
Q 031606 58 LEPPDVPRLAQTARISLTPHEVEEFAPKI 86 (156)
Q Consensus 58 I~kEeVkkIA~LARL~LsEEEle~~~~qL 86 (156)
-+.+++-.||+=+-.++|++|++....+|
T Consensus 25 ~~~e~~~~lA~~~Gf~ft~~el~~~~~el 53 (64)
T TIGR03798 25 EDPEDRVAIAKEAGFEFTGEDLKEAGEEL 53 (64)
T ss_pred CCHHHHHHHHHHcCCCCCHHHHHHHHhhC
Confidence 46889999999999999999998754443
No 26
>PF06580 His_kinase: Histidine kinase; InterPro: IPR010559 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain IPR003594 from INTERPRO and/or IPR003660 from INTERPRO.; GO: 0000155 two-component sensor activity, 0000160 two-component signal transduction system (phosphorelay), 0016021 integral to membrane
Probab=28.22 E-value=1.3e+02 Score=20.80 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=26.6
Q ss_pred hHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHH
Q 031606 61 PDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFG 94 (156)
Q Consensus 61 EeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d 94 (156)
..+..|..+++.+ .++...+...|.+++.|.=
T Consensus 16 NtLn~I~~l~~~~--~~~~~~~i~~ls~~lRy~l 47 (82)
T PF06580_consen 16 NTLNSISWLARID--PEKASEMILSLSDLLRYSL 47 (82)
T ss_pred HHHHHHHHHHHcC--HHHHHHHHHHHHHHHHHHh
Confidence 3567788889888 8889999999999998864
No 27
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=27.39 E-value=91 Score=25.50 Aligned_cols=30 Identities=23% Similarity=0.324 Sum_probs=25.8
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHhccC
Q 031606 70 ARISLTPHEVEEFAPKIRQVIDWFGQLQDV 99 (156)
Q Consensus 70 ARL~LsEEEle~~~~qLn~ILe~~d~L~eV 99 (156)
+.-.|+|+|.+++..+|.++-+-+..|.+|
T Consensus 22 ~~~~LsEeE~eeLr~EL~KvEeEI~TLrqv 51 (162)
T PF04201_consen 22 SEEGLSEEEREELRSELAKVEEEIQTLRQV 51 (162)
T ss_pred CcccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899999999999999999888888776
No 28
>PRK13717 conjugal transfer protein TrbI; Provisional
Probab=27.15 E-value=1.1e+02 Score=24.10 Aligned_cols=29 Identities=3% Similarity=0.183 Sum_probs=24.8
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 031606 64 PRLAQTARISLTPHEVEEFAPKIRQVIDW 92 (156)
Q Consensus 64 kkIA~LARL~LsEEEle~~~~qLn~ILe~ 92 (156)
..+..++..+++|++.+.+...|+..|+-
T Consensus 58 ~F~~Q~~~~~lte~q~e~lt~rF~~aL~~ 86 (128)
T PRK13717 58 AFFDSASQKQLSEAQSKALSARFNTALEA 86 (128)
T ss_pred HHHHHHhccCCCHHHHHHHHHHHHHHHHH
Confidence 45777899999999999999999888763
No 29
>PRK06474 hypothetical protein; Provisional
Probab=26.65 E-value=60 Score=25.93 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=21.4
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHH
Q 031606 70 ARISLTPHEVEEFAPKIRQVIDWFG 94 (156)
Q Consensus 70 ARL~LsEEEle~~~~qLn~ILe~~d 94 (156)
..|.||++|.++|.++|.++++=..
T Consensus 132 ~~L~Lt~ee~~el~~el~~ll~~y~ 156 (178)
T PRK06474 132 VELKLDEEEFEEFQSELNELMIKYY 156 (178)
T ss_pred eeEecCHHHHHHHHHHHHHHHHHHH
Confidence 3577999999999999999887654
No 30
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=26.00 E-value=91 Score=21.64 Aligned_cols=30 Identities=17% Similarity=0.225 Sum_probs=26.1
Q ss_pred CCCChhHHHHHHHHcCCCCCHHHHHHHHHH
Q 031606 56 SSLEPPDVPRLAQTARISLTPHEVEEFAPK 85 (156)
Q Consensus 56 m~I~kEeVkkIA~LARL~LsEEEle~~~~q 85 (156)
..++.+++..|-.|+-+.++.+|+..+...
T Consensus 12 l~l~d~~m~~if~l~~~~vs~~el~a~lrk 41 (68)
T PF07308_consen 12 LDLKDDDMIEIFALAGFEVSKAELSAWLRK 41 (68)
T ss_pred HcCChHHHHHHHHHcCCccCHHHHHHHHCC
Confidence 468899999999999999999999887654
No 31
>TIGR02744 TrbI_Ftype type-F conjugative transfer system protein TrbI. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=24.57 E-value=1.3e+02 Score=23.03 Aligned_cols=28 Identities=4% Similarity=0.194 Sum_probs=24.1
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 031606 64 PRLAQTARISLTPHEVEEFAPKIRQVID 91 (156)
Q Consensus 64 kkIA~LARL~LsEEEle~~~~qLn~ILe 91 (156)
..+..++.-+++|+|.+...+.|+..|+
T Consensus 45 ~F~~q~~~~~lte~q~~~~~~rF~~~L~ 72 (112)
T TIGR02744 45 AFFDSASQKKLSEAQQKALLGRFNALLE 72 (112)
T ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHHH
Confidence 3455689999999999999999999985
No 32
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=24.04 E-value=1.3e+02 Score=22.97 Aligned_cols=45 Identities=9% Similarity=0.188 Sum_probs=35.8
Q ss_pred CCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHH--HHH----HHHHhccC
Q 031606 55 RSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQ--VID----WFGQLQDV 99 (156)
Q Consensus 55 ~m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~--ILe----~~d~L~eV 99 (156)
+-.+|.++|++|.+-+-++++++.+..|.+.|+. |-+ =.++|..|
T Consensus 17 ~~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~sv 67 (112)
T PTZ00373 17 NENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNI 67 (112)
T ss_pred CCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcc
Confidence 3468999999999999999999999999987753 333 34566666
No 33
>cd02062 Nitro_FMN_reductase Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase.
Probab=23.72 E-value=86 Score=21.81 Aligned_cols=27 Identities=11% Similarity=0.228 Sum_probs=19.8
Q ss_pred cCCCCccCCCCCCCChhHHHHHHHHcCCCCC
Q 031606 45 RTRNCSTTTTRSSLEPPDVPRLAQTARISLT 75 (156)
Q Consensus 45 ~~~~~st~~~~m~I~kEeVkkIA~LARL~Ls 75 (156)
++|.|+.+ .|++++++.+.+.++...+
T Consensus 6 S~R~f~~~----~i~~~~l~~l~~~~~~aPs 32 (122)
T cd02062 6 SVRKFTDE----PVPEEVLEKILEAARYAPS 32 (122)
T ss_pred ecccCCCC----CCCHHHHHHHHHHHHhCCC
Confidence 46667542 7899999998888766554
No 34
>PF09754 PAC2: PAC2 family; InterPro: IPR019151 This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass and contains one 20S core particle structure and two 19S regulatory caps. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits [, , , ].; PDB: 3MNF_A 2P90_B 3E35_A 3GAA_D 2WAM_C.
Probab=22.78 E-value=1.4e+02 Score=23.51 Aligned_cols=41 Identities=17% Similarity=0.222 Sum_probs=32.6
Q ss_pred CChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhcc
Q 031606 58 LEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQD 98 (156)
Q Consensus 58 I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~e 98 (156)
....-++.++++-.++++=+++++-.+...+|.+++++|+|
T Consensus 179 aA~~ll~~l~~~~~~~id~~~l~~ead~~~e~~~~~~~l~e 219 (219)
T PF09754_consen 179 AAARLLEALSKLLGLKIDLSDLEEEADNIEEAEEMVEQLEE 219 (219)
T ss_dssp HHHHHHHHHHHHHT---HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhCceeeHHHHHHhcCCHHHHHHHHHHhcC
Confidence 45667899999999999888898888888899999998875
No 35
>PRK10870 transcriptional repressor MprA; Provisional
Probab=22.09 E-value=1.4e+02 Score=23.52 Aligned_cols=28 Identities=14% Similarity=0.346 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHhccCC
Q 031606 73 SLTPHEVEEFAPKIRQVIDWFGQLQDVD 100 (156)
Q Consensus 73 ~LsEEEle~~~~qLn~ILe~~d~L~eVD 100 (156)
.++++|.+.+..-|+.+.+.++.+.+-|
T Consensus 142 ~ls~~e~~~l~~~L~kl~~~l~~~~~~~ 169 (176)
T PRK10870 142 ALSTTEKDQLEQITRKLLSRLDQMEQDG 169 (176)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhhCCCc
Confidence 6899999999999999999988776543
No 36
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.86 E-value=2.1e+02 Score=20.44 Aligned_cols=61 Identities=10% Similarity=0.059 Sum_probs=38.6
Q ss_pred ccccccccccCCCCccCCCCCCCChhHH---HHHHHHcC-CCCCHHHHHHHHHHHHHHHHHHHHhccC
Q 031606 36 YYYDYDYNNRTRNCSTTTTRSSLEPPDV---PRLAQTAR-ISLTPHEVEEFAPKIRQVIDWFGQLQDV 99 (156)
Q Consensus 36 ~~~~~~~~~~~~~~st~~~~m~I~kEeV---kkIA~LAR-L~LsEEEle~~~~qLn~ILe~~d~L~eV 99 (156)
||-..|+.++.+ +..+.-..+.++| +.|..|-+ ++++-+++..+..-++++-..-..+.++
T Consensus 20 ~ye~~Gli~p~r---~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l~~~~~~l~~~~~~~ 84 (98)
T cd01279 20 VYDRLGLVSPAR---TNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQCRSCEH 84 (98)
T ss_pred HHHHCCCCCCCc---CCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 455567776533 2334444555555 45556777 8999999988887777766655555443
No 37
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=21.79 E-value=26 Score=29.04 Aligned_cols=42 Identities=14% Similarity=0.254 Sum_probs=32.6
Q ss_pred CCCChhHHHHHH--------------------HHcCCCCCHHHHHHHHHHHHHHHHHHHHhc
Q 031606 56 SSLEPPDVPRLA--------------------QTARISLTPHEVEEFAPKIRQVIDWFGQLQ 97 (156)
Q Consensus 56 m~I~kEeVkkIA--------------------~LARL~LsEEEle~~~~qLn~ILe~~d~L~ 97 (156)
..||++.++.|. .+|||+++++|.+.+......|.+.+..+.
T Consensus 177 ~~it~~~l~~v~~~E~~l~~~g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~g 238 (252)
T TIGR00268 177 REIDEEKLKMVDEAEEVLRNAGVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIG 238 (252)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcC
Confidence 467877776654 479999999999999988777777766553
No 38
>PF15036 IL34: Interleukin 34; PDB: 4DKF_A 4DKE_A 4DKC_A 4DKD_A 4EXN_A 4EXP_A.
Probab=21.70 E-value=28 Score=28.60 Aligned_cols=81 Identities=15% Similarity=0.103 Sum_probs=36.4
Q ss_pred CChhHHHHHHHHcCC---CCCHHHHH-------------------------HHHHHHHHHHHHHHHh-ccCCCCCCCCcc
Q 031606 58 LEPPDVPRLAQTARI---SLTPHEVE-------------------------EFAPKIRQVIDWFGQL-QDVDLDSVDPAL 108 (156)
Q Consensus 58 I~kEeVkkIA~LARL---~LsEEEle-------------------------~~~~qLn~ILe~~d~L-~eVDTegVEPm~ 108 (156)
+-=|+|-++|+.+|| .+++.|+. ++.+++...+..+.+. .+-.++|||+.-
T Consensus 44 VpYE~VlR~aNitrLq~a~Vs~~~LryLW~~Vsl~a~e~Vq~VLle~HPSwkYl~Ev~~Ll~~v~~~~~~~~~~dvE~~p 123 (169)
T PF15036_consen 44 VPYEGVLRLANITRLQRARVSERELRYLWVLVSLSATESVQEVLLEGHPSWKYLQEVQTLLLDVQQGLKEYRQSDVEVSP 123 (169)
T ss_dssp EEGGG---HHHHHHHHCTT--HHHHHHHHHHHHHHHHHHHHTTS-TTSTTHHHHHHHHHHHHHHHHTTT-----T----H
T ss_pred ccHHHhhhHhhhhHHHhcccCHHHHHHHHHHhhHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHhcccccccccccCc
Confidence 445778888887777 56666655 3445566665555543 335667777764
Q ss_pred cccCCCCCCCC-C-CcccCCCChHHHHHhhhhh
Q 031606 109 RAGSKREKNTL-C-YYPRICAGGTSLIIQLFCL 139 (156)
Q Consensus 109 r~dev~~s~~R-e-Dep~~~~~~~~LL~~~f~~ 139 (156)
++..+. +... . +........++||.|-|..
T Consensus 124 ~ve~vl-sll~e~~~~~~KlVrPKALLDNC~rv 155 (169)
T PF15036_consen 124 RVESVL-SLLNEAPGPGLKLVRPKALLDNCFRV 155 (169)
T ss_dssp HHHHHH-HHHH-STSSSEEEE-HHHHHHHHHHH
T ss_pred cHHHHH-HHHhcCCCCCccccChHHHHHHHHHH
Confidence 432221 1111 1 2233455677999998854
No 39
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=21.28 E-value=1.8e+02 Score=16.60 Aligned_cols=32 Identities=9% Similarity=0.231 Sum_probs=25.0
Q ss_pred CCCCCChhHHHHHHHHcCCCCCHHHHHHHHHH
Q 031606 54 TRSSLEPPDVPRLAQTARISLTPHEVEEFAPK 85 (156)
Q Consensus 54 ~~m~I~kEeVkkIA~LARL~LsEEEle~~~~q 85 (156)
....|+.+++..+........+++++..+...
T Consensus 13 ~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~ 44 (63)
T cd00051 13 GDGTISADELKAALKSLGEGLSEEEIDEMIRE 44 (63)
T ss_pred CCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 34578999999999988888888887765443
No 40
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=20.72 E-value=1.2e+02 Score=24.09 Aligned_cols=38 Identities=26% Similarity=0.380 Sum_probs=26.3
Q ss_pred cccCCCCccCCCCCCCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 031606 43 NNRTRNCSTTTTRSSLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVID 91 (156)
Q Consensus 43 ~~~~~~~st~~~~m~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe 91 (156)
-+.-|+|||-| |.||+++.++|. +++++|.+++..|.+
T Consensus 116 p~~~R~~s~~T--~~vs~~~~~ki~---------~~i~~fRk~i~~i~~ 153 (171)
T PF14394_consen 116 PPEERDFSGLT--MSVSREDYEKIK---------KEIREFRKKIIAIAE 153 (171)
T ss_pred CccccceeeeE--EEeCHHHHHHHH---------HHHHHHHHHHHHHHh
Confidence 34667777655 667888888886 567777777766654
No 41
>PF15335 CAAP1: Caspase activity and apoptosis inhibitor 1
Probab=20.70 E-value=59 Score=22.78 Aligned_cols=16 Identities=19% Similarity=0.322 Sum_probs=13.2
Q ss_pred CCChHHHHHhhhhhee
Q 031606 126 CAGGTSLIIQLFCLLS 141 (156)
Q Consensus 126 ~~~~~~LL~~~f~~~~ 141 (156)
..||++|++|.|+.+.
T Consensus 9 i~Dr~Eml~Q~F~~l~ 24 (64)
T PF15335_consen 9 IDDRKEMLRQCFSVLK 24 (64)
T ss_pred HccHHHHHHHHHHHcC
Confidence 4589999999998753
No 42
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=20.40 E-value=1.7e+02 Score=21.88 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=28.6
Q ss_pred CCChhHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 031606 57 SLEPPDVPRLAQTARISLTPHEVEEFAPKIR 87 (156)
Q Consensus 57 ~I~kEeVkkIA~LARL~LsEEEle~~~~qLn 87 (156)
.||.++|++|.+=+-++++++-+..|.+.|.
T Consensus 16 ~~ta~~I~~IL~aaGveVe~~~~~~~~~aLa 46 (105)
T cd04411 16 ELTEDKIKELLSAAGAEIEPERVKLFLSALN 46 (105)
T ss_pred CCCHHHHHHHHHHcCCCcCHHHHHHHHHHHc
Confidence 3999999999999999999999999998853
No 43
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.13 E-value=1.4e+02 Score=22.14 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=29.3
Q ss_pred CCChhHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHhc
Q 031606 57 SLEPPDVPRLAQTARISLTPHEVEEFAPKIRQVIDWFGQLQ 97 (156)
Q Consensus 57 ~I~kEeVkkIA~LARL~LsEEEle~~~~qLn~ILe~~d~L~ 97 (156)
.++.++.+-+..+.. +++++.+.+...+...+++++.+-
T Consensus 84 ~l~~~~~~ll~~~~~--L~~~~~~~~l~~l~~~~~~~~~~~ 122 (135)
T PRK09706 84 ELSEDQKELLELFDA--LPESEQDAQLSEMRARVENFNKLF 122 (135)
T ss_pred CCCHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 456665554444444 788999999999999999998864
Done!