Query 033207
Match_columns 125
No_of_seqs 71 out of 73
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 11:07:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033207.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033207hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0578 p21-activated serine/t 71.4 2.3 4.9E-05 39.4 1.5 22 104-125 411-436 (550)
2 PF12674 Zn_ribbon_2: Putative 59.1 12 0.00027 26.0 3.0 29 69-97 41-70 (81)
3 COG2166 sufE Cysteine desulfur 56.5 21 0.00046 27.8 4.2 40 49-88 51-95 (144)
4 PF13961 DUF4219: Domain of un 55.4 0.9 2E-05 25.8 -2.6 14 51-64 1-14 (27)
5 PF05922 Inhibitor_I9: Peptida 54.0 23 0.00049 22.3 3.4 61 60-123 3-69 (82)
6 PF10847 DUF2656: Protein of u 51.9 24 0.00052 27.5 3.8 31 55-88 41-71 (132)
7 TIGR03868 F420-O_ABCperi propo 49.7 17 0.00036 28.1 2.7 26 71-97 126-151 (287)
8 cd01148 TroA_a Metal binding p 48.2 23 0.0005 27.3 3.2 24 71-95 124-147 (284)
9 cd01143 YvrC Periplasmic bindi 44.0 20 0.00043 25.6 2.2 20 77-96 98-117 (195)
10 COG0614 FepB ABC-type Fe3+-hyd 43.1 15 0.00033 28.1 1.5 22 76-97 151-172 (319)
11 cd01144 BtuF Cobalamin binding 42.2 16 0.00034 27.4 1.5 23 72-95 91-113 (245)
12 TIGR00013 taut 4-oxalocrotonat 40.0 32 0.0007 21.1 2.4 43 69-111 14-56 (63)
13 PRK02220 4-oxalocrotonate taut 39.3 47 0.001 20.3 3.1 43 69-111 14-56 (61)
14 PRK10576 iron-hydroxamate tran 39.1 52 0.0011 26.0 4.0 23 73-95 128-150 (292)
15 cd01139 TroA_f Periplasmic bin 38.5 49 0.0011 26.4 3.8 24 71-95 130-153 (342)
16 cd01147 HemV-2 Metal binding p 37.7 28 0.00061 26.1 2.2 20 76-95 113-132 (262)
17 cd00491 4Oxalocrotonate_Tautom 35.8 50 0.0011 19.8 2.8 41 69-109 13-53 (58)
18 KOG1684 Enoyl-CoA hydratase [L 35.8 73 0.0016 28.8 4.8 97 1-111 1-99 (401)
19 KOG4079 Putative mitochondrial 35.7 21 0.00044 28.7 1.2 40 69-111 93-135 (169)
20 KOG1257 NADP+-dependent malic 35.3 38 0.00083 31.9 3.1 25 78-103 328-353 (582)
21 PF01497 Peripla_BP_2: Peripla 34.5 81 0.0018 23.1 4.2 23 74-96 96-118 (238)
22 PRK02260 S-ribosylhomocysteina 33.6 61 0.0013 25.6 3.6 31 53-87 81-111 (158)
23 PRK11411 fecB iron-dicitrate t 33.2 63 0.0014 25.6 3.7 24 71-95 134-157 (303)
24 PF08006 DUF1700: Protein of u 32.0 57 0.0012 24.5 3.1 23 71-93 21-46 (181)
25 PF10850 DUF2653: Protein of u 31.9 67 0.0015 23.5 3.3 41 70-113 5-46 (91)
26 TIGR01542 A118_put_portal phag 31.6 51 0.0011 29.6 3.2 42 60-101 413-455 (476)
27 cd01149 HutB Hemin binding pro 31.3 52 0.0011 24.7 2.8 20 76-95 96-115 (235)
28 cd01142 TroA_e Periplasmic bin 30.5 47 0.001 25.6 2.5 22 75-96 122-143 (289)
29 TIGR03659 IsdE heme ABC transp 30.5 48 0.001 26.1 2.5 22 74-95 125-146 (289)
30 PHA01078 putative upper collar 30.4 63 0.0014 27.5 3.3 42 49-90 52-93 (249)
31 cd01146 FhuD Fe3+-siderophore 30.1 79 0.0017 23.9 3.6 23 71-94 97-119 (256)
32 PRK03379 vitamin B12-transport 29.0 45 0.00097 26.1 2.1 20 76-95 109-128 (260)
33 cd04438 DEP_dishevelled DEP (D 28.4 20 0.00044 24.9 0.1 50 46-106 25-74 (84)
34 PF02902 Peptidase_C48: Ulp1 p 27.8 83 0.0018 22.9 3.3 30 73-102 5-34 (216)
35 COG4607 CeuA ABC-type enteroch 27.8 34 0.00074 30.0 1.4 19 80-98 159-177 (320)
36 PTZ00397 macrophage migration 27.3 1.4E+02 0.0031 20.7 4.3 48 60-107 5-52 (116)
37 PRK01964 4-oxalocrotonate taut 26.8 83 0.0018 19.7 2.7 42 69-110 14-55 (64)
38 PF01361 Tautomerase: Tautomer 26.4 91 0.002 19.1 2.8 33 61-93 3-37 (60)
39 cd01140 FatB Siderophore bindi 26.2 64 0.0014 24.6 2.5 20 76-95 109-128 (270)
40 PF08776 VASP_tetra: VASP tetr 25.5 80 0.0017 20.2 2.4 15 72-86 24-38 (40)
41 PRK10957 iron-enterobactin tra 25.1 59 0.0013 25.8 2.2 18 78-95 152-169 (317)
42 PF02664 LuxS: S-Ribosylhomocy 24.8 1.1E+02 0.0024 24.3 3.6 34 53-90 81-114 (157)
43 cd00636 TroA-like Helical back 24.8 69 0.0015 20.6 2.1 25 73-97 97-121 (148)
44 PF14581 SseB_C: SseB protein 24.2 1.6E+02 0.0036 20.1 4.1 35 53-89 45-79 (108)
45 PF01026 TatD_DNase: TatD rela 23.4 1.1E+02 0.0024 23.9 3.4 48 52-99 193-248 (255)
46 cd00126 PAH Pancreatic Hormone 23.3 94 0.002 19.2 2.4 18 64-81 6-23 (36)
47 cd00762 NAD_bind_malic_enz NAD 23.0 91 0.002 26.1 3.0 16 88-103 52-68 (254)
48 TIGR03391 FeS_syn_CsdE cystein 22.7 2.3E+02 0.0049 21.5 4.8 46 49-94 51-103 (138)
49 PRK14048 ferrichrome/ferrioxam 22.7 71 0.0015 26.2 2.3 19 78-96 166-184 (374)
50 PF11767 SET_assoc: Histone ly 22.2 29 0.00063 23.5 -0.0 24 86-109 39-62 (66)
51 COG4594 FecB ABC-type Fe3+-cit 22.0 70 0.0015 28.0 2.2 28 69-97 142-169 (310)
52 COG1854 LuxS LuxS protein invo 21.7 1.8E+02 0.0038 23.5 4.2 32 53-88 81-112 (161)
53 TIGR02778 ligD_pol DNA polymer 21.5 83 0.0018 26.3 2.5 22 65-86 11-32 (245)
54 cd01138 FeuA Periplasmic bindi 21.1 90 0.002 23.4 2.4 22 73-95 97-118 (248)
55 PF07105 DUF1367: Protein of u 21.0 78 0.0017 26.0 2.2 34 53-90 55-90 (196)
56 TIGR02145 Fib_succ_major Fibro 20.9 54 0.0012 25.5 1.2 36 57-97 50-89 (171)
57 KOG4420 Uncharacterized conser 20.5 65 0.0014 28.4 1.7 74 49-122 58-152 (325)
58 PRK15019 CsdA-binding activato 20.2 2.6E+02 0.0057 21.5 4.8 46 49-94 56-108 (147)
No 1
>KOG0578 consensus p21-activated serine/threonine protein kinase [Signal transduction mechanisms]
Probab=71.36 E-value=2.3 Score=39.36 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=20.0
Q ss_pred eeeeeeeeeehhhc----cccCCCCC
Q 033207 104 YYYAFGCKFLKILL----IRSDPYQM 125 (125)
Q Consensus 104 ~yfgF~c~I~Ee~S----lk~lP~~~ 125 (125)
+.||||+.|+|+-+ +-+-||-|
T Consensus 411 tDFGFcaqi~~~~~KR~TmVGTPYWM 436 (550)
T KOG0578|consen 411 TDFGFCAQISEEQSKRSTMVGTPYWM 436 (550)
T ss_pred eeeeeeeccccccCccccccCCCCcc
Confidence 78999999999997 88899987
No 2
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=59.10 E-value=12 Score=26.02 Aligned_cols=29 Identities=21% Similarity=0.225 Sum_probs=25.1
Q ss_pred CCChHHHHHHHHHHHHHHhC-CHHHhhccc
Q 033207 69 YPPRDEIVNGYVKTLASALG-CEEDAKKSI 97 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAkVLG-SeeEAkkkI 97 (125)
..|.+|||+.-++-+++.-| ++|||++.+
T Consensus 41 ~~t~eemie~~~~~~~~~~~~~~~~a~~~~ 70 (81)
T PF12674_consen 41 DITMEEMIEFCVPFMDEFNGMTPEEARKMM 70 (81)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 46999999999999999987 899998643
No 3
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=56.54 E-value=21 Score=27.82 Aligned_cols=40 Identities=28% Similarity=0.511 Sum_probs=34.8
Q ss_pred cccCCCCcceeEEEeeCCCC-----CCChHHHHHHHHHHHHHHhC
Q 033207 49 SLLEGCDYKHWLVVMEAPKG-----YPPRDEIVNGYVKTLASALG 88 (125)
Q Consensus 49 ~L~~Gcdy~HWLVvMe~P~g-----~~sr~emId~Yv~TLAkVLG 88 (125)
-...||...-|++..-..+| ..|.+.||..++.+|..++.
T Consensus 51 n~V~GC~S~vwL~~~~~~~~~~~F~gdSdA~ivrGL~aill~~~~ 95 (144)
T COG2166 51 NPVPGCQSQVWLVTEQNDDGTLHFFGDSDARIVRGLLAILLAAYS 95 (144)
T ss_pred cCCCccccceeEEEeecCCceEEEeccchhHHHHHHHHHHHHHHc
Confidence 46689999999998877654 68999999999999999883
No 4
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=55.43 E-value=0.9 Score=25.79 Aligned_cols=14 Identities=36% Similarity=0.983 Sum_probs=12.3
Q ss_pred cCCCCcceeEEEee
Q 033207 51 LEGCDYKHWLVVME 64 (125)
Q Consensus 51 ~~Gcdy~HWLVvMe 64 (125)
|+|-+|.+|-+.|.
T Consensus 1 l~g~NY~~W~~~M~ 14 (27)
T PF13961_consen 1 LDGTNYSTWKIRMK 14 (27)
T ss_pred CCccCHHHHHHHHH
Confidence 78999999988886
No 5
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=54.02 E-value=23 Score=22.35 Aligned_cols=61 Identities=16% Similarity=0.194 Sum_probs=30.1
Q ss_pred EEEeeCCCCCCChHHHHHHHHHHHHHHhCC----HHHhhccceEEeeceeeeeeeeeehhhc--cccCCC
Q 033207 60 LVVMEAPKGYPPRDEIVNGYVKTLASALGC----EEDAKKSIYSVSTKYYYAFGCKFLKILL--IRSDPY 123 (125)
Q Consensus 60 LVvMe~P~g~~sr~emId~Yv~TLAkVLGS----eeEAkkkIY~vSt~~yfgF~c~I~Ee~S--lk~lP~ 123 (125)
.|+|+.+.. .++..+.-.+-.+..+.+ ....+-++-..-...--||-+.++++.- |+.+|-
T Consensus 3 IV~~k~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~Gfs~~l~~~~i~~L~~~p~ 69 (82)
T PF05922_consen 3 IVVFKDDAS---AASSFSSHKSWQASILKSALKSASSINAKVLYSYDNAFNGFSAKLSEEEIEKLRKDPG 69 (82)
T ss_dssp EEEE-TTST---HHCHHHHHHHHHH----HHHHTH-TTT-EEEEEESSTSSEEEEEE-HHHHHHHHTSTT
T ss_pred EEEECCCCC---cchhHHHHHHHHHHHHhhhhhhhcccCCceEEEEeeeEEEEEEEeCHHHHHHHHcCCC
Confidence 677876533 222344444444433332 1233444444333367899999999887 877773
No 6
>PF10847 DUF2656: Protein of unknown function (DUF2656); InterPro: IPR020325 This entry contains uncharacterised proteins from the cpeY 3'-region. They have no known function, but are found in the phycobilisome.
Probab=51.93 E-value=24 Score=27.49 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=26.3
Q ss_pred CcceeEEEeeCCCCCCChHHHHHHHHHHHHHHhC
Q 033207 55 DYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALG 88 (125)
Q Consensus 55 dy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVLG 88 (125)
+-.||||-++ ...|++||-...++++.+.=-
T Consensus 41 ~hPHW~v~i~---s~lsp~~~~~~~v~aw~~~R~ 71 (132)
T PF10847_consen 41 NHPHWMVEIE---SDLSPDEMAEELVRAWKQYRN 71 (132)
T ss_pred cCCceEEEec---ccCCHHHHHHHHHHHHHHHHH
Confidence 6679999998 778999999999999887643
No 7
>TIGR03868 F420-O_ABCperi proposed F420-0 ABC transporter, periplasmic F420-0 binding protein. This small clade of ABC-type transporter periplasmic binding protein components is found as a three gene cassette along with a permease (TIGR03869) and an ATPase (TIGR03873). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this periplasmic binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
Probab=49.74 E-value=17 Score=28.10 Aligned_cols=26 Identities=8% Similarity=0.253 Sum_probs=19.2
Q ss_pred ChHHHHHHHHHHHHHHhCCHHHhhccc
Q 033207 71 PRDEIVNGYVKTLASALGCEEDAKKSI 97 (125)
Q Consensus 71 sr~emId~Yv~TLAkVLGSeeEAkkkI 97 (125)
+.+++.+. ++.|++++|.|++|++-|
T Consensus 126 ~~~~~~~~-i~~lg~~~g~e~~A~~~i 151 (287)
T TIGR03868 126 TFDDVFAE-ITEVGTIFDVPDAAASLV 151 (287)
T ss_pred CHHHHHHH-HHHHHHHhCCHHHHHHHH
Confidence 45555554 788999999999887643
No 8
>cd01148 TroA_a Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=48.16 E-value=23 Score=27.29 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=15.4
Q ss_pred ChHHHHHHHHHHHHHHhCCHHHhhc
Q 033207 71 PRDEIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 71 sr~emId~Yv~TLAkVLGSeeEAkk 95 (125)
+.+++.+ .++.+++++|.||+|++
T Consensus 124 ~~~~~~~-~~~~lg~~~g~e~~A~~ 147 (284)
T cd01148 124 TLDDVYN-DIRNLGKIFDVEDRADK 147 (284)
T ss_pred CHHHHHH-HHHHHHHHhCCHhHHHH
Confidence 4444444 57778888887776653
No 9
>cd01143 YvrC Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=43.98 E-value=20 Score=25.61 Aligned_cols=20 Identities=25% Similarity=0.385 Sum_probs=14.9
Q ss_pred HHHHHHHHHHhCCHHHhhcc
Q 033207 77 NGYVKTLASALGCEEDAKKS 96 (125)
Q Consensus 77 d~Yv~TLAkVLGSeeEAkkk 96 (125)
.-.+++|++++|.+|+|++-
T Consensus 98 ~~~~~~lg~~~g~~~~a~~~ 117 (195)
T cd01143 98 YDQIELIGKITGAEEEAEKL 117 (195)
T ss_pred HHHHHHHHHHhCChHHHHHH
Confidence 33577889999988887663
No 10
>COG0614 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=43.09 E-value=15 Score=28.14 Aligned_cols=22 Identities=36% Similarity=0.533 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHhCCHHHhhccc
Q 033207 76 VNGYVKTLASALGCEEDAKKSI 97 (125)
Q Consensus 76 Id~Yv~TLAkVLGSeeEAkkkI 97 (125)
+.-=++++++++|.|++|++-|
T Consensus 151 ~~~~i~~lg~~~g~e~~A~~li 172 (319)
T COG0614 151 IKEQIRLLGKALGKEEKAEELI 172 (319)
T ss_pred HHHHHHHHHHHhCcHHHHHHHH
Confidence 3344688999999999997644
No 11
>cd01144 BtuF Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=42.15 E-value=16 Score=27.37 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHHHHhCCHHHhhc
Q 033207 72 RDEIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 72 r~emId~Yv~TLAkVLGSeeEAkk 95 (125)
.+++. --+++||+++|.+++|++
T Consensus 91 ~~~~~-~~~~~lg~~~g~~~~a~~ 113 (245)
T cd01144 91 LDDIL-ADIRRLGTLAGRPARAEE 113 (245)
T ss_pred HHHHH-HHHHHHHHHhCChhHHHH
Confidence 33433 468899999999998854
No 12
>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=40.01 E-value=32 Score=21.14 Aligned_cols=43 Identities=19% Similarity=0.350 Sum_probs=30.7
Q ss_pred CCChHHHHHHHHHHHHHHhCCHHHhhccceEEeeceeeeeeee
Q 033207 69 YPPRDEIVNGYVKTLASALGCEEDAKKSIYSVSTKYYYAFGCK 111 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vSt~~yfgF~c~ 111 (125)
.-.|++++..-.+.|+++||.-+|.-.-+..-.-...||||=.
T Consensus 14 ~eqK~~l~~~it~~l~~~lg~~~~~v~V~i~e~~~~~w~~gG~ 56 (63)
T TIGR00013 14 DEQKRQLIEGVTEAMAETLGANLESIVVIIDEMPKNNYGIGGE 56 (63)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcccEEEEEEEcCHHHeeECCE
Confidence 4578889999999999999966665554445555566777643
No 13
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=39.27 E-value=47 Score=20.33 Aligned_cols=43 Identities=19% Similarity=0.224 Sum_probs=32.6
Q ss_pred CCChHHHHHHHHHHHHHHhCCHHHhhccceEEeeceeeeeeee
Q 033207 69 YPPRDEIVNGYVKTLASALGCEEDAKKSIYSVSTKYYYAFGCK 111 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vSt~~yfgF~c~ 111 (125)
.-.|.++++.-.+.|++++|...|.-.-+..---...||||=.
T Consensus 14 ~eqk~~l~~~it~~l~~~~~~p~~~v~V~i~e~~~~~~~~gG~ 56 (61)
T PRK02220 14 EEQLKALVKDVTAAVSKNTGAPAEHIHVIINEMSKNHYAVGGK 56 (61)
T ss_pred HHHHHHHHHHHHHHHHHHhCcChhhEEEEEEEeChhHeEECCE
Confidence 4577889999999999999976766666666666667777643
No 14
>PRK10576 iron-hydroxamate transporter substrate-binding subunit; Provisional
Probab=39.11 E-value=52 Score=26.04 Aligned_cols=23 Identities=22% Similarity=0.182 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHhCCHHHhhc
Q 033207 73 DEIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 73 ~emId~Yv~TLAkVLGSeeEAkk 95 (125)
-+.+..-++.|++++|.|++|++
T Consensus 128 ~~~~~~~i~~lg~ilG~e~~A~~ 150 (292)
T PRK10576 128 LAVARKSLVELAQRLNLEAAAET 150 (292)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHH
Confidence 45667778999999999988754
No 15
>cd01139 TroA_f Periplasmic binding protein TroA_f. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=38.48 E-value=49 Score=26.39 Aligned_cols=24 Identities=33% Similarity=0.466 Sum_probs=16.8
Q ss_pred ChHHHHHHHHHHHHHHhCCHHHhhc
Q 033207 71 PRDEIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 71 sr~emId~Yv~TLAkVLGSeeEAkk 95 (125)
+-+++.+ -++.|++++|.+++|++
T Consensus 130 ~~~~~~~-~i~~lg~i~g~~~~A~~ 153 (342)
T cd01139 130 PLKNTTP-SMRLLGKALGREERAEE 153 (342)
T ss_pred hhhhHHH-HHHHHHHHhCCHHHHHH
Confidence 3445554 47789999998887754
No 16
>cd01147 HemV-2 Metal binding protein HemV-2. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=37.72 E-value=28 Score=26.14 Aligned_cols=20 Identities=30% Similarity=0.423 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHhCCHHHhhc
Q 033207 76 VNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 76 Id~Yv~TLAkVLGSeeEAkk 95 (125)
+...++.|++++|.+++|++
T Consensus 113 ~~~~i~~lg~~~g~~~~a~~ 132 (262)
T cd01147 113 TPEQIRLLGKVLGKEERAEE 132 (262)
T ss_pred HHHHHHHHHHHhCCHHHHHH
Confidence 35677899999999888774
No 17
>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=35.83 E-value=50 Score=19.78 Aligned_cols=41 Identities=17% Similarity=0.269 Sum_probs=27.0
Q ss_pred CCChHHHHHHHHHHHHHHhCCHHHhhccceEEeeceeeeee
Q 033207 69 YPPRDEIVNGYVKTLASALGCEEDAKKSIYSVSTKYYYAFG 109 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vSt~~yfgF~ 109 (125)
.-.|.++++.-.+.+++++|.-+|.-.-+..-.-...||||
T Consensus 13 ~eqk~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~~~~~~g 53 (58)
T cd00491 13 DEQKRELIERVTEAVSEILGAPEATIVVIIDEMPKENWGIG 53 (58)
T ss_pred HHHHHHHHHHHHHHHHHHhCcCcccEEEEEEEeCchhceEC
Confidence 45677889999999999999655543333333444455554
No 18
>KOG1684 consensus Enoyl-CoA hydratase [Lipid transport and metabolism]
Probab=35.83 E-value=73 Score=28.84 Aligned_cols=97 Identities=22% Similarity=0.158 Sum_probs=57.7
Q ss_pred CchhhhhcccchhHHHHHHhhhcCCCCCCCCcceeccCC-ccccCCCCCcccCCCCcceeEEEeeCCCC-CCChHHHHHH
Q 033207 1 MLRNIILRCPLNLTAAIYRRRHLQSSSPPSSLFFFSSDS-TVTQLTRLPSLLEGCDYKHWLVVMEAPKG-YPPRDEIVNG 78 (125)
Q Consensus 1 ~~~~~~~~~pl~~~a~~~~~~~~~~~~p~s~~~~~s~~s-~~s~l~~~p~L~~Gcdy~HWLVvMe~P~g-~~sr~emId~ 78 (125)
|+|+..+++++...-+.- + +..|.|++-+ .++.-..+++|++|-+... +|+.|.|+- ..=-.|||+.
T Consensus 1 m~~~~~~~~~~s~~~~~~--~--------~~~r~f~~~~~~~~~~~~~~VL~e~~~~~r-~itLNRPKaLNAlnleMv~~ 69 (401)
T KOG1684|consen 1 MLRQKLLKARVSNFLALK--R--------TTSRAFIRMASSVSTDSKDQVLVEGKGCAR-VITLNRPKALNALNLEMVLS 69 (401)
T ss_pred Ccchhhhhhhhcchhhhh--h--------hhccceeecccccccccCCceEEecCCcee-EEEecCchhhccccHHHHHH
Confidence 677777777766443332 1 1233444444 4455555889999866655 889999997 5666799999
Q ss_pred HHHHHHHHhCCHHHhhccceEEeeceeeeeeee
Q 033207 79 YVKTLASALGCEEDAKKSIYSVSTKYYYAFGCK 111 (125)
Q Consensus 79 Yv~TLAkVLGSeeEAkkkIY~vSt~~yfgF~c~ 111 (125)
|...|-+-= .-++++--|--=| +..+||+-
T Consensus 70 ~~~~L~~we-~s~~~k~vIlkgs--~~raFCAG 99 (401)
T KOG1684|consen 70 IYPKLVEWE-KSPLVKLVILKGS--GGRAFCAG 99 (401)
T ss_pred HHHHHHhhc-cCCCceEEEEecC--CCceeecC
Confidence 987664321 1122232233333 36677773
No 19
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=35.65 E-value=21 Score=28.74 Aligned_cols=40 Identities=28% Similarity=0.244 Sum_probs=25.8
Q ss_pred CCChHHHHHHHHHHHHH---HhCCHHHhhccceEEeeceeeeeeee
Q 033207 69 YPPRDEIVNGYVKTLAS---ALGCEEDAKKSIYSVSTKYYYAFGCK 111 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAk---VLGSeeEAkkkIY~vSt~~yfgF~c~ 111 (125)
.-+++||+++.+|||.| +|..||+-|+ +-+--..||.+|+
T Consensus 93 ~~~r~eI~~hl~K~lGKtee~lr~Ee~ek~---~k~nPAnFG~~c~ 135 (169)
T KOG4079|consen 93 GMKREEIEKHLAKTLGKTEEVLRREELEKI---AKLNPANFGSKCE 135 (169)
T ss_pred cccHHHHHHHHHHHhCccHHHHhHHHHHHH---hhcChhhhccccc
Confidence 46899999998887765 4544444333 2345567887775
No 20
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=35.32 E-value=38 Score=31.87 Aligned_cols=25 Identities=36% Similarity=0.535 Sum_probs=18.3
Q ss_pred HHHHHHHHHhC-CHHHhhccceEEeec
Q 033207 78 GYVKTLASALG-CEEDAKKSIYSVSTK 103 (125)
Q Consensus 78 ~Yv~TLAkVLG-SeeEAkkkIY~vSt~ 103 (125)
--+..+.+- | +||||+||||=|.-+
T Consensus 328 l~v~~m~~~-Gl~~eeA~kkIwlvD~~ 353 (582)
T KOG1257|consen 328 LIVMAMVKE-GLSEEEARKKIWLVDSK 353 (582)
T ss_pred HHHHHHHHc-CCCHHHHhccEEEEecC
Confidence 334555555 7 999999999988644
No 21
>PF01497 Peripla_BP_2: Periplasmic binding protein; InterPro: IPR002491 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Most bacterial importers employ a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered to the cell membrane via the acylation of a cysteine residue that is an integral component of a lipoprotein signal sequence. In planta expression of a high-affinity iron-uptake system involving the siderophore chrysobactin in Erwinia chrysanthemi 3937 contributes greatly to invasive growth of this pathogen on its natural host, African violets []. The cobalamin (vitamin B12) and the iron transport systems share many common attributes and probably evolved from the same origin [, ]. The periplasmic-binding domain is composed of two subdomains, each consisting of a central beta-sheet and surrounding alpha-helices, linked by a rigid alpha-helix. The substrate binding site is located in a cleft between the two alpha/beta subdomains [].; GO: 0005488 binding; PDB: 2X4L_A 1N4A_B 1N2Z_B 1N4D_B 4DBL_J 2QI9_F 3EIW_A 3EIX_A 3MWG_A 3MWF_A ....
Probab=34.50 E-value=81 Score=23.06 Aligned_cols=23 Identities=26% Similarity=0.342 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHhCCHHHhhcc
Q 033207 74 EIVNGYVKTLASALGCEEDAKKS 96 (125)
Q Consensus 74 emId~Yv~TLAkVLGSeeEAkkk 96 (125)
+-+.-.++.||+++|-+++|++-
T Consensus 96 ~~~~~~i~~lg~~~g~~~~a~~~ 118 (238)
T PF01497_consen 96 DDWKEQIRQLGKALGKEDQAEAL 118 (238)
T ss_dssp HHHHHHHHHHHHHHTSHHHHHHH
T ss_pred HHHHHHHHHHHHhcccHHHHHHH
Confidence 77778889999999999988753
No 22
>PRK02260 S-ribosylhomocysteinase; Provisional
Probab=33.64 E-value=61 Score=25.62 Aligned_cols=31 Identities=26% Similarity=0.672 Sum_probs=28.4
Q ss_pred CCCcceeEEEeeCCCCCCChHHHHHHHHHHHHHHh
Q 033207 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASAL 87 (125)
Q Consensus 53 Gcdy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVL 87 (125)
||.--+.||+. |.++.+++++...++|..|+
T Consensus 81 GCrTGFYli~~----g~~~~~~i~~l~~~~l~~i~ 111 (158)
T PRK02260 81 GCRTGFYLILI----GTPDEEDVADALKATLEDVL 111 (158)
T ss_pred ccccccEEEEe----CCCCHHHHHHHHHHHHHHHH
Confidence 99999999986 56889999999999999998
No 23
>PRK11411 fecB iron-dicitrate transporter substrate-binding subunit; Provisional
Probab=33.19 E-value=63 Score=25.58 Aligned_cols=24 Identities=13% Similarity=0.221 Sum_probs=18.0
Q ss_pred ChHHHHHHHHHHHHHHhCCHHHhhc
Q 033207 71 PRDEIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 71 sr~emId~Yv~TLAkVLGSeeEAkk 95 (125)
+.++..+ .++.||+++|.|++|++
T Consensus 134 ~~~~~~~-~i~~lg~i~g~e~~a~~ 157 (303)
T PRK11411 134 TYQENLQ-SAAIIGEVLGKKREMQA 157 (303)
T ss_pred CHHHHHH-HHHHHHHHhCCHHHHHH
Confidence 5556555 35789999999988875
No 24
>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=32.05 E-value=57 Score=24.46 Aligned_cols=23 Identities=35% Similarity=0.499 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHHHHHh--C-CHHHh
Q 033207 71 PRDEIVNGYVKTLASAL--G-CEEDA 93 (125)
Q Consensus 71 sr~emId~Yv~TLAkVL--G-SeeEA 93 (125)
.++|++++|.+-..... | ||||+
T Consensus 21 e~~e~l~~Y~e~f~d~~~~G~sEeei 46 (181)
T PF08006_consen 21 EREEILEYYEEYFDDAGEEGKSEEEI 46 (181)
T ss_pred HHHHHHHHHHHHHHHhhhCCCCHHHH
Confidence 57889999988776543 3 55554
No 25
>PF10850 DUF2653: Protein of unknown function (DUF2653); InterPro: IPR020516 This entry contains proteins with no known function.
Probab=31.95 E-value=67 Score=23.55 Aligned_cols=41 Identities=22% Similarity=0.291 Sum_probs=27.6
Q ss_pred CChHHHHHHHHHHHHHHhC-CHHHhhccceEEeeceeeeeeeeee
Q 033207 70 PPRDEIVNGYVKTLASALG-CEEDAKKSIYSVSTKYYYAFGCKFL 113 (125)
Q Consensus 70 ~sr~emId~Yv~TLAkVLG-SeeEAkkkIY~vSt~~yfgF~c~I~ 113 (125)
.+.+|+|++----.|+-=| .-+|-.. ..+|+-++||+|++.
T Consensus 5 l~EqeIiNAvCl~~A~~~~i~P~dVeV---eL~yDdd~GFsAEv~ 46 (91)
T PF10850_consen 5 LSEQEIINAVCLHIAERKGIQPEDVEV---ELMYDDDYGFSAEVW 46 (91)
T ss_pred ccHHHHHHHHHHHHHHhcCCCcccEEE---EEEEecCCCeeEEEE
Confidence 3567788776555555444 3444333 789999999999873
No 26
>TIGR01542 A118_put_portal phage portal protein, putative, A118 family. This model represents a family of phage minor structural proteins. The protein is suggested to be the head-tail connector, or portal protein, on the basis of its position in the phage gene order, its presence in mature phage, its size, and its conservation across a number of complete genomes of tailed phage that lack other candidate portal proteins. Several other known portal protein families lack clear homology to this family and to each other.
Probab=31.63 E-value=51 Score=29.55 Aligned_cols=42 Identities=12% Similarity=0.304 Sum_probs=36.6
Q ss_pred EEEeeCCCC-CCChHHHHHHHHHHHHHHhCCHHHhhccceEEe
Q 033207 60 LVVMEAPKG-YPPRDEIVNGYVKTLASALGCEEDAKKSIYSVS 101 (125)
Q Consensus 60 LVvMe~P~g-~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vS 101 (125)
-|.+||+.+ .+.+++-++.+.|-++.++-|.+++.++.|.++
T Consensus 413 ~v~v~fdDsi~~D~e~e~~~~~~~vaaG~ms~~~yl~k~yg~~ 455 (476)
T TIGR01542 413 TITIDFDDGVFQDEDTTINRYTNAVNAGMIPLKIALQRAWNIT 455 (476)
T ss_pred ceEEecCCccccCHHHHHHHHHHHHHcCCCCHHHHHHHccCCC
Confidence 389999998 678888889999999988889999999988754
No 27
>cd01149 HutB Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=31.33 E-value=52 Score=24.67 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhCCHHHhhc
Q 033207 76 VNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 76 Id~Yv~TLAkVLGSeeEAkk 95 (125)
+..-++.|++++|.|++|++
T Consensus 96 ~~~~~~~lg~i~g~e~~A~~ 115 (235)
T cd01149 96 LLTKIRQVAQALGVPEKGEA 115 (235)
T ss_pred HHHHHHHHHHHhCCHHHHHH
Confidence 44457889999999888765
No 28
>cd01142 TroA_e Periplasmic binding protein TroA_e. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=30.55 E-value=47 Score=25.65 Aligned_cols=22 Identities=27% Similarity=0.235 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHhCCHHHhhcc
Q 033207 75 IVNGYVKTLASALGCEEDAKKS 96 (125)
Q Consensus 75 mId~Yv~TLAkVLGSeeEAkkk 96 (125)
-+...++.||+++|.+++|++-
T Consensus 122 ~~~~~~~~lg~~~g~~~~a~~~ 143 (289)
T cd01142 122 EVKLTIALLGELLGRQEKAEAL 143 (289)
T ss_pred HHHHHHHHHHHHhCcHHHHHHH
Confidence 3456788999999999888754
No 29
>TIGR03659 IsdE heme ABC transporter, heme-binding protein isdE. This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, pfam05031) heme-binding domain. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron.
Probab=30.46 E-value=48 Score=26.08 Aligned_cols=22 Identities=27% Similarity=0.370 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHhCCHHHhhc
Q 033207 74 EIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 74 emId~Yv~TLAkVLGSeeEAkk 95 (125)
+-+...++.+++++|.+++|++
T Consensus 125 ~~~~~~i~~lg~~~G~~~~A~~ 146 (289)
T TIGR03659 125 DGMKKSITELGEKYGREEQAEK 146 (289)
T ss_pred HHHHHHHHHHHHHhCCHHHHHH
Confidence 3344567889999998887754
No 30
>PHA01078 putative upper collar protein
Probab=30.43 E-value=63 Score=27.49 Aligned_cols=42 Identities=24% Similarity=0.410 Sum_probs=35.1
Q ss_pred cccCCCCcceeEEEeeCCCCCCChHHHHHHHHHHHHHHhCCH
Q 033207 49 SLLEGCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALGCE 90 (125)
Q Consensus 49 ~L~~Gcdy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVLGSe 90 (125)
-+.+.|-.-.++|.-++|.-..+-=+||.+|++-||.+-.|+
T Consensus 52 ~~~d~~~~GnfVV~~NK~~~y~~Dy~IieHY~~elaeia~sr 93 (249)
T PHA01078 52 KLYDNCMSGNFVVMQNKPIQYNSDIEIIEHYTDELAEVALSR 93 (249)
T ss_pred HHhcccccCCEEEEeccchhhhcchhHHHHHHHHHHHHHHHH
Confidence 466777666778877888888999999999999999998765
No 31
>cd01146 FhuD Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA-like protein is comprised of two globular subdomains connected by a long alpha helix and binds its specific ligands in the cleft between these domains.
Probab=30.08 E-value=79 Score=23.95 Aligned_cols=23 Identities=35% Similarity=0.354 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHHHHHhCCHHHhh
Q 033207 71 PRDEIVNGYVKTLASALGCEEDAK 94 (125)
Q Consensus 71 sr~emId~Yv~TLAkVLGSeeEAk 94 (125)
+.+++.+ .++.|++++|.+++|+
T Consensus 97 ~~~~~~~-~i~~lg~~~g~~~~a~ 119 (256)
T cd01146 97 WLAEWKE-NLRLIAKALGKEEEAE 119 (256)
T ss_pred cHHHHHH-HHHHHHHHhCcHHHHH
Confidence 3444444 6788999999887664
No 32
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=29.03 E-value=45 Score=26.05 Aligned_cols=20 Identities=20% Similarity=0.190 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHhCCHHHhhc
Q 033207 76 VNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 76 Id~Yv~TLAkVLGSeeEAkk 95 (125)
+...++++++++|.+++|++
T Consensus 109 ~~~~i~~lg~~~g~~~~A~~ 128 (260)
T PRK03379 109 IANALRQLAPWSPQPEKAEQ 128 (260)
T ss_pred HHHHHHHHHHHcCCHHHHHH
Confidence 33457889999998887744
No 33
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=28.37 E-value=20 Score=24.94 Aligned_cols=50 Identities=22% Similarity=0.335 Sum_probs=35.4
Q ss_pred CCCcccCCCCcceeEEEeeCCCCCCChHHHHHHHHHHHHHHhCCHHHhhccceEEeeceee
Q 033207 46 RLPSLLEGCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALGCEEDAKKSIYSVSTKYYY 106 (125)
Q Consensus 46 ~~p~L~~Gcdy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vSt~~yf 106 (125)
.-|.-|-|+|.--||+ +.=.+.-+|+|.+.+=-+.|.+.+ |++|.-++.|
T Consensus 25 ~~p~~F~GsdlVdWL~--~~~~~~~~R~eAv~~g~~Ll~~G~---------i~HV~~~h~F 74 (84)
T cd04438 25 TIPNSFIGSDLVDWLL--SHVEGLTDRREARKYASSLLKLGY---------IRHTVNKITF 74 (84)
T ss_pred ECCccccchHHHHHHH--HhCCCCCCHHHHHHHHHHHHHCCc---------EEecCCCccc
Confidence 3567789999999988 433457799998877666665554 7777655443
No 34
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=27.80 E-value=83 Score=22.89 Aligned_cols=30 Identities=27% Similarity=0.373 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHhCCHHHhhccceEEee
Q 033207 73 DEIVNGYVKTLASALGCEEDAKKSIYSVST 102 (125)
Q Consensus 73 ~emId~Yv~TLAkVLGSeeEAkkkIY~vSt 102 (125)
+++||.|++.|.+-+-++.....+++-+++
T Consensus 5 d~iId~y~~~l~~~~~~~~~~~~~~~~~~~ 34 (216)
T PF02902_consen 5 DSIIDFYLEYLRHRLESENKNSKRVHFFSS 34 (216)
T ss_dssp HHHHHHHHHHHHHHTCCTHHTSTTEEEE-T
T ss_pred HHHHHHHHHHHHHhhccCccCCCcEEEECc
Confidence 689999999999776667777788887775
No 35
>COG4607 CeuA ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=27.77 E-value=34 Score=30.02 Aligned_cols=19 Identities=37% Similarity=0.555 Sum_probs=16.5
Q ss_pred HHHHHHHhCCHHHhhccce
Q 033207 80 VKTLASALGCEEDAKKSIY 98 (125)
Q Consensus 80 v~TLAkVLGSeeEAkkkIY 98 (125)
+++|+++.|-|+||++.+=
T Consensus 159 ~e~Lg~IFgkE~eAk~~~~ 177 (320)
T COG4607 159 IETLGKIFGKEEEAKELLA 177 (320)
T ss_pred HHHHHHHhCchHHHHHHHH
Confidence 5799999999999998763
No 36
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=27.31 E-value=1.4e+02 Score=20.74 Aligned_cols=48 Identities=15% Similarity=0.103 Sum_probs=33.6
Q ss_pred EEEeeCCCCCCChHHHHHHHHHHHHHHhCCHHHhhccceEEeeceeee
Q 033207 60 LVVMEAPKGYPPRDEIVNGYVKTLASALGCEEDAKKSIYSVSTKYYYA 107 (125)
Q Consensus 60 LVvMe~P~g~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vSt~~yfg 107 (125)
.|.++.+.....++++.+..-+.|++++|--|+-++--.+-...-+||
T Consensus 5 ~i~tn~~~~~~~~~~~~~~~~~~l~~~lgkPe~~~~v~~~~~~~m~f~ 52 (116)
T PTZ00397 5 QVSTNVNATDDQADAALSDIENAIADVLGKPLSYIMSGYDYQKHMRFG 52 (116)
T ss_pred EEEecCCCccccHHHHHHHHHHHHHHHhCCChHHEEEEEeCCceEEEC
Confidence 355555555667899999999999999997666555444444444444
No 37
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=26.79 E-value=83 Score=19.67 Aligned_cols=42 Identities=5% Similarity=0.113 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHHHHHhCCHHHhhccceEEeeceeeeeee
Q 033207 69 YPPRDEIVNGYVKTLASALGCEEDAKKSIYSVSTKYYYAFGC 110 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAkVLGSeeEAkkkIY~vSt~~yfgF~c 110 (125)
.-.|.++++.-.+.+++++|--+|+-.-+-.=.-...||||=
T Consensus 14 ~eqk~~l~~~it~~l~~~lg~p~~~v~V~i~e~~~~~w~~gg 55 (64)
T PRK01964 14 EEKIKNLIREVTEAISATLDVPKERVRVIVNEVPSSHWGVAG 55 (64)
T ss_pred HHHHHHHHHHHHHHHHHHhCcChhhEEEEEEEcChHHeeECC
Confidence 557888999999999999996555554444445566777773
No 38
>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=26.38 E-value=91 Score=19.08 Aligned_cols=33 Identities=15% Similarity=0.425 Sum_probs=23.7
Q ss_pred EEeeCCCC--CCChHHHHHHHHHHHHHHhCCHHHh
Q 033207 61 VVMEAPKG--YPPRDEIVNGYVKTLASALGCEEDA 93 (125)
Q Consensus 61 VvMe~P~g--~~sr~emId~Yv~TLAkVLGSeeEA 93 (125)
|..+-++| .-.|++++..-.+.+.+++|...|+
T Consensus 3 I~i~~~~g~~~e~K~~l~~~it~~~~~~lg~~~~~ 37 (60)
T PF01361_consen 3 ITIKIPEGRTAEQKRELAEAITDAVVEVLGIPPER 37 (60)
T ss_dssp EEEEEESTS-HHHHHHHHHHHHHHHHHHHTS-GGG
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHhCcCCCe
Confidence 45555555 3457788999999999999986664
No 39
>cd01140 FatB Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=26.24 E-value=64 Score=24.59 Aligned_cols=20 Identities=40% Similarity=0.582 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhCCHHHhhc
Q 033207 76 VNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 76 Id~Yv~TLAkVLGSeeEAkk 95 (125)
+...++.||+++|.+++|++
T Consensus 109 ~~~~i~~lg~~~g~~~~a~~ 128 (270)
T cd01140 109 VKQNIETLGKIFGKEEEAKE 128 (270)
T ss_pred HHHHHHHHHHHhCcHHHHHH
Confidence 34468999999999888754
No 40
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=25.49 E-value=80 Score=20.18 Aligned_cols=15 Identities=20% Similarity=0.457 Sum_probs=12.0
Q ss_pred hHHHHHHHHHHHHHH
Q 033207 72 RDEIVNGYVKTLASA 86 (125)
Q Consensus 72 r~emId~Yv~TLAkV 86 (125)
|+||||+..+-|.++
T Consensus 24 K~EIIeA~~~eL~r~ 38 (40)
T PF08776_consen 24 KEEIIEAIRQELSRR 38 (40)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcc
Confidence 678888888888764
No 41
>PRK10957 iron-enterobactin transporter periplasmic binding protein; Provisional
Probab=25.09 E-value=59 Score=25.79 Aligned_cols=18 Identities=28% Similarity=0.327 Sum_probs=14.0
Q ss_pred HHHHHHHHHhCCHHHhhc
Q 033207 78 GYVKTLASALGCEEDAKK 95 (125)
Q Consensus 78 ~Yv~TLAkVLGSeeEAkk 95 (125)
..++.|++++|.+++|++
T Consensus 152 ~~~~~lg~~lg~e~~A~~ 169 (317)
T PRK10957 152 ELATQLGEATGLEKQAAA 169 (317)
T ss_pred HHHHHHHHHhCcHHHHHH
Confidence 336899999999888753
No 42
>PF02664 LuxS: S-Ribosylhomocysteinase (LuxS); InterPro: IPR003815 In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. For example, enteric bacteria use quorum sensing to regulate several traits that allow them to establish and maintain infection in their host, including motility, biofilm formation, and virulence-specific genes []. The LuxS/AI-2 system is one of several quorum sensing mechanisms. AI-2 (autoinducer-2) is a signalling molecule that functions in interspecies communication by regulating niche-specific genes with diverse functions in various bacteria, often in response to population density. LuxS (S-ribosylhomocysteinase; 4.4.1.21 from EC) is an autoinducer-production protein that has a metabolic function as a component of the activated methyl cycle. LuxS converts S-ribosylhomocysteine to homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD); DPD can then spontaneously cyclise to active AI-2 [, ]. LuxS is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases []. ; GO: 0005506 iron ion binding, 0009372 quorum sensing; PDB: 1J6X_B 1VGX_A 1INN_B 1VJE_B 1J6V_A 1VH2_A 1J6W_B 1JOE_B 1J98_A 1IE0_A ....
Probab=24.84 E-value=1.1e+02 Score=24.25 Aligned_cols=34 Identities=26% Similarity=0.458 Sum_probs=28.2
Q ss_pred CCCcceeEEEeeCCCCCCChHHHHHHHHHHHHHHhCCH
Q 033207 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALGCE 90 (125)
Q Consensus 53 Gcdy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVLGSe 90 (125)
||.--+.|++.. .++.+++++...++|..|++-+
T Consensus 81 GCrTGFYli~~g----~~~~~~i~~l~~~~l~~i~~~~ 114 (157)
T PF02664_consen 81 GCRTGFYLILWG----DPSSEDIADLLKETLEFILEFE 114 (157)
T ss_dssp TTSSEEEEEEES----S--HHHHHHHHHHHHHHHHT-S
T ss_pred ccccccEEEEeC----CCCHHHHHHHHHHHHHHHHhcC
Confidence 999999999875 5689999999999999999754
No 43
>cd00636 TroA-like Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between two globular domains linked by a single helix. Many of these proteins also possess a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). The TroA-like proteins differ in their fold and ligand-binding mechanism from the PBPI and PBPII proteins, but are structurally similar, however, to the beta-subunit of the nitrogenase molybdenum-iron protein MoFe. Most TroA-like proteins are encoded by ABC-type operons and appear to function as periplasmic components of ABC transporters in metal ion uptake.
Probab=24.77 E-value=69 Score=20.59 Aligned_cols=25 Identities=32% Similarity=0.430 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHhCCHHHhhccc
Q 033207 73 DEIVNGYVKTLASALGCEEDAKKSI 97 (125)
Q Consensus 73 ~emId~Yv~TLAkVLGSeeEAkkkI 97 (125)
-+=+...++.+++.+|-++.|++-+
T Consensus 97 ~~~~~~~i~~lg~~~~~~~~a~~~~ 121 (148)
T cd00636 97 LENIKESIRLIGKALGKEENAEELI 121 (148)
T ss_pred HHHHHHHHHHHHHHHCChHHHHHHH
Confidence 4455667899999999999888643
No 44
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=24.18 E-value=1.6e+02 Score=20.13 Aligned_cols=35 Identities=11% Similarity=0.013 Sum_probs=25.9
Q ss_pred CCCcceeEEEeeCCCCCCChHHHHHHHHHHHHHHhCC
Q 033207 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALGC 89 (125)
Q Consensus 53 Gcdy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVLGS 89 (125)
.++-.||+|+.|.++ ...+++++.--+.+...++.
T Consensus 45 ~~~~~~~li~vd~~~--~~~~~~~~~i~~~~~~~~~~ 79 (108)
T PF14581_consen 45 EDEQPSLLIGVDFDG--EDIEEIFQEIGRAARPYLPD 79 (108)
T ss_pred cCCCceEEEEEeccC--hhHHHHHHHHHHHhhhcCCC
Confidence 578889999999987 56666776666666666654
No 45
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=23.44 E-value=1.1e+02 Score=23.92 Aligned_cols=48 Identities=23% Similarity=0.332 Sum_probs=34.7
Q ss_pred CCCCcceeEEEeeCCC-------CCCChHHHHHHHHHHHHHHhC-CHHHhhccceE
Q 033207 52 EGCDYKHWLVVMEAPK-------GYPPRDEIVNGYVKTLASALG-CEEDAKKSIYS 99 (125)
Q Consensus 52 ~Gcdy~HWLVvMe~P~-------g~~sr~emId~Yv~TLAkVLG-SeeEAkkkIY~ 99 (125)
.-+.-+++|+=-|.|- +.+....+|..=++++|++.| ++||..+.+|.
T Consensus 193 ~~ip~drillETD~P~~~~~~~~~~~~~p~~i~~~~~~la~~~~~~~e~~~~~~~~ 248 (255)
T PF01026_consen 193 KAIPLDRILLETDAPYLAPDPYRGKPNEPSNIPKVAQALAEIKGISLEELAQIIYE 248 (255)
T ss_dssp HHS-GGGEEEE-BTTSSECTTSTTSE--GGGHHHHHHHHHHHHTSTHHHHHHHHHH
T ss_pred hcCChhhEEEcCCCCcCCccccCCCCCChHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4455677788777664 356788888989999999999 89999888764
No 46
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=23.31 E-value=94 Score=19.25 Aligned_cols=18 Identities=17% Similarity=0.195 Sum_probs=13.7
Q ss_pred eCCCCCCChHHHHHHHHH
Q 033207 64 EAPKGYPPRDEIVNGYVK 81 (125)
Q Consensus 64 e~P~g~~sr~emId~Yv~ 81 (125)
+.|++..|.||+..+|-+
T Consensus 6 ~~Pg~~a~~eel~~Y~~~ 23 (36)
T cd00126 6 ENPGDDASPEELRQYLAA 23 (36)
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 346678999999887754
No 47
>cd00762 NAD_bind_malic_enz NAD(P) binding domain of malic enzyme. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glut
Probab=23.00 E-value=91 Score=26.08 Aligned_cols=16 Identities=44% Similarity=0.675 Sum_probs=13.8
Q ss_pred C-CHHHhhccceEEeec
Q 033207 88 G-CEEDAKKSIYSVSTK 103 (125)
Q Consensus 88 G-SeeEAkkkIY~vSt~ 103 (125)
| ++|||+++||-|.-+
T Consensus 52 Gls~e~A~~~i~~vD~~ 68 (254)
T cd00762 52 GISKEEACKRIWXVDRK 68 (254)
T ss_pred CCCHHHHhccEEEECCC
Confidence 5 999999999988654
No 48
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=22.69 E-value=2.3e+02 Score=21.47 Aligned_cols=46 Identities=28% Similarity=0.482 Sum_probs=35.8
Q ss_pred cccCCCCcceeEEEeeCCCC-----CCChHHHHHHHHHHHHHHhC--CHHHhh
Q 033207 49 SLLEGCDYKHWLVVMEAPKG-----YPPRDEIVNGYVKTLASALG--CEEDAK 94 (125)
Q Consensus 49 ~L~~Gcdy~HWLVvMe~P~g-----~~sr~emId~Yv~TLAkVLG--SeeEAk 94 (125)
-...||...-|++.-..-+| .-|-+.||..++..|.+++. +-+|..
T Consensus 51 ~~V~GCqS~VWl~~~~~~dg~~~f~~dSDa~IvkGl~alL~~~~~g~tp~eI~ 103 (138)
T TIGR03391 51 TELTGCENRVWLGHQVLPDGTLHFYGDSEGRIVRGLLAVLLTAVEGKTPEQLL 103 (138)
T ss_pred hccCCcccceeeeeeecCCCEEEEEecCccHHHHHHHHHHHHHHcCCCHHHHH
Confidence 45789999999986522233 45899999999999999997 566654
No 49
>PRK14048 ferrichrome/ferrioxamine B periplasmic transporter; Provisional
Probab=22.67 E-value=71 Score=26.24 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=13.9
Q ss_pred HHHHHHHHHhCCHHHhhcc
Q 033207 78 GYVKTLASALGCEEDAKKS 96 (125)
Q Consensus 78 ~Yv~TLAkVLGSeeEAkkk 96 (125)
.-++.|++++|.||+|++-
T Consensus 166 ~~i~~lG~i~g~ee~A~~l 184 (374)
T PRK14048 166 DNMRLLGKVFEREEQAEDF 184 (374)
T ss_pred HHHHHHHHHhCCHHHHHHH
Confidence 3467888888888877643
No 50
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=22.24 E-value=29 Score=23.48 Aligned_cols=24 Identities=4% Similarity=0.315 Sum_probs=20.2
Q ss_pred HhCCHHHhhccceEEeeceeeeee
Q 033207 86 ALGCEEDAKKSIYSVSTKYYYAFG 109 (125)
Q Consensus 86 VLGSeeEAkkkIY~vSt~~yfgF~ 109 (125)
|.++.+||++|.+.++.+.-|++.
T Consensus 39 vF~~~~Ea~rC~~~~~~~~~f~y~ 62 (66)
T PF11767_consen 39 VFNDSKEAERCFRAEDGTLFFTYR 62 (66)
T ss_pred EECChHHHHHHHHhcCCCEEEEEE
Confidence 456778999999999999888775
No 51
>COG4594 FecB ABC-type Fe3+-citrate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=21.98 E-value=70 Score=28.03 Aligned_cols=28 Identities=29% Similarity=0.488 Sum_probs=22.8
Q ss_pred CCChHHHHHHHHHHHHHHhCCHHHhhccc
Q 033207 69 YPPRDEIVNGYVKTLASALGCEEDAKKSI 97 (125)
Q Consensus 69 ~~sr~emId~Yv~TLAkVLGSeeEAkkkI 97 (125)
.-+-+|-||++ +|.|+.||-|+|-++++
T Consensus 142 ~~dY~eni~s~-~tIakavgKekE~ekrL 169 (310)
T COG4594 142 NEDYQENIDSF-KTIAKAVGKEKEMEKRL 169 (310)
T ss_pred CccHHHHHHHH-HHHHHHhCchHHHHHHH
Confidence 34567888886 78999999999988775
No 52
>COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms]
Probab=21.67 E-value=1.8e+02 Score=23.46 Aligned_cols=32 Identities=22% Similarity=0.562 Sum_probs=28.9
Q ss_pred CCCcceeEEEeeCCCCCCChHHHHHHHHHHHHHHhC
Q 033207 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALG 88 (125)
Q Consensus 53 Gcdy~HWLVvMe~P~g~~sr~emId~Yv~TLAkVLG 88 (125)
||..-+.|++. |.++.++++|....++..||+
T Consensus 81 GCrTGFYm~l~----G~~~~~~i~~~~~~~m~dvl~ 112 (161)
T COG1854 81 GCRTGFYMILI----GTPTSQDIADVLEATMKDVLK 112 (161)
T ss_pred ccccceEEEEE----CCCCHHHHHHHHHHHHHHHHc
Confidence 89999999987 467889999999999999997
No 53
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=21.47 E-value=83 Score=26.31 Aligned_cols=22 Identities=9% Similarity=0.031 Sum_probs=17.4
Q ss_pred CCCCCCChHHHHHHHHHHHHHH
Q 033207 65 APKGYPPRDEIVNGYVKTLASA 86 (125)
Q Consensus 65 ~P~g~~sr~emId~Yv~TLAkV 86 (125)
+|+...||.|.|+||.+.=--.
T Consensus 11 ~P~~g~TK~dl~~YY~~va~~m 32 (245)
T TIGR02778 11 WPAEGITKLDLADYYAAVAPFM 32 (245)
T ss_pred cCCCCCcHHHHHHHHHHHHHHH
Confidence 4667899999999999864433
No 54
>cd01138 FeuA Periplasmic binding protein FeuA. These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=21.07 E-value=90 Score=23.44 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHhCCHHHhhc
Q 033207 73 DEIVNGYVKTLASALGCEEDAKK 95 (125)
Q Consensus 73 ~emId~Yv~TLAkVLGSeeEAkk 95 (125)
+++. ..++.|++++|-+++|++
T Consensus 97 ~~~~-~~i~~lg~~~g~~~~a~~ 118 (248)
T cd01138 97 SDWE-EQLKEIGKLLNKEDEAEK 118 (248)
T ss_pred CCHH-HHHHHHHHHhCcHHHHHH
Confidence 3443 457999999999888765
No 55
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=21.04 E-value=78 Score=25.97 Aligned_cols=34 Identities=38% Similarity=0.620 Sum_probs=25.8
Q ss_pred CCCcceeEEEeeCCCCCCChHH--HHHHHHHHHHHHhCCH
Q 033207 53 GCDYKHWLVVMEAPKGYPPRDE--IVNGYVKTLASALGCE 90 (125)
Q Consensus 53 Gcdy~HWLVvMe~P~g~~sr~e--mId~Yv~TLAkVLGSe 90 (125)
-+-++|| ++-+|.+|++| +|..|++-||...|++
T Consensus 55 ~lgFeyW----~P~gg~is~~E~~lv~g~v~~la~~~g~~ 90 (196)
T PF07105_consen 55 NLGFEYW----EPTGGTISPAERKLVRGFVKFLASYAGSE 90 (196)
T ss_pred HHHHHHc----cCCCCccCHHHHHHHHHHHHHHHHHhCCH
Confidence 3558999 33345566554 7999999999999987
No 56
>TIGR02145 Fib_succ_major Fibrobacter succinogenes major paralogous domain. This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulfide bond formation, are also consistent with an extracytoplasmic location for this domain. This domain can also be found in small numbers of proteins in Chlorobium tepidum and Bacteroides thetaiotaomicron.
Probab=20.89 E-value=54 Score=25.49 Aligned_cols=36 Identities=31% Similarity=0.569 Sum_probs=25.6
Q ss_pred ceeEEEee--CCCC--CCChHHHHHHHHHHHHHHhCCHHHhhccc
Q 033207 57 KHWLVVME--APKG--YPPRDEIVNGYVKTLASALGCEEDAKKSI 97 (125)
Q Consensus 57 ~HWLVvMe--~P~g--~~sr~emId~Yv~TLAkVLGSeeEAkkkI 97 (125)
=-|-.+|| -|.| .||++| -++|.+.+|..+.|-.++
T Consensus 50 Y~w~aa~~~~cP~GWhlPs~~E-----w~~L~~~~g~~~~ag~~L 89 (171)
T TIGR02145 50 YTWAAAMDSICPEGWHLPSTTE-----WNTLFDAVGGKVNAGGKL 89 (171)
T ss_pred EEHHHhccCcCCCCCCCCCHHH-----HHHHHHHhccccchhhhh
Confidence 36889999 4998 899999 356666777655544443
No 57
>KOG4420 consensus Uncharacterized conserved protein (Ganglioside-induced differentiation associated protein 1, GDAP1) [Function unknown]
Probab=20.46 E-value=65 Score=28.35 Aligned_cols=74 Identities=19% Similarity=0.267 Sum_probs=51.9
Q ss_pred cccCCCCcceeEEEeeCCCC----------CCChHHHHHHHHHH------HHHHhCCHHHhhccceEEeec----eeeee
Q 033207 49 SLLEGCDYKHWLVVMEAPKG----------YPPRDEIVNGYVKT------LASALGCEEDAKKSIYSVSTK----YYYAF 108 (125)
Q Consensus 49 ~L~~Gcdy~HWLVvMe~P~g----------~~sr~emId~Yv~T------LAkVLGSeeEAkkkIY~vSt~----~yfgF 108 (125)
.|--|-.++-|...|++-++ .++-.|||||-++| |---+||.+++++-+|..--+ .-|--
T Consensus 58 ~l~~geh~epwFmrlNp~gevPVl~~g~~II~d~tqIIdYvErtf~ger~l~pe~~S~~~d~~l~~e~~l~~lpm~~~t~ 137 (325)
T KOG4420|consen 58 SLPQGEHKEPWFMRLNPGGEVPVLIHGDNIISDYTQIIDYVERTFTGERVLMPEVGSLQHDRVLQYEELLDALPMDAYTH 137 (325)
T ss_pred cCccccccCchheecCCCCCCceEecCCeecccHHHHHHHHHHhhcccccccccccccccHHHHHHHHHHHhcCcchhhc
Confidence 44457788889999996442 36889999999984 556678999999988865321 23446
Q ss_pred eeeeehhhc-cccCC
Q 033207 109 GCKFLKILL-IRSDP 122 (125)
Q Consensus 109 ~c~I~Ee~S-lk~lP 122 (125)
||-|.-|+. ..-.|
T Consensus 138 g~~lh~eL~~~s~iP 152 (325)
T KOG4420|consen 138 GCILHPELTTDSMIP 152 (325)
T ss_pred cccccchhhccccCc
Confidence 777777766 44444
No 58
>PRK15019 CsdA-binding activator; Provisional
Probab=20.24 E-value=2.6e+02 Score=21.45 Aligned_cols=46 Identities=24% Similarity=0.460 Sum_probs=35.7
Q ss_pred cccCCCCcceeEEEeeCCCC-----CCChHHHHHHHHHHHHHHhC--CHHHhh
Q 033207 49 SLLEGCDYKHWLVVMEAPKG-----YPPRDEIVNGYVKTLASALG--CEEDAK 94 (125)
Q Consensus 49 ~L~~Gcdy~HWLVvMe~P~g-----~~sr~emId~Yv~TLAkVLG--SeeEAk 94 (125)
-...||...-|++....-+| .-|-+.||..++..|..++. +-+|..
T Consensus 56 ~~V~GCqS~VWL~~~~~~dg~~~f~~dSDA~IvkGl~alL~~~~~g~tp~eIl 108 (147)
T PRK15019 56 KEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQ 108 (147)
T ss_pred CcCCCcccceeeeeeecCCCEEEEEeeCccHHHHHHHHHHHHHHcCCCHHHHH
Confidence 56789999999975543333 34899999999999999997 566654
Done!