Query psy3546
Match_columns 164
No_of_seqs 165 out of 879
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 19:24:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3546hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00145 DNA_methylase: C-5 cy 100.0 1.7E-29 3.6E-34 202.1 4.6 96 2-117 65-163 (335)
2 COG0270 Dcm Site-specific DNA 99.9 9.6E-28 2.1E-32 204.1 5.1 94 4-117 73-168 (328)
3 cd00315 Cyt_C5_DNA_methylase C 99.9 2.1E-25 4.6E-30 185.8 6.4 94 2-115 66-163 (275)
4 TIGR00675 dcm DNA-methyltransf 99.9 1.1E-24 2.3E-29 184.9 6.6 94 3-116 64-160 (315)
5 KOG0919|consensus 99.9 4.6E-25 9.9E-30 191.9 3.2 97 1-115 72-169 (338)
6 PRK10458 DNA cytosine methylas 99.9 2E-22 4.3E-27 182.3 7.3 94 3-117 174-288 (467)
7 PRK13562 acetolactate synthase 91.4 0.67 1.5E-05 34.5 5.6 48 57-113 3-50 (84)
8 PRK06737 acetolactate synthase 84.4 3.7 8.1E-05 29.7 5.6 42 64-112 8-49 (76)
9 PRK08178 acetolactate synthase 82.6 4.1 8.8E-05 31.0 5.4 43 64-113 14-56 (96)
10 COG4747 ACT domain-containing 80.9 2.6 5.7E-05 34.2 4.1 39 58-103 5-44 (142)
11 PRK11152 ilvM acetolactate syn 75.4 10 0.00022 27.3 5.4 32 64-100 9-40 (76)
12 TIGR00119 acolac_sm acetolacta 69.2 8.6 0.00019 31.0 4.3 32 64-100 7-38 (157)
13 PRK11895 ilvH acetolactate syn 62.0 13 0.00029 30.1 4.1 32 64-100 8-39 (161)
14 PF03793 PASTA: PASTA domain; 61.4 20 0.00043 23.2 4.2 29 63-95 1-29 (63)
15 COG0440 IlvH Acetolactate synt 55.9 16 0.00035 30.2 3.7 45 64-114 10-54 (163)
16 PF01842 ACT: ACT domain; Int 55.1 26 0.00056 21.9 3.8 36 62-102 4-39 (66)
17 COG0414 PanC Panthothenate syn 51.4 29 0.00063 31.2 4.8 56 50-106 12-67 (285)
18 PRK15351 type III secretion sy 50.8 49 0.0011 26.5 5.4 30 2-35 8-37 (124)
19 PF08208 RNA_polI_A34: DNA-dir 49.5 5.5 0.00012 32.1 0.0 6 87-92 120-125 (198)
20 KOG0333|consensus 48.3 22 0.00049 35.1 3.8 67 1-92 479-545 (673)
21 COG2921 Uncharacterized conser 44.9 37 0.00081 25.9 3.8 68 4-88 10-84 (90)
22 PF11432 DUF3197: Protein of u 42.8 23 0.00051 28.0 2.5 30 72-101 57-86 (113)
23 PRK13477 bifunctional pantoate 42.2 41 0.00089 31.9 4.5 52 51-105 13-64 (512)
24 PF08208 RNA_polI_A34: DNA-dir 40.4 9.3 0.0002 30.8 0.0 13 58-70 78-90 (198)
25 cd01979 Pchlide_reductase_N Pc 39.4 39 0.00084 30.0 3.7 71 4-95 117-187 (396)
26 cd04880 ACT_AAAH-PDT-like ACT 38.2 1.2E+02 0.0026 20.1 5.8 48 61-114 2-49 (75)
27 cd04908 ACT_Bt0572_1 N-termina 37.9 74 0.0016 20.7 4.1 30 64-98 7-36 (66)
28 CHL00100 ilvH acetohydroxyacid 36.0 68 0.0015 26.4 4.4 36 64-104 8-44 (174)
29 PF14814 UB2H: Bifunctional tr 35.4 27 0.00059 24.9 1.7 32 76-107 8-39 (85)
30 COG3233 Predicted deacetylase 34.3 1.2E+02 0.0026 26.7 5.8 51 26-92 18-71 (233)
31 cd04889 ACT_PDH-BS-like C-term 33.3 1.1E+02 0.0024 19.0 4.2 32 64-100 4-35 (56)
32 PF07530 PRE_C2HC: Associated 32.2 77 0.0017 22.2 3.6 33 78-112 2-36 (68)
33 PF13710 ACT_5: ACT domain; PD 31.7 56 0.0012 22.1 2.7 25 75-99 4-28 (63)
34 PF14090 HTH_39: Helix-turn-he 31.0 1E+02 0.0022 21.1 4.0 35 77-111 30-67 (70)
35 PRK00907 hypothetical protein; 30.5 23 0.00049 26.5 0.7 30 4-40 12-43 (92)
36 COG0386 BtuE Glutathione perox 29.2 20 0.00042 29.9 0.2 35 64-98 95-135 (162)
37 PF03484 B5: tRNA synthetase B 28.8 23 0.00049 24.2 0.4 20 75-94 19-38 (70)
38 PF00255 GSHPx: Glutathione pe 28.3 13 0.00029 28.2 -0.9 11 3-13 56-66 (108)
39 PRK02842 light-independent pro 27.9 75 0.0016 28.6 3.6 29 67-95 170-198 (427)
40 TIGR01279 DPOR_bchN light-inde 27.3 98 0.0021 27.7 4.3 29 67-95 157-185 (407)
41 PF06375 BLVR: Bovine leukaemi 27.3 17 0.00037 29.7 -0.5 13 98-110 64-76 (154)
42 PF06414 Zeta_toxin: Zeta toxi 27.0 1.3E+02 0.0029 23.6 4.5 33 64-98 97-129 (199)
43 TIGR02081 metW methionine bios 26.7 87 0.0019 24.4 3.4 37 76-113 147-184 (194)
44 cd05777 DNA_polB_delta_exo DED 26.7 2.3E+02 0.0049 23.2 6.0 44 21-89 69-112 (230)
45 PF12017 Tnp_P_element: Transp 26.6 1.2E+02 0.0026 26.1 4.5 41 53-98 179-219 (236)
46 PF02624 YcaO: YcaO-like famil 25.8 67 0.0015 26.8 2.8 84 1-104 92-187 (332)
47 KOG1467|consensus 25.8 95 0.0021 30.4 4.0 46 64-113 390-435 (556)
48 cd05776 DNA_polB_alpha_exo ina 25.5 1.3E+02 0.0028 24.9 4.4 44 21-89 80-123 (234)
49 KOG3988|consensus 24.2 60 0.0013 30.1 2.4 28 76-106 314-341 (378)
50 KOG3042|consensus 23.4 1.4E+02 0.0029 26.8 4.3 54 52-106 16-69 (283)
51 PF03848 TehB: Tellurite resis 23.4 1.5E+02 0.0033 24.5 4.4 55 55-110 91-149 (192)
52 TIGR00587 nfo apurinic endonuc 23.0 1.2E+02 0.0026 25.4 3.8 26 63-88 140-167 (274)
53 KOG2798|consensus 23.0 39 0.00085 31.4 0.9 20 21-40 124-143 (369)
54 cd04885 ACT_ThrD-I Tandem C-te 22.9 67 0.0015 21.3 1.9 19 74-92 49-67 (68)
55 PF01234 NNMT_PNMT_TEMT: NNMT/ 22.9 1.3E+02 0.0028 26.1 4.0 37 76-115 219-256 (256)
56 cd00316 Oxidoreductase_nitroge 22.8 1.5E+02 0.0031 25.5 4.3 20 76-95 167-186 (399)
57 COG3527 AlsD Alpha-acetolactat 22.7 44 0.00094 29.4 1.1 39 63-102 147-185 (234)
58 PHA03108 poly(A) polymerase sm 22.7 1.2E+02 0.0026 27.6 3.9 45 74-118 72-118 (300)
59 PF09582 AnfO_nitrog: Iron onl 22.0 66 0.0014 27.0 2.1 25 62-94 67-91 (202)
60 PF02569 Pantoate_ligase: Pant 21.8 94 0.002 27.6 3.0 37 70-106 31-67 (280)
61 PRK03745 signal recognition pa 21.5 93 0.002 23.8 2.6 30 75-104 32-64 (100)
62 PF08407 Chitin_synth_1N: Chit 21.2 1.2E+02 0.0025 22.3 3.0 25 84-113 54-78 (79)
63 PRK06092 4-amino-4-deoxychoris 21.2 1.4E+02 0.0029 24.7 3.7 38 72-111 197-234 (268)
64 PF07927 YcfA: YcfA-like prote 21.1 98 0.0021 19.7 2.3 18 77-94 1-18 (56)
65 TIGR01121 D_amino_aminoT D-ami 20.8 1.6E+02 0.0035 24.6 4.1 40 71-112 199-238 (276)
66 PRK14336 (dimethylallyl)adenos 20.7 2.3E+02 0.005 25.6 5.3 41 65-107 282-323 (418)
67 PRK07849 4-amino-4-deoxychoris 20.6 1.4E+02 0.003 25.4 3.8 40 70-111 214-253 (292)
68 PHA02768 hypothetical protein; 20.3 48 0.001 23.0 0.8 11 1-11 1-11 (55)
No 1
>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....
Probab=99.95 E-value=1.7e-29 Score=202.14 Aligned_cols=96 Identities=17% Similarity=0.123 Sum_probs=80.9
Q ss_pred CCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHH
Q psy3546 2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRD 78 (164)
Q Consensus 2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d 78 (164)
..-|||||+||.+|.+++.+|+|+.||.+++++|.+++ |+ +|+||||+||..+ ..++
T Consensus 65 l~ggpPCQ~fS~ag~~~~~~d~r~~L~~~~~~~v~~~~----Pk----------------~~~~ENV~~l~~~~~~~~~~ 124 (335)
T PF00145_consen 65 LIGGPPCQGFSIAGKRKGFDDPRNSLFFEFLRIVKELK----PK----------------YFLLENVPGLLSSKNGEVFK 124 (335)
T ss_dssp EEEE---TTTSTTSTHHCCCCHTTSHHHHHHHHHHHHS-----S----------------EEEEEEEGGGGTGGGHHHHH
T ss_pred EEeccCCceEeccccccccccccchhhHHHHHHHhhcc----ce----------------EEEecccceeeccccccccc
Confidence 34689999999999999999999999999999999998 68 5599999999876 5699
Q ss_pred HHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccch
Q psy3546 79 LITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKR 117 (164)
Q Consensus 79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk~ 117 (164)
.|++.|+++||.+++.+|||.+|||||.|+|+++.+.++
T Consensus 125 ~i~~~l~~lGY~v~~~vlna~~yGvPQ~R~R~fivg~r~ 163 (335)
T PF00145_consen 125 EILEELEELGYNVQWRVLNAADYGVPQNRERVFIVGIRK 163 (335)
T ss_dssp HHHHHHHHTTEEEEEEEEEGGGGTSSBE-EEEEEEEEEG
T ss_pred cccccccccceeehhccccHhhCCCCCceeeEEEEEECC
Confidence 999999999999999999999999999995555555444
No 2
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=99.94 E-value=9.6e-28 Score=204.09 Aligned_cols=94 Identities=20% Similarity=0.186 Sum_probs=85.1
Q ss_pred cCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc--hHHHHHH
Q psy3546 4 IDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS--RSRDLIT 81 (164)
Q Consensus 4 ~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s--~~~d~I~ 81 (164)
=|||||+||.+|.+++.+|+|++||++++++|..++ |+ +|+||||+||..+ ..++.|+
T Consensus 73 gGpPCQ~FS~aG~r~~~~D~R~~L~~~~~r~I~~~~----P~----------------~fv~ENV~gl~~~~~~~~~~i~ 132 (328)
T COG0270 73 GGPPCQDFSIAGKRRGYDDPRGSLFLEFIRLIEQLR----PK----------------FFVLENVKGLLSSKGQTFDEIK 132 (328)
T ss_pred eCCCCcchhhcCcccCCcCccceeeHHHHHHHHhhC----CC----------------EEEEecCchHHhcCchHHHHHH
Confidence 389999999999999999999999999999999999 57 6699999999875 6899999
Q ss_pred HHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccch
Q psy3546 82 SMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKR 117 (164)
Q Consensus 82 s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk~ 117 (164)
+.|+++||.+.+.||||.||||||+|+++++.+.++
T Consensus 133 ~~L~~~GY~~~~~ilna~dyGvPQ~ReRvfiig~~~ 168 (328)
T COG0270 133 KELEELGYGVEFNILNAADYGVPQSRERVFIVGFRR 168 (328)
T ss_pred HHHHHcCCcchHheeeHHhcCCCCCccEEEEEEecC
Confidence 999999999999999999999999996655555443
No 3
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=99.92 E-value=2.1e-25 Score=185.76 Aligned_cols=94 Identities=18% Similarity=0.209 Sum_probs=84.3
Q ss_pred CCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chHHH
Q psy3546 2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRSRD 78 (164)
Q Consensus 2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~~d 78 (164)
...|+|||+||.+|.+++.+|+|+.|+.+++++|..++ |+ +|+||||+||.. +..++
T Consensus 66 l~~gpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~----P~----------------~~v~ENV~g~~~~~~~~~~~ 125 (275)
T cd00315 66 LTGGFPCQPFSIAGKRKGFEDTRGTLFFEIIRILKEKK----PK----------------YFLLENVKGLLTHDNGNTLK 125 (275)
T ss_pred EEeCCCChhhhHHhhcCCCCCchHHHHHHHHHHHHhcC----CC----------------EEEEEcCcchhccCchHHHH
Confidence 35689999999999999999999999999999999998 68 559999999986 67899
Q ss_pred HHHHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEeccc
Q psy3546 79 LITSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKKK 115 (164)
Q Consensus 79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~rk 115 (164)
.|++.|+++||.+.+.+|||.+|||||.| |+|+++-.
T Consensus 126 ~i~~~l~~~GY~~~~~~l~a~~~GvPQ~R~R~~~ia~~ 163 (275)
T cd00315 126 VILNTLEELGYNVYWKLLNASDYGVPQNRERVFIIGIR 163 (275)
T ss_pred HHHHHHHhCCcEEEEEEEEHHHcCCCCCCcEEEEEEEe
Confidence 99999999999999999999999999999 55555443
No 4
>TIGR00675 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.91 E-value=1.1e-24 Score=184.90 Aligned_cols=94 Identities=19% Similarity=0.239 Sum_probs=83.1
Q ss_pred CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHHH
Q psy3546 3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRDL 79 (164)
Q Consensus 3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d~ 79 (164)
.-|+|||+||.+|.+++.+|+|+.||.+++++|.+++ |+ +|+||||+||..+ ..++.
T Consensus 64 ~gg~PCq~fS~ag~~~~~~d~r~~L~~~~~r~i~~~~----P~----------------~~v~ENV~~l~~~~~~~~~~~ 123 (315)
T TIGR00675 64 LGGFPCQPFSIAGKRKGFEDTRGTLFFEIVRILKEKK----PK----------------FFLLENVKGLVSHDKGRTFKV 123 (315)
T ss_pred EecCCCcccchhcccCCCCCchhhHHHHHHHHHhhcC----CC----------------EEEeeccHHHHhcccchHHHH
Confidence 4689999999999999999999999999999999998 68 5599999999753 57899
Q ss_pred HHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546 80 ITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK 116 (164)
Q Consensus 80 I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk 116 (164)
|+++|..+||.+.+.+||+.||||||.|+|+++.+.+
T Consensus 124 i~~~l~~~GY~v~~~~l~a~dyGvPQ~R~R~f~ia~r 160 (315)
T TIGR00675 124 IIETLEELGYKVYYKVLNAKDFGVPQNRERIYIVGFR 160 (315)
T ss_pred HHHHHHhCCCEEEEEEEcHHHCCCCCCccEEEEEEEe
Confidence 9999999999999999999999999999555444444
No 5
>KOG0919|consensus
Probab=99.90 E-value=4.6e-25 Score=191.87 Aligned_cols=97 Identities=30% Similarity=0.431 Sum_probs=92.4
Q ss_pred CCCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHH
Q psy3546 1 MASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLI 80 (164)
Q Consensus 1 ~~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I 80 (164)
|.....|||||++.|+|+|+.|+|+++|.+++.+|++++. .|. || +||||+||+.|..++.+
T Consensus 72 m~lMSPpCQPfTRiG~q~D~~D~Rs~aflhil~~lP~~q~--LPe---------------YI-L~ENVkGFE~S~ar~~~ 133 (338)
T KOG0919|consen 72 MLLMSPPCQPFTRIGLQRDTEDKRSDAFLHILGLLPECQE--LPE---------------YI-LMENVKGFESSQARNQF 133 (338)
T ss_pred eEeeCCCCCchhhhcccccccCchhHHHHHHHhhhhhhhh--hhH---------------HH-HHhhcccchhhhHHHHH
Confidence 5567899999999999999999999999999999999985 788 89 99999999999999999
Q ss_pred HHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEeccc
Q psy3546 81 TSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKKK 115 (164)
Q Consensus 81 ~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~rk 115 (164)
++.|+++||++++|+|+|++||||++| |||+++|.
T Consensus 134 i~~lencGf~~~EfiLsPtqfniPNsR~Ryy~iArl 169 (338)
T KOG0919|consen 134 IESLENCGFHWREFILSPTQFNIPNSRYRYYCIARL 169 (338)
T ss_pred HHHHHhcCchhhheeccccccCCCCcchheeehhhh
Confidence 999999999999999999999999999 99998874
No 6
>PRK10458 DNA cytosine methylase; Provisional
Probab=99.87 E-value=2e-22 Score=182.26 Aligned_cols=94 Identities=17% Similarity=0.212 Sum_probs=79.7
Q ss_pred CcCCCCCcccccCcCCC--------C-CCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC
Q psy3546 3 SIDYASNSDPGTGLQKD--------I-ADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73 (164)
Q Consensus 3 ~~~fPCQ~FS~aG~rkd--------~-~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~ 73 (164)
.-||||||||.+|.++. . +|+|++||.+++++|.+.+ |+ +|+||||+||.+
T Consensus 174 ~gGpPCQ~FS~AG~~k~~~~gr~~g~~~d~rg~Lf~~~~rii~~~k----Pk----------------~fvlENV~gl~s 233 (467)
T PRK10458 174 LAGFPCQPFSLAGVSKKNSLGRAHGFECETQGTLFFDVARIIDAKR----PA----------------IFVLENVKNLKS 233 (467)
T ss_pred EEcCCCCccchhcccccccccccccccCCccccHHHHHHHHHHHhC----CC----------------EEEEeCcHhhhc
Confidence 45999999999997542 2 3889999999999999998 68 569999999976
Q ss_pred c---hHHHHHHHHHHhCCCeEE---------EEEeCCCCCCCCCcceEEEecccch
Q psy3546 74 S---RSRDLITSMLTRAGFRFQ---------EFLLSPTQFGTSLYTEWLRNKKKKR 117 (164)
Q Consensus 74 s---~~~d~I~s~L~~~GY~v~---------~~lLnatdfGVPQ~Rr~~i~~rkk~ 117 (164)
+ ..++.|++.|.++||.+. +.||||.+| |||.|+|+++.+.++
T Consensus 234 ~~~g~~f~~i~~~L~~lGY~v~~~~~~g~~~~~vlna~~f-VPQ~R~RvfiVg~r~ 288 (467)
T PRK10458 234 HDKGKTFRIIMQTLDELGYDVADAEDNGPDDPKIIDGKHF-LPQHRERIVLVGFRR 288 (467)
T ss_pred ccccHHHHHHHHHHHHcCCeEEeccccCcccceEeehhhC-CCccCcEEEEEEEeC
Confidence 4 589999999999999996 589999999 999996666555553
No 7
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=91.38 E-value=0.67 Score=34.48 Aligned_cols=48 Identities=13% Similarity=0.105 Sum_probs=36.3
Q ss_pred cccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546 57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK 113 (164)
Q Consensus 57 ~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~ 113 (164)
+-||. ++||.+|. ...|...|++.||++...-+.++. .|...|+-|+.
T Consensus 3 ~~isv--lVeN~~GV-----L~Rit~lFsRRg~NI~SLtvg~Te--~~~iSRmtivv 50 (84)
T PRK13562 3 RILKL--QVADQVST-----LNRITSAFVRLQYNIDTLHVTHSE--QPGISNMEIQV 50 (84)
T ss_pred EEEEE--EEECCCCH-----HHHHHHHHhccCcCeeeEEecccC--CCCceEEEEEE
Confidence 34554 59999984 578999999999999999998885 55555555443
No 8
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=84.38 E-value=3.7 Score=29.66 Aligned_cols=42 Identities=19% Similarity=0.142 Sum_probs=32.8
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEe
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRN 112 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~ 112 (164)
+++|-|| ....|+..|.+.||++...-+.|+. .|...|..++
T Consensus 8 ~v~n~pG-----VL~Ri~~lf~rRgfNI~Sl~vg~te--~~~~sriti~ 49 (76)
T PRK06737 8 VIHNDPS-----VLLRISGIFARRGYYISSLNLNERD--TSGVSEMKLT 49 (76)
T ss_pred EEecCCC-----HHHHHHHHHhccCcceEEEEecccC--CCCeeEEEEE
Confidence 5999998 4578999999999999988888775 5555454444
No 9
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=82.59 E-value=4.1 Score=31.01 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=33.6
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK 113 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~ 113 (164)
++||.||. ...|...|++.||.+......|+. .|...|+.|+.
T Consensus 14 lv~N~pGV-----L~RIaglFsRRgyNIeSLtvg~te--~~~iSRmtivv 56 (96)
T PRK08178 14 TVRNHPGV-----MSHVCGLFARRAFNVEGILCLPIQ--DGDKSRIWLLV 56 (96)
T ss_pred EEECCcCH-----HHHHHHHHhcCCcCeeeEEEeecC--CCCceEEEEEE
Confidence 59999984 578999999999999988777764 67765555544
No 10
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=80.87 E-value=2.6 Score=34.22 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=30.5
Q ss_pred ccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEE-EeCCCCCCC
Q psy3546 58 KLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEF-LLSPTQFGT 103 (164)
Q Consensus 58 ~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~-lLnatdfGV 103 (164)
|.|.| +||-||= +-..++.|.++|-++..+ +-++.+||+
T Consensus 5 QISvF--lENk~GR-----L~~~~~~L~eagINiRA~tiAdt~dFGI 44 (142)
T COG4747 5 QISVF--LENKPGR-----LASVANKLKEAGINIRAFTIADTGDFGI 44 (142)
T ss_pred EEEEE--ecCCcch-----HHHHHHHHHHcCCceEEEEeccccCcce
Confidence 56655 9999973 345678889999999766 678999997
No 11
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=75.39 E-value=10 Score=27.29 Aligned_cols=32 Identities=6% Similarity=0.150 Sum_probs=27.7
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQ 100 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatd 100 (164)
+++|-|| ....|+..|.+.||++...-+.++.
T Consensus 9 ~v~n~pG-----VL~Ri~~lf~rRGfnI~sl~v~~t~ 40 (76)
T PRK11152 9 KARFRPE-----VLERVLRVVRHRGFQVCSMNMTQNT 40 (76)
T ss_pred EEECCcc-----HHHHHHHHHhcCCeeeeeEEeeecC
Confidence 6999997 5678999999999999998887775
No 12
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=69.25 E-value=8.6 Score=31.01 Aligned_cols=32 Identities=25% Similarity=0.494 Sum_probs=28.1
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQ 100 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatd 100 (164)
++||-|| .+..|...|.+.||++....+.|++
T Consensus 7 ~ven~pG-----vL~rI~~lf~rrg~NI~Sl~v~~t~ 38 (157)
T TIGR00119 7 LVENEPG-----VLSRVAGLFTRRGFNIESLTVGPTE 38 (157)
T ss_pred EEcCCCc-----HHHHHHHHHHhCCceEEEEEEeecC
Confidence 6999997 4578999999999999999888884
No 13
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=62.05 E-value=13 Score=30.10 Aligned_cols=32 Identities=19% Similarity=0.463 Sum_probs=27.8
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQ 100 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatd 100 (164)
+++|-|| .+..|...|.+.||++....+.|++
T Consensus 8 ~veN~pG-----vL~rI~~lf~rrg~NI~Sl~v~~te 39 (161)
T PRK11895 8 LVENEPG-----VLSRVAGLFSRRGYNIESLTVGPTE 39 (161)
T ss_pred EEcCCCc-----HHHHHHHHHHhCCCcEEEEEeeecC
Confidence 6999997 4578999999999999998888874
No 14
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=61.35 E-value=20 Score=23.20 Aligned_cols=29 Identities=24% Similarity=0.391 Sum_probs=19.8
Q ss_pred EEeecCcCCCCchHHHHHHHHHHhCCCeEEEEE
Q psy3546 63 FRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFL 95 (164)
Q Consensus 63 Fl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~l 95 (164)
+.|+||.|+ +.+...+.|+.+|+.+...-
T Consensus 1 V~vPd~~g~----~~~~a~~~l~~~g~~~~~~~ 29 (63)
T PF03793_consen 1 VTVPDLVGM----TYDEAKSILEAAGLTVNVVE 29 (63)
T ss_dssp EEE-TTTTS----BHHHHHHHHHHTT-EEEEEE
T ss_pred CCCCCcCCC----cHHHHHHHHHHCCCEEEEEE
Confidence 368899873 56788889999999765443
No 15
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=55.92 E-value=16 Score=30.22 Aligned_cols=45 Identities=18% Similarity=0.262 Sum_probs=36.5
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecc
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKK 114 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~r 114 (164)
+++|-+|.+ ..++..|.+.||++....+.+++-.. .+|-+++..+
T Consensus 10 lv~ne~GvL-----sRv~glfsrRG~NIeSltv~~tE~~~-~SRiTivv~g 54 (163)
T COG0440 10 LVENEPGVL-----SRVTGLFSRRGYNIESLTVGPTETPG-LSRITIVVSG 54 (163)
T ss_pred EEECCCCee-----ehhhHHHHhcCcccceEEEEecCCCC-ceEEEEEEcC
Confidence 699999864 46788899999999999999998665 5676666665
No 16
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=55.11 E-value=26 Score=21.87 Aligned_cols=36 Identities=19% Similarity=0.269 Sum_probs=27.9
Q ss_pred EEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCC
Q psy3546 62 IFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102 (164)
Q Consensus 62 iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfG 102 (164)
.+.++|.||+ +..+++.|.+.|+.+.........=+
T Consensus 4 ~v~~~drpG~-----l~~v~~~la~~~inI~~~~~~~~~~~ 39 (66)
T PF01842_consen 4 RVIVPDRPGI-----LADVTEILADHGINIDSISQSSDKDG 39 (66)
T ss_dssp EEEEETSTTH-----HHHHHHHHHHTTEEEEEEEEEEESST
T ss_pred EEEcCCCCCH-----HHHHHHHHHHcCCCHHHeEEEecCCC
Confidence 3479999984 57899999999999988776665433
No 17
>COG0414 PanC Panthothenate synthetase [Coenzyme metabolism]
Probab=51.41 E-value=29 Score=31.20 Aligned_cols=56 Identities=18% Similarity=0.236 Sum_probs=40.6
Q ss_pred hhhhccccccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCc
Q psy3546 50 QAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLY 106 (164)
Q Consensus 50 ~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~ 106 (164)
++++.|++.---|-+++-. |.++......|...-...+..|-...+||+|||-+..
T Consensus 12 ~~~~~~r~~gk~Vg~VPTM-G~LH~GHlsLVr~A~~~~d~VVVSIFVNP~QFg~~ED 67 (285)
T COG0414 12 QAIKALRKEGKRVGLVPTM-GNLHEGHLSLVRRAKKENDVVVVSIFVNPLQFGPNED 67 (285)
T ss_pred HHHHHHHHcCCEEEEEcCC-cccchHHHHHHHHHhhcCCeEEEEEEeChhhcCCchh
Confidence 4555676654344344433 5566667788888888999999999999999998654
No 18
>PRK15351 type III secretion system protein SsaP; Provisional
Probab=50.80 E-value=49 Score=26.46 Aligned_cols=30 Identities=17% Similarity=0.169 Sum_probs=20.1
Q ss_pred CCcCCCCCcccccCcCCCCCCccchHHHHHHHhc
Q psy3546 2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETI 35 (164)
Q Consensus 2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI 35 (164)
.|+|.|||++...+- +.+-.+.|..++.-+
T Consensus 8 ~~~~~~~~~~~~~~~----~~~grt~F~qLM~Q~ 37 (124)
T PRK15351 8 GSLGLPCQSYQDDNE----AEAERMDFEQLMHQA 37 (124)
T ss_pred cccCCcccccccccc----cccccchHHHHHhhc
Confidence 489999999875442 334446677777644
No 19
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=49.47 E-value=5.5 Score=32.12 Aligned_cols=6 Identities=17% Similarity=0.301 Sum_probs=0.0
Q ss_pred CCCeEE
Q psy3546 87 AGFRFQ 92 (164)
Q Consensus 87 ~GY~v~ 92 (164)
.||...
T Consensus 120 ~G~~~~ 125 (198)
T PF08208_consen 120 FGYGSP 125 (198)
T ss_dssp ------
T ss_pred CCCCcc
Confidence 455443
No 20
>KOG0333|consensus
Probab=48.31 E-value=22 Score=35.08 Aligned_cols=67 Identities=22% Similarity=0.344 Sum_probs=41.9
Q ss_pred CCCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHH
Q psy3546 1 MASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLI 80 (164)
Q Consensus 1 ~~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I 80 (164)
|+|||+.-++-+..-..--..+.-.. +..++++|..++. |. .| ++-|.+ ...|.|
T Consensus 479 ~vtig~~gk~~~rveQ~v~m~~ed~k-~kkL~eil~~~~~---pp---------------iI-IFvN~k-----k~~d~l 533 (673)
T KOG0333|consen 479 VVTIGSAGKPTPRVEQKVEMVSEDEK-RKKLIEILESNFD---PP---------------II-IFVNTK-----KGADAL 533 (673)
T ss_pred EEEeccCCCCccchheEEEEecchHH-HHHHHHHHHhCCC---CC---------------EE-EEEech-----hhHHHH
Confidence 46788887777765422111122222 7788888888853 56 34 677765 345777
Q ss_pred HHHHHhCCCeEE
Q psy3546 81 TSMLTRAGFRFQ 92 (164)
Q Consensus 81 ~s~L~~~GY~v~ 92 (164)
-..|+.+||++.
T Consensus 534 Ak~LeK~g~~~~ 545 (673)
T KOG0333|consen 534 AKILEKAGYKVT 545 (673)
T ss_pred HHHHhhccceEE
Confidence 777888887764
No 21
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=44.91 E-value=37 Score=25.93 Aligned_cols=68 Identities=18% Similarity=0.247 Sum_probs=39.8
Q ss_pred cCCCCCccc--ccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhh-----hhccccccceEEEeecCcCCCCchH
Q psy3546 4 IDYASNSDP--GTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQA-----VKGWKRKLSGIFRTPNVKGFEGSRS 76 (164)
Q Consensus 4 ~~fPCQ~FS--~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~-----~~~~~~~~~~iFl~ENVkGf~~s~~ 76 (164)
|-|||- |+ ..| +++-.|-..++++|...-| ..|+.+. -+|=---+|..|..+|+. -
T Consensus 10 ~eFPc~-F~~KVmG------~a~~~l~~~vv~vvqr~ap----~~~~~~~~~k~SSkGnY~svsI~i~A~~~E------Q 72 (90)
T COG2921 10 LEFPCT-FTYKVMG------AAGPELEDQVVEVVQRHAP----GDYTPRVSWKPSSKGNYLSVSITIRATNIE------Q 72 (90)
T ss_pred eECCcc-ceeeehc------ccchhHHHHHHHHHHHHCC----cccCceeeeccCCCCceEEEEEEEEECCHH------H
Confidence 679997 65 445 4455788889999998884 5444433 222222344444555543 3
Q ss_pred HHHHHHHHHhCC
Q psy3546 77 RDLITSMLTRAG 88 (164)
Q Consensus 77 ~d~I~s~L~~~G 88 (164)
.+.|..+|+..+
T Consensus 73 ~e~ly~eL~~~~ 84 (90)
T COG2921 73 VEALYRELRKHE 84 (90)
T ss_pred HHHHHHHHhhCC
Confidence 456666666543
No 22
>PF11432 DUF3197: Protein of unknown function (DUF3197); InterPro: IPR024443 This domain, whose function is unknown, is found in bacterial proteins.; PDB: 1WN9_A 1WNA_A.
Probab=42.80 E-value=23 Score=28.01 Aligned_cols=30 Identities=40% Similarity=0.641 Sum_probs=24.8
Q ss_pred CCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q psy3546 72 EGSRSRDLITSMLTRAGFRFQEFLLSPTQF 101 (164)
Q Consensus 72 ~~s~~~d~I~s~L~~~GY~v~~~lLnatdf 101 (164)
.+.+...+++..|.+.|-.+.+.||+|++|
T Consensus 57 ~G~~ALaELv~wl~~~G~~f~EaVl~p~e~ 86 (113)
T PF11432_consen 57 EGERALAELVRWLQERGARFYEAVLSPSEF 86 (113)
T ss_dssp THHHHHHHHHHHHHHTT-EEEEEEE-GGGH
T ss_pred cHHHHHHHHHHHHHHcCCchhheecCHHHH
Confidence 455678999999999999999999999987
No 23
>PRK13477 bifunctional pantoate ligase/cytidylate kinase; Provisional
Probab=42.17 E-value=41 Score=31.93 Aligned_cols=52 Identities=15% Similarity=0.178 Sum_probs=36.4
Q ss_pred hhhccccccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCC
Q psy3546 51 AVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSL 105 (164)
Q Consensus 51 ~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ 105 (164)
.+..|+++ +.. +++-. |-++.....+|..+-..+...|-...+||+|||-+.
T Consensus 13 ~~~~~~~~-~ig-~VPTM-G~LH~GHlsLi~~A~~~~d~vVvSIFVNP~QF~~~e 64 (512)
T PRK13477 13 WLRQQRSE-TIG-FVPTM-GALHQGHLSLIRRARQENDVVLVSIFVNPLQFGPNE 64 (512)
T ss_pred HHHHhcCC-cEE-EECCC-cchhHHHHHHHHHHHHhCCEEEEEEccCcccCCCch
Confidence 34556655 444 33333 334556678888888889998999999999999763
No 24
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=40.39 E-value=9.3 Score=30.82 Aligned_cols=13 Identities=0% Similarity=0.146 Sum_probs=3.4
Q ss_pred ccceEEEeecCcC
Q psy3546 58 KLSGIFRTPNVKG 70 (164)
Q Consensus 58 ~~~~iFl~ENVkG 70 (164)
.++.+|.|.=+..
T Consensus 78 ~~~~~~~I~e~~~ 90 (198)
T PF08208_consen 78 PFDRFLHISEIVQ 90 (198)
T ss_dssp --SEEEEEEE---
T ss_pred CcceEEEEEEecC
Confidence 3334444443333
No 25
>cd01979 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=39.43 E-value=39 Score=29.96 Aligned_cols=71 Identities=18% Similarity=0.200 Sum_probs=39.7
Q ss_pred cCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHHHHH
Q psy3546 4 IDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSM 83 (164)
Q Consensus 4 ~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~ 83 (164)
+|+|+-+.+..|-..+..+.-..++..++..+..-. . .|. -| |+.|........+|...
T Consensus 117 ~~~pvi~v~t~gf~g~~~~G~~~~~~alv~~~~~~~-~-~~~---------------~V----nliG~~~~~d~~el~~l 175 (396)
T cd01979 117 IGVPILVASASGLDYTFTQGEDTVLAALVPRCPEKP-S-PER---------------SL----VLVGSLPDIVEDQLRRE 175 (396)
T ss_pred CCCcEEEeeCCCccccHHHHHHHHHHHHhhhccccc-C-CCC---------------ce----EEEEeCCcchHHHHHHH
Confidence 456666666555433223333456666666553211 1 122 12 55555444457889999
Q ss_pred HHhCCCeEEEEE
Q psy3546 84 LTRAGFRFQEFL 95 (164)
Q Consensus 84 L~~~GY~v~~~l 95 (164)
|+.+|+++..++
T Consensus 176 L~~~Gi~v~~~~ 187 (396)
T cd01979 176 LEQLGIPVVGFL 187 (396)
T ss_pred HHHcCCeEEEEe
Confidence 999999996544
No 26
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=38.21 E-value=1.2e+02 Score=20.11 Aligned_cols=48 Identities=13% Similarity=0.179 Sum_probs=32.9
Q ss_pred eEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecc
Q psy3546 61 GIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKK 114 (164)
Q Consensus 61 ~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~r 114 (164)
.+|.++|-|| +...+++.|...|.++....-.|.. +.+....+|+-.-
T Consensus 2 l~~~l~d~pG-----~L~~vL~~f~~~~vni~~I~Srp~~-~~~~~~~f~id~~ 49 (75)
T cd04880 2 LVFSLKNKPG-----ALAKALKVFAERGINLTKIESRPSR-KGLWEYEFFVDFE 49 (75)
T ss_pred EEEEeCCcCC-----HHHHHHHHHHHCCCCEEEEEeeecC-CCCceEEEEEEEE
Confidence 4567888775 4788999999999998877544543 3444455555544
No 27
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=37.87 E-value=74 Score=20.74 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=23.8
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSP 98 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLna 98 (164)
.++|-|| .+..|++.|.+.|+.+......+
T Consensus 7 ~v~d~pG-----~La~v~~~l~~~~inI~~i~~~~ 36 (66)
T cd04908 7 FLENKPG-----RLAAVTEILSEAGINIRALSIAD 36 (66)
T ss_pred EEcCCCC-----hHHHHHHHHHHCCCCEEEEEEEe
Confidence 6888886 45789999999999997776544
No 28
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=36.02 E-value=68 Score=26.38 Aligned_cols=36 Identities=25% Similarity=0.465 Sum_probs=28.5
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCC-CCCCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPT-QFGTS 104 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnat-dfGVP 104 (164)
+.+|-||+ ...|...|.+.||++......++ +-|++
T Consensus 8 lv~n~PGV-----L~RIt~lFsrRg~NIesLsv~~t~~~~~s 44 (174)
T CHL00100 8 LVEDESGV-----LTRIAGLFARRGFNIESLAVGPAEQKGIS 44 (174)
T ss_pred EEeCcCCH-----HHHHHHHHHhCCCCeeEEEeeEcCCCCcc
Confidence 69999985 57899999999999988776553 44555
No 29
>PF14814 UB2H: Bifunctional transglycosylase second domain; PDB: 3FWL_A 3VMA_A.
Probab=35.35 E-value=27 Score=24.94 Aligned_cols=32 Identities=19% Similarity=0.134 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcc
Q psy3546 76 SRDLITSMLTRAGFRFQEFLLSPTQFGTSLYT 107 (164)
Q Consensus 76 ~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~R 107 (164)
+.+.|+.+|+.+||+-...+-.|-+|-+..++
T Consensus 8 s~~~l~~eL~~LgYR~v~~~~~pG~y~~~g~~ 39 (85)
T PF14814_consen 8 SPAQLEQELELLGYRKVSNPDRPGEYSRSGNR 39 (85)
T ss_dssp -HHHHHHHHHHTT-EE-SS--STTEEEEETTE
T ss_pred CHHHHHHHHHHcCCCcCCCCCCCeEEEEECCE
Confidence 46899999999999988888888887555544
No 30
>COG3233 Predicted deacetylase [General function prediction only]
Probab=34.26 E-value=1.2e+02 Score=26.71 Aligned_cols=51 Identities=12% Similarity=0.025 Sum_probs=35.5
Q ss_pred hHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcC---CCCchHHHHHHHHHHhCCCeEE
Q psy3546 26 TALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKG---FEGSRSRDLITSMLTRAGFRFQ 92 (164)
Q Consensus 26 ~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkG---f~~s~~~d~I~s~L~~~GY~v~ 92 (164)
.-++.+.++|.++.+ .|. +++++++|-.| +..+.-|-.+++.+.+.||.+.
T Consensus 18 ~~~~~i~~~ide~~~--~~~--------------t~lLViPn~~~~~~l~~d~rf~~~l~~r~e~Gdel~ 71 (233)
T COG3233 18 PTLSNIDAAIDEYGA--QNS--------------TVLLVIPNHANDYPLSKDPRFVDLLTEREEEGDELV 71 (233)
T ss_pred hhHHHHHHHHHHhCC--CCc--------------eEEEEeeccCCCCCcccChHHHHHHHHHHhcCCEEE
Confidence 345666677777764 233 35578999876 4556667788888888999874
No 31
>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A
Probab=33.28 E-value=1.1e+02 Score=19.04 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=24.8
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQ 100 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatd 100 (164)
.++|.||. ...+++.|.+.|..+......+..
T Consensus 4 ~~~d~~G~-----l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 4 FVENKPGR-----LAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EeCCCCCh-----HHHHHHHHHHcCCCEeeEEEEEcc
Confidence 68888873 567889999999999877665554
No 32
>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth. These proteins are possibly involved in RNA binding or single strand DNA binding.
Probab=32.20 E-value=77 Score=22.21 Aligned_cols=33 Identities=12% Similarity=0.137 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCeEEEEEeCCCC--CCCCCcceEEEe
Q psy3546 78 DLITSMLTRAGFRFQEFLLSPTQ--FGTSLYTEWLRN 112 (164)
Q Consensus 78 d~I~s~L~~~GY~v~~~lLnatd--fGVPQ~Rr~~i~ 112 (164)
+.|.++|...||.+. ++.++.. .+.|+ +-+|+.
T Consensus 2 ~~I~~~L~~~G~~v~-~i~~~~~~~~k~pl-~mf~ve 36 (68)
T PF07530_consen 2 EEIKEELKDQGHPVR-NIHNMHSRNTKKPL-NMFFVE 36 (68)
T ss_pred HHHHHHHHHcCCceE-EEEccccCCCCCCc-eEEEEe
Confidence 579999999999997 4545443 36676 444443
No 33
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=31.67 E-value=56 Score=22.09 Aligned_cols=25 Identities=28% Similarity=0.523 Sum_probs=20.4
Q ss_pred hHHHHHHHHHHhCCCeEEEEEeCCC
Q psy3546 75 RSRDLITSMLTRAGFRFQEFLLSPT 99 (164)
Q Consensus 75 ~~~d~I~s~L~~~GY~v~~~lLnat 99 (164)
..+..|+..|.+.||.+....+.++
T Consensus 4 GvL~Ri~~vf~rRg~nI~sl~v~~~ 28 (63)
T PF13710_consen 4 GVLNRITGVFRRRGFNIESLSVGPT 28 (63)
T ss_dssp THHHHHHHHHHTTT-EECEEEEEE-
T ss_pred HHHHHHHHHHhcCCeEEeeEEeeec
Confidence 4678999999999999999888874
No 34
>PF14090 HTH_39: Helix-turn-helix domain
Probab=31.03 E-value=1e+02 Score=21.09 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCCeEEEE-EeCCCCCCCCCcc--eEEE
Q psy3546 77 RDLITSMLTRAGFRFQEF-LLSPTQFGTSLYT--EWLR 111 (164)
Q Consensus 77 ~d~I~s~L~~~GY~v~~~-lLnatdfGVPQ~R--r~~i 111 (164)
...-+.+|.+.||.|... +-.++..|.+..| +|.+
T Consensus 30 ~~aRI~eLR~~G~~I~t~~~~~~~~~g~~~~rva~Y~L 67 (70)
T PF14090_consen 30 LAARISELRKKGYPIVTEWVTVPTEDGRPHRRVARYSL 67 (70)
T ss_pred HHHHHHHHHHcCCeeeEEEEEeeccCCCcCCCEEEEEe
Confidence 456677899999999754 5667788998865 4444
No 35
>PRK00907 hypothetical protein; Provisional
Probab=30.50 E-value=23 Score=26.53 Aligned_cols=30 Identities=13% Similarity=0.027 Sum_probs=20.6
Q ss_pred cCCCCCccc--ccCcCCCCCCccchHHHHHHHhccccCC
Q psy3546 4 IDYASNSDP--GTGLQKDIADARCTALSYLIETIPANFP 40 (164)
Q Consensus 4 ~~fPCQ~FS--~aG~rkd~~D~R~~L~~~~iriI~~~~p 40 (164)
|.|||. |+ ..|. +...+...+++++....|
T Consensus 12 iEFPc~-fpiKVmG~------a~~~l~~~V~~vv~~h~p 43 (92)
T PRK00907 12 FQFPGT-FELSAMGT------AERGLETELPRLLAATGV 43 (92)
T ss_pred EecCCC-CeEEEEEc------CchhHHHHHHHHHHHhCC
Confidence 789994 76 4563 334577788888887764
No 36
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=29.19 E-value=20 Score=29.95 Aligned_cols=35 Identities=14% Similarity=0.252 Sum_probs=19.5
Q ss_pred EeecCcCCCCchHHHHHHHHH------HhCCCeEEEEEeCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSML------TRAGFRFQEFLLSP 98 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L------~~~GY~v~~~lLna 98 (164)
---+|.|=..+..+..+.+.- ......|.-||++.
T Consensus 95 ~Ki~VnG~~a~PLy~~L~~~~~g~~~~~~IkWNFtKFLvdr 135 (162)
T COG0386 95 SKIDVNGKNAHPLYKYLKEQKPGKLGGKDIKWNFTKFLVDR 135 (162)
T ss_pred eEEeecCCCCCcHHHHHHhcCCCCccCCccceeeEEEEEcC
Confidence 334666665566666666553 22334556667664
No 37
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=28.79 E-value=23 Score=24.25 Aligned_cols=20 Identities=30% Similarity=0.546 Sum_probs=14.7
Q ss_pred hHHHHHHHHHHhCCCeEEEE
Q psy3546 75 RSRDLITSMLTRAGFRFQEF 94 (164)
Q Consensus 75 ~~~d~I~s~L~~~GY~v~~~ 94 (164)
-+.+.+.+.|+++||.+...
T Consensus 19 i~~~~i~~~L~~lg~~~~~~ 38 (70)
T PF03484_consen 19 ISPEEIIKILKRLGFKVEKI 38 (70)
T ss_dssp --HHHHHHHHHHTT-EEEE-
T ss_pred CCHHHHHHHHHHCCCEEEEC
Confidence 35689999999999999874
No 38
>PF00255 GSHPx: Glutathione peroxidase; InterPro: IPR000889 Glutathione peroxidase (GSHPx) (1.11.1.9 from EC) is an enzyme that catalyses the reduction of hydroxyperoxides by glutathione [, ]. Its main function is to protect against the damaging effect of endogenously formed hydroxyperoxides. In higher vertebrates, several forms of GSHPx are known, including a ubiquitous cytosolic form (GSHPx-1), a gastrointestinal cytosolic form (GSHPx-GI), a plasma secreted form (GSHPx-P), and an epididymal secretory form (GSHPx-EP). In addition to these characterised forms, the sequence of a protein of unknown function [] has been shown to be evolutionary related to those of GSHPx's. In filarial nematode parasites, the major soluble cuticular protein (gp29) is a secreted GSHPx, which may provide a mechanism of resistance to the immune reaction of the mammalian host by neutralising the products of the oxidative burst of leukocytes []. The Escherichia coli protein btuE, a periplasmic protein involved in vitamin B12 transport, is evolutionarily related to GSHPxs, although the significance of this relationship is unclear. The structure of bovine seleno-glutathione peroxidase has been determined []. The protein belongs to the alpha-beta class, with a 3 layer(aba) sandwich architecture. The catalyic site of GSHPx contains a conserved residue which is either a cysteine or, in many eukaryotic GSHPx, a selenocysteine []. ; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 3E0U_A 2VUP_A 2RM5_A 2RM6_A 3DWV_B 2P31_B 2R37_B 1GP1_B 2F8A_B 3KIJ_C ....
Probab=28.33 E-value=13 Score=28.22 Aligned_cols=11 Identities=9% Similarity=0.138 Sum_probs=8.8
Q ss_pred CcCCCCCcccc
Q psy3546 3 SIDYASNSDPG 13 (164)
Q Consensus 3 ~~~fPCQ~FS~ 13 (164)
-|||||+.|-.
T Consensus 56 ILaFPcnqFg~ 66 (108)
T PF00255_consen 56 ILAFPCNQFGN 66 (108)
T ss_dssp EEEEEBSTTTT
T ss_pred EEeeehHHhcc
Confidence 37999999863
No 39
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=27.86 E-value=75 Score=28.60 Aligned_cols=29 Identities=21% Similarity=0.239 Sum_probs=19.9
Q ss_pred cCcCCCCchHHHHHHHHHHhCCCeEEEEE
Q psy3546 67 NVKGFEGSRSRDLITSMLTRAGFRFQEFL 95 (164)
Q Consensus 67 NVkGf~~s~~~d~I~s~L~~~GY~v~~~l 95 (164)
|+.|........+|...|+.+|+++...+
T Consensus 170 niiG~~~~~d~~el~~lL~~~Gi~v~~~l 198 (427)
T PRK02842 170 VLVGSLADVVEDQLTLEFKKLGIGVVGFL 198 (427)
T ss_pred EEEEeCCcchHHHHHHHHHHcCCeeEEEe
Confidence 45554433345789999999999986444
No 40
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme involved in bacteriochlorophyll biosynthesis. This subunit shows homology to the nitrogenase molybdenum-iron protein NifN.
Probab=27.28 E-value=98 Score=27.73 Aligned_cols=29 Identities=21% Similarity=0.211 Sum_probs=21.5
Q ss_pred cCcCCCCchHHHHHHHHHHhCCCeEEEEE
Q psy3546 67 NVKGFEGSRSRDLITSMLTRAGFRFQEFL 95 (164)
Q Consensus 67 NVkGf~~s~~~d~I~s~L~~~GY~v~~~l 95 (164)
|+.|+.......+|...|+.+|.++...+
T Consensus 157 niiG~~~~~d~~elk~lL~~~Gi~v~~~l 185 (407)
T TIGR01279 157 VLVGSVNDIVADQLRLELKQLGIPVVGFL 185 (407)
T ss_pred EEEeccChhhHHHHHHHHHHcCCeEEEEe
Confidence 56676554456889999999999996433
No 41
>PF06375 BLVR: Bovine leukaemia virus receptor (BLVR); InterPro: IPR010474 Bovine leukemia virus (BLV) is one of the most common infectious cattle viruses, with between 30 and 40% of cows in the United States being infected. It is closely related to the human T-cell leukaemia virus type 1 (HTLV-1) and has highly conserved envelope glycoprotein functional domains []. BLV is an oncogenic C-type retrovirus, which results in the animals developing a malignant lymphoma. BLV, like the human and simian T cell leukaemia viruses, is a deltaretrovirus. 182 residues at the amino-terminal of the BLV envelope glycoprotein surface unit encompass the receptor-binding domain. The metabolic activity in B cells, T cells, and thymocytes is indicated by the expression of the BLV-binding receptor []. A candidate gene of the receptor (BLVR) is related, but unique, to a gene family of the delta subunit of the adaptor protein (AP) complex 3, AP-3 []. The AP-3 complex is not clathrin-associated but is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. ; PDB: 4AFI_B.
Probab=27.25 E-value=17 Score=29.75 Aligned_cols=13 Identities=8% Similarity=-0.284 Sum_probs=4.9
Q ss_pred CCCCCCCCcceEE
Q psy3546 98 PTQFGTSLYTEWL 110 (164)
Q Consensus 98 atdfGVPQ~Rr~~ 110 (164)
-+|.++.+.....
T Consensus 64 ~sdkYl~~~~~~~ 76 (154)
T PF06375_consen 64 GSDKYLKQQQERR 76 (154)
T ss_dssp S-SSEEESST---
T ss_pred hhHHHHHHHHhhh
Confidence 3455556665444
No 42
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=27.02 E-value=1.3e+02 Score=23.63 Aligned_cols=33 Identities=6% Similarity=0.101 Sum_probs=20.8
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCC
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSP 98 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLna 98 (164)
++|.+- ........++..|.+.||.+.-.++..
T Consensus 97 i~E~tl--~~~~~~~~~~~~~k~~GY~v~l~~v~~ 129 (199)
T PF06414_consen 97 IFEGTL--SNPSKLRKLIREAKAAGYKVELYYVAV 129 (199)
T ss_dssp EEE--T--TSSHHHHHHHHHHHCTT-EEEEEEE--
T ss_pred EEecCC--CChhHHHHHHHHHHcCCceEEEEEEEC
Confidence 578764 234556669999999999998776654
No 43
>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=26.69 E-value=87 Score=24.40 Aligned_cols=37 Identities=11% Similarity=0.133 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEec
Q psy3546 76 SRDLITSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNK 113 (164)
Q Consensus 76 ~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~ 113 (164)
+.+.+.+.|.++||.+.+...-+.| |+|-.- +||-+.
T Consensus 147 s~~~~~~ll~~~Gf~v~~~~~~~~~-~~~~~~~~~~~~~ 184 (194)
T TIGR02081 147 TIADFEDLCGELNLRILDRAAFDVD-GRGGREVRWFPNL 184 (194)
T ss_pred cHHHHHHHHHHCCCEEEEEEEeccc-cccccccccCccc
Confidence 5788999999999999887766654 666553 666554
No 44
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=26.66 E-value=2.3e+02 Score=23.20 Aligned_cols=44 Identities=11% Similarity=0.038 Sum_probs=31.3
Q ss_pred CCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHHHHHHHhCCC
Q psy3546 21 ADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGF 89 (164)
Q Consensus 21 ~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY 89 (164)
+++| .|+..|+.+|.... |+ |++-=|+-||. +..|++....+|-
T Consensus 69 ~~E~-eLL~~f~~~i~~~D----PD----------------ii~GyN~~~FD----l~yL~~R~~~l~i 112 (230)
T cd05777 69 ETEE-ELLLAWRDFVQEVD----PD----------------IITGYNICNFD----LPYLLERAKALKL 112 (230)
T ss_pred CCHH-HHHHHHHHHHHhcC----CC----------------EEEEecCCCCC----HHHHHHHHHHhCC
Confidence 4566 59999999999998 68 44778888763 4455555555543
No 45
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=26.65 E-value=1.2e+02 Score=26.13 Aligned_cols=41 Identities=15% Similarity=0.151 Sum_probs=30.0
Q ss_pred hccccccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCC
Q psy3546 53 KGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSP 98 (164)
Q Consensus 53 ~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLna 98 (164)
+.||.-+-|. + |- -.+...+..|++.|.++||.|...+-|.
T Consensus 179 ~~WKQpi~~~--f-~t--~m~~~~l~~iI~~l~~~g~~VvAivsD~ 219 (236)
T PF12017_consen 179 KSWKQPIYFD--F-DT--SMDADILKNIIEKLHEIGYNVVAIVSDM 219 (236)
T ss_pred hcCCccEEEE--e-cC--cCCHHHHHHHHHHHHHCCCEEEEEECCC
Confidence 4799888333 2 43 2345678899999999999998887554
No 46
>PF02624 YcaO: YcaO-like family; InterPro: IPR003776 This domain comprises the whole of a protein in Methanocaldococcus jannaschii (Methanococcus jannaschii) and Methanobacterium thermoautotrophicum, all but the N-terminal 60 residues from a protein of Mycobacterium tuberculosis, and all but the C-terminal 180 residues from a protein in Haemophilus influenzae and Escherichia coli, among proteins from published complete genomes.
Probab=25.84 E-value=67 Score=26.78 Aligned_cols=84 Identities=20% Similarity=0.252 Sum_probs=0.0
Q ss_pred CCCcCCCCC---------cccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCC
Q psy3546 1 MASIDYASN---------SDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGF 71 (164)
Q Consensus 1 ~~~~~fPCQ---------~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf 71 (164)
|+.+.+|+. .-++..-..+.+++-...+.++||-=..+. -|..+++.. .+. .
T Consensus 92 ~~~~~~~~~~~~~~~~~~~S~G~A~g~s~~eA~~~al~E~iERda~~~--------------~w~~~~~~~-~i~----~ 152 (332)
T PF02624_consen 92 LVYVFYPYRDGEPLFFYSTSNGLAAGNSLEEAILHALLEVIERDAFSL--------------WWYNRLPPP-RID----D 152 (332)
T ss_pred HHHhcCCCCCcccccccCCCCEEcCCCCHHHHHHHHHHHHHHHHHHHH--------------HHHhcCCCC-eEe----c
Q ss_pred CCchHHHHHHHHHHh---CCCeEEEEEeCCCCCCCC
Q psy3546 72 EGSRSRDLITSMLTR---AGFRFQEFLLSPTQFGTS 104 (164)
Q Consensus 72 ~~s~~~d~I~s~L~~---~GY~v~~~lLnatdfGVP 104 (164)
........|...+.. .|+++..+-++. ++|||
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~v~l~dit~-~~~vp 187 (332)
T PF02624_consen 153 VLDPTLPELLERLERLREAGLEVRLFDITN-DFGVP 187 (332)
T ss_pred ccCcCCHHHHHHHHHhhcCceEEEEEECCC-CCCce
No 47
>KOG1467|consensus
Probab=25.75 E-value=95 Score=30.38 Aligned_cols=46 Identities=13% Similarity=0.124 Sum_probs=36.0
Q ss_pred EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546 64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK 113 (164)
Q Consensus 64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~ 113 (164)
++.-=|+|+|- .++..|...||.+.+.++++..|=.+-.+.+|+.+
T Consensus 390 VVDSRP~~EG~----~~lr~Lv~~GinctYv~I~a~syim~evtkvfLGa 435 (556)
T KOG1467|consen 390 VVDSRPNLEGR----KLLRRLVDRGINCTYVLINAASYIMLEVTKVFLGA 435 (556)
T ss_pred EEeCCCCcchH----HHHHHHHHcCCCeEEEEehhHHHHHHhcceeeech
Confidence 77777888875 56777888999999999999999665556666543
No 48
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=25.46 E-value=1.3e+02 Score=24.87 Aligned_cols=44 Identities=16% Similarity=0.366 Sum_probs=32.9
Q ss_pred CCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHHHHHHHhCCC
Q psy3546 21 ADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGF 89 (164)
Q Consensus 21 ~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY 89 (164)
+++| .|+..|+..|..+. |+ |++-=|+-||. ++.|++.+..+|-
T Consensus 80 ~~E~-~LL~~f~~~i~~~D----PD----------------iivG~Ni~~fd----l~~L~~R~~~l~i 123 (234)
T cd05776 80 ENER-ALLNFFLAKLQKID----PD----------------VLVGHDLEGFD----LDVLLSRIQELKV 123 (234)
T ss_pred CCHH-HHHHHHHHHHhhcC----CC----------------EEEeeccCCCC----HHHHHHHHHHhCC
Confidence 5666 69999999999998 78 54778888763 5666666666543
No 49
>KOG3988|consensus
Probab=24.23 E-value=60 Score=30.10 Aligned_cols=28 Identities=21% Similarity=0.286 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhCCCeEEEEEeCCCCCCCCCc
Q psy3546 76 SRDLITSMLTRAGFRFQEFLLSPTQFGTSLY 106 (164)
Q Consensus 76 ~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~ 106 (164)
..+.|--||..+||.-. .||.+||.|-.
T Consensus 314 dma~iAPmL~~LGYDp~---anpPnYgkpd~ 341 (378)
T KOG3988|consen 314 DMADIAPMLAILGYDPY---ANPPNYGKPDP 341 (378)
T ss_pred HHHHHHHHHHHhCCCCC---CCCCCCCCCCH
Confidence 46788999999999864 68999999863
No 50
>KOG3042|consensus
Probab=23.45 E-value=1.4e+02 Score=26.85 Aligned_cols=54 Identities=13% Similarity=0.218 Sum_probs=38.3
Q ss_pred hhccccccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCc
Q psy3546 52 VKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLY 106 (164)
Q Consensus 52 ~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~ 106 (164)
+..|+.+-.-|=+++-. |-+++..+..+.+.+...-|.+....+||.||.-|+.
T Consensus 16 ~~~~R~~g~tIgfVPTM-G~LHeGH~SLvrqs~~~~~~tVVSIfVNP~QF~pteD 69 (283)
T KOG3042|consen 16 TQELRETGETIGFVPTM-GCLHEGHASLVRQSVKENTYTVVSIFVNPSQFAPTED 69 (283)
T ss_pred HHHHHhcCCeEEEeccc-ccccccHHHHHHHHHhhCceEEEEEEechhhcCChhH
Confidence 34444443344222222 4456777889999999999999999999999988775
No 51
>PF03848 TehB: Tellurite resistance protein TehB; InterPro: IPR015985 Tellurite resistance protein TehB is part of a tellurite-reducing operon tehA and tehB. When present in high copy number, TehB is responsible for potassium tellurite resistance, probably by increasing the reduction rate of tellurite to metallic tellurium within the bacterium. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases []. Conformational changes in TehB are observed upon binding of both tellurite and SAM, suggesting that TehB utilises a methyltransferase activity in the detoxification of tellurite. This entry represents the methyltransferase domain found in all TehB proteins.; PDB: 2KW5_A 3MER_B 3M70_A 2I6G_A 4DQ0_D 2XVA_B 2XVM_A.
Probab=23.44 E-value=1.5e+02 Score=24.54 Aligned_cols=55 Identities=15% Similarity=0.153 Sum_probs=32.7
Q ss_pred cccccceEEEeecCcCCCCchHHHHHHHHHHhC----CCeEEEEEeCCCCCCCCCcceEE
Q psy3546 55 WKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRA----GFRFQEFLLSPTQFGTSLYTEWL 110 (164)
Q Consensus 55 ~~~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~----GY~v~~~lLnatdfGVPQ~Rr~~ 110 (164)
|....++| +-.-|-.|.....+..|+..+..+ ||.+.+...+..+||.|..-.++
T Consensus 91 ~~~~yD~I-~st~v~~fL~~~~~~~i~~~m~~~~~pGG~~li~~~~~~~d~p~~~~~~f~ 149 (192)
T PF03848_consen 91 FPEEYDFI-VSTVVFMFLQRELRPQIIENMKAATKPGGYNLIVTFMETPDYPCPSPFPFL 149 (192)
T ss_dssp -TTTEEEE-EEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS--SS--S--
T ss_pred ccCCcCEE-EEEEEeccCCHHHHHHHHHHHHhhcCCcEEEEEEEecccCCCCCCCCCCcc
Confidence 33445555 445677788877788888888765 89998777888899988654443
No 52
>TIGR00587 nfo apurinic endonuclease (APN1). All proteins in this family for which functions are known are 5' AP endonculeases that are used in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.00 E-value=1.2e+02 Score=25.37 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=17.2
Q ss_pred EEeecCcCCCC--chHHHHHHHHHHhCC
Q psy3546 63 FRTPNVKGFEG--SRSRDLITSMLTRAG 88 (164)
Q Consensus 63 Fl~ENVkGf~~--s~~~d~I~s~L~~~G 88 (164)
+.+||++|..+ ..+.+++...|...+
T Consensus 140 l~lEN~~~~~~~l~~~~~el~~ll~~~~ 167 (274)
T TIGR00587 140 ILLENMAGQGSELGRSFEELAYIIKVIV 167 (274)
T ss_pred EEEEeCCCCCCccCCCHHHHHHHHHhcC
Confidence 58999998753 345566666665444
No 53
>KOG2798|consensus
Probab=22.99 E-value=39 Score=31.41 Aligned_cols=20 Identities=25% Similarity=0.363 Sum_probs=18.0
Q ss_pred CCccchHHHHHHHhccccCC
Q psy3546 21 ADARCTALSYLIETIPANFP 40 (164)
Q Consensus 21 ~D~R~~L~~~~iriI~~~~p 40 (164)
.-+|..++.-+|+-|..++|
T Consensus 124 ~~ERd~~ykpii~~l~~lfp 143 (369)
T KOG2798|consen 124 QRERDQLYKPIIEELNSLFP 143 (369)
T ss_pred chhhhhhhhhHHHHHHhhCC
Confidence 35789999999999999997
No 54
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.94 E-value=67 Score=21.27 Aligned_cols=19 Identities=11% Similarity=0.235 Sum_probs=16.3
Q ss_pred chHHHHHHHHHHhCCCeEE
Q psy3546 74 SRSRDLITSMLTRAGFRFQ 92 (164)
Q Consensus 74 s~~~d~I~s~L~~~GY~v~ 92 (164)
....+.|+..|.+.||.+.
T Consensus 49 ~~~~~~i~~~L~~~G~~~~ 67 (68)
T cd04885 49 REDLAELKERLEALGYPYV 67 (68)
T ss_pred HHHHHHHHHHHHHcCCCcc
Confidence 4678999999999999864
No 55
>PF01234 NNMT_PNMT_TEMT: NNMT/PNMT/TEMT family; InterPro: IPR000940 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed 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. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Several cytoplasmic vertebrate methyltransferases are evolutionary related [], including nicotinamide N-methyltransferase (2.1.1.1 from EC) (NNMT); phenylethanolamine N-methyltransferase (2.1.1.28 from EC) (PNMT); and thioether S-methyltransferase (2.1.1.96 from EC) (TEMT). NNMT catalyzes the N-methylation of nicotinamide and other pyridines to form pyridinium ions. This activity is important for the biotransformation of many drugs and xenobiotic compounds. PNMT catalyzes the last step in catecholamine biosynthesis, the conversion of noradrenalin to adrenalin; and TEMT catalyzes the methylation of dimethyl sulphide into trimethylsulphonium. These three enzymes use S-adenosyl-L-methionine as the methyl donor. They are proteins of 30 to 32 kDa.; GO: 0008168 methyltransferase activity; PDB: 2IIP_C 3ROD_A 2OBF_A 3HCA_B 2ONY_B 3KR1_A 2OPB_B 3KQP_B 2AN4_B 3KQM_A ....
Probab=22.86 E-value=1.3e+02 Score=26.15 Aligned_cols=37 Identities=22% Similarity=0.384 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEeccc
Q psy3546 76 SRDLITSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKKK 115 (164)
Q Consensus 76 ~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~rk 115 (164)
.-+.+.+.|+++||.+...- .+++++.+. -.|++++|
T Consensus 219 ~ee~v~~al~~aG~~i~~~~---~~~~~~d~~~~~f~~a~K 256 (256)
T PF01234_consen 219 NEEFVREALEEAGFDIEDLE---KQSKVSDYEGMFFLVARK 256 (256)
T ss_dssp -HHHHHHHHHHTTEEEEEEE---G-TTTB---EEEEEEEEE
T ss_pred CHHHHHHHHHHcCCEEEecc---cccCcCCCCcEEEEEEeC
Confidence 46899999999999998777 278888886 56666554
No 56
>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molec
Probab=22.76 E-value=1.5e+02 Score=25.49 Aligned_cols=20 Identities=15% Similarity=0.358 Sum_probs=16.3
Q ss_pred HHHHHHHHHHhCCCeEEEEE
Q psy3546 76 SRDLITSMLTRAGFRFQEFL 95 (164)
Q Consensus 76 ~~d~I~s~L~~~GY~v~~~l 95 (164)
...+|..+|+.+|+++...+
T Consensus 167 d~~el~~ll~~~G~~v~~~~ 186 (399)
T cd00316 167 DLRELKRLLEEMGIRVNALF 186 (399)
T ss_pred hHHHHHHHHHHcCCcEEEEc
Confidence 56899999999999986543
No 57
>COG3527 AlsD Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.74 E-value=44 Score=29.37 Aligned_cols=39 Identities=26% Similarity=0.248 Sum_probs=28.3
Q ss_pred EEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCC
Q psy3546 63 FRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102 (164)
Q Consensus 63 Fl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfG 102 (164)
|-.|||.|..-+-.--+..+.|.-+||+++. +=+---||
T Consensus 147 f~~Env~GtiVGf~tP~~~~Gl~v~GyHlHF-itDdrtfG 185 (234)
T COG3527 147 FEFENVKGTIVGFWTPEYFEGLAVAGYHLHF-ITDDRTFG 185 (234)
T ss_pred eEEeecCceEEEecChHHhcccccCceEEEE-eecCcccc
Confidence 5899999987664456788889999999763 33444444
No 58
>PHA03108 poly(A) polymerase small subunit; Provisional
Probab=22.67 E-value=1.2e+02 Score=27.63 Aligned_cols=45 Identities=7% Similarity=0.025 Sum_probs=33.0
Q ss_pred chHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCc--ceEEEecccchh
Q psy3546 74 SRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLY--TEWLRNKKKKRK 118 (164)
Q Consensus 74 s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~--Rr~~i~~rkk~~ 118 (164)
+.....+.+.+..+||.+.|.++||.+|-.+.. +..-++-++=++
T Consensus 72 G~HI~~L~~lf~~lg~~ikw~LiDp~~h~~~Le~l~nV~Li~~f~de 118 (300)
T PHA03108 72 GTHIRYLRDHFYSLGVVIKWMLIDGRKHDPILNGLRDVTLVTRFVDE 118 (300)
T ss_pred CccHHHHHHHHHhcCCCeEEEEECCCcccHhhcCCCcEEeeHhhcCH
Confidence 456788899999999999999999999976554 344444444333
No 59
>PF09582 AnfO_nitrog: Iron only nitrogenase protein AnfO (AnfO_nitrog); InterPro: IPR014287 Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species.
Probab=22.05 E-value=66 Score=26.99 Aligned_cols=25 Identities=40% Similarity=0.574 Sum_probs=17.2
Q ss_pred EEEeecCcCCCCchHHHHHHHHHHhCCCeEEEE
Q psy3546 62 IFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEF 94 (164)
Q Consensus 62 iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~ 94 (164)
||+..+|.|+.- +.|.++||++.+.
T Consensus 67 ifV~~~v~Gi~y--------~~Le~~g~~iWe~ 91 (202)
T PF09582_consen 67 IFVAKSVSGIPY--------SLLEKAGFSIWES 91 (202)
T ss_pred EEEEccccCccH--------HHHHHCCcEEEEE
Confidence 789999999742 3455667766554
No 60
>PF02569 Pantoate_ligase: Pantoate-beta-alanine ligase; InterPro: IPR003721 D-Pantothenate is synthesized via four enzymes from ketoisovalerate, which is an intermediate of branched-chain amino acid synthesis []. Pantoate-beta-alanine ligase, also know as pantothenate synthase, (6.3.2.1 from EC) catalyzes the formation of pantothenate from pantoate and alanine in the pantothenate biosynthesis pathway [].; GO: 0004592 pantoate-beta-alanine ligase activity, 0015940 pantothenate biosynthetic process; PDB: 3MUE_C 1V8F_B 1UFV_A 2X3F_B 1MOP_A 3COY_B 3IOC_A 1N2E_A 3IVX_A 1N2H_A ....
Probab=21.82 E-value=94 Score=27.57 Aligned_cols=37 Identities=22% Similarity=0.248 Sum_probs=26.2
Q ss_pred CCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCc
Q psy3546 70 GFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLY 106 (164)
Q Consensus 70 Gf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~ 106 (164)
|-++......|-.+-..+...+-...+||+|||-+..
T Consensus 31 GaLHeGHlsLi~~A~~~~d~vVVSIFVNP~QF~~~eD 67 (280)
T PF02569_consen 31 GALHEGHLSLIRRARAENDVVVVSIFVNPTQFGPNED 67 (280)
T ss_dssp SS--HHHHHHHHHHHHHSSEEEEEE---GGGSSTTSH
T ss_pred chhhHHHHHHHHHHHhCCCEEEEEECcCcccCCCcch
Confidence 4445667788888888999999999999999998753
No 61
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=21.50 E-value=93 Score=23.82 Aligned_cols=30 Identities=20% Similarity=0.257 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHhCCCeE-EEE--EeCCCCCCCC
Q psy3546 75 RSRDLITSMLTRAGFRF-QEF--LLSPTQFGTS 104 (164)
Q Consensus 75 ~~~d~I~s~L~~~GY~v-~~~--lLnatdfGVP 104 (164)
.+.++|...+..+||.+ ... -..|.++|.|
T Consensus 32 P~~~EI~~a~~~lgl~~~~~E~~K~yPr~~g~~ 64 (100)
T PRK03745 32 PTLEEIVDAAEALGFKVIEVDREKLNPRLSGID 64 (100)
T ss_pred CCHHHHHHHHHHcCCCcEeeccCCCCCCccCCc
Confidence 46789999999999998 333 4899999986
No 62
>PF08407 Chitin_synth_1N: Chitin synthase N-terminal; InterPro: IPR013616 This is the N-terminal domain of Chitin synthase (IPR004834 from INTERPRO). ; GO: 0004100 chitin synthase activity
Probab=21.24 E-value=1.2e+02 Score=22.30 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=18.8
Q ss_pred HHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546 84 LTRAGFRFQEFLLSPTQFGTSLYTEWLRNK 113 (164)
Q Consensus 84 L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~ 113 (164)
|.+.||. |-+..||.|-.++.+|+.
T Consensus 54 F~~~gyt-----LR~~~y~~pR~tEl~Ivi 78 (79)
T PF08407_consen 54 FTEDGYT-----LRQVLYGPPRETELFIVI 78 (79)
T ss_pred HhHcCcE-----echhhcCCCCccEEEEEE
Confidence 4455665 567889999999999874
No 63
>PRK06092 4-amino-4-deoxychorismate lyase; Reviewed
Probab=21.24 E-value=1.4e+02 Score=24.70 Aligned_cols=38 Identities=18% Similarity=0.197 Sum_probs=28.8
Q ss_pred CCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEE
Q psy3546 72 EGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLR 111 (164)
Q Consensus 72 ~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i 111 (164)
..+-++..+++.+.++|+.|++..|++.|. .+..+.|+
T Consensus 197 L~GitR~~vl~~~~~~g~~v~e~~i~~~dL--~~adevfl 234 (268)
T PRK06092 197 VAGVMRQFILELLAQSGYPVVEVDASLEEL--LQADEVFI 234 (268)
T ss_pred cccHHHHHHHHHHHHcCCeEEEEECCHHHH--hhCCEEEE
Confidence 345578999999999999999999988874 33344544
No 64
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=21.07 E-value=98 Score=19.67 Aligned_cols=18 Identities=22% Similarity=0.294 Sum_probs=13.4
Q ss_pred HHHHHHHHHhCCCeEEEE
Q psy3546 77 RDLITSMLTRAGFRFQEF 94 (164)
Q Consensus 77 ~d~I~s~L~~~GY~v~~~ 94 (164)
++++...|..+||.+...
T Consensus 1 ~~el~k~L~~~G~~~~r~ 18 (56)
T PF07927_consen 1 WRELIKLLEKAGFEEVRQ 18 (56)
T ss_dssp -HHHHHHHHHTT-EEEEE
T ss_pred ChHHHHHHHHCCCEEecC
Confidence 468899999999998643
No 65
>TIGR01121 D_amino_aminoT D-amino acid aminotransferase. Specificity is broad for various D-amino acids, and differs among members of the family; the family is designated equivalog, but with this caveat attached.
Probab=20.76 E-value=1.6e+02 Score=24.56 Aligned_cols=40 Identities=13% Similarity=0.086 Sum_probs=30.1
Q ss_pred CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEe
Q psy3546 71 FEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRN 112 (164)
Q Consensus 71 f~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~ 112 (164)
+..+-+++.+++.+..+|+.+.+.-|++.+. .+..+.|+.
T Consensus 199 ~L~GitR~~vl~~a~~~g~~v~e~~i~~~el--~~ade~flt 238 (276)
T TIGR01121 199 ILNGITRMVILACAEENGIPVKEEPFTKEEL--LNADEVFVS 238 (276)
T ss_pred CCcCHHHHHHHHHHHHCCCeEEEEeCCHHHH--hcCCEEEEe
Confidence 3445678999999999999999998888875 333455543
No 66
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.75 E-value=2.3e+02 Score=25.55 Aligned_cols=41 Identities=12% Similarity=0.079 Sum_probs=27.6
Q ss_pred eecCcCCCCchHHHHHHHHHHhCCCeE-EEEEeCCCCCCCCCcc
Q psy3546 65 TPNVKGFEGSRSRDLITSMLTRAGFRF-QEFLLSPTQFGTSLYT 107 (164)
Q Consensus 65 ~ENVkGf~~s~~~d~I~s~L~~~GY~v-~~~lLnatdfGVPQ~R 107 (164)
|=..|| ++...+...++.+.++++.. ..+.++| .=|+|-+.
T Consensus 282 IvGfPG-ET~edf~~tl~fi~~~~~~~~~v~~ysp-~pGT~a~~ 323 (418)
T PRK14336 282 IVGFPS-ETEEQFNQSYKLMADIGYDAIHVAAYSP-RPQTVAAR 323 (418)
T ss_pred EEECCC-CCHHHHHHHHHHHHhcCCCEEEeeecCC-CCCChhHh
Confidence 334444 45567888889999999875 4556665 44777764
No 67
>PRK07849 4-amino-4-deoxychorismate lyase; Provisional
Probab=20.61 E-value=1.4e+02 Score=25.39 Aligned_cols=40 Identities=10% Similarity=0.102 Sum_probs=30.0
Q ss_pred CCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEE
Q psy3546 70 GFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLR 111 (164)
Q Consensus 70 Gf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i 111 (164)
|++.+-+++.+++.+.+.|+.+.+..+++.+. .+..+.|+
T Consensus 214 giL~GItR~~vie~~~~~g~~v~er~i~~~eL--~~Adevfl 253 (292)
T PRK07849 214 GILPGTTQAALFEVAREKGWDCEYRALRPADL--FAADGVWL 253 (292)
T ss_pred CCCccHHHHHHHHHHHHcCCceEEEECCHHHH--hhCCEEEE
Confidence 44556689999999999999999998888773 33344544
No 68
>PHA02768 hypothetical protein; Provisional
Probab=20.30 E-value=48 Score=22.98 Aligned_cols=11 Identities=27% Similarity=0.289 Sum_probs=9.1
Q ss_pred CCCcCCCCCcc
Q psy3546 1 MASIDYASNSD 11 (164)
Q Consensus 1 ~~~~~fPCQ~F 11 (164)
||-|||+|.-.
T Consensus 1 ~~~~~y~C~~C 11 (55)
T PHA02768 1 MALLGYECPIC 11 (55)
T ss_pred CcccccCcchh
Confidence 88999999753
Done!