Query 029048
Match_columns 200
No_of_seqs 86 out of 88
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 06:39:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029048.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029048hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05922 Inhibitor_I9: Peptida 95.4 0.022 4.7E-07 39.1 3.6 69 80-154 2-75 (82)
2 PF12674 Zn_ribbon_2: Putative 55.2 17 0.00037 27.2 3.4 29 91-119 41-70 (81)
3 TIGR00683 nanA N-acetylneurami 45.0 49 0.0011 28.9 5.1 68 76-153 96-163 (290)
4 TIGR03868 F420-O_ABCperi propo 44.8 26 0.00056 29.1 3.2 26 93-119 126-151 (287)
5 cd01143 YvrC Periplasmic bindi 38.9 31 0.00067 26.5 2.7 22 98-119 97-118 (195)
6 COG0614 FepB ABC-type Fe3+-hyd 37.3 25 0.00053 29.1 2.0 22 98-119 151-172 (319)
7 cd01144 BtuF Cobalamin binding 37.3 25 0.00053 28.4 2.0 25 94-119 91-115 (245)
8 PF10847 DUF2656: Protein of u 37.0 53 0.0012 27.4 3.9 31 76-110 41-71 (132)
9 cd01148 TroA_a Metal binding p 36.9 50 0.0011 27.4 3.8 26 92-118 123-148 (284)
10 KOG1276 Protoporphyrinogen oxi 36.0 30 0.00064 34.2 2.6 46 64-116 381-427 (491)
11 cd01139 TroA_f Periplasmic bin 35.7 61 0.0013 27.8 4.2 24 93-117 130-153 (342)
12 PF01497 Peripla_BP_2: Peripla 35.3 87 0.0019 24.7 4.8 24 96-119 96-119 (238)
13 PRK10576 iron-hydroxamate tran 34.2 43 0.00094 28.5 3.1 25 94-118 127-151 (292)
14 cd01147 HemV-2 Metal binding p 33.1 47 0.001 26.9 3.0 21 98-118 113-133 (262)
15 cd00954 NAL N-Acetylneuraminic 31.2 1.1E+02 0.0025 26.4 5.2 59 87-153 105-163 (288)
16 cd01146 FhuD Fe3+-siderophore 30.6 87 0.0019 25.5 4.2 23 93-116 97-119 (256)
17 PF13961 DUF4219: Domain of un 30.1 3.7 8.1E-05 24.9 -2.9 14 72-85 1-14 (27)
18 PRK11411 fecB iron-dicitrate t 29.2 62 0.0013 27.6 3.2 25 93-118 134-158 (303)
19 KOG4079 Putative mitochondrial 28.8 37 0.00079 29.2 1.7 49 91-144 93-144 (169)
20 PRK04147 N-acetylneuraminate l 28.3 1.3E+02 0.0029 26.0 5.1 61 86-155 107-167 (293)
21 cd01149 HutB Hemin binding pro 28.1 71 0.0015 25.8 3.2 21 98-118 96-116 (235)
22 TIGR03659 IsdE heme ABC transp 27.4 67 0.0014 27.2 3.1 22 96-117 125-146 (289)
23 COG1854 LuxS LuxS protein invo 27.0 1.7E+02 0.0037 25.3 5.4 32 74-110 81-112 (161)
24 cd01142 TroA_e Periplasmic bin 26.0 73 0.0016 26.5 3.0 21 98-118 123-143 (289)
25 COG4607 CeuA ABC-type enteroch 25.8 44 0.00096 31.4 1.8 22 101-122 158-179 (320)
26 cd01140 FatB Siderophore bindi 24.9 80 0.0017 25.9 3.0 20 98-117 109-128 (270)
27 PRK03379 vitamin B12-transport 24.7 68 0.0015 26.9 2.7 24 93-117 105-128 (260)
28 COG1448 TyrB Aspartate/tyrosin 23.6 1E+02 0.0022 29.8 3.8 60 65-143 170-229 (396)
29 KOG0578 p21-activated serine/t 23.5 29 0.00064 34.6 0.3 25 122-147 408-434 (550)
30 cd01851 GBP Guanylate-binding 23.2 1E+02 0.0022 25.9 3.3 33 78-110 59-92 (224)
31 PRK11630 hypothetical protein; 23.1 65 0.0014 27.2 2.2 36 102-142 17-53 (206)
32 KOG1670 Translation initiation 22.6 1.3E+02 0.0028 26.9 4.0 28 79-111 110-137 (212)
33 KOG1412 Aspartate aminotransfe 22.3 1.1E+02 0.0024 29.6 3.8 52 63-132 174-225 (410)
34 cd00952 CHBPH_aldolase Trans-o 22.1 2.2E+02 0.0047 25.2 5.4 59 86-152 111-169 (309)
35 PF01026 TatD_DNase: TatD rela 20.6 1.2E+02 0.0025 25.6 3.3 51 71-121 191-248 (255)
36 TIGR00013 taut 4-oxalocrotonat 20.6 78 0.0017 20.9 1.8 43 91-133 14-56 (63)
37 PF02617 ClpS: ATP-dependent C 20.3 1.1E+02 0.0024 22.0 2.7 59 78-143 5-64 (82)
38 cd00636 TroA-like Helical back 20.2 1.1E+02 0.0024 21.1 2.6 24 96-119 98-121 (148)
39 KOG1257 NADP+-dependent malic 20.1 95 0.0021 31.4 3.0 23 101-124 329-352 (582)
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=95.39 E-value=0.022 Score=39.11 Aligned_cols=69 Identities=22% Similarity=0.412 Sum_probs=42.6
Q ss_pred eEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHH----HHhhc-cceeeecceeeeeeeeCHHHHHhhhCCCcccceEec
Q 029048 80 WLIVMEFPKDPAPTREQMIETYLNTLATVLGSME----EAKKN-MYAFSTTTYTGFQCTVSEETSEKFKGDKYVNGEIIP 154 (200)
Q Consensus 80 WLVvMd~P~~~~pSr~EmId~Yv~TLAkVLGSEE----EAKkk-IYsvSt~tyfGF~c~IdEE~S~KLkGd~~VnG~IvP 154 (200)
.+|+|+.+ .+.++.++...+-++..|.+.. ..+-+ +|.+.. .--||.+.+++++.++|+.+|.|. -|.|
T Consensus 2 YIV~~k~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~-~~~Gfs~~l~~~~i~~L~~~p~V~-~Ve~ 75 (82)
T PF05922_consen 2 YIVVFKDD----ASAASSFSSHKSWQASILKSALKSASSINAKVLYSYDN-AFNGFSAKLSEEEIEKLRKDPGVK-SVEP 75 (82)
T ss_dssp EEEEE-TT----STHHCHHHHHHHHHH----HHHHTH-TTT-EEEEEESS-TSSEEEEEE-HHHHHHHHTSTTEE-EEEE
T ss_pred EEEEECCC----CCcchhHHHHHHHHHHHHhhhhhhhcccCCceEEEEee-eEEEEEEEeCHHHHHHHHcCCCeE-EEEe
Confidence 47888866 3334456666666665554321 12223 676766 789999999999999999999888 4444
No 2
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=55.23 E-value=17 Score=27.20 Aligned_cols=29 Identities=38% Similarity=0.391 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHHHHHHhC-CHHHHhhcc
Q 029048 91 APTREQMIETYLNTLATVLG-SMEEAKKNM 119 (200)
Q Consensus 91 ~pSr~EmId~Yv~TLAkVLG-SEEEAKkkI 119 (200)
+-|.+|||+.-++-|++.-| ++|||++-+
T Consensus 41 ~~t~eemie~~~~~~~~~~~~~~~~a~~~~ 70 (81)
T PF12674_consen 41 DITMEEMIEFCVPFMDEFNGMTPEEARKMM 70 (81)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 56899999999999999987 899998754
No 3
>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=45.02 E-value=49 Score=28.93 Aligned_cols=68 Identities=13% Similarity=0.042 Sum_probs=45.1
Q ss_pred CCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeeeeeCHHHHHhhhCCCcccceEe
Q 029048 76 DYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKGDKYVNGEII 153 (200)
Q Consensus 76 Dy~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLkGd~~VnG~Iv 153 (200)
.....+|++ |---.++.++|++||-+.++.+- +--.-||++-.. .|..|+.|+..+|...|-|-|.--
T Consensus 96 Gad~v~v~~--P~y~~~~~~~i~~yf~~v~~~~~----~lpv~lYn~P~~----tg~~l~~~~i~~L~~~pnv~giK~ 163 (290)
T TIGR00683 96 GYDCLSAVT--PFYYKFSFPEIKHYYDTIIAETG----GLNMIVYSIPFL----TGVNMGIEQFGELYKNPKVLGVKF 163 (290)
T ss_pred CCCEEEEeC--CcCCCCCHHHHHHHHHHHHhhCC----CCCEEEEeCccc----cccCcCHHHHHHHhcCCCEEEEEe
Confidence 334455533 55667899999999987776421 112347887643 266899999999997676665443
No 4
>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=44.80 E-value=26 Score=29.14 Aligned_cols=26 Identities=12% Similarity=0.240 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhhcc
Q 029048 93 TREQMIETYLNTLATVLGSMEEAKKNM 119 (200)
Q Consensus 93 Sr~EmId~Yv~TLAkVLGSEEEAKkkI 119 (200)
+.+++.+. ++.||++||.||+|++-|
T Consensus 126 ~~~~~~~~-i~~lg~~~g~e~~A~~~i 151 (287)
T TIGR03868 126 TFDDVFAE-ITEVGTIFDVPDAAASLV 151 (287)
T ss_pred CHHHHHHH-HHHHHHHhCCHHHHHHHH
Confidence 45555544 889999999999988643
No 5
>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=38.90 E-value=31 Score=26.53 Aligned_cols=22 Identities=27% Similarity=0.388 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhCCHHHHhhcc
Q 029048 98 IETYLNTLATVLGSMEEAKKNM 119 (200)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkkI 119 (200)
+.-.++.||+++|-+|+|++.|
T Consensus 97 ~~~~~~~lg~~~g~~~~a~~~~ 118 (195)
T cd01143 97 IYDQIELIGKITGAEEEAEKLV 118 (195)
T ss_pred HHHHHHHHHHHhCChHHHHHHH
Confidence 3346889999999999999865
No 6
>COG0614 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=37.31 E-value=25 Score=29.07 Aligned_cols=22 Identities=27% Similarity=0.421 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHhCCHHHHhhcc
Q 029048 98 IETYLNTLATVLGSMEEAKKNM 119 (200)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkkI 119 (200)
+.--+++||++||.|++|++-|
T Consensus 151 ~~~~i~~lg~~~g~e~~A~~li 172 (319)
T COG0614 151 IKEQIRLLGKALGKEEKAEELI 172 (319)
T ss_pred HHHHHHHHHHHhCcHHHHHHHH
Confidence 4556789999999999997654
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=37.25 E-value=25 Score=28.37 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHhhcc
Q 029048 94 REQMIETYLNTLATVLGSMEEAKKNM 119 (200)
Q Consensus 94 r~EmId~Yv~TLAkVLGSEEEAKkkI 119 (200)
.+++. -.+++||++||.+|+|++.+
T Consensus 91 ~~~~~-~~~~~lg~~~g~~~~a~~~~ 115 (245)
T cd01144 91 LDDIL-ADIRRLGTLAGRPARAEELA 115 (245)
T ss_pred HHHHH-HHHHHHHHHhCChhHHHHHH
Confidence 34443 46899999999999996643
No 8
>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=36.96 E-value=53 Score=27.44 Aligned_cols=31 Identities=16% Similarity=0.409 Sum_probs=26.2
Q ss_pred CCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhC
Q 029048 76 DYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLG 110 (200)
Q Consensus 76 Dy~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLG 110 (200)
+--||||-++ ..-+++||-...++++.+.=-
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 5679999999 577899999999999987643
No 9
>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=36.92 E-value=50 Score=27.39 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHHHHHHHhCCHHHHhhc
Q 029048 92 PTREQMIETYLNTLATVLGSMEEAKKN 118 (200)
Q Consensus 92 pSr~EmId~Yv~TLAkVLGSEEEAKkk 118 (200)
.+.+++.+ .++.|++++|.||+|++-
T Consensus 123 ~~~~~~~~-~~~~lg~~~g~e~~A~~~ 148 (284)
T cd01148 123 ATLDDVYN-DIRNLGKIFDVEDRADKL 148 (284)
T ss_pred CCHHHHHH-HHHHHHHHhCCHhHHHHH
Confidence 35555555 688999999998887653
No 10
>KOG1276 consensus Protoporphyrinogen oxidase [Coenzyme transport and metabolism]
Probab=35.98 E-value=30 Score=34.18 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=37.7
Q ss_pred CCCCcccccCCCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhC-CHHHHh
Q 029048 64 NEPRETIMLPGCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLG-SMEEAK 116 (200)
Q Consensus 64 ~~~~~tiLf~GCDy~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLG-SEEEAK 116 (200)
.+++-|.+.-||-+.||-+ -.+|++|+|+.--.-|.+-|| ++|++.
T Consensus 381 ~s~~vtvm~gg~~~~n~~~-------~~~S~ee~~~~v~~alq~~Lgi~~~P~~ 427 (491)
T KOG1276|consen 381 PSPKVTVMMGGGGSTNTSL-------AVPSPEELVNAVTSALQKMLGISNKPVS 427 (491)
T ss_pred CCceEEEEecccccccCcC-------CCCCHHHHHHHHHHHHHHHhCCCCCccc
Confidence 3457788888998888864 478999999999999999999 666653
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=35.73 E-value=61 Score=27.80 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=17.9
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhh
Q 029048 93 TREQMIETYLNTLATVLGSMEEAKK 117 (200)
Q Consensus 93 Sr~EmId~Yv~TLAkVLGSEEEAKk 117 (200)
+-+++.+ -++.||+++|.+|+|++
T Consensus 130 ~~~~~~~-~i~~lg~i~g~~~~A~~ 153 (342)
T cd01139 130 PLKNTTP-SMRLLGKALGREERAEE 153 (342)
T ss_pred hhhhHHH-HHHHHHHHhCCHHHHHH
Confidence 4455554 58899999999988854
No 12
>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=35.26 E-value=87 Score=24.66 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHhCCHHHHhhcc
Q 029048 96 QMIETYLNTLATVLGSMEEAKKNM 119 (200)
Q Consensus 96 EmId~Yv~TLAkVLGSEEEAKkkI 119 (200)
+-+.-.++.||++||-+++|++-|
T Consensus 96 ~~~~~~i~~lg~~~g~~~~a~~~~ 119 (238)
T PF01497_consen 96 DDWKEQIRQLGKALGKEDQAEALI 119 (238)
T ss_dssp HHHHHHHHHHHHHHTSHHHHHHHH
T ss_pred HHHHHHHHHHHHhcccHHHHHHHH
Confidence 667888999999999999988643
No 13
>PRK10576 iron-hydroxamate transporter substrate-binding subunit; Provisional
Probab=34.18 E-value=43 Score=28.52 Aligned_cols=25 Identities=20% Similarity=0.093 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHhhc
Q 029048 94 REQMIETYLNTLATVLGSMEEAKKN 118 (200)
Q Consensus 94 r~EmId~Yv~TLAkVLGSEEEAKkk 118 (200)
.-+.+...++.|+++||.|++|++-
T Consensus 127 ~~~~~~~~i~~lg~ilG~e~~A~~l 151 (292)
T PRK10576 127 PLAVARKSLVELAQRLNLEAAAETH 151 (292)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 3456777899999999999988753
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=33.10 E-value=47 Score=26.87 Aligned_cols=21 Identities=29% Similarity=0.341 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHhCCHHHHhhc
Q 029048 98 IETYLNTLATVLGSMEEAKKN 118 (200)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkk 118 (200)
+...++.||+++|.+++|++-
T Consensus 113 ~~~~i~~lg~~~g~~~~a~~~ 133 (262)
T cd01147 113 TPEQIRLLGKVLGKEERAEEL 133 (262)
T ss_pred HHHHHHHHHHHhCCHHHHHHH
Confidence 457789999999999988754
No 15
>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=31.19 E-value=1.1e+02 Score=26.36 Aligned_cols=59 Identities=14% Similarity=0.045 Sum_probs=39.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeeeeeCHHHHHhhhCCCcccceEe
Q 029048 87 PKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKGDKYVNGEII 153 (200)
Q Consensus 87 P~~~~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLkGd~~VnG~Iv 153 (200)
|---.++.+|++++|.+.+..+=+ ----||+.-.. .|+.|+.++..+|...|-|-|.-.
T Consensus 105 P~y~~~~~~~i~~~~~~v~~a~~~----lpi~iYn~P~~----tg~~l~~~~~~~L~~~pnivgiK~ 163 (288)
T cd00954 105 PFYYKFSFEEIKDYYREIIAAAAS----LPMIIYHIPAL----TGVNLTLEQFLELFEIPNVIGVKF 163 (288)
T ss_pred CCCCCCCHHHHHHHHHHHHHhcCC----CCEEEEeCccc----cCCCCCHHHHHHHhcCCCEEEEEe
Confidence 444568999999999887654301 11236766432 277999999999997666655443
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=30.64 E-value=87 Score=25.54 Aligned_cols=23 Identities=30% Similarity=0.281 Sum_probs=16.2
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHh
Q 029048 93 TREQMIETYLNTLATVLGSMEEAK 116 (200)
Q Consensus 93 Sr~EmId~Yv~TLAkVLGSEEEAK 116 (200)
+.+++. ..++.|++++|-+|+|+
T Consensus 97 ~~~~~~-~~i~~lg~~~g~~~~a~ 119 (256)
T cd01146 97 WLAEWK-ENLRLIAKALGKEEEAE 119 (256)
T ss_pred cHHHHH-HHHHHHHHHhCcHHHHH
Confidence 344444 47889999999887664
No 17
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=30.06 E-value=3.7 Score=24.94 Aligned_cols=14 Identities=43% Similarity=0.942 Sum_probs=11.3
Q ss_pred cCCCCCceeEEEEc
Q 029048 72 LPGCDYNHWLIVME 85 (200)
Q Consensus 72 f~GCDy~HWLVvMd 85 (200)
|+|-+|.+|-+.|.
T Consensus 1 l~g~NY~~W~~~M~ 14 (27)
T PF13961_consen 1 LDGTNYSTWKIRMK 14 (27)
T ss_pred CCccCHHHHHHHHH
Confidence 67889999987774
No 18
>PRK11411 fecB iron-dicitrate transporter substrate-binding subunit; Provisional
Probab=29.25 E-value=62 Score=27.57 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=19.2
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhhc
Q 029048 93 TREQMIETYLNTLATVLGSMEEAKKN 118 (200)
Q Consensus 93 Sr~EmId~Yv~TLAkVLGSEEEAKkk 118 (200)
+.++..+ .++.||++||.|++|++-
T Consensus 134 ~~~~~~~-~i~~lg~i~g~e~~a~~~ 158 (303)
T PRK11411 134 TYQENLQ-SAAIIGEVLGKKREMQAR 158 (303)
T ss_pred CHHHHHH-HHHHHHHHhCCHHHHHHH
Confidence 5566655 468899999999999853
No 19
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=28.79 E-value=37 Score=29.24 Aligned_cols=49 Identities=22% Similarity=0.250 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHHH---HhCCHHHHhhccceeeecceeeeeeeeCHHHHHhhhC
Q 029048 91 APTREQMIETYLNTLAT---VLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKG 144 (200)
Q Consensus 91 ~pSr~EmId~Yv~TLAk---VLGSEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLkG 144 (200)
.-+++||++..++||.| +|--||+-|+. -+.-..||..|+ -++.-++.|
T Consensus 93 ~~~r~eI~~hl~K~lGKtee~lr~Ee~ek~~---k~nPAnFG~~c~--R~CiCEv~G 144 (169)
T KOG4079|consen 93 GMKREEIEKHLAKTLGKTEEVLRREELEKIA---KLNPANFGSKCE--RQCICEVQG 144 (169)
T ss_pred cccHHHHHHHHHHHhCccHHHHhHHHHHHHh---hcChhhhccccc--ceEEEecCC
Confidence 55789999887777754 45444444433 344577887775 234444444
No 20
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=28.34 E-value=1.3e+02 Score=26.01 Aligned_cols=61 Identities=11% Similarity=0.045 Sum_probs=40.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeeeeeCHHHHHhhhCCCcccceEecC
Q 029048 86 FPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKGDKYVNGEIIPC 155 (200)
Q Consensus 86 ~P~~~~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLkGd~~VnG~IvPr 155 (200)
.|---.++.++|+++|.+.+..+ + ----||++.. . -|+.|+.|+..+|...|-|-|.---.
T Consensus 107 ~P~y~~~~~~~l~~~f~~va~a~-~----lPv~iYn~P~--~--tg~~l~~~~l~~L~~~pnvvgiK~s~ 167 (293)
T PRK04147 107 TPFYYPFSFEEICDYYREIIDSA-D----NPMIVYNIPA--L--TGVNLSLDQFNELFTLPKVIGVKQTA 167 (293)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhC-C----CCEEEEeCch--h--hccCCCHHHHHHHhcCCCEEEEEeCC
Confidence 45556778899988887765542 1 1233666542 2 36699999999999777776655433
No 21
>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=28.08 E-value=71 Score=25.78 Aligned_cols=21 Identities=24% Similarity=0.289 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHhCCHHHHhhc
Q 029048 98 IETYLNTLATVLGSMEEAKKN 118 (200)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkk 118 (200)
+..-++.|+++||-|++|++-
T Consensus 96 ~~~~~~~lg~i~g~e~~A~~l 116 (235)
T cd01149 96 LLTKIRQVAQALGVPEKGEAL 116 (235)
T ss_pred HHHHHHHHHHHhCCHHHHHHH
Confidence 444688999999999988753
No 22
>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=27.41 E-value=67 Score=27.21 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHhCCHHHHhh
Q 029048 96 QMIETYLNTLATVLGSMEEAKK 117 (200)
Q Consensus 96 EmId~Yv~TLAkVLGSEEEAKk 117 (200)
+-+...++.||++||-+++|++
T Consensus 125 ~~~~~~i~~lg~~~G~~~~A~~ 146 (289)
T TIGR03659 125 DGMKKSITELGEKYGREEQAEK 146 (289)
T ss_pred HHHHHHHHHHHHHhCCHHHHHH
Confidence 3355568999999999998865
No 23
>COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms]
Probab=26.97 E-value=1.7e+02 Score=25.28 Aligned_cols=32 Identities=25% Similarity=0.586 Sum_probs=29.1
Q ss_pred CCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhC
Q 029048 74 GCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLG 110 (200)
Q Consensus 74 GCDy~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLG 110 (200)
||.--+.|++.. .|+-++++|....++.-||+
T Consensus 81 GCrTGFYm~l~G-----~~~~~~i~~~~~~~m~dvl~ 112 (161)
T COG1854 81 GCRTGFYMILIG-----TPTSQDIADVLEATMKDVLK 112 (161)
T ss_pred ccccceEEEEEC-----CCCHHHHHHHHHHHHHHHHc
Confidence 999999999975 56789999999999999997
No 24
>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=26.03 E-value=73 Score=26.50 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHhCCHHHHhhc
Q 029048 98 IETYLNTLATVLGSMEEAKKN 118 (200)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKkk 118 (200)
+...++.||+++|.+++|++-
T Consensus 123 ~~~~~~~lg~~~g~~~~a~~~ 143 (289)
T cd01142 123 VKLTIALLGELLGRQEKAEAL 143 (289)
T ss_pred HHHHHHHHHHHhCcHHHHHHH
Confidence 556789999999999988754
No 25
>COG4607 CeuA ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=25.81 E-value=44 Score=31.40 Aligned_cols=22 Identities=32% Similarity=0.478 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCHHHHhhcccee
Q 029048 101 YLNTLATVLGSMEEAKKNMYAF 122 (200)
Q Consensus 101 Yv~TLAkVLGSEEEAKkkIYsv 122 (200)
=+++|+++.|-|+|||+.+=++
T Consensus 158 n~e~Lg~IFgkE~eAk~~~~~i 179 (320)
T COG4607 158 NIETLGKIFGKEEEAKELLADI 179 (320)
T ss_pred HHHHHHHHhCchHHHHHHHHHH
Confidence 4679999999999999887443
No 26
>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=24.87 E-value=80 Score=25.89 Aligned_cols=20 Identities=35% Similarity=0.626 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHhCCHHHHhh
Q 029048 98 IETYLNTLATVLGSMEEAKK 117 (200)
Q Consensus 98 Id~Yv~TLAkVLGSEEEAKk 117 (200)
+...++.||+++|.+|+|++
T Consensus 109 ~~~~i~~lg~~~g~~~~a~~ 128 (270)
T cd01140 109 VKQNIETLGKIFGKEEEAKE 128 (270)
T ss_pred HHHHHHHHHHHhCcHHHHHH
Confidence 34469999999999988764
No 27
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=24.75 E-value=68 Score=26.93 Aligned_cols=24 Identities=33% Similarity=0.278 Sum_probs=17.4
Q ss_pred CHHHHHHHHHHHHHHHhCCHHHHhh
Q 029048 93 TREQMIETYLNTLATVLGSMEEAKK 117 (200)
Q Consensus 93 Sr~EmId~Yv~TLAkVLGSEEEAKk 117 (200)
+-++ +...+++|++++|.+++|++
T Consensus 105 ~~~~-~~~~i~~lg~~~g~~~~A~~ 128 (260)
T PRK03379 105 SIEQ-IANALRQLAPWSPQPEKAEQ 128 (260)
T ss_pred CHHH-HHHHHHHHHHHcCCHHHHHH
Confidence 3444 44468899999999988754
No 28
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=23.58 E-value=1e+02 Score=29.83 Aligned_cols=60 Identities=27% Similarity=0.519 Sum_probs=40.8
Q ss_pred CCCcccccCCCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeeeeeCHHHHHhhh
Q 029048 65 EPRETIMLPGCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFK 143 (200)
Q Consensus 65 ~~~~tiLf~GCDy~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLk 143 (200)
+..+.+|+-|| ...|.+-+||.+|-.+ |+.++ +.+.+--+---.|+||+.-|+|+ ++.|+
T Consensus 170 ~~~~vvLLH~C--------cHNPTG~D~t~~qW~~-----l~~~~-----~~r~lip~~D~AYQGF~~GleeD-a~~lR 229 (396)
T COG1448 170 PEGSVVLLHGC--------CHNPTGIDPTEEQWQE-----LADLI-----KERGLIPFFDIAYQGFADGLEED-AYALR 229 (396)
T ss_pred CCCCEEEEecC--------CCCCCCCCCCHHHHHH-----HHHHH-----HHcCCeeeeehhhhhhccchHHH-HHHHH
Confidence 66678899999 5689999999988643 23333 13444444444999999997666 44444
No 29
>KOG0578 consensus p21-activated serine/threonine protein kinase [Signal transduction mechanisms]
Probab=23.52 E-value=29 Score=34.56 Aligned_cols=25 Identities=36% Similarity=0.505 Sum_probs=18.0
Q ss_pred eeecceeeeeeeeCHHHHHhhh--CCCc
Q 029048 122 FSTTTYTGFQCTVSEETSEKFK--GDKY 147 (200)
Q Consensus 122 vSt~tyfGF~c~IdEE~S~KLk--Gd~~ 147 (200)
|.- +.||||+.|+++.++.=. |-||
T Consensus 408 vKl-tDFGFcaqi~~~~~KR~TmVGTPY 434 (550)
T KOG0578|consen 408 VKL-TDFGFCAQISEEQSKRSTMVGTPY 434 (550)
T ss_pred EEE-eeeeeeeccccccCccccccCCCC
Confidence 444 899999999999974333 5444
No 30
>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=23.19 E-value=1e+02 Score=25.92 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=26.5
Q ss_pred ceeEEEEcCCCCCCCCHHH-HHHHHHHHHHHHhC
Q 029048 78 NHWLIVMEFPKDPAPTREQ-MIETYLNTLATVLG 110 (200)
Q Consensus 78 ~HWLVvMd~P~~~~pSr~E-mId~Yv~TLAkVLG 110 (200)
++++|+||.|+-..+.+.+ +.|.-+-.||..|-
T Consensus 59 ~~~v~~lDteG~~~~~~~~~~~~~~~~~l~~lls 92 (224)
T cd01851 59 EHAVLLLDTEGTDGRERGEFEDDARLFALATLLS 92 (224)
T ss_pred cceEEEEecCCcCccccCchhhhhHHHHHHHHHh
Confidence 5899999999988887777 77777777777653
No 31
>PRK11630 hypothetical protein; Provisional
Probab=23.15 E-value=65 Score=27.17 Aligned_cols=36 Identities=14% Similarity=0.387 Sum_probs=26.8
Q ss_pred HHHHHHHhCCHHHHhhccceeeecceeeeeeee-CHHHHHhh
Q 029048 102 LNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTV-SEETSEKF 142 (200)
Q Consensus 102 v~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~I-dEE~S~KL 142 (200)
++..+++|. +-.|-.+-|+|-||++|.. +++..++|
T Consensus 17 i~~a~~~L~-----~G~vi~~PTdTvYgL~~d~~n~~Av~~l 53 (206)
T PRK11630 17 INQAVEIVR-----KGGVIVYPTDSGYALGCKIEDKNAMERI 53 (206)
T ss_pred HHHHHHHHH-----CCCEEEEeCCChHhhhcCCCCHHHHHHH
Confidence 344455552 3469999999999999997 67777777
No 32
>KOG1670 consensus Translation initiation factor 4F, cap-binding subunit (eIF-4E) and related cap-binding proteins [Translation, ribosomal structure and biogenesis]
Probab=22.62 E-value=1.3e+02 Score=26.88 Aligned_cols=28 Identities=29% Similarity=0.618 Sum_probs=23.4
Q ss_pred eeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCC
Q 029048 79 HWLIVMEFPKDPAPTREQMIETYLNTLATVLGS 111 (200)
Q Consensus 79 HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLGS 111 (200)
.|+|++++- +++++=...+.||..++|-
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 799998742 6788888899999999993
No 33
>KOG1412 consensus Aspartate aminotransferase/Glutamic oxaloacetic transaminase AAT2/GOT1 [Amino acid transport and metabolism]
Probab=22.29 E-value=1.1e+02 Score=29.60 Aligned_cols=52 Identities=37% Similarity=0.634 Sum_probs=41.7
Q ss_pred CCCCCcccccCCCCCceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeee
Q 029048 63 SNEPRETIMLPGCDYNHWLIVMEFPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQC 132 (200)
Q Consensus 63 ~~~~~~tiLf~GCDy~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c 132 (200)
+.|....+++.+|-+| |.+-+||+||-+. +|.|+ .+|+++-+=-..|.||-.
T Consensus 174 ~APe~si~iLhaCAhN--------PTGmDPT~EQW~q-----ia~vi-----k~k~lf~fFDiAYQGfAS 225 (410)
T KOG1412|consen 174 SAPEGSIIILHACAHN--------PTGMDPTREQWKQ-----IADVI-----KSKNLFPFFDIAYQGFAS 225 (410)
T ss_pred hCCCCcEEeeeccccC--------CCCCCCCHHHHHH-----HHHHH-----HhcCceeeeehhhccccc
Confidence 3477888999999664 8899999999764 46776 467788888889999964
No 34
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=22.13 E-value=2.2e+02 Score=25.21 Aligned_cols=59 Identities=12% Similarity=0.048 Sum_probs=38.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeeeeeCHHHHHhhhCCCcccceE
Q 029048 86 FPKDPAPTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFKGDKYVNGEI 152 (200)
Q Consensus 86 ~P~~~~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLkGd~~VnG~I 152 (200)
.|---.++.+++++||-+ +|...+ +.---||++-. .+ +..|+.|+..+|...|.|-|.-
T Consensus 111 ~P~y~~~~~~~l~~yf~~-va~a~~---~lPv~iYn~P~--~t--g~~l~~~~l~~L~~~pnivgiK 169 (309)
T cd00952 111 RPMWLPLDVDTAVQFYRD-VAEAVP---EMAIAIYANPE--AF--KFDFPRAAWAELAQIPQVVAAK 169 (309)
T ss_pred CCcCCCCCHHHHHHHHHH-HHHhCC---CCcEEEEcCch--hc--CCCCCHHHHHHHhcCCCEEEEE
Confidence 444456788888888844 444331 12334777653 22 4699999999999777666643
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=20.63 E-value=1.2e+02 Score=25.61 Aligned_cols=51 Identities=22% Similarity=0.359 Sum_probs=38.3
Q ss_pred ccCCCCCceeEEEEcCCC------CCCCCHHHHHHHHHHHHHHHhC-CHHHHhhccce
Q 029048 71 MLPGCDYNHWLIVMEFPK------DPAPTREQMIETYLNTLATVLG-SMEEAKKNMYA 121 (200)
Q Consensus 71 Lf~GCDy~HWLVvMd~P~------~~~pSr~EmId~Yv~TLAkVLG-SEEEAKkkIYs 121 (200)
++--+.-+++||=.|.|- .+.+....+|..=+++||++.| ++||+.+.+|.
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 345567789999999874 2367778889999999999999 99999998875
No 36
>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=20.56 E-value=78 Score=20.90 Aligned_cols=43 Identities=19% Similarity=0.173 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHHHHhCCHHHHhhccceeeecceeeeeee
Q 029048 91 APTREQMIETYLNTLATVLGSMEEAKKNMYAFSTTTYTGFQCT 133 (200)
Q Consensus 91 ~pSr~EmId~Yv~TLAkVLGSEEEAKkkIYsvSt~tyfGF~c~ 133 (200)
.-.|++++..-.+.|+.+||.-+|+-.-+..-.-...||||=.
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 3467788888999999999966665554444444466777643
No 37
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=20.33 E-value=1.1e+02 Score=21.98 Aligned_cols=59 Identities=27% Similarity=0.313 Sum_probs=36.2
Q ss_pred ceeEEEEcCCCCCCCCHHHHHHHHHHHHHHHhC-CHHHHhhccceeeecceeeeeeeeCHHHHHhhh
Q 029048 78 NHWLIVMEFPKDPAPTREQMIETYLNTLATVLG-SMEEAKKNMYAFSTTTYTGFQCTVSEETSEKFK 143 (200)
Q Consensus 78 ~HWLVvMd~P~~~~pSr~EmId~Yv~TLAkVLG-SEEEAKkkIYsvSt~tyfGF~c~IdEE~S~KLk 143 (200)
..|.|++=. |+.-|-++.|+ .|.+++| |+++|.+.+-.+-...- +....-+.|.++..+
T Consensus 5 ~~~~vvL~N--De~ht~~~Vi~----~L~~~~~~s~~~A~~~a~~v~~~G~-avv~~~~~e~ae~~~ 64 (82)
T PF02617_consen 5 DMYRVVLWN--DEVHTFEQVID----VLRRVFGCSEEQARQIAMEVHREGR-AVVGTGSREEAEEYA 64 (82)
T ss_dssp -EEEEEEE----SSSBHHHHHH----HHHHHC---HHHHHHHHHHHHHHSE-EEEEEEEHHHHHHHH
T ss_pred CceEEEEEc--CCCCCHHHHHH----HHHHHHCCCHHHHHHHHHHHhHcCC-EeeeeCCHHHHHHHH
Confidence 567776653 56777777665 5677778 99999999887766444 444455555555443
No 38
>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=20.23 E-value=1.1e+02 Score=21.14 Aligned_cols=24 Identities=21% Similarity=0.356 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHhCCHHHHhhcc
Q 029048 96 QMIETYLNTLATVLGSMEEAKKNM 119 (200)
Q Consensus 96 EmId~Yv~TLAkVLGSEEEAKkkI 119 (200)
+=+.-.++.|++.||-++.|++-+
T Consensus 98 ~~~~~~i~~lg~~~~~~~~a~~~~ 121 (148)
T cd00636 98 ENIKESIRLIGKALGKEENAEELI 121 (148)
T ss_pred HHHHHHHHHHHHHHCChHHHHHHH
Confidence 336677899999999899988754
No 39
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=20.15 E-value=95 Score=31.39 Aligned_cols=23 Identities=26% Similarity=0.453 Sum_probs=17.0
Q ss_pred HHHHHHHHhC-CHHHHhhccceeee
Q 029048 101 YLNTLATVLG-SMEEAKKNMYAFST 124 (200)
Q Consensus 101 Yv~TLAkVLG-SEEEAKkkIYsvSt 124 (200)
-+..|.+- | +||||+|+||=+.-
T Consensus 329 ~v~~m~~~-Gl~~eeA~kkIwlvD~ 352 (582)
T KOG1257|consen 329 IVMAMVKE-GLSEEEARKKIWLVDS 352 (582)
T ss_pred HHHHHHHc-CCCHHHHhccEEEEec
Confidence 34444444 7 99999999998764
Done!