Query psy14414
Match_columns 76
No_of_seqs 14 out of 16
Neff 2.0
Searched_HMMs 46136
Date Fri Aug 16 19:14:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14414.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14414hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2132|consensus 97.7 2.2E-05 4.7E-10 62.9 3.1 59 16-74 281-354 (355)
2 PF08200 Phage_1_1: Bacterioph 80.5 0.54 1.2E-05 28.7 0.0 11 45-55 1-11 (45)
3 PHA00453 hypothetical protein 74.4 1.1 2.4E-05 27.0 0.2 15 45-59 1-15 (41)
4 TIGR00013 taut 4-oxalocrotonat 67.5 5.9 0.00013 22.2 2.2 26 36-61 12-37 (63)
5 COG5404 SulA SOS-response cell 59.3 11 0.00024 28.2 2.9 40 36-75 68-114 (169)
6 TIGR02740 TraF-like TraF-like 58.1 14 0.0003 27.3 3.3 28 45-73 83-110 (271)
7 KOG0860|consensus 56.3 8.4 0.00018 27.0 1.8 12 42-53 42-54 (116)
8 PTZ00397 macrophage migration 52.9 20 0.00043 22.8 3.0 28 34-61 10-37 (116)
9 cd07921 PCA_45_Doxase_A_like S 52.1 8.4 0.00018 26.5 1.2 20 33-52 42-62 (106)
10 PRK02220 4-oxalocrotonate taut 51.6 19 0.00041 20.1 2.4 26 36-61 12-37 (61)
11 PF00725 3HCDH: 3-hydroxyacyl- 48.3 34 0.00074 20.5 3.4 30 42-71 52-82 (97)
12 PF13728 TraF: F plasmid trans 47.4 38 0.00083 24.3 4.0 49 22-71 3-62 (215)
13 cd06154 YjgF_YER057c_UK114_lik 46.0 19 0.00042 22.9 2.1 25 38-62 43-67 (119)
14 PF09734 Tau95: RNA polymerase 45.3 16 0.00034 27.0 1.8 30 31-68 4-37 (310)
15 cd07321 Extradiol_Dioxygenase_ 45.2 13 0.00028 23.3 1.2 21 33-53 32-53 (77)
16 PF01361 Tautomerase: Tautomer 45.0 26 0.00056 19.6 2.3 25 37-61 12-36 (60)
17 PRK07217 replication factor A; 43.7 30 0.00065 27.5 3.3 24 50-74 252-275 (311)
18 cd07924 PCA_45_Doxase_A The A 43.7 17 0.00036 25.7 1.7 20 33-52 50-70 (121)
19 cd06155 eu_AANH_C_1 A group of 42.9 23 0.0005 22.0 2.1 41 20-60 7-47 (101)
20 COG0285 FolC Folylpolyglutamat 42.4 31 0.00066 28.0 3.2 29 48-76 27-78 (427)
21 PRK02289 4-oxalocrotonate taut 42.0 26 0.00057 20.1 2.1 26 36-61 12-37 (60)
22 cd00448 YjgF_YER057c_UK114_fam 41.5 25 0.00054 20.7 2.0 25 37-61 30-54 (107)
23 PF07746 LigA: Aromatic-ring-o 41.1 18 0.00038 23.6 1.4 21 33-53 27-48 (88)
24 PF03241 HpaB: 4-hydroxyphenyl 40.5 5.1 0.00011 28.7 -1.3 54 2-64 119-172 (205)
25 cd07925 LigA_like_1 The A subu 39.7 21 0.00046 24.6 1.7 20 33-52 42-62 (106)
26 PRK01271 4-oxalocrotonate taut 38.8 28 0.00062 21.9 2.0 27 36-62 13-39 (76)
27 PF07179 SseB: SseB protein N- 38.1 41 0.00088 20.2 2.6 27 48-74 1-28 (124)
28 PF01042 Ribonuc_L-PSP: Endori 38.0 24 0.00052 22.3 1.6 23 38-60 42-64 (121)
29 PF09409 PUB: PUB domain; Int 38.0 38 0.00082 20.6 2.5 24 39-62 4-27 (87)
30 PRK01964 4-oxalocrotonate taut 37.8 42 0.00091 19.1 2.5 27 35-61 11-37 (64)
31 PF13621 Cupin_8: Cupin-like d 37.6 18 0.00039 23.9 1.0 12 17-28 238-249 (251)
32 PF13308 YARHG: YARHG domain 37.2 10 0.00022 23.6 -0.2 21 8-28 40-60 (81)
33 TIGR03610 RutC pyrimidine util 37.1 30 0.00065 22.7 2.0 40 21-60 26-71 (127)
34 PF03271 EB1: EB1-like C-termi 37.0 20 0.00044 20.6 1.1 25 43-67 11-35 (43)
35 PF14850 Pro_dh-DNA_bdg: DNA-b 36.4 23 0.00049 24.7 1.4 20 32-56 8-27 (114)
36 cd02198 YjgH_like YjgH belongs 36.3 36 0.00078 21.3 2.2 24 38-61 32-55 (111)
37 PF03195 DUF260: Protein of un 35.2 33 0.00072 22.7 2.0 28 41-70 35-62 (101)
38 PRK13703 conjugal pilus assemb 33.6 1.1E+02 0.0023 23.2 4.7 32 39-71 53-85 (248)
39 KOG0859|consensus 33.5 30 0.00064 26.8 1.8 14 40-53 137-150 (217)
40 cd00491 4Oxalocrotonate_Tautom 33.3 46 0.001 18.0 2.1 26 36-61 11-36 (58)
41 cd06156 eu_AANH_C_2 A group of 33.2 37 0.0008 22.1 2.0 18 38-55 32-49 (118)
42 COG4709 Predicted membrane pro 32.6 43 0.00093 25.4 2.5 27 49-75 43-69 (195)
43 TIGR00004 endoribonuclease L-P 32.5 43 0.00093 21.2 2.1 24 38-61 47-70 (124)
44 PF14164 YqzH: YqzH-like prote 30.9 32 0.00069 22.0 1.3 11 47-57 5-15 (64)
45 TIGR03384 betaine_BetI transcr 30.7 1.1E+02 0.0023 19.4 3.8 29 44-72 130-160 (189)
46 PRK00745 4-oxalocrotonate taut 29.2 73 0.0016 17.7 2.5 24 36-59 12-35 (62)
47 COG0815 Lnt Apolipoprotein N-a 28.7 29 0.00063 28.4 1.1 26 19-50 415-440 (518)
48 smart00591 RWD domain in RING 27.7 92 0.002 18.3 2.9 29 31-59 61-91 (107)
49 PF13167 GTP-bdg_N: GTP-bindin 27.5 34 0.00073 22.5 1.0 19 31-53 62-80 (95)
50 cd03308 CmuA_CmuC_like CmuA_Cm 27.1 1E+02 0.0022 23.5 3.7 27 44-70 187-213 (378)
51 TIGR02792 PCA_ligA protocatech 27.1 28 0.00062 24.5 0.7 20 33-52 47-67 (117)
52 PF03549 Tir_receptor_M: Trans 26.6 28 0.0006 22.7 0.5 12 7-18 19-30 (66)
53 COG1942 Uncharacterized protei 26.3 67 0.0015 20.0 2.2 26 36-61 13-38 (69)
54 PRK13377 protocatechuate 4,5-d 26.0 31 0.00066 24.7 0.7 20 33-52 53-73 (129)
55 cd06150 YjgF_YER057c_UK114_lik 25.9 66 0.0014 19.9 2.1 21 38-58 28-48 (105)
56 cd07923 Gallate_dioxygenase_C 25.9 27 0.00059 23.5 0.4 20 33-52 34-54 (94)
57 PRK13378 protocatechuate 4,5-d 24.7 34 0.00073 24.1 0.7 20 33-52 53-73 (117)
58 PLN02433 uroporphyrinogen deca 24.4 83 0.0018 23.5 2.7 25 46-70 154-178 (345)
59 cd06152 YjgF_YER057c_UK114_lik 24.1 78 0.0017 20.4 2.3 24 38-61 33-57 (114)
60 PHA02696 hypothetical protein; 23.7 47 0.001 22.3 1.2 17 37-53 56-72 (79)
61 PRK01005 V-type ATP synthase s 23.5 1.8E+02 0.0039 21.3 4.3 24 48-71 97-120 (207)
62 PF06744 DUF1215: Protein of u 23.1 65 0.0014 20.9 1.8 15 60-74 41-55 (125)
63 PRK07218 replication factor A; 23.1 94 0.002 25.3 3.0 26 48-74 357-382 (423)
64 PF10796 Anti-adapt_IraP: Sigm 22.9 81 0.0018 20.9 2.2 25 37-61 41-65 (87)
65 PF03730 Ku_C: Ku70/Ku80 C-ter 22.6 21 0.00045 22.2 -0.6 11 7-17 8-18 (96)
66 TIGR02739 TraF type-F conjugat 22.6 2E+02 0.0043 21.8 4.5 37 36-73 57-94 (256)
67 KOG0414|consensus 22.5 1E+02 0.0022 29.1 3.4 38 38-75 615-653 (1251)
68 PF13524 Glyco_trans_1_2: Glyc 22.2 1.7E+02 0.0037 16.8 3.8 30 46-75 50-82 (92)
69 PF15397 DUF4618: Domain of un 22.2 84 0.0018 24.3 2.5 21 31-51 112-132 (258)
70 PF14863 Alkyl_sulf_dimr: Alky 22.1 92 0.002 21.5 2.4 47 23-71 43-98 (141)
71 cd00580 CHMI 5-carboxymethyl-2 22.0 96 0.0021 19.7 2.4 27 35-61 70-96 (113)
72 COG0251 TdcF Putative translat 21.9 78 0.0017 21.0 2.0 50 13-62 19-74 (130)
73 PF08006 DUF1700: Protein of u 21.9 82 0.0018 21.4 2.1 18 49-66 43-60 (181)
74 PRK00423 tfb transcription ini 21.5 1.6E+02 0.0035 22.1 3.8 21 46-66 116-136 (310)
75 PF05069 Phage_tail_S: Phage v 21.3 1.7E+02 0.0036 19.3 3.5 25 45-69 3-27 (148)
76 PRK13379 protocatechuate 4,5-d 21.0 44 0.00095 23.6 0.7 20 33-52 54-74 (119)
77 COG4598 HisP ABC-type histidin 20.8 1E+02 0.0023 24.3 2.8 37 33-70 148-196 (256)
78 TIGR01498 folK 2-amino-4-hydro 20.8 1E+02 0.0022 20.7 2.4 24 31-54 56-79 (127)
79 PF08546 ApbA_C: Ketopantoate 20.8 1.4E+02 0.003 18.5 2.8 19 58-76 74-92 (125)
80 COG0319 Predicted metal-depend 20.6 45 0.00096 23.6 0.6 18 21-38 56-73 (153)
81 cd01645 RT_Rtv RT_Rtv: Reverse 20.6 72 0.0016 22.1 1.7 21 33-53 6-26 (213)
82 PF15460 SAS4: Something about 20.6 1.2E+02 0.0025 20.4 2.6 25 43-69 20-44 (101)
No 1
>KOG2132|consensus
Probab=97.75 E-value=2.2e-05 Score=62.91 Aligned_cols=59 Identities=25% Similarity=0.195 Sum_probs=49.2
Q ss_pred ccceeeeeecC-CCCC-c----------eecc-CCcchhhHHHHhHHHHH--HHHhcChhHHHHHHHHHHhccc
Q psy14414 16 KVSQVSWKPKT-KPTG-D----------IEYP-LKGHQKVAILRNIEKMV--AEALQNQEEVSHLMRALVLGRY 74 (76)
Q Consensus 16 ~~~sVnfwyk~-~P~p-~----------I~yP-L~~~QKVaImRNIEKML--~eAL~D~~EVg~Llr~lVlGRY 74 (76)
|+-.+.+|+.+ .+.| + +++| |+.++|++++|+++.|| +|+|.+|.+..+++|++-.+++
T Consensus 281 k~i~l~~p~~s~~lyP~d~~~~~tsqvdvenPdlk~fp~~~k~~~l~~lL~pGe~L~iP~kwwhyvrs~d~s~s 354 (355)
T KOG2132|consen 281 KRIRLYPPEDSGALYPTDTYLLETSQVDVENPDLKAFPKFAKARFLDCLLEPGEALFIPPKWWHYVRSLDKSFS 354 (355)
T ss_pred eEEEEecCcccCCCCCccchhhcccccccCCCChhhhhHHHHHHHHHHhcCCchhccccHHHhhhhhhcccccc
Confidence 34455667773 3334 5 8899 99999999999999999 9999999999999999987765
No 2
>PF08200 Phage_1_1: Bacteriophage 1.1 Protein ; InterPro: IPR013232 Gene 1.1 in Bacteriophage T7 encodes a 42 amino acid protein, rich in basic amino acids suggesting its interaction with nucleic acids []. Many homologues are present in different T7 and T3-like bacteriophage.
Probab=80.52 E-value=0.54 Score=28.69 Aligned_cols=11 Identities=45% Similarity=0.700 Sum_probs=9.3
Q ss_pred HHhHHHHHHHH
Q psy14414 45 LRNIEKMVAEA 55 (76)
Q Consensus 45 mRNIEKML~eA 55 (76)
|||+|||--.+
T Consensus 1 MRNFEK~tkr~ 11 (45)
T PF08200_consen 1 MRNFEKMTKRN 11 (45)
T ss_pred CccHHhhhhcc
Confidence 89999998764
No 3
>PHA00453 hypothetical protein
Probab=74.37 E-value=1.1 Score=26.95 Aligned_cols=15 Identities=40% Similarity=0.592 Sum_probs=11.4
Q ss_pred HHhHHHHHHHHhcCh
Q psy14414 45 LRNIEKMVAEALQNQ 59 (76)
Q Consensus 45 mRNIEKML~eAL~D~ 59 (76)
|||.|||-..+=...
T Consensus 1 MRNFEKmtrk~nr~~ 15 (41)
T PHA00453 1 MRNFEKMTKRSNRNA 15 (41)
T ss_pred CccHHHHHHHhhhhh
Confidence 899999987754433
No 4
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=67.47 E-value=5.9 Score=22.22 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=23.2
Q ss_pred CCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
++..||-++.+.|=..|.+.||-|.+
T Consensus 12 rt~eqK~~l~~~it~~l~~~lg~~~~ 37 (63)
T TIGR00013 12 RTDEQKRQLIEGVTEAMAETLGANLE 37 (63)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 67899999999999999999987654
No 5
>COG5404 SulA SOS-response cell division inhibitor, blocks FtsZ ring formation [Cell division and chromosome partitioning]
Probab=59.31 E-value=11 Score=28.19 Aligned_cols=40 Identities=33% Similarity=0.461 Sum_probs=32.1
Q ss_pred CCcchhhHH--HH----hHHH-HHHHHhcChhHHHHHHHHHHhcccC
Q psy14414 36 LKGHQKVAI--LR----NIEK-MVAEALQNQEEVSHLMRALVLGRYT 75 (76)
Q Consensus 36 L~~~QKVaI--mR----NIEK-ML~eAL~D~~EVg~Llr~lVlGRYt 75 (76)
|+++||.+= +| |+|| |+..++....-|....+++.+|||.
T Consensus 68 ltPqqkLsreWl~~sGLp~~kv~ql~q~~p~~tle~m~~ALrtGnys 114 (169)
T COG5404 68 LTPQQKLSREWLQASGLPLTKVMQLSQLSPCHTVESMVRALRTGNYS 114 (169)
T ss_pred hCCHHHHHHHHHHHcCCCHHHHHHHhhcCcHHHHHHHHHHHHcCCce
Confidence 577888652 11 7888 5678999999999999999999994
No 6
>TIGR02740 TraF-like TraF-like protein. This protein is related to the F-type conjugation system pilus assembly proteins TraF (TIGR02739)and TrbB (TIGR02738) both of which exhibit a thioredoxin fold. The protein represented by this model has the same length and architecture as TraF, but lacks the CXXC-motif found in TrbB and believed to be responsible for the disulfide isomerase activity of that protein.
Probab=58.10 E-value=14 Score=27.34 Aligned_cols=28 Identities=18% Similarity=0.235 Sum_probs=20.7
Q ss_pred HHhHHHHHHHHhcChhHHHHHHHHHHhcc
Q psy14414 45 LRNIEKMVAEALQNQEEVSHLMRALVLGR 73 (76)
Q Consensus 45 mRNIEKML~eAL~D~~EVg~Llr~lVlGR 73 (76)
-+|+++.+..|+-+|++ ....+-|.+-|
T Consensus 83 ~~~~~~~~~~Ai~~Pt~-env~~y~~lq~ 110 (271)
T TIGR02740 83 RENLPELRDKAIDNPTP-ENVRAYLEAQR 110 (271)
T ss_pred HHHHHHHHHHHHhCCCH-HHHHHHHHHHH
Confidence 38999999999999985 55555554433
No 7
>KOG0860|consensus
Probab=56.30 E-value=8.4 Score=26.98 Aligned_cols=12 Identities=50% Similarity=0.880 Sum_probs=9.9
Q ss_pred hHHHH-hHHHHHH
Q psy14414 42 VAILR-NIEKMVA 53 (76)
Q Consensus 42 VaImR-NIEKML~ 53 (76)
+.||| ||||.|.
T Consensus 42 v~IMr~NV~KVlE 54 (116)
T KOG0860|consen 42 VDIMRENVEKVLE 54 (116)
T ss_pred HHHHHHhHHHHHH
Confidence 57887 8999985
No 8
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=52.93 E-value=20 Score=22.77 Aligned_cols=28 Identities=25% Similarity=0.256 Sum_probs=25.2
Q ss_pred ccCCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 34 YPLKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 34 yPL~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
-|++..|+-+++.-+-+.|+++||-|++
T Consensus 10 ~~~~~~~~~~~~~~~~~~l~~~lgkPe~ 37 (116)
T PTZ00397 10 VNATDDQADAALSDIENAIADVLGKPLS 37 (116)
T ss_pred CCCccccHHHHHHHHHHHHHHHhCCChH
Confidence 4667788999999999999999999987
No 9
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=52.08 E-value=8.4 Score=26.47 Aligned_cols=20 Identities=30% Similarity=0.532 Sum_probs=16.4
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|+|+..||-||+ |+..+|+
T Consensus 42 ~~gLTeEe~~AV~~rD~~~Li 62 (106)
T cd07921 42 KFGLTEEQKQAVLDRDWLRLL 62 (106)
T ss_pred HcCCCHHHHHHHHhCCHHHHH
Confidence 6999999999998 4666665
No 10
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=51.56 E-value=19 Score=20.09 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=22.8
Q ss_pred CCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
++..||-++.+-|=..|.+++|-|.+
T Consensus 12 rs~eqk~~l~~~it~~l~~~~~~p~~ 37 (61)
T PRK02220 12 RTEEQLKALVKDVTAAVSKNTGAPAE 37 (61)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcChh
Confidence 57899999999999999999997643
No 11
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=48.27 E-value=34 Score=20.49 Aligned_cols=30 Identities=23% Similarity=0.335 Sum_probs=23.6
Q ss_pred hHHHHhHHHHHHHHhcCh-hHHHHHHHHHHh
Q psy14414 42 VAILRNIEKMVAEALQNQ-EEVSHLMRALVL 71 (76)
Q Consensus 42 VaImRNIEKML~eAL~D~-~EVg~Llr~lVl 71 (76)
..++.+|-+-+.++++|+ .+..++++.|+.
T Consensus 52 l~~~~~~~~~~~~~~~~~~~~~~~~l~~mv~ 82 (97)
T PF00725_consen 52 LDVVYHILEYLAAALGDRAFRPSPLLKEMVE 82 (97)
T ss_dssp HHHHHHHHHHHHHHHCCGGGSS-HHHHHHHH
T ss_pred chHHHHHHHHHHHhcCCCcCCchHHHHHHHH
Confidence 456778888899999999 556899998874
No 12
>PF13728 TraF: F plasmid transfer operon protein
Probab=47.39 E-value=38 Score=24.30 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=30.1
Q ss_pred eeecCCCCC-ce---ecc------CCcchhhH-HHHhHHHHHHHHhcChhHHHHHHHHHHh
Q psy14414 22 WKPKTKPTG-DI---EYP------LKGHQKVA-ILRNIEKMVAEALQNQEEVSHLMRALVL 71 (76)
Q Consensus 22 fwyk~~P~p-~I---~yP------L~~~QKVa-ImRNIEKML~eAL~D~~EVg~Llr~lVl 71 (76)
|||...|.+ +. .-| ....+.++ +=.|+|+.+..|+-+|+ .-...+-|.+
T Consensus 3 ~WY~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~Ai~~PT-~eNv~~y~~l 62 (215)
T PF13728_consen 3 FWYEEPPKPKEPEPKPKPAPPAQSPSATESMEWFRENLEEALDQAIDNPT-PENVRAYLRL 62 (215)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHH
Confidence 788777665 11 111 22234444 55699999999999998 4445544443
No 13
>cd06154 YjgF_YER057c_UK114_like_6 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=46.02 E-value=19 Score=22.91 Aligned_cols=25 Identities=36% Similarity=0.250 Sum_probs=20.5
Q ss_pred cchhhHHHHhHHHHHHHHhcChhHH
Q psy14414 38 GHQKVAILRNIEKMVAEALQNQEEV 62 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eAL~D~~EV 62 (76)
..|=..+++||++.|.+|-++.+.|
T Consensus 43 ~~Q~~~~~~ni~~~L~~aG~~~~dV 67 (119)
T cd06154 43 YEQTRQCLEIIEAALAEAGASLEDV 67 (119)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHE
Confidence 3788899999999999987776543
No 14
>PF09734 Tau95: RNA polymerase III transcription factor (TF)IIIC subunit; InterPro: IPR019136 Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents subunit 5 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable []. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.
Probab=45.25 E-value=16 Score=27.00 Aligned_cols=30 Identities=33% Similarity=0.653 Sum_probs=23.4
Q ss_pred ceeccCCcchhhHHH----HhHHHHHHHHhcChhHHHHHHHH
Q psy14414 31 DIEYPLKGHQKVAIL----RNIEKMVAEALQNQEEVSHLMRA 68 (76)
Q Consensus 31 ~I~yPL~~~QKVaIm----RNIEKML~eAL~D~~EVg~Llr~ 68 (76)
-||||. +. +|++||| ++||-...|...+..
T Consensus 4 ~VE~Pg-------~V~~~~~n~dkai-~tLGG~~~Is~~~~~ 37 (310)
T PF09734_consen 4 AVEYPG-------IVSPTSKNVDKAI-ETLGGIEAISKALDS 37 (310)
T ss_pred EEEcCc-------EecccCCCHHHHH-HHhCCHHHHHHHHcC
Confidence 378885 56 8999976 789999999887653
No 15
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=45.19 E-value=13 Score=23.27 Aligned_cols=21 Identities=33% Similarity=0.596 Sum_probs=17.0
Q ss_pred eccCCcchhhHHH-HhHHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMVA 53 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML~ 53 (76)
+|+|+..||-||+ |.+++|+.
T Consensus 32 ~~~Lt~eE~~al~~rD~~~L~~ 53 (77)
T cd07321 32 EYGLTPEEKAALLARDVGALYV 53 (77)
T ss_pred HcCCCHHHHHHHHcCCHHHHHH
Confidence 6999999999987 56777653
No 16
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=45.03 E-value=26 Score=19.59 Aligned_cols=25 Identities=28% Similarity=0.276 Sum_probs=21.3
Q ss_pred CcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 37 KGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 37 ~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
+..||-++.+-|=..+.++||-|.+
T Consensus 12 ~~e~K~~l~~~it~~~~~~lg~~~~ 36 (60)
T PF01361_consen 12 TAEQKRELAEAITDAVVEVLGIPPE 36 (60)
T ss_dssp -HHHHHHHHHHHHHHHHHHHTS-GG
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCCC
Confidence 5789999999999999999998865
No 17
>PRK07217 replication factor A; Reviewed
Probab=43.71 E-value=30 Score=27.48 Aligned_cols=24 Identities=33% Similarity=0.570 Sum_probs=20.4
Q ss_pred HHHHHHhcChhHHHHHHHHHHhccc
Q psy14414 50 KMVAEALQNQEEVSHLMRALVLGRY 74 (76)
Q Consensus 50 KML~eAL~D~~EVg~Llr~lVlGRY 74 (76)
.|-.+|| |++.|-..++..++|||
T Consensus 252 ~~a~dal-d~~vv~~~i~~~llGr~ 275 (311)
T PRK07217 252 QMAMDAL-DTGVVLDELKEKLLGRY 275 (311)
T ss_pred HHHHHhh-chhhHHHHHHHhhcCce
Confidence 4555777 88999999999999998
No 18
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=43.68 E-value=17 Score=25.73 Aligned_cols=20 Identities=35% Similarity=0.753 Sum_probs=16.3
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|||+..||-||. |+.-.||
T Consensus 50 ~~~Lteeqr~aV~~RD~~~li 70 (121)
T cd07924 50 KWPMTEEQKQAVLARDYNRML 70 (121)
T ss_pred HcCCCHHHHHHHHHhhHHHHH
Confidence 6999999999986 5666665
No 19
>cd06155 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=42.94 E-value=23 Score=22.00 Aligned_cols=41 Identities=7% Similarity=-0.070 Sum_probs=26.9
Q ss_pred eeeeecCCCCCceeccCCcchhhHHHHhHHHHHHHHhcChh
Q psy14414 20 VSWKPKTKPTGDIEYPLKGHQKVAILRNIEKMVAEALQNQE 60 (76)
Q Consensus 20 Vnfwyk~~P~p~I~yPL~~~QKVaImRNIEKML~eAL~D~~ 60 (76)
=+|+|-+|-++.-.-.=-..|=..+++||++.|.+|=.+.+
T Consensus 7 g~~v~vSG~~~~~~~~d~~~Q~~~v~~ni~~~L~~aG~~~~ 47 (101)
T cd06155 7 GGLLWISNVTASESDETVEEQMESIFSKLREILQSNGLSLS 47 (101)
T ss_pred CCEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHHcCCCHH
Confidence 36777777665110001237999999999999999855443
No 20
>COG0285 FolC Folylpolyglutamate synthase [Coenzyme metabolism]
Probab=42.38 E-value=31 Score=27.95 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=22.8
Q ss_pred HHHH--HHHHhcChh---------------HHHHHHHHHHh------cccCC
Q psy14414 48 IEKM--VAEALQNQE---------------EVSHLMRALVL------GRYTE 76 (76)
Q Consensus 48 IEKM--L~eAL~D~~---------------EVg~Llr~lVl------GRYte 76 (76)
+|+| |.+.||+|+ -+..+|++|.. |+||+
T Consensus 27 L~Ri~~ll~~LGnP~~~~~vIhVaGTNGKGSt~afl~siL~~aG~~VG~yTS 78 (427)
T COG0285 27 LERISRLLERLGNPQKSPPVIHVAGTNGKGSTCAFLESILREAGYKVGVYTS 78 (427)
T ss_pred hHHHHHHHHHcCCccccCCeEEEeCCCCchhHHHHHHHHHHHcCCCceEECC
Confidence 5666 899999994 46678888877 88885
No 21
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=42.02 E-value=26 Score=20.08 Aligned_cols=26 Identities=23% Similarity=0.323 Sum_probs=23.0
Q ss_pred CCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
++..||-++++=|=+.+.+++|-|.+
T Consensus 12 rs~EqK~~L~~~it~a~~~~~~~p~~ 37 (60)
T PRK02289 12 RSQEQKNALAREVTEVVSRIAKAPKE 37 (60)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 46789999999999999999998754
No 22
>cd00448 YjgF_YER057c_UK114_family YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=41.49 E-value=25 Score=20.73 Aligned_cols=25 Identities=20% Similarity=0.207 Sum_probs=20.1
Q ss_pred CcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 37 KGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 37 ~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
-..|=..+++||++.|.++-++.+.
T Consensus 30 ~~~Q~~~~~~ni~~~L~~~g~~~~~ 54 (107)
T cd00448 30 IEAQTRQALENLEAVLEAAGGSLDD 54 (107)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHH
Confidence 3468889999999999999776443
No 23
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=41.05 E-value=18 Score=23.61 Aligned_cols=21 Identities=33% Similarity=0.574 Sum_probs=14.9
Q ss_pred eccCCcchhhHHH-HhHHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMVA 53 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML~ 53 (76)
+|+|+..||-||. |.+.+|+.
T Consensus 27 ~~~Lt~eer~av~~rD~~~L~~ 48 (88)
T PF07746_consen 27 EYGLTEEERQAVLDRDWLALIA 48 (88)
T ss_dssp CCT--HHHHHHHHCT-HHHHHH
T ss_pred HcCCCHHHHHHHHcCCHHHHHH
Confidence 6999999999998 67877763
No 24
>PF03241 HpaB: 4-hydroxyphenylacetate 3-hydroxylase C terminal; InterPro: IPR024719 This C-terminal domain is found in HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This domain is also found in pyoverdin chromophore biosynthetic protein PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=40.48 E-value=5.1 Score=28.67 Aligned_cols=54 Identities=15% Similarity=0.268 Sum_probs=33.7
Q ss_pred CCCCCCCCCCccccccceeeeeecCCCCCceeccCCcchhhHHHHhHHHHHHHHhcChhHHHH
Q psy14414 2 SPNFKSDFENPDLQKVSQVSWKPKTKPTGDIEYPLKGHQKVAILRNIEKMVAEALQNQEEVSH 64 (76)
Q Consensus 2 ~~~~~~~~~~~~~~~~~sVnfwyk~~P~p~I~yPL~~~QKVaImRNIEKML~eAL~D~~EVg~ 64 (76)
.|..+ ||+||++.+.- .=.+++.+. ..+.+|+.++|-++.+.+.++|--.++-.
T Consensus 119 ~Ps~~-Df~npe~~~~l--~kYl~g~~~------~~aeeR~rl~rLawDl~~s~fg~r~~~ye 172 (205)
T PF03241_consen 119 LPSEA-DFDNPEIGPYL--DKYLQGANG------VSAEERVRLFRLAWDLTGSEFGGRQELYE 172 (205)
T ss_dssp ---HH-HHH-TTTHHHH--HHHT-BTTT------C-HHHHHHHHHHHHHHHTSHHHHHHHHHH
T ss_pred CCCHH-HhCCcchhHHH--HHHhcccCC------CCHHHHHHHHHHHHHHhcCcchhhhHhhh
Confidence 46666 99999876543 222333323 24789999999999999988876655543
No 25
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=39.71 E-value=21 Score=24.62 Aligned_cols=20 Identities=30% Similarity=0.522 Sum_probs=16.0
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|||+..||-||. |+.-.||
T Consensus 42 ~~~Lteeqr~av~~RD~~~li 62 (106)
T cd07925 42 KFGLTPEQKQAVRNRDVLRML 62 (106)
T ss_pred HcCCCHHHHHHHHHhhHHHHH
Confidence 6999999999997 5565555
No 26
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=38.76 E-value=28 Score=21.92 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=24.1
Q ss_pred CCcchhhHHHHhHHHHHHHHhcChhHH
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQEEV 62 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~~EV 62 (76)
++..||-++.+-|=+.+.++||-+.++
T Consensus 13 ~s~EqK~~La~~iT~a~~~~lg~~~e~ 39 (76)
T PRK01271 13 LDEEQKAALAADITDVIIRHLNSKDSS 39 (76)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcce
Confidence 688999999999999999999977653
No 27
>PF07179 SseB: SseB protein N-terminal domain; InterPro: IPR009839 This family consists of several SseB proteins, which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli [] and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon [].
Probab=38.08 E-value=41 Score=20.23 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=21.8
Q ss_pred HHHHHHHHhcC-hhHHHHHHHHHHhccc
Q psy14414 48 IEKMVAEALQN-QEEVSHLMRALVLGRY 74 (76)
Q Consensus 48 IEKML~eAL~D-~~EVg~Llr~lVlGRY 74 (76)
+|+.|.++..+ +.....++++|..++|
T Consensus 1 Le~al~~~~~~~~~~~~~~~~~L~~a~~ 28 (124)
T PF07179_consen 1 LEEALAAFAEETEEDEEAFLEALLKAEV 28 (124)
T ss_pred CHHHHHHHHhCCHHHHHHHHHHHhhCeE
Confidence 47788888888 7888889999987765
No 28
>PF01042 Ribonuc_L-PSP: Endoribonuclease L-PSP; InterPro: IPR006175 This domain is found in endoribonuclease, that is active on single-stranded mRNA and inhibits protein synthesis by cleavage of mRNA []. Previously it was thought to inhibit protein synthesis initiation []. This endoribonuclease may also be involved in the regulation of purine biosynthesis []. ; PDB: 3GTZ_B 3V4D_E 1J7H_A 3R0P_D 2IG8_A 1QD9_B 3L7Q_E 3VCZ_A 3QUW_A 2EWC_K ....
Probab=38.04 E-value=24 Score=22.30 Aligned_cols=23 Identities=30% Similarity=0.345 Sum_probs=18.4
Q ss_pred cchhhHHHHhHHHHHHHHhcChh
Q psy14414 38 GHQKVAILRNIEKMVAEALQNQE 60 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eAL~D~~ 60 (76)
..|=..+++||++.|.+|=.+.+
T Consensus 42 ~~Q~~~~l~ni~~~L~~~G~~~~ 64 (121)
T PF01042_consen 42 EEQTRQALDNIERILAAAGASLD 64 (121)
T ss_dssp HHHHHHHHHHHHHHHHHTTS-GG
T ss_pred HHHHHHHHHhhhhhhhcCCCcce
Confidence 57889999999999998755543
No 29
>PF09409 PUB: PUB domain; InterPro: IPR018997 The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain []. This domain is also found on other proteins linked to the ubiquitin-proteasome system. ; PDB: 2CM0_A 2CCQ_A 2D5U_A 2HPL_A 2HPJ_A.
Probab=37.98 E-value=38 Score=20.62 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=19.7
Q ss_pred chhhHHHHhHHHHHHHHhcChhHH
Q psy14414 39 HQKVAILRNIEKMVAEALQNQEEV 62 (76)
Q Consensus 39 ~QKVaImRNIEKML~eAL~D~~EV 62 (76)
.|+...++.++|+|.+.+.+|++-
T Consensus 4 ~~~~~al~~L~~il~NI~~~P~~~ 27 (87)
T PF09409_consen 4 EAFQKALETLEKILSNILSNPNEE 27 (87)
T ss_dssp HHHHHHHHHHHHHHHHHHHSTT-C
T ss_pred HHHHHHHHHHHHHHHHHccCCCcc
Confidence 467788899999999999999863
No 30
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=37.83 E-value=42 Score=19.09 Aligned_cols=27 Identities=11% Similarity=0.241 Sum_probs=23.2
Q ss_pred cCCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 35 PLKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 35 PL~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
..+..||-++.+.|=+.|.+.||=|.+
T Consensus 11 grt~eqk~~l~~~it~~l~~~lg~p~~ 37 (64)
T PRK01964 11 GRPEEKIKNLIREVTEAISATLDVPKE 37 (64)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcChh
Confidence 357799999999999999999987654
No 31
>PF13621 Cupin_8: Cupin-like domain; PDB: 3AL6_C 3AL5_C 2XUM_A 2Y0I_A 1MZE_A 3KCY_A 1MZF_A 1YCI_A 2ILM_A 1H2L_A ....
Probab=37.58 E-value=18 Score=23.92 Aligned_cols=12 Identities=17% Similarity=-0.017 Sum_probs=8.5
Q ss_pred cceeeeeecCCC
Q psy14414 17 VSQVSWKPKTKP 28 (76)
Q Consensus 17 ~~sVnfwyk~~P 28 (76)
--||||||+..+
T Consensus 238 sisvn~w~~~~~ 249 (251)
T PF13621_consen 238 SISVNYWFRTPF 249 (251)
T ss_dssp EEEEEEEEESS-
T ss_pred EEEEEEEecccc
Confidence 348999998764
No 32
>PF13308 YARHG: YARHG domain
Probab=37.21 E-value=10 Score=23.63 Aligned_cols=21 Identities=24% Similarity=0.059 Sum_probs=17.8
Q ss_pred CCCCccccccceeeeeecCCC
Q psy14414 8 DFENPDLQKVSQVSWKPKTKP 28 (76)
Q Consensus 8 ~~~~~~~~~~~sVnfwyk~~P 28 (76)
.|.+++||..-+=.-||++.+
T Consensus 40 ~F~~~~l~~yF~~~~WY~~~~ 60 (81)
T PF13308_consen 40 CFKSQDLQAYFSSKSWYKPEY 60 (81)
T ss_pred CCCCHHHHHHHcCCCccCCCc
Confidence 588899998888777999888
No 33
>TIGR03610 RutC pyrimidine utilization protein C. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the endoribonuclease L-PSP family defined by pfam01042.
Probab=37.15 E-value=30 Score=22.68 Aligned_cols=40 Identities=13% Similarity=0.029 Sum_probs=27.0
Q ss_pred eeeecCCCCC-c----eecc-CCcchhhHHHHhHHHHHHHHhcChh
Q psy14414 21 SWKPKTKPTG-D----IEYP-LKGHQKVAILRNIEKMVAEALQNQE 60 (76)
Q Consensus 21 nfwyk~~P~p-~----I~yP-L~~~QKVaImRNIEKML~eAL~D~~ 60 (76)
++=|-+|.++ + +-.| =-..|=..+++||++.|.+|=++.+
T Consensus 26 ~~v~vSGq~~~d~~g~~~~~~d~~~Q~~~~l~ni~~iL~~aG~~~~ 71 (127)
T TIGR03610 26 GVVYVSGTLPFDKDNNVVHVGDAAAQTRHVLETIKSVIETAGGTMD 71 (127)
T ss_pred CEEEEeccCCcCCCCCeeCCCCHHHHHHHHHHHHHHHHHHcCCCHH
Confidence 6667666654 1 2122 2346999999999999999855443
No 34
>PF03271 EB1: EB1-like C-terminal motif; InterPro: IPR004953 A group of microtubule-associated proteins called +TIPs (plus end tracking proteins), including EB1 (end-binding protein 1) family proteins, label growing microtubules ends specifically in diverse organisms and are implicated in spindle dynamics, chromosome segregation, and directing microtubules toward cortical sites. EB1 members have a bipartite composition: the N-terminal CH domain (IPR001715 from INTERPRO) mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polarity determinants. The EB1-C domain comprises a unique EB1-like sequence motif that acts as a binding site for other +TIP proteins. It interacts with the carboxy terminus of the adenomatous polyposis coli (APC) tumor suppressor, a well conserved +TIP phosphoprotein with a pivotal function in cell cycle regulation. Another binding partner of the EB1-C domain is the well conserved +TIP protein dynactin, a component of the large cytoplasmic dynein/dynactin complex [, , ]. The ~80-residue EB1-C domain starts with a long smoothly curved helix (alpha1), which is followed by a hairpin connection leading to a short second helix (alpha2) running antiparallel to alpha1. The two parallel alpha1 helices of the EB1-C domain dimer wrap around each other in a slightly left-handed supercoil. The two alpha2 helices run antiparallel to helices alpha1 and form a similar fork in the opposite orientation and rotated by 90 degrees. As a result, two helical segments from each monomer form a four-helix bundle. The side chain forming the hydrophobic core of this bundle are highly conserved [, , ]. Some protein known to contain an EB1-C domain are listed below: Yeast protein BIM1. Fission yeast microtubule integrity protein mal3. Vertebrate microtubule-associated protein RP/EB family member 1 (EB1). Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1). Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3). ; GO: 0008017 microtubule binding; PDB: 3TQ7_B 4E61_B 2HKQ_A 1YIG_B 3GJO_B 2HL5_B 1YIB_A 1WU9_A 1TXQ_B.
Probab=36.97 E-value=20 Score=20.59 Aligned_cols=25 Identities=32% Similarity=0.485 Sum_probs=16.9
Q ss_pred HHHHhHHHHHHHHhcChhHHHHHHH
Q psy14414 43 AILRNIEKMVAEALQNQEEVSHLMR 67 (76)
Q Consensus 43 aImRNIEKML~eAL~D~~EVg~Llr 67 (76)
+-+|+||-++.++-++.++..++..
T Consensus 11 ~KLR~IE~l~q~~~~~~~~~~~~~~ 35 (43)
T PF03271_consen 11 NKLRDIEILCQEANESENEPKDLIK 35 (43)
T ss_dssp HHHHHHHHHHHHHCHHCCTC--HHH
T ss_pred HHHHHHHHHHhhccccCcchhHHHH
Confidence 4579999999998766655544443
No 35
>PF14850 Pro_dh-DNA_bdg: DNA-binding domain of Proline dehydrogenase; PDB: 2FZM_A 3E2Q_A 3E2S_A 2FZN_A 1K87_A 1TJ2_A 3ITG_B 3E2R_A 1TJ1_A 1TIW_A ....
Probab=36.44 E-value=23 Score=24.70 Aligned_cols=20 Identities=45% Similarity=0.660 Sum_probs=14.7
Q ss_pred eeccCCcchhhHHHHhHHHHHHHHh
Q psy14414 32 IEYPLKGHQKVAILRNIEKMVAEAL 56 (76)
Q Consensus 32 I~yPL~~~QKVaImRNIEKML~eAL 56 (76)
-||+|+.+-=|++|. |+|||
T Consensus 8 ~EY~Lss~EGvaLMc-----LAEAL 27 (114)
T PF14850_consen 8 QEYSLSSQEGVALMC-----LAEAL 27 (114)
T ss_dssp HCTT--HHHHHHHHH-----HHHHH
T ss_pred HHcCCCcHHHHHHHH-----HHHHH
Confidence 379999999999997 56665
No 36
>cd02198 YjgH_like YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=36.28 E-value=36 Score=21.33 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=19.3
Q ss_pred cchhhHHHHhHHHHHHHHhcChhH
Q psy14414 38 GHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eAL~D~~E 61 (76)
..|=..+++||++.|.+|=++.+.
T Consensus 32 ~~Q~~~~~~ni~~~L~~aG~~~~d 55 (111)
T cd02198 32 EAQFRLAFQNLGAVLEAAGCSFDD 55 (111)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHH
Confidence 368888999999999998555543
No 37
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=35.17 E-value=33 Score=22.72 Aligned_cols=28 Identities=43% Similarity=0.477 Sum_probs=20.7
Q ss_pred hhHHHHhHHHHHHHHhcChhHHHHHHHHHH
Q psy14414 41 KVAILRNIEKMVAEALQNQEEVSHLMRALV 70 (76)
Q Consensus 41 KVaImRNIEKML~eAL~D~~EVg~Llr~lV 70 (76)
||==..||-|||.++ +|++=....++|+
T Consensus 35 kvFG~sni~k~L~~~--~~~~R~~a~~Sl~ 62 (101)
T PF03195_consen 35 KVFGVSNISKMLQEL--PPEQREDAMRSLV 62 (101)
T ss_pred HHHchhHHHHHHHhC--CccchhhHHHHHH
Confidence 344468999999987 6776677777775
No 38
>PRK13703 conjugal pilus assembly protein TraF; Provisional
Probab=33.58 E-value=1.1e+02 Score=23.23 Aligned_cols=32 Identities=19% Similarity=0.304 Sum_probs=22.5
Q ss_pred chhhHHH-HhHHHHHHHHhcChhHHHHHHHHHHh
Q psy14414 39 HQKVAIL-RNIEKMVAEALQNQEEVSHLMRALVL 71 (76)
Q Consensus 39 ~QKVaIm-RNIEKML~eAL~D~~EVg~Llr~lVl 71 (76)
-|+++.+ +|+++-+..|+-+|++ -...+-|.+
T Consensus 53 ~e~~~~l~~~~~~~~~~Ai~~Pt~-ENv~~y~~l 85 (248)
T PRK13703 53 MEKLAVLQTATKRALYEAILYPGV-ENFVKYFRL 85 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCH-HHHHHHHHH
Confidence 3666666 7999999999999965 444444443
No 39
>KOG0859|consensus
Probab=33.51 E-value=30 Score=26.78 Aligned_cols=14 Identities=36% Similarity=0.522 Sum_probs=11.4
Q ss_pred hhhHHHHhHHHHHH
Q psy14414 40 QKVAILRNIEKMVA 53 (76)
Q Consensus 40 QKVaImRNIEKML~ 53 (76)
=|=-+|+||||.|.
T Consensus 137 vk~vM~eNIekvld 150 (217)
T KOG0859|consen 137 VKGVMMENIEKVLD 150 (217)
T ss_pred HHHHHHHHHHHHHh
Confidence 35668999999985
No 40
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=33.27 E-value=46 Score=18.04 Aligned_cols=26 Identities=23% Similarity=0.328 Sum_probs=22.0
Q ss_pred CCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
.+..||-++.+-|=..|.+.+|-|.+
T Consensus 11 rt~eqk~~l~~~i~~~l~~~~g~~~~ 36 (58)
T cd00491 11 RTDEQKRELIERVTEAVSEILGAPEA 36 (58)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 45789999999999999999976654
No 41
>cd06156 eu_AANH_C_2 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the second of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=33.25 E-value=37 Score=22.08 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=15.4
Q ss_pred cchhhHHHHhHHHHHHHH
Q psy14414 38 GHQKVAILRNIEKMVAEA 55 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eA 55 (76)
..|=..+|+||+..|.+|
T Consensus 32 ~~Q~~qal~Ni~~vL~~a 49 (118)
T cd06156 32 TLQAVLSLQHLERVAKAM 49 (118)
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 358888999999999886
No 42
>COG4709 Predicted membrane protein [Function unknown]
Probab=32.61 E-value=43 Score=25.44 Aligned_cols=27 Identities=15% Similarity=0.099 Sum_probs=21.9
Q ss_pred HHHHHHHhcChhHHHHHHHHHHhcccC
Q psy14414 49 EKMVAEALQNQEEVSHLMRALVLGRYT 75 (76)
Q Consensus 49 EKML~eAL~D~~EVg~Llr~lVlGRYt 75 (76)
|--++..||||.|+..=.++=+.+|+-
T Consensus 43 E~EI~~~LG~P~eiA~ei~s~~~~k~~ 69 (195)
T COG4709 43 EEEIAKDLGDPKEIAAEILSERGIKKE 69 (195)
T ss_pred HHHHHHHhCCHHHHHHHHHHHccchHH
Confidence 566788999999999888887776653
No 43
>TIGR00004 endoribonuclease L-PSP, putative. This protein was described initially as an inhibitor of protein synthesis intiation but is now viewed as an endoribonuclease active on single-stranded mRNA. The cleavage of mRNA is responsible for the inhibition of protein synthesis. A role in purine regulation has also been suggested.
Probab=32.51 E-value=43 Score=21.16 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=19.8
Q ss_pred cchhhHHHHhHHHHHHHHhcChhH
Q psy14414 38 GHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eAL~D~~E 61 (76)
..|=..+++||++.|.+|-++.+.
T Consensus 47 ~~Q~~~~~~ni~~~L~~aG~~~~d 70 (124)
T TIGR00004 47 AEQAEQVLENLKAILEAAGLSLDD 70 (124)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHH
Confidence 368899999999999998766554
No 44
>PF14164 YqzH: YqzH-like protein
Probab=30.90 E-value=32 Score=21.97 Aligned_cols=11 Identities=45% Similarity=0.646 Sum_probs=9.7
Q ss_pred hHHHHHHHHhc
Q psy14414 47 NIEKMVAEALQ 57 (76)
Q Consensus 47 NIEKML~eAL~ 57 (76)
=||||+..+|+
T Consensus 5 ~I~Kmi~~~l~ 15 (64)
T PF14164_consen 5 LIEKMIINCLR 15 (64)
T ss_pred HHHHHHHHHHH
Confidence 38999999997
No 45
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=30.68 E-value=1.1e+02 Score=19.37 Aligned_cols=29 Identities=21% Similarity=0.288 Sum_probs=21.7
Q ss_pred HHHhHHHHHHHHhc--ChhHHHHHHHHHHhc
Q psy14414 44 ILRNIEKMVAEALQ--NQEEVSHLMRALVLG 72 (76)
Q Consensus 44 ImRNIEKML~eAL~--D~~EVg~Llr~lVlG 72 (76)
+..++++.+.+.+. |+..+..++.+++.|
T Consensus 130 ~~~~l~~~l~~~~~~~~~~~~a~~~~~~~~G 160 (189)
T TIGR03384 130 LHSNLMSELRQLLPREQAERAAEGLAALIDG 160 (189)
T ss_pred HHHHHHHHHHhhcCcchHHHHHHHHHHHHHH
Confidence 44577777776654 788899888888877
No 46
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=29.24 E-value=73 Score=17.69 Aligned_cols=24 Identities=21% Similarity=0.250 Sum_probs=21.3
Q ss_pred CCcchhhHHHHhHHHHHHHHhcCh
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQ 59 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~ 59 (76)
.+..||-++.+-|=..|.+.||=|
T Consensus 12 rs~eqk~~l~~~it~~l~~~~~~p 35 (62)
T PRK00745 12 RTVEQKRKLVEEITRVTVETLGCP 35 (62)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCC
Confidence 578899999999999999999933
No 47
>COG0815 Lnt Apolipoprotein N-acyltransferase [Cell envelope biogenesis, outer membrane]
Probab=28.75 E-value=29 Score=28.41 Aligned_cols=26 Identities=15% Similarity=-0.139 Sum_probs=19.5
Q ss_pred eeeeeecCCCCCceeccCCcchhhHHHHhHHH
Q psy14414 19 QVSWKPKTKPTGDIEYPLKGHQKVAILRNIEK 50 (76)
Q Consensus 19 sVnfwyk~~P~p~I~yPL~~~QKVaImRNIEK 50 (76)
|=+=||..+..| .-|..+|.||+||-
T Consensus 415 SNDAWf~~s~~p------~QH~~~a~~RAiE~ 440 (518)
T COG0815 415 SNDAWFGGSWGP------YQHFQQARVRAVEL 440 (518)
T ss_pred ccccccCCCcch------HHHHHHHHHHHHhc
Confidence 445688887776 35788999999993
No 48
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=27.70 E-value=92 Score=18.31 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=21.4
Q ss_pred ceecc--CCcchhhHHHHhHHHHHHHHhcCh
Q psy14414 31 DIEYP--LKGHQKVAILRNIEKMVAEALQNQ 59 (76)
Q Consensus 31 ~I~yP--L~~~QKVaImRNIEKML~eAL~D~ 59 (76)
.++-+ |...|+-.+.+.+.+++.+-+|.+
T Consensus 61 ~~~~~~~l~~~~~~~l~~~l~~~~~e~~g~~ 91 (107)
T smart00591 61 SLLNSEGLSDEQLAELLKKLEEIAEENLGEV 91 (107)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHHHHhCCCE
Confidence 44444 777888888888888888877664
No 49
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=27.52 E-value=34 Score=22.52 Aligned_cols=19 Identities=32% Similarity=0.387 Sum_probs=15.5
Q ss_pred ceeccCCcchhhHHHHhHHHHHH
Q psy14414 31 DIEYPLKGHQKVAILRNIEKMVA 53 (76)
Q Consensus 31 ~I~yPL~~~QKVaImRNIEKML~ 53 (76)
.+-.+|++.| .||+||.++
T Consensus 62 vfd~~Lsp~Q----~rNLe~~~~ 80 (95)
T PF13167_consen 62 VFDNELSPSQ----QRNLEKALG 80 (95)
T ss_pred EECCCCCHHH----HHHHHHHHC
Confidence 4567999999 499999875
No 50
>cd03308 CmuA_CmuC_like CmuA_CmuC_like: uncharacterized protein family similar to uroporphyrinogen decarboxylase (URO-D) and the methyltransferases CmuA and CmuC.
Probab=27.14 E-value=1e+02 Score=23.53 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=25.0
Q ss_pred HHHhHHHHHHHHhcChhHHHHHHHHHH
Q psy14414 44 ILRNIEKMVAEALQNQEEVSHLMRALV 70 (76)
Q Consensus 44 ImRNIEKML~eAL~D~~EVg~Llr~lV 70 (76)
.+|.+|+++.....+|++|-.||..+.
T Consensus 187 ~l~g~~~~~~~l~~~Pe~v~~ll~~~t 213 (378)
T cd03308 187 YLRGFKGISIDLRRRPEKVAEACEAVT 213 (378)
T ss_pred HHhCHHHHHHHHHHCHHHHHHHHHHHH
Confidence 789999999999999999999998765
No 51
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=27.13 E-value=28 Score=24.49 Aligned_cols=20 Identities=35% Similarity=0.581 Sum_probs=15.6
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|||+..||-+|. |+.=.||
T Consensus 47 ~~~Lt~eqk~av~~RD~~~li 67 (117)
T TIGR02792 47 EWNLTPAQKQAVLARDLNACI 67 (117)
T ss_pred HcCCCHHHHHHHHhhhHHHHH
Confidence 6999999999997 4555554
No 52
>PF03549 Tir_receptor_M: Translocated intimin receptor (Tir) intimin-binding domain; InterPro: IPR003536 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Enteropathogenic and entero- haemorrhagic Escherichia coli secrete the bacterial adhesion mediation molecule intimin [], which targets the translocated intimin receptor, Tir. Tir is secreted by the bacteria and is embedded in the target cell's plasma membrane []. This facilitates bacterial cell attachment to the host. ; GO: 0005515 protein binding; PDB: 2ZWK_F 2ZQK_D 1F02_T.
Probab=26.63 E-value=28 Score=22.67 Aligned_cols=12 Identities=58% Similarity=0.886 Sum_probs=9.9
Q ss_pred CCCCCccccccc
Q psy14414 7 SDFENPDLQKVS 18 (76)
Q Consensus 7 ~~~~~~~~~~~~ 18 (76)
.-|.|||-|||.
T Consensus 19 eafqnp~nqkvn 30 (66)
T PF03549_consen 19 EAFQNPDNQKVN 30 (66)
T ss_dssp HHCTSGGGEEEE
T ss_pred HHhcCcccceec
Confidence 458999999975
No 53
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=26.25 E-value=67 Score=20.02 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=22.5
Q ss_pred CCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 36 LKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 36 L~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
++.+||-+|-.-|=.++.+.||-+.+
T Consensus 13 ~~~~~K~~la~~vT~~~~~~lg~~~~ 38 (69)
T COG1942 13 LDEEQKAELAAEVTEVTVETLGKDPS 38 (69)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 56788999999999999999997654
No 54
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=25.99 E-value=31 Score=24.72 Aligned_cols=20 Identities=35% Similarity=0.786 Sum_probs=15.7
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|||+..||-||. |+.=.||
T Consensus 53 e~~Lteeqr~aV~~RD~~~li 73 (129)
T PRK13377 53 EWPMTEEQKQAVLARDLNRCI 73 (129)
T ss_pred HcCCCHHHHHHHHhhhHHHHH
Confidence 6999999999986 5555554
No 55
>cd06150 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=25.89 E-value=66 Score=19.92 Aligned_cols=21 Identities=29% Similarity=0.362 Sum_probs=17.2
Q ss_pred cchhhHHHHhHHHHHHHHhcC
Q psy14414 38 GHQKVAILRNIEKMVAEALQN 58 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eAL~D 58 (76)
..|=-.+++||++.|.++=.+
T Consensus 28 ~~Q~~~~~~nl~~~L~~~G~~ 48 (105)
T cd06150 28 TGQTRQVLAKIDALLAEAGSD 48 (105)
T ss_pred HHHHHHHHHHHHHHHHHcCCC
Confidence 478889999999999987433
No 56
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=25.88 E-value=27 Score=23.49 Aligned_cols=20 Identities=20% Similarity=0.215 Sum_probs=15.5
Q ss_pred eccCCcchhhHHHH-hHHHHH
Q psy14414 33 EYPLKGHQKVAILR-NIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaImR-NIEKML 52 (76)
+|+|+..||-+|++ ++=+|+
T Consensus 34 e~gLt~Ee~~av~~rD~~~li 54 (94)
T cd07923 34 EAGLTEEERTLIRNRDWIGMI 54 (94)
T ss_pred HcCCCHHHHHHHHcchHHHHH
Confidence 69999999999984 554444
No 57
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=24.69 E-value=34 Score=24.10 Aligned_cols=20 Identities=35% Similarity=0.556 Sum_probs=15.3
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|||+..||-+|. |+.=.||
T Consensus 53 ~~~Lteeqk~aV~~RD~~~mi 73 (117)
T PRK13378 53 KYGLNEEQKEAIRNRDVLQLL 73 (117)
T ss_pred HcCCCHHHHHHHHhhhHHHHH
Confidence 6999999999997 4444444
No 58
>PLN02433 uroporphyrinogen decarboxylase
Probab=24.42 E-value=83 Score=23.52 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=20.2
Q ss_pred HhHHHHHHHHhcChhHHHHHHHHHH
Q psy14414 46 RNIEKMVAEALQNQEEVSHLMRALV 70 (76)
Q Consensus 46 RNIEKML~eAL~D~~EVg~Llr~lV 70 (76)
|++|+++.....||+.|..+|..+.
T Consensus 154 ~~~~~~~~~l~~~Pe~v~~ll~~it 178 (345)
T PLN02433 154 KNYKVIKKMAFTAPEVLHALLDKLT 178 (345)
T ss_pred ccHHHHHHHHHhCHHHHHHHHHHHH
Confidence 3488888888889999998887664
No 59
>cd06152 YjgF_YER057c_UK114_like_4 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=24.08 E-value=78 Score=20.42 Aligned_cols=24 Identities=17% Similarity=0.122 Sum_probs=19.1
Q ss_pred cchhhHHHHhHHHHHHHHh-cChhH
Q psy14414 38 GHQKVAILRNIEKMVAEAL-QNQEE 61 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eAL-~D~~E 61 (76)
..|=-.+++||++.|.+|= .+.+.
T Consensus 33 ~~Q~~~~~~Nl~~~L~~aG~~~~~d 57 (114)
T cd06152 33 EEEIDQAFDNVELALKAAGGKGWEQ 57 (114)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCHHH
Confidence 4788899999999999885 45443
No 60
>PHA02696 hypothetical protein; Provisional
Probab=23.68 E-value=47 Score=22.26 Aligned_cols=17 Identities=47% Similarity=0.767 Sum_probs=14.0
Q ss_pred CcchhhHHHHhHHHHHH
Q psy14414 37 KGHQKVAILRNIEKMVA 53 (76)
Q Consensus 37 ~~~QKVaImRNIEKML~ 53 (76)
-++|-||+|||+-+..+
T Consensus 56 DgkQvVaLlR~vsrvva 72 (79)
T PHA02696 56 DGKQVVALLRAVSRVVA 72 (79)
T ss_pred cHHHHHHHHHHhHHHhc
Confidence 47899999999977654
No 61
>PRK01005 V-type ATP synthase subunit E; Provisional
Probab=23.49 E-value=1.8e+02 Score=21.26 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=21.6
Q ss_pred HHHHHHHHhcChhHHHHHHHHHHh
Q psy14414 48 IEKMVAEALQNQEEVSHLMRALVL 71 (76)
Q Consensus 48 IEKML~eAL~D~~EVg~Llr~lVl 71 (76)
++++|.++|.||+=+..|+..+|.
T Consensus 97 ~~~lv~~~~~d~~~l~~lI~~~v~ 120 (207)
T PRK01005 97 LGEWLEHVLTDPEVSAKLIQALVQ 120 (207)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHH
Confidence 789999999999999999988875
No 62
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=23.12 E-value=65 Score=20.92 Aligned_cols=15 Identities=40% Similarity=0.654 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHhccc
Q psy14414 60 EEVSHLMRALVLGRY 74 (76)
Q Consensus 60 ~EVg~Llr~lVlGRY 74 (76)
.||.+..+..+.|||
T Consensus 41 ~~V~~~~~~~i~gRY 55 (125)
T PF06744_consen 41 AEVYPFCRQAIAGRY 55 (125)
T ss_pred HHHHHHHHHHhcCCC
Confidence 579999999999999
No 63
>PRK07218 replication factor A; Provisional
Probab=23.07 E-value=94 Score=25.25 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=21.0
Q ss_pred HHHHHHHHhcChhHHHHHHHHHHhccc
Q psy14414 48 IEKMVAEALQNQEEVSHLMRALVLGRY 74 (76)
Q Consensus 48 IEKML~eAL~D~~EVg~Llr~lVlGRY 74 (76)
+.+|..+|| |.+.|-..++..++|||
T Consensus 357 a~~~~~~~~-d~~~v~~~i~~~llG~~ 382 (423)
T PRK07218 357 AEELAREAM-DKDVVAEDIRERLVGRE 382 (423)
T ss_pred HHHHHHhhh-cchhhHHHHHHhhcCcE
Confidence 346777776 77888889999999998
No 64
>PF10796 Anti-adapt_IraP: Sigma-S stabilisation anti-adaptor protein ; InterPro: IPR019732 This entry is conserved in Enterobacteriaceae. It is one of a series of proteins, expressed by these bacteria in response to stress, that help to regulate Sigma-S, the stationary phase sigma factor of Escherichia coli and Salmonella. IraP is essential for Sigma-S stabilisation in some but not all starvation conditions []. ; GO: 0005737 cytoplasm
Probab=22.87 E-value=81 Score=20.86 Aligned_cols=25 Identities=16% Similarity=0.306 Sum_probs=21.1
Q ss_pred CcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 37 KGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 37 ~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
...|.-+|..|||+-+..|+.+.++
T Consensus 41 ~~~~~~~~i~~I~~Ai~~a~~~~~~ 65 (87)
T PF10796_consen 41 DQGGRQEMIESIEKAIEDASPSSDV 65 (87)
T ss_pred CcchHHHHHHHHHHHHHHhcccCCc
Confidence 5677888999999999999987654
No 65
>PF03730 Ku_C: Ku70/Ku80 C-terminal arm; InterPro: IPR005160 The Ku heterodimer (composed of Ku70 P12956 from SWISSPROT and Ku80 P13010 from SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C-terminal arm. This alpha helical region embraces the beta-barrel domain IPR006164 from INTERPRO of the opposite subunit [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0006303 double-strand break repair via nonhomologous end joining; PDB: 1JEY_B 1JEQ_B 1RW2_A 3RZ9_B 3RZX_B.
Probab=22.64 E-value=21 Score=22.23 Aligned_cols=11 Identities=45% Similarity=0.812 Sum_probs=7.2
Q ss_pred CCCCCcccccc
Q psy14414 7 SDFENPDLQKV 17 (76)
Q Consensus 7 ~~~~~~~~~~~ 17 (76)
+.|+||-||+.
T Consensus 8 ~~~~NP~LQ~h 18 (96)
T PF03730_consen 8 DKFPNPSLQRH 18 (96)
T ss_dssp CCS--HHHHHH
T ss_pred CCcCCchHHHH
Confidence 57999999974
No 66
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.
Probab=22.64 E-value=2e+02 Score=21.81 Aligned_cols=37 Identities=19% Similarity=0.355 Sum_probs=26.1
Q ss_pred CCcchhhHHH-HhHHHHHHHHhcChhHHHHHHHHHHhcc
Q psy14414 36 LKGHQKVAIL-RNIEKMVAEALQNQEEVSHLMRALVLGR 73 (76)
Q Consensus 36 L~~~QKVaIm-RNIEKML~eAL~D~~EVg~Llr~lVlGR 73 (76)
+++-|+++.+ +|+++.+..|+-+|++ ....+-|.+-|
T Consensus 57 ~~~~~~~~~l~~~~~~~~~~Ai~~Pt~-ENv~~y~~lq~ 94 (256)
T TIGR02739 57 LSPTEQMKLLRQETKEALNQAILNPSV-ENFARYMRLQR 94 (256)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHhCCCH-HHHHHHHHHHH
Confidence 4555666655 5899999999999984 55555555433
No 67
>KOG0414|consensus
Probab=22.47 E-value=1e+02 Score=29.10 Aligned_cols=38 Identities=18% Similarity=0.384 Sum_probs=34.1
Q ss_pred cchhhHHHHhHHHHHHHH-hcChhHHHHHHHHHHhcccC
Q psy14414 38 GHQKVAILRNIEKMVAEA-LQNQEEVSHLMRALVLGRYT 75 (76)
Q Consensus 38 ~~QKVaImRNIEKML~eA-L~D~~EVg~Llr~lVlGRYt 75 (76)
.|-+.+|-+|.=|.+.+| .||-.-+-.+|..+|.+||-
T Consensus 615 ~~e~~~ia~NL~~l~~~~s~~d~~slE~vl~~lv~~~~I 653 (1251)
T KOG0414|consen 615 ASEASSIAQNLSKLLIDASIGDLTSLEEVLCELVARGYI 653 (1251)
T ss_pred hhHHHHHHHHHHHHHhcccccchhhHHHHHHHHHhCCCc
Confidence 345588999999999999 99999999999999999984
No 68
>PF13524 Glyco_trans_1_2: Glycosyl transferases group 1
Probab=22.24 E-value=1.7e+02 Score=16.80 Aligned_cols=30 Identities=30% Similarity=0.385 Sum_probs=20.5
Q ss_pred HhHHHHHHHHhcChhH---HHHHHHHHHhcccC
Q psy14414 46 RNIEKMVAEALQNQEE---VSHLMRALVLGRYT 75 (76)
Q Consensus 46 RNIEKML~eAL~D~~E---Vg~Llr~lVlGRYt 75 (76)
..+...+...|.||++ ++.-.+..|+-+||
T Consensus 50 ~el~~~i~~ll~~~~~~~~ia~~a~~~v~~~~t 82 (92)
T PF13524_consen 50 EELAEKIEYLLENPEERRRIAKNARERVLKRHT 82 (92)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhCC
Confidence 4566677888899987 44555666766665
No 69
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=22.21 E-value=84 Score=24.32 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=18.3
Q ss_pred ceeccCCcchhhHHHHhHHHH
Q psy14414 31 DIEYPLKGHQKVAILRNIEKM 51 (76)
Q Consensus 31 ~I~yPL~~~QKVaImRNIEKM 51 (76)
+=+||+++-|=..++|||+..
T Consensus 112 D~EYPvK~vqIa~L~rqlq~l 132 (258)
T PF15397_consen 112 DHEYPVKAVQIANLVRQLQQL 132 (258)
T ss_pred hhhhhHHHHHHHHHHHHHHHH
Confidence 458999999999999999864
No 70
>PF14863 Alkyl_sulf_dimr: Alkyl sulfatase dimerisation; PDB: 2YHE_C 2CG2_A 2CG3_A 2CFU_A 2CFZ_A.
Probab=22.10 E-value=92 Score=21.52 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=21.8
Q ss_pred eecCCCCCceeccCCcchh----hHHHHhHHHHHHHH---h--cChhHHHHHHHHHHh
Q psy14414 23 KPKTKPTGDIEYPLKGHQK----VAILRNIEKMVAEA---L--QNQEEVSHLMRALVL 71 (76)
Q Consensus 23 wyk~~P~p~I~yPL~~~QK----VaImRNIEKML~eA---L--~D~~EVg~Llr~lVl 71 (76)
||-|-|+ .+ +||.+.++ |+.|--.+++|..| + ||...+..|+..++.
T Consensus 43 WfDgnP~-~L-~pl~p~~~A~~~v~l~GG~d~vl~~A~~~~~~gd~~wA~~L~d~l~~ 98 (141)
T PF14863_consen 43 WFDGNPA-NL-NPLPPEEEAKRYVELAGGADKVLERAQAALAAGDYQWAAELLDHLVF 98 (141)
T ss_dssp S--S-GG-GT-S---HHHHHHHHHHHTTCHHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred ccCCCcc-cc-CCCChHHHHHHHHHHcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 8999998 47 88887765 44443444444332 2 455555555555543
No 71
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=21.95 E-value=96 Score=19.69 Aligned_cols=27 Identities=11% Similarity=-0.023 Sum_probs=23.4
Q ss_pred cCCcchhhHHHHhHHHHHHHHhcChhH
Q psy14414 35 PLKGHQKVAILRNIEKMVAEALQNQEE 61 (76)
Q Consensus 35 PL~~~QKVaImRNIEKML~eAL~D~~E 61 (76)
..+..||-++.+.|-..|.+.|+.+-+
T Consensus 70 GRs~eqK~~l~~~i~~~l~~~~~~~~~ 96 (113)
T cd00580 70 GRSEEQKQELSEALLAALRAHLAPVFA 96 (113)
T ss_pred CCCHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 467789999999999999999988744
No 72
>COG0251 TdcF Putative translation initiation inhibitor, yjgF family [Translation, ribosomal structure and biogenesis]
Probab=21.88 E-value=78 Score=20.98 Aligned_cols=50 Identities=18% Similarity=0.004 Sum_probs=34.1
Q ss_pred cccccceeeeeecCCCCC-c----eecc-CCcchhhHHHHhHHHHHHHHhcChhHH
Q psy14414 13 DLQKVSQVSWKPKTKPTG-D----IEYP-LKGHQKVAILRNIEKMVAEALQNQEEV 62 (76)
Q Consensus 13 ~~~~~~sVnfwyk~~P~p-~----I~yP-L~~~QKVaImRNIEKML~eAL~D~~EV 62 (76)
--|-+..-+|=|-+|..| + +.-+ =-..|=...+.||+..|.+|..+.+.|
T Consensus 19 yS~av~~~~~vfvSGQi~~~~~g~~v~~~d~~~Q~~~~l~ni~a~L~~aG~~~~~V 74 (130)
T COG0251 19 YSQAVVAGGLVFVSGQIPLDPTGELVGGEDIEAQTRQALANIKAVLEAAGSTLDDV 74 (130)
T ss_pred ccceEEECCEEEEeCcCCcCCCCcccCCCCHHHHHHHHHHHHHHHHHHcCCCHHHE
Confidence 334455566778888776 1 2122 234677889999999999999876654
No 73
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.88 E-value=82 Score=21.36 Aligned_cols=18 Identities=17% Similarity=0.337 Sum_probs=12.6
Q ss_pred HHHHHHHhcChhHHHHHH
Q psy14414 49 EKMVAEALQNQEEVSHLM 66 (76)
Q Consensus 49 EKML~eAL~D~~EVg~Ll 66 (76)
|.-+.+.||||+|+..=+
T Consensus 43 Eeeii~~LG~P~~iA~~i 60 (181)
T PF08006_consen 43 EEEIIAELGSPKEIAREI 60 (181)
T ss_pred HHHHHHHcCCHHHHHHHH
Confidence 455667899999876533
No 74
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.51 E-value=1.6e+02 Score=22.09 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=14.1
Q ss_pred HhHHHHHHHHhcChhHHHHHH
Q psy14414 46 RNIEKMVAEALQNQEEVSHLM 66 (76)
Q Consensus 46 RNIEKML~eAL~D~~EVg~Ll 66 (76)
.+-|+.|..|+..-.+++..|
T Consensus 116 ~~~er~l~~a~~~I~~~~~~L 136 (310)
T PRK00423 116 NAAERNLAFALSELDRIASQL 136 (310)
T ss_pred ChHhHHHHHHHHHHHHHHHHc
Confidence 355888888886655555543
No 75
>PF05069 Phage_tail_S: Phage virion morphogenesis family ; InterPro: IPR006522 This entry represents a number of known and suspected phage virion morphogenesis proteins. The S protein from phage P2 is thought to act in tail completion and stable head joining [].
Probab=21.32 E-value=1.7e+02 Score=19.26 Aligned_cols=25 Identities=12% Similarity=0.351 Sum_probs=18.8
Q ss_pred HHhHHHHHHHHhcChhHHHHHHHHH
Q psy14414 45 LRNIEKMVAEALQNQEEVSHLMRAL 69 (76)
Q Consensus 45 mRNIEKML~eAL~D~~EVg~Llr~l 69 (76)
+..|+++|..+...+.+..+|++.+
T Consensus 3 ~~~l~~~L~~L~~~~~~~~~l~~~i 27 (148)
T PF05069_consen 3 LEQLQRALERLAAQPKDRRPLLRKI 27 (148)
T ss_pred HHHHHHHHHHHHhChHhHHHHHHHH
Confidence 3567888888777788887777765
No 76
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=21.00 E-value=44 Score=23.63 Aligned_cols=20 Identities=30% Similarity=0.257 Sum_probs=15.3
Q ss_pred eccCCcchhhHHH-HhHHHHH
Q psy14414 33 EYPLKGHQKVAIL-RNIEKMV 52 (76)
Q Consensus 33 ~yPL~~~QKVaIm-RNIEKML 52 (76)
+|||+..||-+|. |+.=.||
T Consensus 54 ~~~Lt~eqk~aV~~RDw~~mi 74 (119)
T PRK13379 54 EAGLTEQEKELIRARDWLGLV 74 (119)
T ss_pred HcCCCHHHHHHHHhccHHHHH
Confidence 6999999999987 4554444
No 77
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=20.82 E-value=1e+02 Score=24.34 Aligned_cols=37 Identities=35% Similarity=0.579 Sum_probs=24.5
Q ss_pred eccCC----cchhhHHHHhH----HHHHH----HHhcChhHHHHHHHHHH
Q psy14414 33 EYPLK----GHQKVAILRNI----EKMVA----EALQNQEEVSHLMRALV 70 (76)
Q Consensus 33 ~yPL~----~~QKVaImRNI----EKML~----eAL~D~~EVg~Llr~lV 70 (76)
.||-. -||++||-|-+ +-||- .|| ||+-||..|+-|.
T Consensus 148 ~YP~~LSGGQQQR~aIARaLameP~vmLFDEPTSAL-DPElVgEVLkv~~ 196 (256)
T COG4598 148 AYPAHLSGGQQQRVAIARALAMEPEVMLFDEPTSAL-DPELVGEVLKVMQ 196 (256)
T ss_pred cCccccCchHHHHHHHHHHHhcCCceEeecCCcccC-CHHHHHHHHHHHH
Confidence 57743 47999998864 22332 233 8999999887663
No 78
>TIGR01498 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. This model describes the folate biosynthesis enzyme 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. Alternate names include 6-hydroxymethyl-7,8-dihydropterin diphosphokinase and 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (HPPK). The extreme C-terminal region, of typically eight to thirty residues, is not included in the model. This enzyme may be found as a fusion protein with other enzymes of folate biosynthesis.
Probab=20.77 E-value=1e+02 Score=20.65 Aligned_cols=24 Identities=25% Similarity=0.416 Sum_probs=20.2
Q ss_pred ceeccCCcchhhHHHHhHHHHHHH
Q psy14414 31 DIEYPLKGHQKVAILRNIEKMVAE 54 (76)
Q Consensus 31 ~I~yPL~~~QKVaImRNIEKML~e 54 (76)
.++--|++++=.+++++||+-++.
T Consensus 56 ~~~T~l~p~~Ll~~l~~IE~~~GR 79 (127)
T TIGR01498 56 EVETTLAPRELLALLQAIEAELGR 79 (127)
T ss_pred EEEeCCCHHHHHHHHHHHHHHhCC
Confidence 366678999999999999998774
No 79
>PF08546 ApbA_C: Ketopantoate reductase PanE/ApbA C terminal; InterPro: IPR013752 This is the C-terminal domain of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, 1.1.1.169 from EC. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway []. ApbA and PanE are allelic []. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway []. ; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 1YJQ_A 1KS9_A 2OFP_A 1YON_A 2EW2_B 3EGO_B 3HN2_D 3GHY_B 3G17_E 3HWR_B ....
Probab=20.76 E-value=1.4e+02 Score=18.50 Aligned_cols=19 Identities=26% Similarity=0.434 Sum_probs=12.3
Q ss_pred ChhHHHHHHHHHHhcccCC
Q psy14414 58 NQEEVSHLMRALVLGRYTE 76 (76)
Q Consensus 58 D~~EVg~Llr~lVlGRYte 76 (76)
.+.....+++++..||.||
T Consensus 74 ~~~~~~SM~~D~~~gr~tE 92 (125)
T PF08546_consen 74 TPDNRSSMLQDIEAGRPTE 92 (125)
T ss_dssp TTTT--HHHHHHHTTB--S
T ss_pred cCCccccHHHHHHHccccc
Confidence 4556888999999999886
No 80
>COG0319 Predicted metal-dependent hydrolase [General function prediction only]
Probab=20.63 E-value=45 Score=23.61 Aligned_cols=18 Identities=28% Similarity=0.645 Sum_probs=13.1
Q ss_pred eeeecCCCCCceeccCCc
Q psy14414 21 SWKPKTKPTGDIEYPLKG 38 (76)
Q Consensus 21 nfwyk~~P~p~I~yPL~~ 38 (76)
.|+-|-+||.+|+||+-.
T Consensus 56 ~yR~kD~pTDVLSFp~~e 73 (153)
T COG0319 56 EYRGKDKPTDVLSFPYNE 73 (153)
T ss_pred HHcCCCCCCceEEecCCC
Confidence 355666777799999874
No 81
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=20.60 E-value=72 Score=22.06 Aligned_cols=21 Identities=14% Similarity=0.327 Sum_probs=19.2
Q ss_pred eccCCcchhhHHHHhHHHHHH
Q psy14414 33 EYPLKGHQKVAILRNIEKMVA 53 (76)
Q Consensus 33 ~yPL~~~QKVaImRNIEKML~ 53 (76)
.||++..|+-++-+=|+++|.
T Consensus 6 ~~p~~~~~~~~~~~~i~~ll~ 26 (213)
T cd01645 6 QWPLTEEKLEALTELVTEQLK 26 (213)
T ss_pred ccCCCHHHHHHHHHHHHHHHH
Confidence 599999999999999999885
No 82
>PF15460 SAS4: Something about silencing, SAS, complex subunit 4
Probab=20.58 E-value=1.2e+02 Score=20.40 Aligned_cols=25 Identities=32% Similarity=0.515 Sum_probs=15.5
Q ss_pred HHHHhHHHHHHHHhcChhHHHHHHHHH
Q psy14414 43 AILRNIEKMVAEALQNQEEVSHLMRAL 69 (76)
Q Consensus 43 aImRNIEKML~eAL~D~~EVg~Llr~l 69 (76)
.-|||+||. .|+.....+..+|..|
T Consensus 20 krm~n~ek~--r~~~E~d~L~~lle~L 44 (101)
T PF15460_consen 20 KRMRNIEKE--RAQHEKDRLQRLLEKL 44 (101)
T ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHH
Confidence 369999984 4555555555555443
Done!