Query psy16163
Match_columns 85
No_of_seqs 131 out of 208
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 22:24:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16163.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16163hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1700|consensus 97.8 8.9E-06 1.9E-10 60.1 1.2 35 2-37 42-76 (200)
2 PF00412 LIM: LIM domain; Int 95.6 0.0032 7E-08 36.3 0.1 25 2-27 34-58 (58)
3 KOG1700|consensus 94.7 0.014 3E-07 43.2 1.1 35 2-36 143-177 (200)
4 COG0723 QcrA Rieske Fe-S prote 55.5 6.8 0.00015 27.7 1.3 20 11-32 121-140 (177)
5 KOG4239|consensus 53.9 3 6.5E-05 34.2 -0.9 26 55-80 39-64 (348)
6 KOG1703|consensus 53.5 5 0.00011 32.9 0.4 28 2-30 397-424 (479)
7 COG0194 Gmk Guanylate kinase [ 45.9 23 0.00049 26.8 2.8 47 13-67 3-65 (191)
8 KOG4440|consensus 43.5 15 0.00033 33.3 1.7 37 17-63 754-790 (993)
9 PF10281 Ish1: Putative stress 38.5 37 0.0008 18.6 2.3 18 51-68 19-37 (38)
10 PF07967 zf-C3HC: C3HC zinc fi 32.5 30 0.00065 23.5 1.5 16 56-71 2-17 (133)
11 TIGR01416 Rieske_proteo ubiqui 32.4 28 0.00061 25.1 1.4 17 13-31 131-147 (174)
12 PF00355 Rieske: Rieske [2Fe-2 31.4 28 0.0006 21.4 1.1 20 13-34 59-79 (97)
13 PF07526 POX: Associated with 31.4 15 0.00033 26.0 -0.1 17 58-74 79-99 (140)
14 PF09373 PMBR: Pseudomurein-bi 30.2 22 0.00048 19.2 0.4 20 54-73 3-22 (33)
15 PF11918 DUF3436: Domain of un 29.7 62 0.0013 20.2 2.4 18 50-67 32-49 (55)
16 cd03470 Rieske_cytochrome_bc1 29.0 35 0.00077 23.4 1.4 18 13-32 83-100 (126)
17 PF08846 DUF1816: Domain of un 28.4 36 0.00077 21.9 1.2 19 52-70 25-43 (68)
18 smart00574 POX domain associat 28.1 19 0.00041 26.2 -0.1 18 58-75 79-100 (140)
19 PF08586 Rsc14: RSC complex, R 27.1 38 0.00082 23.5 1.3 14 51-64 82-95 (101)
20 KOG1432|consensus 26.8 42 0.0009 28.0 1.7 24 10-36 315-338 (379)
21 KOG1044|consensus 23.6 26 0.00057 31.0 -0.0 24 7-31 172-195 (670)
22 cd03469 Rieske_RO_Alpha_N Ries 22.1 60 0.0013 20.6 1.5 19 12-32 57-75 (118)
23 PF07627 PSCyt3: Protein of un 21.5 17 0.00037 24.6 -1.3 25 10-36 64-88 (101)
24 TIGR01213 conserved hypothetic 21.4 32 0.0007 28.5 0.1 20 15-35 8-27 (388)
25 PHA03010 hypothetical protein; 21.3 42 0.00091 28.7 0.7 18 65-82 382-399 (546)
No 1
>KOG1700|consensus
Probab=97.77 E-value=8.9e-06 Score=60.06 Aligned_cols=35 Identities=40% Similarity=0.635 Sum_probs=33.0
Q ss_pred ccccccccceecCeeeecCCccccccCCccccCCcc
Q psy16163 2 TVTNTSVTYTHKGVPYCHVPCYGALFGPQLFGHGTR 37 (85)
Q Consensus 2 K~Ldsg~~aehdgk~YC~k~CY~klFGPkG~G~G~~ 37 (85)
|+|+++++++|++++|| +.||.+.|||+|+|++.+
T Consensus 42 k~l~~~~~~~~e~~~yc-~~~~~~~~~~~~~~~~~~ 76 (200)
T KOG1700|consen 42 KTLTLSGYSEHEGVPYC-KNCHVAQFGPKGGGFGKG 76 (200)
T ss_pred ccccccccccccccccc-ccchHhhhCccccccccc
Confidence 78999999999999999 699999999999999974
No 2
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=95.64 E-value=0.0032 Score=36.33 Aligned_cols=25 Identities=36% Similarity=0.760 Sum_probs=21.8
Q ss_pred ccccccccceecCeeeecCCcccccc
Q psy16163 2 TVTNTSVTYTHKGVPYCHVPCYGALF 27 (85)
Q Consensus 2 K~Ldsg~~aehdgk~YC~k~CY~klF 27 (85)
+.|.++.+.+.+++||| +.||.++|
T Consensus 34 ~~l~~~~~~~~~~~~~C-~~c~~~~f 58 (58)
T PF00412_consen 34 KPLNDGDFYEKDGKPYC-KDCYQKRF 58 (58)
T ss_dssp CBTTTSSEEEETTEEEE-HHHHHHHT
T ss_pred CccCCCeeEeECCEEEC-HHHHhhhC
Confidence 46778889999999999 69999987
No 3
>KOG1700|consensus
Probab=94.71 E-value=0.014 Score=43.19 Aligned_cols=35 Identities=17% Similarity=0.212 Sum_probs=32.4
Q ss_pred ccccccccceecCeeeecCCccccccCCccccCCc
Q psy16163 2 TVTNTSVTYTHKGVPYCHVPCYGALFGPQLFGHGT 36 (85)
Q Consensus 2 K~Ldsg~~aehdgk~YC~k~CY~klFGPkG~G~G~ 36 (85)
+.|++++.+++++.+||.+.|++.++|+.+++.+.
T Consensus 143 ~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~~ 177 (200)
T KOG1700|consen 143 KKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNEGF 177 (200)
T ss_pred cccCCcchhhcCCccccchhhheeecCCCcccccc
Confidence 57999999999999999889999999999998875
No 4
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=55.49 E-value=6.8 Score=27.65 Aligned_cols=20 Identities=30% Similarity=0.698 Sum_probs=17.5
Q ss_pred eecCeeeecCCccccccCCccc
Q psy16163 11 THKGVPYCHVPCYGALFGPQLF 32 (85)
Q Consensus 11 ehdgk~YC~k~CY~klFGPkG~ 32 (85)
..++.++| +||+..|-|.|.
T Consensus 121 ~~~~~~~C--PCHGS~yd~~g~ 140 (177)
T COG0723 121 GAEGGFFC--PCHGSRYDPDGG 140 (177)
T ss_pred CCCCeEEc--cCCCCeEcCCCC
Confidence 45688999 899999999985
No 5
>KOG4239|consensus
Probab=53.88 E-value=3 Score=34.17 Aligned_cols=26 Identities=19% Similarity=0.006 Sum_probs=23.2
Q ss_pred CCChhHHHHHhhhhheeeeCccceeE
Q psy16163 55 NMPRSHLESKLNLYNQYYDGKSGEIR 80 (85)
Q Consensus 55 ~i~r~~l~s~LktYN~y~e~k~~~i~ 80 (85)
.|...++|=.+|+||+|+++.+++.+
T Consensus 39 ~~~p~~~lv~~r~~~~~~~g~~~~~~ 64 (348)
T KOG4239|consen 39 HIQPLELLVPLRGHNFYTAGLLLPTW 64 (348)
T ss_pred ccCcccceeecccccccccccccccc
Confidence 66778888889999999999999988
No 6
>KOG1703|consensus
Probab=53.55 E-value=5 Score=32.89 Aligned_cols=28 Identities=29% Similarity=0.573 Sum_probs=24.2
Q ss_pred ccccccccceecCeeeecCCccccccCCc
Q psy16163 2 TVTNTSVTYTHKGVPYCHVPCYGALFGPQ 30 (85)
Q Consensus 2 K~Ldsg~~aehdgk~YC~k~CY~klFGPk 30 (85)
+.|.+..+-+++++||| ..||-++|+++
T Consensus 397 ~~~~~~~~~~~~~~pyc-e~~~~~~~~~~ 424 (479)
T KOG1703|consen 397 KPLKNSSFFESDGEPYC-EDHYKKLFTTK 424 (479)
T ss_pred CCCCCCcccccCCccch-hhhHhhhcccc
Confidence 56778888999999999 59999999955
No 7
>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]
Probab=45.92 E-value=23 Score=26.80 Aligned_cols=47 Identities=21% Similarity=0.137 Sum_probs=32.7
Q ss_pred cCeeeecCCccccccCCccccCCc------------cceeeeecccccc----CCCCCCCChhHHHHHhhh
Q psy16163 13 KGVPYCHVPCYGALFGPQLFGHGT------------RVESHTSFGKVEN----KPCGSNMPRSHLESKLNL 67 (85)
Q Consensus 13 dgk~YC~k~CY~klFGPkG~G~G~------------~~~sh~~~~~~~~----~~~~~~i~r~~l~s~Lkt 67 (85)
.|.++| +.||.|.|=++ -+.|||+..+-.. +-|. +|++.+|+++++.
T Consensus 3 ~G~l~v-------lsgPSG~GKsTl~k~L~~~~~l~~SVS~TTR~pR~gEv~G~dY~-Fvs~~EF~~~i~~ 65 (191)
T COG0194 3 KGLLIV-------LSGPSGVGKSTLVKALLEDDKLRFSVSATTRKPRPGEVDGVDYF-FVTEEEFEELIER 65 (191)
T ss_pred CceEEE-------EECCCCCCHHHHHHHHHhhcCeEEEEEeccCCCCCCCcCCceeE-eCCHHHHHHHHhc
Confidence 456666 68999988774 3567776655322 3333 8999999999874
No 8
>KOG4440|consensus
Probab=43.52 E-value=15 Score=33.31 Aligned_cols=37 Identities=30% Similarity=0.529 Sum_probs=28.6
Q ss_pred eecCCccccccCCccccCCccceeeeeccccccCCCCCCCChhHHHH
Q psy16163 17 YCHVPCYGALFGPQLFGHGTRVESHTSFGKVENKPCGSNMPRSHLES 63 (85)
Q Consensus 17 YC~k~CY~klFGPkG~G~G~~~~sh~~~~~~~~~~~~~~i~r~~l~s 63 (85)
-|.-.--+.|||-.|||.|- +.+.||-++|+=+=|.+
T Consensus 754 ~CeLvT~GeLFgRSgyGIGl----------qK~SPWt~~vtlaIL~~ 790 (993)
T KOG4440|consen 754 KCELVTTGELFGRSGYGIGL----------QKDSPWTQNVTLAILKS 790 (993)
T ss_pred ccceEecccccccccccccc----------ccCCCCcchhhHHHHHh
Confidence 35444568899999999997 78899998887655543
No 9
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=38.47 E-value=37 Score=18.58 Aligned_cols=18 Identities=17% Similarity=0.137 Sum_probs=12.3
Q ss_pred CCCCCC-ChhHHHHHhhhh
Q psy16163 51 PCGSNM-PRSHLESKLNLY 68 (85)
Q Consensus 51 ~~~~~i-~r~~l~s~LktY 68 (85)
|..... +|++|+.++|.+
T Consensus 19 ~~~~~~~~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 19 PVPKSAKTRDELLKLAKKN 37 (38)
T ss_pred CCCCCCCCHHHHHHHHHHh
Confidence 333444 899999888754
No 10
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 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 zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=32.45 E-value=30 Score=23.50 Aligned_cols=16 Identities=13% Similarity=0.314 Sum_probs=14.0
Q ss_pred CChhHHHHHhhhhhee
Q psy16163 56 MPRSHLESKLNLYNQY 71 (85)
Q Consensus 56 i~r~~l~s~LktYN~y 71 (85)
-+|.+|+..|+||+..
T Consensus 2 ~~r~~~l~RL~Tf~~~ 17 (133)
T PF07967_consen 2 WDREDFLRRLETFKSL 17 (133)
T ss_pred CCHHHHHHHHHHcccc
Confidence 3699999999999974
No 11
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=32.41 E-value=28 Score=25.12 Aligned_cols=17 Identities=35% Similarity=0.837 Sum_probs=14.5
Q ss_pred cCeeeecCCccccccCCcc
Q psy16163 13 KGVPYCHVPCYGALFGPQL 31 (85)
Q Consensus 13 dgk~YC~k~CY~klFGPkG 31 (85)
.+.++| +||+..|.+.|
T Consensus 131 ~~~~~C--PcHgs~Fd~~G 147 (174)
T TIGR01416 131 KGGFFC--PCHGSHYDTAG 147 (174)
T ss_pred CCEEEe--CCCCCEECCCC
Confidence 356999 89999999975
No 12
>PF00355 Rieske: Rieske [2Fe-2S] domain; InterPro: IPR017941 There are multiple types of iron-sulphur clusters which are grouped into three main categories based on their atomic content: [2Fe-2S], [3Fe-4S], [4Fe-4S] (see PDOC00176 from PROSITEDOC), and other hybrid or mixed metal types. Two general types of [2Fe-2S] clusters are known and they differ in their coordinating residues. The ferredoxin-type [2Fe-2S] clusters are coordinated to the protein by four cysteine residues (see PDOC00175 from PROSITEDOC). The Rieske-type [2Fe-2S] cluster is coordinated to its protein by two cysteine residues and two histidine residues [, ]. The structure of several Rieske domains has been solved []. It contains three layers of antiparallel beta sheets forming two beta sandwiches. Both beta sandwiches share the central sheet 2. The metal-binding site is at the top of the beta sandwich formed by the sheets 2 and 3. The Fe1 iron of the Rieske cluster is coordinated by two cysteines while the other iron Fe2 is coordinated by two histidines. Two inorganic sulphide ions bridge the two iron ions forming a flat, rhombic cluster. Rieske-type iron-sulphur clusters are common to electron transfer chains of mitochondria and chloroplast and to non-haem iron oxygenase systems: The Rieske protein of the Ubiquinol-cytochrome c reductase (1.10.2.2 from EC) (also known as the bc1 complex or complex III), a complex of the electron transport chains of mitochondria and of some aerobic prokaryotes; it catalyses the oxidoreduction of ubiquinol and cytochrome c. The Rieske protein of chloroplastic plastoquinone-plastocyanin reductase (1.10.99.1 from EC) (also known as the b6f complex). It is functionally similar to the bc1 complex and catalyses the oxidoreduction of plastoquinol and cytochrome f. Bacterial naphthalene 1,2-dioxygenase subunit alpha, a component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol. Bacterial 3-phenylpropionate dioxygenase ferredoxin subunit. Bacterial toluene monoxygenase. Bacterial biphenyl dioxygenase. ; GO: 0016491 oxidoreductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 2XRX_A 2XR8_O 2XSH_G 2XSO_I 2YFI_C 2YFL_A 2YFJ_K 1G8J_D 1G8K_D 1NYK_B ....
Probab=31.44 E-value=28 Score=21.44 Aligned_cols=20 Identities=35% Similarity=0.464 Sum_probs=16.4
Q ss_pred cCeeeecCCccccccCCc-cccC
Q psy16163 13 KGVPYCHVPCYGALFGPQ-LFGH 34 (85)
Q Consensus 13 dgk~YC~k~CY~klFGPk-G~G~ 34 (85)
++.+.| +|++..|.+. |--.
T Consensus 59 ~~~i~C--p~Hg~~Fd~~tG~~~ 79 (97)
T PF00355_consen 59 GGVIVC--PCHGWRFDLDTGECV 79 (97)
T ss_dssp TTEEEE--TTTTEEEETTTSBEE
T ss_pred cCEEEe--CCcCCEEeCCCceEe
Confidence 578999 8999999999 6433
No 13
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=31.35 E-value=15 Score=26.00 Aligned_cols=17 Identities=47% Similarity=0.757 Sum_probs=13.8
Q ss_pred hhHHHHHh----hhhheeeeC
Q psy16163 58 RSHLESKL----NLYNQYYDG 74 (85)
Q Consensus 58 r~~l~s~L----ktYN~y~e~ 74 (85)
|+.|+++| +.||+||++
T Consensus 79 K~KLl~mL~eVd~RY~qY~~Q 99 (140)
T PF07526_consen 79 KAKLLSMLDEVDRRYRQYYDQ 99 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 67788888 579999975
No 14
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=30.22 E-value=22 Score=19.22 Aligned_cols=20 Identities=10% Similarity=0.333 Sum_probs=18.2
Q ss_pred CCCChhHHHHHhhhhheeee
Q psy16163 54 SNMPRSHLESKLNLYNQYYD 73 (85)
Q Consensus 54 ~~i~r~~l~s~LktYN~y~e 73 (85)
..|++++++..++..+.|++
T Consensus 3 ~~i~~~~~~d~a~rv~~f~~ 22 (33)
T PF09373_consen 3 GTISKEEYLDMASRVNNFYE 22 (33)
T ss_pred ceecHHHHHHHHHHHHHHHH
Confidence 37999999999999999995
No 15
>PF11918 DUF3436: Domain of unknown function (DUF3436); InterPro: IPR024591 This uncharacterised N-terminal domain is associated with the interphotoreceptor retinol-binding protein family. It is about 50 amino acids in length and has two conserved sequence motifs: DPRL and SYEP.
Probab=29.69 E-value=62 Score=20.18 Aligned_cols=18 Identities=22% Similarity=0.265 Sum_probs=14.9
Q ss_pred CCCCCCCChhHHHHHhhh
Q psy16163 50 KPCGSNMPRSHLESKLNL 67 (85)
Q Consensus 50 ~~~~~~i~r~~l~s~Lkt 67 (85)
-|--+++|.+||++.|++
T Consensus 32 ~p~~~~Lt~EqLla~lq~ 49 (55)
T PF11918_consen 32 PPALPNLTPEQLLAMLQK 49 (55)
T ss_pred CCCCCCcCHHHHHHHHHh
Confidence 455579999999999985
No 16
>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=28.99 E-value=35 Score=23.36 Aligned_cols=18 Identities=28% Similarity=0.645 Sum_probs=15.1
Q ss_pred cCeeeecCCccccccCCccc
Q psy16163 13 KGVPYCHVPCYGALFGPQLF 32 (85)
Q Consensus 13 dgk~YC~k~CY~klFGPkG~ 32 (85)
.+.++| +||+..|-..|-
T Consensus 83 ~~~~~C--PcHgs~Fdl~G~ 100 (126)
T cd03470 83 YGGFFC--PCHGSHYDASGR 100 (126)
T ss_pred CCEEEe--cCcCCEECCCCe
Confidence 467999 899999999753
No 17
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=28.43 E-value=36 Score=21.85 Aligned_cols=19 Identities=26% Similarity=0.253 Sum_probs=15.7
Q ss_pred CCCCCChhHHHHHhhhhhe
Q psy16163 52 CGSNMPRSHLESKLNLYNQ 70 (85)
Q Consensus 52 ~~~~i~r~~l~s~LktYN~ 70 (85)
|||+++|+++.+.+-.|=.
T Consensus 25 FGPF~s~~eA~~~~~gyie 43 (68)
T PF08846_consen 25 FGPFDSREEAEAALPGYIE 43 (68)
T ss_pred eCCcCCHHHHHHHhccHHH
Confidence 6789999999998877643
No 18
>smart00574 POX domain associated with HOX domains.
Probab=28.05 E-value=19 Score=26.16 Aligned_cols=18 Identities=33% Similarity=0.634 Sum_probs=13.2
Q ss_pred hhHHHHHh----hhhheeeeCc
Q psy16163 58 RSHLESKL----NLYNQYYDGK 75 (85)
Q Consensus 58 r~~l~s~L----ktYN~y~e~k 75 (85)
|+.|+++| +.||+||++=
T Consensus 79 k~kLl~mL~eVd~RY~qY~~qm 100 (140)
T smart00574 79 KAKLLSMLEEVDRRYKHYYEQM 100 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 34577777 6899999763
No 19
>PF08586 Rsc14: RSC complex, Rsc14/Ldb7 subunit; InterPro: IPR013895 RSC is an ATP-dependent chromatin remodelling complex found in yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7 interact physically and/or functionally with Rsc3, Rsc30, and Htl1 to form a module important for a broad range of RSC functions [].
Probab=27.14 E-value=38 Score=23.50 Aligned_cols=14 Identities=43% Similarity=0.591 Sum_probs=11.9
Q ss_pred CCCCCCChhHHHHH
Q psy16163 51 PCGSNMPRSHLESK 64 (85)
Q Consensus 51 ~~~~~i~r~~l~s~ 64 (85)
=.|..+||.+|+||
T Consensus 82 LLGgyVPr~QLEsL 95 (101)
T PF08586_consen 82 LLGGYVPRQQLESL 95 (101)
T ss_pred cccCcCCHHHHHhh
Confidence 35789999999997
No 20
>KOG1432|consensus
Probab=26.84 E-value=42 Score=28.01 Aligned_cols=24 Identities=33% Similarity=0.487 Sum_probs=18.4
Q ss_pred ceecCeeeecCCccccccCCccccCCc
Q psy16163 10 YTHKGVPYCHVPCYGALFGPQLFGHGT 36 (85)
Q Consensus 10 aehdgk~YC~k~CY~klFGPkG~G~G~ 36 (85)
++++++++- ||+.-+|=.|||+++
T Consensus 315 ~~~k~~~wl---CygGgaGyggYg~~g 338 (379)
T KOG1432|consen 315 GELKGELWL---CYGGGAGYGGYGIGG 338 (379)
T ss_pred cccCCeEEE---EecCCCccCCcCcCC
Confidence 344555554 999999999999875
No 21
>KOG1044|consensus
Probab=23.62 E-value=26 Score=31.03 Aligned_cols=24 Identities=38% Similarity=0.682 Sum_probs=19.2
Q ss_pred cccceecCeeeecCCccccccCCcc
Q psy16163 7 SVTYTHKGVPYCHVPCYGALFGPQL 31 (85)
Q Consensus 7 g~~aehdgk~YC~k~CY~klFGPkG 31 (85)
|-.-.+||+||| -.||.+.||-|=
T Consensus 172 gey~skdg~pyc-e~dy~~~fgvkc 195 (670)
T KOG1044|consen 172 GEYMSKDGVPYC-EKDYQAKFGVKC 195 (670)
T ss_pred ceeeccCCCcch-hhhhhhhcCeeh
Confidence 334568999999 599999999873
No 22
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=22.11 E-value=60 Score=20.63 Aligned_cols=19 Identities=21% Similarity=0.286 Sum_probs=15.8
Q ss_pred ecCeeeecCCccccccCCccc
Q psy16163 12 HKGVPYCHVPCYGALFGPQLF 32 (85)
Q Consensus 12 hdgk~YC~k~CY~klFGPkG~ 32 (85)
.++.+.| +||+..|...|-
T Consensus 57 ~~~~i~C--p~Hg~~Fd~~G~ 75 (118)
T cd03469 57 NAGRLVC--PYHGWTYDLDGK 75 (118)
T ss_pred CCCEEEC--CCCCCEECCCCc
Confidence 4567999 899999999953
No 23
>PF07627 PSCyt3: Protein of unknown function (DUF1588); InterPro: IPR013039 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=21.46 E-value=17 Score=24.57 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=20.0
Q ss_pred ceecCeeeecCCccccccCCccccCCc
Q psy16163 10 YTHKGVPYCHVPCYGALFGPQLFGHGT 36 (85)
Q Consensus 10 aehdgk~YC~k~CY~klFGPkG~G~G~ 36 (85)
..|...+.| ..|+. ++-|=||++=.
T Consensus 64 ~~h~~~~~C-a~CH~-~iDP~Gf~fE~ 88 (101)
T PF07627_consen 64 EQHTENPAC-ASCHR-KIDPLGFAFEN 88 (101)
T ss_pred HhhcCCCcH-HHHhh-hhCccchhhhc
Confidence 346677889 59999 89999988765
No 24
>TIGR01213 conserved hypothetical protein TIGR01213. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.
Probab=21.44 E-value=32 Score=28.46 Aligned_cols=20 Identities=35% Similarity=0.775 Sum_probs=17.2
Q ss_pred eeeecCCccccccCCccccCC
Q psy16163 15 VPYCHVPCYGALFGPQLFGHG 35 (85)
Q Consensus 15 k~YC~k~CY~klFGPkG~G~G 35 (85)
-|-|+ .|.+++|+-.|+|.+
T Consensus 8 ~plCd-~CLGR~Fa~~~~gl~ 27 (388)
T TIGR01213 8 YPLCD-RCLGRLFAKLGHGTS 27 (388)
T ss_pred CCCCc-cccchhhhhhccCCC
Confidence 36795 999999999999975
No 25
>PHA03010 hypothetical protein; Provisional
Probab=21.25 E-value=42 Score=28.72 Aligned_cols=18 Identities=39% Similarity=0.608 Sum_probs=15.4
Q ss_pred hhhhheeeeCccceeEee
Q psy16163 65 LNLYNQYYDGKSGEIRSR 82 (85)
Q Consensus 65 LktYN~y~e~k~~~i~~r 82 (85)
=|+|||||+-++.+|-+.
T Consensus 382 Nki~NgyyNtet~EI~ss 399 (546)
T PHA03010 382 NKIFNCYYNTESEEIFSS 399 (546)
T ss_pred CeeeeeEEecccceeeeh
Confidence 378999999999998774
Done!