Query 038876
Match_columns 127
No_of_seqs 116 out of 809
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 04:09:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038876.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038876hhsearch_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 1.8E-40 3.8E-45 233.1 6.1 110 8-125 1-110 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 60.2 12 0.00027 19.3 2.4 22 16-37 3-24 (27)
3 smart00707 RPEL Repeat in Dros 57.4 6.2 0.00013 20.2 0.9 14 11-24 6-19 (26)
4 PF07960 CBP4: CBP4; InterPro 56.6 6.2 0.00013 27.9 1.2 12 14-25 29-40 (128)
5 PF06214 SLAM: Signaling lymph 48.1 3.9 8.4E-05 28.4 -0.9 49 26-76 74-123 (126)
6 cd00490 Met_repressor_MetJ Met 46.7 22 0.00047 23.7 2.5 38 15-58 50-87 (103)
7 PF13822 ACC_epsilon: Acyl-CoA 46.2 11 0.00024 23.0 1.0 9 15-23 10-18 (62)
8 COG3060 MetJ Transcriptional r 45.9 15 0.00032 24.3 1.6 38 15-58 51-88 (105)
9 PF09174 Maf1: Maf1 regulator; 45.0 6.5 0.00014 29.0 -0.2 14 42-55 137-150 (179)
10 PF01473 CW_binding_1: Putativ 44.1 16 0.00035 16.7 1.2 9 67-75 7-15 (19)
11 PRK05264 transcriptional repre 43.1 25 0.00053 23.6 2.3 38 15-58 51-88 (105)
12 PHA00692 hypothetical protein 42.2 9.4 0.0002 23.5 0.2 10 7-16 36-45 (74)
13 PF02180 BH4: Bcl-2 homology r 41.4 25 0.00055 18.1 1.7 21 17-37 4-24 (27)
14 PF01340 MetJ: Met Apo-repress 38.0 25 0.00055 23.4 1.8 38 15-58 50-87 (104)
15 PF02755 RPEL: RPEL repeat; I 36.5 21 0.00046 18.1 1.0 12 13-24 8-19 (26)
16 PLN02417 dihydrodipicolinate s 33.9 29 0.00062 27.1 1.8 18 7-25 102-119 (280)
17 cd00954 NAL N-Acetylneuraminic 33.4 29 0.00063 27.0 1.8 18 8-26 103-120 (288)
18 TIGR02313 HpaI-NOT-DapA 2,4-di 32.1 33 0.00072 26.9 1.9 18 7-25 101-118 (294)
19 PF10107 Endonuc_Holl: Endonuc 31.3 12 0.00026 27.3 -0.6 18 2-19 79-96 (156)
20 PF07131 DUF1382: Protein of u 31.0 36 0.00078 20.9 1.5 14 10-23 22-39 (61)
21 cd00952 CHBPH_aldolase Trans-o 30.3 35 0.00076 27.0 1.8 19 6-25 108-126 (309)
22 PRK02079 pyrroloquinoline quin 29.7 32 0.0007 22.4 1.3 15 1-15 1-15 (88)
23 PF02375 JmjN: jmjN domain; I 29.5 27 0.00058 18.9 0.7 11 13-23 2-12 (34)
24 cd00950 DHDPS Dihydrodipicolin 28.0 43 0.00092 25.8 1.9 29 7-37 101-129 (284)
25 TIGR00674 dapA dihydrodipicoli 27.6 49 0.0011 25.7 2.2 19 7-26 99-117 (285)
26 PRK03170 dihydrodipicolinate s 26.5 48 0.001 25.7 2.0 29 7-37 102-130 (292)
27 PRK04147 N-acetylneuraminate l 26.0 47 0.001 25.9 1.8 28 8-37 106-133 (293)
28 COG4472 Uncharacterized protei 22.7 58 0.0012 21.3 1.4 11 19-29 74-84 (88)
29 PF06042 DUF925: Bacterial pro 22.1 44 0.00095 24.4 0.9 33 22-57 19-51 (163)
30 PF12375 DUF3653: Phage protei 21.7 29 0.00062 22.1 -0.1 23 1-23 4-26 (76)
31 TIGR02935 probable nitrogen fi 21.5 58 0.0013 23.3 1.4 22 16-37 24-45 (140)
32 COG0442 ProS Prolyl-tRNA synth 21.0 71 0.0015 27.5 2.0 26 12-37 104-130 (500)
33 PRK05473 hypothetical protein; 20.9 69 0.0015 21.1 1.5 11 19-29 74-84 (86)
34 TIGR03249 KdgD 5-dehydro-4-deo 20.5 73 0.0016 24.9 1.9 29 7-37 105-133 (296)
35 PF03540 TFIID_30kDa: Transcri 20.5 76 0.0017 18.8 1.5 11 18-28 4-14 (51)
36 PRK14390 hypothetical protein; 20.3 55 0.0012 20.2 0.9 45 5-54 10-54 (63)
37 PRK03620 5-dehydro-4-deoxygluc 20.2 71 0.0015 25.1 1.8 29 7-37 107-135 (303)
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=1.8e-40 Score=233.07 Aligned_cols=110 Identities=40% Similarity=0.683 Sum_probs=78.9
Q ss_pred CCCCeeECCChHHHHHHHHHhhhcCCCCCcccCccccccCCCCCCccccccCCCCccCCCCcEEEEeccccccCCCCccc
Q 038876 8 LPHGFQFRPSDEELIEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSEIWDSHGGPFLNADEDLYFFTHLKKKFSKGSRID 87 (127)
Q Consensus 8 lp~G~rF~PTDeELi~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~L~~~~~~~~~~~~~~wyFF~~~~~k~~~g~R~~ 87 (127)
|||||||+|||+|||.+||++|+.|.++|. ..+|+++|||++|||+|+..+. ..+++|||||++++++.++.|.+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~-~~~i~~~Diy~~~P~~L~~~~~----~~~~~~yFF~~~~~~~~~~~r~~ 75 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPC-EDVIHDVDIYSAHPWELPAKFK----GGDEEWYFFSPRKKKYPNGGRPN 75 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGGS-GGGCHHHSS----S-SSEEEEEEE----------S-
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCc-ccceeecccCccChHHhhhhcc----CCCceEEEEEecccccCCccccc
Confidence 899999999999999999999999999887 5789999999999999995322 25679999999999998999999
Q ss_pred ceecCCCceEeeccCCceEEeCCCceEEEEEEEEEEEe
Q 038876 88 RKVGSSGGTWQGEDAGKDIVSGQSKIKIGSKKRFRYEK 125 (127)
Q Consensus 88 R~~g~~~G~W~~~g~~~~I~~~~~~~~iG~kk~l~f~~ 125 (127)
|++ ++|+||++|+.++|.+. ++++||+|++|+||.
T Consensus 76 R~~--~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~ 110 (129)
T PF02365_consen 76 RVT--GGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYS 110 (129)
T ss_dssp EEE--TTEEEEEECEEEEEEE--TTCEEEEEEEEEEEE
T ss_pred ccc--cceEEeecccccccccc-cceeeeeEEEEEEEe
Confidence 987 69999999999999986 578999999999995
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=60.20 E-value=12 Score=19.28 Aligned_cols=22 Identities=23% Similarity=0.125 Sum_probs=17.1
Q ss_pred CChHHHHHHHHHhhhcCCCCCc
Q 038876 16 PSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 16 PTDeELi~~YL~~K~~g~~lp~ 37 (127)
.+-.|||.+|+.-|+.-+..+.
T Consensus 3 ~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 3 LDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred cchHHHHHHHHHHHHhhcCCCC
Confidence 3568999999999998665543
No 3
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=57.40 E-value=6.2 Score=20.21 Aligned_cols=14 Identities=43% Similarity=0.589 Sum_probs=11.3
Q ss_pred CeeECCChHHHHHH
Q 038876 11 GFQFRPSDEELIEH 24 (127)
Q Consensus 11 G~rF~PTDeELi~~ 24 (127)
....+||.||||..
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 45689999999973
No 4
>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=56.63 E-value=6.2 Score=27.88 Aligned_cols=12 Identities=42% Similarity=0.866 Sum_probs=10.1
Q ss_pred ECCChHHHHHHH
Q 038876 14 FRPSDEELIEHY 25 (127)
Q Consensus 14 F~PTDeELi~~Y 25 (127)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 479999999875
No 5
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=48.15 E-value=3.9 Score=28.41 Aligned_cols=49 Identities=20% Similarity=0.045 Sum_probs=25.9
Q ss_pred HHhhhcCCCCCcccCcccc-ccCCCCCCccccccCCCCccCCCCcEEEEecc
Q 038876 26 LKKKDSGIFIPLAEYFIRD-CNLYQEKPSEIWDSHGGPFLNADEDLYFFTHL 76 (127)
Q Consensus 26 L~~K~~g~~lp~~~~~I~~-~Dvy~~~P~~L~~~~~~~~~~~~~~wyFF~~~ 76 (127)
.++||..-+++. ..--+. -|=|.+|+..|.-..-.+ ..+++-|||.+-.
T Consensus 74 vkkKIvSldl~e-g~sp~yledgY~FhlEnLsL~Il~S-rkE~EGWYfmtlE 123 (126)
T PF06214_consen 74 VKKKIVSLDLSE-GGSPRYLEDGYKFHLENLSLEILES-RKEDEGWYFMTLE 123 (126)
T ss_dssp --EEEEEE-TTS--SS-EESSSSEEEETTTTEEEETT---GGG-EEEEEEEE
T ss_pred hhheEEEecccc-CCCccccccccEEecccceeehhcc-ccccCceEEEEee
Confidence 356676666655 122222 278888988886542222 2256789998754
No 6
>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=46.68 E-value=22 Score=23.67 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=29.9
Q ss_pred CCChHHHHHHHHHhhhcCCCCCcccCccccccCCCCCCcccccc
Q 038876 15 RPSDEELIEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSEIWDS 58 (127)
Q Consensus 15 ~PTDeELi~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~L~~~ 58 (127)
+-|..||++.-...-..|+|||. |.|+-...|..+|+.
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~------D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD------DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC------hhhhhhcCcccccHH
Confidence 34667888776667778999998 678888888888874
No 7
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=46.18 E-value=11 Score=22.99 Aligned_cols=9 Identities=56% Similarity=0.907 Sum_probs=7.6
Q ss_pred CCChHHHHH
Q 038876 15 RPSDEELIE 23 (127)
Q Consensus 15 ~PTDeELi~ 23 (127)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999864
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=45.88 E-value=15 Score=24.34 Aligned_cols=38 Identities=24% Similarity=0.371 Sum_probs=29.9
Q ss_pred CCChHHHHHHHHHhhhcCCCCCcccCccccccCCCCCCcccccc
Q 038876 15 RPSDEELIEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSEIWDS 58 (127)
Q Consensus 15 ~PTDeELi~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~L~~~ 58 (127)
+-|..||++.-...-..|+|||. +.|+-..-|.++|+.
T Consensus 51 hatnsellceaflhaftgqplpt------d~dl~ker~deipe~ 88 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT------DADLRKERSDEIPEA 88 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC------cHHHHHhccccchHH
Confidence 34667888776667778999998 778888888888874
No 9
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=44.96 E-value=6.5 Score=29.00 Aligned_cols=14 Identities=29% Similarity=0.888 Sum_probs=7.6
Q ss_pred cccccCCCCCCccc
Q 038876 42 IRDCNLYQEKPSEI 55 (127)
Q Consensus 42 I~~~Dvy~~~P~~L 55 (127)
+.+||||++.|..-
T Consensus 137 l~~C~iYsy~pd~~ 150 (179)
T PF09174_consen 137 LKDCDIYSYNPDSD 150 (179)
T ss_dssp GGG-EEEEE---GG
T ss_pred ccCceEEEEccCCC
Confidence 56799999999543
No 10
>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=44.15 E-value=16 Score=16.66 Aligned_cols=9 Identities=22% Similarity=0.837 Sum_probs=7.0
Q ss_pred CCcEEEEec
Q 038876 67 DEDLYFFTH 75 (127)
Q Consensus 67 ~~~wyFF~~ 75 (127)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 578999953
No 11
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=43.10 E-value=25 Score=23.56 Aligned_cols=38 Identities=24% Similarity=0.317 Sum_probs=29.7
Q ss_pred CCChHHHHHHHHHhhhcCCCCCcccCccccccCCCCCCcccccc
Q 038876 15 RPSDEELIEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSEIWDS 58 (127)
Q Consensus 15 ~PTDeELi~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~L~~~ 58 (127)
+-|..||++.-...-..|+|||. |-|+-...|..+|+.
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~------D~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD------DEDLRKERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC------hhhhhhcCcccchHH
Confidence 34667888776667778999998 678888888888863
No 12
>PHA00692 hypothetical protein
Probab=42.16 E-value=9.4 Score=23.48 Aligned_cols=10 Identities=40% Similarity=0.737 Sum_probs=8.0
Q ss_pred CCCCCeeECC
Q 038876 7 FLPHGFQFRP 16 (127)
Q Consensus 7 ~lp~G~rF~P 16 (127)
..||||||--
T Consensus 36 eyppgfrfgg 45 (74)
T PHA00692 36 EYPPGFRFGG 45 (74)
T ss_pred ecCCCccccc
Confidence 5799999953
No 13
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=41.39 E-value=25 Score=18.13 Aligned_cols=21 Identities=29% Similarity=0.256 Sum_probs=16.0
Q ss_pred ChHHHHHHHHHhhhcCCCCCc
Q 038876 17 SDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 17 TDeELi~~YL~~K~~g~~lp~ 37 (127)
+-+|||.+|+.-|+.-+..+.
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~w 24 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYVW 24 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTSTS
T ss_pred cHHHHHHHHHHHHhhhcCCCC
Confidence 357999999999997655443
No 14
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=37.98 E-value=25 Score=23.41 Aligned_cols=38 Identities=24% Similarity=0.360 Sum_probs=22.8
Q ss_pred CCChHHHHHHHHHhhhcCCCCCcccCccccccCCCCCCcccccc
Q 038876 15 RPSDEELIEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSEIWDS 58 (127)
Q Consensus 15 ~PTDeELi~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~L~~~ 58 (127)
+-|..||++.-...-..|+|||. |.|+-...|..+|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~------D~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT------DDDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------------TTGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC------hhhhhhcCCccchHH
Confidence 45777888776667778999998 668888888888863
No 15
>PF02755 RPEL: RPEL repeat; InterPro: IPR004018 The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that Q9VZY2 from SWISSPROT contains a SAP domain that is also implicated in DNA binding.; PDB: 2YJE_M 2V52_M 2YJF_M 2V51_E.
Probab=36.53 E-value=21 Score=18.11 Aligned_cols=12 Identities=50% Similarity=0.822 Sum_probs=6.8
Q ss_pred eECCChHHHHHH
Q 038876 13 QFRPSDEELIEH 24 (127)
Q Consensus 13 rF~PTDeELi~~ 24 (127)
..+|+-+|||..
T Consensus 8 ~~RP~~~eLv~r 19 (26)
T PF02755_consen 8 SQRPTREELVER 19 (26)
T ss_dssp HT---HHHHHHT
T ss_pred hcCCCHHHHHHc
Confidence 358999999963
No 16
>PLN02417 dihydrodipicolinate synthase
Probab=33.93 E-value=29 Score=27.05 Aligned_cols=18 Identities=28% Similarity=0.517 Sum_probs=14.4
Q ss_pred CCCCCeeECCChHHHHHHH
Q 038876 7 FLPHGFQFRPSDEELIEHY 25 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~Y 25 (127)
-+|| +.|.||++||+.||
T Consensus 102 ~~~P-~y~~~~~~~i~~~f 119 (280)
T PLN02417 102 HINP-YYGKTSQEGLIKHF 119 (280)
T ss_pred EcCC-ccCCCCHHHHHHHH
Confidence 3556 55899999999987
No 17
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=33.44 E-value=29 Score=27.05 Aligned_cols=18 Identities=22% Similarity=0.198 Sum_probs=13.5
Q ss_pred CCCCeeECCChHHHHHHHH
Q 038876 8 LPHGFQFRPSDEELIEHYL 26 (127)
Q Consensus 8 lp~G~rF~PTDeELi~~YL 26 (127)
+||- .|.||++||+.||.
T Consensus 103 ~~P~-y~~~~~~~i~~~~~ 120 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYR 120 (288)
T ss_pred eCCC-CCCCCHHHHHHHHH
Confidence 4554 47899999998763
No 18
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=32.08 E-value=33 Score=26.92 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=14.0
Q ss_pred CCCCCeeECCChHHHHHHH
Q 038876 7 FLPHGFQFRPSDEELIEHY 25 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~Y 25 (127)
-+||-| |.||++||+.||
T Consensus 101 v~pP~y-~~~~~~~l~~~f 118 (294)
T TIGR02313 101 VIVPYY-NKPNQEALYDHF 118 (294)
T ss_pred EcCccC-CCCCHHHHHHHH
Confidence 345554 899999999976
No 19
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=31.29 E-value=12 Score=27.29 Aligned_cols=18 Identities=22% Similarity=0.403 Sum_probs=13.8
Q ss_pred CCCCCCCCCCeeECCChH
Q 038876 2 QEHRPFLPHGFQFRPSDE 19 (127)
Q Consensus 2 ~~~~~~lp~G~rF~PTDe 19 (127)
.++-.++-|+|.++|+|.
T Consensus 79 ~EqlaP~lp~F~ynP~D~ 96 (156)
T PF10107_consen 79 SEQLAPFLPEFPYNPKDA 96 (156)
T ss_pred HHHhhhccCCCCCChhhh
Confidence 345566779999999985
No 20
>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=30.96 E-value=36 Score=20.87 Aligned_cols=14 Identities=43% Similarity=0.776 Sum_probs=10.6
Q ss_pred CCeeECC----ChHHHHH
Q 038876 10 HGFQFRP----SDEELIE 23 (127)
Q Consensus 10 ~G~rF~P----TDeELi~ 23 (127)
.|+||.| ||+|+..
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999999 6777643
No 21
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=30.30 E-value=35 Score=27.03 Aligned_cols=19 Identities=5% Similarity=0.044 Sum_probs=15.0
Q ss_pred CCCCCCeeECCChHHHHHHH
Q 038876 6 PFLPHGFQFRPSDEELIEHY 25 (127)
Q Consensus 6 ~~lp~G~rF~PTDeELi~~Y 25 (127)
+-+|| +.|.||++||+.||
T Consensus 108 lv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 108 MLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EECCC-cCCCCCHHHHHHHH
Confidence 34566 56899999999977
No 22
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=29.69 E-value=32 Score=22.43 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCeeEC
Q 038876 1 MQEHRPFLPHGFQFR 15 (127)
Q Consensus 1 m~~~~~~lp~G~rF~ 15 (127)
|.+....||+||||+
T Consensus 1 ~~~~~p~l~~~~rl~ 15 (88)
T PRK02079 1 DRNQVPTLRPGYRFQ 15 (88)
T ss_pred CCCCCcccCCCcccc
Confidence 456667899999887
No 23
>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=29.48 E-value=27 Score=18.87 Aligned_cols=11 Identities=36% Similarity=0.594 Sum_probs=5.3
Q ss_pred eECCChHHHHH
Q 038876 13 QFRPSDEELIE 23 (127)
Q Consensus 13 rF~PTDeELi~ 23 (127)
-|+||.||.-+
T Consensus 2 vf~Pt~eEF~d 12 (34)
T PF02375_consen 2 VFYPTMEEFKD 12 (34)
T ss_dssp EE---HHHHS-
T ss_pred cccCCHHHHhC
Confidence 38999999754
No 24
>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=27.96 E-value=43 Score=25.84 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=18.5
Q ss_pred CCCCCeeECCChHHHHHHHHHhhhcCCCCCc
Q 038876 7 FLPHGFQFRPSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~YL~~K~~g~~lp~ 37 (127)
-+||.| |.||++||+.|| +.=+...++|.
T Consensus 101 ~~~P~~-~~~~~~~l~~~~-~~ia~~~~~pi 129 (284)
T cd00950 101 VVTPYY-NKPSQEGLYAHF-KAIAEATDLPV 129 (284)
T ss_pred Eccccc-CCCCHHHHHHHH-HHHHhcCCCCE
Confidence 456644 889999999865 43333334554
No 25
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=27.60 E-value=49 Score=25.67 Aligned_cols=19 Identities=21% Similarity=0.499 Sum_probs=14.2
Q ss_pred CCCCCeeECCChHHHHHHHH
Q 038876 7 FLPHGFQFRPSDEELIEHYL 26 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~YL 26 (127)
-+||-| |.||++||+.||.
T Consensus 99 v~pP~y-~~~~~~~i~~~~~ 117 (285)
T TIGR00674 99 VVTPYY-NKPTQEGLYQHFK 117 (285)
T ss_pred EcCCcC-CCCCHHHHHHHHH
Confidence 345554 7899999999774
No 26
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=26.51 E-value=48 Score=25.72 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=18.7
Q ss_pred CCCCCeeECCChHHHHHHHHHhhhcCCCCCc
Q 038876 7 FLPHGFQFRPSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~YL~~K~~g~~lp~ 37 (127)
-+||-| |.||++||+.|| +.=+...++|.
T Consensus 102 ~~pP~~-~~~~~~~i~~~~-~~ia~~~~~pv 130 (292)
T PRK03170 102 VVTPYY-NKPTQEGLYQHF-KAIAEATDLPI 130 (292)
T ss_pred ECCCcC-CCCCHHHHHHHH-HHHHhcCCCCE
Confidence 356655 889999999865 33333334554
No 27
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=26.00 E-value=47 Score=25.90 Aligned_cols=28 Identities=18% Similarity=0.126 Sum_probs=17.7
Q ss_pred CCCCeeECCChHHHHHHHHHhhhcCCCCCc
Q 038876 8 LPHGFQFRPSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 8 lp~G~rF~PTDeELi~~YL~~K~~g~~lp~ 37 (127)
+||- -|.||++||+.|| +.=+...++|.
T Consensus 106 ~~P~-y~~~~~~~l~~~f-~~va~a~~lPv 133 (293)
T PRK04147 106 VTPF-YYPFSFEEICDYY-REIIDSADNPM 133 (293)
T ss_pred eCCc-CCCCCHHHHHHHH-HHHHHhCCCCE
Confidence 3444 4899999999865 33333345665
No 28
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.73 E-value=58 Score=21.29 Aligned_cols=11 Identities=55% Similarity=0.848 Sum_probs=9.1
Q ss_pred HHHHHHHHHhh
Q 038876 19 EELIEHYLKKK 29 (127)
Q Consensus 19 eELi~~YL~~K 29 (127)
||||.+||+.+
T Consensus 74 EElvk~YLk~~ 84 (88)
T COG4472 74 EELVKYYLKGN 84 (88)
T ss_pred HHHHHHHHhhc
Confidence 79999999754
No 29
>PF06042 DUF925: Bacterial protein of unknown function (DUF925); InterPro: IPR009267 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2LA3_A.
Probab=22.10 E-value=44 Score=24.43 Aligned_cols=33 Identities=15% Similarity=0.064 Sum_probs=19.6
Q ss_pred HHHHHHhhhcCCCCCcccCccccccCCCCCCccccc
Q 038876 22 IEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSEIWD 57 (127)
Q Consensus 22 i~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~L~~ 57 (127)
|.......+.|.+.. ..|.|+||.-+||.++..
T Consensus 19 vrn~VWn~L~g~~~~---~~i~DiDviYfD~~d~s~ 51 (163)
T PF06042_consen 19 VRNTVWNHLHGRPPS---TPINDIDVIYFDPSDLSY 51 (163)
T ss_dssp HHHHHHGGGTTS-TT------SEEEEEE--T-TS-H
T ss_pred HHHHHHHHhcCCCCC---CCCCceeEEEeCCCCCCH
Confidence 556677788888765 488999999999977764
No 30
>PF12375 DUF3653: Phage protein; InterPro: IPR021077 This entry represents a phage protein found in bacteria and viruses, they are typically between 112 and 194 amino acids in length. Note that many members are hypothetical proteins.
Probab=21.70 E-value=29 Score=22.13 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCeeECCChHHHHH
Q 038876 1 MQEHRPFLPHGFQFRPSDEELIE 23 (127)
Q Consensus 1 m~~~~~~lp~G~rF~PTDeELi~ 23 (127)
|+...+-.|.|.+|.|.|-+-..
T Consensus 4 ~~~~~LiTPeGr~~~p~~l~~~~ 26 (76)
T PF12375_consen 4 FQGGRLITPEGRRFSPQDLEWWS 26 (76)
T ss_pred eeCCeEECCCCCccCHHHHHHHH
Confidence 44566789999999999876554
No 31
>TIGR02935 probable nitrogen fixation protein. Members of this protein family, called DUF269 by Pfam model pfam03270, are strictly limited to nitrogen-fixing species, although not universal among them. The gene typically is found next to the nifX gene (see TIGRFAMs model TIGR02663).
Probab=21.46 E-value=58 Score=23.35 Aligned_cols=22 Identities=36% Similarity=0.573 Sum_probs=17.5
Q ss_pred CChHHHHHHHHHhhhcCCCCCc
Q 038876 16 PSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 16 PTDeELi~~YL~~K~~g~~lp~ 37 (127)
=||++|+..|+.-|-.-+.+|.
T Consensus 24 ~sDe~lL~pfIvtke~rr~ipi 45 (140)
T TIGR02935 24 KSDAELLAPYIVTKEERREIPI 45 (140)
T ss_pred CChHHHHHhhcCCHHHhccCCC
Confidence 4899999999987777666664
No 32
>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.98 E-value=71 Score=27.54 Aligned_cols=26 Identities=31% Similarity=0.511 Sum_probs=22.8
Q ss_pred eeECCChHHHHHHHHHhhhcC-CCCCc
Q 038876 12 FQFRPSDEELIEHYLKKKDSG-IFIPL 37 (127)
Q Consensus 12 ~rF~PTDeELi~~YL~~K~~g-~~lp~ 37 (127)
|-++||-||+|..+.+.+|.+ .+||.
T Consensus 104 l~L~PTsEe~it~~~~~~i~SYkdLPl 130 (500)
T COG0442 104 LALRPTSEEVITDMFRKWIRSYKDLPL 130 (500)
T ss_pred eeeCCCcHHHHHHHHHHHhhhhhhCCc
Confidence 568999999999999999997 56887
No 33
>PRK05473 hypothetical protein; Provisional
Probab=20.89 E-value=69 Score=21.07 Aligned_cols=11 Identities=55% Similarity=0.909 Sum_probs=8.6
Q ss_pred HHHHHHHHHhh
Q 038876 19 EELIEHYLKKK 29 (127)
Q Consensus 19 eELi~~YL~~K 29 (127)
||||.+||..+
T Consensus 74 EeLv~~Yl~~~ 84 (86)
T PRK05473 74 EELVKSYLKGN 84 (86)
T ss_pred HHHHHHHHHhc
Confidence 78899998654
No 34
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=20.54 E-value=73 Score=24.90 Aligned_cols=29 Identities=17% Similarity=0.211 Sum_probs=18.1
Q ss_pred CCCCCeeECCChHHHHHHHHHhhhcCCCCCc
Q 038876 7 FLPHGFQFRPSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~YL~~K~~g~~lp~ 37 (127)
-+|| |-|.||+++|+.||- .=+...++|.
T Consensus 105 ~~pP-~y~~~s~~~i~~~f~-~v~~a~~~pv 133 (296)
T TIGR03249 105 LLPP-YLINGEQEGLYAHVE-AVCESTDLGV 133 (296)
T ss_pred ECCC-CCCCCCHHHHHHHHH-HHHhccCCCE
Confidence 4566 447899999998763 2233334654
No 35
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=20.46 E-value=76 Score=18.76 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=9.0
Q ss_pred hHHHHHHHHHh
Q 038876 18 DEELIEHYLKK 28 (127)
Q Consensus 18 DeELi~~YL~~ 28 (127)
.+||+.|||..
T Consensus 4 PD~v~~~yL~~ 14 (51)
T PF03540_consen 4 PDEVTDYYLER 14 (51)
T ss_pred CHHHHHHHHHH
Confidence 47999999975
No 36
>PRK14390 hypothetical protein; Provisional
Probab=20.30 E-value=55 Score=20.21 Aligned_cols=45 Identities=16% Similarity=0.110 Sum_probs=25.2
Q ss_pred CCCCCCCeeECCChHHHHHHHHHhhhcCCCCCcccCccccccCCCCCCcc
Q 038876 5 RPFLPHGFQFRPSDEELIEHYLKKKDSGIFIPLAEYFIRDCNLYQEKPSE 54 (127)
Q Consensus 5 ~~~lp~G~rF~PTDeELi~~YL~~K~~g~~lp~~~~~I~~~Dvy~~~P~~ 54 (127)
..-+|+-+||.||=-|=...-+++.- .+.. ....-.-|..++||-
T Consensus 10 Sp~~~~~CRf~PTCS~Ya~~Ai~~~G---~~kG--~~l~~~RilRC~P~~ 54 (63)
T PRK14390 10 SPFFGPRCRFIPSCSSYGYEAITRHG---PWKG--GWLTLRRLSRCHPLT 54 (63)
T ss_pred CCCCCCCCCcCccHHHHHHHHHHHhC---cHHH--HHHHHHHHhcCCCCC
Confidence 45688999999997665443333221 1221 222223677777763
No 37
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=20.21 E-value=71 Score=25.15 Aligned_cols=29 Identities=17% Similarity=0.197 Sum_probs=18.3
Q ss_pred CCCCCeeECCChHHHHHHHHHhhhcCCCCCc
Q 038876 7 FLPHGFQFRPSDEELIEHYLKKKDSGIFIPL 37 (127)
Q Consensus 7 ~lp~G~rF~PTDeELi~~YL~~K~~g~~lp~ 37 (127)
-+|| +.|.||+++|+.||- .=+...++|.
T Consensus 107 ~~pP-~y~~~~~~~i~~~f~-~va~~~~lpi 135 (303)
T PRK03620 107 LLPP-YLTEAPQEGLAAHVE-AVCKSTDLGV 135 (303)
T ss_pred ECCC-CCCCCCHHHHHHHHH-HHHHhCCCCE
Confidence 3455 567899999998763 2233335664
Done!