Query 042525
Match_columns 68
No_of_seqs 111 out of 317
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:04:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042525.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042525hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03492 Methyltransf_7: SAM d 100.0 1.1E-36 2.4E-41 223.9 3.0 68 1-68 54-128 (334)
2 PLN02668 indole-3-acetate carb 100.0 4.8E-35 1E-39 221.0 5.0 67 1-67 100-182 (386)
3 PF08241 Methyltransf_11: Meth 86.7 0.63 1.4E-05 26.1 2.1 28 33-60 46-73 (95)
4 KOG2940 Predicted methyltransf 86.0 0.22 4.7E-06 37.8 -0.2 24 43-66 133-156 (325)
5 cd05721 IgV_CTLA-4 Immunoglobu 68.9 3.3 7.2E-05 27.2 1.5 26 42-67 10-43 (115)
6 KOG3010 Methyltransferase [Gen 63.1 2.9 6.4E-05 31.2 0.5 17 44-60 97-113 (261)
7 COG2226 UbiE Methylase involve 55.1 3.4 7.3E-05 29.9 -0.4 32 36-67 108-139 (238)
8 PF13489 Methyltransf_23: Meth 55.1 8.8 0.00019 23.6 1.6 22 41-62 72-93 (161)
9 PRK05785 hypothetical protein; 53.2 4.1 9E-05 28.3 -0.2 29 36-64 99-127 (226)
10 PRK10258 biotin biosynthesis p 53.2 9.3 0.0002 26.2 1.6 21 42-62 98-118 (251)
11 PRK14103 trans-aconitate 2-met 52.3 8.5 0.00019 26.6 1.3 26 36-62 79-104 (255)
12 PLN02232 ubiquinone biosynthes 48.2 13 0.00028 24.3 1.6 27 36-62 33-59 (160)
13 PRK01683 trans-aconitate 2-met 47.0 13 0.00028 25.5 1.5 22 41-62 87-108 (258)
14 TIGR02072 BioC biotin biosynth 45.8 13 0.00029 24.3 1.4 27 36-62 87-113 (240)
15 KOG1541 Predicted protein carb 41.3 15 0.00032 27.7 1.2 22 42-63 107-128 (270)
16 TIGR02727 MTHFS_bact 5,10-meth 39.5 13 0.00028 24.8 0.6 38 28-66 129-169 (181)
17 TIGR03488 cas_Cas5p CRISPR-ass 39.3 5 0.00011 29.2 -1.5 30 30-59 28-58 (237)
18 PLN02233 ubiquinone biosynthes 39.0 22 0.00048 25.1 1.7 20 43-62 141-160 (261)
19 PF08436 DXP_redisom_C: 1-deox 38.3 12 0.00026 23.7 0.3 26 16-41 8-38 (84)
20 PRK10333 5-formyltetrahydrofol 37.8 15 0.00032 24.9 0.6 38 28-66 123-164 (182)
21 PF08242 Methyltransf_12: Meth 37.7 17 0.00036 21.1 0.8 16 46-61 65-80 (99)
22 PRK06202 hypothetical protein; 36.8 20 0.00043 24.4 1.2 19 44-62 126-144 (232)
23 TIGR02081 metW methionine bios 34.4 22 0.00048 23.5 1.1 20 43-62 71-90 (194)
24 TIGR02752 MenG_heptapren 2-hep 31.1 46 0.00099 22.3 2.2 29 34-62 101-129 (231)
25 TIGR03127 RuMP_HxlB 6-phospho 28.5 19 0.00041 23.6 -0.0 29 11-39 15-43 (179)
26 PF06441 EHN: Epoxide hydrolas 25.6 35 0.00077 21.8 0.9 12 29-40 96-107 (112)
27 PF01209 Ubie_methyltran: ubiE 24.4 60 0.0013 22.9 1.9 27 36-62 105-131 (233)
28 cd05005 SIS_PHI Hexulose-6-pho 24.0 20 0.00044 23.5 -0.5 29 11-39 18-46 (179)
29 PRK10886 DnaA initiator-associ 21.9 45 0.00097 23.2 0.9 15 23-37 38-52 (196)
30 COG0743 Dxr 1-deoxy-D-xylulose 20.8 66 0.0014 25.4 1.7 27 15-41 148-179 (385)
31 PF01812 5-FTHF_cyc-lig: 5-for 20.2 27 0.00059 23.1 -0.5 38 28-65 131-173 (186)
No 1
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=100.00 E-value=1.1e-36 Score=223.88 Aligned_cols=68 Identities=54% Similarity=0.940 Sum_probs=53.6
Q ss_pred CceEEEEeCCCCCCcHHHHhhcCCCC-------ccceEEecccccccccccCCceeEEEcccccccccCCCCCCC
Q 042525 1 TQEFRIFFNDHTSNDFNTLFKSLPPE-------RNYFAASVPGAFYGALISQGIIASVNSSHSVRWLSSVPNEVE 68 (68)
Q Consensus 1 ~~e~~v~~nDlP~NDFn~lF~~l~~~-------~~~f~~~vpgSFy~rlfP~~Svh~~~Ss~alhWLS~~P~~l~ 68 (68)
+|||||+|||||+||||+||++|++. ++||++|||||||+||||++||||+||++|||||||+|+++.
T Consensus 54 ~~e~~v~~nDlP~NDFn~lF~~l~~~~~~~~~~~~~f~~gvpgSFy~rLfP~~Svh~~~Ss~alHWLS~vP~~l~ 128 (334)
T PF03492_consen 54 PPEFQVFFNDLPSNDFNTLFKSLPSFQQSLKKFRNYFVSGVPGSFYGRLFPSNSVHFGHSSYALHWLSQVPEELV 128 (334)
T ss_dssp --EEEEEEEE-TTS-HHHHHHCHHHHHHHHHHTTSEEEEEEES-TTS--S-TT-EEEEEEES-TTB-SSS-CCCC
T ss_pred CCeEEEEeCCCCCccHHHHHHhChhhhhccCCCceEEEEecCchhhhccCCCCceEEEEEechhhhcccCCcccc
Confidence 48999999999999999999999876 699999999999999999999999999999999999999873
No 2
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=100.00 E-value=4.8e-35 Score=221.03 Aligned_cols=67 Identities=54% Similarity=0.924 Sum_probs=62.6
Q ss_pred CceEEEEeCCCCCCcHHHHhhcCCCC----------------ccceEEecccccccccccCCceeEEEcccccccccCCC
Q 042525 1 TQEFRIFFNDHTSNDFNTLFKSLPPE----------------RNYFAASVPGAFYGALISQGIIASVNSSHSVRWLSSVP 64 (68)
Q Consensus 1 ~~e~~v~~nDlP~NDFn~lF~~l~~~----------------~~~f~~~vpgSFy~rlfP~~Svh~~~Ss~alhWLS~~P 64 (68)
+||+||++||||+||||+||++|+++ ++||++|||||||+||||++||||+||++|||||||+|
T Consensus 100 ~pe~qv~~nDLP~NDFNtlF~~L~~~~~~~~~~~~~~~~~~~~~~f~~gvpGSFY~RLfP~~Slh~~~Ss~slHWLS~vP 179 (386)
T PLN02668 100 PPEFSAFFSDLPSNDFNTLFQLLPPLANYGGSMEECLAASGHRSYFAAGVPGSFYRRLFPARSIDVFHSAFSLHWLSQVP 179 (386)
T ss_pred CCcceEEecCCCCCCHHHHHhhchhhhhhhcchhhhccccCCCceEEEecCccccccccCCCceEEEEeeccceecccCc
Confidence 47999999999999999999999752 24999999999999999999999999999999999999
Q ss_pred CCC
Q 042525 65 NEV 67 (68)
Q Consensus 65 ~~l 67 (68)
+++
T Consensus 180 ~~l 182 (386)
T PLN02668 180 ESV 182 (386)
T ss_pred hhh
Confidence 986
No 3
>PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B ....
Probab=86.71 E-value=0.63 Score=26.13 Aligned_cols=28 Identities=14% Similarity=0.018 Sum_probs=21.6
Q ss_pred ecccccccccccCCceeEEEcccccccc
Q 042525 33 SVPGAFYGALISQGIIASVNSSHSVRWL 60 (68)
Q Consensus 33 ~vpgSFy~rlfP~~Svh~~~Ss~alhWL 60 (68)
-+-+++..--+|++|+|.+++..++||+
T Consensus 46 ~~~~d~~~l~~~~~sfD~v~~~~~~~~~ 73 (95)
T PF08241_consen 46 FRQGDAEDLPFPDNSFDVVFSNSVLHHL 73 (95)
T ss_dssp EEESBTTSSSS-TT-EEEEEEESHGGGS
T ss_pred heeehHHhCccccccccccccccceeec
Confidence 3445666668899999999999999998
No 4
>KOG2940 consensus Predicted methyltransferase [General function prediction only]
Probab=85.96 E-value=0.22 Score=37.77 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=21.9
Q ss_pred ccCCceeEEEcccccccccCCCCC
Q 042525 43 ISQGIIASVNSSHSVRWLSSVPNE 66 (68)
Q Consensus 43 fP~~Svh~~~Ss~alhWLS~~P~~ 66 (68)
|-++|+|+++||.++||....|..
T Consensus 133 f~ens~DLiisSlslHW~NdLPg~ 156 (325)
T KOG2940|consen 133 FKENSVDLIISSLSLHWTNDLPGS 156 (325)
T ss_pred ccccchhhhhhhhhhhhhccCchH
Confidence 778999999999999999999863
No 5
>cd05721 IgV_CTLA-4 Immunoglobulin (Ig) domain of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). IgV_CTLA-4: domain similar to the variable(v)-type immunoglobulin (Ig) domain found in cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). CTLA-4 is involved in the regulation of T cell response, acting as an inhibitor of intracellular signalling. CTLA-4 is similar to CD28, a T cell co-receptor protein that recognizes the B7 proteins (CD80 and CD86). CD28 binding of the B7 proteins occurs after the presentation of antigen to the T cell receptor (TCR) via the peptide-MHC complex on the surface of an antigen presenting cell (APC). CTLA-4 also binds the B7 molecules with a higher affinity than does CD28. The B7/CTLA-4 interaction generates inhibitory signals down-regulating the response, and may prevent T cell activation by weak TCR signals. CD28 and CTLA-4 then elicit opposing signals in the regulation of T cell responsiveness and homeostasis. T cell activation leads to increased
Probab=68.87 E-value=3.3 Score=27.22 Aligned_cols=26 Identities=23% Similarity=0.193 Sum_probs=19.2
Q ss_pred cccCCceeEEE-------cc-cccccccCCCCCC
Q 042525 42 LISQGIIASVN-------SS-HSVRWLSSVPNEV 67 (68)
Q Consensus 42 lfP~~Svh~~~-------Ss-~alhWLS~~P~~l 67 (68)
+.|.+++-+.+ |+ +.++|+.|+|.++
T Consensus 10 v~p~~sv~LsC~~sg~~~s~e~~~~wvRq~pg~l 43 (115)
T cd05721 10 ASSNGAASLVCEYTYNGFSKEFRASLLKGADSAV 43 (115)
T ss_pred EcCCCCEEEEEEecCCccccEEEEEEEEeCCCCc
Confidence 45666766655 34 8999999999864
No 6
>KOG3010 consensus Methyltransferase [General function prediction only]
Probab=63.08 E-value=2.9 Score=31.22 Aligned_cols=17 Identities=12% Similarity=0.560 Sum_probs=15.7
Q ss_pred cCCceeEEEcccccccc
Q 042525 44 SQGIIASVNSSHSVRWL 60 (68)
Q Consensus 44 P~~Svh~~~Ss~alhWL 60 (68)
+++|||++.++-|+||.
T Consensus 97 ~e~SVDlI~~Aqa~HWF 113 (261)
T KOG3010|consen 97 GEESVDLITAAQAVHWF 113 (261)
T ss_pred CCcceeeehhhhhHHhh
Confidence 48999999999999995
No 7
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=55.09 E-value=3.4 Score=29.93 Aligned_cols=32 Identities=13% Similarity=0.181 Sum_probs=26.1
Q ss_pred cccccccccCCceeEEEcccccccccCCCCCC
Q 042525 36 GAFYGALISQGIIASVNSSHSVRWLSSVPNEV 67 (68)
Q Consensus 36 gSFy~rlfP~~Svh~~~Ss~alhWLS~~P~~l 67 (68)
|..-+=-||++|.|.+..++.|+++.+.++.|
T Consensus 108 ~dAe~LPf~D~sFD~vt~~fglrnv~d~~~aL 139 (238)
T COG2226 108 GDAENLPFPDNSFDAVTISFGLRNVTDIDKAL 139 (238)
T ss_pred echhhCCCCCCccCEEEeeehhhcCCCHHHHH
Confidence 45555569999999999999999998876543
No 8
>PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C ....
Probab=55.08 E-value=8.8 Score=23.59 Aligned_cols=22 Identities=9% Similarity=0.164 Sum_probs=19.0
Q ss_pred ccccCCceeEEEcccccccccC
Q 042525 41 ALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 41 rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
...|+++.|++++..+|||+..
T Consensus 72 ~~~~~~~fD~i~~~~~l~~~~d 93 (161)
T PF13489_consen 72 PPFPDGSFDLIICNDVLEHLPD 93 (161)
T ss_dssp HHCHSSSEEEEEEESSGGGSSH
T ss_pred hhccccchhhHhhHHHHhhccc
Confidence 3468899999999999999874
No 9
>PRK05785 hypothetical protein; Provisional
Probab=53.23 E-value=4.1 Score=28.28 Aligned_cols=29 Identities=17% Similarity=0.172 Sum_probs=21.8
Q ss_pred cccccccccCCceeEEEcccccccccCCC
Q 042525 36 GAFYGALISQGIIASVNSSHSVRWLSSVP 64 (68)
Q Consensus 36 gSFy~rlfP~~Svh~~~Ss~alhWLS~~P 64 (68)
|++-.-=++++|.|.+++++++||+...+
T Consensus 99 ~d~~~lp~~d~sfD~v~~~~~l~~~~d~~ 127 (226)
T PRK05785 99 GSFEALPFRDKSFDVVMSSFALHASDNIE 127 (226)
T ss_pred echhhCCCCCCCEEEEEecChhhccCCHH
Confidence 34333346799999999999999976543
No 10
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=53.17 E-value=9.3 Score=26.18 Aligned_cols=21 Identities=14% Similarity=0.284 Sum_probs=18.2
Q ss_pred cccCCceeEEEcccccccccC
Q 042525 42 LISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 42 lfP~~Svh~~~Ss~alhWLS~ 62 (68)
-++.++.|+++|..++||...
T Consensus 98 ~~~~~~fD~V~s~~~l~~~~d 118 (251)
T PRK10258 98 PLATATFDLAWSNLAVQWCGN 118 (251)
T ss_pred cCCCCcEEEEEECchhhhcCC
Confidence 367889999999999999754
No 11
>PRK14103 trans-aconitate 2-methyltransferase; Provisional
Probab=52.25 E-value=8.5 Score=26.63 Aligned_cols=26 Identities=15% Similarity=0.276 Sum_probs=20.6
Q ss_pred cccccccccCCceeEEEcccccccccC
Q 042525 36 GAFYGALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 36 gSFy~rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
+.. ..+.+.++.|+++|..++||+..
T Consensus 79 ~d~-~~~~~~~~fD~v~~~~~l~~~~d 104 (255)
T PRK14103 79 GDV-RDWKPKPDTDVVVSNAALQWVPE 104 (255)
T ss_pred cCh-hhCCCCCCceEEEEehhhhhCCC
Confidence 443 45667789999999999999864
No 12
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=48.22 E-value=13 Score=24.29 Aligned_cols=27 Identities=11% Similarity=0.060 Sum_probs=20.1
Q ss_pred cccccccccCCceeEEEcccccccccC
Q 042525 36 GAFYGALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 36 gSFy~rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
|...+=-+++++.|.+.+.+++||+..
T Consensus 33 ~d~~~lp~~~~~fD~v~~~~~l~~~~d 59 (160)
T PLN02232 33 GDAIDLPFDDCEFDAVTMGYGLRNVVD 59 (160)
T ss_pred echhhCCCCCCCeeEEEecchhhcCCC
Confidence 343332367889999999999999754
No 13
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=47.01 E-value=13 Score=25.55 Aligned_cols=22 Identities=14% Similarity=0.351 Sum_probs=18.5
Q ss_pred ccccCCceeEEEcccccccccC
Q 042525 41 ALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 41 rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
.+.|.++.|+++|..++||+..
T Consensus 87 ~~~~~~~fD~v~~~~~l~~~~d 108 (258)
T PRK01683 87 SWQPPQALDLIFANASLQWLPD 108 (258)
T ss_pred ccCCCCCccEEEEccChhhCCC
Confidence 4457789999999999999854
No 14
>TIGR02072 BioC biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.
Probab=45.79 E-value=13 Score=24.33 Aligned_cols=27 Identities=11% Similarity=0.224 Sum_probs=22.1
Q ss_pred cccccccccCCceeEEEcccccccccC
Q 042525 36 GAFYGALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 36 gSFy~rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
++.-+..+++++.|++++..++||+..
T Consensus 87 ~d~~~~~~~~~~fD~vi~~~~l~~~~~ 113 (240)
T TIGR02072 87 GDAEKLPLEDSSFDLIVSNLALQWCDD 113 (240)
T ss_pred cchhhCCCCCCceeEEEEhhhhhhccC
Confidence 455566678899999999999999854
No 15
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=41.35 E-value=15 Score=27.67 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=19.2
Q ss_pred cccCCceeEEEcccccccccCC
Q 042525 42 LISQGIIASVNSSHSVRWLSSV 63 (68)
Q Consensus 42 lfP~~Svh~~~Ss~alhWLS~~ 63 (68)
=|++++.|=++|-.|++||=.+
T Consensus 107 pfrpGtFDg~ISISAvQWLcnA 128 (270)
T KOG1541|consen 107 PFRPGTFDGVISISAVQWLCNA 128 (270)
T ss_pred CCCCCccceEEEeeeeeeeccc
Confidence 3789999999999999999654
No 16
>TIGR02727 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase. This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism.
Probab=39.50 E-value=13 Score=24.84 Aligned_cols=38 Identities=11% Similarity=0.203 Sum_probs=24.4
Q ss_pred cceEEecccccccccccCCcee---EEEcccccccccCCCCC
Q 042525 28 NYFAASVPGAFYGALISQGIIA---SVNSSHSVRWLSSVPNE 66 (68)
Q Consensus 28 ~~f~~~vpgSFy~rlfP~~Svh---~~~Ss~alhWLS~~P~~ 66 (68)
+-+=.|.||.||+|.+..-.-. +|. ++..+.+.++|.+
T Consensus 129 ~G~RLG~GgGyYDR~L~~~~~~~~~igv-~~~~q~~~~lp~e 169 (181)
T TIGR02727 129 RGYRLGYGGGYYDRFLANLKGKTVVVGL-AFDFQLVDELPRE 169 (181)
T ss_pred CCccccCCcchHHHHHHhcccCCCEEEE-EecceeeCccCCC
Confidence 4456789999999998753211 333 3566666666643
No 17
>TIGR03488 cas_Cas5p CRISPR-associated protein, Cas5p family. CC Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pgingi (Porphyromonas gingivalis) subtype, but shows some sequence similarity to genes of the Cas5 type (see TIGR02593).
Probab=39.29 E-value=5 Score=29.22 Aligned_cols=30 Identities=27% Similarity=0.566 Sum_probs=20.0
Q ss_pred eEEecccccccc-cccCCceeEEEccccccc
Q 042525 30 FAASVPGAFYGA-LISQGIIASVNSSHSVRW 59 (68)
Q Consensus 30 f~~~vpgSFy~r-lfP~~Svh~~~Ss~alhW 59 (68)
.++-.|||||.. ++|++-+=-|.--+.|.|
T Consensus 28 mvselpgsfykal~~p~k~iicgl~envlgw 58 (237)
T TIGR03488 28 MVSELPGSFYKALLVPDKHIICGLFENVLGW 58 (237)
T ss_pred HHHhCchhHHHHhcCCcchhhhhhhhhhhhc
Confidence 567799999987 567776544444444444
No 18
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=39.02 E-value=22 Score=25.12 Aligned_cols=20 Identities=5% Similarity=0.111 Sum_probs=17.7
Q ss_pred ccCCceeEEEcccccccccC
Q 042525 43 ISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 43 fP~~Svh~~~Ss~alhWLS~ 62 (68)
+|+++.|.+++++++||+..
T Consensus 141 ~~~~sfD~V~~~~~l~~~~d 160 (261)
T PLN02233 141 FDDCYFDAITMGYGLRNVVD 160 (261)
T ss_pred CCCCCEeEEEEecccccCCC
Confidence 67899999999999999753
No 19
>PF08436 DXP_redisom_C: 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; InterPro: IPR013644 1-deoxy-D-xylulose 5-phosphate reductoisomerase synthesises 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate in a single step by intramolecular rearrangement and reduction and is responsible for terpenoid biosynthesis in some organisms []. In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the non-mevalonate pathway for isoprenoid biosynthesis. The enzyme requires Mn2+, Co2+ or Mg2+ for activity, with the first being most effective. This domain is found to the C terminus of IPR013512 from INTERPRO domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases.; GO: 0005515 protein binding; PDB: 3AUA_A 3AU9_B 3AU8_B 3A14_A 3A06_A 2Y1D_B 4AIC_A 2JD0_B 2Y1C_B 2JD1_A ....
Probab=38.31 E-value=12 Score=23.68 Aligned_cols=26 Identities=19% Similarity=0.383 Sum_probs=19.4
Q ss_pred HHHHhhcCCCC-----ccceEEecccccccc
Q 042525 16 FNTLFKSLPPE-----RNYFAASVPGAFYGA 41 (68)
Q Consensus 16 Fn~lF~~l~~~-----~~~f~~~vpgSFy~r 41 (68)
-|.+|+.|... ++++..|.||-|+++
T Consensus 8 HsAifQ~L~~~~~~~v~~i~lTASGGpFr~~ 38 (84)
T PF08436_consen 8 HSAIFQCLQGEKREEVEKIILTASGGPFRDK 38 (84)
T ss_dssp HHHHHHHSGHHHHCTEEEEEEEE--STTTTS
T ss_pred HHHHHHHCCCCCccccCEEEEECcchhhCCC
Confidence 47899999754 478999999999875
No 20
>PRK10333 5-formyltetrahydrofolate cyclo-ligase family protein; Provisional
Probab=37.76 E-value=15 Score=24.92 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=25.5
Q ss_pred cceEEecccccccccccCCc----eeEEEcccccccccCCCCC
Q 042525 28 NYFAASVPGAFYGALISQGI----IASVNSSHSVRWLSSVPNE 66 (68)
Q Consensus 28 ~~f~~~vpgSFy~rlfP~~S----vh~~~Ss~alhWLS~~P~~ 66 (68)
+-+=.|.||.||+|.++.-+ .-+|. ++..+.+.++|.+
T Consensus 123 ~G~RLG~GgGyYDR~L~~~~~~~~~~igl-a~~~Q~~~~ip~e 164 (182)
T PRK10333 123 YGQRLGMGGGFYDRTLQNWQHYKTQPVGY-AHDCQLVEKLPVE 164 (182)
T ss_pred CCCcccCCcchHHHHHHHhcccCCcEEEE-eeeeEEeCCcCCC
Confidence 44667899999999998522 22444 4556667777753
No 21
>PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A.
Probab=37.71 E-value=17 Score=21.11 Aligned_cols=16 Identities=19% Similarity=0.138 Sum_probs=9.3
Q ss_pred CceeEEEccccccccc
Q 042525 46 GIIASVNSSHSVRWLS 61 (68)
Q Consensus 46 ~Svh~~~Ss~alhWLS 61 (68)
++.|+++++.++||+.
T Consensus 65 ~~fD~V~~~~vl~~l~ 80 (99)
T PF08242_consen 65 ESFDLVVASNVLHHLE 80 (99)
T ss_dssp ---SEEEEE-TTS--S
T ss_pred cccceehhhhhHhhhh
Confidence 7999999999999993
No 22
>PRK06202 hypothetical protein; Provisional
Probab=36.77 E-value=20 Score=24.40 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=17.0
Q ss_pred cCCceeEEEcccccccccC
Q 042525 44 SQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 44 P~~Svh~~~Ss~alhWLS~ 62 (68)
++++.|+++++.++||+..
T Consensus 126 ~~~~fD~V~~~~~lhh~~d 144 (232)
T PRK06202 126 EGERFDVVTSNHFLHHLDD 144 (232)
T ss_pred cCCCccEEEECCeeecCCh
Confidence 6789999999999999864
No 23
>TIGR02081 metW methionine biosynthesis protein MetW. This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized.
Probab=34.43 E-value=22 Score=23.54 Aligned_cols=20 Identities=10% Similarity=0.014 Sum_probs=17.6
Q ss_pred ccCCceeEEEcccccccccC
Q 042525 43 ISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 43 fP~~Svh~~~Ss~alhWLS~ 62 (68)
+++++.|++++..++||+..
T Consensus 71 ~~~~sfD~Vi~~~~l~~~~d 90 (194)
T TIGR02081 71 FPDKSFDYVILSQTLQATRN 90 (194)
T ss_pred cCCCCcCEEEEhhHhHcCcC
Confidence 57889999999999999854
No 24
>TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.
Probab=31.06 E-value=46 Score=22.27 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=21.1
Q ss_pred cccccccccccCCceeEEEcccccccccC
Q 042525 34 VPGAFYGALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 34 vpgSFy~rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
+.|...+--+|.++.|++++..++||++.
T Consensus 101 ~~~d~~~~~~~~~~fD~V~~~~~l~~~~~ 129 (231)
T TIGR02752 101 VHGNAMELPFDDNSFDYVTIGFGLRNVPD 129 (231)
T ss_pred EEechhcCCCCCCCccEEEEecccccCCC
Confidence 33444443467889999999999999754
No 25
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=28.53 E-value=19 Score=23.56 Aligned_cols=29 Identities=10% Similarity=0.156 Sum_probs=21.3
Q ss_pred CCCCcHHHHhhcCCCCccceEEecccccc
Q 042525 11 HTSNDFNTLFKSLPPERNYFAASVPGAFY 39 (68)
Q Consensus 11 lP~NDFn~lF~~l~~~~~~f~~~vpgSFy 39 (68)
+..+++..+.+.+...+++|+.|+++|.+
T Consensus 15 l~~~~~~~~~~~l~~a~~I~i~G~G~S~~ 43 (179)
T TIGR03127 15 IDEEELDKLADKIIKAKRIFVAGAGRSGL 43 (179)
T ss_pred CCHHHHHHHHHHHHhCCEEEEEecCHHHH
Confidence 34456666666776667899999999864
No 26
>PF06441 EHN: Epoxide hydrolase N terminus; InterPro: IPR010497 This entry represents the N-terminal region of the eukaryotic epoxide hydrolase protein. Epoxide hydrolases (3.3.2.3 from EC) comprise a group of functionally related enzymes that catalyse the addition of water to oxirane compounds (epoxides), thereby usually generating vicinal trans-diols. EHs have been found in all types of living organisms, including mammals, invertebrates, plants, fungi and bacteria. In animals, the major interest in EH is directed towards their detoxification capacity for epoxides since they are important safeguards against the cytotoxic and genotoxic potential of oxirane derivatives that are often reactive electrophiles because of the high tension of the three-membered ring system and the strong polarisation of the C--O bonds. This is of significant relevance because epoxides are frequent intermediary metabolites, which arise during the biotransformation of foreign compounds []. This domain is often found in conjunction with IPR000073 from INTERPRO.; GO: 0004301 epoxide hydrolase activity, 0009636 response to toxin, 0016020 membrane; PDB: 3G0I_B 3G02_A 1QO7_A.
Probab=25.63 E-value=35 Score=21.85 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=6.7
Q ss_pred ceEEeccccccc
Q 042525 29 YFAASVPGAFYG 40 (68)
Q Consensus 29 ~f~~~vpgSFy~ 40 (68)
++.-|-||||++
T Consensus 96 ll~HGWPgSf~E 107 (112)
T PF06441_consen 96 LLLHGWPGSFLE 107 (112)
T ss_dssp EEE--SS--GGG
T ss_pred EEECCCCccHHh
Confidence 678899999986
No 27
>PF01209 Ubie_methyltran: ubiE/COQ5 methyltransferase family; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities []. Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity; PDB: 1VL5_C.
Probab=24.41 E-value=60 Score=22.86 Aligned_cols=27 Identities=15% Similarity=0.161 Sum_probs=16.2
Q ss_pred cccccccccCCceeEEEcccccccccC
Q 042525 36 GAFYGALISQGIIASVNSSHSVRWLSS 62 (68)
Q Consensus 36 gSFy~rlfP~~Svh~~~Ss~alhWLS~ 62 (68)
|+.-.==+|++|.|.+.+++++|-+..
T Consensus 105 ~da~~lp~~d~sfD~v~~~fglrn~~d 131 (233)
T PF01209_consen 105 GDAEDLPFPDNSFDAVTCSFGLRNFPD 131 (233)
T ss_dssp -BTTB--S-TT-EEEEEEES-GGG-SS
T ss_pred cCHHHhcCCCCceeEEEHHhhHHhhCC
Confidence 444443489999999999999998754
No 28
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=23.95 E-value=20 Score=23.54 Aligned_cols=29 Identities=7% Similarity=0.148 Sum_probs=20.2
Q ss_pred CCCCcHHHHhhcCCCCccceEEecccccc
Q 042525 11 HTSNDFNTLFKSLPPERNYFAASVPGAFY 39 (68)
Q Consensus 11 lP~NDFn~lF~~l~~~~~~f~~~vpgSFy 39 (68)
+...+...+.+.+...+++|+.|+++|.+
T Consensus 18 l~~~~l~~~~~~i~~a~~I~i~G~G~S~~ 46 (179)
T cd05005 18 IDEEELDKLISAILNAKRIFVYGAGRSGL 46 (179)
T ss_pred cCHHHHHHHHHHHHhCCeEEEEecChhHH
Confidence 33445556666665667899999998865
No 29
>PRK10886 DnaA initiator-associating protein DiaA; Provisional
Probab=21.90 E-value=45 Score=23.16 Aligned_cols=15 Identities=7% Similarity=0.002 Sum_probs=12.3
Q ss_pred CCCCccceEEecccc
Q 042525 23 LPPERNYFAASVPGA 37 (68)
Q Consensus 23 l~~~~~~f~~~vpgS 37 (68)
+...+++|++|+|||
T Consensus 38 l~~~~rI~~~G~GgS 52 (196)
T PRK10886 38 LLNGNKILCCGNGTS 52 (196)
T ss_pred HHcCCEEEEEECcHH
Confidence 344578999999999
No 30
>COG0743 Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Lipid metabolism]
Probab=20.85 E-value=66 Score=25.41 Aligned_cols=27 Identities=22% Similarity=0.466 Sum_probs=22.3
Q ss_pred cHHHHhhcCCCC-----ccceEEecccccccc
Q 042525 15 DFNTLFKSLPPE-----RNYFAASVPGAFYGA 41 (68)
Q Consensus 15 DFn~lF~~l~~~-----~~~f~~~vpgSFy~r 41 (68)
.-|.+|+.|+.. .++...|.||.|++.
T Consensus 148 EH~AifQ~L~~~~~~~v~~iiLTASGGpFR~~ 179 (385)
T COG0743 148 EHNAIFQCLQGETQKGVKKIILTASGGPFRDK 179 (385)
T ss_pred hhHHHHHHcCccccCcceEEEEecCCCCcCCC
Confidence 468999999865 368999999999874
No 31
>PF01812 5-FTHF_cyc-lig: 5-formyltetrahydrofolate cyclo-ligase family; InterPro: IPR002698 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase 6.3.3.2 from EC catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+ []. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin [].; GO: 0005524 ATP binding, 0030272 5-formyltetrahydrofolate cyclo-ligase activity, 0009396 folic acid-containing compound biosynthetic process; PDB: 1WKC_A 1SBQ_A 1U3G_A 1U3F_B 1YDM_B 1SOU_A 2JCB_B 3HY6_A 3HY4_A 3HXT_A ....
Probab=20.20 E-value=27 Score=23.13 Aligned_cols=38 Identities=11% Similarity=0.202 Sum_probs=19.5
Q ss_pred cceEEecccccccccccCCce-----eEEEcccccccccCCCC
Q 042525 28 NYFAASVPGAFYGALISQGII-----ASVNSSHSVRWLSSVPN 65 (68)
Q Consensus 28 ~~f~~~vpgSFy~rlfP~~Sv-----h~~~Ss~alhWLS~~P~ 65 (68)
+-+=.|-||-||+|.+..-.- -.+--++..+.+.++|.
T Consensus 131 ~G~RLG~GgGyYDR~L~~~~~~~~~~~~igl~~~~q~~~~iP~ 173 (186)
T PF01812_consen 131 NGNRLGYGGGYYDRFLARLPPGRKKPLKIGLAFDFQIVDDIPV 173 (186)
T ss_dssp TSBEE-SSSTHHHHHHHHHTS-SS--EEEEEE-GGGEES----
T ss_pred CCCeEecCCCHHHhHHHhhhcccCCCeEEEEeehhheeCCCCC
Confidence 445678899999998764432 22223345556666664
Done!