Query 033208
Match_columns 125
No_of_seqs 45 out of 47
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 11:08:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033208.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033208hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11876 petM cytochrome b6-f 99.4 2.9E-13 6.4E-18 82.3 3.5 30 90-119 2-31 (32)
2 PF08041 PetM: PetM family of 99.3 2.3E-12 5.1E-17 77.9 3.0 30 91-120 1-30 (31)
3 PRK00523 hypothetical protein; 37.3 41 0.0009 23.7 2.8 16 101-116 12-27 (72)
4 PLN02237 glyceraldehyde-3-phos 36.2 28 0.0006 31.3 2.3 30 37-68 27-56 (442)
5 PF06024 DUF912: Nucleopolyhed 34.7 34 0.00074 24.2 2.1 29 94-122 66-94 (101)
6 PRK01844 hypothetical protein; 33.4 52 0.0011 23.2 2.8 16 101-116 11-26 (72)
7 PF01102 Glycophorin_A: Glycop 32.9 46 0.001 25.0 2.7 28 93-120 67-94 (122)
8 COG4674 Uncharacterized ABC-ty 31.9 26 0.00057 29.8 1.4 20 30-49 4-24 (249)
9 PF03672 UPF0154: Uncharacteri 28.9 43 0.00092 23.1 1.8 13 104-116 7-19 (64)
10 COG2991 Uncharacterized protei 27.7 68 0.0015 23.1 2.7 24 93-116 3-26 (77)
11 COG0411 LivG ABC-type branched 27.5 23 0.00051 29.8 0.3 17 34-50 7-24 (250)
12 PTZ00382 Variant-specific surf 27.4 29 0.00063 24.6 0.8 21 96-116 73-93 (96)
13 KOG3488 Dolichol phosphate-man 27.2 66 0.0014 23.3 2.6 24 95-118 53-76 (81)
14 PF01837 DUF39: Domain of unkn 24.9 40 0.00086 29.7 1.3 48 3-50 28-75 (340)
15 PF07885 Ion_trans_2: Ion chan 24.3 1.2E+02 0.0025 19.4 3.1 36 81-117 42-77 (79)
16 cd06153 YjgF_YER057c_UK114_lik 24.1 1.2E+02 0.0027 21.4 3.5 40 29-71 12-51 (114)
17 PF03591 AzlC: AzlC protein; 23.8 2.8E+02 0.0062 20.3 5.5 45 57-114 94-138 (143)
18 PF11808 DUF3329: Domain of un 23.2 1.2E+02 0.0026 20.9 3.2 24 91-114 7-30 (90)
19 PF07297 DPM2: Dolichol phosph 22.4 1.2E+02 0.0025 21.5 3.0 27 93-119 49-75 (78)
20 PF11772 EpuA: DNA-directed RN 21.4 48 0.001 21.4 0.8 20 96-115 4-23 (47)
21 TIGR01167 LPXTG_anchor LPXTG-m 21.3 79 0.0017 17.5 1.7 20 95-115 10-29 (34)
22 cd06155 eu_AANH_C_1 A group of 21.1 1.3E+02 0.0027 20.5 3.0 38 25-70 3-40 (101)
No 1
>PRK11876 petM cytochrome b6-f complex subunit PetM; Reviewed
Probab=99.39 E-value=2.9e-13 Score=82.27 Aligned_cols=30 Identities=47% Similarity=0.686 Sum_probs=28.9
Q ss_pred hhhHHHHHHHHHHHHHHHHhhhhhhheeeh
Q 033208 90 ASEIFRIAAIMNGLVLIGVAVGFVLLRIEA 119 (125)
Q Consensus 90 agEIf~iA~im~~LtLVGlavGFvLLrvea 119 (125)
++|||++|+|||+|||||+++||+|||||+
T Consensus 2 a~EIf~~A~i~~~LvlvGlalGf~LLkiqg 31 (32)
T PRK11876 2 ASEIFGIAALFWVLIPVGLAGGALLLKLQG 31 (32)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHheeeec
Confidence 689999999999999999999999999985
No 2
>PF08041 PetM: PetM family of cytochrome b6f complex subunit 7; InterPro: IPR012595 This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta haem's and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin [].; GO: 0009512 cytochrome b6f complex; PDB: 2ZT9_F 1Q90_M 2E76_F 2E75_F 2E74_F 2D2C_S 1VF5_S.
Probab=99.28 E-value=2.3e-12 Score=77.88 Aligned_cols=30 Identities=60% Similarity=0.997 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhheeehh
Q 033208 91 SEIFRIAAIMNGLVLIGVAVGFVLLRIEAS 120 (125)
Q Consensus 91 gEIf~iA~im~~LtLVGlavGFvLLrvea~ 120 (125)
+|||++|.|||+|||||+++||+|||||..
T Consensus 1 ~EIf~~a~i~~~lvlvGla~Gf~LLkiQG~ 30 (31)
T PF08041_consen 1 GEIFNIAVICFGLVLVGLALGFVLLKIQGG 30 (31)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTT-
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHhheeecC
Confidence 699999999999999999999999999754
No 3
>PRK00523 hypothetical protein; Provisional
Probab=37.33 E-value=41 Score=23.75 Aligned_cols=16 Identities=19% Similarity=0.565 Sum_probs=12.6
Q ss_pred HHHHHHHHhhhhhhhe
Q 033208 101 NGLVLIGVAVGFVLLR 116 (125)
Q Consensus 101 ~~LtLVGlavGFvLLr 116 (125)
....|+|+++||++.|
T Consensus 12 i~~li~G~~~Gffiar 27 (72)
T PRK00523 12 IPLLIVGGIIGYFVSK 27 (72)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3447789999999876
No 4
>PLN02237 glyceraldehyde-3-phosphate dehydrogenase B
Probab=36.15 E-value=28 Score=31.34 Aligned_cols=30 Identities=30% Similarity=0.499 Sum_probs=19.9
Q ss_pred ccccCCcccccceeeecccccHHHHHHHHHHh
Q 033208 37 LNSFGGLKAQNSLTSLGMPVSTEQAFAKIVSS 68 (125)
Q Consensus 37 lnsfgGLKa~N~V~~LG~pv~teq~FAkvvss 68 (125)
+..|.|||+...+.. +. -++|..|...+.+
T Consensus 27 ~~~~~g~~~~~~~~~-~~-~~~~~~~~~~~~~ 56 (442)
T PLN02237 27 VAEFSGLRASSCVTF-AK-NAREASFFDVVAS 56 (442)
T ss_pred ccccccccccccccc-cc-cccchhHHHHhhh
Confidence 889999999776543 33 3455566555555
No 5
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=34.70 E-value=34 Score=24.23 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHhhhhhhheeehhhh
Q 033208 94 FRIAAIMNGLVLIGVAVGFVLLRIEASVE 122 (125)
Q Consensus 94 f~iA~im~~LtLVGlavGFvLLrvea~ve 122 (125)
+.+.+++..|+|+-+..-|+.||-++-..
T Consensus 66 i~lls~v~IlVily~IyYFVILRer~~~~ 94 (101)
T PF06024_consen 66 ISLLSFVCILVILYAIYYFVILRERQKSI 94 (101)
T ss_pred HHHHHHHHHHHHHhhheEEEEEecccccc
Confidence 34444555667778888999999876543
No 6
>PRK01844 hypothetical protein; Provisional
Probab=33.35 E-value=52 Score=23.24 Aligned_cols=16 Identities=38% Similarity=0.632 Sum_probs=12.4
Q ss_pred HHHHHHHHhhhhhhhe
Q 033208 101 NGLVLIGVAVGFVLLR 116 (125)
Q Consensus 101 ~~LtLVGlavGFvLLr 116 (125)
..-.|+|+++||++.|
T Consensus 11 I~~li~G~~~Gff~ar 26 (72)
T PRK01844 11 VVALVAGVALGFFIAR 26 (72)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3445779999999876
No 7
>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=32.94 E-value=46 Score=25.04 Aligned_cols=28 Identities=21% Similarity=0.355 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhheeehh
Q 033208 93 IFRIAAIMNGLVLIGVAVGFVLLRIEAS 120 (125)
Q Consensus 93 If~iA~im~~LtLVGlavGFvLLrvea~ 120 (125)
+.-|-++|.|++++-+.+-|++.|...-
T Consensus 67 ~~Ii~gv~aGvIg~Illi~y~irR~~Kk 94 (122)
T PF01102_consen 67 IGIIFGVMAGVIGIILLISYCIRRLRKK 94 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHS--
T ss_pred eehhHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3344577888888888889999887643
No 8
>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]
Probab=31.87 E-value=26 Score=29.78 Aligned_cols=20 Identities=50% Similarity=0.924 Sum_probs=17.8
Q ss_pred ceEEEeecc-ccCCcccccce
Q 033208 30 KVSYITGLN-SFGGLKAQNSL 49 (125)
Q Consensus 30 ~v~~i~gln-sfgGLKa~N~V 49 (125)
.+.|++|++ ||||.||.|++
T Consensus 4 ~iL~~~~vsVsF~GF~Aln~l 24 (249)
T COG4674 4 IILYLDGVSVSFGGFKALNDL 24 (249)
T ss_pred ceEEEeceEEEEcceeeeeee
Confidence 678889987 89999999986
No 9
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=28.92 E-value=43 Score=23.08 Aligned_cols=13 Identities=31% Similarity=0.963 Sum_probs=10.7
Q ss_pred HHHHHhhhhhhhe
Q 033208 104 VLIGVAVGFVLLR 116 (125)
Q Consensus 104 tLVGlavGFvLLr 116 (125)
.++|+++||++.|
T Consensus 7 li~G~~~Gff~ar 19 (64)
T PF03672_consen 7 LIVGAVIGFFIAR 19 (64)
T ss_pred HHHHHHHHHHHHH
Confidence 3679999999876
No 10
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.69 E-value=68 Score=23.12 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhe
Q 033208 93 IFRIAAIMNGLVLIGVAVGFVLLR 116 (125)
Q Consensus 93 If~iA~im~~LtLVGlavGFvLLr 116 (125)
.|-+....|.|+.+|+++||..-|
T Consensus 3 t~lltFg~Fllvi~gMsiG~I~kr 26 (77)
T COG2991 3 TFLLTFGIFLLVIAGMSIGYIFKR 26 (77)
T ss_pred cHHHHHHHHHHHHHHHhHhhheec
Confidence 356777889999999999998654
No 11
>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]
Probab=27.46 E-value=23 Score=29.81 Aligned_cols=17 Identities=47% Similarity=0.919 Sum_probs=13.4
Q ss_pred Eeec-cccCCccccccee
Q 033208 34 ITGL-NSFGGLKAQNSLT 50 (125)
Q Consensus 34 i~gl-nsfgGLKa~N~V~ 50 (125)
++++ +.||||+|.|+|.
T Consensus 7 v~~l~k~FGGl~Al~~Vs 24 (250)
T COG0411 7 VRGLSKRFGGLTAVNDVS 24 (250)
T ss_pred eccceeecCCEEEEecee
Confidence 4444 5899999999984
No 12
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=27.39 E-value=29 Score=24.63 Aligned_cols=21 Identities=19% Similarity=0.194 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHhhhhhhhe
Q 033208 96 IAAIMNGLVLIGVAVGFVLLR 116 (125)
Q Consensus 96 iA~im~~LtLVGlavGFvLLr 116 (125)
|+++.....|||+++.|++.|
T Consensus 73 vg~~~~v~~lv~~l~w~f~~r 93 (96)
T PTZ00382 73 VAVVAVVGGLVGFLCWWFVCR 93 (96)
T ss_pred eehhhHHHHHHHHHhheeEEe
Confidence 334444456677777777766
No 13
>KOG3488 consensus Dolichol phosphate-mannose regulatory protein (DPM2) [Posttranslational modification, protein turnover, chaperones]
Probab=27.17 E-value=66 Score=23.31 Aligned_cols=24 Identities=33% Similarity=0.444 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHhhhhhhheee
Q 033208 95 RIAAIMNGLVLIGVAVGFVLLRIE 118 (125)
Q Consensus 95 ~iA~im~~LtLVGlavGFvLLrve 118 (125)
-+|+-.+.|.|+|+.++++.||-.
T Consensus 53 Pvaagl~ll~lig~Fis~vMlKsk 76 (81)
T KOG3488|consen 53 PVAAGLFLLCLIGTFISLVMLKSK 76 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhcc
Confidence 467788999999999999999854
No 14
>PF01837 DUF39: Domain of unknown function DUF39; InterPro: IPR002708 This domain, whose function is not known, is about 320 residues long and is found in proteins that have two C-terminal CBS domains, IPR000644 from INTERPRO. The protein O26943 from SWISSPROT is described as inosine-5'-monophosphate dehydrogenase related protein VIII, based on the sequence simarity it shares to the CBS domains.
Probab=24.91 E-value=40 Score=29.69 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=38.1
Q ss_pred ccccccCcchhhhhhhcccccccccccceEEEeeccccCCccccccee
Q 033208 3 TASATLSPATFISATAAAGSCRRRRSVKVSYITGLNSFGGLKAQNSLT 50 (125)
Q Consensus 3 ta~A~~~p~ti~~~~~~~g~~~~r~~~~v~~i~glnsfgGLKa~N~V~ 50 (125)
.+.+||.|-.=+.+..+++++.+.....-+++-|...|+||-+---..
T Consensus 28 VTtgTfg~M~ssga~lnfg~~~P~i~~~~v~LNgV~ay~GlgaVD~~l 75 (340)
T PF01837_consen 28 VTTGTFGPMCSSGAFLNFGHSDPPIKMEKVWLNGVPAYGGLGAVDLYL 75 (340)
T ss_pred EecccccccccceeEEECCCCCCCeeEEEEEECCEEccccceEEEEEE
Confidence 356777777777788889998888777889999999999976655443
No 15
>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []. ; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....
Probab=24.30 E-value=1.2e+02 Score=19.39 Aligned_cols=36 Identities=19% Similarity=0.384 Sum_probs=28.8
Q ss_pred cccccccchhhhHHHHHHHHHHHHHHHHhhhhhhhee
Q 033208 81 GVLTSTCNAASEIFRIAAIMNGLVLIGVAVGFVLLRI 117 (125)
Q Consensus 81 GAlss~c~~agEIf~iA~im~~LtLVGlavGFvLLrv 117 (125)
|-+..+ +..+.++.+--+++++.+.++.++...-.+
T Consensus 42 GDi~p~-t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l 77 (79)
T PF07885_consen 42 GDIVPQ-TPAGRIFTIIYMLIGIFLFALFLSVLASVL 77 (79)
T ss_dssp SSSSTS-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccCC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445555 788999999999999999999988765443
No 16
>cd06153 YjgF_YER057c_UK114_like_5 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=24.12 E-value=1.2e+02 Score=21.42 Aligned_cols=40 Identities=15% Similarity=0.217 Sum_probs=30.1
Q ss_pred cceEEEeeccccCCcccccceeeecccccHHHHHHHHHHhhcc
Q 033208 29 VKVSYITGLNSFGGLKAQNSLTSLGMPVSTEQAFAKIVSSVRA 71 (125)
Q Consensus 29 ~~v~~i~glnsfgGLKa~N~V~~LG~pv~teq~FAkvvsslk~ 71 (125)
++..||-|.-+.. ++..+..-++.--++|+|.++..-|+.
T Consensus 12 g~~v~vSGq~~~d---~~g~~~~~d~~~Q~~~~l~ni~~~L~~ 51 (114)
T cd06153 12 RTHLFISGTASIV---GHGTVHPGDVEAQTRETLENIEALLEA 51 (114)
T ss_pred CcEEEEEeECcCC---CCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 6789999986654 344454557778889999999999983
No 17
>PF03591 AzlC: AzlC protein; InterPro: IPR011606 Some proteins in this entry are encoded by a gene, which is a part of the azl operon. This operon is involved in branched-chain amino acid transport []. Overexpression of this gene results in resistance to a leucine analogue, 4-azaleucine. The protein has 5 potential transmembrane motifs.
Probab=23.77 E-value=2.8e+02 Score=20.33 Aligned_cols=45 Identities=18% Similarity=0.262 Sum_probs=31.8
Q ss_pred cHHHHHHHHHHhhccCCCCCCccccccccccchhhhHHHHHHHHHHHHHHHHhhhhhh
Q 033208 57 STEQAFAKIVSSVRAPGKGEGQSGGVLTSTCNAASEIFRIAAIMNGLVLIGVAVGFVL 114 (125)
Q Consensus 57 ~teq~FAkvvsslk~~s~gkg~~GGAlss~c~~agEIf~iA~im~~LtLVGlavGFvL 114 (125)
=||+.||-.....+ ++.+ +. ....+.++..+...-.+|-.+|.++
T Consensus 94 ltDe~fa~~~~~~~--~~~~--~~---------~~~~~g~~~~~~~~W~~gt~~G~~~ 138 (143)
T PF03591_consen 94 LTDESFAVAMSRFQ--PNPP--DR---------HAYYLGLGLLLYLSWVLGTALGALL 138 (143)
T ss_pred HHHHHHHHHHHHhc--cCCc--ch---------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999998877665 2221 11 5678888888888877788887765
No 18
>PF11808 DUF3329: Domain of unknown function (DUF3329); InterPro: IPR021766 This family of proteins are functionally uncharacterised. This family is only found in bacteria. ; GO: 0004673 protein histidine kinase activity
Probab=23.24 E-value=1.2e+02 Score=20.86 Aligned_cols=24 Identities=21% Similarity=0.480 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhh
Q 033208 91 SEIFRIAAIMNGLVLIGVAVGFVL 114 (125)
Q Consensus 91 gEIf~iA~im~~LtLVGlavGFvL 114 (125)
.|+.+++.+.....+||..+|.+.
T Consensus 7 ~~l~~l~~~~l~~~lvG~~~g~~~ 30 (90)
T PF11808_consen 7 RELWRLLLLLLAAALVGWLFGHLW 30 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHH
Confidence 467777777777788887777653
No 19
>PF07297 DPM2: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2); InterPro: IPR009914 This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2 [].; GO: 0009059 macromolecule biosynthetic process, 0030176 integral to endoplasmic reticulum membrane
Probab=22.41 E-value=1.2e+02 Score=21.55 Aligned_cols=27 Identities=26% Similarity=0.556 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhheeeh
Q 033208 93 IFRIAAIMNGLVLIGVAVGFVLLRIEA 119 (125)
Q Consensus 93 If~iA~im~~LtLVGlavGFvLLrvea 119 (125)
+.-+...+.++.+||.-+|++++|=++
T Consensus 49 ~lP~~lll~~~~~vg~f~g~vmik~~~ 75 (78)
T PF07297_consen 49 ILPIFLLLLGLSGVGTFLGYVMIKSKK 75 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 344556778888999999999998544
No 20
>PF11772 EpuA: DNA-directed RNA polymerase subunit beta; InterPro: IPR024596 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the short 60-residue long bacterial family that is the beta subunit of the DNA-directed RNA polymerase, likely to be 2.7.7.6 from EC It is membrane-bound and is referred to by the name EpuA.
Probab=21.37 E-value=48 Score=21.39 Aligned_cols=20 Identities=15% Similarity=0.381 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHhhhhhhh
Q 033208 96 IAAIMNGLVLIGVAVGFVLL 115 (125)
Q Consensus 96 iA~im~~LtLVGlavGFvLL 115 (125)
+..++.....+|+.+||..+
T Consensus 4 V~lL~~~~l~iGlmIGY~vi 23 (47)
T PF11772_consen 4 VLLLAILALAIGLMIGYGVI 23 (47)
T ss_pred HHHHHHHHHHHHHHeeeeee
Confidence 45667777788999999754
No 21
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=21.29 E-value=79 Score=17.48 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHhhhhhhh
Q 033208 95 RIAAIMNGLVLIGVAVGFVLL 115 (125)
Q Consensus 95 ~iA~im~~LtLVGlavGFvLL 115 (125)
....+..+++++++ .++++.
T Consensus 10 ~~~~~~~G~~l~~~-~~~~~~ 29 (34)
T TIGR01167 10 NSLLLLLGLLLLGL-GGLLLR 29 (34)
T ss_pred cHHHHHHHHHHHHH-HHHHhe
Confidence 34444455555555 444443
No 22
>cd06155 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=21.14 E-value=1.3e+02 Score=20.47 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=28.0
Q ss_pred cccccceEEEeeccccCCcccccceeeecccccHHHHHHHHHHhhc
Q 033208 25 RRRSVKVSYITGLNSFGGLKAQNSLTSLGMPVSTEQAFAKIVSSVR 70 (125)
Q Consensus 25 ~r~~~~v~~i~glnsfgGLKa~N~V~~LG~pv~teq~FAkvvsslk 70 (125)
.|+.++..|+-|.-+..- .-++---++|+|.++..-|+
T Consensus 3 ~~~~g~~v~vSG~~~~~~--------~~d~~~Q~~~v~~ni~~~L~ 40 (101)
T cd06155 3 QNRTGGLLWISNVTASES--------DETVEEQMESIFSKLREILQ 40 (101)
T ss_pred eEEECCEEEEecCCCCCC--------CCCHHHHHHHHHHHHHHHHH
Confidence 466788889888765542 33555678899999999998
Done!