Query 030868
Match_columns 170
No_of_seqs 93 out of 101
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 05:48:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030868.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030868hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02341 RcbX: RbcX protein; 100.0 2.7E-46 5.8E-51 287.1 13.2 105 56-165 7-111 (111)
2 PF12112 DUF3579: Protein of u 51.8 5.5 0.00012 30.2 0.3 26 75-100 61-86 (92)
3 cd00131 PAX Paired Box domain 32.6 2.1E+02 0.0045 22.0 6.4 40 60-99 24-63 (128)
4 PRK00116 ruvA Holliday junctio 31.6 2E+02 0.0044 23.5 6.5 47 44-95 75-129 (192)
5 cd02518 GT2_SpsF SpsF is a gly 31.5 57 0.0012 26.3 3.2 29 70-98 196-225 (233)
6 cd06457 M3A_MIP Peptidase M3 m 30.0 2.8E+02 0.0061 25.6 7.8 94 62-159 26-129 (458)
7 PF12234 Rav1p_C: RAVE protein 29.8 1.3E+02 0.0027 29.9 5.8 72 56-127 481-554 (631)
8 PRK05686 fliG flagellar motor 29.6 2.5E+02 0.0053 25.0 7.2 48 99-148 78-125 (339)
9 cd06258 Peptidase_M3_like The 28.9 1.6E+02 0.0034 25.6 5.7 61 68-132 6-66 (365)
10 PRK15337 type III secretion sy 28.9 2.9E+02 0.0064 27.7 8.1 48 63-113 494-541 (686)
11 PF14677 FANCI_S3: FANCI solen 28.6 88 0.0019 26.6 4.0 25 85-110 191-215 (219)
12 PF02268 TFIIA_gamma_N: Transc 28.1 71 0.0015 21.6 2.7 22 105-126 18-39 (49)
13 smart00351 PAX Paired Box doma 28.0 2.7E+02 0.0059 21.1 6.7 44 70-113 34-91 (125)
14 PF06690 DUF1188: Protein of u 26.1 33 0.00072 30.4 1.0 40 42-108 96-138 (252)
15 PF01820 Dala_Dala_lig_N: D-al 24.1 28 0.00061 26.2 0.2 23 50-80 7-29 (117)
16 PF08740 BCS1_N: BCS1 N termin 23.9 1.8E+02 0.0038 22.9 4.8 20 83-102 34-53 (187)
17 TIGR01987 HI0074 nucleotidyltr 22.5 2.6E+02 0.0056 21.7 5.3 36 90-125 66-105 (123)
18 PF14102 Caps_synth_CapC: Caps 22.2 1.2E+02 0.0027 23.4 3.5 46 39-84 15-63 (121)
19 PF05823 Gp-FAR-1: Nematode fa 21.7 3.3E+02 0.0072 21.8 6.0 38 51-88 19-58 (154)
20 PF03052 Adeno_52K: Adenoviral 21.6 5.3E+02 0.011 22.2 9.0 102 43-160 67-179 (201)
21 PF06503 DUF1101: Protein of u 20.8 45 0.00098 30.8 0.9 74 57-131 46-121 (360)
22 PF09722 DUF2384: Protein of u 20.6 1.2E+02 0.0026 19.6 2.7 30 47-80 22-51 (54)
23 TIGR02865 spore_II_E stage II 20.6 7.3E+02 0.016 24.8 9.2 74 66-144 373-449 (764)
24 PF06540 GMAP: Galanin message 20.3 1.6E+02 0.0034 21.1 3.4 26 50-75 16-41 (62)
25 PHA00771 head assembly protein 20.2 65 0.0014 26.4 1.6 17 39-55 62-78 (151)
26 TIGR00207 fliG flagellar motor 20.0 6.4E+02 0.014 22.6 8.0 89 55-150 143-254 (338)
No 1
>PF02341 RcbX: RbcX protein; InterPro: IPR003435 The RbcX protein has been identified as having a possible chaperonin-like function []. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RubisCO in Anabaena sp. (strain CA / ATCC 33047). RbcX has been shown to possess a chaperonin-like function assisting correct folding of RubisCO in Escherichia coli expression studies and is needed for RubisCO to reach its maximal activity [].; PDB: 2PEM_B 2PEI_L 2PEK_A 2Z46_E 2Z44_A 2PEJ_F 2PEN_D 2PEQ_B 2Z45_A 3Q20_A ....
Probab=100.00 E-value=2.7e-46 Score=287.09 Aligned_cols=105 Identities=43% Similarity=0.692 Sum_probs=101.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCCHHHHHHHHHhcccCChhhHHHHHHHHHHHhhccc
Q 030868 56 EAKGAKHLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVRSAYCKRDF 135 (170)
Q Consensus 56 E~kaak~L~~yfTy~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LA~RIMevR~~ya~~~F 135 (170)
.+|||++|++||||+|||||++||+||||+.|.||++|+++||++|||+||++||+|+ ++||+|||+||+|||+++|
T Consensus 7 ~kdtak~L~~yfTy~Avr~Vl~QL~etnp~~~~wL~~F~~~~~~~DGd~fl~~L~~e~---~~LA~RIM~vR~~la~~~~ 83 (111)
T PF02341_consen 7 AKDTAKVLQSYFTYQAVRTVLAQLYETNPPAYIWLYNFLSRNPLQDGDAFLEALMREN---QELALRIMEVREHLAEEVF 83 (111)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHSTCSSHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCccHHHHHHHHHHHC---HHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999999999999999999999999999999997 9999999999999999998
Q ss_pred chHHHHHHHHHHHHHHhHHHHHHHHhhhcc
Q 030868 136 EWDNLKRLAIKTVDESNTRLMRDYVLETSH 165 (170)
Q Consensus 136 eWd~lk~la~k~i~~~N~~LMRe~l~et~~ 165 (170)
|| +++++.+.|+++|+++||+||+++++
T Consensus 84 d~--l~em~~~~I~~~N~e~~R~~L~r~t~ 111 (111)
T PF02341_consen 84 DF--LPEMVREGIQQANMELMRQYLERMTQ 111 (111)
T ss_dssp GG--HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HH--hHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 87 99999999999999999999999874
No 2
>PF12112 DUF3579: Protein of unknown function (DUF3579); InterPro: IPR021969 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif. ; PDB: 2L9D_A.
Probab=51.82 E-value=5.5 Score=30.24 Aligned_cols=26 Identities=23% Similarity=0.506 Sum_probs=21.7
Q ss_pred HHHHhhccChhhHHHHHHHHhcCCCC
Q 030868 75 ITAQLQSYNPEAYKELMEFLERHPLN 100 (170)
Q Consensus 75 Vl~QL~e~np~~y~wL~~Fl~~~pl~ 100 (170)
|=.+|+..+|.+|..+++|...|.|+
T Consensus 61 Vd~~L~~~~P~af~fvm~FA~dN~L~ 86 (92)
T PF12112_consen 61 VDERLRDIEPMAFDFVMNFAKDNDLQ 86 (92)
T ss_dssp EETHHHHH-HHHHHHHHHHHHHHTEE
T ss_pred EccHhhhcChHHHHHHHHHHHHCCCe
Confidence 44678999999999999999998874
No 3
>cd00131 PAX Paired Box domain
Probab=32.64 E-value=2.1e+02 Score=22.01 Aligned_cols=40 Identities=18% Similarity=0.050 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCC
Q 030868 60 AKHLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPL 99 (170)
Q Consensus 60 ak~L~~yfTy~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl 99 (170)
++++.-|-.=...+.|..+|.=.-+..+.|+..|-++..+
T Consensus 24 ~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v 63 (128)
T cd00131 24 QRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSI 63 (128)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence 3444444455566777777776677899999999976544
No 4
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=31.58 E-value=2e+02 Score=23.53 Aligned_cols=47 Identities=13% Similarity=0.078 Sum_probs=29.8
Q ss_pred ceeecCCCCCChhhHHHHHHHHHHHHHHHH----H----HHHHhhccChhhHHHHHHHHh
Q 030868 44 KMYVPGFGEASPEAKGAKHLHNFFTYIAVR----I----ITAQLQSYNPEAYKELMEFLE 95 (170)
Q Consensus 44 km~Vp~fGG~sPE~kaak~L~~yfTy~AvR----~----Vl~QL~e~np~~y~wL~~Fl~ 95 (170)
..-|||.| .|+|..|.+.|+.-.+. - -|.++.+.++..+.-+...+.
T Consensus 75 L~~i~GIG-----pk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 75 LISVSGVG-----PKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HhcCCCCC-----HHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 35588888 57888888888864443 2 334455667766655554444
No 5
>cd02518 GT2_SpsF SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration.
Probab=31.48 E-value=57 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=18.6
Q ss_pred HHHHHHHHHhhccChh-hHHHHHHHHhcCC
Q 030868 70 IAVRIITAQLQSYNPE-AYKELMEFLERHP 98 (170)
Q Consensus 70 ~AvR~Vl~QL~e~np~-~y~wL~~Fl~~~p 98 (170)
..++.+...|+..|++ -+.|+.+|+++||
T Consensus 196 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p 225 (233)
T cd02518 196 ELIKEIYEALYPKNPDFSLEDIIELLDKNP 225 (233)
T ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhCh
Confidence 3445555666666655 5777777777776
No 6
>cd06457 M3A_MIP Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that show similarity to the Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both, nuclear and mitochondrial encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. It cleaves intermediate-size proteins initially processed by mitochondrial processing peptidase (MPP) to yield a processing intermediate with a typical N-terminal octapeptide that is sequentially cleaved by MIP to mature-size protein. MIP cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tri-carboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. It has been suggested that the human MIP (HMIP polypeptide; gene symbo
Probab=30.02 E-value=2.8e+02 Score=25.57 Aligned_cols=94 Identities=16% Similarity=0.135 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCCHHHHHHHHHhcccCChhhHHHHHHHHHHHhhcc-------
Q 030868 62 HLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVRSAYCKRD------- 134 (170)
Q Consensus 62 ~L~~yfTy~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LA~RIMevR~~ya~~~------- 134 (170)
....|-..+..|.-++||-++..-+..-|.+=+.. .+.+=.+||..|.+.. ..+|.+-++.=..+++++
T Consensus 26 n~~il~~l~~lR~e~A~llGy~sya~~~l~~~ma~-spe~v~~fL~~l~~~~---~p~~~~e~~~L~~~~~~~~~~~~~~ 101 (458)
T cd06457 26 QLELLEELLSSRAELAQLLGFESYAHRALRGKMAK-NPENVMEFLTELSEKL---RPRAEEELAVLRDMKRKVLGKPLSS 101 (458)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcC-CHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHhcCCCcCC
Confidence 33467778899999999999986655555544443 3556678999998886 778888776544454433
Q ss_pred ---cchHHHHHHHHHHHHHHhHHHHHHH
Q 030868 135 ---FEWDNLKRLAIKTVDESNTRLMRDY 159 (170)
Q Consensus 135 ---FeWd~lk~la~k~i~~~N~~LMRe~ 159 (170)
.||..+.+...+.--+.+.+.+|+|
T Consensus 102 L~pwD~~yy~~~~~~~~~~~d~~~l~~Y 129 (458)
T cd06457 102 LAPWDRDYYTGQYRQSRFDSEPSNLSPY 129 (458)
T ss_pred CCHHHHHHHHHHHHHhhcCCChHHhccc
Confidence 2444455544444333445555544
No 7
>PF12234 Rav1p_C: RAVE protein 1 C terminal; InterPro: IPR022033 This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C-terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.
Probab=29.81 E-value=1.3e+02 Score=29.89 Aligned_cols=72 Identities=18% Similarity=0.120 Sum_probs=44.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcc-ChhhHHHHH-HHHhcCCCCCHHHHHHHHHhcccCChhhHHHHHHHH
Q 030868 56 EAKGAKHLHNFFTYIAVRIITAQLQSY-NPEAYKELM-EFLERHPLNDGDKFCADLMRESSRHKGLALRILEVR 127 (170)
Q Consensus 56 E~kaak~L~~yfTy~AvR~Vl~QL~e~-np~~y~wL~-~Fl~~~pl~DGd~fL~~Lmre~~~~~~LA~RIMevR 127 (170)
-+||..++.+++-=.-.=++++-|+|- |.|.+.+|. +++--.-+.+||.|++...-=-=++++.|.|.+...
T Consensus 481 l~dAv~V~~~~l~D~qLAi~i~Rl~e~d~gp~~~~ll~~~vLp~a~~~~d~wl~s~~~W~L~~~~~ai~~Li~~ 554 (631)
T PF12234_consen 481 LKDAVNVCLRQLNDPQLAIAIARLYEGDNGPVLKKLLEEHVLPEAIKEGDRWLASWAFWMLGDYDEAIRALISP 554 (631)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHcCCCchHHHHHHHHhhhccccccCCHHHHHHHHHhcCCHHHHHHHHhcC
Confidence 466666666666555556666666443 456665544 566656667999999985422212267888877543
No 8
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=29.62 E-value=2.5e+02 Score=24.96 Aligned_cols=48 Identities=19% Similarity=0.196 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHhcccCChhhHHHHHHHHHHHhhcccchHHHHHHHHHHH
Q 030868 99 LNDGDKFCADLMRESSRHKGLALRILEVRSAYCKRDFEWDNLKRLAIKTV 148 (170)
Q Consensus 99 l~DGd~fL~~Lmre~~~~~~LA~RIMevR~~ya~~~FeWd~lk~la~k~i 148 (170)
..+|..|++.++... .+++.|..||.--..--. .|-|+.+..+--+.|
T Consensus 78 ~~gg~~~~~~iL~~~-l~~~~a~~il~~i~~~~~-~~~fe~L~~ld~~~l 125 (339)
T PRK05686 78 LMGGIDYARSLLEKA-LGEEKADSILERILESLG-TSGFDFLRKMDPQQL 125 (339)
T ss_pred cCChHHHHHHHHHHH-cCHHHHHHHHHHHhcccc-CchHHHHhcCCHHHH
Confidence 468999999999751 127788888865332222 377888866543333
No 9
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=28.93 E-value=1.6e+02 Score=25.64 Aligned_cols=61 Identities=21% Similarity=0.170 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCCHHHHHHHHHhcccCChhhHHHHHHHHHHHhh
Q 030868 68 TYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVRSAYCK 132 (170)
Q Consensus 68 Ty~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LA~RIMevR~~ya~ 132 (170)
.++-+|.-++|+-+++...-.+|.+++.. .+.+=+.|+..|-+.- +.++.++++....+++
T Consensus 6 ~lv~lr~e~A~~lGy~~~~d~~l~~~~~~-~~e~v~~f~~~l~~~~---~p~~~~~~~~l~~~~~ 66 (365)
T cd06258 6 ELVSLRNQLARLLGYENFADYKLALQEAK-SPETVEGFFEELKRKL---RPLLAKLREEISAAKQ 66 (365)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHhcC-CHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Confidence 45667888999989976667777777776 6778899999997775 6788888887766554
No 10
>PRK15337 type III secretion system protein InvA; Provisional
Probab=28.91 E-value=2.9e+02 Score=27.75 Aligned_cols=48 Identities=19% Similarity=0.329 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCCHHHHHHHHHhcc
Q 030868 63 LHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRES 113 (170)
Q Consensus 63 L~~yfTy~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~ 113 (170)
...+|+++-|+-.+++|++.+|..-.+|-+ .-|++.=-+=|+.|++|+
T Consensus 494 a~ellg~qev~~Lld~l~~~~p~Lv~elp~---~l~l~~i~~VLq~LL~E~ 541 (686)
T PRK15337 494 INEFFGIQETKHLLDQLEKKYPDLLKEVYR---HATVQRISEVLQRLLSER 541 (686)
T ss_pred HHHHcCHHHHHHHHHHHHHHCHHHHHHHhc---cCCHHHHHHHHHHHHhcC
Confidence 678999999999999999999987766522 233444445666777664
No 11
>PF14677 FANCI_S3: FANCI solenoid 3; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=28.57 E-value=88 Score=26.55 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=17.1
Q ss_pred hhHHHHHHHHhcCCCCCHHHHHHHHH
Q 030868 85 EAYKELMEFLERHPLNDGDKFCADLM 110 (170)
Q Consensus 85 ~~y~wL~~Fl~~~pl~DGd~fL~~Lm 110 (170)
+.|.|+.+|...+++.|-. ++.+|+
T Consensus 191 q~~~W~~~~ck~~~l~d~~-~~k~ll 215 (219)
T PF14677_consen 191 QMLSWTLKFCKENSLEDSS-FCKGLL 215 (219)
T ss_dssp HHHHHHHHHHHS---S-HH-HHHHHH
T ss_pred HHHHHHHHHHHhcCCCcHH-HHHHHH
Confidence 4799999999999998865 777776
No 12
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=28.07 E-value=71 Score=21.58 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=16.5
Q ss_pred HHHHHHhcccCChhhHHHHHHH
Q 030868 105 FCADLMRESSRHKGLALRILEV 126 (170)
Q Consensus 105 fL~~Lmre~~~~~~LA~RIMev 126 (170)
=|.+|+.++.-.|.||++||..
T Consensus 18 tLDeli~~~~I~p~La~kVL~~ 39 (49)
T PF02268_consen 18 TLDELIQEGKITPQLAMKVLEQ 39 (49)
T ss_dssp HHHHHHHTTSS-HHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHHH
Confidence 3567788876679999999964
No 13
>smart00351 PAX Paired Box domain.
Probab=28.03 E-value=2.7e+02 Score=21.13 Aligned_cols=44 Identities=25% Similarity=0.163 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhccChhhHHHHHHHHhcCCCCC----H----------HHHHHHHHhcc
Q 030868 70 IAVRIITAQLQSYNPEAYKELMEFLERHPLND----G----------DKFCADLMRES 113 (170)
Q Consensus 70 ~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~D----G----------d~fL~~Lmre~ 113 (170)
...+.+-.+|.=.-+..|.|+..|-++..+.. | +.||.++.+++
T Consensus 34 ~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~ 91 (125)
T smart00351 34 VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQEN 91 (125)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHC
Confidence 34555556666566779999999987655433 2 45677666665
No 14
>PF06690 DUF1188: Protein of unknown function (DUF1188); InterPro: IPR009573 This family consists of several hypothetical archaeal proteins of around 260 residues in length, which seem to be specific to Methanobacterium, Methanococcus and Methanopyrus species. The function of this family is unknown.
Probab=26.12 E-value=33 Score=30.39 Aligned_cols=40 Identities=28% Similarity=0.641 Sum_probs=32.1
Q ss_pred CCceeec--CCCCCChhhHHHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCCH-HHHHHH
Q 030868 42 CQKMYVP--GFGEASPEAKGAKHLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDG-DKFCAD 108 (170)
Q Consensus 42 ~~km~Vp--~fGG~sPE~kaak~L~~yfTy~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~DG-d~fL~~ 108 (170)
..-++|. ||||.+|+ +|+..||++. +.++|-.|| |..|..
T Consensus 96 ~~DlIID~TGlGGv~~~---------------------~Ls~~~p~v~------IVEdP~~~~sD~~I~~ 138 (252)
T PF06690_consen 96 NPDLIIDTTGLGGVDPD---------------------FLSKFNPKVF------IVEDPKGDGSDKTIYE 138 (252)
T ss_pred CCCEEEECCCCCCCCHH---------------------HHhccCCCEE------EEECCCccCcchhhhh
Confidence 4558888 99999996 6788899864 888999988 777654
No 15
>PF01820 Dala_Dala_lig_N: D-ala D-ala ligase N-terminus; InterPro: IPR011127 This entry represents the N-terminal region of the D-alanine--D-alanine ligase enzyme (6.3.2.4 from EC) which is thought to be involved in substrate binding []. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [].; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005618 cell wall; PDB: 4EG0_B 3E5N_A 3RFC_A 3R5F_A 1IOV_A 1IOW_A 2DLN_A 3Q1K_D 3I12_C 3N8D_B ....
Probab=24.11 E-value=28 Score=26.20 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=16.7
Q ss_pred CCCCChhhHHHHHHHHHHHHHHHHHHHHHhh
Q 030868 50 FGEASPEAKGAKHLHNFFTYIAVRIITAQLQ 80 (170)
Q Consensus 50 fGG~sPE~kaak~L~~yfTy~AvR~Vl~QL~ 80 (170)
|||.|+|++++- +..+.|+.+|.
T Consensus 7 fGG~S~EheVSl--------~Sa~~v~~~L~ 29 (117)
T PF01820_consen 7 FGGRSSEHEVSL--------RSARNVYEALD 29 (117)
T ss_dssp EETSSTTHHHHH--------HHHHHHHHHSH
T ss_pred eccCchhHHHHH--------HHHHHHHHHHh
Confidence 799999999863 34556666663
No 16
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=23.92 E-value=1.8e+02 Score=22.87 Aligned_cols=20 Identities=35% Similarity=0.650 Sum_probs=17.1
Q ss_pred ChhhHHHHHHHHhcCCCCCH
Q 030868 83 NPEAYKELMEFLERHPLNDG 102 (170)
Q Consensus 83 np~~y~wL~~Fl~~~pl~DG 102 (170)
+-+.|.||+.+++++|....
T Consensus 34 ~D~~Y~~lm~Wls~q~~~~~ 53 (187)
T PF08740_consen 34 DDEAYDWLMRWLSSQPFSKR 53 (187)
T ss_pred CCHHHHHHHHHHhhCCcccc
Confidence 55799999999999999653
No 17
>TIGR01987 HI0074 nucleotidyltransferase substrate binding protein, HI0074 family. The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (pfam01909).
Probab=22.45 E-value=2.6e+02 Score=21.72 Aligned_cols=36 Identities=19% Similarity=0.122 Sum_probs=24.1
Q ss_pred HHHHHhcCCCCCHHHHHHHHHhcccC----ChhhHHHHHH
Q 030868 90 LMEFLERHPLNDGDKFCADLMRESSR----HKGLALRILE 125 (170)
Q Consensus 90 L~~Fl~~~pl~DGd~fL~~Lmre~~~----~~~LA~RIMe 125 (170)
+......+-+.||+.|++-|-..|-- |.+.|..|..
T Consensus 66 ir~A~~~glI~d~~~W~~ml~~RN~tsHtYde~~a~~i~~ 105 (123)
T TIGR01987 66 LKEAFRAGLIGDESLWIAMLDDRNITSHTYDQEKAREIYA 105 (123)
T ss_pred HHHHHHcCCcCCHHHHHHHHHHhCcccccCCHHHHHHHHH
Confidence 44455666779999999998766531 3556666654
No 18
>PF14102 Caps_synth_CapC: Capsule biosynthesis CapC
Probab=22.22 E-value=1.2e+02 Score=23.41 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=36.8
Q ss_pred cccCCceeecCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHhhccCh
Q 030868 39 TIHCQKMYVPGF---GEASPEAKGAKHLHNFFTYIAVRIITAQLQSYNP 84 (170)
Q Consensus 39 ~~~~~km~Vp~f---GG~sPE~kaak~L~~yfTy~AvR~Vl~QL~e~np 84 (170)
-.+++.++|||+ -=.+|.+-....+.+..||..+|.+..-.-=+..
T Consensus 15 G~~~gGlivPgylAl~~~~P~~l~~~~~~s~lt~~i~~~l~~~~ilyGR 63 (121)
T PF14102_consen 15 GWSPGGLIVPGYLALYLDQPVRLLVTLLISLLTYLIVRLLSRRTILYGR 63 (121)
T ss_pred CCCCCCEeeHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHhhhcccH
Confidence 567899999973 2278999999999999999999888776544443
No 19
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=21.71 E-value=3.3e+02 Score=21.75 Aligned_cols=38 Identities=21% Similarity=0.369 Sum_probs=12.1
Q ss_pred CCCChhhHH--HHHHHHHHHHHHHHHHHHHhhccChhhHH
Q 030868 51 GEASPEAKG--AKHLHNFFTYIAVRIITAQLQSYNPEAYK 88 (170)
Q Consensus 51 GG~sPE~ka--ak~L~~yfTy~AvR~Vl~QL~e~np~~y~ 88 (170)
++-+||.|+ ..+..+|-+|...--+++-|.+-+|..|.
T Consensus 19 ~~Lt~eeK~~lkev~~~~~~~~~~de~i~~LK~ksP~L~~ 58 (154)
T PF05823_consen 19 KNLTPEEKAELKEVAKNYAKFKNEDEMIAALKEKSPSLYE 58 (154)
T ss_dssp HH--TTTHHHHHHHHTT-------TTHHHHHHHH-HHHHH
T ss_pred HcCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCHHHHH
Confidence 444555322 23444444444433444444444554443
No 20
>PF03052 Adeno_52K: Adenoviral protein L1 52/55-kDa; InterPro: IPR004292 The adenoviral protein 52K (named after the earliest known 52kDa members) is a DNA-binding protein []. The adenoviral 52K protein is encoded by a late gene [] in various adenoviruses including the avian adenovirus: chicken embryo lethal orphan (CELO) virus []. The adenoviral protein L1 52/55 kDa is expressed in both the early and late stages of infection which suggests that it could play multiple roles in the viral life cycle. The L1 52/55 kDa protein interacts with the viral IVa2 protein and is required for DNA packaging [, ]. L1 53/55 kDa is required to mediate stable association between the viral DNA and empty capsid []. This entry represents the adenoviral 52kDa-like protein and includes proteins involved in virion assembly.; GO: 0019068 virion assembly
Probab=21.56 E-value=5.3e+02 Score=22.21 Aligned_cols=102 Identities=19% Similarity=0.268 Sum_probs=53.4
Q ss_pred CceeecCCCCCChhh---HHHHHHHHHHHHHHHHHHHHHhhc--------cChhhHHHHHHHHhcCCCCCHHHHHHHHHh
Q 030868 43 QKMYVPGFGEASPEA---KGAKHLHNFFTYIAVRIITAQLQS--------YNPEAYKELMEFLERHPLNDGDKFCADLMR 111 (170)
Q Consensus 43 ~km~Vp~fGG~sPE~---kaak~L~~yfTy~AvR~Vl~QL~e--------~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmr 111 (170)
+.+|+|.+.|.||-+ +||. |....-+-..--+..|-.= .-|+.+.-|+.+.. |+++++.
T Consensus 67 ~~DF~~~~~g~s~a~ah~~AA~-L~~~~~~T~~~E~~~q~~fn~~vrtll~R~e~~lGL~yl~d---------f~~~~~~ 136 (201)
T PF03052_consen 67 PEDFKEEFPGFSPAQAHMVAAE-LHRAYEQTEKYEVSFQDTFNNHVRTLLWRPEVPLGLYYLWD---------FVQAYVE 136 (201)
T ss_pred hhhcCCCcccccHHHHHHHHHH-HhHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhHHHHHHHH---------HHHHHHh
Confidence 557788899999884 3333 3333333333333333210 13555555655543 7777777
Q ss_pred cccCChhhHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhHHHHHHHH
Q 030868 112 ESSRHKGLALRILEVRSAYCKRDFEWDNLKRLAIKTVDESNTRLMRDYV 160 (170)
Q Consensus 112 e~~~~~~LA~RIMevR~~ya~~~FeWd~lk~la~k~i~~~N~~LMRe~l 160 (170)
.++ ...|..-+..+ ....+ |+..-+-+.-.|.+.+-+.+++-+
T Consensus 137 ~P~-~~~Lt~ql~li--~qh~~---~~~~lR~~l~~i~e~~~~Wl~DLi 179 (201)
T PF03052_consen 137 NPN-SKALTAQLFLI--VQHGR---DNGTLREALPDIAEPESEWLRDLI 179 (201)
T ss_pred CCC-chhhHHHHHHH--HHhcc---cchHHHHHhhhhcccccHHHHHHH
Confidence 753 22332222221 12233 666666667777777766666544
No 21
>PF06503 DUF1101: Protein of unknown function (DUF1101); InterPro: IPR010521 This entry is represented by Maize rough dwarf virus (MRDV), S6; it is a family of uncharacterised viral proteins.
Probab=20.83 E-value=45 Score=30.83 Aligned_cols=74 Identities=18% Similarity=0.400 Sum_probs=51.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH-hhccChhhHHHHHHHHhcCCC-CCHHHHHHHHHhcccCChhhHHHHHHHHHHHh
Q 030868 57 AKGAKHLHNFFTYIAVRIITAQ-LQSYNPEAYKELMEFLERHPL-NDGDKFCADLMRESSRHKGLALRILEVRSAYC 131 (170)
Q Consensus 57 ~kaak~L~~yfTy~AvR~Vl~Q-L~e~np~~y~wL~~Fl~~~pl-~DGd~fL~~Lmre~~~~~~LA~RIMevR~~ya 131 (170)
.+++-.|.+||++++++.--.- +.+..|+.|.+|+ |.+.-+. -|=+.|+-.||-.+.--+.|..-|+..=..|.
T Consensus 46 ~~p~m~Lsdy~s~vs~~f~~e~~~~el~p~ly~dl~-f~d~~~~dVDLn~l~wqll~~nqD~~aL~vNiLrm~~t~~ 121 (360)
T PF06503_consen 46 TSPKMALSDYFSSVSITFDQEMRIPELDPPLYGDLH-FHDHYTQDVDLNLLCWQLLSSNQDSRALCVNILRMYDTYS 121 (360)
T ss_pred CCCceehhhhhheeEeeccCcccCCCCCcccccchH-HHhhccccccHHHHHHHHhcCCccHHHHHHHHHHHHHHHh
Confidence 4567789999999999875433 5788999999986 4655444 47789999998776222556555554444443
No 22
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=20.65 E-value=1.2e+02 Score=19.58 Aligned_cols=30 Identities=13% Similarity=0.028 Sum_probs=18.4
Q ss_pred ecCCCCCChhhHHHHHHHHHHHHHHHHHHHHHhh
Q 030868 47 VPGFGEASPEAKGAKHLHNFFTYIAVRIITAQLQ 80 (170)
Q Consensus 47 Vp~fGG~sPE~kaak~L~~yfTy~AvR~Vl~QL~ 80 (170)
.|+|||.+|-.=. .+---...|+-.|++++
T Consensus 22 ~~~l~g~~Plel~----~t~~G~~~V~~~L~~~~ 51 (54)
T PF09722_consen 22 NPALGGRTPLELL----RTEAGAERVLDYLDRIE 51 (54)
T ss_pred HHHhCCCCHHHHH----cChHHHHHHHHHHHHHH
Confidence 3579999997432 23444556666666654
No 23
>TIGR02865 spore_II_E stage II sporulation protein E. Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs.
Probab=20.64 E-value=7.3e+02 Score=24.85 Aligned_cols=74 Identities=14% Similarity=0.116 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHHhhcccchHHHHH
Q 030868 66 FFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRES---SRHKGLALRILEVRSAYCKRDFEWDNLKR 142 (170)
Q Consensus 66 yfTy~AvR~Vl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~---~~~~~LA~RIMevR~~ya~~~FeWd~lk~ 142 (170)
+-||.+..-++.++++..... ..+-+.+.++=++- ++|++.+-..= ..|...-.|+.|-|+.+++. ++.+.+
T Consensus 373 ~~Ty~~~~~l~~~~e~~~~~~-~~~p~~~~~~C~r~-~~~~~~~~~~~~~~~~n~~w~~rl~e~R~~va~Q---l~~~s~ 447 (764)
T TIGR02865 373 DYTYSAMEELIENLEEKKDPN-SKLPDEFERKCIKR-KELINTTEDILNNYIINEMWRKRLEEGRRLVAEQ---LKGVAE 447 (764)
T ss_pred HHHHHHHHHHHHHHHhcCCch-hhhhHHHHHhCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 458999998999988877655 67777776555543 44766654321 11366789999999999997 666654
Q ss_pred HH
Q 030868 143 LA 144 (170)
Q Consensus 143 la 144 (170)
..
T Consensus 448 ~l 449 (764)
T TIGR02865 448 SV 449 (764)
T ss_pred HH
Confidence 43
No 24
>PF06540 GMAP: Galanin message associated peptide (GMAP); InterPro: IPR013068 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [].
Probab=20.32 E-value=1.6e+02 Score=21.06 Aligned_cols=26 Identities=12% Similarity=0.364 Sum_probs=21.9
Q ss_pred CCCCChhhHHHHHHHHHHHHHHHHHH
Q 030868 50 FGEASPEAKGAKHLHNFFTYIAVRII 75 (170)
Q Consensus 50 fGG~sPE~kaak~L~~yfTy~AvR~V 75 (170)
|+...||.++-.++..|+||.=++-.
T Consensus 16 ~~r~l~d~nivrTiiEFLtfLhLKEa 41 (62)
T PF06540_consen 16 FDRPLADDNIVRTIIEFLTFLHLKEA 41 (62)
T ss_pred ccCCCchhHHHHHHHHHHHHHHHHHh
Confidence 67667999999999999999877653
No 25
>PHA00771 head assembly protein
Probab=20.19 E-value=65 Score=26.40 Aligned_cols=17 Identities=35% Similarity=0.694 Sum_probs=15.0
Q ss_pred cccCCceeecCCCCCCh
Q 030868 39 TIHCQKMYVPGFGEASP 55 (170)
Q Consensus 39 ~~~~~km~Vp~fGG~sP 55 (170)
-.+|+-||-|+|-|.|.
T Consensus 62 ~~ecHa~y~P~fRG~ya 78 (151)
T PHA00771 62 TFDCHAMYLPEIRGFSK 78 (151)
T ss_pred EEEEEeeeCccccchhH
Confidence 46899999999998886
No 26
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=20.01 E-value=6.4e+02 Score=22.56 Aligned_cols=89 Identities=19% Similarity=0.219 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHH--HHHhhccChhhHHHH----HHHHh----cCCCCCHHHHHHHHHhccc----------
Q 030868 55 PEAKGAKHLHNFFTYIAVRII--TAQLQSYNPEAYKEL----MEFLE----RHPLNDGDKFCADLMRESS---------- 114 (170)
Q Consensus 55 PE~kaak~L~~yfTy~AvR~V--l~QL~e~np~~y~wL----~~Fl~----~~pl~DGd~fL~~Lmre~~---------- 114 (170)
|...||++|..|=.-....|+ +++|+..+|+.-..+ .+|+. ...-.+|-..++.++..-+
T Consensus 143 ~p~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~~~~~~~~~il~~ 222 (338)
T TIGR00207 143 DPAQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINLMDRKTEKTIITS 222 (338)
T ss_pred CHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHhCCchHHHHHHHH
Q ss_pred ---CChhhHHHHHHHHHHHhhcccchHHHHHHHHHHHHH
Q 030868 115 ---RHKGLALRILEVRSAYCKRDFEWDNLKRLAIKTVDE 150 (170)
Q Consensus 115 ---~~~~LA~RIMevR~~ya~~~FeWd~lk~la~k~i~~ 150 (170)
.|+++|.+| -+..|.++.+-++--+.|..
T Consensus 223 L~~~dp~la~~I-------r~~mF~Fedl~~ld~~~l~~ 254 (338)
T TIGR00207 223 LEEFDPELAEEI-------KKEMFVFEDIVDLDDRSIQR 254 (338)
T ss_pred HHHhCHHHHHHH-------HHHccCHHHHhcCCHHHHHH
Done!