Query 038974
Match_columns 134
No_of_seqs 104 out of 820
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 05:08:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038974hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 3.9E-46 8.4E-51 264.4 8.0 121 2-125 1-129 (129)
2 PHA00692 hypothetical protein 49.7 7 0.00015 24.2 0.5 8 2-9 37-44 (74)
3 PF07960 CBP4: CBP4; InterPro 42.0 13 0.00029 26.4 1.0 10 9-18 30-40 (128)
4 PF13822 ACC_epsilon: Acyl-CoA 35.5 20 0.00044 22.0 1.0 9 9-17 10-18 (62)
5 smart00707 RPEL Repeat in Dros 31.3 35 0.00077 17.5 1.3 12 6-17 7-18 (26)
6 COG3060 MetJ Transcriptional r 28.6 38 0.00083 22.6 1.4 38 9-53 51-90 (105)
7 PF07131 DUF1382: Protein of u 27.5 70 0.0015 19.8 2.4 20 4-23 22-48 (61)
8 cd00490 Met_repressor_MetJ Met 27.1 69 0.0015 21.5 2.5 37 9-52 50-88 (103)
9 PF01473 CW_binding_1: Putativ 27.0 44 0.00095 15.2 1.1 7 58-64 8-14 (19)
10 PF02375 JmjN: jmjN domain; I 26.7 38 0.00082 18.4 1.0 19 7-26 2-23 (34)
11 PF12323 HTH_OrfB_IS605: Helix 25.7 39 0.00085 19.0 1.0 11 6-16 7-17 (46)
12 PF08672 APC2: Anaphase promot 24.5 57 0.0012 19.9 1.6 19 8-26 31-49 (60)
13 PRK10154 hypothetical protein; 24.2 42 0.00092 23.9 1.1 21 101-121 78-101 (134)
14 cd00950 DHDPS Dihydrodipicolin 24.0 85 0.0018 24.4 2.9 24 2-26 102-125 (284)
15 PF08990 Docking: Erythronolid 24.0 43 0.00094 17.3 0.9 13 10-22 2-14 (27)
16 PRK05264 transcriptional repre 23.4 84 0.0018 21.2 2.3 37 9-52 51-89 (105)
17 PRK14390 hypothetical protein; 23.1 39 0.00085 21.0 0.7 14 1-14 12-25 (63)
18 TIGR03874 4cys_cytochr c-type 22.9 61 0.0013 23.4 1.8 23 4-26 93-119 (143)
19 PF08970 Sda: Sporulation inhi 22.6 87 0.0019 18.3 2.0 17 10-26 4-21 (46)
20 smart00265 BH4 BH4 Bcl-2 homol 21.0 1E+02 0.0022 15.9 1.9 17 10-26 3-20 (27)
21 COG0020 UppS Undecaprenyl pyro 21.0 71 0.0015 25.1 1.9 35 12-50 172-210 (245)
22 PF05848 CtsR: Firmicute trans 20.9 1.3E+02 0.0029 22.0 3.2 37 12-50 4-44 (152)
23 PF11141 DUF2914: Protein of u 20.5 1.4E+02 0.003 18.4 2.8 21 79-104 42-62 (66)
24 PF12043 DUF3527: Domain of un 20.1 2.6E+02 0.0055 23.3 5.0 82 39-131 29-112 (346)
25 PF10807 DUF2541: Protein of u 20.1 61 0.0013 23.1 1.2 20 101-120 78-100 (134)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=3.9e-46 Score=264.38 Aligned_cols=121 Identities=33% Similarity=0.596 Sum_probs=90.2
Q ss_pred CCCCceEcCChHHHHH-HHHHhHcCCCCCCCC-CceEeccCCCCCCcccchhcccCCCccEEEEeeccc-cCCCC-ceee
Q 038974 2 LPPGVVFNPTEEDRVS-YLIGKVSGHTDGGGS-YFIQDIQLCEHEPWELLSLAHDCCHQQMYFTHLRSR-YHSEM-VYRE 77 (134)
Q Consensus 2 LP~G~rF~PtDeELi~-YL~~k~~g~~~~~~~-~~I~~~Dvy~~~Pw~L~~~~~~~~~~~~yFF~~~~~-~~~g~-~~R~ 77 (134)
|||||||+|||+|||. ||.+|+.+. +++. .+|.++|||+.|||+|+..... .+++||||+++++ +.+|. .+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~--~~~~~~~i~~~Diy~~~P~~L~~~~~~-~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGE--PLPCEDVIHDVDIYSAHPWELPAKFKG-GDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT---HHCS-CHSEE--GGGS-GGGCHHHSSS--SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCC--CCCcccceeecccCccChHHhhhhccC-CCceEEEEEecccccCCccccccc
Confidence 8999999999999999 999999999 6665 7899999999999999953222 3379999999998 77776 8899
Q ss_pred eccceeeecCCCceEeCCCCceEEEEEEEEEEe----cCCCCCeEEEEEEeC
Q 038974 78 AVCGFWKNLGLSSYINDKGGKPVAVKKSLNYYK----KDVKTQWLMTCTHFC 125 (134)
Q Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~kk~~~fy~----~~~kt~W~M~Ey~l~ 125 (134)
+++|+||++|+.++|.+.+|++||+|++|+||. ++.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999988889999999999996 567999999999984
No 2
>PHA00692 hypothetical protein
Probab=49.73 E-value=7 Score=24.21 Aligned_cols=8 Identities=50% Similarity=1.136 Sum_probs=6.5
Q ss_pred CCCCceEc
Q 038974 2 LPPGVVFN 9 (134)
Q Consensus 2 LP~G~rF~ 9 (134)
.||||||-
T Consensus 37 yppgfrfg 44 (74)
T PHA00692 37 YPPGFRFG 44 (74)
T ss_pred cCCCcccc
Confidence 58999985
No 3
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=41.96 E-value=13 Score=26.41 Aligned_cols=10 Identities=50% Similarity=0.876 Sum_probs=8.8
Q ss_pred cCChHHHHH-H
Q 038974 9 NPTEEDRVS-Y 18 (134)
Q Consensus 9 ~PtDeELi~-Y 18 (134)
.||||||+. |
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 699999998 5
No 4
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=35.50 E-value=20 Score=22.00 Aligned_cols=9 Identities=44% Similarity=0.811 Sum_probs=8.0
Q ss_pred cCChHHHHH
Q 038974 9 NPTEEDRVS 17 (134)
Q Consensus 9 ~PtDeELi~ 17 (134)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999976
No 5
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=31.30 E-value=35 Score=17.50 Aligned_cols=12 Identities=25% Similarity=0.318 Sum_probs=10.2
Q ss_pred ceEcCChHHHHH
Q 038974 6 VVFNPTEEDRVS 17 (134)
Q Consensus 6 ~rF~PtDeELi~ 17 (134)
...+|+.+|||.
T Consensus 7 l~~RP~~eeLv~ 18 (26)
T smart00707 7 LSQRPTREELEE 18 (26)
T ss_pred HHcCCCHHHHHH
Confidence 457899999997
No 6
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=28.59 E-value=38 Score=22.55 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=28.7
Q ss_pred cCChHHHHH--HHHHhHcCCCCCCCCCceEeccCCCCCCcccchhcc
Q 038974 9 NPTEEDRVS--YLIGKVSGHTDGGGSYFIQDIQLCEHEPWELLSLAH 53 (134)
Q Consensus 9 ~PtDeELi~--YL~~k~~g~~~~~~~~~I~~~Dvy~~~Pw~L~~~~~ 53 (134)
|-|..||++ ||. -..|+ |+|. +.|+-...|.++|+.+.
T Consensus 51 hatnsellceaflh-aftgq--plpt----d~dl~ker~deipe~ak 90 (105)
T COG3060 51 HATNSELLCEAFLH-AFTGQ--PLPT----DADLRKERSDEIPEAAK 90 (105)
T ss_pred hhhhHHHHHHHHHH-HHcCC--CCCC----cHHHHHhccccchHHHH
Confidence 457788888 554 56788 8874 67888888999998763
No 7
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=27.48 E-value=70 Score=19.76 Aligned_cols=20 Identities=35% Similarity=0.497 Sum_probs=13.0
Q ss_pred CCceEcC----ChHHHHH---HHHHhH
Q 038974 4 PGVVFNP----TEEDRVS---YLIGKV 23 (134)
Q Consensus 4 ~G~rF~P----tDeELi~---YL~~k~ 23 (134)
.|+||.| ||+|... -|..|+
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kL 48 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKL 48 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHH
Confidence 5999998 5666544 444554
No 8
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=27.12 E-value=69 Score=21.47 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=28.4
Q ss_pred cCChHHHHH--HHHHhHcCCCCCCCCCceEeccCCCCCCcccchhc
Q 038974 9 NPTEEDRVS--YLIGKVSGHTDGGGSYFIQDIQLCEHEPWELLSLA 52 (134)
Q Consensus 9 ~PtDeELi~--YL~~k~~g~~~~~~~~~I~~~Dvy~~~Pw~L~~~~ 52 (134)
|-|..||++ ||. -..|+ |+|. +.|+-...|.++|..+
T Consensus 50 HATNSELLCEAFLH-AfTGQ--PLP~----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLH-AFTGQ--PLPD----DADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHH-HhcCC--CCCC----hhhhhhcCcccccHHH
Confidence 457789998 665 46788 8885 5688888899998865
No 9
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=27.00 E-value=44 Score=15.23 Aligned_cols=7 Identities=14% Similarity=0.467 Sum_probs=5.6
Q ss_pred ccEEEEe
Q 038974 58 QQMYFTH 64 (134)
Q Consensus 58 ~~~yFF~ 64 (134)
+.||||.
T Consensus 8 ~~wYy~~ 14 (19)
T PF01473_consen 8 GNWYYFD 14 (19)
T ss_dssp TEEEEET
T ss_pred CEEEEeC
Confidence 7899983
No 10
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=26.70 E-value=38 Score=18.41 Aligned_cols=19 Identities=32% Similarity=0.532 Sum_probs=9.5
Q ss_pred eEcCChHHHHH---HHHHhHcCC
Q 038974 7 VFNPTEEDRVS---YLIGKVSGH 26 (134)
Q Consensus 7 rF~PtDeELi~---YL~~k~~g~ 26 (134)
.|+||.||--+ ||.. +...
T Consensus 2 vf~Pt~eEF~dp~~yi~~-i~~~ 23 (34)
T PF02375_consen 2 VFYPTMEEFKDPIKYISS-IEPE 23 (34)
T ss_dssp EE---HHHHS-HHHHHHH-HHHT
T ss_pred cccCCHHHHhCHHHHHHH-HHHH
Confidence 48999999988 5544 4433
No 11
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=25.74 E-value=39 Score=18.99 Aligned_cols=11 Identities=27% Similarity=0.359 Sum_probs=8.7
Q ss_pred ceEcCChHHHH
Q 038974 6 VVFNPTEEDRV 16 (134)
Q Consensus 6 ~rF~PtDeELi 16 (134)
||+.||+++..
T Consensus 7 ~rl~Pt~~Q~~ 17 (46)
T PF12323_consen 7 YRLYPTKEQEE 17 (46)
T ss_pred EEEecCHHHHH
Confidence 68899998754
No 12
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=24.52 E-value=57 Score=19.92 Aligned_cols=19 Identities=16% Similarity=0.174 Sum_probs=14.6
Q ss_pred EcCChHHHHHHHHHhHcCC
Q 038974 8 FNPTEEDRVSYLIGKVSGH 26 (134)
Q Consensus 8 F~PtDeELi~YL~~k~~g~ 26 (134)
|..|.+||-.||-.++...
T Consensus 31 ~~~s~~eL~~fL~~lv~e~ 49 (60)
T PF08672_consen 31 YDISLEELQEFLDRLVEEG 49 (60)
T ss_dssp TT--HHHHHHHHHHHHHTT
T ss_pred CCCCHHHHHHHHHHHHHCC
Confidence 5677888888999999887
No 13
>PRK10154 hypothetical protein; Provisional
Probab=24.19 E-value=42 Score=23.88 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=16.1
Q ss_pred EEEEEEEEEe---cCCCCCeEEEE
Q 038974 101 AVKKSLNYYK---KDVKTQWLMTC 121 (134)
Q Consensus 101 G~kk~~~fy~---~~~kt~W~M~E 121 (134)
|..++|.|+. ++..|+|+=--
T Consensus 78 g~s~tl~f~~~lk~~q~T~W~~~~ 101 (134)
T PRK10154 78 SASQSLNIPSEIKEGQTTDWININ 101 (134)
T ss_pred CCceEEecchhhccCCccccEEcc
Confidence 3448899988 78999998544
No 14
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=24.01 E-value=85 Score=24.42 Aligned_cols=24 Identities=13% Similarity=0.155 Sum_probs=17.7
Q ss_pred CCCCceEcCChHHHHHHHHHhHcCC
Q 038974 2 LPPGVVFNPTEEDRVSYLIGKVSGH 26 (134)
Q Consensus 2 LP~G~rF~PtDeELi~YL~~k~~g~ 26 (134)
+||.| |.|++++|+.|.+.-+...
T Consensus 102 ~~P~~-~~~~~~~l~~~~~~ia~~~ 125 (284)
T cd00950 102 VTPYY-NKPSQEGLYAHFKAIAEAT 125 (284)
T ss_pred ccccc-CCCCHHHHHHHHHHHHhcC
Confidence 46644 8899999999777666554
No 15
>PF08990 Docking: Erythronolide synthase docking; InterPro: IPR015083 The N-terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function []. ; GO: 0016740 transferase activity, 0048037 cofactor binding; PDB: 2HG4_E.
Probab=23.97 E-value=43 Score=17.29 Aligned_cols=13 Identities=23% Similarity=0.281 Sum_probs=7.9
Q ss_pred CChHHHHHHHHHh
Q 038974 10 PTEEDRVSYLIGK 22 (134)
Q Consensus 10 PtDeELi~YL~~k 22 (134)
++++.|.+||+.=
T Consensus 2 ~~e~kLr~YLkr~ 14 (27)
T PF08990_consen 2 ANEDKLRDYLKRV 14 (27)
T ss_dssp --HCHHHHHHHHH
T ss_pred CcHHHHHHHHHHH
Confidence 3566777799753
No 16
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=23.36 E-value=84 Score=21.21 Aligned_cols=37 Identities=19% Similarity=0.215 Sum_probs=28.3
Q ss_pred cCChHHHHH--HHHHhHcCCCCCCCCCceEeccCCCCCCcccchhc
Q 038974 9 NPTEEDRVS--YLIGKVSGHTDGGGSYFIQDIQLCEHEPWELLSLA 52 (134)
Q Consensus 9 ~PtDeELi~--YL~~k~~g~~~~~~~~~I~~~Dvy~~~Pw~L~~~~ 52 (134)
|-|..||++ ||. -..|+ |+|. +-|+-...|-++|..+
T Consensus 51 HATNSELLCEAFLH-A~TGQ--PLP~----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLH-AFTGQ--PLPD----DEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHH-HHcCC--CCCC----hhhhhhcCcccchHHH
Confidence 457789998 665 46788 8885 5688888899998765
No 17
>PRK14390 hypothetical protein; Provisional
Probab=23.11 E-value=39 Score=21.05 Aligned_cols=14 Identities=21% Similarity=0.420 Sum_probs=11.3
Q ss_pred CCCCCceEcCChHH
Q 038974 1 MLPPGVVFNPTEED 14 (134)
Q Consensus 1 ~LP~G~rF~PtDeE 14 (134)
.+|+-.||.||=.|
T Consensus 12 ~~~~~CRf~PTCS~ 25 (63)
T PRK14390 12 FFGPRCRFIPSCSS 25 (63)
T ss_pred CCCCCCCcCccHHH
Confidence 36889999999665
No 18
>TIGR03874 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Probab=22.85 E-value=61 Score=23.42 Aligned_cols=23 Identities=22% Similarity=0.167 Sum_probs=18.3
Q ss_pred CCceEcCChH-HH---HHHHHHhHcCC
Q 038974 4 PGVVFNPTEE-DR---VSYLIGKVSGH 26 (134)
Q Consensus 4 ~G~rF~PtDe-EL---i~YL~~k~~g~ 26 (134)
|+|.-..+|+ || +.||+....|.
T Consensus 93 PaF~~~LsD~~eIa~L~~YLR~~~~g~ 119 (143)
T TIGR03874 93 PAFGDNPNVMCYLDDLYVYLRARGTDA 119 (143)
T ss_pred CCccccCCcHHHHHHHHHHHHhccCCC
Confidence 7888899987 44 44999988887
No 19
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=22.63 E-value=87 Score=18.30 Aligned_cols=17 Identities=12% Similarity=-0.011 Sum_probs=12.4
Q ss_pred CChHHHHH-HHHHhHcCC
Q 038974 10 PTEEDRVS-YLIGKVSGH 26 (134)
Q Consensus 10 PtDeELi~-YL~~k~~g~ 26 (134)
=||+.||. |.+.+-.+-
T Consensus 4 LSDe~LiesY~~A~el~L 21 (46)
T PF08970_consen 4 LSDELLIESYHKAIELNL 21 (46)
T ss_dssp S-HHHHHHHHHHHHHTT-
T ss_pred ccHHHHHHHHHHHHHhCC
Confidence 37999999 998876665
No 20
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=21.05 E-value=1e+02 Score=15.92 Aligned_cols=17 Identities=24% Similarity=0.282 Sum_probs=13.9
Q ss_pred CChHHHHH-HHHHhHcCC
Q 038974 10 PTEEDRVS-YLIGKVSGH 26 (134)
Q Consensus 10 PtDeELi~-YL~~k~~g~ 26 (134)
.+-.|||. |+.-|+.-.
T Consensus 3 ~~nRelV~~yv~yKLsQr 20 (27)
T smart00265 3 LDNRELVVDYVTYKLSQN 20 (27)
T ss_pred cchHHHHHHHHHHHHhhc
Confidence 35689999 999998766
No 21
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=21.02 E-value=71 Score=25.10 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=25.3
Q ss_pred hHHHHH-HHHHhHcCCCCCCCCCceEe---ccCCCCCCcccch
Q 038974 12 EEDRVS-YLIGKVSGHTDGGGSYFIQD---IQLCEHEPWELLS 50 (134)
Q Consensus 12 DeELi~-YL~~k~~g~~~~~~~~~I~~---~Dvy~~~Pw~L~~ 50 (134)
|||++. ||.. .+. |-|+-+|.+ ..+-.+-||++.-
T Consensus 172 ~e~~i~~~L~~--~~~--pdpDLlIRTsGe~RlSnFllWQ~aY 210 (245)
T COG0020 172 DEELISSHLYT--SGL--PDPDLLIRTSGEQRLSNFLLWQSAY 210 (245)
T ss_pred CHHHHHHhhcc--cCC--CCCCEEEeCCCcccccccHHHHHHh
Confidence 688888 9988 555 545556665 4777888999865
No 22
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=20.92 E-value=1.3e+02 Score=21.95 Aligned_cols=37 Identities=16% Similarity=0.145 Sum_probs=23.5
Q ss_pred hHHHHH-HHHHhHcCCCCCCCCCceEe---ccCCCCCCcccch
Q 038974 12 EEDRVS-YLIGKVSGHTDGGGSYFIQD---IQLCEHEPWELLS 50 (134)
Q Consensus 12 DeELi~-YL~~k~~g~~~~~~~~~I~~---~Dvy~~~Pw~L~~ 50 (134)
=.++|. ||+..+... +-..-.|.- +|-+.|-|.++--
T Consensus 4 lSD~IE~yik~lL~~s--~~~~ieIqR~eLA~~F~CvPSQINY 44 (152)
T PF05848_consen 4 LSDIIEQYIKQLLEES--EEGQIEIQRNELAERFNCVPSQINY 44 (152)
T ss_dssp HHHHHHHHHHHHHCTS--TTSEEEE-HHHHHHHTTS-THHHHH
T ss_pred HHHHHHHHHHHHHHhC--CCCeEEEeHHHHHHHhCCchhhhhe
Confidence 357899 999998887 211112332 2668999999954
No 23
>PF11141 DUF2914: Protein of unknown function (DUF2914); InterPro: IPR022606 This bacterial family of proteins has no known function.
Probab=20.46 E-value=1.4e+02 Score=18.38 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=14.7
Q ss_pred ccceeeecCCCceEeCCCCceEEEEE
Q 038974 79 VCGFWKNLGLSSYINDKGGKPVAVKK 104 (134)
Q Consensus 79 ~~G~Wk~~g~~~~i~~~~g~~iG~kk 104 (134)
..|-|+.. |.+.+|++||..+
T Consensus 42 ~~G~WrV~-----V~~~~G~~l~~~~ 62 (66)
T PF11141_consen 42 QPGDWRVE-----VVDEDGQVLGSLR 62 (66)
T ss_pred CCcCEEEE-----EEcCCCCEEEEEE
Confidence 45667755 6777888888754
No 24
>PF12043 DUF3527: Domain of unknown function (DUF3527); InterPro: IPR021916 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.
Probab=20.10 E-value=2.6e+02 Score=23.28 Aligned_cols=82 Identities=16% Similarity=0.108 Sum_probs=42.8
Q ss_pred cCCCCCCcccchhcccCCCccEEEEeeccccCCCCceeeeccceeeecCCCceEeCCCCceEEEEEEEEEEe-cCCCCC-
Q 038974 39 QLCEHEPWELLSLAHDCCHQQMYFTHLRSRYHSEMVYREAVCGFWKNLGLSSYINDKGGKPVAVKKSLNYYK-KDVKTQ- 116 (134)
Q Consensus 39 Dvy~~~Pw~L~~~~~~~~~~~~yFF~~~~~~~~g~~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~kk~~~fy~-~~~kt~- 116 (134)
|||....|.+--...... +-.|-|.-.+ .++-+.|.|...+....= .+.+||..++=.+.. ...+.+
T Consensus 29 ~VlaAt~~k~~~~~~~~~-~~vYTFhs~~-------e~KKks~~w~~~~~k~k~---~~~iVGQMkVSss~~~~~~~~~~ 97 (346)
T PF12043_consen 29 EVLAATMWKSGSSDKNDL-NWVYTFHSIK-------EVKKKSGSWINSGDKNKS---SSNIVGQMKVSSSLSSEPSKQGS 97 (346)
T ss_pred cEEEEEEeeccccccccc-ceEEEEEeec-------cccccccccccccccccC---CcceEEEEEeeeeeeecccCCcc
Confidence 677777777642211111 2335444331 112236667766532211 226899988866655 222222
Q ss_pred eEEEEEEeCCCCCCc
Q 038974 117 WLMTCTHFCTITSIR 131 (134)
Q Consensus 117 W~M~Ey~l~~~~~~~ 131 (134)
=+..||.|-+.+.++
T Consensus 98 s~~~EFVLf~~~~~~ 112 (346)
T PF12043_consen 98 SMVTEFVLFGVDHAR 112 (346)
T ss_pred eeEEEEEEEeccccc
Confidence 477799988865543
No 25
>PF10807 DUF2541: Protein of unknown function (DUF2541); InterPro: IPR020240 This entry represents proteins found in the Gammaproteobacteria that have no known function.
Probab=20.05 E-value=61 Score=23.13 Aligned_cols=20 Identities=20% Similarity=0.529 Sum_probs=15.5
Q ss_pred EEEEEEEEEe---cCCCCCeEEE
Q 038974 101 AVKKSLNYYK---KDVKTQWLMT 120 (134)
Q Consensus 101 G~kk~~~fy~---~~~kt~W~M~ 120 (134)
|.-++|.|+. ++.+|+|+--
T Consensus 78 g~s~~l~~~~~ikeg~tT~Wi~i 100 (134)
T PF10807_consen 78 GESQTLNFPRSIKEGQTTDWINI 100 (134)
T ss_pred ccceEEcccccccCCCccCcEEe
Confidence 4447888888 7899999855
Done!