Query psy12486
Match_columns 148
No_of_seqs 105 out of 175
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 20:34:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12486hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4455|consensus 100.0 2.5E-33 5.3E-38 208.9 4.5 103 5-112 4-110 (110)
2 PF07019 Rab5ip: Rab5-interact 99.9 2.3E-24 5E-29 151.3 3.2 76 26-106 6-81 (81)
3 KOG3415|consensus 98.7 7.9E-09 1.7E-13 78.9 2.3 80 26-110 48-127 (129)
4 PF06839 zf-GRF: GRF zinc fing 72.6 1.7 3.7E-05 27.2 0.7 12 136-147 17-28 (45)
5 PF01102 Glycophorin_A: Glycop 64.1 5 0.00011 30.8 1.9 12 36-47 68-79 (122)
6 PRK13682 hypothetical protein; 55.6 23 0.00049 23.6 3.7 20 36-55 8-27 (51)
7 COG5487 Small integral membran 53.1 34 0.00074 23.0 4.2 18 37-54 9-26 (54)
8 PF07043 DUF1328: Protein of u 46.3 51 0.0011 20.7 4.0 22 37-58 4-25 (39)
9 PHA00024 IX minor coat protein 30.2 36 0.00078 20.8 1.4 17 94-110 8-24 (33)
10 PF04418 DUF543: Domain of unk 23.7 81 0.0018 22.2 2.5 11 36-46 36-46 (75)
11 PF13940 Ldr_toxin: Toxin Ldr, 23.7 39 0.00084 20.9 0.7 15 31-45 10-26 (35)
12 PF03613 EIID-AGA: PTS system 22.2 1.4E+02 0.0029 25.5 4.0 32 36-67 117-148 (264)
No 1
>KOG4455|consensus
Probab=99.98 E-value=2.5e-33 Score=208.86 Aligned_cols=103 Identities=42% Similarity=0.791 Sum_probs=96.7
Q ss_pred CCCCCCCCCccCHHHHHhhhc----cccccccchhhhhHhhhhhhccccchhhHHHHHHHHHHHHHHHHHHhCCCccccc
Q psy12486 5 KSSKPGDHTAYSELACAKQCS----CGRVLPAHLWLPLSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYF 80 (148)
Q Consensus 5 ~~~~~~~~~~~s~e~v~~N~~----~r~l~~~~d~sll~Gi~AGILGLtgl~GFlfy~i~~ll~sll~~~k~~~~~~~YF 80 (148)
.+.+..+++.++++|++.|+| +|+.+ |+++|++||||||||+.||+||+++.++.++++.+||+++|.+||
T Consensus 4 s~~~~~~~~~~s~aav~nN~kvl~f~Rt~~-----s~i~G~aAGILGltg~~GFi~Y~l~~~i~~il~~~K~~~~~~kyf 78 (110)
T KOG4455|consen 4 SKAEEVFIPIYSTAAVRNNKKVLEFVRTSS-----SAIAGCAAGILGLTGLHGFIFYFLSVLILSILLVLKAGGQWGKYF 78 (110)
T ss_pred chhhhcCCcchhHHHHhcCHHHHHHHHHHH-----HHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHCCCHHhhc
Confidence 344567889999999999999 66666 999999999999999999999999999889999999999999999
Q ss_pred cccceeeecCcccchhhhHHHHHhhhhhhhee
Q psy12486 81 LNRKSLLTNGFVGGLCTYVLFWTFFYTMGDKW 112 (148)
Q Consensus 81 ~s~~~i~~~g~~~~L~~FVL~WTl~Y~lVhvy 112 (148)
++|.++|++++++|+++|||+||+.|+|||+|
T Consensus 79 ~s~~~~f~~~f~~Gl~tyVl~Wtf~Y~lv~~~ 110 (110)
T KOG4455|consen 79 QSRRNLFTESFLGGLTTYVLAWTFFYGLVHVY 110 (110)
T ss_pred CchhHHHHHHHhchHHHHHHHHHHHhhhhccC
Confidence 99999999999999999999999999999997
No 2
>PF07019 Rab5ip: Rab5-interacting protein (Rab5ip)
Probab=99.89 E-value=2.3e-24 Score=151.25 Aligned_cols=76 Identities=45% Similarity=0.861 Sum_probs=72.6
Q ss_pred cccccccchhhhhHhhhhhhccccchhhHHHHHHHHHHHHHHHHHHhCCCccccccccceeeecCcccchhhhHHHHHhh
Q psy12486 26 CGRVLPAHLWLPLSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYFLNRKSLLTNGFVGGLCTYVLFWTFF 105 (148)
Q Consensus 26 ~r~l~~~~d~sll~Gi~AGILGLtgl~GFlfy~i~~ll~sll~~~k~~~~~~~YF~s~~~i~~~g~~~~L~~FVL~WTl~ 105 (148)
+||++ |+++|++||||||||+.||++|++++++++.+++.|+++++++||.+++|+++||+++++++|||+||++
T Consensus 6 ~r~~~-----a~~~Gi~aGILgLtg~~Gf~~f~~~~~~~s~~~~~~~~~~~~~~f~~~~~i~~~g~~~~l~~Fvl~Wtl~ 80 (81)
T PF07019_consen 6 CRQII-----ALLAGIAAGILGLTGLYGFIFFFLSSFLVSLLYYAKAGFPDEDYFGGPWEIFTEGFFSGLSTFVLFWTLF 80 (81)
T ss_pred HHHHH-----HHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHHHhcCChhhhcCCHHHHHHhhhhchHHHHHHHhhee
Confidence 45677 9999999999999999999999999999999988899999999999999999999999999999999998
Q ss_pred h
Q psy12486 106 Y 106 (148)
Q Consensus 106 Y 106 (148)
|
T Consensus 81 Y 81 (81)
T PF07019_consen 81 Y 81 (81)
T ss_pred C
Confidence 8
No 3
>KOG3415|consensus
Probab=98.69 E-value=7.9e-09 Score=78.93 Aligned_cols=80 Identities=23% Similarity=0.409 Sum_probs=68.3
Q ss_pred cccccccchhhhhHhhhhhhccccchhhHHHHHHHHHHHHHHHHHHhCCCccccccccceeeecCcccchhhhHHHHHhh
Q psy12486 26 CGRVLPAHLWLPLSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYFLNRKSLLTNGFVGGLCTYVLFWTFF 105 (148)
Q Consensus 26 ~r~l~~~~d~sll~Gi~AGILGLtgl~GFlfy~i~~ll~sll~~~k~~~~~~~YF~s~~~i~~~g~~~~L~~FVL~WTl~ 105 (148)
.||+. +++.|++-||+.|+|.-|.+.|...+..+.-+|+.+-..-.++=|-+-.++.-||++..+.+|.+.|+.+
T Consensus 48 ~rQVi-----~l~lGviwGi~pL~G~l~iv~f~~issgIvy~y~~~~~~VDEee~GG~weL~kEGf~asfa~FlvtWIi~ 122 (129)
T KOG3415|consen 48 IRQVI-----GLILGVIWGIIPLVGFLGIVLFLGISSGIVYLYYANFLKVDEEEYGGHWELLKEGFMASFALFLVTWIIF 122 (129)
T ss_pred HHHHH-----HHHHHHHHhhchhhhHHHHHHHHHhhhhHHHHHHHHHHhcCHHHhCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78888 9999999999999999999999888777777776555544444455558999999999999999999999
Q ss_pred hhhhh
Q psy12486 106 YTMGD 110 (148)
Q Consensus 106 Y~lVh 110 (148)
|++.|
T Consensus 123 Yt~~h 127 (129)
T KOG3415|consen 123 YTLAH 127 (129)
T ss_pred Hhhhc
Confidence 99988
No 4
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=72.55 E-value=1.7 Score=27.18 Aligned_cols=12 Identities=50% Similarity=1.068 Sum_probs=10.5
Q ss_pred ccCCCCcccccc
Q psy12486 136 PIPNQGMEFYSC 147 (148)
Q Consensus 136 ~~~~~~~~~~~~ 147 (148)
.-+|+||.||.|
T Consensus 17 ~~~N~GR~Fy~C 28 (45)
T PF06839_consen 17 TGPNPGRRFYKC 28 (45)
T ss_pred CCCCCCCcceEC
Confidence 458999999998
No 5
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=64.11 E-value=5 Score=30.76 Aligned_cols=12 Identities=33% Similarity=0.570 Sum_probs=10.7
Q ss_pred hhhHhhhhhhcc
Q psy12486 36 LPLSGCTAGILG 47 (148)
Q Consensus 36 sll~Gi~AGILG 47 (148)
.+++|+.|||+|
T Consensus 68 ~Ii~gv~aGvIg 79 (122)
T PF01102_consen 68 GIIFGVMAGVIG 79 (122)
T ss_dssp HHHHHHHHHHHH
T ss_pred ehhHHHHHHHHH
Confidence 789999999987
No 6
>PRK13682 hypothetical protein; Provisional
Probab=55.63 E-value=23 Score=23.59 Aligned_cols=20 Identities=25% Similarity=0.431 Sum_probs=16.6
Q ss_pred hhhHhhhhhhccccchhhHH
Q psy12486 36 LPLSGCTAGILGLTGFYGFG 55 (148)
Q Consensus 36 sll~Gi~AGILGLtgl~GFl 55 (148)
-++..++||++|.+|+.|-.
T Consensus 8 FliiA~iA~~lGF~GiAg~a 27 (51)
T PRK13682 8 FLVIALIAAVLGFGGIAGAA 27 (51)
T ss_pred HHHHHHHHHHhccchHHHHH
Confidence 45678899999999999843
No 7
>COG5487 Small integral membrane protein [Function unknown]
Probab=53.14 E-value=34 Score=22.98 Aligned_cols=18 Identities=33% Similarity=0.473 Sum_probs=14.5
Q ss_pred hhHhhhhhhccccchhhH
Q psy12486 37 PLSGCTAGILGLTGFYGF 54 (148)
Q Consensus 37 ll~Gi~AGILGLtgl~GF 54 (148)
++.-++||.||..|+.|-
T Consensus 9 lvialIa~~lGFgGiaga 26 (54)
T COG5487 9 LVIALIAGALGFGGIAGA 26 (54)
T ss_pred HHHHHHHHHhCcccHHHH
Confidence 456778999999999874
No 8
>PF07043 DUF1328: Protein of unknown function (DUF1328); InterPro: IPR009760 This entry represents several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown but is thought to be a membrane protein.; GO: 0005886 plasma membrane
Probab=46.30 E-value=51 Score=20.71 Aligned_cols=22 Identities=27% Similarity=0.422 Sum_probs=17.8
Q ss_pred hhHhhhhhhccccchhhHHHHH
Q psy12486 37 PLSGCTAGILGLTGFYGFGFYV 58 (148)
Q Consensus 37 ll~Gi~AGILGLtgl~GFlfy~ 58 (148)
++..++||++|.+|+.|-..=.
T Consensus 4 liiAliAg~lGF~Giag~a~~i 25 (39)
T PF07043_consen 4 LIIALIAGVLGFGGIAGTAAGI 25 (39)
T ss_pred HHHHHHHHHcCcccHHHHHHHH
Confidence 5678899999999999875443
No 9
>PHA00024 IX minor coat protein
Probab=30.21 E-value=36 Score=20.79 Aligned_cols=17 Identities=29% Similarity=0.604 Sum_probs=13.2
Q ss_pred chhhhHHHHHhhhhhhh
Q psy12486 94 GLCTYVLFWTFFYTMGD 110 (148)
Q Consensus 94 ~L~~FVL~WTl~Y~lVh 110 (148)
-+..|+|-|++.|++..
T Consensus 8 ffgA~ilG~~l~~~Il~ 24 (33)
T PHA00024 8 FFGAYILGWALFYGILV 24 (33)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35678999999998753
No 10
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. These proteins contain a conserved N-terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Probab=23.72 E-value=81 Score=22.20 Aligned_cols=11 Identities=18% Similarity=-0.085 Sum_probs=6.1
Q ss_pred hhhHhhhhhhc
Q psy12486 36 LPLSGCTAGIL 46 (148)
Q Consensus 36 sll~Gi~AGIL 46 (148)
++++|+++++|
T Consensus 36 G~~~G~~~s~l 46 (75)
T PF04418_consen 36 GFGIGVVFSLL 46 (75)
T ss_pred hhhHHHHHHHH
Confidence 55566555544
No 11
>PF13940 Ldr_toxin: Toxin Ldr, type I toxin-antitoxin system
Probab=23.71 E-value=39 Score=20.88 Aligned_cols=15 Identities=20% Similarity=0.078 Sum_probs=10.3
Q ss_pred ccchh--hhhHhhhhhh
Q psy12486 31 PAHLW--LPLSGCTAGI 45 (148)
Q Consensus 31 ~~~d~--sll~Gi~AGI 45 (148)
.-||+ -+++|+++++
T Consensus 10 ~WhDLAAP~iagIi~s~ 26 (35)
T PF13940_consen 10 FWHDLAAPIIAGIIASL 26 (35)
T ss_pred HHHHhHhHHHHHHHHHH
Confidence 34888 5677777765
No 12
>PF03613 EIID-AGA: PTS system mannose/fructose/sorbose family IID component; InterPro: IPR004704 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=22.22 E-value=1.4e+02 Score=25.54 Aligned_cols=32 Identities=13% Similarity=0.049 Sum_probs=24.4
Q ss_pred hhhHhhhhhhccccchhhHHHHHHHHHHHHHH
Q psy12486 36 LPLSGCTAGILGLTGFYGFGFYVLAVIGLWVL 67 (148)
Q Consensus 36 sll~Gi~AGILGLtgl~GFlfy~i~~ll~sll 67 (148)
-+.+|++++.--=-++.|-++|++.+.+..+.
T Consensus 117 pI~~~i~~~la~~Gn~lGpil~~~~~~~~~~~ 148 (264)
T PF03613_consen 117 PILASIAASLALQGNILGPILFLLLYNIIHFF 148 (264)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHHHHHHHH
Confidence 55666777766666888999999998887655
Done!