Query 032201
Match_columns 145
No_of_seqs 89 out of 91
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 10:57:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032201.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032201hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05922 Inhibitor_I9: Peptida 91.4 0.28 6E-06 32.1 3.3 61 80-145 2-67 (82)
2 PF12674 Zn_ribbon_2: Putative 60.5 12 0.00027 26.6 3.3 29 91-119 41-70 (81)
3 TIGR03868 F420-O_ABCperi propo 53.2 16 0.00035 28.9 3.1 26 93-119 126-151 (287)
4 cd01143 YvrC Periplasmic bindi 47.1 19 0.00042 26.4 2.5 22 98-119 97-118 (195)
5 cd01148 TroA_a Metal binding p 46.1 30 0.00065 27.3 3.7 25 92-117 123-147 (284)
6 COG0614 FepB ABC-type Fe3+-hyd 45.8 15 0.00033 28.9 1.9 23 98-120 151-173 (319)
7 cd01144 BtuF Cobalamin binding 45.0 16 0.00034 28.1 1.8 25 94-119 91-115 (245)
8 KOG1276 Protoporphyrinogen oxi 44.0 19 0.00041 33.9 2.6 45 65-116 382-427 (491)
9 PF10847 DUF2656: Protein of u 44.0 38 0.00083 27.0 3.9 30 76-109 41-70 (132)
10 PF01497 Peripla_BP_2: Peripla 42.5 61 0.0013 24.3 4.7 23 96-118 96-118 (238)
11 cd01139 TroA_f Periplasmic bin 41.8 44 0.00096 27.3 4.1 25 93-118 130-154 (342)
12 PRK10576 iron-hydroxamate tran 41.7 28 0.00061 28.3 3.0 24 94-117 127-150 (292)
13 PF13961 DUF4219: Domain of un 40.7 1.8 3.9E-05 25.1 -3.0 14 72-85 1-14 (27)
14 cd01147 HemV-2 Metal binding p 39.5 32 0.0007 26.5 2.8 21 98-118 113-133 (262)
15 PRK11411 fecB iron-dicitrate t 37.6 38 0.00082 27.5 3.1 26 93-119 134-159 (303)
16 cd01146 FhuD Fe3+-siderophore 37.4 60 0.0013 25.2 4.1 25 93-118 97-121 (256)
17 KOG1412 Aspartate aminotransfe 37.4 46 0.00099 30.7 3.8 53 62-132 173-225 (410)
18 cd01149 HutB Hemin binding pro 35.1 47 0.001 25.6 3.1 21 98-118 96-116 (235)
19 KOG4079 Putative mitochondrial 35.0 25 0.00055 28.8 1.7 40 91-133 93-135 (169)
20 TIGR03659 IsdE heme ABC transp 34.4 43 0.00094 27.0 3.0 22 96-117 125-146 (289)
21 cd01142 TroA_e Periplasmic bin 33.0 47 0.001 26.3 2.9 22 98-119 123-144 (289)
22 COG1448 TyrB Aspartate/tyrosin 32.4 59 0.0013 30.0 3.7 57 64-138 169-225 (396)
23 cd01140 FatB Siderophore bindi 32.2 50 0.0011 25.8 2.9 20 98-117 109-128 (270)
24 PRK03379 vitamin B12-transport 31.3 44 0.00096 26.7 2.5 24 93-117 105-128 (260)
25 COG4607 CeuA ABC-type enteroch 30.1 33 0.00072 30.8 1.7 21 101-121 158-178 (320)
26 PRK11630 hypothetical protein; 30.0 33 0.00072 27.5 1.6 36 102-142 17-53 (206)
27 KOG1670 Translation initiation 27.6 99 0.0021 26.4 4.1 28 79-111 110-137 (212)
28 cd00636 TroA-like Helical back 26.7 70 0.0015 21.1 2.5 24 96-119 98-121 (148)
29 KOG1257 NADP+-dependent malic 25.8 65 0.0014 31.1 2.9 24 101-125 329-353 (582)
30 PRK10957 iron-enterobactin tra 25.2 67 0.0014 26.1 2.6 17 101-117 153-169 (317)
31 cd01851 GBP Guanylate-binding 25.1 92 0.002 24.9 3.3 32 78-109 59-91 (224)
32 TIGR00013 taut 4-oxalocrotonat 25.0 63 0.0014 20.3 1.9 44 91-134 14-57 (63)
33 PF08006 DUF1700: Protein of u 24.9 96 0.0021 23.9 3.3 26 90-115 18-46 (181)
34 KOG0578 p21-activated serine/t 24.5 26 0.00055 33.4 0.1 18 122-140 408-425 (550)
35 PF01026 TatD_DNase: TatD rela 24.3 1.1E+02 0.0023 24.6 3.6 51 71-121 191-248 (255)
36 cd01138 FeuA Periplasmic bindi 24.2 80 0.0017 24.4 2.7 19 99-117 100-118 (248)
37 PRK14048 ferrichrome/ferrioxam 24.1 73 0.0016 26.8 2.7 20 100-119 166-185 (374)
38 PF04970 LRAT: Lecithin retino 23.8 41 0.00088 24.3 1.0 22 64-85 7-28 (125)
39 PRK02260 S-ribosylhomocysteina 23.6 99 0.0021 25.0 3.2 31 74-109 81-111 (158)
40 PF01282 Ribosomal_S24e: Ribos 23.3 1.6E+02 0.0036 20.9 4.0 42 82-130 3-44 (84)
41 cd00954 NAL N-Acetylneuraminic 22.9 1.8E+02 0.0038 24.0 4.7 50 87-144 105-154 (288)
42 PRK02220 4-oxalocrotonate taut 22.6 1.1E+02 0.0024 19.1 2.8 43 90-132 13-55 (61)
43 cd00491 4Oxalocrotonate_Tautom 22.3 90 0.0019 19.1 2.2 41 91-131 13-53 (58)
44 PF07105 DUF1367: Protein of u 21.7 1E+02 0.0022 25.9 3.0 36 71-112 53-90 (196)
45 PF14581 SseB_C: SseB protein 21.6 1.9E+02 0.0041 20.3 4.1 34 74-110 45-78 (108)
46 TIGR00683 nanA N-acetylneurami 21.1 2E+02 0.0043 24.0 4.6 59 76-144 96-154 (290)
47 PF01876 RNase_P_p30: RNase P 21.1 80 0.0017 23.6 2.1 17 103-119 130-147 (150)
48 PF02664 LuxS: S-Ribosylhomocy 21.0 2.1E+02 0.0046 23.2 4.6 34 74-112 81-114 (157)
49 COG1854 LuxS LuxS protein invo 20.9 1.8E+02 0.004 23.9 4.3 82 12-110 22-112 (161)
50 PF08776 VASP_tetra: VASP tetr 20.7 1.2E+02 0.0025 19.9 2.5 15 94-108 24-38 (40)
51 PF08947 BPS: BPS (Between PH 20.6 49 0.0011 22.5 0.8 10 80-89 7-16 (49)
52 PLN02150 terpene synthase/cycl 20.4 49 0.0011 23.9 0.9 20 98-121 10-30 (96)
53 PRK08187 pyruvate kinase; Vali 20.3 99 0.0021 28.8 3.0 30 89-118 434-482 (493)
No 1
>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=91.40 E-value=0.28 Score=32.08 Aligned_cols=61 Identities=20% Similarity=0.394 Sum_probs=35.5
Q ss_pred eEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCH----HHHhcc-cceeeecceeeeeeeeCHHHHhhhhCC
Q 032201 80 WLIVMEFPKDPAPTREQMIETYLNTLATVLGSM----EEAKKN-MYAFSTTTYTGFQCTVSEETSEKFKGV 145 (145)
Q Consensus 80 WLVvMe~P~~~~psr~emId~Yv~TLAkVLGSE----EEAKkk-IYsvSt~tyfGF~c~I~EE~S~klk~l 145 (145)
.+|+|+.+. +.++..+...+-++..+.+- ...+-+ +|.+.. .--||.+.++++..++|+..
T Consensus 2 YIV~~k~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~-~~~Gfs~~l~~~~i~~L~~~ 67 (82)
T PF05922_consen 2 YIVVFKDDA----SAASSFSSHKSWQASILKSALKSASSINAKVLYSYDN-AFNGFSAKLSEEEIEKLRKD 67 (82)
T ss_dssp EEEEE-TTS----THHCHHHHHHHHHH----HHHHTH-TTT-EEEEEESS-TSSEEEEEE-HHHHHHHHTS
T ss_pred EEEEECCCC----CcchhHHHHHHHHHHHHhhhhhhhcccCCceEEEEee-eEEEEEEEeCHHHHHHHHcC
Confidence 478888663 33334556666666555432 122333 676766 78999999999999999863
No 2
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=60.46 E-value=12 Score=26.64 Aligned_cols=29 Identities=38% Similarity=0.391 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHHHHHHhC-CHHHHhccc
Q 032201 91 APTREQMIETYLNTLATVLG-SMEEAKKNM 119 (145)
Q Consensus 91 ~psr~emId~Yv~TLAkVLG-SEEEAKkkI 119 (145)
+-|.+|||+.-++-+++.-| ++|||++-+
T Consensus 41 ~~t~eemie~~~~~~~~~~~~~~~~a~~~~ 70 (81)
T PF12674_consen 41 DITMEEMIEFCVPFMDEFNGMTPEEARKMM 70 (81)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 56899999999999999987 899998753
No 3
>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=53.20 E-value=16 Score=28.93 Aligned_cols=26 Identities=12% Similarity=0.240 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhccc
Q 032201 93 TREQMIETYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 93 sr~emId~Yv~TLAkVLGSEEEAKkkI 119 (145)
+.+++.+. ++.||+++|.||+|++-|
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 789999999999987643
No 4
>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=47.13 E-value=19 Score=26.38 Aligned_cols=22 Identities=27% Similarity=0.388 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhCCHHHHhccc
Q 032201 98 IETYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkkI 119 (145)
+.-.++.|++++|-+|+|++-|
T Consensus 97 ~~~~~~~lg~~~g~~~~a~~~~ 118 (195)
T cd01143 97 IYDQIELIGKITGAEEEAEKLV 118 (195)
T ss_pred HHHHHHHHHHHhCChHHHHHHH
Confidence 3346889999999999887743
No 5
>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=46.10 E-value=30 Score=27.34 Aligned_cols=25 Identities=16% Similarity=0.306 Sum_probs=18.4
Q ss_pred CCHHHHHHHHHHHHHHHhCCHHHHhc
Q 032201 92 PTREQMIETYLNTLATVLGSMEEAKK 117 (145)
Q Consensus 92 psr~emId~Yv~TLAkVLGSEEEAKk 117 (145)
.+.+++.+ .++.+++++|.||+|++
T Consensus 123 ~~~~~~~~-~~~~lg~~~g~e~~A~~ 147 (284)
T cd01148 123 ATLDDVYN-DIRNLGKIFDVEDRADK 147 (284)
T ss_pred CCHHHHHH-HHHHHHHHhCCHhHHHH
Confidence 34555555 68889999999888765
No 6
>COG0614 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=45.78 E-value=15 Score=28.91 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHhCCHHHHhcccc
Q 032201 98 IETYLNTLATVLGSMEEAKKNMY 120 (145)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkkIY 120 (145)
+.--++++|+++|.|++|++-|-
T Consensus 151 ~~~~i~~lg~~~g~e~~A~~li~ 173 (319)
T COG0614 151 IKEQIRLLGKALGKEEKAEELIA 173 (319)
T ss_pred HHHHHHHHHHHhCcHHHHHHHHH
Confidence 44567899999999999987553
No 7
>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=45.01 E-value=16 Score=28.14 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHhccc
Q 032201 94 REQMIETYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 94 r~emId~Yv~TLAkVLGSEEEAKkkI 119 (145)
.+++. -.+++||+++|.+|+|++.+
T Consensus 91 ~~~~~-~~~~~lg~~~g~~~~a~~~~ 115 (245)
T cd01144 91 LDDIL-ADIRRLGTLAGRPARAEELA 115 (245)
T ss_pred HHHHH-HHHHHHHHHhCChhHHHHHH
Confidence 34433 46899999999999996543
No 8
>KOG1276 consensus Protoporphyrinogen oxidase [Coenzyme transport and metabolism]
Probab=44.04 E-value=19 Score=33.91 Aligned_cols=45 Identities=22% Similarity=0.437 Sum_probs=36.4
Q ss_pred CCCcccccCCCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhC-CHHHHh
Q 032201 65 EPRETIMLPGCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLG-SMEEAK 116 (145)
Q Consensus 65 ~~~~tiLf~GcDy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVLG-SEEEAK 116 (145)
.++-|.+.-||-+.||-+ -.+|++|.++.--+-|.+-|| ++|++.
T Consensus 382 s~~vtvm~gg~~~~n~~~-------~~~S~ee~~~~v~~alq~~Lgi~~~P~~ 427 (491)
T KOG1276|consen 382 SPKVTVMMGGGGSTNTSL-------AVPSPEELVNAVTSALQKMLGISNKPVS 427 (491)
T ss_pred CceEEEEecccccccCcC-------CCCCHHHHHHHHHHHHHHHhCCCCCccc
Confidence 447777888888887754 478999999999999999999 666653
No 9
>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=44.03 E-value=38 Score=26.99 Aligned_cols=30 Identities=17% Similarity=0.418 Sum_probs=25.8
Q ss_pred CCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHh
Q 032201 76 DYNHWLIVMEFPKDPAPTREQMIETYLNTLATVL 109 (145)
Q Consensus 76 Dy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVL 109 (145)
+--||||-++ ..-+++||-...++++.+.=
T Consensus 41 ~hPHW~v~i~----s~lsp~~~~~~~v~aw~~~R 70 (132)
T PF10847_consen 41 NHPHWMVEIE----SDLSPDEMAEELVRAWKQYR 70 (132)
T ss_pred cCCceEEEec----ccCCHHHHHHHHHHHHHHHH
Confidence 5689999999 57789999999999998764
No 10
>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=42.52 E-value=61 Score=24.34 Aligned_cols=23 Identities=17% Similarity=0.242 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHhCCHHHHhcc
Q 032201 96 QMIETYLNTLATVLGSMEEAKKN 118 (145)
Q Consensus 96 emId~Yv~TLAkVLGSEEEAKkk 118 (145)
+-+.-.++.||+++|-+++|++-
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 66788899999999999998754
No 11
>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=41.79 E-value=44 Score=27.30 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=18.5
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhcc
Q 032201 93 TREQMIETYLNTLATVLGSMEEAKKN 118 (145)
Q Consensus 93 sr~emId~Yv~TLAkVLGSEEEAKkk 118 (145)
+-+++.+ -++.||+++|.+|+|++-
T Consensus 130 ~~~~~~~-~i~~lg~i~g~~~~A~~l 154 (342)
T cd01139 130 PLKNTTP-SMRLLGKALGREERAEEF 154 (342)
T ss_pred hhhhHHH-HHHHHHHHhCCHHHHHHH
Confidence 4455554 588999999999988653
No 12
>PRK10576 iron-hydroxamate transporter substrate-binding subunit; Provisional
Probab=41.69 E-value=28 Score=28.27 Aligned_cols=24 Identities=21% Similarity=0.080 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHhc
Q 032201 94 REQMIETYLNTLATVLGSMEEAKK 117 (145)
Q Consensus 94 r~emId~Yv~TLAkVLGSEEEAKk 117 (145)
.-+.+...++.|++++|.|++|++
T Consensus 127 ~~~~~~~~i~~lg~ilG~e~~A~~ 150 (292)
T PRK10576 127 PLAVARKSLVELAQRLNLEAAAET 150 (292)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHH
Confidence 345667789999999999998865
No 13
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=40.68 E-value=1.8 Score=25.11 Aligned_cols=14 Identities=43% Similarity=0.942 Sum_probs=11.4
Q ss_pred cCCCCCceeEEEEc
Q 032201 72 LPGCDYNHWLIVME 85 (145)
Q Consensus 72 f~GcDy~HWLVvMe 85 (145)
|+|-+|.+|-+.|.
T Consensus 1 l~g~NY~~W~~~M~ 14 (27)
T PF13961_consen 1 LDGTNYSTWKIRMK 14 (27)
T ss_pred CCccCHHHHHHHHH
Confidence 67889999987774
No 14
>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=39.47 E-value=32 Score=26.50 Aligned_cols=21 Identities=29% Similarity=0.341 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHhCCHHHHhcc
Q 032201 98 IETYLNTLATVLGSMEEAKKN 118 (145)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkk 118 (145)
+...++.||+++|.+++|++-
T Consensus 113 ~~~~i~~lg~~~g~~~~a~~~ 133 (262)
T cd01147 113 TPEQIRLLGKVLGKEERAEEL 133 (262)
T ss_pred HHHHHHHHHHHhCCHHHHHHH
Confidence 457789999999999988753
No 15
>PRK11411 fecB iron-dicitrate transporter substrate-binding subunit; Provisional
Probab=37.65 E-value=38 Score=27.52 Aligned_cols=26 Identities=19% Similarity=0.328 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhccc
Q 032201 93 TREQMIETYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 93 sr~emId~Yv~TLAkVLGSEEEAKkkI 119 (145)
+.++..+ .++.||+++|.|++|++-|
T Consensus 134 ~~~~~~~-~i~~lg~i~g~e~~a~~~i 159 (303)
T PRK11411 134 TYQENLQ-SAAIIGEVLGKKREMQARI 159 (303)
T ss_pred CHHHHHH-HHHHHHHHhCCHHHHHHHH
Confidence 5566655 4688999999999998543
No 16
>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=37.41 E-value=60 Score=25.24 Aligned_cols=25 Identities=32% Similarity=0.262 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhcc
Q 032201 93 TREQMIETYLNTLATVLGSMEEAKKN 118 (145)
Q Consensus 93 sr~emId~Yv~TLAkVLGSEEEAKkk 118 (145)
+.+++. ..++.|++++|-+|+|+.-
T Consensus 97 ~~~~~~-~~i~~lg~~~g~~~~a~~~ 121 (256)
T cd01146 97 WLAEWK-ENLRLIAKALGKEEEAEKL 121 (256)
T ss_pred cHHHHH-HHHHHHHHHhCcHHHHHHH
Confidence 344444 4788999999988877543
No 17
>KOG1412 consensus Aspartate aminotransferase/Glutamic oxaloacetic transaminase AAT2/GOT1 [Amino acid transport and metabolism]
Probab=37.37 E-value=46 Score=30.71 Aligned_cols=53 Identities=36% Similarity=0.623 Sum_probs=42.1
Q ss_pred CCCCCCcccccCCCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeeee
Q 032201 62 SSNEPRETIMLPGCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQC 132 (145)
Q Consensus 62 s~~~~~~tiLf~GcDy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c 132 (145)
.+-|.+..+++.+|-+| |.+-+||+||-+. +|.|+ .+|+++-+=-..|+||-.
T Consensus 173 ~~APe~si~iLhaCAhN--------PTGmDPT~EQW~q-----ia~vi-----k~k~lf~fFDiAYQGfAS 225 (410)
T KOG1412|consen 173 ESAPEGSIIILHACAHN--------PTGMDPTREQWKQ-----IADVI-----KSKNLFPFFDIAYQGFAS 225 (410)
T ss_pred hhCCCCcEEeeeccccC--------CCCCCCCHHHHHH-----HHHHH-----HhcCceeeeehhhccccc
Confidence 33588889999999664 8899999999764 46676 567788887789999953
No 18
>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=35.11 E-value=47 Score=25.59 Aligned_cols=21 Identities=24% Similarity=0.289 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHhCCHHHHhcc
Q 032201 98 IETYLNTLATVLGSMEEAKKN 118 (145)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkk 118 (145)
+..-++.|++++|.|++|++-
T Consensus 96 ~~~~~~~lg~i~g~e~~A~~l 116 (235)
T cd01149 96 LLTKIRQVAQALGVPEKGEAL 116 (235)
T ss_pred HHHHHHHHHHHhCCHHHHHHH
Confidence 444688999999999988753
No 19
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=35.02 E-value=25 Score=28.84 Aligned_cols=40 Identities=25% Similarity=0.254 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHHHHH---HhCCHHHHhcccceeeecceeeeeee
Q 032201 91 APTREQMIETYLNTLAT---VLGSMEEAKKNMYAFSTTTYTGFQCT 133 (145)
Q Consensus 91 ~psr~emId~Yv~TLAk---VLGSEEEAKkkIYsvSt~tyfGF~c~ 133 (145)
.-+++||++..++||.| +|..||+-|+. -+.-..||..|+
T Consensus 93 ~~~r~eI~~hl~K~lGKtee~lr~Ee~ek~~---k~nPAnFG~~c~ 135 (169)
T KOG4079|consen 93 GMKREEIEKHLAKTLGKTEEVLRREELEKIA---KLNPANFGSKCE 135 (169)
T ss_pred cccHHHHHHHHHHHhCccHHHHhHHHHHHHh---hcChhhhccccc
Confidence 55799999987777764 45444444433 234567777764
No 20
>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=34.40 E-value=43 Score=27.00 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHhCCHHHHhc
Q 032201 96 QMIETYLNTLATVLGSMEEAKK 117 (145)
Q Consensus 96 emId~Yv~TLAkVLGSEEEAKk 117 (145)
+-+...++.+|+++|.+++|++
T Consensus 125 ~~~~~~i~~lg~~~G~~~~A~~ 146 (289)
T TIGR03659 125 DGMKKSITELGEKYGREEQAEK 146 (289)
T ss_pred HHHHHHHHHHHHHhCCHHHHHH
Confidence 3355568999999999998865
No 21
>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=32.99 E-value=47 Score=26.33 Aligned_cols=22 Identities=23% Similarity=0.372 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHhCCHHHHhccc
Q 032201 98 IETYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkkI 119 (145)
+...++.||+++|.+++|++-|
T Consensus 123 ~~~~~~~lg~~~g~~~~a~~~~ 144 (289)
T cd01142 123 VKLTIALLGELLGRQEKAEALV 144 (289)
T ss_pred HHHHHHHHHHHhCcHHHHHHHH
Confidence 5567899999999999988643
No 22
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=32.42 E-value=59 Score=29.97 Aligned_cols=57 Identities=28% Similarity=0.532 Sum_probs=39.6
Q ss_pred CCCCcccccCCCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeeeeeeCHHH
Q 032201 64 NEPRETIMLPGCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEET 138 (145)
Q Consensus 64 ~~~~~tiLf~GcDy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~I~EE~ 138 (145)
-+.++.+|+-|| ...|.+-+||++|=.+ |+.++ +++.+--+=--.|+||+.-++|+.
T Consensus 169 a~~~~vvLLH~C--------cHNPTG~D~t~~qW~~-----l~~~~-----~~r~lip~~D~AYQGF~~GleeDa 225 (396)
T COG1448 169 APEGSVVLLHGC--------CHNPTGIDPTEEQWQE-----LADLI-----KERGLIPFFDIAYQGFADGLEEDA 225 (396)
T ss_pred CCCCCEEEEecC--------CCCCCCCCCCHHHHHH-----HHHHH-----HHcCCeeeeehhhhhhccchHHHH
Confidence 377788899999 5689999999998643 23333 134444443449999999987764
No 23
>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=32.15 E-value=50 Score=25.80 Aligned_cols=20 Identities=35% Similarity=0.626 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHhCCHHHHhc
Q 032201 98 IETYLNTLATVLGSMEEAKK 117 (145)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKk 117 (145)
+...++.||+++|.+|+|++
T Consensus 109 ~~~~i~~lg~~~g~~~~a~~ 128 (270)
T cd01140 109 VKQNIETLGKIFGKEEEAKE 128 (270)
T ss_pred HHHHHHHHHHHhCcHHHHHH
Confidence 34569999999999988864
No 24
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=31.30 E-value=44 Score=26.75 Aligned_cols=24 Identities=33% Similarity=0.278 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhc
Q 032201 93 TREQMIETYLNTLATVLGSMEEAKK 117 (145)
Q Consensus 93 sr~emId~Yv~TLAkVLGSEEEAKk 117 (145)
+-++ +...+++|++++|.+++|++
T Consensus 105 ~~~~-~~~~i~~lg~~~g~~~~A~~ 128 (260)
T PRK03379 105 SIEQ-IANALRQLAPWSPQPEKAEQ 128 (260)
T ss_pred CHHH-HHHHHHHHHHHcCCHHHHHH
Confidence 3444 34468899999999988855
No 25
>COG4607 CeuA ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=30.09 E-value=33 Score=30.77 Aligned_cols=21 Identities=33% Similarity=0.485 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCHHHHhcccce
Q 032201 101 YLNTLATVLGSMEEAKKNMYA 121 (145)
Q Consensus 101 Yv~TLAkVLGSEEEAKkkIYs 121 (145)
=+++|+++.|-|+|||+.+=+
T Consensus 158 n~e~Lg~IFgkE~eAk~~~~~ 178 (320)
T COG4607 158 NIETLGKIFGKEEEAKELLAD 178 (320)
T ss_pred HHHHHHHHhCchHHHHHHHHH
Confidence 467999999999999987643
No 26
>PRK11630 hypothetical protein; Provisional
Probab=29.95 E-value=33 Score=27.53 Aligned_cols=36 Identities=14% Similarity=0.391 Sum_probs=26.3
Q ss_pred HHHHHHHhCCHHHHhcccceeeecceeeeeeee-CHHHHhhh
Q 032201 102 LNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTV-SEETSEKF 142 (145)
Q Consensus 102 v~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~I-~EE~S~kl 142 (145)
++..+++| .+-.|-.+-|+|-||.+|.. +++..++|
T Consensus 17 i~~a~~~L-----~~G~vi~~PTdTvYgL~~d~~n~~Av~~l 53 (206)
T PRK11630 17 INQAVEIV-----RKGGVIVYPTDSGYALGCKIEDKNAMERI 53 (206)
T ss_pred HHHHHHHH-----HCCCEEEEeCCChHhhhcCCCCHHHHHHH
Confidence 34445555 23469999999999999997 66777666
No 27
>KOG1670 consensus Translation initiation factor 4F, cap-binding subunit (eIF-4E) and related cap-binding proteins [Translation, ribosomal structure and biogenesis]
Probab=27.61 E-value=99 Score=26.35 Aligned_cols=28 Identities=29% Similarity=0.618 Sum_probs=23.1
Q ss_pred eeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCC
Q 032201 79 HWLIVMEFPKDPAPTREQMIETYLNTLATVLGS 111 (145)
Q Consensus 79 HWLVvMe~P~~~~psr~emId~Yv~TLAkVLGS 111 (145)
.|+|++++- +++++=...+.||...+|-
T Consensus 110 rW~~~~~k~-----~k~~lD~~WL~tLlalIGE 137 (212)
T KOG1670|consen 110 RWLITVPKS-----GKAELDELWLETLLALIGE 137 (212)
T ss_pred eEEEEecCc-----chhhHHHHHHHHHHHHHhh
Confidence 799988742 6788888899999999984
No 28
>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=26.71 E-value=70 Score=21.12 Aligned_cols=24 Identities=21% Similarity=0.356 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHhCCHHHHhccc
Q 032201 96 QMIETYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 96 emId~Yv~TLAkVLGSEEEAKkkI 119 (145)
+=+.-.++.+++.||-+++|++-+
T Consensus 98 ~~~~~~i~~lg~~~~~~~~a~~~~ 121 (148)
T cd00636 98 ENIKESIRLIGKALGKEENAEELI 121 (148)
T ss_pred HHHHHHHHHHHHHHCChHHHHHHH
Confidence 336677899999999999998754
No 29
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=25.81 E-value=65 Score=31.09 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=17.4
Q ss_pred HHHHHHHHhC-CHHHHhcccceeeec
Q 032201 101 YLNTLATVLG-SMEEAKKNMYAFSTT 125 (145)
Q Consensus 101 Yv~TLAkVLG-SEEEAKkkIYsvSt~ 125 (145)
-+..+.+- | +||||+++||=+.-+
T Consensus 329 ~v~~m~~~-Gl~~eeA~kkIwlvD~~ 353 (582)
T KOG1257|consen 329 IVMAMVKE-GLSEEEARKKIWLVDSK 353 (582)
T ss_pred HHHHHHHc-CCCHHHHhccEEEEecC
Confidence 34444544 7 999999999987643
No 30
>PRK10957 iron-enterobactin transporter periplasmic binding protein; Provisional
Probab=25.18 E-value=67 Score=26.14 Aligned_cols=17 Identities=18% Similarity=0.188 Sum_probs=14.4
Q ss_pred HHHHHHHHhCCHHHHhc
Q 032201 101 YLNTLATVLGSMEEAKK 117 (145)
Q Consensus 101 Yv~TLAkVLGSEEEAKk 117 (145)
.++.|+++||.+|+|++
T Consensus 153 ~~~~lg~~lg~e~~A~~ 169 (317)
T PRK10957 153 LATQLGEATGLEKQAAA 169 (317)
T ss_pred HHHHHHHHhCcHHHHHH
Confidence 36899999999998864
No 31
>cd01851 GBP Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein
Probab=25.12 E-value=92 Score=24.91 Aligned_cols=32 Identities=22% Similarity=0.290 Sum_probs=25.3
Q ss_pred ceeEEEEcCCCCCCCCHHH-HHHHHHHHHHHHh
Q 032201 78 NHWLIVMEFPKDPAPTREQ-MIETYLNTLATVL 109 (145)
Q Consensus 78 ~HWLVvMe~P~~~~psr~e-mId~Yv~TLAkVL 109 (145)
++++|+||.|+-..+.+.+ +.|.-+-.|+..|
T Consensus 59 ~~~v~~lDteG~~~~~~~~~~~~~~~~~l~~ll 91 (224)
T cd01851 59 EHAVLLLDTEGTDGRERGEFEDDARLFALATLL 91 (224)
T ss_pred cceEEEEecCCcCccccCchhhhhHHHHHHHHH
Confidence 5899999999987887777 7777777776655
No 32
>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=24.95 E-value=63 Score=20.32 Aligned_cols=44 Identities=18% Similarity=0.182 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeeeeee
Q 032201 91 APTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTV 134 (145)
Q Consensus 91 ~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~I 134 (145)
.-.|++++..-.+.|+++||.-+|+-.-+..-.-...||||=..
T Consensus 14 ~eqK~~l~~~it~~l~~~lg~~~~~v~V~i~e~~~~~w~~gG~~ 57 (63)
T TIGR00013 14 DEQKRQLIEGVTEAMAETLGANLESIVVIIDEMPKNNYGIGGEL 57 (63)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcccEEEEEEEcCHHHeeECCEE
Confidence 44677888888999999999665555444443444677776443
No 33
>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=24.93 E-value=96 Score=23.86 Aligned_cols=26 Identities=35% Similarity=0.496 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHHHHHHHh--C-CHHHH
Q 032201 90 PAPTREQMIETYLNTLATVL--G-SMEEA 115 (145)
Q Consensus 90 ~~psr~emId~Yv~TLAkVL--G-SEEEA 115 (145)
|+-.++|++++|.+-..... | ||||+
T Consensus 18 p~~e~~e~l~~Y~e~f~d~~~~G~sEeei 46 (181)
T PF08006_consen 18 PEEEREEILEYYEEYFDDAGEEGKSEEEI 46 (181)
T ss_pred CHHHHHHHHHHHHHHHHHhhhCCCCHHHH
Confidence 34468899999987776543 3 56654
No 34
>KOG0578 consensus p21-activated serine/threonine protein kinase [Signal transduction mechanisms]
Probab=24.54 E-value=26 Score=33.44 Aligned_cols=18 Identities=39% Similarity=0.445 Sum_probs=14.5
Q ss_pred eeecceeeeeeeeCHHHHh
Q 032201 122 FSTTTYTGFQCTVSEETSE 140 (145)
Q Consensus 122 vSt~tyfGF~c~I~EE~S~ 140 (145)
|.- +.||||+.|+++..+
T Consensus 408 vKl-tDFGFcaqi~~~~~K 425 (550)
T KOG0578|consen 408 VKL-TDFGFCAQISEEQSK 425 (550)
T ss_pred EEE-eeeeeeeccccccCc
Confidence 344 799999999999863
No 35
>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=24.33 E-value=1.1e+02 Score=24.60 Aligned_cols=51 Identities=22% Similarity=0.359 Sum_probs=38.1
Q ss_pred ccCCCCCceeEEEEcCCC------CCCCCHHHHHHHHHHHHHHHhC-CHHHHhcccce
Q 032201 71 MLPGCDYNHWLIVMEFPK------DPAPTREQMIETYLNTLATVLG-SMEEAKKNMYA 121 (145)
Q Consensus 71 Lf~GcDy~HWLVvMe~P~------~~~psr~emId~Yv~TLAkVLG-SEEEAKkkIYs 121 (145)
+..-+.-+++||=.|.|- .+.+...++|..=+++||++.| ++||+.+.+|.
T Consensus 191 ~~~~ip~drillETD~P~~~~~~~~~~~~~p~~i~~~~~~la~~~~~~~e~~~~~~~~ 248 (255)
T PF01026_consen 191 LIKAIPLDRILLETDAPYLAPDPYRGKPNEPSNIPKVAQALAEIKGISLEELAQIIYE 248 (255)
T ss_dssp HHHHS-GGGEEEE-BTTSSECTTSTTSE--GGGHHHHHHHHHHHHTSTHHHHHHHHHH
T ss_pred HHhcCChhhEEEcCCCCcCCccccCCCCCChHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 335567788999999873 2367788889999999999999 99999998875
No 36
>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=24.21 E-value=80 Score=24.36 Aligned_cols=19 Identities=32% Similarity=0.480 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhCCHHHHhc
Q 032201 99 ETYLNTLATVLGSMEEAKK 117 (145)
Q Consensus 99 d~Yv~TLAkVLGSEEEAKk 117 (145)
...++.|+++||-+++|++
T Consensus 100 ~~~i~~lg~~~g~~~~a~~ 118 (248)
T cd01138 100 EEQLKEIGKLLNKEDEAEK 118 (248)
T ss_pred HHHHHHHHHHhCcHHHHHH
Confidence 3468999999999988876
No 37
>PRK14048 ferrichrome/ferrioxamine B periplasmic transporter; Provisional
Probab=24.14 E-value=73 Score=26.85 Aligned_cols=20 Identities=20% Similarity=0.219 Sum_probs=15.8
Q ss_pred HHHHHHHHHhCCHHHHhccc
Q 032201 100 TYLNTLATVLGSMEEAKKNM 119 (145)
Q Consensus 100 ~Yv~TLAkVLGSEEEAKkkI 119 (145)
.-++.|++++|.||+|++-|
T Consensus 166 ~~i~~lG~i~g~ee~A~~li 185 (374)
T PRK14048 166 DNMRLLGKVFEREEQAEDFA 185 (374)
T ss_pred HHHHHHHHHhCCHHHHHHHH
Confidence 45788999999999887543
No 38
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=23.79 E-value=41 Score=24.30 Aligned_cols=22 Identities=32% Similarity=0.604 Sum_probs=16.9
Q ss_pred CCCCcccccCCCCCceeEEEEc
Q 032201 64 NEPRETIMLPGCDYNHWLIVME 85 (145)
Q Consensus 64 ~~~~~tiLf~GcDy~HWLVvMe 85 (145)
..+.+-|.++..-|+||-|++.
T Consensus 7 ~~~GD~I~~~r~~y~H~gIYvG 28 (125)
T PF04970_consen 7 LKPGDHIEVPRGLYEHWGIYVG 28 (125)
T ss_dssp --TT-EEEEEETTEEEEEEEEE
T ss_pred CCCCCEEEEecCCccEEEEEec
Confidence 3567888899999999999876
No 39
>PRK02260 S-ribosylhomocysteinase; Provisional
Probab=23.55 E-value=99 Score=25.04 Aligned_cols=31 Identities=32% Similarity=0.651 Sum_probs=28.2
Q ss_pred CCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHh
Q 032201 74 GCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVL 109 (145)
Q Consensus 74 GcDy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVL 109 (145)
||.--+.||+.. .++.++|++...++|..|+
T Consensus 81 GCrTGFYli~~g-----~~~~~~i~~l~~~~l~~i~ 111 (158)
T PRK02260 81 GCRTGFYLILIG-----TPDEEDVADALKATLEDVL 111 (158)
T ss_pred ccccccEEEEeC-----CCCHHHHHHHHHHHHHHHH
Confidence 999999999974 5778999999999999998
No 40
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=23.26 E-value=1.6e+02 Score=20.87 Aligned_cols=42 Identities=26% Similarity=0.394 Sum_probs=26.0
Q ss_pred EEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeee
Q 032201 82 IVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGF 130 (145)
Q Consensus 82 VvMe~P~~~~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF 130 (145)
|....|+.+-|||.|+.+ -||+.+|. -+..|+=.+..+.||=
T Consensus 3 ~~v~h~g~~Tpsr~ei~~----klA~~~~~---~~~~ivv~~~~t~fG~ 44 (84)
T PF01282_consen 3 FEVLHPGKPTPSRKEIRE----KLAAMLNV---DPDLIVVFGIKTEFGG 44 (84)
T ss_dssp EEEE-SSSSS--HHHHHH----HHHHHHTS---TGCCEEEEEEEESSSS
T ss_pred EEEECCCCCCCCHHHHHH----HHHHHhCC---CCCeEEEeccEecCCC
Confidence 456678889999999975 57888876 2344555555555553
No 41
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=22.88 E-value=1.8e+02 Score=24.01 Aligned_cols=50 Identities=14% Similarity=0.094 Sum_probs=32.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeeeeeeCHHHHhhhhC
Q 032201 87 PKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKG 144 (145)
Q Consensus 87 P~~~~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~I~EE~S~klk~ 144 (145)
|---.++.+|+++||.+.+..+=+ ----||+.-..+ |..|+.|+..+|.+
T Consensus 105 P~y~~~~~~~i~~~~~~v~~a~~~----lpi~iYn~P~~t----g~~l~~~~~~~L~~ 154 (288)
T cd00954 105 PFYYKFSFEEIKDYYREIIAAAAS----LPMIIYHIPALT----GVNLTLEQFLELFE 154 (288)
T ss_pred CCCCCCCHHHHHHHHHHHHHhcCC----CCEEEEeCcccc----CCCCCHHHHHHHhc
Confidence 434568999999999887654201 112367665322 67888888888764
No 42
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=22.58 E-value=1.1e+02 Score=19.07 Aligned_cols=43 Identities=5% Similarity=-0.004 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeeee
Q 032201 90 PAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQC 132 (145)
Q Consensus 90 ~~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c 132 (145)
..-.|.++++.--+.|++++|...|.-.-+..---...+|||-
T Consensus 13 s~eqk~~l~~~it~~l~~~~~~p~~~v~V~i~e~~~~~~~~gG 55 (61)
T PRK02220 13 TEEQLKALVKDVTAAVSKNTGAPAEHIHVIINEMSKNHYAVGG 55 (61)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcChhhEEEEEEEeChhHeEECC
Confidence 3446778888889999999997666655554544446666664
No 43
>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=22.26 E-value=90 Score=19.13 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeee
Q 032201 91 APTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQ 131 (145)
Q Consensus 91 ~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~ 131 (145)
.-.|.++++.-.+.|++++|.-+|.-.-+..-.-...||||
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 33577788888899999999655543333333333555555
No 44
>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=21.74 E-value=1e+02 Score=25.95 Aligned_cols=36 Identities=19% Similarity=0.401 Sum_probs=29.7
Q ss_pred ccCCCCCceeEEEEcCCCCCCCCHHH--HHHHHHHHHHHHhCCH
Q 032201 71 MLPGCDYNHWLIVMEFPKDPAPTREQ--MIETYLNTLATVLGSM 112 (145)
Q Consensus 71 Lf~GcDy~HWLVvMe~P~~~~psr~e--mId~Yv~TLAkVLGSE 112 (145)
||.=| |+|| -|.++..|++| +|.-|++-||...|++
T Consensus 53 LL~lg-FeyW-----~P~gg~is~~E~~lv~g~v~~la~~~g~~ 90 (196)
T PF07105_consen 53 LLNLG-FEYW-----EPTGGTISPAERKLVRGFVKFLASYAGSE 90 (196)
T ss_pred HHHHH-HHHc-----cCCCCccCHHHHHHHHHHHHHHHHHhCCH
Confidence 55444 8999 58888888776 6999999999999987
No 45
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=21.63 E-value=1.9e+02 Score=20.31 Aligned_cols=34 Identities=15% Similarity=0.123 Sum_probs=23.3
Q ss_pred CCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhC
Q 032201 74 GCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLG 110 (145)
Q Consensus 74 GcDy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVLG 110 (145)
.++-.||+|+.|..+ ...+++++.--+.+...++
T Consensus 45 ~~~~~~~li~vd~~~---~~~~~~~~~i~~~~~~~~~ 78 (108)
T PF14581_consen 45 EDEQPSLLIGVDFDG---EDIEEIFQEIGRAARPYLP 78 (108)
T ss_pred cCCCceEEEEEeccC---hhHHHHHHHHHHHhhhcCC
Confidence 567789999999986 4455666555555555553
No 46
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=21.13 E-value=2e+02 Score=24.01 Aligned_cols=59 Identities=12% Similarity=0.019 Sum_probs=37.8
Q ss_pred CCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhcccceeeecceeeeeeeeCHHHHhhhhC
Q 032201 76 DYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKG 144 (145)
Q Consensus 76 Dy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~I~EE~S~klk~ 144 (145)
.....+|. .|.--.++.+||++||-+.++++- +--.-||++-.. .|..|+.|+..+|.+
T Consensus 96 Gad~v~v~--~P~y~~~~~~~i~~yf~~v~~~~~----~lpv~lYn~P~~----tg~~l~~~~i~~L~~ 154 (290)
T TIGR00683 96 GYDCLSAV--TPFYYKFSFPEIKHYYDTIIAETG----GLNMIVYSIPFL----TGVNMGIEQFGELYK 154 (290)
T ss_pred CCCEEEEe--CCcCCCCCHHHHHHHHHHHHhhCC----CCCEEEEeCccc----cccCcCHHHHHHHhc
Confidence 33444443 355567899999999987765421 122347887643 256888888888754
No 47
>PF01876 RNase_P_p30: RNase P subunit p30; InterPro: IPR002738 Members of this protein family are part of the ribonuclease P complex () that takes part in endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor. This process is essential for tRNA processing.; GO: 0004540 ribonuclease activity, 0008033 tRNA processing; PDB: 1V77_A 2CZV_A.
Probab=21.13 E-value=80 Score=23.63 Aligned_cols=17 Identities=53% Similarity=0.608 Sum_probs=12.7
Q ss_pred HHHHHHhC-CHHHHhccc
Q 032201 103 NTLATVLG-SMEEAKKNM 119 (145)
Q Consensus 103 ~TLAkVLG-SEEEAKkkI 119 (145)
--|+..|| ++++||+.|
T Consensus 130 ~~l~~~lGl~~~~a~~av 147 (150)
T PF01876_consen 130 INLLALLGLSEEEAKKAV 147 (150)
T ss_dssp HHHHHHTT--HHHHHHTT
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 34677999 999999875
No 48
>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=20.98 E-value=2.1e+02 Score=23.23 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=28.2
Q ss_pred CCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCH
Q 032201 74 GCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSM 112 (145)
Q Consensus 74 GcDy~HWLVvMe~P~~~~psr~emId~Yv~TLAkVLGSE 112 (145)
||.--+.||+.. .++.+++++...++|..|+.-+
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 999999999986 5678999999999999999744
No 49
>COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms]
Probab=20.86 E-value=1.8e+02 Score=23.92 Aligned_cols=82 Identities=21% Similarity=0.373 Sum_probs=51.5
Q ss_pred cCCccCCC--CCcccccccCCCCCC--CCCccccccchhh---hcccCCCCCCCCCCCCCCCCccccc--CCCCCceeEE
Q 032201 12 SKPLLSSR--PQLTLGLRVGSPTLR--LPSRAHSRSILTV---RAGATDSEYSSKRSSSNEPRETIML--PGCDYNHWLI 82 (145)
Q Consensus 12 ~k~l~~~~--~~~~~~~~~~~~~~~--~p~~~~~~~~~~~---~~~~~~~~ys~~~~s~~~~~~tiLf--~GcDy~HWLV 82 (145)
.|+-+-++ -.+.+++||-.|+-. .|..+++.--+.+ |....+. -++|=| -||.--+.|+
T Consensus 22 ~~~~~~~~Gd~It~fDiRf~qPNke~m~~~~iHTlEHL~A~~iRnh~~g~------------~~iID~SPMGCrTGFYm~ 89 (161)
T COG1854 22 AKTMTGPKGDVITKFDIRFCQPNKEIMPPAGIHTLEHLLAGFIRNHLNGN------------VEIIDISPMGCRTGFYMI 89 (161)
T ss_pred cccccCCCCCEEEEeEEEEecCChhhCCccchhhHHHHHHHHHHhcccCc------------eeEEEecCcccccceEEE
Confidence 44444333 355677787777655 4556666442222 3222211 122211 3999999999
Q ss_pred EEcCCCCCCCCHHHHHHHHHHHHHHHhC
Q 032201 83 VMEFPKDPAPTREQMIETYLNTLATVLG 110 (145)
Q Consensus 83 vMe~P~~~~psr~emId~Yv~TLAkVLG 110 (145)
+.. .|+.++++|....++.-||+
T Consensus 90 l~G-----~~~~~~i~~~~~~~m~dvl~ 112 (161)
T COG1854 90 LIG-----TPTSQDIADVLEATMKDVLK 112 (161)
T ss_pred EEC-----CCCHHHHHHHHHHHHHHHHc
Confidence 985 56789999999999999997
No 50
>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=20.71 E-value=1.2e+02 Score=19.90 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHH
Q 032201 94 REQMIETYLNTLATV 108 (145)
Q Consensus 94 r~emId~Yv~TLAkV 108 (145)
|+||||+..+-|.++
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 51
>PF08947 BPS: BPS (Between PH and SH2) ; InterPro: IPR015042 The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor []. ; PDB: 2AUH_B.
Probab=20.59 E-value=49 Score=22.49 Aligned_cols=10 Identities=30% Similarity=0.604 Sum_probs=6.0
Q ss_pred eEEEEcCCCC
Q 032201 80 WLIVMEFPKD 89 (145)
Q Consensus 80 WLVvMe~P~~ 89 (145)
=||.|||-+.
T Consensus 7 slVaMDFsG~ 16 (49)
T PF08947_consen 7 SLVAMDFSGQ 16 (49)
T ss_dssp --EEEE-SSS
T ss_pred ceEEeeecCC
Confidence 4799999974
No 52
>PLN02150 terpene synthase/cyclase family protein
Probab=20.40 E-value=49 Score=23.93 Aligned_cols=20 Identities=25% Similarity=0.483 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHhC-CHHHHhcccce
Q 032201 98 IETYLNTLATVLG-SMEEAKKNMYA 121 (145)
Q Consensus 98 Id~Yv~TLAkVLG-SEEEAKkkIYs 121 (145)
|+||.+-= | |||||.+.|-.
T Consensus 10 IeCYMke~----g~seeeA~~~i~~ 30 (96)
T PLN02150 10 VNCYMKQH----GVTKEEAVSELKK 30 (96)
T ss_pred HHHHhccC----CCCHHHHHHHHHH
Confidence 67776642 6 88888877643
No 53
>PRK08187 pyruvate kinase; Validated
Probab=20.30 E-value=99 Score=28.76 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHH-------------------HHHHHHHhCCHHHHhcc
Q 032201 89 DPAPTREQMIETY-------------------LNTLATVLGSMEEAKKN 118 (145)
Q Consensus 89 ~~~psr~emId~Y-------------------v~TLAkVLGSEEEAKkk 118 (145)
.+.|||+||-|.+ |++|++++...|+.|.|
T Consensus 434 ~p~PTRAEvtDvAnadgaDavMLs~G~ypveaV~~l~~I~~~~e~~~~k 482 (493)
T PRK08187 434 KGLPSRAEMTDAAMAARAECVMLNKGPYLVEAVTFLDDLLARMDGHQHK 482 (493)
T ss_pred CCCCchHHHHHHHhhcCCCEEeecCCCCHHHHHHHHHHHHHHHHHhhhc
Confidence 4789999998876 56777777666655544
Done!