Query psy11705
Match_columns 81
No_of_seqs 36 out of 38
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 16:48:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11705.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11705hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15114 UPF0640: Uncharacteri 100.0 1.4E-46 3E-51 244.0 6.0 68 4-73 2-69 (69)
2 PF06305 DUF1049: Protein of u 59.4 15 0.00033 21.5 3.0 50 17-76 12-61 (68)
3 PRK10628 LigB family dioxygena 51.9 6.7 0.00015 30.0 0.8 13 26-38 208-220 (246)
4 PF14142 YrzO: YrzO-like prote 51.6 16 0.00035 22.4 2.3 17 29-45 5-21 (46)
5 TIGR00852 pts-Glc PTS system, 50.9 10 0.00022 28.5 1.6 18 24-41 3-20 (289)
6 PF06522 B12D: NADH-ubiquinone 50.5 7.8 0.00017 24.4 0.8 13 28-40 6-18 (73)
7 TIGR02002 PTS-II-BC-glcB PTS s 37.9 19 0.00042 29.8 1.4 29 11-43 56-84 (502)
8 PF08365 IGF2_C: Insulin-like 37.6 23 0.0005 22.5 1.5 12 56-67 5-16 (56)
9 PF05965 FYRC: F/Y rich C-term 37.6 25 0.00053 21.9 1.6 24 5-28 59-82 (86)
10 PF00876 Innexin: Innexin; In 35.7 22 0.00048 27.5 1.4 23 19-41 79-101 (348)
11 PF04741 InvH: InvH outer memb 33.8 21 0.00046 26.4 1.0 15 25-39 4-18 (147)
12 TIGR02986 restrict_Alw26I type 29.1 45 0.00097 28.3 2.2 21 44-64 30-51 (424)
13 PF01757 Acyl_transf_3: Acyltr 24.4 73 0.0016 21.1 2.2 15 27-41 47-61 (340)
14 PF13150 DUF3989: Protein of u 23.6 57 0.0012 21.5 1.6 45 7-61 12-56 (85)
15 PRK00888 ftsB cell division pr 22.9 2.4E+02 0.0052 18.7 4.5 41 31-76 7-47 (105)
16 TIGR01996 PTS-II-BC-sucr PTS s 22.3 49 0.0011 26.9 1.3 26 11-40 153-178 (461)
17 TIGR00727 ISP4_OPT small oligo 21.5 53 0.0011 28.7 1.4 17 24-40 572-588 (681)
18 PF02411 MerT: MerT mercuric t 21.1 44 0.00096 23.0 0.7 29 23-64 47-75 (116)
19 PF12052 VGCC_beta4Aa_N: Volta 20.8 1.1E+02 0.0023 18.6 2.2 17 60-76 24-40 (42)
20 PF10777 YlaC: Inner membrane 20.5 22 0.00047 26.5 -1.0 9 51-59 140-148 (155)
21 PF09665 RE_Alw26IDE: Type II 20.3 81 0.0018 27.4 2.2 21 44-64 30-51 (511)
No 1
>PF15114 UPF0640: Uncharacterised protein family UPF0640
Probab=100.00 E-value=1.4e-46 Score=244.00 Aligned_cols=68 Identities=62% Similarity=1.137 Sum_probs=65.7
Q ss_pred hhhhHHHHHHHHhcCCCcccchhhhhHHHHhhhhhhhhhheeeeeecCcchhhhHHhhHHHHHHHHHHhh
Q psy11705 4 FFYSLRLKRLLKAWPGQKYFGIYRFLPLFFGVGAALEFAMIKWEVNNGEINFYKTYKRNQAVILAEERLS 73 (81)
Q Consensus 4 ~~~s~~ikrll~~~PGK~rfG~YRflP~FF~lGaamE~~MIn~~v~~G~~nFYdvyrRkqae~~~e~rl~ 73 (81)
..+|++|++||++||||++||+|||||+||||||||||+||||+| |+|||||||||||||++||+|++
T Consensus 2 ~~~s~~i~~ll~~~PGK~~fG~YRFLP~FF~lGaalE~~MIn~~v--G~~~FY~tykrrqae~~~e~rl~ 69 (69)
T PF15114_consen 2 FLRSRRIRRLLDLWPGKRRFGIYRFLPLFFVLGAALEWSMINWRV--GKENFYDTYKRRQAERQVEQRLK 69 (69)
T ss_pred chhHHHHHHHHHHCCCccccchhhhhHHHHHhhhhheEEEEEEee--CceeHHHHHHHHHHHHHHHHhcC
Confidence 458999999999999999999999999999999999999999999 99999999999999999999974
No 2
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=59.42 E-value=15 Score=21.49 Aligned_cols=50 Identities=20% Similarity=0.214 Sum_probs=27.4
Q ss_pred cCCCcccchhhhhHHHHhhhhhhhhhheeeeeecCcchhhhHHhhHHHHHHHHHHhhhhh
Q psy11705 17 WPGQKYFGIYRFLPLFFGVGAALEFAMIKWEVNNGEINFYKTYKRNQAVILAEERLSKLE 76 (81)
Q Consensus 17 ~PGK~rfG~YRflP~FF~lGaamE~~MIn~~v~~G~~nFYdvyrRkqae~~~e~rl~~~~ 76 (81)
+|+.-....+=++=++|++|+.+=|++- .....+.|..-+..++++++.+
T Consensus 12 ~~~~~~~pl~l~il~~f~~G~llg~l~~----------~~~~~~~r~~~~~~~k~l~~le 61 (68)
T PF06305_consen 12 LFGQFPLPLGLLILIAFLLGALLGWLLS----------LPSRLRLRRRIRRLRKELKKLE 61 (68)
T ss_pred EeeeccchHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHH
Confidence 3343333444456678888888777653 2233455555555555555543
No 3
>PRK10628 LigB family dioxygenase; Provisional
Probab=51.92 E-value=6.7 Score=30.04 Aligned_cols=13 Identities=38% Similarity=0.759 Sum_probs=11.3
Q ss_pred hhhhHHHHhhhhh
Q psy11705 26 YRFLPLFFGVGAA 38 (81)
Q Consensus 26 YRflP~FF~lGaa 38 (81)
=-|+|+|+++||+
T Consensus 208 EH~lPL~~alGAa 220 (246)
T PRK10628 208 EHYLPLLYVLGAW 220 (246)
T ss_pred HHHHHHHHHhcCC
Confidence 3589999999996
No 4
>PF14142 YrzO: YrzO-like protein
Probab=51.63 E-value=16 Score=22.39 Aligned_cols=17 Identities=47% Similarity=0.745 Sum_probs=15.6
Q ss_pred hHHHHhhhhhhhhhhee
Q psy11705 29 LPLFFGVGAALEFAMIK 45 (81)
Q Consensus 29 lP~FF~lGaamE~~MIn 45 (81)
|-+||..|-|-|..-||
T Consensus 5 llff~a~gvacelaain 21 (46)
T PF14142_consen 5 LLFFFAAGVACELAAIN 21 (46)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 56899999999999998
No 5
>TIGR00852 pts-Glc PTS system, maltose and glucose-specific subfamily, IIC component. permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the E. coli PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli. Most, but not all Scr permeases of other bacteria also lack a IIA domain. This model is specific for the IIC domain of the Glc family PTS transporters.
Probab=50.94 E-value=10 Score=28.54 Aligned_cols=18 Identities=50% Similarity=0.968 Sum_probs=15.6
Q ss_pred chhhhhHHHHhhhhhhhh
Q psy11705 24 GIYRFLPLFFGVGAALEF 41 (81)
Q Consensus 24 G~YRflP~FF~lGaamE~ 41 (81)
.++.|||++|+.++|-.+
T Consensus 3 ~~F~fLPil~a~saak~f 20 (289)
T TIGR00852 3 AAFFFLPLLFAIGAAKGF 20 (289)
T ss_pred hHHHHHHHHHHHHHHHHh
Confidence 679999999999888765
No 6
>PF06522 B12D: NADH-ubiquinone reductase complex 1 MLRQ subunit; InterPro: IPR010530 The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear [] and is found in plants [], insects, fungi and higher metazoans []. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation [].
Probab=50.51 E-value=7.8 Score=24.39 Aligned_cols=13 Identities=46% Similarity=0.761 Sum_probs=10.7
Q ss_pred hhHHHHhhhhhhh
Q psy11705 28 FLPLFFGVGAALE 40 (81)
Q Consensus 28 flP~FF~lGaamE 40 (81)
.+|||+++|+|+=
T Consensus 6 l~PL~~~vg~a~~ 18 (73)
T PF06522_consen 6 LYPLFVIVGVAVG 18 (73)
T ss_pred ccchHHHHHHHHH
Confidence 4799999998864
No 7
>TIGR02002 PTS-II-BC-glcB PTS system, glucose-specific IIBC component. This model represents the combined B and C domains of the PTS transport system enzyme II specific for glucose transport. Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name "PTS system, glucose-specific IIABC component" while the B. subtilus enzyme also contains an enzyme III domain which appears to act independently of the enzyme II domains. This family is most closely related to the N-acetylglucosamine-specific PTS enzymes (TIGR01998).
Probab=37.87 E-value=19 Score=29.83 Aligned_cols=29 Identities=38% Similarity=0.624 Sum_probs=22.7
Q ss_pred HHHHHhcCCCcccchhhhhHHHHhhhhhhhhhh
Q psy11705 11 KRLLKAWPGQKYFGIYRFLPLFFGVGAALEFAM 43 (81)
Q Consensus 11 krll~~~PGK~rfG~YRflP~FF~lGaamE~~M 43 (81)
-.+++.. |. .++.|||++|++|+|..+..
T Consensus 56 ~~~l~~~-g~---avF~~LPilfai~~A~~f~~ 84 (502)
T TIGR02002 56 SKVMEAA-GG---IIFANLPLIFAIGVALGLAG 84 (502)
T ss_pred HHHHHHH-HH---HHHHHhHHHHHHHHHHHhcC
Confidence 3445544 44 89999999999999988876
No 8
>PF08365 IGF2_C: Insulin-like growth factor II E-peptide; InterPro: IPR013576 The insulin family of proteins groups together several evolutionarily related active peptides []: these include insulin [, ], relaxin [, ], insect prothoracicotropic hormone (bombyxin) [], insulin-like growth factors (IGF1 and IGF2) [, ], mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP) (gene INSL4), locust insulin-related peptide (LIRP), molluscan insulin-related peptides (MIP), and Caenorhabditis elegans insulin-like peptides. The 3D structures of a number of family members have been determined [, , ]. The fold comprises two polypeptide chains (A and B) linked by two disulphide bonds: all share a conserved arrangement of 4 cysteines in their A chain, the first of which is linked by a disulphide bond to the third, while the second and fourth are linked by interchain disulphide bonds to cysteines in the B chain. Insulin is found in many animals, and is involved in the regulation of normal glucose homeostasis. It also has other specific physiological effects, such as increasing the permeability of cells to monosaccharides, amino acids and fatty acids, and accelerating glycolysis and glycogen synthesis in the liver []. Insulin exerts its effects by interaction with a cell-surface receptor, which may also result in the promotion of cell growth []. Insulin is synthesised as a prepropeptide from which an endoplasmic reticulum-targeting sequence is cleaved to yield proinsulin. The sequence of prosinsulin contains 2 well-conserved regions (designated A and B), separated by an intervening connecting region (C), which is variable between species []. The connecting region is cleaved, liberating the active protein, which contains the A and B chains, held together by 2 disulphide bonds []. Insulin-like Growth Factor Binding Proteins (IGFBP) are a group of vertebrate secreted proteins, which bind to IGF-I and IGF-II with high affinity and modulate the biological actions of IGFs. The IGFBP family has six distinct subgroups, IGFBP-1 through 6, based on conservation of gene (intron-exon) organisation, structural similarity, and binding affinity for IGFs. Across species, IGFBP-5 exhibits the most sequence conservation, while IGFBP-6 exhibits the least sequence conservation. The IGFBPs contain inhibitor domain homologues, which are related to MEROPS protease inhibitor family I31 (equistatin, clan IX). All IGFBPs share a common domain architecture (IPR000867 from INTERPRO:IPR000716 from INTERPRO). While the N-terminal (IPR000867 from INTERPRO, IGF binding protein domain), and the C-terminal (IPR000716 from INTERPRO, thyroglobulin type-1 repeat) domains are conserved across vertebrate species, the mid-region is highly variable with respect to protease cleavage sites and phosphorylation and glycosylation sites. IGFBPs contain 16-18 conserved cysteines located in the N-terminal and the C-terminal regions, which form 8-9 disulphide bonds []. As demonstrated for human IGFBP-5, the N terminus is the primary binding site for IGF. This region, comprised of Val49, Tyr50, Pro62 and Lys68-Leu75, forms a hydrophobic patch on the surface of the protein []. The C terminus is also required for high affinity IGF binding, as well as for binding to the extracellular matrix [] and for nuclear translocation [, ] of IGFBP-3 and -5. IGFBPs are unusually pleiotropic molecules. Like other binding proteins, IGFBP can prolong the half-life of IGFs via high affinity binding of the ligands. In addition to functioning as simple carrier proteins, serum IGFBPs also serve to regulate the endocrine and paracrine/autocrine actions of IGF by modulating the IGF available to bind to signalling IGF-I receptors [, ]. Furthermore, IGFBPs can function as growth modulators independent of IGFs. For example, IGFBP-5 stimulates markers of bone formation in osteoblasts lacking functional IGFs []. The binding of IGFBP to its putative receptor on the cell membrane may stimulate the signalling pathway independent of an IGF receptor, to mediate the effects of IGFBPs in certain target cell types. IGFBP-1 and -2, but not other IGFBPs, contain a C-terminal Arg-Gly-Asp integrin-binding motif. Thus, IGFBP-1 can also stimulate cell migration of CHO and human trophoblast cells through an action mediated by alpha 5 beta 1 integrin []. Finally, IGFBPs transported into the nucleus (via the nuclear localisation signal) may also exert IGF-independent effects by transcriptional activation of genes. This domain is the C-terminal domain of insulin-like growth factor II proteins (IGF-2, also see IPR004825 from INTERPRO) in vertebrates and seems to represent the E-peptide [, ].
Probab=37.61 E-value=23 Score=22.49 Aligned_cols=12 Identities=33% Similarity=0.614 Sum_probs=10.2
Q ss_pred hhHHhhHHHHHH
Q psy11705 56 YKTYKRNQAVIL 67 (81)
Q Consensus 56 YdvyrRkqae~~ 67 (81)
||||+||.|++.
T Consensus 5 yd~WqrksaqRL 16 (56)
T PF08365_consen 5 YDVWQRKSAQRL 16 (56)
T ss_pred hhHHHHHHHHHH
Confidence 899999888873
No 9
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=37.56 E-value=25 Score=21.91 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=17.5
Q ss_pred hhhHHHHHHHHhcCCCcccchhhh
Q psy11705 5 FYSLRLKRLLKAWPGQKYFGIYRF 28 (81)
Q Consensus 5 ~~s~~ikrll~~~PGK~rfG~YRf 28 (81)
+.+..|.++|+.+||-...--|+|
T Consensus 59 ls~p~V~~lie~Lp~a~~c~~Y~f 82 (86)
T PF05965_consen 59 LSNPAVQRLIESLPGADKCSNYKF 82 (86)
T ss_dssp TTSHHHHHHHTTSTTGGG-TT---
T ss_pred CCCHHHHHHHHhCCCcchhhcCCc
Confidence 467889999999999988777765
No 10
>PF00876 Innexin: Innexin; InterPro: IPR000990 The pannexin family combines invertebrate gap junction proteins and their vertebrate homologs. These proteins have been named innexins []. Gap junctions are composed of membrane proteins, which form a channel permeable for ions and small molecules connecting cytoplasm of adjacent cells. Although gap junctions provide similar functions in all multicellular organisms, until recently it was believed that vertebrates and invertebrates use unrelated proteins for this purpose. While the connexins family of gap junction proteins is well- characterised in vertebrates, no homologs have been found in invertebrates. In turn, gap junction molecules with no sequence homology to connexins have been identified in insects and nematodes. It has been suggested that these proteins are specific invertebrate gap junctions, and they were thus named innexins (invertebrate analog of connexins) []. As innexin homologs were recently identified in other taxonomic groups including vertebrates, indicating their ubiquitous distribution in the animal kingdom, they were called pannexins (from the Latin pan-all, throughout, and nexus-connection, bond) [, , ]. Genomes of vertebrates carry probably a conserved set of 3 pannexin paralogs (PANX1, PANX2 and PANX3). Invertebrate genomes may contain more than a dozen pannexin (innexin) genes. Vinnexins, viral homologs of pannexins/innexins, were identified in Polydnaviruses that occur in obligate symbiotic associations with parasitoid wasps. It was suggested that virally encoded vinnexin proteins may function to alter gap junction proteins in infected host cells, possibly modifying cell-cell communication during encapsulation responses in parasitized insects [, ]. Structurally pannexins are simillar to connexins. Both types of protein consist of a cytoplasmic N-terminal domain, followed by four transmembrane segments that delimit two extracellular and one cytoplasmic loops; the C- terminal domain is cytoplasmic.; GO: 0005921 gap junction
Probab=35.73 E-value=22 Score=27.46 Aligned_cols=23 Identities=17% Similarity=0.463 Sum_probs=19.1
Q ss_pred CCcccchhhhhHHHHhhhhhhhh
Q psy11705 19 GQKYFGIYRFLPLFFGVGAALEF 41 (81)
Q Consensus 19 GK~rfG~YRflP~FF~lGaamE~ 41 (81)
.++..+.|.|+|++.++-|+|=+
T Consensus 79 ~~~~i~YYQWVPfiL~lQA~lfy 101 (348)
T PF00876_consen 79 EKREISYYQWVPFILLLQAILFY 101 (348)
T ss_pred ccceEeeehhhHHHHHHHHHHHH
Confidence 45678999999999999998743
No 11
>PF04741 InvH: InvH outer membrane lipoprotein; InterPro: IPR006830 This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion [, ].; GO: 0009405 pathogenesis
Probab=33.80 E-value=21 Score=26.36 Aligned_cols=15 Identities=40% Similarity=0.817 Sum_probs=13.0
Q ss_pred hhhhhHHHHhhhhhh
Q psy11705 25 IYRFLPLFFGVGAAL 39 (81)
Q Consensus 25 ~YRflP~FF~lGaam 39 (81)
.|.-||+|+++|.|-
T Consensus 4 fysclpvf~ligcaq 18 (147)
T PF04741_consen 4 FYSCLPVFLLIGCAQ 18 (147)
T ss_pred hhhhhhHHHHhhhcc
Confidence 588899999999873
No 12
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=29.10 E-value=45 Score=28.33 Aligned_cols=21 Identities=33% Similarity=0.809 Sum_probs=16.5
Q ss_pred eeeeeecCc-chhhhHHhhHHH
Q psy11705 44 IKWEVNNGE-INFYKTYKRNQA 64 (81)
Q Consensus 44 In~~v~~G~-~nFYdvyrRkqa 64 (81)
|+|.+..+. +.||++|.+|.+
T Consensus 30 I~W~~~s~~~~gF~~~~q~R~a 51 (424)
T TIGR02986 30 ISWQVSSKKTTGFYTYYQARRA 51 (424)
T ss_pred eEEEecCCCCccchHHHHHHHH
Confidence 889886554 569999998865
No 13
>PF01757 Acyl_transf_3: Acyltransferase family; InterPro: IPR002656 This entry contains a range of acyltransferase enzymes as well as yet uncharacterised proteins from Caenorhabditis elegans. It also includes the protein OatA. The pathogenic bacteria, Staphylococcus aureus, is able to cause persistent infections due to its ability to resist the immune defence system. Lysozyme, a cell wall-lytic enzyme, is one of the first defence compounds induced in serum and tissues after the onset of infection. S. aureus has complete resistance to lysozyme action by O-acetylating its peptidoglycan (PG) by O-acetyltransferase (OatA) [, ]. Staphylococcus bacteria are one of the only bacterial genera that are resistant to lysozyme and tend to colonise the skin and mucosa of humans and animals []. OatA is an integral membrane protein. This entry also includes NolL proteins. NolL-dependent acetylation is specific for the fucosyl penta-N-acetylglucosamine species. In addition, the NolL protein caused elevated production of lipo-chitin oligosaccharides (LCOs). The NolL protein obtained from Rhizobium loti (Mesorhizobium loti) functions as an acetyl transferase [].; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=24.36 E-value=73 Score=21.08 Aligned_cols=15 Identities=33% Similarity=0.388 Sum_probs=11.9
Q ss_pred hhhHHHHhhhhhhhh
Q psy11705 27 RFLPLFFGVGAALEF 41 (81)
Q Consensus 27 RflP~FF~lGaamE~ 41 (81)
--+|+||++.|-+=.
T Consensus 47 ~~v~~Ff~iSG~~~~ 61 (340)
T PF01757_consen 47 FAVPLFFFISGYLLA 61 (340)
T ss_pred hHHHHHHHHHHHHHH
Confidence 358999999887655
No 14
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=23.58 E-value=57 Score=21.47 Aligned_cols=45 Identities=20% Similarity=0.184 Sum_probs=31.8
Q ss_pred hHHHHHHHHhcCCCcccchhhhhHHHHhhhhhhhhhheeeeeecCcchhhhHHhh
Q psy11705 7 SLRLKRLLKAWPGQKYFGIYRFLPLFFGVGAALEFAMIKWEVNNGEINFYKTYKR 61 (81)
Q Consensus 7 s~~ikrll~~~PGK~rfG~YRflP~FF~lGaamE~~MIn~~v~~G~~nFYdvyrR 61 (81)
..++|++++.+|.++|..+ +=..|++-|++=..|+ -..+|+.=|.
T Consensus 12 ~~~Lr~~c~~Lsp~~R~~v---vl~ml~~fa~l~ly~~-------~~ai~~~Gk~ 56 (85)
T PF13150_consen 12 DDRLRRYCGRLSPKQRLRV---VLVMLVLFAALCLYMT-------VSAIYDIGKE 56 (85)
T ss_pred HHHHHHHHhcCCHHHHHHH---HHHHHHHHHHHHHHHH-------HHHHHHhccC
Confidence 3679999999999988765 4455566666666676 2567777543
No 15
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=22.91 E-value=2.4e+02 Score=18.75 Aligned_cols=41 Identities=17% Similarity=0.304 Sum_probs=25.4
Q ss_pred HHHhhhhhhhhhheeeeeecCcchhhhHHhhHHHHHHHHHHhhhhh
Q psy11705 31 LFFGVGAALEFAMIKWEVNNGEINFYKTYKRNQAVILAEERLSKLE 76 (81)
Q Consensus 31 ~FF~lGaamE~~MIn~~v~~G~~nFYdvyrRkqae~~~e~rl~~~~ 76 (81)
+++++-+.+.+.++. |.-++-+..+-++-..+.++++++.+
T Consensus 7 vll~ll~~l~y~l~~-----g~~G~~~~~~l~~q~~~~~~e~~~l~ 47 (105)
T PRK00888 7 LLLALLVWLQYSLWF-----GKNGILDYWRVNDQVAAQQQTNAKLK 47 (105)
T ss_pred HHHHHHHHHHHHHhc-----cCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666777777774 77777666555555555555555443
No 16
>TIGR01996 PTS-II-BC-sucr PTS system, sucrose-specific IIBC component. This family is closely related to the trehalose transporting PTS IIBC enzymes and the B and C domains of each are described by subfamily-domain level TIGRFAMs models (TIGR00826 and TIGR00852, respectively).
Probab=22.28 E-value=49 Score=26.87 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=17.8
Q ss_pred HHHHHhcCCCcccchhhhhHHHHhhhhhhh
Q psy11705 11 KRLLKAWPGQKYFGIYRFLPLFFGVGAALE 40 (81)
Q Consensus 11 krll~~~PGK~rfG~YRflP~FF~lGaamE 40 (81)
-.+++.. |+ .++.|||++|+.++|=+
T Consensus 153 ~~il~~i-~~---a~f~fLPil~a~s~AKk 178 (461)
T TIGR01996 153 AEMINVF-TS---TAFAFLPILIGFSAAKR 178 (461)
T ss_pred HHHHHHH-HH---HHHHHHHHHHHHHHHHH
Confidence 3445444 44 78999999999776543
No 17
>TIGR00727 ISP4_OPT small oligopeptide transporter, OPT family. This model represents a family of transporters of small oligopeptides, demonstrated experimentally in three different species of yeast. A set of related proteins from the plant Arabidopsis thaliana forms an outgroup to the yeast set by neighbor joining analysis but is remarkably well conserved and is predicted here to have equivalent function.
Probab=21.53 E-value=53 Score=28.70 Aligned_cols=17 Identities=35% Similarity=0.495 Sum_probs=15.2
Q ss_pred chhhhhHHHHhhhhhhh
Q psy11705 24 GIYRFLPLFFGVGAALE 40 (81)
Q Consensus 24 G~YRflP~FF~lGaamE 40 (81)
|.|..||.||++||++=
T Consensus 572 ~~Y~~l~~~fliGa~~p 588 (681)
T TIGR00727 572 YIYPGLKWFWLIGACIG 588 (681)
T ss_pred CcchHHHHHHHHHHHHH
Confidence 37999999999999983
No 18
>PF02411 MerT: MerT mercuric transport protein; InterPro: IPR003457 MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerA).; GO: 0015097 mercury ion transmembrane transporter activity, 0015694 mercury ion transport, 0016020 membrane
Probab=21.14 E-value=44 Score=23.02 Aligned_cols=29 Identities=24% Similarity=0.548 Sum_probs=18.1
Q ss_pred cchhhhhHHHHhhhhhhhhhheeeeeecCcchhhhHHhhHHH
Q psy11705 23 FGIYRFLPLFFGVGAALEFAMIKWEVNNGEINFYKTYKRNQA 64 (81)
Q Consensus 23 fG~YRflP~FF~lGaamE~~MIn~~v~~G~~nFYdvyrRkqa 64 (81)
+.+|| |+|.++-.+. -.-.||+.||++++
T Consensus 47 lepyR--p~fi~~tl~~-----------lg~a~~~~yr~~~~ 75 (116)
T PF02411_consen 47 LEPYR--PYFIALTLLF-----------LGYAFWRLYRPRKA 75 (116)
T ss_pred HHhHH--HHHHHHHHHH-----------HHHHHHHHHccccc
Confidence 46777 7776554332 23678999987653
No 19
>PF12052 VGCC_beta4Aa_N: Voltage gated calcium channel subunit beta domain 4Aa N terminal; InterPro: IPR000584 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. Co-expression of beta subunit mRNA with alpha-1 subunit mRNA in xenopus oocytes produces increased calcium currents, which are accompanied by a shift in the voltage-dependence of activation to more negative membrane potentials. Conversely, microinjection of antisense oligonucleotides to beta subunit mRNA produces decreased calcium currents and shifts voltage-dependent activation to more positive membrane potentials. There are four distinct beta subunits: beta-1, beta-2, beta-3 and beta-4; and the magnitude of the shift in the voltage-dependence of activation of change to membrane potentials varies with the particular subtype []. This entry represents the beta subunits found in L-type voltage-gated calcium channels.; GO: 0005245 voltage-gated calcium channel activity, 0006816 calcium ion transport, 0051925 regulation of calcium ion transport via voltage-gated calcium channel activity; PDB: 1T0J_A 1T0H_A 2D46_A 1T3S_A 1T3L_A 4DEY_A 4DEX_A 1VYT_B 1VYU_A.
Probab=20.85 E-value=1.1e+02 Score=18.55 Aligned_cols=17 Identities=29% Similarity=0.190 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHHhhhhh
Q psy11705 60 KRNQAVILAEERLSKLE 76 (81)
Q Consensus 60 rRkqae~~~e~rl~~~~ 76 (81)
-|+.+|+++..+|+.+.
T Consensus 24 lRre~erqA~~QLekAk 40 (42)
T PF12052_consen 24 LRREAERQALAQLEKAK 40 (42)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 57888999888887764
No 20
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=20.47 E-value=22 Score=26.49 Aligned_cols=9 Identities=67% Similarity=1.412 Sum_probs=4.8
Q ss_pred CcchhhhHH
Q psy11705 51 GEINFYKTY 59 (81)
Q Consensus 51 G~~nFYdvy 59 (81)
|+..|||||
T Consensus 140 gei~FYDVy 148 (155)
T PF10777_consen 140 GEISFYDVY 148 (155)
T ss_pred CceeEEEeE
Confidence 455555554
No 21
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=20.31 E-value=81 Score=27.42 Aligned_cols=21 Identities=38% Similarity=0.893 Sum_probs=15.5
Q ss_pred eeeeeecC-cchhhhHHhhHHH
Q psy11705 44 IKWEVNNG-EINFYKTYKRNQA 64 (81)
Q Consensus 44 In~~v~~G-~~nFYdvyrRkqa 64 (81)
|+|.+..+ .+.||++|.+|-+
T Consensus 30 I~W~a~s~~~~gF~~t~q~R~~ 51 (511)
T PF09665_consen 30 IQWEAPSNRTSGFYDTYQKRRA 51 (511)
T ss_pred eEEEecCCCCCcchHHHHHHHH
Confidence 67777544 3569999998865
Done!