Query 033054
Match_columns 128
No_of_seqs 114 out of 687
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 09:15:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033054.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033054hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3386 Copper transporter [In 100.0 2.2E-34 4.8E-39 213.1 13.2 108 1-108 15-143 (155)
2 PF04145 Ctr: Ctr copper trans 100.0 1.1E-35 2.4E-40 214.1 3.7 102 2-103 1-144 (144)
3 PF11446 DUF2897: Protein of u 93.4 0.072 1.6E-06 33.1 2.3 28 82-109 1-28 (55)
4 COG3763 Uncharacterized protei 78.2 1.9 4E-05 28.2 2.0 22 86-107 8-29 (71)
5 PF06800 Sugar_transport: Suga 64.9 73 0.0016 25.7 9.0 92 13-107 91-186 (269)
6 COG3086 RseC Positive regulato 63.1 20 0.00043 26.6 4.8 46 64-112 79-130 (150)
7 PF03672 UPF0154: Uncharacteri 62.8 7.9 0.00017 24.8 2.3 21 87-107 2-22 (64)
8 PF13829 DUF4191: Domain of un 60.2 17 0.00037 28.6 4.3 49 70-118 38-86 (224)
9 PF15050 SCIMP: SCIMP protein 59.5 7.4 0.00016 28.1 2.0 19 85-103 7-28 (133)
10 PF14012 DUF4229: Protein of u 56.0 12 0.00026 23.9 2.4 38 76-113 18-61 (69)
11 PRK11677 hypothetical protein; 55.5 11 0.00024 27.4 2.3 18 88-105 6-23 (134)
12 PF11772 EpuA: DNA-directed RN 54.0 4.2 9.2E-05 24.4 -0.0 26 88-113 8-33 (47)
13 COG2991 Uncharacterized protei 51.0 14 0.0003 24.3 2.0 21 85-105 7-27 (77)
14 PRK01844 hypothetical protein; 47.8 22 0.00047 23.3 2.6 20 88-107 10-29 (72)
15 PF01062 Bestrophin: Bestrophi 43.1 63 0.0014 25.2 5.1 43 70-112 225-267 (293)
16 PRK00523 hypothetical protein; 41.4 31 0.00068 22.5 2.6 20 88-107 11-30 (72)
17 PF06376 DUF1070: Protein of u 41.1 22 0.00047 20.0 1.6 13 70-82 15-27 (34)
18 PF06612 DUF1146: Protein of u 40.9 30 0.00066 20.6 2.3 14 36-49 3-16 (48)
19 PF12072 DUF3552: Domain of un 39.5 29 0.00062 26.4 2.6 21 87-107 5-25 (201)
20 PRK10929 putative mechanosensi 39.1 3.4E+02 0.0074 26.4 10.0 78 23-100 832-915 (1109)
21 PHA00024 IX minor coat protein 38.5 55 0.0012 18.2 2.9 26 82-107 2-27 (33)
22 TIGR02327 int_mem_ywzB conserv 38.0 32 0.00069 22.1 2.2 17 88-104 40-56 (68)
23 PF10031 DUF2273: Small integr 34.4 1.1E+02 0.0023 18.5 5.2 31 71-101 14-48 (51)
24 COG3105 Uncharacterized protei 32.4 47 0.001 24.2 2.6 17 88-104 11-27 (138)
25 PRK15051 4-amino-4-deoxy-L-ara 30.8 1.8E+02 0.0038 19.8 10.5 46 61-107 37-89 (111)
26 COG5336 Uncharacterized protei 30.5 1.6E+02 0.0035 20.9 4.9 53 59-113 50-102 (116)
27 PRK02898 cobalt transport prot 29.9 40 0.00086 23.4 1.8 27 60-102 64-90 (100)
28 PF08636 Pkr1: ER protein Pkr1 29.3 1.7E+02 0.0037 19.2 5.9 45 51-98 14-60 (75)
29 PRK10255 PTS system N-acetyl g 29.1 1.1E+02 0.0023 27.8 4.8 34 69-102 74-112 (648)
30 PRK14853 nhaA pH-dependent sod 28.3 3.9E+02 0.0084 23.0 10.2 56 52-107 332-395 (423)
31 COG0472 Rfe UDP-N-acetylmuramy 27.4 1.9E+02 0.0041 23.7 5.6 24 84-107 188-211 (319)
32 PF12270 Cyt_c_ox_IV: Cytochro 27.1 79 0.0017 23.1 3.0 18 86-103 39-56 (137)
33 PF12273 RCR: Chitin synthesis 27.1 66 0.0014 22.5 2.6 22 28-49 5-26 (130)
34 PF10112 Halogen_Hydrol: 5-bro 27.0 2.7E+02 0.0058 20.7 6.4 25 79-103 24-48 (199)
35 PF12273 RCR: Chitin synthesis 26.0 84 0.0018 22.0 3.0 28 89-116 8-35 (130)
36 PF06305 DUF1049: Protein of u 26.0 83 0.0018 19.1 2.6 20 86-105 22-41 (68)
37 PRK10862 SoxR reducing system 25.6 2.3E+02 0.0049 20.7 5.3 24 85-108 103-126 (154)
38 PF04246 RseC_MucC: Positive r 21.8 2.8E+02 0.0062 19.2 6.2 25 85-109 96-120 (135)
39 PF04206 MtrE: Tetrahydrometha 21.6 1E+02 0.0023 24.8 3.0 43 62-107 57-99 (269)
40 COG4657 RnfA Predicted NADH:ub 21.3 3.8E+02 0.0083 20.5 6.7 25 58-82 127-151 (193)
41 PF09578 Spore_YabQ: Spore cor 20.6 2.4E+02 0.0053 18.0 8.8 71 30-104 4-79 (80)
42 COG4906 Predicted membrane pro 20.5 4.1E+02 0.0088 24.1 6.6 29 21-49 286-314 (696)
43 KOG2322 N-methyl-D-aspartate r 20.4 3.3E+02 0.0073 21.7 5.6 68 17-93 76-145 (237)
44 PF15179 Myc_target_1: Myc tar 20.2 2.1E+02 0.0045 22.2 4.2 28 88-115 25-55 (197)
45 PRK10489 enterobactin exporter 20.1 1.7E+02 0.0037 23.5 4.1 17 106-122 400-416 (417)
46 PLN03223 Polycystin cation cha 20.1 7.5E+02 0.016 25.2 8.7 59 37-106 1297-1355(1634)
No 1
>KOG3386 consensus Copper transporter [Inorganic ion transport and metabolism]
Probab=100.00 E-value=2.2e-34 Score=213.07 Aligned_cols=108 Identities=33% Similarity=0.563 Sum_probs=98.6
Q ss_pred CeeeeEEccCceeEecCCCccCChHHHHHHHHHHHHHHHHHHHHHHhhhh-----c---CC-C--------Cc----hHH
Q 033054 1 MGHITFFWGTNTEILFPGWPGESFSCYILALIFVFMISLTVEWISHAKLI-----K---SG-I--------SN----VAS 59 (128)
Q Consensus 1 mM~M~F~~~~~~~lLF~~W~~~t~~~~~~s~i~vf~la~~~e~l~~~r~~-----~---p~-~--------~~----~~~ 59 (128)
+|.|+|||+..+++||++|+++|+++|+++|+++|++|+++|+||..|+. + |. + .+ ...
T Consensus 15 ~m~M~f~~~~~~~iLF~~W~~~s~~~~~ls~i~iflla~l~E~Lk~~r~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ 94 (155)
T KOG3386|consen 15 MMMMFFHFKTIETILFSSWHITSAGGMALSCIAIFLLAVLYEALKFGREKLFRWQQLRQPTGHGHEIPLSGPSKLLNSAS 94 (155)
T ss_pred ceEEEEecCceeEEEEcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCccccccCcchhhhhHH
Confidence 69999999988999999999999999999999999999999999999963 1 10 0 01 467
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhccccc
Q 033054 60 GILQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIFGSQVF 108 (128)
Q Consensus 60 ~l~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f~~~~~ 108 (128)
|++|+++|.+|.++||+|||++||||+|+++||++|+++||++|+.+..
T Consensus 95 h~~qt~l~~~Q~~~sY~LMLifMtfN~~l~Lavv~Ga~~G~flF~~~~~ 143 (155)
T KOG3386|consen 95 HLIQTLLYVVQLGFSYLLMLIFMTFNGYLFLAVVLGAGVGYFLFGSLTF 143 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhhhhheeeeccc
Confidence 9999999999999999999999999999999999999999999999886
No 2
>PF04145 Ctr: Ctr copper transporter family; InterPro: IPR007274 The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionines probably coordinate copper during the process of metal transport.; GO: 0005375 copper ion transmembrane transporter activity, 0035434 copper ion transmembrane transport, 0016021 integral to membrane; PDB: 2LS4_A 2LS2_A 2LS3_A.
Probab=100.00 E-value=1.1e-35 Score=214.13 Aligned_cols=102 Identities=26% Similarity=0.543 Sum_probs=58.6
Q ss_pred eeeeEEccC-ceeEecCCCccCChHHHHHHHHHHHHHHHHHHHHHHhhhh------c-----------CC--------C-
Q 033054 2 GHITFFWGT-NTEILFPGWPGESFSCYILALIFVFMISLTVEWISHAKLI------K-----------SG--------I- 54 (128)
Q Consensus 2 M~M~F~~~~-~~~lLF~~W~~~t~~~~~~s~i~vf~la~~~e~l~~~r~~------~-----------p~--------~- 54 (128)
|+|+|||+. ++++||++|+++|.++|+++|+++|++|+++|+||.+|.. + ++ +
T Consensus 1 M~M~F~~~~~~~~lLF~~W~~~s~~~~~~sci~~f~lav~~e~L~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (144)
T PF04145_consen 1 MSMYFHWGTIRDCLLFKSWKPSSAGAYVGSCIGVFLLAVLYEFLKALRRRLERRWARRRSRRASCSSSESRSRSDASSKS 80 (144)
T ss_dssp ------------------------HHHHHHHHHHHHHHHHTTT-------------------------------------
T ss_pred CeeEEEcCCCccEEEeCCcEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccCcccCCCccccccc
Confidence 899999997 9999999999999999999999999999999999999853 0 00 0
Q ss_pred ---------------CchHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHh
Q 033054 55 ---------------SNVASGILQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIF 103 (128)
Q Consensus 55 ---------------~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f 103 (128)
.....|++|+++|++|+++||+|||+|||||+|+++||++|.++||++|
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~Y~LMLvvMTyN~~l~~aVv~G~~~G~~~F 144 (144)
T PF04145_consen 81 SPSPSSTSPRSSRRRWFWSQHLIRALLHFVQVLLGYLLMLVVMTYNVYLFIAVVLGAGLGYFLF 144 (144)
T ss_dssp ---------------------SHHHHHHHHHHHHHHHHHHHHHHTT--SSSHHHHHHTTSS-GG
T ss_pred ccccccccccCCCCCccHHHHHHHHHHHHHHHHHHHHHHHhhhheeHHHHHHHHHHHHHheeeC
Confidence 0134689999999999999999999999999999999999999999987
No 3
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=93.40 E-value=0.072 Score=33.12 Aligned_cols=28 Identities=14% Similarity=0.159 Sum_probs=24.4
Q ss_pred HhhhHHHHHHHHHHHHHHHHHhcccccc
Q 033054 82 MSFNIGVLLAAVAGYSVGFLIFGSQVFR 109 (128)
Q Consensus 82 MTfN~~l~~avi~G~~iG~~~f~~~~~~ 109 (128)
|+.|+|+++.+++|..+|.+.-=+++..
T Consensus 1 ~~~~~wlIIviVlgvIigNia~LK~sAk 28 (55)
T PF11446_consen 1 STWNPWLIIVIVLGVIIGNIAALKYSAK 28 (55)
T ss_pred CcchhhHHHHHHHHHHHhHHHHHHHhcc
Confidence 6899999999999999999998666543
No 4
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.20 E-value=1.9 Score=28.16 Aligned_cols=22 Identities=36% Similarity=0.529 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHhcccc
Q 033054 86 IGVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 86 ~~l~~avi~G~~iG~~~f~~~~ 107 (128)
.++.+|.++|...|||+-.+..
T Consensus 8 l~ivl~ll~G~~~G~fiark~~ 29 (71)
T COG3763 8 LLIVLALLAGLIGGFFIARKQM 29 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5678899999999998876655
No 5
>PF06800 Sugar_transport: Sugar transport protein; InterPro: IPR010651 This is a family of bacterial sugar transporters approximately 300 residues long. Members include glucose uptake proteins [], ribose transport proteins, and several putative and hypothetical membrane proteins probably involved in sugar transport across bacterial membranes.; GO: 0015144 carbohydrate transmembrane transporter activity, 0034219 carbohydrate transmembrane transport, 0016021 integral to membrane
Probab=64.87 E-value=73 Score=25.71 Aligned_cols=92 Identities=14% Similarity=0.211 Sum_probs=52.2
Q ss_pred eEecCCCccCChHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhhh---H-HH
Q 033054 13 EILFPGWPGESFSCYILALIFVFMISLTVEWISHAKLIKSGISNVASGILQTLMYAFRIGLAYLVMLAVMSFN---I-GV 88 (128)
Q Consensus 13 ~lLF~~W~~~t~~~~~~s~i~vf~la~~~e~l~~~r~~~p~~~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN---~-~l 88 (128)
.++|.+|+..+..-+-..-+.+...++ .+...|+.+.+..+...+..+.++..+-.+++|...-+..-+. . -.
T Consensus 91 v~~fgEW~~~~~~~~G~~Al~liiiGv---~lts~~~~~~~~~~~~~~~~kgi~~Ll~stigy~~Y~~~~~~~~~~~~~~ 167 (269)
T PF06800_consen 91 VLFFGEWTTTTQKIIGFLALVLIIIGV---ILTSYQDKKSDKSSSKSNMKKGILALLISTIGYWIYSVIPKAFHVSGWSA 167 (269)
T ss_pred HhhcCCCCCcchHHHHHHHHHHHHHHH---HHhccccccccccccccchhhHHHHHHHHHHHHHHHHHHHHhcCCChhHh
Confidence 467999987654433222222333333 3444454432211123444556666666777777665554432 2 26
Q ss_pred HHHHHHHHHHHHHHhcccc
Q 033054 89 LLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 89 ~~avi~G~~iG~~~f~~~~ 107 (128)
++-=.+|..+|.++|....
T Consensus 168 ~lPqaiGm~i~a~i~~~~~ 186 (269)
T PF06800_consen 168 FLPQAIGMLIGAFIFNLFS 186 (269)
T ss_pred HHHHHHHHHHHHHHHhhcc
Confidence 7777889999999998755
No 6
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=63.09 E-value=20 Score=26.62 Aligned_cols=46 Identities=22% Similarity=0.332 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhh------hHHHHHHHHHHHHHHHHHhcccccccCC
Q 033054 64 TLMYAFRIGLAYLVMLAVMSF------NIGVLLAAVAGYSVGFLIFGSQVFRNNL 112 (128)
Q Consensus 64 ~~l~~~~~~l~YlLMLivMTf------N~~l~~avi~G~~iG~~~f~~~~~~~~~ 112 (128)
.++|.+... .+++.++++ ..+..+.+++|.++|+++-.+...+.+.
T Consensus 79 ~LvYi~PL~---~l~v~~~La~~L~~~e~~~~~~~~lg~~l~fl~~r~ysRkl~~ 130 (150)
T COG3086 79 LLVYIFPLV---GLFLGAILAQYLFFSELIVIFGAFLGLALGFLLARRYSRKLAK 130 (150)
T ss_pred HHHHHHHHH---HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 456666654 344444442 3567888999999999999888765555
No 7
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=62.79 E-value=7.9 Score=24.76 Aligned_cols=21 Identities=29% Similarity=0.520 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHhcccc
Q 033054 87 GVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 87 ~l~~avi~G~~iG~~~f~~~~ 107 (128)
.++++.++|.++|+++-.+..
T Consensus 2 ~iilali~G~~~Gff~ar~~~ 22 (64)
T PF03672_consen 2 LIILALIVGAVIGFFIARKYM 22 (64)
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999865554
No 8
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=60.19 E-value=17 Score=28.64 Aligned_cols=49 Identities=14% Similarity=0.147 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhcccccccCCcCCCCC
Q 033054 70 RIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIFGSQVFRNNLKIEPYQ 118 (128)
Q Consensus 70 ~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f~~~~~~~~~~~~~~~ 118 (128)
-+.++.++.++.=+.=.++++++.+|..++-++|+++..+-...-.|+|
T Consensus 38 ~~~v~v~ig~l~~~~~~~~i~gi~~g~l~am~vl~rra~ra~Y~qieGq 86 (224)
T PF13829_consen 38 PIAVFVLIGLLFGSWWYWLIIGILLGLLAAMIVLSRRAQRAAYAQIEGQ 86 (224)
T ss_pred HHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3344555555555555678999999999999999999876666555554
No 9
>PF15050 SCIMP: SCIMP protein
Probab=59.50 E-value=7.4 Score=28.06 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=12.0
Q ss_pred hHHHHHHH---HHHHHHHHHHh
Q 033054 85 NIGVLLAA---VAGYSVGFLIF 103 (128)
Q Consensus 85 N~~l~~av---i~G~~iG~~~f 103 (128)
|.|+++|| +++.++|..+|
T Consensus 7 nFWiiLAVaII~vS~~lglIly 28 (133)
T PF15050_consen 7 NFWIILAVAIILVSVVLGLILY 28 (133)
T ss_pred chHHHHHHHHHHHHHHHHHHHH
Confidence 56666664 45666776666
No 10
>PF14012 DUF4229: Protein of unknown function (DUF4229)
Probab=55.98 E-value=12 Score=23.93 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=28.6
Q ss_pred HHHHHHHhhh------HHHHHHHHHHHHHHHHHhcccccccCCc
Q 033054 76 LVMLAVMSFN------IGVLLAAVAGYSVGFLIFGSQVFRNNLK 113 (128)
Q Consensus 76 lLMLivMTfN------~~l~~avi~G~~iG~~~f~~~~~~~~~~ 113 (128)
.++++..... ....+|++++..++|++|.+.+.+-+.+
T Consensus 18 vi~~v~~~~~~~~p~~~~~l~A~vis~~lS~~ll~~~R~~~~~~ 61 (69)
T PF14012_consen 18 VIWLVGLLIGVEVPLLVAALLALVISMPLSYVLLRRLRDRASAD 61 (69)
T ss_pred HHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555 6788999999999999998887654443
No 11
>PRK11677 hypothetical protein; Provisional
Probab=55.53 E-value=11 Score=27.39 Aligned_cols=18 Identities=22% Similarity=0.372 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHhcc
Q 033054 88 VLLAAVAGYSVGFLIFGS 105 (128)
Q Consensus 88 l~~avi~G~~iG~~~f~~ 105 (128)
.++++++|.++|+++-..
T Consensus 6 a~i~livG~iiG~~~~R~ 23 (134)
T PRK11677 6 ALIGLVVGIIIGAVAMRF 23 (134)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 457777788888777654
No 12
>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=53.97 E-value=4.2 Score=24.39 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHhcccccccCCc
Q 033054 88 VLLAAVAGYSVGFLIFGSQVFRNNLK 113 (128)
Q Consensus 88 l~~avi~G~~iG~~~f~~~~~~~~~~ 113 (128)
.+++.++|..+||.+.|...+.+..+
T Consensus 8 ~~~~l~iGlmIGY~viG~G~p~~vf~ 33 (47)
T PF11772_consen 8 AILALAIGLMIGYGVIGDGNPFDVFS 33 (47)
T ss_pred HHHHHHHHHHeeeeeeCCCCHHHhCC
Confidence 56788999999999998876554443
No 13
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.05 E-value=14 Score=24.34 Aligned_cols=21 Identities=29% Similarity=0.708 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHHhcc
Q 033054 85 NIGVLLAAVAGYSVGFLIFGS 105 (128)
Q Consensus 85 N~~l~~avi~G~~iG~~~f~~ 105 (128)
..++|+.|++|.++||.+-..
T Consensus 7 tFg~Fllvi~gMsiG~I~krk 27 (77)
T COG2991 7 TFGIFLLVIAGMSIGYIFKRK 27 (77)
T ss_pred HHHHHHHHHHHHhHhhheecc
Confidence 457899999999999975433
No 14
>PRK01844 hypothetical protein; Provisional
Probab=47.78 E-value=22 Score=23.29 Aligned_cols=20 Identities=35% Similarity=0.534 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHhcccc
Q 033054 88 VLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 88 l~~avi~G~~iG~~~f~~~~ 107 (128)
.+++.++|.++|+|+-.+..
T Consensus 10 ~I~~li~G~~~Gff~ark~~ 29 (72)
T PRK01844 10 GVVALVAGVALGFFIARKYM 29 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 36788899999998865544
No 15
>PF01062 Bestrophin: Bestrophin, RFP-TM, chloride channel; InterPro: IPR021134 Bestrophin is a 68kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterised by a depressed light peak in the electrooculogram []. VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif. Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak []. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties []. This entry also includes a number of hypothetical proteins belonging to protein family UPF0187.
Probab=43.14 E-value=63 Score=25.25 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhcccccccCC
Q 033054 70 RIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIFGSQVFRNNL 112 (128)
Q Consensus 70 ~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f~~~~~~~~~ 112 (128)
+.+..|++.+.+.--+..-..++++...++++.+|....+..-
T Consensus 225 ~~l~~y~~~lPf~l~~~~~~~~~~~~~l~~~~~~gl~~ig~~l 267 (293)
T PF01062_consen 225 RFLYIYLLLLPFGLVDSLGWLTPPITFLVSFFFLGLEEIGEEL 267 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677776666655555566888888999999998876543
No 16
>PRK00523 hypothetical protein; Provisional
Probab=41.38 E-value=31 Score=22.54 Aligned_cols=20 Identities=10% Similarity=0.235 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhcccc
Q 033054 88 VLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 88 l~~avi~G~~iG~~~f~~~~ 107 (128)
.+++.++|.++|+|+-.+..
T Consensus 11 ~i~~li~G~~~Gffiark~~ 30 (72)
T PRK00523 11 GIPLLIVGGIIGYFVSKKMF 30 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45678889999998865544
No 17
>PF06376 DUF1070: Protein of unknown function (DUF1070); InterPro: IPR009424 This entry represents the arabinogalactan peptide family found in plants [].
Probab=41.11 E-value=22 Score=19.96 Aligned_cols=13 Identities=38% Similarity=0.853 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHH
Q 033054 70 RIGLAYLVMLAVM 82 (128)
Q Consensus 70 ~~~l~YlLMLivM 82 (128)
.-.++|+||+++-
T Consensus 15 Dqgiay~Lm~~Al 27 (34)
T PF06376_consen 15 DQGIAYMLMLVAL 27 (34)
T ss_pred hHHHHHHHHHHHH
Confidence 3568899998763
No 18
>PF06612 DUF1146: Protein of unknown function (DUF1146); InterPro: IPR009526 Members of this protein family are small, typically about 80 residues in length, and are highly hydrophobic. The gene is found so far only in a subset of the firmicutes in association with genes of the ATP synthase F1 complex or NADH-quinone oxidoreductase. This family includes YwzB from Bacillus subtilis.
Probab=40.90 E-value=30 Score=20.62 Aligned_cols=14 Identities=14% Similarity=0.171 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHhhh
Q 033054 36 MISLTVEWISHAKL 49 (128)
Q Consensus 36 ~la~~~e~l~~~r~ 49 (128)
+.++.+.++...|.
T Consensus 3 fI~la~~aLq~l~~ 16 (48)
T PF06612_consen 3 FIALAFWALQSLRW 16 (48)
T ss_pred eHHHHHHHHHhcCH
Confidence 34455556666653
No 19
>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
Probab=39.48 E-value=29 Score=26.38 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHhcccc
Q 033054 87 GVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 87 ~l~~avi~G~~iG~~~f~~~~ 107 (128)
..++++++|.++||++..+..
T Consensus 5 ~~i~~~~vG~~~G~~~~~~~~ 25 (201)
T PF12072_consen 5 IAIVALIVGIGIGYLVRKKIN 25 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 467888999999999876543
No 20
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=39.09 E-value=3.4e+02 Score=26.39 Aligned_cols=78 Identities=13% Similarity=0.191 Sum_probs=43.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHhhh--h--cCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH--HHH
Q 033054 23 SFSCYILALIFVFMISLTVEWISHAKL--I--KSGISNVASGILQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAV--AGY 96 (128)
Q Consensus 23 t~~~~~~s~i~vf~la~~~e~l~~~r~--~--~p~~~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi--~G~ 96 (128)
|.+..+.+.+.+++..++.+.++..-+ . +.+-++....++.++...+-.+++.+..|-.+-.|..-+.+++ +|.
T Consensus 832 tl~~ll~AllIliv~~~l~r~l~~lle~~l~~~~~l~~~~~~~i~~l~~y~I~~ig~l~~L~~lGI~~t~l~al~galGV 911 (1109)
T PRK10929 832 TLGSVLIAILVFIITTQLVRNLPALLELALLQHLDLTPGTGYAITTITKYLLMLIGGLVGFSMIGIEWSKLQWLVAALGV 911 (1109)
T ss_pred eHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCChhHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence 346666666665555566666654322 1 1222334456666666666667777777777777765443333 344
Q ss_pred HHHH
Q 033054 97 SVGF 100 (128)
Q Consensus 97 ~iG~ 100 (128)
++|+
T Consensus 912 gIGf 915 (1109)
T PRK10929 912 GLGF 915 (1109)
T ss_pred HHHH
Confidence 4443
No 21
>PHA00024 IX minor coat protein
Probab=38.51 E-value=55 Score=18.22 Aligned_cols=26 Identities=19% Similarity=0.114 Sum_probs=19.4
Q ss_pred HhhhHHHHHHHHHHHHHHHHHhcccc
Q 033054 82 MSFNIGVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 82 MTfN~~l~~avi~G~~iG~~~f~~~~ 107 (128)
|.+=++.+-|-++|.++||-+-.-++
T Consensus 2 ~~~l~~ffgA~ilG~~l~~~Il~FKk 27 (33)
T PHA00024 2 MSYLGYFFGAYILGWALFYGILVFKK 27 (33)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55667788899999999987654443
No 22
>TIGR02327 int_mem_ywzB conserved hypothetical integral membrane protein. Members of this protein family are small, typically about 80 residues in length, and are highly hydrophobic. The gene is found so far only in a subset of the Firmicutes in association with genes of the ATP synthase F1 complex or NADH-quinone oxidoreductase. This family includes ywzB from Bacillus subtilis; Pfam model pfam06612 describes the same family as Protein of unknown function DUF1146.
Probab=38.00 E-value=32 Score=22.13 Aligned_cols=17 Identities=35% Similarity=0.677 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHhc
Q 033054 88 VLLAAVAGYSVGFLIFG 104 (128)
Q Consensus 88 l~~avi~G~~iG~~~f~ 104 (128)
+++|+++|+.++.|+.+
T Consensus 40 vllaIalGylvs~FfL~ 56 (68)
T TIGR02327 40 VLIAIALGYTVSHFFLE 56 (68)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45677777777777653
No 23
>PF10031 DUF2273: Small integral membrane protein (DUF2273); InterPro: IPR018730 Members of this family of hypothetical bacterial proteins have no known function.
Probab=34.42 E-value=1.1e+02 Score=18.45 Aligned_cols=31 Identities=26% Similarity=0.456 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHhhhHH----HHHHHHHHHHHHHH
Q 033054 71 IGLAYLVMLAVMSFNIG----VLLAAVAGYSVGFL 101 (128)
Q Consensus 71 ~~l~YlLMLivMTfN~~----l~~avi~G~~iG~~ 101 (128)
..++.++=++++++-.| +++.+++|..+|..
T Consensus 14 ~~~G~ila~l~l~~GF~~tl~i~~~~~iG~~iG~~ 48 (51)
T PF10031_consen 14 GLIGLILALLILTFGFWKTLFILLFAAIGYYIGKY 48 (51)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666777777666 66677778888765
No 24
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.37 E-value=47 Score=24.23 Aligned_cols=17 Identities=35% Similarity=0.509 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHhc
Q 033054 88 VLLAAVAGYSVGFLIFG 104 (128)
Q Consensus 88 l~~avi~G~~iG~~~f~ 104 (128)
..++.++|.+||+++-.
T Consensus 11 a~igLvvGi~IG~li~R 27 (138)
T COG3105 11 ALIGLVVGIIIGALIAR 27 (138)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46788899999998863
No 25
>PRK15051 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional
Probab=30.82 E-value=1.8e+02 Score=19.85 Aligned_cols=46 Identities=20% Similarity=0.170 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh-------hhHHHHHHHHHHHHHHHHHhcccc
Q 033054 61 ILQTLMYAFRIGLAYLVMLAVMS-------FNIGVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 61 l~~~~l~~~~~~l~YlLMLivMT-------fN~~l~~avi~G~~iG~~~f~~~~ 107 (128)
+....+-.+++.+++.++..+|. |-.+- ++.+....+|+++|+.+.
T Consensus 37 l~~~~~~~~~~~l~~~~~~~al~~iplg~Ay~~~~-l~~v~~~~~~~l~f~E~l 89 (111)
T PRK15051 37 VLWLGLALACLGLAMVLWLLVLQNVPVGIAYPMLS-LNFVWVTLAAVKLWHEPV 89 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCChHHHHHHHH-HHHHHHHHHHHHHhCCCC
Confidence 34455556778888888877776 44455 667777888999987765
No 26
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.52 E-value=1.6e+02 Score=20.91 Aligned_cols=53 Identities=13% Similarity=0.209 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhcccccccCCc
Q 033054 59 SGILQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIFGSQVFRNNLK 113 (128)
Q Consensus 59 ~~l~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f~~~~~~~~~~ 113 (128)
..++..++ +-+.++|++==.+=|=-.++++-.++|.+.|.+.--|..-.++.|
T Consensus 50 sefIsGil--VGa~iG~llD~~agTsPwglIv~lllGf~AG~lnv~Rsag~va~~ 102 (116)
T COG5336 50 SEFISGIL--VGAGIGWLLDKFAGTSPWGLIVFLLLGFGAGVLNVLRSAGKVAEQ 102 (116)
T ss_pred HHHHHHHH--HHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 34555544 346788888888899999999999999999999987776555554
No 27
>PRK02898 cobalt transport protein CbiN; Provisional
Probab=29.90 E-value=40 Score=23.40 Aligned_cols=27 Identities=30% Similarity=0.754 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 033054 60 GILQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLI 102 (128)
Q Consensus 60 ~l~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~ 102 (128)
.=+.++|+.+|..++ |.++|+.+||+-
T Consensus 64 GEiESLLFaLQAAiG----------------AgiIgY~lG~~~ 90 (100)
T PRK02898 64 GEIESLLFALQAALG----------------AGIIGYILGYYK 90 (100)
T ss_pred chHHHHHHHHHHHHh----------------hhhhheeeeehh
Confidence 347799999999987 677888888764
No 28
>PF08636 Pkr1: ER protein Pkr1; InterPro: IPR013945 Pkr1 has been identified as an ER protein of unknown function.
Probab=29.34 E-value=1.7e+02 Score=19.18 Aligned_cols=45 Identities=16% Similarity=0.147 Sum_probs=27.1
Q ss_pred cCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH--HHHHHHHHH
Q 033054 51 KSGISNVASGILQTLMYAFRIGLAYLVMLAVMSFNIGVL--LAAVAGYSV 98 (128)
Q Consensus 51 ~p~~~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN~~l~--~avi~G~~i 98 (128)
.|+++|......+.....++.. ++=|+..|+|.-++ ..+.+|...
T Consensus 14 tPG~tp~li~a~n~sF~~L~~~---l~~Ll~~t~niHfivL~~l~~~Lw~ 60 (75)
T PF08636_consen 14 TPGTTPTLIIATNVSFAALFLV---LLALLFLTYNIHFIVLSFLALGLWA 60 (75)
T ss_pred CCCCChHHHHHHHHHHHHHHHH---HHHHHHHccCHHHHHHHHHHHHHHH
Confidence 5787776655666666666665 55667777777643 334444433
No 29
>PRK10255 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional
Probab=29.10 E-value=1.1e+02 Score=27.84 Aligned_cols=34 Identities=26% Similarity=0.460 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHH-----hhhHHHHHHHHHHHHHHHHH
Q 033054 69 FRIGLAYLVMLAVM-----SFNIGVLLAAVAGYSVGFLI 102 (128)
Q Consensus 69 ~~~~l~YlLMLivM-----TfN~~l~~avi~G~~iG~~~ 102 (128)
+...++|++|..+| +.|.++|..+++|...++.-
T Consensus 74 la~~v~yl~~~~~~~~~~~~~~~gvfgGIi~G~i~a~l~ 112 (648)
T PRK10255 74 LAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAY 112 (648)
T ss_pred HHHHHHHHHHHHHHHHHhhhhchhhhhhhHHHHHHHHHH
Confidence 34567777777664 45889999999999987643
No 30
>PRK14853 nhaA pH-dependent sodium/proton antiporter; Provisional
Probab=28.34 E-value=3.9e+02 Score=23.05 Aligned_cols=56 Identities=13% Similarity=0.106 Sum_probs=35.5
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHH-HHHHh-------hhHHHHHHHHHHHHHHHHHhcccc
Q 033054 52 SGISNVASGILQTLMYAFRIGLAYLVM-LAVMS-------FNIGVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 52 p~~~~~~~~l~~~~l~~~~~~l~YlLM-LivMT-------fN~~l~~avi~G~~iG~~~f~~~~ 107 (128)
|+.-...+-..-+++-++-.++|-+.= |..-+ =-.+++++-++...+|+.++....
T Consensus 332 P~~~~~~~l~gv~~L~GIGFTmSlFI~~LAf~~~~~~~~~aKigil~~S~~s~~~G~~~l~~~~ 395 (423)
T PRK14853 332 DDDLTWIDVFGVALLAGIGFTVSLLIGELAFGGGSARDDAVKVGVLTGSLIAALLASVLLRLRN 395 (423)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 443333444556888888888886554 33311 124678888888889998885443
No 31
>COG0472 Rfe UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]
Probab=27.39 E-value=1.9e+02 Score=23.68 Aligned_cols=24 Identities=33% Similarity=0.477 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhcccc
Q 033054 84 FNIGVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 84 fN~~l~~avi~G~~iG~~~f~~~~ 107 (128)
+...++.++++|+.+|++.|++..
T Consensus 188 ~~~~~~~~al~ga~LGFL~~N~~P 211 (319)
T COG0472 188 GELALICAALAGACLGFLWFNFYP 211 (319)
T ss_pred hhHHHHHHHHHHHHHHHHHhcCCh
Confidence 555688999999999999999876
No 32
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=27.14 E-value=79 Score=23.09 Aligned_cols=18 Identities=17% Similarity=0.440 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 033054 86 IGVLLAAVAGYSVGFLIF 103 (128)
Q Consensus 86 ~~l~~avi~G~~iG~~~f 103 (128)
+.+.++..++..+|.++-
T Consensus 39 ~aL~ls~~l~~mig~yl~ 56 (137)
T PF12270_consen 39 VALVLSGGLALMIGFYLR 56 (137)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 346667777777765544
No 33
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=27.06 E-value=66 Score=22.53 Aligned_cols=22 Identities=9% Similarity=0.205 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhh
Q 033054 28 ILALIFVFMISLTVEWISHAKL 49 (128)
Q Consensus 28 ~~s~i~vf~la~~~e~l~~~r~ 49 (128)
++.+|+++++.++.-+....|+
T Consensus 5 ~~iii~~i~l~~~~~~~~~rRR 26 (130)
T PF12273_consen 5 FAIIIVAILLFLFLFYCHNRRR 26 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444443
No 34
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=27.02 E-value=2.7e+02 Score=20.73 Aligned_cols=25 Identities=16% Similarity=0.367 Sum_probs=14.0
Q ss_pred HHHHhhhHHHHHHHHHHHHHHHHHh
Q 033054 79 LAVMSFNIGVLLAAVAGYSVGFLIF 103 (128)
Q Consensus 79 LivMTfN~~l~~avi~G~~iG~~~f 103 (128)
.....++...++++++|.+.+...+
T Consensus 24 ~~~~~~~~~~~l~~l~~~~~~~~~~ 48 (199)
T PF10112_consen 24 VSFFGFDHSFLLSLLIGAVAFAVVY 48 (199)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 3344455555566666666555544
No 35
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=26.00 E-value=84 Score=22.00 Aligned_cols=28 Identities=14% Similarity=0.110 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHhcccccccCCcCCC
Q 033054 89 LLAAVAGYSVGFLIFGSQVFRNNLKIEP 116 (128)
Q Consensus 89 ~~avi~G~~iG~~~f~~~~~~~~~~~~~ 116 (128)
++.+++-..++.+++.+++.++..++..
T Consensus 8 ii~~i~l~~~~~~~~~rRR~r~G~~P~~ 35 (130)
T PF12273_consen 8 IIVAILLFLFLFYCHNRRRRRRGLQPIY 35 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCcC
Confidence 3344444455556666666666444443
No 36
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.96 E-value=83 Score=19.10 Aligned_cols=20 Identities=25% Similarity=0.389 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHhcc
Q 033054 86 IGVLLAAVAGYSVGFLIFGS 105 (128)
Q Consensus 86 ~~l~~avi~G~~iG~~~f~~ 105 (128)
..++++.++|..+|.++...
T Consensus 22 l~il~~f~~G~llg~l~~~~ 41 (68)
T PF06305_consen 22 LLILIAFLLGALLGWLLSLP 41 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45667777777777766543
No 37
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=25.60 E-value=2.3e+02 Score=20.69 Aligned_cols=24 Identities=25% Similarity=0.301 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHHHHHHHHhccccc
Q 033054 85 NIGVLLAAVAGYSVGFLIFGSQVF 108 (128)
Q Consensus 85 N~~l~~avi~G~~iG~~~f~~~~~ 108 (128)
+.+.+++.++|.++||++-.....
T Consensus 103 e~~~~~~~~~g~~~g~~~~r~~~~ 126 (154)
T PRK10862 103 DLAALCGALLGGVGGFLLARGLSR 126 (154)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 778888999999999888875543
No 38
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=21.85 E-value=2.8e+02 Score=19.23 Aligned_cols=25 Identities=28% Similarity=0.457 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHHHHHHhcccccc
Q 033054 85 NIGVLLAAVAGYSVGFLIFGSQVFR 109 (128)
Q Consensus 85 N~~l~~avi~G~~iG~~~f~~~~~~ 109 (128)
+.+.+++-++|.++||++-.....+
T Consensus 96 e~~~~l~~l~~l~~~~~~~~~~~~~ 120 (135)
T PF04246_consen 96 ELWAILGGLLGLALGFLILRLFDRR 120 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 7888999999999999988766543
No 39
>PF04206 MtrE: Tetrahydromethanopterin S-methyltransferase, subunit E ; InterPro: IPR005780 This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. 5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0006814 sodium ion transport, 0005737 cytoplasm, 0012506 vesicle membrane
Probab=21.58 E-value=1e+02 Score=24.80 Aligned_cols=43 Identities=26% Similarity=0.356 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhcccc
Q 033054 62 LQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIFGSQV 107 (128)
Q Consensus 62 ~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f~~~~ 107 (128)
..++.-.+.-.++|.|| ..++.-.++|+++|..++-++-+-..
T Consensus 57 aygl~~ai~g~iA~~lm---~~~~~~~i~ai~~Ga~vAa~v~g~ya 99 (269)
T PF04206_consen 57 AYGLWCAIAGAIAWALM---SAFGLNPILAIAIGAAVAALVHGVYA 99 (269)
T ss_pred hhhHHHHHHHHHHHHHH---HHcCccHHHHHHHHHHHHHHHHHHHH
Confidence 34566667777788777 34556689999999999988766543
No 40
>COG4657 RnfA Predicted NADH:ubiquinone oxidoreductase, subunit RnfA [Energy production and conversion]
Probab=21.26 E-value=3.8e+02 Score=20.49 Aligned_cols=25 Identities=20% Similarity=0.594 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033054 58 ASGILQTLMYAFRIGLAYLVMLAVM 82 (128)
Q Consensus 58 ~~~l~~~~l~~~~~~l~YlLMLivM 82 (128)
..++.+++.|++...+||-|-++.+
T Consensus 127 ~~~f~qsv~~gf~a~lGfslvmvlf 151 (193)
T COG4657 127 GHNFLQSVVYGFGAALGFSLVMVLF 151 (193)
T ss_pred hhhHHHHHHHHhhhHhhHHHHHHHH
Confidence 4678999999999999988776543
No 41
>PF09578 Spore_YabQ: Spore cortex protein YabQ (Spore_YabQ); InterPro: IPR019074 This protein is predicted to span the membrane several times. It is only found in genomes of species that perform sporulation, such as Bacillus subtilis, Clostridium tetani, and other members of the Firmicutes (low-GC Gram-positive bacteria). Mutation of this sigmaE-dependent gene blocks development of the spore cortex. The length of the C-terminal region, which includes some hydrophobic regions, is variable.
Probab=20.65 E-value=2.4e+02 Score=18.01 Aligned_cols=71 Identities=10% Similarity=0.167 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhhh-----HHHHHHHHHHHHHHHHHhc
Q 033054 30 ALIFVFMISLTVEWISHAKLIKSGISNVASGILQTLMYAFRIGLAYLVMLAVMSFN-----IGVLLAAVAGYSVGFLIFG 104 (128)
Q Consensus 30 s~i~vf~la~~~e~l~~~r~~~p~~~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN-----~~l~~avi~G~~iG~~~f~ 104 (128)
++..=+.+++.+..++..|+..|.+ +....+.+.+...+....-+. .....| .++++++++|..+-+..++
T Consensus 4 ~~~~G~~lg~~yD~~r~~r~~~~~~-~~~~~i~DllfWl~~~~~~F~---~l~~~N~G~iR~Y~~lg~~~G~~lY~~~ls 79 (80)
T PF09578_consen 4 SILSGIILGFLYDLYRVFRRVFRHS-RWLTGIEDLLFWLLAALIVFY---FLYWTNYGEIRFYIFLGILLGMILYFRLLS 79 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccc-hHHHHHHHHHHHHHHHHHHHH---HHHHccceeeeHHHHHHHHHHHHHHHHHhc
Confidence 3344457899999999999875332 233444444444443333222 223334 4588899998888766654
No 42
>COG4906 Predicted membrane protein [Function unknown]
Probab=20.54 E-value=4.1e+02 Score=24.08 Aligned_cols=29 Identities=24% Similarity=0.383 Sum_probs=26.1
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033054 21 GESFSCYILALIFVFMISLTVEWISHAKL 49 (128)
Q Consensus 21 ~~t~~~~~~s~i~vf~la~~~e~l~~~r~ 49 (128)
.++..++.-.+.++|...+.+|.+..+|+
T Consensus 286 ~n~~~~flsvl~Fif~f~F~~e~lalaRq 314 (696)
T COG4906 286 KNSDYGFLSVLLFIFQFSFIYEILALARQ 314 (696)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778889999999999999999999996
No 43
>KOG2322 consensus N-methyl-D-aspartate receptor glutamate-binding subunit [Signal transduction mechanisms]
Probab=20.40 E-value=3.3e+02 Score=21.69 Aligned_cols=68 Identities=22% Similarity=0.288 Sum_probs=38.6
Q ss_pred CCCccCChHHHHHHHHHHHHHHHHHH-HHHHhhhhcCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH-HHHHHH
Q 033054 17 PGWPGESFSCYILALIFVFMISLTVE-WISHAKLIKSGISNVASGILQTLMYAFRIGLAYLVMLAVMSFNIG-VLLAAV 93 (128)
Q Consensus 17 ~~W~~~t~~~~~~s~i~vf~la~~~e-~l~~~r~~~p~~~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN~~-l~~avi 93 (128)
+.|.-++++.| ..|+.+|+...+.- .....|+.- ...-+ ++-......++.++++.-.||.- +..|++
T Consensus 76 ~~~v~~~~~~~-~~~~~vf~vt~l~l~c~~~~r~k~-----P~N~i---lL~iFT~a~s~~~g~~~a~~~~~~VL~Al~ 145 (237)
T KOG2322|consen 76 QDFVRRNPALY-WALIVVFIVTYLSLACCEGLRRKS-----PVNLI---LLGIFTLAEAFMTGLVTAFYDAKVVLLALI 145 (237)
T ss_pred HHHHHhCcHHH-HHHHHHHHHHHHHHHccCcccccC-----cHHHh---HHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 56778888888 55555555544322 222222111 11222 33335578899999999999954 333433
No 44
>PF15179 Myc_target_1: Myc target protein 1
Probab=20.21 E-value=2.1e+02 Score=22.15 Aligned_cols=28 Identities=18% Similarity=0.121 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHH---hcccccccCCcCC
Q 033054 88 VLLAAVAGYSVGFLI---FGSQVFRNNLKIE 115 (128)
Q Consensus 88 l~~avi~G~~iG~~~---f~~~~~~~~~~~~ 115 (128)
+++++++|..||-++ |.+...+++...+
T Consensus 25 F~vSm~iGLviG~li~~LltwlSRRRASa~I 55 (197)
T PF15179_consen 25 FCVSMAIGLVIGALIWALLTWLSRRRASARI 55 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 455666677666544 4566666666533
No 45
>PRK10489 enterobactin exporter EntS; Provisional
Probab=20.11 E-value=1.7e+02 Score=23.50 Aligned_cols=17 Identities=29% Similarity=0.257 Sum_probs=9.5
Q ss_pred cccccCCcCCCCCCCCC
Q 033054 106 QVFRNNLKIEPYQDLSD 122 (128)
Q Consensus 106 ~~~~~~~~~~~~~~~~~ 122 (128)
...++.+++|++++.+|
T Consensus 400 ~~~~~~~~~~~~~~~~~ 416 (417)
T PRK10489 400 GELRRFRQTPPEVDASD 416 (417)
T ss_pred ccccccccccccCCCCC
Confidence 34455555666666665
No 46
>PLN03223 Polycystin cation channel protein; Provisional
Probab=20.09 E-value=7.5e+02 Score=25.17 Aligned_cols=59 Identities=20% Similarity=0.222 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhccc
Q 033054 37 ISLTVEWISHAKLIKSGISNVASGILQTLMYAFRIGLAYLVMLAVMSFNIGVLLAAVAGYSVGFLIFGSQ 106 (128)
Q Consensus 37 la~~~e~l~~~r~~~p~~~~~~~~l~~~~l~~~~~~l~YlLMLivMTfN~~l~~avi~G~~iG~~~f~~~ 106 (128)
+.++...+|.+|.++ =++....+.+++.....=+.+|++|+.++-+ .=+.+|+++||..
T Consensus 1297 IlIFLsiLKfLRLLR--FNPrL~vLt~TLrrAapDLa~F~IIF~IVF~---------AFAqLG~LLFGt~ 1355 (1634)
T PLN03223 1297 INIILLLGRILKLMD--FQPRLGVITRTLWLAGADLMHFFVIFGMVFV---------GYAFIGHVIFGNA 1355 (1634)
T ss_pred HHHHHHHHHHHHHhc--cChhHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHhccC
Confidence 345555556666553 1123455666777777777777777655422 1223566777654
Done!