Query 044408
Match_columns 93
No_of_seqs 106 out of 556
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 03:01:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044408.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044408hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3386 Copper transporter [In 99.8 8E-21 1.7E-25 137.0 7.5 74 2-75 51-145 (155)
2 PF04145 Ctr: Ctr copper trans 99.8 6.9E-21 1.5E-25 130.5 1.8 48 21-68 97-144 (144)
3 PF11446 DUF2897: Protein of u 89.9 0.26 5.7E-06 30.2 2.0 28 47-74 1-28 (55)
4 PF01062 Bestrophin: Bestrophi 77.6 15 0.00033 27.5 7.1 57 33-89 223-279 (293)
5 PF08636 Pkr1: ER protein Pkr1 74.9 17 0.00036 23.6 5.8 48 13-63 11-60 (75)
6 PRK15051 4-amino-4-deoxy-L-ara 73.7 24 0.00052 23.5 7.0 70 2-72 8-89 (111)
7 PRK11431 multidrug efflux syst 69.4 31 0.00068 23.2 7.1 67 2-71 8-81 (105)
8 PF13829 DUF4191: Domain of un 68.4 7.6 0.00016 29.9 3.6 48 36-83 39-86 (224)
9 PF06295 DUF1043: Protein of u 67.3 3.6 7.9E-05 28.5 1.6 19 52-70 1-19 (128)
10 PF03672 UPF0154: Uncharacteri 63.8 6.9 0.00015 24.8 2.2 19 52-70 2-20 (64)
11 PRK11677 hypothetical protein; 61.0 7.7 0.00017 27.6 2.3 20 51-70 4-23 (134)
12 PRK10650 multidrug efflux syst 59.2 53 0.0012 22.3 6.6 67 2-71 14-87 (109)
13 PF04206 MtrE: Tetrahydrometha 55.2 13 0.00028 29.4 2.8 60 27-89 57-116 (269)
14 PRK00972 tetrahydromethanopter 53.2 12 0.00027 29.9 2.5 42 27-72 64-105 (292)
15 PF14012 DUF4229: Protein of u 51.8 40 0.00086 21.1 4.2 46 26-74 6-57 (69)
16 PRK01844 hypothetical protein; 49.7 18 0.00039 23.4 2.4 18 53-70 10-27 (72)
17 PF06376 DUF1070: Protein of u 48.8 17 0.00036 20.4 1.9 14 34-47 14-27 (34)
18 COG3763 Uncharacterized protei 48.8 19 0.00042 23.3 2.4 21 51-71 8-28 (71)
19 COG2991 Uncharacterized protei 48.3 15 0.00032 24.1 1.9 22 51-73 8-29 (77)
20 PF14362 DUF4407: Domain of un 44.8 49 0.0011 25.3 4.6 28 46-73 38-65 (301)
21 PRK00523 hypothetical protein; 42.8 27 0.00058 22.6 2.4 18 53-70 11-28 (72)
22 PF12072 DUF3552: Domain of un 42.8 23 0.0005 26.0 2.4 19 52-70 5-23 (201)
23 PRK10452 multidrug efflux syst 41.7 1.2E+02 0.0025 20.9 6.9 66 2-71 9-82 (120)
24 PF06939 DUF1286: Protein of u 41.6 54 0.0012 23.0 3.9 47 17-64 59-108 (114)
25 PRK09541 emrE multidrug efflux 39.8 1.2E+02 0.0025 20.5 7.0 67 2-71 9-82 (110)
26 PF07784 DUF1622: Protein of u 39.3 47 0.001 21.4 3.2 14 29-42 60-73 (77)
27 PF10112 Halogen_Hydrol: 5-bro 39.0 1.4E+02 0.003 21.5 6.0 26 43-68 23-48 (199)
28 TIGR01113 mtrE N5-methyltetrah 36.7 28 0.0006 27.8 2.1 43 27-72 57-99 (283)
29 COG0472 Rfe UDP-N-acetylmuramy 36.1 68 0.0015 25.4 4.3 25 49-73 188-212 (319)
30 PRK10255 PTS system N-acetyl g 36.1 61 0.0013 28.5 4.3 34 34-67 74-112 (648)
31 PF10031 DUF2273: Small integr 34.1 1E+02 0.0023 18.3 4.4 31 36-66 14-48 (51)
32 PRK02919 oxaloacetate decarbox 33.5 97 0.0021 20.2 4.0 26 36-62 7-32 (82)
33 PF06612 DUF1146: Protein of u 32.3 45 0.00098 19.6 2.1 12 3-14 5-16 (48)
34 PF11772 EpuA: DNA-directed RN 30.6 26 0.00056 20.8 0.8 20 52-71 7-26 (47)
35 COG2076 EmrE Membrane transpor 30.5 1.8E+02 0.0039 19.9 6.2 67 2-71 9-82 (106)
36 PRK02898 cobalt transport prot 29.4 44 0.00095 22.9 1.9 39 12-67 52-90 (100)
37 TIGR02327 int_mem_ywzB conserv 29.4 54 0.0012 20.7 2.2 17 53-69 40-56 (68)
38 COG3105 Uncharacterized protei 29.3 54 0.0012 23.7 2.4 18 52-69 10-27 (138)
39 PF06305 DUF1049: Protein of u 29.1 64 0.0014 19.0 2.5 20 51-70 22-41 (68)
40 COG5336 Uncharacterized protei 28.9 1.7E+02 0.0037 20.6 4.8 50 22-73 48-97 (116)
41 PF12273 RCR: Chitin synthesis 27.7 74 0.0016 21.6 2.8 22 54-75 8-29 (130)
42 COG4828 Predicted membrane pro 26.6 89 0.0019 21.8 3.0 18 21-38 51-68 (113)
43 PF04113 Gpi16: Gpi16 subunit, 26.2 50 0.0011 28.4 2.1 22 46-67 509-530 (564)
44 PHA00024 IX minor coat protein 24.5 68 0.0015 17.9 1.8 26 47-72 2-27 (33)
45 PRK14855 nhaA pH-dependent sod 24.1 4.1E+02 0.0088 22.4 7.0 62 16-77 351-419 (423)
46 PRK10862 SoxR reducing system 22.8 2.4E+02 0.0052 19.9 4.8 22 50-71 103-124 (154)
47 PF15179 Myc_target_1: Myc tar 22.1 74 0.0016 24.2 2.1 16 53-68 25-40 (197)
48 PF02116 STE2: Fungal pheromon 22.1 1.4E+02 0.0031 23.5 3.8 23 24-47 31-53 (284)
49 PF05545 FixQ: Cbb3-type cytoc 21.9 48 0.001 19.0 0.9 6 63-68 23-28 (49)
50 COG4239 ABC-type uncharacteriz 21.3 3.7E+02 0.0079 22.1 6.0 47 23-73 129-175 (341)
51 TIGR01594 holin_lambda phage h 20.6 2.8E+02 0.0061 18.7 4.8 43 21-66 44-86 (107)
52 PF07444 Ycf66_N: Ycf66 protei 20.5 86 0.0019 20.6 2.0 23 47-69 3-25 (84)
No 1
>KOG3386 consensus Copper transporter [Inorganic ion transport and metabolism]
Probab=99.83 E-value=8e-21 Score=136.96 Aligned_cols=74 Identities=31% Similarity=0.525 Sum_probs=63.0
Q ss_pred hHHHHHHHhhccc-----cc---c------------CCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 044408 2 FSLTVDWISHMKL-----IK---S------------GINN-VASGILRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAG 60 (93)
Q Consensus 2 la~~~E~l~~~~~-----~k---~------------g~~~-~~~~l~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG 60 (93)
+|+++|+|+..|. .+ | .... ...|++|+++|.+|++++|+|||++||||+|+++|+++|
T Consensus 51 la~l~E~Lk~~r~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~h~~qt~l~~~Q~~~sY~LMLifMtfN~~l~Lavv~G 130 (155)
T KOG3386|consen 51 LAVLYEALKFGREKLFRWQQLRQPTGHGHEIPLSGPSKLLNSASHLIQTLLYVVQLGFSYLLMLIFMTFNGYLFLAVVLG 130 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccCCCccccccCcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence 6899999997553 11 1 1111 567999999999999999999999999999999999999
Q ss_pred hhhhHhhhccccccC
Q 044408 61 YSAGFFIFGSQVFRN 75 (93)
Q Consensus 61 ~~~G~~~F~~~~~~~ 75 (93)
+++||++|+.++...
T Consensus 131 a~~G~flF~~~~~~~ 145 (155)
T KOG3386|consen 131 AGVGYFLFGSLTFTP 145 (155)
T ss_pred HhhhhheeeeccccC
Confidence 999999999998833
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=99.81 E-value=6.9e-21 Score=130.55 Aligned_cols=48 Identities=33% Similarity=0.604 Sum_probs=39.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhh
Q 044408 21 NVASGILRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIF 68 (93)
Q Consensus 21 ~~~~~l~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F 68 (93)
+...|++|+++|++|.+++|+|||+|||||+|+|+||++|.++||++|
T Consensus 97 ~~~~~~~~~~l~~~~~~l~Y~LMLvvMTyN~~l~~aVv~G~~~G~~~F 144 (144)
T PF04145_consen 97 FWSQHLIRALLHFVQVLLGYLLMLVVMTYNVYLFIAVVLGAGLGYFLF 144 (144)
T ss_dssp -----SHHHHHHHHHHHHHHHHHHHHHHTT--SSSHHHHHHTTSS-GG
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhhhheeHHHHHHHHHHHHHheeeC
Confidence 357799999999999999999999999999999999999999999998
No 3
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=89.85 E-value=0.26 Score=30.22 Aligned_cols=28 Identities=14% Similarity=0.091 Sum_probs=24.1
Q ss_pred HhhhHHHHHHHHHHhhhhHhhhcccccc
Q 044408 47 MSFNIGVLLAAVAGYSAGFFIFGSQVFR 74 (93)
Q Consensus 47 MTfN~~i~~avilG~~~G~~~F~~~~~~ 74 (93)
|+.|+|+++.+++|..+|...-=+++.+
T Consensus 1 ~~~~~wlIIviVlgvIigNia~LK~sAk 28 (55)
T PF11446_consen 1 STWNPWLIIVIVLGVIIGNIAALKYSAK 28 (55)
T ss_pred CcchhhHHHHHHHHHHHhHHHHHHHhcc
Confidence 7899999999999999999988655543
No 4
>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=77.56 E-value=15 Score=27.50 Aligned_cols=57 Identities=25% Similarity=0.313 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhccccccCCccCCCCCCCCCCC
Q 044408 33 AFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQVFRNNFKIEPYQDLSDLP 89 (93)
Q Consensus 33 ~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~~~~~~~~~~~~~~~~l~ 89 (93)
.-++...|++++.+..-+..-...+++...++++++|.+..+..-+.+=+.+..|+|
T Consensus 223 ~~~~l~~y~~~lPf~l~~~~~~~~~~~~~l~~~~~~gl~~ig~~ledPFg~d~~dlp 279 (293)
T PF01062_consen 223 LSRFLYIYLLLLPFGLVDSLGWLTPPITFLVSFFFLGLEEIGEELEDPFGNDPNDLP 279 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcCCCcCc
Confidence 344556678777777666666666888889999999999887766544455566776
No 5
>PF08636 Pkr1: ER protein Pkr1; InterPro: IPR013945 Pkr1 has been identified as an ER protein of unknown function.
Probab=74.85 E-value=17 Score=23.64 Aligned_cols=48 Identities=21% Similarity=0.169 Sum_probs=29.1
Q ss_pred cccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH--HHHHHHHHhhh
Q 044408 13 KLIKSGINNVASGILRTLMYAFRFGLAYLAMLPVMSFNIG--VLLAAVAGYSA 63 (93)
Q Consensus 13 ~~~k~g~~~~~~~l~~a~l~~~q~~l~YlLMLivMTfN~~--i~~avilG~~~ 63 (93)
...+||++|......+.....++..+ +-|+..|+|.= +...+.+|.+.
T Consensus 11 sIftPG~tp~li~a~n~sF~~L~~~l---~~Ll~~t~niHfivL~~l~~~Lw~ 60 (75)
T PF08636_consen 11 SIFTPGTTPTLIIATNVSFAALFLVL---LALLFLTYNIHFIVLSFLALGLWA 60 (75)
T ss_pred HccCCCCChHHHHHHHHHHHHHHHHH---HHHHHHccCHHHHHHHHHHHHHHH
Confidence 35689999876666666666666554 44566666654 44444444443
No 6
>PRK15051 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional
Probab=73.69 E-value=24 Score=23.54 Aligned_cols=70 Identities=16% Similarity=0.048 Sum_probs=42.7
Q ss_pred hHHHHHHHhhcccccc-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHh-------hhHHHHHHHHHHhhhhHhhhc
Q 044408 2 FSLTVDWISHMKLIKS-----GINNVASGILRTLMYAFRFGLAYLAMLPVMS-------FNIGVLLAAVAGYSAGFFIFG 69 (93)
Q Consensus 2 la~~~E~l~~~~~~k~-----g~~~~~~~l~~a~l~~~q~~l~YlLMLivMT-------fN~~i~~avilG~~~G~~~F~ 69 (93)
+|++.|.....-+.+. .+...+..+....+-.+++++++.++..+|. |-.+- ++.+....+|+++|+
T Consensus 8 ~ai~~ev~g~~~lK~s~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~~al~~iplg~Ay~~~~-l~~v~~~~~~~l~f~ 86 (111)
T PRK15051 8 FASLLSVAGQLCQKQATRPVAIGKRRKHIVLWLGLALACLGLAMVLWLLVLQNVPVGIAYPMLS-LNFVWVTLAAVKLWH 86 (111)
T ss_pred HHHHHHHHHHHHHHHHhccCCcchhhhHHHHHHHHHHHHHHHHHHHHHHHHhhCChHHHHHHHH-HHHHHHHHHHHHHhC
Confidence 4667777765332211 1111122244455556788888888887776 44455 677788889999997
Q ss_pred ccc
Q 044408 70 SQV 72 (93)
Q Consensus 70 ~~~ 72 (93)
.+.
T Consensus 87 E~l 89 (111)
T PRK15051 87 EPV 89 (111)
T ss_pred CCC
Confidence 653
No 7
>PRK11431 multidrug efflux system protein; Provisional
Probab=69.44 E-value=31 Score=23.16 Aligned_cols=67 Identities=9% Similarity=0.092 Sum_probs=44.9
Q ss_pred hHHHHHHHhhccccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHH-------hhhHHHHHHHHHHhhhhHhhhccc
Q 044408 2 FSLTVDWISHMKLIKSGINNVASGILRTLMYAFRFGLAYLAMLPVM-------SFNIGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 2 la~~~E~l~~~~~~k~g~~~~~~~l~~a~l~~~q~~l~YlLMLivM-------TfN~~i~~avilG~~~G~~~F~~~ 71 (93)
+|+..|.+...-..+..+.. +..-++...+-+.++|.++-.+| .|-.|--+.++.-..+|.+.|+.+
T Consensus 8 ~Ai~~Ev~~t~~Lk~s~gf~---~~~~~~~~i~~~~~sf~~Ls~al~~ip~gvaYAvW~GiG~v~~~lig~~~f~e~ 81 (105)
T PRK11431 8 IAGLLEVVWAVGLKYTHGFS---RLTPSIITVTAMIVSMALLAWAMKSLPVGTAYAVWTGIGAVGAAITGIVLLGES 81 (105)
T ss_pred HHHHHHHHHHHHHHhhhCCc---cHHHHHHHHHHHHHHHHHHHHHHhhCCcHhHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 57778888776554432211 33334445666677777776665 677777788888889999999765
No 8
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=68.37 E-value=7.6 Score=29.94 Aligned_cols=48 Identities=15% Similarity=0.140 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhccccccCCccCCCCC
Q 044408 36 FGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQVFRNNFKIEPYQ 83 (93)
Q Consensus 36 ~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~~~~~~~~~~~~ 83 (93)
..++.++.++.=+.=.++++++.+|..++.++|+++.-+..+...|++
T Consensus 39 ~~v~v~ig~l~~~~~~~~i~gi~~g~l~am~vl~rra~ra~Y~qieGq 86 (224)
T PF13829_consen 39 IAVFVLIGLLFGSWWYWLIIGILLGLLAAMIVLSRRAQRAAYAQIEGQ 86 (224)
T ss_pred HHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 344445555555555668899999999999999998776666544433
No 9
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=67.33 E-value=3.6 Score=28.47 Aligned_cols=19 Identities=26% Similarity=0.349 Sum_probs=15.5
Q ss_pred HHHHHHHHHhhhhHhhhcc
Q 044408 52 GVLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 52 ~i~~avilG~~~G~~~F~~ 70 (93)
|++++.++|.++|+++...
T Consensus 1 y~~i~lvvG~iiG~~~~r~ 19 (128)
T PF06295_consen 1 YAIIGLVVGLIIGFLIGRL 19 (128)
T ss_pred ChHHHHHHHHHHHHHHHHH
Confidence 5788899999999998654
No 10
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=63.76 E-value=6.9 Score=24.79 Aligned_cols=19 Identities=37% Similarity=0.595 Sum_probs=15.7
Q ss_pred HHHHHHHHHhhhhHhhhcc
Q 044408 52 GVLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 52 ~i~~avilG~~~G~~~F~~ 70 (93)
.++++.++|.++|+|+-.+
T Consensus 2 ~iilali~G~~~Gff~ar~ 20 (64)
T PF03672_consen 2 LIILALIVGAVIGFFIARK 20 (64)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 4678999999999998654
No 11
>PRK11677 hypothetical protein; Provisional
Probab=61.02 E-value=7.7 Score=27.58 Aligned_cols=20 Identities=20% Similarity=0.130 Sum_probs=15.2
Q ss_pred HHHHHHHHHHhhhhHhhhcc
Q 044408 51 IGVLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 51 ~~i~~avilG~~~G~~~F~~ 70 (93)
.+.++++++|.++|+++-+.
T Consensus 4 ~~a~i~livG~iiG~~~~R~ 23 (134)
T PRK11677 4 EYALIGLVVGIIIGAVAMRF 23 (134)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 34568888899999888754
No 12
>PRK10650 multidrug efflux system protein MdtI; Provisional
Probab=59.23 E-value=53 Score=22.25 Aligned_cols=67 Identities=13% Similarity=0.205 Sum_probs=43.8
Q ss_pred hHHHHHHHhhccccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHH-------hhhHHHHHHHHHHhhhhHhhhccc
Q 044408 2 FSLTVDWISHMKLIKSGINNVASGILRTLMYAFRFGLAYLAMLPVM-------SFNIGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 2 la~~~E~l~~~~~~k~g~~~~~~~l~~a~l~~~q~~l~YlLMLivM-------TfN~~i~~avilG~~~G~~~F~~~ 71 (93)
+|++.|.....-..+..+ ..+..-++...+-+.++|.++-.+| .|-.|--+.++.-..+|.+.|+.+
T Consensus 14 ~Ai~~Ev~~t~~Lk~s~g---f~~~~~~~~~~~~~~~sf~~Ls~al~~lpvgvAYAvW~GiG~v~~~~ig~~~f~e~ 87 (109)
T PRK10650 14 LAIVLEIVANIFLKFSDG---FRRKIYGILSLAAVLAAFSALSQAVKGIDLSVAYALWGGFGIAATLAAGWILFGQR 87 (109)
T ss_pred HHHHHHHHHHHHHHHhcC---CcchHHHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 467777777655543322 1233345666677788888886666 566666777777778888888764
No 13
>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=55.20 E-value=13 Score=29.45 Aligned_cols=60 Identities=18% Similarity=0.175 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhccccccCCccCCCCCCCCCCC
Q 044408 27 LRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQVFRNNFKIEPYQDLSDLP 89 (93)
Q Consensus 27 ~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~~~~~~~~~~~~~~~~l~ 89 (93)
..+++.++--.++|.|| ..++.-.++++++|..++-++-+......---+...+|++++|
T Consensus 57 aygl~~ai~g~iA~~lm---~~~~~~~i~ai~~Ga~vAa~v~g~ya~taylGR~~s~~~F~QP 116 (269)
T PF04206_consen 57 AYGLWCAIAGAIAWALM---SAFGLNPILAIAIGAAVAALVHGVYATTAYLGRIASQKRFGQP 116 (269)
T ss_pred hhhHHHHHHHHHHHHHH---HHcCccHHHHHHHHHHHHHHHHHHHHHHHHhhhHhhHhhcCCC
Confidence 34677778888888877 3455568899999999998887654331100011235666665
No 14
>PRK00972 tetrahydromethanopterin S-methyltransferase subunit E; Provisional
Probab=53.24 E-value=12 Score=29.85 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhcccc
Q 044408 27 LRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQV 72 (93)
Q Consensus 27 ~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~ 72 (93)
..+++.++--.++|.+| .|.+| ..+++++|..++-++-+...
T Consensus 64 aygl~~ai~g~vA~~lm--~~~~~--~vlAi~~Ga~vaa~vhg~ya 105 (292)
T PRK00972 64 AYGLWCAIAGAVAWALM--AFGLN--PVLAIIVGAGVAALVHGVYA 105 (292)
T ss_pred hhHHHHHHHHHHHHHHH--HcCcc--HHHHHHHHHHHHHHHHHHHH
Confidence 35677788888888888 55555 45699999999988876543
No 15
>PF14012 DUF4229: Protein of unknown function (DUF4229)
Probab=51.82 E-value=40 Score=21.11 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh------HHHHHHHHHHhhhhHhhhcccccc
Q 044408 26 ILRTLMYAFRFGLAYLAMLPVMSFN------IGVLLAAVAGYSAGFFIFGSQVFR 74 (93)
Q Consensus 26 l~~a~l~~~q~~l~YlLMLivMTfN------~~i~~avilG~~~G~~~F~~~~~~ 74 (93)
+.|-.++..- ...++++.+... ....++++++..++|++|++.+.+
T Consensus 6 l~Rl~lfv~~---~~vi~~v~~~~~~~~p~~~~~l~A~vis~~lS~~ll~~~R~~ 57 (69)
T PF14012_consen 6 LARLGLFVVL---FAVIWLVGLLIGVEVPLLVAALLALVISMPLSYVLLRRLRDR 57 (69)
T ss_pred HHHHHHHHHH---HHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444333 334555555555 668899999999999999875554
No 16
>PRK01844 hypothetical protein; Provisional
Probab=49.72 E-value=18 Score=23.43 Aligned_cols=18 Identities=44% Similarity=0.632 Sum_probs=14.4
Q ss_pred HHHHHHHHhhhhHhhhcc
Q 044408 53 VLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 53 i~~avilG~~~G~~~F~~ 70 (93)
.+++.++|.+.|||+-++
T Consensus 10 ~I~~li~G~~~Gff~ark 27 (72)
T PRK01844 10 GVVALVAGVALGFFIARK 27 (72)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 467889999999998654
No 17
>PF06376 DUF1070: Protein of unknown function (DUF1070); InterPro: IPR009424 This entry represents the arabinogalactan peptide family found in plants [].
Probab=48.84 E-value=17 Score=20.44 Aligned_cols=14 Identities=36% Similarity=0.684 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHH
Q 044408 34 FRFGLAYLAMLPVM 47 (93)
Q Consensus 34 ~q~~l~YlLMLivM 47 (93)
+.-+++|+||+++-
T Consensus 14 iDqgiay~Lm~~Al 27 (34)
T PF06376_consen 14 IDQGIAYMLMLVAL 27 (34)
T ss_pred hhHHHHHHHHHHHH
Confidence 34578999998753
No 18
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.80 E-value=19 Score=23.30 Aligned_cols=21 Identities=43% Similarity=0.668 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhhhhHhhhccc
Q 044408 51 IGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 51 ~~i~~avilG~~~G~~~F~~~ 71 (93)
.++.+|.++|...|||+-.+.
T Consensus 8 l~ivl~ll~G~~~G~fiark~ 28 (71)
T COG3763 8 LLIVLALLAGLIGGFFIARKQ 28 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 467789999999998887653
No 19
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.32 E-value=15 Score=24.10 Aligned_cols=22 Identities=32% Similarity=0.739 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhhhhHhhhccccc
Q 044408 51 IGVLLAAVAGYSAGFFIFGSQVF 73 (93)
Q Consensus 51 ~~i~~avilG~~~G~~~F~~~~~ 73 (93)
.++|+.+++|..+||. |++++.
T Consensus 8 Fg~Fllvi~gMsiG~I-~krk~I 29 (77)
T COG2991 8 FGIFLLVIAGMSIGYI-FKRKSI 29 (77)
T ss_pred HHHHHHHHHHHhHhhh-eecccc
Confidence 4789999999999985 555555
No 20
>PF14362 DUF4407: Domain of unknown function (DUF4407)
Probab=44.84 E-value=49 Score=25.27 Aligned_cols=28 Identities=29% Similarity=0.281 Sum_probs=22.2
Q ss_pred HHhhhHHHHHHHHHHhhhhHhhhccccc
Q 044408 46 VMSFNIGVLLAAVAGYSAGFFIFGSQVF 73 (93)
Q Consensus 46 vMTfN~~i~~avilG~~~G~~~F~~~~~ 73 (93)
.+++......++.+|...|.++|.-++.
T Consensus 38 ~~~~~~~~~~ai~~glvwgl~I~~lDR~ 65 (301)
T PF14362_consen 38 YTVFGGPVWAAIPFGLVWGLVIFNLDRF 65 (301)
T ss_pred HHHhccchHHHHHHHHHHHHHHHHHHHH
Confidence 4455555699999999999999977655
No 21
>PRK00523 hypothetical protein; Provisional
Probab=42.84 E-value=27 Score=22.64 Aligned_cols=18 Identities=17% Similarity=0.298 Sum_probs=14.1
Q ss_pred HHHHHHHHhhhhHhhhcc
Q 044408 53 VLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 53 i~~avilG~~~G~~~F~~ 70 (93)
++++.++|.+.|||+-++
T Consensus 11 ~i~~li~G~~~Gffiark 28 (72)
T PRK00523 11 GIPLLIVGGIIGYFVSKK 28 (72)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 456788999999988654
No 22
>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=42.75 E-value=23 Score=25.96 Aligned_cols=19 Identities=16% Similarity=0.399 Sum_probs=15.4
Q ss_pred HHHHHHHHHhhhhHhhhcc
Q 044408 52 GVLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 52 ~i~~avilG~~~G~~~F~~ 70 (93)
..++++++|.++||++...
T Consensus 5 ~~i~~~~vG~~~G~~~~~~ 23 (201)
T PF12072_consen 5 IAIVALIVGIGIGYLVRKK 23 (201)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4678889999999998654
No 23
>PRK10452 multidrug efflux system protein MdtJ; Provisional
Probab=41.67 E-value=1.2e+02 Score=20.95 Aligned_cols=66 Identities=6% Similarity=0.070 Sum_probs=41.8
Q ss_pred hHHHHHHHhhccccc-cCCcccHHHHHHHHHHHHHHHHHHHHHHHHH-------hhhHHHHHHHHHHhhhhHhhhccc
Q 044408 2 FSLTVDWISHMKLIK-SGINNVASGILRTLMYAFRFGLAYLAMLPVM-------SFNIGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 2 la~~~E~l~~~~~~k-~g~~~~~~~l~~a~l~~~q~~l~YlLMLivM-------TfN~~i~~avilG~~~G~~~F~~~ 71 (93)
+|++.|.....-... .+.+. ....++..+-+.++|.++-.+| .|-.|--+.++.-..+|.++|+.+
T Consensus 9 ~Ai~~Ev~~t~~LK~s~g~~~----~~~~~~~i~~~~~sf~~ls~al~~lplsiAYavw~GiG~v~~~~ig~~~f~E~ 82 (120)
T PRK10452 9 LAIATEITGTLSMKWASVSEG----NGGFILMLVMISLSYIFLSFAVKKIALGVAYALWEGIGILFITLFSVLLFDES 82 (120)
T ss_pred HHHHHHHHHHHHHHhhccCCC----cHHHHHHHHHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 477788877765543 22222 2234556666777777776666 355555566777778888888765
No 24
>PF06939 DUF1286: Protein of unknown function (DUF1286); InterPro: IPR009705 This entry is represented by Sulfolobus virus STSV1, Orf8. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical archaeal proteins of around 120 residues in length. All members of this family seem to be Sulfolobus species specific. The function of this family is unknown.
Probab=41.63 E-value=54 Score=23.02 Aligned_cols=47 Identities=23% Similarity=0.334 Sum_probs=32.0
Q ss_pred cCCcccHHHHHHHHHHHHHHHHHHHHHHHHHh---hhHHHHHHHHHHhhhh
Q 044408 17 SGINNVASGILRTLMYAFRFGLAYLAMLPVMS---FNIGVLLAAVAGYSAG 64 (93)
Q Consensus 17 ~g~~~~~~~l~~a~l~~~q~~l~YlLMLivMT---fN~~i~~avilG~~~G 64 (93)
|..+|..+-+.|++..++-..+- +.++..+. +|.-+.++++.|...|
T Consensus 59 ~~RTPlTHT~pRSv~WGli~slp-~i~~l~~~~~~~~~~il~~Ll~Gvl~G 108 (114)
T PF06939_consen 59 PVRTPLTHTLPRSVLWGLIPSLP-LIILLYYYYGYFNYIILLALLSGVLVG 108 (114)
T ss_pred eecCCCccCcchhhHHHHHHHHH-HHHHHHHHhcchHHHHHHHHHhhhccc
Confidence 55678888889999888777665 23333322 3456788888887766
No 25
>PRK09541 emrE multidrug efflux protein; Reviewed
Probab=39.77 E-value=1.2e+02 Score=20.46 Aligned_cols=67 Identities=9% Similarity=0.041 Sum_probs=40.5
Q ss_pred hHHHHHHHhhccccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHH-------hhhHHHHHHHHHHhhhhHhhhccc
Q 044408 2 FSLTVDWISHMKLIKSGINNVASGILRTLMYAFRFGLAYLAMLPVM-------SFNIGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 2 la~~~E~l~~~~~~k~g~~~~~~~l~~a~l~~~q~~l~YlLMLivM-------TfN~~i~~avilG~~~G~~~F~~~ 71 (93)
+|+..|.+...-.....+. .+..-++...+-+.++|.++-.+| .|-.|--+.++.-..+|.+.|+.+
T Consensus 9 ~a~~~Ev~~~~~lK~s~gf---~~~~~~i~~~~~~~~sf~~l~~al~~ipl~iAYavw~GlG~v~~~l~g~~~f~e~ 82 (110)
T PRK09541 9 GAILAEVIGTTLMKFSEGF---TRLWPSVGTIICYCASFWLLAQTLAYIPTGIAYAIWSGVGIVLISLLSWGFFGQR 82 (110)
T ss_pred HHHHHHHHHHHHHHHhcCC---CchhHHHHHHHHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4777888777654433321 233344455556677777665555 355555566666677888888764
No 26
>PF07784 DUF1622: Protein of unknown function (DUF1622); InterPro: IPR012427 This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species.
Probab=39.31 E-value=47 Score=21.36 Aligned_cols=14 Identities=21% Similarity=0.278 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHH
Q 044408 29 TLMYAFRFGLAYLA 42 (93)
Q Consensus 29 a~l~~~q~~l~YlL 42 (93)
+.+-.++..++|+|
T Consensus 60 a~Iv~IRt~Ls~~L 73 (77)
T PF07784_consen 60 AAIVLIRTFLSYFL 73 (77)
T ss_pred HHHHHHHHHHHHHH
Confidence 44444444444443
No 27
>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=39.04 E-value=1.4e+02 Score=21.49 Aligned_cols=26 Identities=19% Similarity=0.387 Sum_probs=15.4
Q ss_pred HHHHHhhhHHHHHHHHHHhhhhHhhh
Q 044408 43 MLPVMSFNIGVLLAAVAGYSAGFFIF 68 (93)
Q Consensus 43 MLivMTfN~~i~~avilG~~~G~~~F 68 (93)
......++...++++++|.+.+..++
T Consensus 23 ~~~~~~~~~~~~l~~l~~~~~~~~~~ 48 (199)
T PF10112_consen 23 LVSFFGFDHSFLLSLLIGAVAFAVVY 48 (199)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 34444556666667777776665544
No 28
>TIGR01113 mtrE N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit E. coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase 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.
Probab=36.66 E-value=28 Score=27.79 Aligned_cols=43 Identities=16% Similarity=0.120 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhcccc
Q 044408 27 LRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQV 72 (93)
Q Consensus 27 ~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~ 72 (93)
..+++.++--.++|.||... +.-.++++++|..++-++-+...
T Consensus 57 aygl~~~i~g~vA~~l~~~~---~~~~ilAi~~Ga~vaa~v~~~ya 99 (283)
T TIGR01113 57 SYGLYCGIAGAVAYVLMSYF---GLPPLIALAVGAVIAALVHLAYA 99 (283)
T ss_pred hhHHHHHHHHHHHHHHHHhc---CCchHHHHHHHHHHHHHHHHHHH
Confidence 35677778888888887433 44567899999999988876543
No 29
>COG0472 Rfe UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]
Probab=36.11 E-value=68 Score=25.37 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHhhhhHhhhccccc
Q 044408 49 FNIGVLLAAVAGYSAGFFIFGSQVF 73 (93)
Q Consensus 49 fN~~i~~avilG~~~G~~~F~~~~~ 73 (93)
+...++.+.++|+.+||+.|++.+.
T Consensus 188 ~~~~~~~~al~ga~LGFL~~N~~PA 212 (319)
T COG0472 188 GELALICAALAGACLGFLWFNFYPA 212 (319)
T ss_pred hhHHHHHHHHHHHHHHHHHhcCChh
Confidence 4455888999999999999998775
No 30
>PRK10255 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional
Probab=36.07 E-value=61 Score=28.48 Aligned_cols=34 Identities=24% Similarity=0.433 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHh-----hhHHHHHHHHHHhhhhHhh
Q 044408 34 FRFGLAYLAMLPVMS-----FNIGVLLAAVAGYSAGFFI 67 (93)
Q Consensus 34 ~q~~l~YlLMLivMT-----fN~~i~~avilG~~~G~~~ 67 (93)
+.-.++|++|..+|. .|.++|..+++|+..++..
T Consensus 74 la~~v~yl~~~~~~~~~~~~~~~gvfgGIi~G~i~a~l~ 112 (648)
T PRK10255 74 LAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAY 112 (648)
T ss_pred HHHHHHHHHHHHHHHHHhhhhchhhhhhhHHHHHHHHHH
Confidence 445678888877753 4888999999999887643
No 31
>PF10031 DUF2273: Small integral membrane protein (DUF2273); InterPro: IPR018730 Members of this family of hypothetical bacterial proteins have no known function.
Probab=34.09 E-value=1e+02 Score=18.25 Aligned_cols=31 Identities=26% Similarity=0.417 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHhhhHH----HHHHHHHHhhhhHh
Q 044408 36 FGLAYLAMLPVMSFNIG----VLLAAVAGYSAGFF 66 (93)
Q Consensus 36 ~~l~YlLMLivMTfN~~----i~~avilG~~~G~~ 66 (93)
..++.++=++++++-.+ +++.+.+|..+|..
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 56667777777764
No 32
>PRK02919 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=33.46 E-value=97 Score=20.17 Aligned_cols=26 Identities=19% Similarity=0.186 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHhh
Q 044408 36 FGLAYLAMLPVMSFNIGVLLAAVAGYS 62 (93)
Q Consensus 36 ~~l~YlLMLivMTfN~~i~~avilG~~ 62 (93)
+.=+--+|++-|.+ +.+|+++++.+.
T Consensus 7 l~~gl~lMvlGMg~-VfvFL~lLI~~i 32 (82)
T PRK02919 7 LGEGFTLMFLGMGF-VLAFLFLLIFAI 32 (82)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 34455678888888 788888877654
No 33
>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=32.35 E-value=45 Score=19.61 Aligned_cols=12 Identities=8% Similarity=0.130 Sum_probs=5.7
Q ss_pred HHHHHHHhhccc
Q 044408 3 SLTVDWISHMKL 14 (93)
Q Consensus 3 a~~~E~l~~~~~ 14 (93)
++..-.|+.-+|
T Consensus 5 ~la~~aLq~l~~ 16 (48)
T PF06612_consen 5 ALAFWALQSLRW 16 (48)
T ss_pred HHHHHHHHhcCH
Confidence 444445555444
No 34
>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=30.55 E-value=26 Score=20.75 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=16.5
Q ss_pred HHHHHHHHHhhhhHhhhccc
Q 044408 52 GVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 52 ~i~~avilG~~~G~~~F~~~ 71 (93)
..+++.++|+.+||-+.|..
T Consensus 7 L~~~~l~iGlmIGY~viG~G 26 (47)
T PF11772_consen 7 LAILALAIGLMIGYGVIGDG 26 (47)
T ss_pred HHHHHHHHHHHeeeeeeCCC
Confidence 35778899999999988764
No 35
>COG2076 EmrE Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]
Probab=30.50 E-value=1.8e+02 Score=19.89 Aligned_cols=67 Identities=13% Similarity=0.279 Sum_probs=42.1
Q ss_pred hHHHHHHHhhccccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHH-------hhhHHHHHHHHHHhhhhHhhhccc
Q 044408 2 FSLTVDWISHMKLIKSGINNVASGILRTLMYAFRFGLAYLAMLPVM-------SFNIGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 2 la~~~E~l~~~~~~k~g~~~~~~~l~~a~l~~~q~~l~YlLMLivM-------TfN~~i~~avilG~~~G~~~F~~~ 71 (93)
+|.+.|.....-.......+ +...+++-.+-+.++|.+.-.+| .|-+|--+.++....+|.++|+.+
T Consensus 9 lAi~~EV~~~~~lK~s~gf~---~~~~~il~~v~~~~sf~~Ls~alk~ipvgvAYAiW~GiG~v~~~l~g~~~f~E~ 82 (106)
T COG2076 9 LAILLEVVGTTLLKYSDGFT---RLWPSILTIVGYGLSFYLLSLALKTIPLGVAYAIWTGIGIVGTALVGVLLFGES 82 (106)
T ss_pred HHHHHHHHHHHHHHHHhccc---ccchHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence 56777877765554333211 22234444555666666654433 577778888888899999999764
No 36
>PRK02898 cobalt transport protein CbiN; Provisional
Probab=29.45 E-value=44 Score=22.85 Aligned_cols=39 Identities=23% Similarity=0.462 Sum_probs=25.3
Q ss_pred ccccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhh
Q 044408 12 MKLIKSGINNVASGILRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFI 67 (93)
Q Consensus 12 ~~~~k~g~~~~~~~l~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~ 67 (93)
.||.+|-=.|- ..=+.++|+.+|..++ +.++|..+||+-
T Consensus 52 ~PWf~PlwEPP-sGEiESLLFaLQAAiG----------------AgiIgY~lG~~~ 90 (100)
T PRK02898 52 EPWFEPLWEPP-SGEIESLLFALQAALG----------------AGIIGYILGYYK 90 (100)
T ss_pred cccccccccCC-cchHHHHHHHHHHHHh----------------hhhhheeeeehh
Confidence 45654332221 2345789999999988 667777777764
No 37
>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=29.44 E-value=54 Score=20.73 Aligned_cols=17 Identities=35% Similarity=0.710 Sum_probs=12.7
Q ss_pred HHHHHHHHhhhhHhhhc
Q 044408 53 VLLAAVAGYSAGFFIFG 69 (93)
Q Consensus 53 i~~avilG~~~G~~~F~ 69 (93)
+++|+.+|..++.|+.+
T Consensus 40 vllaIalGylvs~FfL~ 56 (68)
T TIGR02327 40 VLIAIALGYTVSHFFLE 56 (68)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 56778888888877764
No 38
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.26 E-value=54 Score=23.68 Aligned_cols=18 Identities=28% Similarity=0.298 Sum_probs=15.0
Q ss_pred HHHHHHHHHhhhhHhhhc
Q 044408 52 GVLLAAVAGYSAGFFIFG 69 (93)
Q Consensus 52 ~i~~avilG~~~G~~~F~ 69 (93)
+..++.++|.++|+.+-+
T Consensus 10 ~a~igLvvGi~IG~li~R 27 (138)
T COG3105 10 YALIGLVVGIIIGALIAR 27 (138)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 467888999999999874
No 39
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=29.12 E-value=64 Score=19.02 Aligned_cols=20 Identities=20% Similarity=0.306 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhhhhHhhhcc
Q 044408 51 IGVLLAAVAGYSAGFFIFGS 70 (93)
Q Consensus 51 ~~i~~avilG~~~G~~~F~~ 70 (93)
..++++.++|..+|.++.-.
T Consensus 22 l~il~~f~~G~llg~l~~~~ 41 (68)
T PF06305_consen 22 LLILIAFLLGALLGWLLSLP 41 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45677777888888776643
No 40
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.91 E-value=1.7e+02 Score=20.56 Aligned_cols=50 Identities=14% Similarity=0.209 Sum_probs=40.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhccccc
Q 044408 22 VASGILRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQVF 73 (93)
Q Consensus 22 ~~~~l~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~~ 73 (93)
...+++..++-+ ++++|++==.+=|=..++++-.++|.+.|++.-.++.-
T Consensus 48 lssefIsGilVG--a~iG~llD~~agTsPwglIv~lllGf~AG~lnv~Rsag 97 (116)
T COG5336 48 LSSEFISGILVG--AGIGWLLDKFAGTSPWGLIVFLLLGFGAGVLNVLRSAG 97 (116)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345666666554 67888888889999999999999999999998866544
No 41
>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=27.68 E-value=74 Score=21.59 Aligned_cols=22 Identities=14% Similarity=0.218 Sum_probs=11.1
Q ss_pred HHHHHHHhhhhHhhhccccccC
Q 044408 54 LLAAVAGYSAGFFIFGSQVFRN 75 (93)
Q Consensus 54 ~~avilG~~~G~~~F~~~~~~~ 75 (93)
|+.+++-.+++++++.+++.++
T Consensus 8 ii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 8 IIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHhhc
Confidence 3344444455555555655555
No 42
>COG4828 Predicted membrane protein [Function unknown]
Probab=26.55 E-value=89 Score=21.85 Aligned_cols=18 Identities=6% Similarity=0.373 Sum_probs=9.1
Q ss_pred ccHHHHHHHHHHHHHHHH
Q 044408 21 NVASGILRTLMYAFRFGL 38 (93)
Q Consensus 21 ~~~~~l~~a~l~~~q~~l 38 (93)
+...++-+=+.+++++.+
T Consensus 51 ~iRkelt~ki~fgLEf~i 68 (113)
T COG4828 51 SIRKELTNKIAFGLEFLI 68 (113)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344455555555555444
No 43
>PF04113 Gpi16: Gpi16 subunit, GPI transamidase component; InterPro: IPR007245 GPI (glycosyl phosphatidyl inositol) transamidase is a multiprotein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase adds glycosylphosphatidylinositols (GPIs) to newly synthesized proteins. Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif [].; GO: 0016021 integral to membrane, 0042765 GPI-anchor transamidase complex
Probab=26.19 E-value=50 Score=28.42 Aligned_cols=22 Identities=23% Similarity=0.394 Sum_probs=19.9
Q ss_pred HHhhhHHHHHHHHHHhhhhHhh
Q 044408 46 VMSFNIGVLLAAVAGYSAGFFI 67 (93)
Q Consensus 46 vMTfN~~i~~avilG~~~G~~~ 67 (93)
.|-||+-.+.+++++.++|-..
T Consensus 509 SMPyNVI~lt~Tv~Al~FG~i~ 530 (564)
T PF04113_consen 509 SMPYNVIILTCTVMALAFGSIF 530 (564)
T ss_pred CccchhhHHHHHHHHHHHHHHH
Confidence 5999999999999999999763
No 44
>PHA00024 IX minor coat protein
Probab=24.54 E-value=68 Score=17.90 Aligned_cols=26 Identities=19% Similarity=0.065 Sum_probs=18.8
Q ss_pred HhhhHHHHHHHHHHhhhhHhhhcccc
Q 044408 47 MSFNIGVLLAAVAGYSAGFFIFGSQV 72 (93)
Q Consensus 47 MTfN~~i~~avilG~~~G~~~F~~~~ 72 (93)
|.+=++.|-|-++|-++||-+-.-++
T Consensus 2 ~~~l~~ffgA~ilG~~l~~~Il~FKk 27 (33)
T PHA00024 2 MSYLGYFFGAYILGWALFYGILVFKK 27 (33)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56667788888899888886654433
No 45
>PRK14855 nhaA pH-dependent sodium/proton antiporter; Provisional
Probab=24.07 E-value=4.1e+02 Score=22.40 Aligned_cols=62 Identities=18% Similarity=0.028 Sum_probs=43.4
Q ss_pred ccCCcccHHHHHHHHHHHHHHHHHHHHH-HHHH------hhhHHHHHHHHHHhhhhHhhhccccccCCc
Q 044408 16 KSGINNVASGILRTLMYAFRFGLAYLAM-LPVM------SFNIGVLLAAVAGYSAGFFIFGSQVFRNNF 77 (93)
Q Consensus 16 k~g~~~~~~~l~~a~l~~~q~~l~YlLM-LivM------TfN~~i~~avilG~~~G~~~F~~~~~~~~~ 77 (93)
.|...+|.+-..-+++-++-++.|-++= |..- .=-.+++++-++...+|+.+......+.+.
T Consensus 351 lP~g~~w~~l~gv~~LaGIGFTmSLFIa~LAF~~~~~~~~aKigIL~~S~~aai~G~~~L~~~~~~~~~ 419 (423)
T PRK14855 351 LPRRVNWLHMLGAGLLAGIGFTMSLFISNLAFADAALLTQAKLGVLAASVLAALLGAGWLWWAVRGQPG 419 (423)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 4777788888888999999999996553 3330 112468888888888999888544444444
No 46
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=22.82 E-value=2.4e+02 Score=19.95 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHhhhhHhhhccc
Q 044408 50 NIGVLLAAVAGYSAGFFIFGSQ 71 (93)
Q Consensus 50 N~~i~~avilG~~~G~~~F~~~ 71 (93)
+.+.+++.++|.++||++-+..
T Consensus 103 e~~~~~~~~~g~~~g~~~~r~~ 124 (154)
T PRK10862 103 DLAALCGALLGGVGGFLLARGL 124 (154)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 6677888899999998887653
No 47
>PF15179 Myc_target_1: Myc target protein 1
Probab=22.14 E-value=74 Score=24.24 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=10.7
Q ss_pred HHHHHHHHhhhhHhhh
Q 044408 53 VLLAAVAGYSAGFFIF 68 (93)
Q Consensus 53 i~~avilG~~~G~~~F 68 (93)
+++++++|+.+|-++|
T Consensus 25 F~vSm~iGLviG~li~ 40 (197)
T PF15179_consen 25 FCVSMAIGLVIGALIW 40 (197)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4566777777776665
No 48
>PF02116 STE2: Fungal pheromone mating factor STE2 GPCR; InterPro: IPR000366 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). Little is known about the structure and function of the mating factor receptors, STE2 and STE3. It is believed, however, that they are integral membrane proteins that may be involved in the response to mating factors on the cell membrane [, , ]. The amino acid sequences of both receptors contain high proportions of hydrophobic residues grouped into 7 domains, in a manner reminiscent of the rhodopsins and other receptors believed to interact with G-proteins. However, while a similar 3D framework has been proposed to account for this, there is no significant sequence similarity either between STE2 and STE3, or between these and the rhodopsin-type family: the receptors thus bear their own unique '7TM' signatures.; GO: 0004932 mating-type factor pheromone receptor activity, 0016020 membrane; PDB: 2K9P_A.
Probab=22.09 E-value=1.4e+02 Score=23.49 Aligned_cols=23 Identities=22% Similarity=0.442 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 044408 24 SGILRTLMYAFRFGLAYLAMLPVM 47 (93)
Q Consensus 24 ~~l~~a~l~~~q~~l~YlLMLivM 47 (93)
..+-.++.|+.|.+.+ ++||++|
T Consensus 31 ~~~~~~I~yg~qiGA~-~~llivL 53 (284)
T PF02116_consen 31 YNVRTAINYGVQIGAC-LLLLIVL 53 (284)
T ss_dssp HHHHHHHHHHHHHHHH-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHH
Confidence 3566789999999999 6666555
No 49
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=21.91 E-value=48 Score=18.99 Aligned_cols=6 Identities=33% Similarity=0.805 Sum_probs=2.2
Q ss_pred hhHhhh
Q 044408 63 AGFFIF 68 (93)
Q Consensus 63 ~G~~~F 68 (93)
+|..++
T Consensus 23 ~gi~~w 28 (49)
T PF05545_consen 23 IGIVIW 28 (49)
T ss_pred HHHHHH
Confidence 333333
No 50
>COG4239 ABC-type uncharacterized transport system, permease component [General function prediction only]
Probab=21.27 E-value=3.7e+02 Score=22.09 Aligned_cols=47 Identities=26% Similarity=0.472 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHhhhccccc
Q 044408 23 ASGILRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFFIFGSQVF 73 (93)
Q Consensus 23 ~~~l~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~~F~~~~~ 73 (93)
-+++..-++|+.+..+=+-|+|..-+ ..+.|.+|+..|||=+.-+..
T Consensus 129 gRDV~ARliygfRiSvLfgL~lT~~S----aliGv~~GA~qGyfgg~vdL~ 175 (341)
T COG4239 129 GRDVLARLIYGFRISVLFGLSLTLIS----ALIGVLAGALQGYFGGWVDLL 175 (341)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhhhhccchHHH
Confidence 56788889999999888888877644 566778888888876544443
No 51
>TIGR01594 holin_lambda phage holin, lambda family. This model represents one of a large number of mutally dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda.
Probab=20.65 E-value=2.8e+02 Score=18.72 Aligned_cols=43 Identities=21% Similarity=0.279 Sum_probs=23.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhHh
Q 044408 21 NVASGILRTLMYAFRFGLAYLAMLPVMSFNIGVLLAAVAGYSAGFF 66 (93)
Q Consensus 21 ~~~~~l~~a~l~~~q~~l~YlLMLivMTfN~~i~~avilG~~~G~~ 66 (93)
.+.+.++.+++.+. ++....-..=.|..---+++.+|..+||.
T Consensus 44 ~~~~~llea~mCg~---la~~~~~~l~~~g~~~~~a~~~g~~IGfl 86 (107)
T TIGR01594 44 KFKRKLIDALMCAA---IALVAASALDFLGLPTSLSPFLGGMIGFV 86 (107)
T ss_pred cHHHHHHHHHHHHH---HHHHHHHHHHHcCCcHHHHHHHhhheeec
Confidence 47788888888873 22222222122222234566777777764
No 52
>PF07444 Ycf66_N: Ycf66 protein N-terminus; InterPro: IPR010004 This entry represents Ycf66, a protein that is restricted to the chloroplasts of simple plants and algae. It is also found in the cyanobacteria. The function is unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=20.49 E-value=86 Score=20.64 Aligned_cols=23 Identities=13% Similarity=0.119 Sum_probs=16.7
Q ss_pred HhhhHHHHHHHHHHhhhhHhhhc
Q 044408 47 MSFNIGVLLAAVAGYSAGFFIFG 69 (93)
Q Consensus 47 MTfN~~i~~avilG~~~G~~~F~ 69 (93)
+++|...+++++++.+-.-+.|-
T Consensus 3 ~~~~~~~iLgi~l~~~~~~Ly~l 25 (84)
T PF07444_consen 3 FGFGPSYILGIILILGGLALYFL 25 (84)
T ss_pred cccCHHHHHHHHHHHHHHHHHHH
Confidence 67888888888888765555553
Done!