Query 031335
Match_columns 161
No_of_seqs 131 out of 1016
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 12:38:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031335hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1058 CinA Predicted nucleot 100.0 7.5E-31 1.6E-35 214.0 12.4 138 12-154 101-248 (255)
2 PRK00549 competence damage-ind 100.0 6.8E-29 1.5E-33 215.3 15.5 138 18-159 106-254 (414)
3 PRK03673 hypothetical protein; 100.0 2.1E-28 4.5E-33 211.0 14.6 139 16-159 105-250 (396)
4 PRK03670 competence damage-ind 100.0 5.1E-28 1.1E-32 197.8 15.1 125 18-152 114-245 (252)
5 TIGR00200 cinA_nterm competenc 99.9 6.4E-25 1.4E-29 190.4 14.8 139 17-159 105-255 (413)
6 PRK01215 competence damage-ind 99.9 2.9E-24 6.4E-29 176.7 15.0 131 17-153 108-254 (264)
7 cd00885 cinA Competence-damage 99.6 6.5E-16 1.4E-20 119.7 3.7 60 17-79 104-169 (170)
8 PF00994 MoCF_biosynth: Probab 93.4 0.042 9.2E-07 40.8 1.5 34 43-78 103-143 (144)
9 smart00852 MoCF_biosynth Proba 88.1 0.61 1.3E-05 34.1 3.3 44 26-71 89-133 (135)
10 TIGR00177 molyb_syn molybdenum 84.7 1.2 2.6E-05 33.1 3.4 32 39-72 106-140 (144)
11 COG2921 Uncharacterized conser 76.8 14 0.0003 25.8 6.2 58 93-150 18-82 (90)
12 cd07027 RNAP_RPB11_like RPB11 73.0 17 0.00037 24.8 5.9 54 100-153 20-79 (83)
13 cd07029 RNAP_I_III_AC19 AC19 s 71.2 23 0.0005 24.2 6.2 53 100-152 20-78 (85)
14 PF00408 PGM_PMM_IV: Phosphogl 68.6 17 0.00037 23.6 5.0 37 116-152 36-72 (73)
15 COG1761 RPB11 DNA-directed RNA 65.9 28 0.00062 24.7 5.9 54 100-153 26-85 (99)
16 PF00936 BMC: BMC domain; Int 65.1 28 0.0006 23.0 5.5 45 114-159 25-69 (75)
17 PRK00907 hypothetical protein; 58.4 60 0.0013 22.6 7.1 56 95-150 23-84 (92)
18 PRK01146 DNA-directed RNA poly 56.5 58 0.0013 22.2 6.0 54 100-153 22-81 (85)
19 PF03808 Glyco_tran_WecB: Glyc 54.6 67 0.0015 24.4 6.8 29 94-122 53-82 (172)
20 PF13656 RNA_pol_L_2: RNA poly 53.6 57 0.0012 21.7 5.5 53 100-152 12-70 (77)
21 cd07053 BMC_PduT_repeat1 1,2-p 53.1 66 0.0014 21.5 6.2 46 114-160 24-69 (76)
22 cd06926 RNAP_II_RPB11 RPB11 su 52.9 59 0.0013 22.5 5.7 54 100-153 28-87 (93)
23 PF05036 SPOR: Sporulation rel 51.4 57 0.0012 20.3 5.2 57 97-154 13-71 (76)
24 cd06927 RNAP_L L subunit of Ar 51.3 75 0.0016 21.6 5.9 54 100-153 20-79 (83)
25 PRK09417 mogA molybdenum cofac 50.0 17 0.00036 28.8 2.8 15 55-71 129-144 (193)
26 TIGR02667 moaB_proteo molybden 46.0 23 0.00049 26.9 2.9 24 55-80 127-152 (163)
27 PRK00341 hypothetical protein; 45.2 1E+02 0.0022 21.3 6.8 56 95-150 23-83 (91)
28 PRK02047 hypothetical protein; 44.1 1E+02 0.0023 21.2 7.2 56 95-150 22-83 (91)
29 COG1925 FruB Phosphotransferas 42.6 30 0.00065 23.9 2.8 24 127-150 59-83 (88)
30 PTZ00302 N-acetylglucosamine-p 42.0 88 0.0019 29.0 6.5 53 102-154 527-580 (585)
31 PRK10897 phosphohistidinoprote 40.6 54 0.0012 22.6 3.9 27 127-153 61-88 (90)
32 cd00758 MoCF_BD MoCF_BD: molyb 40.1 14 0.0003 26.9 0.9 20 55-76 111-132 (133)
33 cd07049 BMC_EutL_repeat1 ethan 40.1 92 0.002 22.3 5.1 58 95-155 32-100 (103)
34 cd03086 PGM3 PGM3 (phosphogluc 39.6 1.2E+02 0.0027 27.4 7.0 40 112-151 473-512 (513)
35 PF03135 CagE_TrbE_VirB: CagE, 38.8 1.3E+02 0.0029 23.2 6.4 37 115-157 143-179 (205)
36 cd00886 MogA_MoaB MogA_MoaB fa 38.0 37 0.00081 25.2 3.0 24 54-79 123-147 (152)
37 COG1839 Uncharacterized conser 37.8 1.8E+02 0.004 22.2 7.2 58 103-160 30-87 (162)
38 PF06183 DinI: DinI-like famil 37.0 1.2E+02 0.0025 19.7 5.6 31 104-137 12-42 (65)
39 KOG1794 N-Acetylglucosamine ki 36.3 49 0.0011 28.3 3.6 60 94-154 37-97 (336)
40 PRK03604 moaC bifunctional mol 34.0 43 0.00093 28.5 3.0 22 55-78 278-300 (312)
41 PRK11169 leucine-responsive tr 32.7 1.6E+02 0.0035 22.0 5.8 71 72-149 18-98 (164)
42 cd04905 ACT_CM-PDT C-terminal 32.6 1.4E+02 0.003 19.3 6.7 53 100-152 13-70 (80)
43 PF04359 DUF493: Protein of un 32.1 1.4E+02 0.003 19.9 4.8 60 91-150 11-77 (85)
44 PRK10850 PTS system phosphohis 31.4 98 0.0021 21.0 4.0 22 127-148 59-80 (85)
45 cd03084 phosphohexomutase The 31.2 91 0.002 26.3 4.6 32 120-151 323-354 (355)
46 PRK13780 phosphocarrier protei 31.0 62 0.0014 22.1 3.0 15 127-141 59-73 (88)
47 cd03089 PMM_PGM The phosphoman 30.9 1.1E+02 0.0024 26.7 5.2 31 121-151 412-442 (443)
48 PF13083 KH_4: KH domain; PDB: 30.5 1.5E+02 0.0033 19.0 6.4 40 101-140 3-42 (73)
49 PF02391 MoaE: MoaE protein; 28.3 2.2E+02 0.0049 20.3 5.9 57 96-153 52-114 (117)
50 smart00877 BMC Bacterial micro 27.9 1.8E+02 0.0039 19.1 6.3 40 114-154 24-63 (75)
51 PF09883 DUF2110: Uncharacteri 27.9 3.4E+02 0.0073 22.2 7.9 56 95-154 8-65 (225)
52 PRK14320 glmM phosphoglucosami 27.7 91 0.002 27.3 4.1 35 120-154 406-440 (443)
53 PF14492 EFG_II: Elongation Fa 27.6 1.8E+02 0.0039 18.9 6.4 63 87-153 4-68 (75)
54 PRK14318 glmM phosphoglucosami 27.2 1E+02 0.0022 27.0 4.4 35 120-154 411-445 (448)
55 PRK15468 carboxysome structura 27.1 1.9E+02 0.0041 21.0 4.9 51 94-150 45-95 (111)
56 PLN02895 phosphoacetylglucosam 27.0 2.7E+02 0.0058 25.7 7.1 36 118-153 517-552 (562)
57 PF03927 NapD: NapD protein; 26.8 2E+02 0.0043 19.1 6.0 46 101-149 16-61 (79)
58 PRK14317 glmM phosphoglucosami 26.6 90 0.002 27.6 3.9 35 120-154 428-462 (465)
59 PF01193 RNA_pol_L: RNA polyme 26.4 1.7E+02 0.0038 18.4 4.7 53 100-152 10-65 (66)
60 PRK14324 glmM phosphoglucosami 26.1 1.5E+02 0.0032 26.1 5.1 37 118-154 406-442 (446)
61 PRK14322 glmM phosphoglucosami 25.7 1.2E+02 0.0027 26.3 4.6 34 120-153 395-428 (429)
62 PRK14323 glmM phosphoglucosami 25.6 1.2E+02 0.0027 26.4 4.6 34 120-153 403-436 (440)
63 PRK10887 glmM phosphoglucosami 25.4 1.2E+02 0.0026 26.6 4.4 34 120-153 407-440 (443)
64 PRK14316 glmM phosphoglucosami 24.9 1.3E+02 0.0029 26.3 4.6 35 119-153 408-442 (448)
65 PRK09662 GspL-like protein; Pr 24.2 4E+02 0.0086 22.4 7.1 54 99-152 204-263 (286)
66 PRK04998 hypothetical protein; 24.2 2.3E+02 0.0051 19.1 6.7 56 95-150 21-80 (88)
67 PRK09542 manB phosphomannomuta 24.2 1.9E+02 0.0041 25.4 5.5 32 122-153 412-443 (445)
68 COG3622 Hfi Hydroxypyruvate is 23.5 69 0.0015 26.6 2.4 65 54-126 146-213 (260)
69 TIGR00696 wecB_tagA_cpsF bacte 23.5 3.5E+02 0.0075 20.8 7.6 28 94-121 53-80 (177)
70 TIGR01455 glmM phosphoglucosam 23.4 1.6E+02 0.0034 25.8 4.8 34 120-153 409-442 (443)
71 PRK14319 glmM phosphoglucosami 23.3 1.3E+02 0.0028 26.2 4.3 34 120-153 390-423 (430)
72 cd04931 ACT_PAH ACT domain of 23.1 2.5E+02 0.0055 19.1 6.5 55 100-154 26-84 (90)
73 PF06778 Chlor_dismutase: Chlo 22.4 3.9E+02 0.0085 21.0 7.3 53 103-155 11-67 (193)
74 PRK14434 acylphosphatase; Prov 22.2 2.5E+02 0.0053 19.3 4.7 35 119-153 33-67 (92)
75 cd06533 Glyco_transf_WecG_TagA 21.8 3.6E+02 0.0077 20.3 8.9 28 94-121 51-78 (171)
76 PRK14314 glmM phosphoglucosami 21.8 1.3E+02 0.0028 26.5 3.9 34 120-153 413-446 (450)
77 cd05805 MPG1_transferase GTP-m 21.0 2E+02 0.0043 25.1 5.0 31 121-151 410-440 (441)
78 cd04878 ACT_AHAS N-terminal AC 20.6 2E+02 0.0044 17.0 4.0 23 127-150 42-64 (72)
79 cd04880 ACT_AAAH-PDT-like ACT 20.3 2.4E+02 0.0052 17.8 6.6 53 100-152 11-68 (75)
80 PRK14321 glmM phosphoglucosami 20.2 2.1E+02 0.0046 25.1 5.0 28 126-153 416-443 (449)
81 TIGR01046 S10_Arc_S20_Euk ribo 20.2 2.1E+02 0.0046 20.0 4.0 26 128-153 2-27 (99)
No 1
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=99.97 E-value=7.5e-31 Score=213.98 Aligned_cols=138 Identities=23% Similarity=0.296 Sum_probs=119.7
Q ss_pred CCCCCCCCCCCCHhhhcccccCCCCceeeeCCCCcccEEEec----eEEEecCCCCch-hHHHHHH-HHHHHHhCCCCCC
Q 031335 12 QPYNLGSQETFGIQISQMALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLM 85 (161)
Q Consensus 12 ~~~~~~~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i~----~v~~LPG~~vP~-m~~m~~~-v~p~L~~~~~~~~ 85 (161)
..|...++.+++++|+|||++|+|| ++|+||+|+|||+.++ +||+||| ||+ |++||+. +.|++... + ..
T Consensus 101 ~~~~~~r~~~~~~~~~K~A~~P~Ga-~~l~NpvG~APG~~v~~~~~~v~~lPG--vP~Em~~M~e~~~~~~l~~~-~-~~ 175 (255)
T COG1058 101 EEKYAKRGREMTEANRKQAMLPEGA-EVLDNPVGTAPGFVVEGNGKNVYVLPG--VPSEMKPMFENVLLPLLTGR-F-PS 175 (255)
T ss_pred HHHHHhcCCCCChhhhhhccCCCCC-EeCCCCCCCCCeeEEecCCeEEEEeCC--CCHHHHHHHHHHHHHHhhcc-C-CC
Confidence 3445567899999999999999999 9999999999999998 7999999 999 9999985 56777664 3 22
Q ss_pred CcEEEEEEE-ecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEE---EEEEecCHHHHHHHHHHHHHHccC
Q 031335 86 EPYTSKSLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLI---ISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 86 ~~~~~~~l~-~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~---lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
..+++++++ +|++||.|++.|++++.++++++|+|||+.++...+ |+.+++|++.++++.+++..++.+
T Consensus 176 ~~~~~~~~~~~gi~ES~la~~L~~i~~~~~~~~i~s~p~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~i~~ 248 (255)
T COG1058 176 TKYYSRVLRVFGIGESSLAPTLKDLQDEQPNVTIASYPKDGEVRLRELVIRAEARDEEEADALLRWLEGRLRA 248 (255)
T ss_pred CceEEEEEEEcCCChHHHHHHHHHHHhcCCCCEEEecCCCCceeccceEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 568899998 799999999999999999999999999999888554 888889999988888888776654
No 2
>PRK00549 competence damage-inducible protein A; Provisional
Probab=99.96 E-value=6.8e-29 Score=215.30 Aligned_cols=138 Identities=17% Similarity=0.183 Sum_probs=119.7
Q ss_pred CCCCCCHhhhcccccCCCCceeeeCCCCcccEEEec----eEEEecCCCCch-hHHHHHH-HHHHHHhCCCCCCCcEEEE
Q 031335 18 SQETFGIQISQMALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSK 91 (161)
Q Consensus 18 ~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i~----~v~~LPG~~vP~-m~~m~~~-v~p~L~~~~~~~~~~~~~~ 91 (161)
++..++++|+|||++|+|| ++|+||+|||||++++ .+|+||| ||+ |++||+. ++|+|++. +.....++++
T Consensus 106 ~~~~~~~~n~kqA~~P~ga-~~l~N~~GtApG~~~~~~~~~i~~lPG--vP~Em~~m~~~~v~p~l~~~-~~~~~~~~~~ 181 (414)
T PRK00549 106 RGREMTENNRKQALIPEGA-TVLPNPVGTAPGMIIEVDGKTYIVLPG--PPSELKPMFEEYVVPYLSSA-KGTGEVLYSR 181 (414)
T ss_pred cCCCCChHHHHhhcCCCCC-EECcCCCCcCCeEEEEECCEEEEEeCC--CcHHHHHHHHHHhHHHHHhh-cCCCceEEEE
Confidence 4668999999999999999 9999999999999997 4999999 999 9999985 89999753 2222457788
Q ss_pred EEE-ecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHH----HHHHHHHHHHccCCceEe
Q 031335 92 SLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARI----EAAIESLFKKFHRGAFSE 159 (161)
Q Consensus 92 ~l~-~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~----~~a~~~l~~~l~~~i~~~ 159 (161)
.++ +|++||+|++.|.++...++++++|+||+.+.++|+|++++.+++.+ +++.++|++++++++|++
T Consensus 182 ~l~~~gi~Es~l~~~L~~l~~~~~~v~ig~~~~~~~~~vrl~~~~~~~~~~~~~~~~~~~~i~~~lg~~~~~~ 254 (414)
T PRK00549 182 VLRFFGIGESQLATTLRDLIDNQTNPTIAPYAKDGEVTLRLTAKARSEEEAEKLIDPLEEEIRDRVGDYFYGY 254 (414)
T ss_pred EEEEcCCCHHHHHHHHHHHHhcCCCCEEEECccCCEEEEEEEEecCCHHHHHHHHHHHHHHHHHHhccceecC
Confidence 887 79999999999999988888999999999877899999999987654 456778899999999974
No 3
>PRK03673 hypothetical protein; Provisional
Probab=99.96 E-value=2.1e-28 Score=210.96 Aligned_cols=139 Identities=18% Similarity=0.124 Sum_probs=119.7
Q ss_pred CCCCCCCCHhhhcccccCCCCceeeeCCCCcccEEEec----eEEEecCCCCch-hHHHHH-HHHHHHHhCCCCCCCcEE
Q 031335 16 LGSQETFGIQISQMALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWN-CLIELLRSGGLSLMEPYT 89 (161)
Q Consensus 16 ~~~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i~----~v~~LPG~~vP~-m~~m~~-~v~p~L~~~~~~~~~~~~ 89 (161)
..+++.|+++|+|||++|+|| ++|+||+|||||++++ .+|+||| ||+ |++||+ .++|+|+.. +.....++
T Consensus 105 ~~~~~~m~~~n~kQA~~P~ga-~~l~N~~GtApG~~~~~~~~~i~~LPG--vP~Emk~M~~~~v~p~L~~~-~~~~~~~~ 180 (396)
T PRK03673 105 AERGRVMAPSNRKQAELPASA-EMIDNPVGTACGFALQLNRCLMFFTPG--VPSEFKVMVEQEILPRLRER-FSLPEPPL 180 (396)
T ss_pred HhcCCCCChhHHhhccCCCCC-eeccCCCccCCcEEEEECCEEEEEECC--ChHHHHHHHHHHHHHHHHhh-cCCCCceE
Confidence 345678999999999999999 9999999999999996 3999999 999 999997 589999764 32223456
Q ss_pred EEEEE-ecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccCCceEe
Q 031335 90 SKSLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFSE 159 (161)
Q Consensus 90 ~~~l~-~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~~i~~~ 159 (161)
++.++ +|++||++++.|.++.. .+++++|+|++.++++++|+.++.+.+.++++.++|++++++++|++
T Consensus 181 ~~~l~~~Gi~ES~l~~~l~~l~~-~~~~~i~~~~~~~~v~vrlt~~~~~~~~~~~~~~~i~~~lg~~v~~~ 250 (396)
T PRK03673 181 CLRLTTFGRSESDLAQSLDPLPL-PPGVVMGYRSSMPIIELKLTGPASQRQAMEQLWQQVRRVAGQSVIFE 250 (396)
T ss_pred EEEEEECCCCHHHHHHHHHHHhc-CCCCEEeecCCCCeEEEEEEEccCCHHHHHHHHHHHHHHhCCcEEEe
Confidence 77777 79999999999999852 34899999999988999999999887668889999999999999974
No 4
>PRK03670 competence damage-inducible protein A; Provisional
Probab=99.96 E-value=5.1e-28 Score=197.77 Aligned_cols=125 Identities=19% Similarity=0.210 Sum_probs=109.3
Q ss_pred CCCCCCHhhhcccccCCCCceeeeCCCCcccEEEec----eEEEecCCCCch-hHHHHHH-HHHHHHhCCCCCCCcEEEE
Q 031335 18 SQETFGIQISQMALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSK 91 (161)
Q Consensus 18 ~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i~----~v~~LPG~~vP~-m~~m~~~-v~p~L~~~~~~~~~~~~~~ 91 (161)
.+.+++++|.|||++|+|| ++|+|++|+|||++++ ++|+||| ||+ |++||+. ++|+|.. .+++++
T Consensus 114 ~~~~~~~~~~kmA~~P~ga-~~l~N~~g~ApG~~~~~~~~~v~~lPG--vP~e~~~M~~~~v~p~l~~------~~~~~~ 184 (252)
T PRK03670 114 DDPTLNEARKKMAYLPEGA-EPLENTEGAAPGAYIEHKGTKIFVLPG--MPREMKAMLEKEVLPRLGE------RKFVQK 184 (252)
T ss_pred cccccChHHHheeCCCCCC-EECCCCCCcCceEEEEECCeEEEEeCC--ChHHHHHHHHHHHHHhhcc------CCeEEE
Confidence 3457899999999999999 9999999999999997 7999999 999 9999985 8998844 235666
Q ss_pred EEE-ecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHc
Q 031335 92 SLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 152 (161)
Q Consensus 92 ~l~-~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l 152 (161)
.+. ++.+||+|++.|++++++++ |+|||||+..+.+++|+++|.|++.++++.+++++..
T Consensus 185 ~~~~~~~~Es~la~~l~~~~~~~~-v~igSyP~~~~~~~~l~~~g~~~~~~~~a~~~l~~~~ 245 (252)
T PRK03670 185 KFLAEITDESKLAPILEEALERFN-VKIHSSPKGFGKYIGIIIFAEDEEEIEKAVEFMEERG 245 (252)
T ss_pred EEEeCCCCHHHHHHHHHHHHHHCC-ceEecCCCCCCCcEEEEEEECCHHHHHHHHHHHHHhC
Confidence 666 68999999999999999995 9999999833457999999999999999999997643
No 5
>TIGR00200 cinA_nterm competence/damage-inducible protein CinA N-terminal domain. cinA is a DNA damage- or competence-inducible protein that is polycistronic with recA in a number of species
Probab=99.93 E-value=6.4e-25 Score=190.39 Aligned_cols=139 Identities=16% Similarity=0.095 Sum_probs=117.5
Q ss_pred CCCCCCCHhhhcccccCCCCceeeeCCCCcccEEEe-c----eEEEecCCCCch-hHHHHH-HHHHHHHhCCCCCCCcEE
Q 031335 17 GSQETFGIQISQMALLPEGTTELLHHDKLLLPLIKC-Q----NVIILTATNVTE-LDKEWN-CLIELLRSGGLSLMEPYT 89 (161)
Q Consensus 17 ~~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i-~----~v~~LPG~~vP~-m~~m~~-~v~p~L~~~~~~~~~~~~ 89 (161)
.++.+++++|.|||++|+|| ++|+|++|+|||+++ . .|++||| ||. |++||+ .+.|+|+.. +.....++
T Consensus 105 ~~g~~~~~~n~kqA~~p~ga-~~l~N~~G~APG~~~~~~~~~~i~~LPG--~P~e~~~m~~~~v~p~l~~~-~~~~~~~~ 180 (413)
T TIGR00200 105 ETGRVMAPNNRKQALLPAGA-EFLANPVGTAPGMFAVQLNRCLMLFTPG--VPSEFRVMVEHEALPRLRER-FSLPQPIV 180 (413)
T ss_pred hcCCCCChHHHHhcCCCCCC-EECCCCCCCCCeeEEEecCCEEEEEeCC--CcHHHHHHHHHHhhHHHHHh-cCCCceEE
Confidence 34668999999999999999 999999999999655 2 2788999 999 999998 478999754 32223577
Q ss_pred EEEEE-ecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHH----HHHHHHHHHHccCCceEe
Q 031335 90 SKSLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARI----EAAIESLFKKFHRGAFSE 159 (161)
Q Consensus 90 ~~~l~-~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~----~~a~~~l~~~l~~~i~~~ 159 (161)
++.++ +|++||++++.|.++...++++++++|++.++++++++.++.+.+.. +++.++|++++++++|++
T Consensus 181 ~~~~~~~Gi~ES~l~~~l~~~~~~~~~~~~~~~~~~~~v~vrl~~~~~~~~~a~~~~~~~~~~i~~~lg~~~~~~ 255 (413)
T TIGR00200 181 SLVLRFFGIGESQLEADLADSLDTLTNPTGAPMAYRGEVPLRELKLTGPESEQQRAMEKLWLDIKRVAGQSVIGE 255 (413)
T ss_pred EEEEEECCCCHHHHHHHHHHHHhcCCCCeEEEecCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHhCcceecc
Confidence 88887 79999999999999987778899999999888999999999876543 457889999999999974
No 6
>PRK01215 competence damage-inducible protein A; Provisional
Probab=99.92 E-value=2.9e-24 Score=176.71 Aligned_cols=131 Identities=15% Similarity=0.190 Sum_probs=108.1
Q ss_pred CCCCCCCHhhhcccccCCCCceeeeCCCCcccEEEec----eEEEecCCCCch-hHHHHHH-HHHHHHhCCCCCCCcEEE
Q 031335 17 GSQETFGIQISQMALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTS 90 (161)
Q Consensus 17 ~~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i~----~v~~LPG~~vP~-m~~m~~~-v~p~L~~~~~~~~~~~~~ 90 (161)
.++..++++|.|||++|+|| ++|+|+.|||||+++. .||+||| ||. |+.||+. +.|+|++. +...+++
T Consensus 108 ~~~~~~~~~~~k~A~~P~ga-~~l~N~~Gtapg~~~~~~~~~i~~LPG--~P~e~~~m~~~~v~p~l~~~---~~~~~~~ 181 (264)
T PRK01215 108 KRGIPLTPERKKMAMMPPGA-VPLENPVGTAPGILIEHGGKDIVALPG--VPREMEAIFENFVEPLLKNR---PPLKYYE 181 (264)
T ss_pred hcCCCCChhHHheeeCCCCC-EecCCCCCcCCeEEEEECCEEEEEeCC--ChHHHHHHHHHHHHHHHhcc---CCCcEEE
Confidence 35678899999999999999 9999999999999985 4999999 999 9999985 88999753 1245778
Q ss_pred EEEE-ecCChhHHHHHHHhhhhhCCCcEEEE-----eeecCCccEEEEEEecCHHHH----HHHHHHHHHHcc
Q 031335 91 KSLT-TNLSDLEAAQPLSKLCLEFPDLHIGC-----YRKSRQGPLIISFEGKDQARI----EAAIESLFKKFH 153 (161)
Q Consensus 91 ~~l~-~gi~ES~la~~L~~l~~~~~~v~igs-----yp~~~~~~v~lt~~g~d~~~~----~~a~~~l~~~l~ 153 (161)
++++ +|++||++++.|.++..+++++++|| |++.++++|+|++++.+.+.+ +++.+.|++++.
T Consensus 182 ~~~~~~Gi~Es~l~~~l~~l~~~~~~~~~~s~p~~~~~~~~~v~vrl~~~~~~~~~~~~~~~~~~~~i~~~~~ 254 (264)
T PRK01215 182 DSILVEGVMESDLAPYVKELVKKYDRVYVKSHPKGYEVSKPILEIQIAGSGEREEEAKVKVEKVLEELKELIK 254 (264)
T ss_pred EEEEECCCCHHHHHHHHHHHHHhCCCCEEecCccceecCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHHH
Confidence 8888 79999999999999988889999954 466666789999988876554 345556666654
No 7
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=99.59 E-value=6.5e-16 Score=119.70 Aligned_cols=60 Identities=23% Similarity=0.288 Sum_probs=54.0
Q ss_pred CCCCCCCHhhhcccccCCCCceeeeCCCCcccEEEec----eEEEecCCCCch-hHHHHH-HHHHHHHh
Q 031335 17 GSQETFGIQISQMALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWN-CLIELLRS 79 (161)
Q Consensus 17 ~~~~~~~~~~~rqA~vPega~~~l~N~~GtAPG~~i~----~v~~LPG~~vP~-m~~m~~-~v~p~L~~ 79 (161)
.+...+++++.|||++|+|| ++|.|++|+|||++++ ++|+||| ||+ |++||+ .+.|+|++
T Consensus 104 ~~~~~~~~~~~r~a~~p~ga-~~i~N~~G~apg~~~~~~~~~i~~lPG--~P~e~~~m~~~~~~~~l~~ 169 (170)
T cd00885 104 RRGREMTEANLKQAMLPEGA-TLLPNPVGTAPGFSVEHNGKNVFLLPG--VPSEMKPMLEEEVLPRLRE 169 (170)
T ss_pred hcCCccChhhhheecCCCCC-EECcCCCCEeeEEEEEeCCeEEEEECC--ChHHHHHHHHHHHHHHHhc
Confidence 34456889999999999999 9999999999999997 6999999 999 999998 68898854
No 8
>PF00994 MoCF_biosynth: Probable molybdopterin binding domain; InterPro: IPR001453 Eukaryotic and prokaryotic molybdoenzymes require a molybdopterin cofactor (MoCF) for their activity. The biosynthesis of this cofactor involves a complex multistep enzymatic pathway. One of the eukaryotic proteins involved in this pathway is the Drosophila protein cinnamon [] which is highly similar to gephyrin, a rat microtubule-associated protein which was thought to anchor the glycine receptor to subsynaptic microtubules. Cinnamon and gephyrin are evolutionary related, in their N-terminal half, to the Escherichia coli MoCF biosynthesis proteins mog/chlG and moaB/chlA2 and, in their C-terminal half, to E. coli moeA/chlE.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 3TCR_B 1O8O_B 1O8Q_G 1EAV_D 1O8N_C 1UUX_A 1UUY_A 2G2C_A 2G4R_C 3K6A_F ....
Probab=93.38 E-value=0.042 Score=40.75 Aligned_cols=34 Identities=24% Similarity=0.112 Sum_probs=25.1
Q ss_pred CCCcccEEEec-----eEEEecCCCCch-hHHHHHHH-HHHHH
Q 031335 43 DKLLLPLIKCQ-----NVIILTATNVTE-LDKEWNCL-IELLR 78 (161)
Q Consensus 43 ~~GtAPG~~i~-----~v~~LPG~~vP~-m~~m~~~v-~p~L~ 78 (161)
|.++++++.++ .+|.||| .|. ++.+|+.+ .|.|+
T Consensus 103 p~~~~~~~~~~~~~~~~v~~LPG--~P~~~~~~~~~~v~P~L~ 143 (144)
T PF00994_consen 103 PTGLAPGAYLSRKGGKPVFGLPG--NPVAAKVMLEVLVLPLLR 143 (144)
T ss_dssp TCETEGGGGGTSSETTEEEEE-S--SHHHHHHHHHHHHHHHHH
T ss_pred ccceeeEEEeeCCCCcEEEEcCC--CHHHHHHHHHHHHHHhcC
Confidence 44567765553 4999999 999 99999864 59885
No 9
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=88.11 E-value=0.61 Score=34.05 Aligned_cols=44 Identities=16% Similarity=0.029 Sum_probs=31.8
Q ss_pred hhcccccCCCCceeeeCCCCcccEEEeceEEEecCCCCch-hHHHHH
Q 031335 26 ISQMALLPEGTTELLHHDKLLLPLIKCQNVIILTATNVTE-LDKEWN 71 (161)
Q Consensus 26 ~~rqA~vPega~~~l~N~~GtAPG~~i~~v~~LPG~~vP~-m~~m~~ 71 (161)
..++++.|-+.+.+..|+.+.++|+.-+.|+.||| .|. +..+|+
T Consensus 89 ~~~~~~~Pg~~~~~~~~~~~~~~g~~~~~i~~LPG--~P~~~~~~~~ 133 (135)
T smart00852 89 GFGEAMRPGGAPTVLANLSGTAPGFRGKLVFGLPG--SPVAARAMLE 133 (135)
T ss_pred ChhhhhcccCCccccccccCcCCeEeCcEEEECCC--CHHHHHHHHH
Confidence 35678888766233347788888875346999999 998 877664
No 10
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=84.71 E-value=1.2 Score=33.11 Aligned_cols=32 Identities=6% Similarity=-0.174 Sum_probs=24.7
Q ss_pred eeeCCCCcccEEEec--eEEEecCCCCch-hHHHHHH
Q 031335 39 LLHHDKLLLPLIKCQ--NVIILTATNVTE-LDKEWNC 72 (161)
Q Consensus 39 ~l~N~~GtAPG~~i~--~v~~LPG~~vP~-m~~m~~~ 72 (161)
+.-+|-+++.+..++ -|+.||| .|. ...+|+.
T Consensus 106 ~~~~PG~~~~~~~~~~~~v~~LPG--~P~aa~~~~~~ 140 (144)
T TIGR00177 106 VLSRPGKPATAGVRGGTLIFGLPG--NPVSALVTFEV 140 (144)
T ss_pred hhCCCCCceEEEEECCEEEEECCC--CHHHHHHHHHH
Confidence 356777777777776 3999999 998 8888864
No 11
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=76.82 E-value=14 Score=25.79 Aligned_cols=58 Identities=14% Similarity=0.201 Sum_probs=42.0
Q ss_pred EE-ecCChhHHHHHHHhhhhhC-CC---cEEEEeeecCCc--cEEEEEEecCHHHHHHHHHHHHH
Q 031335 93 LT-TNLSDLEAAQPLSKLCLEF-PD---LHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 93 l~-~gi~ES~la~~L~~l~~~~-~~---v~igsyp~~~~~--~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
++ .|....++++.+-++.+++ |+ .++..-|+..+. .|++++++.+.+.++.+...|.+
T Consensus 18 ~KVmG~a~~~l~~~vv~vvqr~ap~~~~~~~~~k~SSkGnY~svsI~i~A~~~EQ~e~ly~eL~~ 82 (90)
T COG2921 18 YKVMGAAGPELEDQVVEVVQRHAPGDYTPRVSWKPSSKGNYLSVSITIRATNIEQVEALYRELRK 82 (90)
T ss_pred eeehcccchhHHHHHHHHHHHHCCcccCceeeeccCCCCceEEEEEEEEECCHHHHHHHHHHHhh
Confidence 44 6877777888887776665 43 445556655443 59999999999999988888775
No 12
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=72.95 E-value=17 Score=24.78 Aligned_cols=54 Identities=13% Similarity=0.110 Sum_probs=37.7
Q ss_pred hHHHHHHHhhhhhCCCcEEEEeeecC--C--ccEEEEEEe-cC-HHHHHHHHHHHHHHcc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYRKSR--Q--GPLIISFEG-KD-QARIEAAIESLFKKFH 153 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp~~~--~--~~v~lt~~g-~d-~~~~~~a~~~l~~~l~ 153 (161)
-++...|+....+.|+|.++.|-... . ..++|...+ .+ .+.+.+|++.|.+.+.
T Consensus 20 HTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~ 79 (83)
T cd07027 20 HTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYE 79 (83)
T ss_pred chHHHHHHHHHhcCCCeeEEEEecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 56888888777778999999886422 2 346776665 33 4567888888877654
No 13
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=71.23 E-value=23 Score=24.23 Aligned_cols=53 Identities=15% Similarity=0.202 Sum_probs=36.5
Q ss_pred hHHHHHHHhhhhhCCCcEEEEeeecC--C--ccEEEEEEe-cC-HHHHHHHHHHHHHHc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYRKSR--Q--GPLIISFEG-KD-QARIEAAIESLFKKF 152 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp~~~--~--~~v~lt~~g-~d-~~~~~~a~~~l~~~l 152 (161)
-++...|+....+.|+|.++.|-... . ..++|..++ .+ .+.+.+|++.|.+.+
T Consensus 20 HTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~ 78 (85)
T cd07029 20 HTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQIC 78 (85)
T ss_pred cchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHH
Confidence 56888888877778999999996422 2 346776665 34 355677777776654
No 14
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=68.60 E-value=17 Score=23.56 Aligned_cols=37 Identities=11% Similarity=0.167 Sum_probs=29.4
Q ss_pred cEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHc
Q 031335 116 LHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 152 (161)
Q Consensus 116 v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l 152 (161)
..+-..|+..+..+|+.+++.+++.+++..+.+.+.+
T Consensus 36 ~~l~vR~SgTEP~iRv~~Ea~~~~~~~~~~~~i~~~i 72 (73)
T PF00408_consen 36 WRLLVRPSGTEPKIRVYVEAPDEEELEEIAEEIAEAI 72 (73)
T ss_dssp EEEEEEEESSSSEEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred eEEEEECCCCCceEEEEEEeCCHHHHHHHHHHHHHhh
Confidence 4444888877777999999999998888888777654
No 15
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=65.94 E-value=28 Score=24.68 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=36.0
Q ss_pred hHHHHHHHhhhhhCCCcEEEEeeecC--C--ccEEEEEEec-C-HHHHHHHHHHHHHHcc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYRKSR--Q--GPLIISFEGK-D-QARIEAAIESLFKKFH 153 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp~~~--~--~~v~lt~~g~-d-~~~~~~a~~~l~~~l~ 153 (161)
-++...|+....+-++|.+++|--.. . ..++|...++ | .+.+.+|+..+.+.+.
T Consensus 26 HTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~ 85 (99)
T COG1761 26 HTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKILKDLE 85 (99)
T ss_pred chHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 55788888766677899999885332 2 2477777766 5 3556777776666543
No 16
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=65.14 E-value=28 Score=23.04 Aligned_cols=45 Identities=13% Similarity=0.183 Sum_probs=34.8
Q ss_pred CCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccCCceEe
Q 031335 114 PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFSE 159 (161)
Q Consensus 114 ~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~~i~~~ 159 (161)
-+|++..+-....+...+.+.| |.+.++.+.+..++..++.+++.
T Consensus 25 a~V~l~~~~~~~~g~~~~~i~G-~vs~V~~Av~a~~~~~~~~~v~~ 69 (75)
T PF00936_consen 25 ANVELVEIELICGGKVTVIITG-DVSAVKAAVDAAEEAAGKKLVSS 69 (75)
T ss_dssp SSEEEEEEEEESTTEEEEEEEE-SHHHHHHHHHHHHHHHHHTEEEE
T ss_pred CCEEEEEEEecCCCeEEEEEEE-CHHHHHHHHHHHHHHHhhceeeE
Confidence 4888888877767788888888 78888888888888777655544
No 17
>PRK00907 hypothetical protein; Provisional
Probab=58.36 E-value=60 Score=22.60 Aligned_cols=56 Identities=16% Similarity=0.169 Sum_probs=39.8
Q ss_pred ecCChhHHHHHHHhhhhhC-C---CcEEEEeeecCCc--cEEEEEEecCHHHHHHHHHHHHH
Q 031335 95 TNLSDLEAAQPLSKLCLEF-P---DLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 95 ~gi~ES~la~~L~~l~~~~-~---~v~igsyp~~~~~--~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
.|.....+.+.+.++..++ | .-.+...++..+. .+++++...+++.++++.+.|.+
T Consensus 23 mG~a~~~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~GkY~Svtv~i~ats~eQld~iY~~L~~ 84 (92)
T PRK00907 23 MGTAERGLETELPRLLAATGVELLQERISWKHSSSGKYVSVRIGFRAESREQYDAAHQALRD 84 (92)
T ss_pred EEcCchhHHHHHHHHHHHhCCCCCcCcEEeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 5777777888777765544 4 3456667766543 48888888899988888887765
No 18
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=56.54 E-value=58 Score=22.20 Aligned_cols=54 Identities=19% Similarity=0.218 Sum_probs=37.3
Q ss_pred hHHHHHHHhhhhhCCCcEEEEeeecCC--c--cEEEEEEe-cC-HHHHHHHHHHHHHHcc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--G--PLIISFEG-KD-QARIEAAIESLFKKFH 153 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp~~~~--~--~v~lt~~g-~d-~~~~~~a~~~l~~~l~ 153 (161)
-++...|+....+.|+|.++.|-.... . .++|...+ .+ .+.+.+|++.|.+.+.
T Consensus 22 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~ 81 (85)
T PRK01146 22 HTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCD 81 (85)
T ss_pred chHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 568888887777789999999864432 2 36666663 34 3556888888777654
No 19
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=54.61 E-value=67 Score=24.37 Aligned_cols=29 Identities=17% Similarity=0.127 Sum_probs=23.7
Q ss_pred EecCChhHHHHHHHhhhhhCCCcEEE-Eee
Q 031335 94 TTNLSDLEAAQPLSKLCLEFPDLHIG-CYR 122 (161)
Q Consensus 94 ~~gi~ES~la~~L~~l~~~~~~v~ig-syp 122 (161)
.+|-.|..+++..+.+...+|++.|. +++
T Consensus 53 llG~~~~~~~~~~~~l~~~yP~l~ivg~~~ 82 (172)
T PF03808_consen 53 LLGGSEEVLEKAAANLRRRYPGLRIVGYHH 82 (172)
T ss_pred EEeCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence 37999999899899999999988765 444
No 20
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=53.62 E-value=57 Score=21.75 Aligned_cols=53 Identities=25% Similarity=0.295 Sum_probs=34.4
Q ss_pred hHHHHHHHhhhhhCCCcEEEEee--ecCCcc--EEEEEEec-C-HHHHHHHHHHHHHHc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYR--KSRQGP--LIISFEGK-D-QARIEAAIESLFKKF 152 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp--~~~~~~--v~lt~~g~-d-~~~~~~a~~~l~~~l 152 (161)
-++...|+....+.|+|.++.|- |.-+.. +++..++. + .+.+.+|++.+.+.+
T Consensus 12 HTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~ 70 (77)
T PF13656_consen 12 HTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGITPIEALKKALEDLIKIC 70 (77)
T ss_dssp HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence 56788888777777999999885 333444 55555554 3 345677777666554
No 21
>cd07053 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=53.13 E-value=66 Score=21.47 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=33.1
Q ss_pred CCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccCCceEee
Q 031335 114 PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFSEV 160 (161)
Q Consensus 114 ~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~~i~~~~ 160 (161)
-+|++..|-....++..+.++| |-+.++.+.+.-++..+..+++..
T Consensus 24 a~V~l~~~~~~~~Gk~~vii~G-dvsaV~~Av~a~~~~~~~~~v~~~ 69 (76)
T cd07053 24 ANVELVLAKTICPGKYIIIVSG-DVGAVQAAVDAGKEIGGKYVVDSF 69 (76)
T ss_pred CceEEEEEEeecCCEEEEEEEE-cHHHHHHHHHHHHHHhCCcEEEEE
Confidence 4899888876666777777777 456677888877777776666543
No 22
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=52.94 E-value=59 Score=22.54 Aligned_cols=54 Identities=19% Similarity=0.259 Sum_probs=36.1
Q ss_pred hHHHHHHHhhhhhCCCcEEEEeeecC--C--ccEEEEEEe-cC-HHHHHHHHHHHHHHcc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYRKSR--Q--GPLIISFEG-KD-QARIEAAIESLFKKFH 153 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp~~~--~--~~v~lt~~g-~d-~~~~~~a~~~l~~~l~ 153 (161)
-+|...|+....+.|+|.++.|.... . ..++|..++ .+ .+.+.+|++.|.+.+.
T Consensus 28 HTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~ 87 (93)
T cd06926 28 HTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITDLISELS 87 (93)
T ss_pred chHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Confidence 56888888777778999999997432 2 235665555 23 3556777777776553
No 23
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=51.40 E-value=57 Score=20.31 Aligned_cols=57 Identities=19% Similarity=0.065 Sum_probs=32.0
Q ss_pred CChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEe-cCHHHHHHHHHHHH-HHccC
Q 031335 97 LSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEG-KDQARIEAAIESLF-KKFHR 154 (161)
Q Consensus 97 i~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g-~d~~~~~~a~~~l~-~~l~~ 154 (161)
-.++.....+.++....++..+ .....+...-+|.+-. .+.++++++...|+ ....+
T Consensus 13 ~~~~~A~~~~~~l~~~g~~~~~-~~~~~~~~~yrV~~G~f~~~~~A~~~~~~l~~~~~~~ 71 (76)
T PF05036_consen 13 SSEENAERLLAKLKKKGPDAYV-VQVSKGGPWYRVRVGPFSSREEAEAALRKLKKAAGPD 71 (76)
T ss_dssp S-HHHHHHHHHHHHHHT------EEEEEETTCEEEEECCECTCCHHHHHHHHHHHHHTS-
T ss_pred CCHHHHHHHHHHHHhcCCCcce-EEEecCCceEEEEECCCCCHHHHHHHHHHHhHhhCCC
Confidence 4667778888888877665544 3333334445555543 56677788888888 44433
No 24
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=51.34 E-value=75 Score=21.56 Aligned_cols=54 Identities=19% Similarity=0.208 Sum_probs=37.3
Q ss_pred hHHHHHHHhhhhhCCCcEEEEeeecC--C--ccEEEEEEe-cC-HHHHHHHHHHHHHHcc
Q 031335 100 LEAAQPLSKLCLEFPDLHIGCYRKSR--Q--GPLIISFEG-KD-QARIEAAIESLFKKFH 153 (161)
Q Consensus 100 S~la~~L~~l~~~~~~v~igsyp~~~--~--~~v~lt~~g-~d-~~~~~~a~~~l~~~l~ 153 (161)
-++...|+....+.|+|.++.|-... . ..++|...+ .+ .+.+.+|++.|.+.+.
T Consensus 20 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~ 79 (83)
T cd06927 20 HTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCE 79 (83)
T ss_pred chHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Confidence 56788888777777999999986433 2 246666665 33 3566888888777654
No 25
>PRK09417 mogA molybdenum cofactor biosynthesis protein MogA; Provisional
Probab=50.03 E-value=17 Score=28.75 Aligned_cols=15 Identities=13% Similarity=0.297 Sum_probs=14.0
Q ss_pred EEEecCCCCch-hHHHHH
Q 031335 55 VIILTATNVTE-LDKEWN 71 (161)
Q Consensus 55 v~~LPG~~vP~-m~~m~~ 71 (161)
|+.||| .|. ++.+|+
T Consensus 129 I~nLPG--Sp~a~~~~le 144 (193)
T PRK09417 129 IINLPG--QPKSIKETLE 144 (193)
T ss_pred EEECCC--CHHHHHHHHH
Confidence 889999 999 999998
No 26
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=46.00 E-value=23 Score=26.94 Aligned_cols=24 Identities=21% Similarity=0.368 Sum_probs=19.4
Q ss_pred EEEecCCCCch-hHHHHH-HHHHHHHhC
Q 031335 55 VIILTATNVTE-LDKEWN-CLIELLRSG 80 (161)
Q Consensus 55 v~~LPG~~vP~-m~~m~~-~v~p~L~~~ 80 (161)
||.||| .|. ...+|+ .+.|.|...
T Consensus 127 v~~LPG--~P~aa~~~~~~~v~P~l~~~ 152 (163)
T TIGR02667 127 VFCLPG--STGACRTAWDKIIAAQLDAR 152 (163)
T ss_pred EEECCC--CHHHHHHHHHHHHHHHHHHH
Confidence 999999 998 878887 578888543
No 27
>PRK00341 hypothetical protein; Provisional
Probab=45.17 E-value=1e+02 Score=21.29 Aligned_cols=56 Identities=5% Similarity=0.020 Sum_probs=38.2
Q ss_pred ecCChhHHHHHHHhhhhhCC---CcEEEEeeecCCc--cEEEEEEecCHHHHHHHHHHHHH
Q 031335 95 TNLSDLEAAQPLSKLCLEFP---DLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 95 ~gi~ES~la~~L~~l~~~~~---~v~igsyp~~~~~--~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
.|.....+.+.+.++..++- .-.+.+-++.++. .+.+++...+++.+++..+.|.+
T Consensus 23 iG~~~~~~~~~V~~iv~~~~~~~~~~~~~k~Ss~GkY~S~tv~i~~~s~~q~~~iy~~L~~ 83 (91)
T PRK00341 23 IGDTGVGFKDLVIEILQKHADVDLSTLAERQSSNGKYTTVQLHIVATDEDQLQDINSALRA 83 (91)
T ss_pred EEcCchhHHHHHHHHHHHhCCCcccceeeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 57777777777777665542 2345556655443 37788888888888888887765
No 28
>PRK02047 hypothetical protein; Provisional
Probab=44.12 E-value=1e+02 Score=21.16 Aligned_cols=56 Identities=16% Similarity=0.160 Sum_probs=38.8
Q ss_pred ecCChhHHHHHHHhhhhhC-CC---cEEEEeeecCCc--cEEEEEEecCHHHHHHHHHHHHH
Q 031335 95 TNLSDLEAAQPLSKLCLEF-PD---LHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 95 ~gi~ES~la~~L~~l~~~~-~~---v~igsyp~~~~~--~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
.|..+..+.+.+.++..++ ++ -.+.+-++..+. .+.+++...+++.+++..+.|.+
T Consensus 22 IG~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~GkY~Svtv~v~v~s~eq~~~iY~~L~~ 83 (91)
T PRK02047 22 MGKAHPEFADTIFKVVSVHDPEFDLEKIEERPSSGGNYTGLTITVRATSREQLDNIYRALTG 83 (91)
T ss_pred EEeCcHhHHHHHHHHHHHhCCCCccCceEEccCCCCeEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 5766677777777776655 33 446677766543 37777778888888888777765
No 29
>COG1925 FruB Phosphotransferase system, HPr-related proteins [Carbohydrate transport and metabolism]
Probab=42.58 E-value=30 Score=23.91 Aligned_cols=24 Identities=29% Similarity=0.325 Sum_probs=15.6
Q ss_pred ccEEEEEEecCHHHH-HHHHHHHHH
Q 031335 127 GPLIISFEGKDQARI-EAAIESLFK 150 (161)
Q Consensus 127 ~~v~lt~~g~d~~~~-~~a~~~l~~ 150 (161)
..++|+++|.|++++ ++..+.+.+
T Consensus 59 ~~i~i~a~G~de~~Al~aL~~li~~ 83 (88)
T COG1925 59 DEIELSAEGEDEEEALEALSELIES 83 (88)
T ss_pred CEEEEEEeCccHHHHHHHHHHHHHh
Confidence 469999999997643 444444444
No 30
>PTZ00302 N-acetylglucosamine-phosphate mutase; Provisional
Probab=41.97 E-value=88 Score=28.99 Aligned_cols=53 Identities=4% Similarity=-0.018 Sum_probs=35.6
Q ss_pred HHHHHHhhhhhC-CCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 102 AAQPLSKLCLEF-PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 102 la~~L~~l~~~~-~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
+++.+..+...+ ++=.+-..|+..+.-||+.+++++++.+++..+++.+.+.+
T Consensus 527 Lq~~id~~~~~~~~~gr~lvRpSGTEp~vRvyaEA~t~~~a~~l~~~v~~~v~~ 580 (585)
T PTZ00302 527 LQDKIDAIVSKYDNAARAFIRPSGTEPVVRVYAEAPTLEQADELANEVKGLVLR 580 (585)
T ss_pred HHHHHHHHHhhccCCceEEEEcCCCCcEEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 445555554444 33234466665566799999999999888888887776643
No 31
>PRK10897 phosphohistidinoprotein-hexose phosphotransferase component of N-regulated PTS system (Npr); Provisional
Probab=40.60 E-value=54 Score=22.56 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=17.1
Q ss_pred ccEEEEEEecCHHHH-HHHHHHHHHHcc
Q 031335 127 GPLIISFEGKDQARI-EAAIESLFKKFH 153 (161)
Q Consensus 127 ~~v~lt~~g~d~~~~-~~a~~~l~~~l~ 153 (161)
..|+++++|.|++++ +++.+.+.+.|+
T Consensus 61 ~~i~v~~~G~De~~A~~~l~~~~~~~~~ 88 (90)
T PRK10897 61 RQIEVEATGPQEEEALAAVIALFNSGFD 88 (90)
T ss_pred CEEEEEEECcCHHHHHHHHHHHHHhccC
Confidence 359999999997643 444444444443
No 32
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=40.15 E-value=14 Score=26.88 Aligned_cols=20 Identities=10% Similarity=0.200 Sum_probs=15.7
Q ss_pred EEEecCCCCch-hHHHHHH-HHHH
Q 031335 55 VIILTATNVTE-LDKEWNC-LIEL 76 (161)
Q Consensus 55 v~~LPG~~vP~-m~~m~~~-v~p~ 76 (161)
++.||| .|. ...+|.. +.|.
T Consensus 111 i~~LPG--~p~a~~~~~~~~v~p~ 132 (133)
T cd00758 111 IINLPG--SPKSALTTFEALVLPA 132 (133)
T ss_pred EEECCC--CHHHHHHHHHHhheec
Confidence 899999 998 8788864 5553
No 33
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=40.11 E-value=92 Score=22.29 Aligned_cols=58 Identities=12% Similarity=0.218 Sum_probs=37.5
Q ss_pred ecCChhHHHHHHHhhhhhCCCcEEEEeeecC-----------CccEEEEEEecCHHHHHHHHHHHHHHccCC
Q 031335 95 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR-----------QGPLIISFEGKDQARIEAAIESLFKKFHRG 155 (161)
Q Consensus 95 ~gi~ES~la~~L~~l~~~~~~v~igsyp~~~-----------~~~v~lt~~g~d~~~~~~a~~~l~~~l~~~ 155 (161)
...+|..+.. .+...+--+|+++ |++.. .+.|.+.+.|.|.++++.+.+...+.+...
T Consensus 32 ~~~~e~~iiA--~DeAtKaa~vev~-~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 32 ADSDDVTYTA--LDEATKAAEVEVV-YARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred eCCCcceeeh--hhhhhhhcCeEEE-EEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 4566644322 1223334589999 56554 345777788889999999888887776543
No 34
>cd03086 PGM3 PGM3 (phosphoglucomutase 3), also known as PAGM (phosphoacetylglucosamine mutase) and AGM1 (N-acetylglucosamine-phosphate mutase), is an essential enzyme found in eukaryotes that reversibly catalyzes the conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate as part of the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway. UDP-GlcNAc is an essential metabolite that serves as the biosynthetic precursor of many glycoproteins and mucopolysaccharides. AGM1 is a member of the alpha-D-phosphohexomutase superfamily, which catalyzes the intramolecular phosphoryl transfer of sugar substrates. The alpha-D-phosphohexomutases have four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=39.57 E-value=1.2e+02 Score=27.40 Aligned_cols=40 Identities=5% Similarity=0.003 Sum_probs=29.6
Q ss_pred hCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHH
Q 031335 112 EFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 151 (161)
Q Consensus 112 ~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~ 151 (161)
.+.+=.+=..|+..+.-||+.+++++++.+++..+++.+.
T Consensus 473 ~~~~gr~lVRpSGTEp~iRvyaEA~t~~~~~~l~~~i~~~ 512 (513)
T cd03086 473 KYNNGRAFVRPSGTEDVVRVYAEAATQEEADELANEVAEL 512 (513)
T ss_pred cCCCeeEEEecCCCCcEEEEEEEeCCHHHHHHHHHHHHhh
Confidence 3333234466766666799999999999999988888764
No 35
>PF03135 CagE_TrbE_VirB: CagE, TrbE, VirB family, component of type IV transporter system; InterPro: IPR018145 This domain is found in (amongst others): the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration []. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro []. Similar type IV transport systems are also found in other bacteria. This domain is also found in proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.; GO: 0005524 ATP binding
Probab=38.82 E-value=1.3e+02 Score=23.16 Aligned_cols=37 Identities=14% Similarity=0.317 Sum_probs=28.5
Q ss_pred CcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccCCce
Q 031335 115 DLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAF 157 (161)
Q Consensus 115 ~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~~i~ 157 (161)
.+.+|.| +..|.+.++|++.+++..+.+.+.|...-|
T Consensus 143 ~~~~G~~------~~~i~v~~~~~~~l~~~~~~v~~~l~~~G~ 179 (205)
T PF03135_consen 143 RVSFGYY------HFTIVVFADDPEELDDKVAEVSSALNNLGF 179 (205)
T ss_pred Ceeeeee------EEEEEEEcCCHHHHHHHHHHHHHHHHHCCC
Confidence 4566655 477889999999999999998888765443
No 36
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=37.95 E-value=37 Score=25.22 Aligned_cols=24 Identities=8% Similarity=0.159 Sum_probs=17.6
Q ss_pred eEEEecCCCCch-hHHHHHHHHHHHHh
Q 031335 54 NVIILTATNVTE-LDKEWNCLIELLRS 79 (161)
Q Consensus 54 ~v~~LPG~~vP~-m~~m~~~v~p~L~~ 79 (161)
-++.||| .|. ....|+.+.|.|+.
T Consensus 123 ~v~~LPG--~P~aa~~~~~~v~P~l~~ 147 (152)
T cd00886 123 LIFNLPG--SPKAVREALEVILPELPH 147 (152)
T ss_pred EEEECCC--CHHHHHHHHHHHHHHHHH
Confidence 3899999 996 55555558888754
No 37
>COG1839 Uncharacterized conserved protein [Function unknown]
Probab=37.82 E-value=1.8e+02 Score=22.20 Aligned_cols=58 Identities=22% Similarity=0.359 Sum_probs=37.8
Q ss_pred HHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccCCceEee
Q 031335 103 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFSEV 160 (161)
Q Consensus 103 a~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~~i~~~~ 160 (161)
++.-+.+....|++++|.--.-..++--++-+|.|++..+.|.+-.++.-..+.|.-+
T Consensus 30 eDL~ealvt~vP~~kfgiAf~EAsg~rLvR~~GND~eL~~lA~ena~~I~AGHvFVI~ 87 (162)
T COG1839 30 EDLYEALVTAVPGLKFGIAFNEASGPRLVRYTGNDEELVKLAIENALKIGAGHVFVIL 87 (162)
T ss_pred HHHHHHHHhcCCCceEEEEeecccCCeeEEecCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence 3333444555688888876544445544667788888877887777776666776543
No 38
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=37.01 E-value=1.2e+02 Score=19.70 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=14.7
Q ss_pred HHHHhhhhhCCCcEEEEeeecCCccEEEEEEecC
Q 031335 104 QPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKD 137 (161)
Q Consensus 104 ~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d 137 (161)
+..+.+...||+..+-.-+... --|++.|..
T Consensus 12 EL~kRl~~~yPd~~v~Vr~~s~---~~l~v~g~~ 42 (65)
T PF06183_consen 12 ELTKRLHRQYPDAEVRVRPGSA---NGLSVSGGK 42 (65)
T ss_dssp HHHHHHHHH-SS-EEEEEEESS----EEEEES--
T ss_pred HHHHHHHHHCCCceEeeeeccc---CccccCCcC
Confidence 3344667778987766655432 235555543
No 39
>KOG1794 consensus N-Acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=36.25 E-value=49 Score=28.32 Aligned_cols=60 Identities=15% Similarity=0.187 Sum_probs=36.8
Q ss_pred EecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecC-HHHHHHHHHHHHHHccC
Q 031335 94 TTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKD-QARIEAAIESLFKKFHR 154 (161)
Q Consensus 94 ~~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d-~~~~~~a~~~l~~~l~~ 154 (161)
++.+++..+++.++++..+- ..+-|.-++..-..+-|.++|.| ++..++.+++++..++.
T Consensus 37 h~~ig~~~~~~rie~~i~~A-~~k~g~d~~~~lr~lgL~lSg~d~e~~~~~lv~~~R~~fps 97 (336)
T KOG1794|consen 37 HWLIGSTTCASRIEDMIREA-KEKAGWDKKGPLRSLGLGLSGTDQEDKNRKLVTEFRDKFPS 97 (336)
T ss_pred cccCCchHHHHHHHHHHHHH-HhhcCCCccCccceeeeecccCCchhHHHHHHHHHHHhccc
Confidence 46777777777777664332 12223333222234778888766 45568888888888874
No 40
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional
Probab=33.97 E-value=43 Score=28.49 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=17.8
Q ss_pred EEEecCCCCch-hHHHHHHHHHHHH
Q 031335 55 VIILTATNVTE-LDKEWNCLIELLR 78 (161)
Q Consensus 55 v~~LPG~~vP~-m~~m~~~v~p~L~ 78 (161)
||.||| .|. ....|+.++|.|.
T Consensus 278 I~~LPG--~P~aa~~~~~~llp~l~ 300 (312)
T PRK03604 278 VVALPG--SPGGASDALAVLLPALF 300 (312)
T ss_pred EEECCC--CHHHHHHHHHHHHHHHH
Confidence 899999 997 7777887777663
No 41
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=32.73 E-value=1.6e+02 Score=22.01 Aligned_cols=71 Identities=11% Similarity=0.064 Sum_probs=39.6
Q ss_pred HHHHHHHhCCCCCCCcEEEEEEE--ecCChhHHHHHHHhhhhhCCCcEEEEeeecC----C--c--cEEEEEEecCHHHH
Q 031335 72 CLIELLRSGGLSLMEPYTSKSLT--TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR----Q--G--PLIISFEGKDQARI 141 (161)
Q Consensus 72 ~v~p~L~~~~~~~~~~~~~~~l~--~gi~ES~la~~L~~l~~~~~~v~igsyp~~~----~--~--~v~lt~~g~d~~~~ 141 (161)
.++..|+.. .......|- +|++++.+..++++|.+. ++--|+.+..+ + . -+.+++++...+.+
T Consensus 18 ~IL~~Lq~d-----~R~s~~eiA~~lglS~~tv~~Ri~rL~~~--GvI~~~~~~v~p~~lg~~~~a~v~i~~~~~~~~~~ 90 (164)
T PRK11169 18 NILNELQKD-----GRISNVELSKRVGLSPTPCLERVRRLERQ--GFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVF 90 (164)
T ss_pred HHHHHhccC-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCeEEEEEEECHHHhCCCEEEEEEEEEcCCChHHH
Confidence 466667543 122224442 799999999999999765 44334443322 1 1 24455544444445
Q ss_pred HHHHHHHH
Q 031335 142 EAAIESLF 149 (161)
Q Consensus 142 ~~a~~~l~ 149 (161)
+++.+.+.
T Consensus 91 ~~~~~~l~ 98 (164)
T PRK11169 91 EQFNAAVQ 98 (164)
T ss_pred HHHHHHHh
Confidence 55544443
No 42
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=32.64 E-value=1.4e+02 Score=19.25 Aligned_cols=53 Identities=17% Similarity=0.137 Sum_probs=33.3
Q ss_pred hHHHHHHHhhhhhCCC-cEEEEeeecCC-c--cEEEEEEec-CHHHHHHHHHHHHHHc
Q 031335 100 LEAAQPLSKLCLEFPD-LHIGCYRKSRQ-G--PLIISFEGK-DQARIEAAIESLFKKF 152 (161)
Q Consensus 100 S~la~~L~~l~~~~~~-v~igsyp~~~~-~--~v~lt~~g~-d~~~~~~a~~~l~~~l 152 (161)
..+++.++.+.+..-+ .++.++|.... . .+++.+++. +.+.++++.+.|++..
T Consensus 13 G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~~ 70 (80)
T cd04905 13 GALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRLT 70 (80)
T ss_pred CHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhC
Confidence 3477777766554334 37888887442 2 356666665 4566778888777744
No 43
>PF04359 DUF493: Protein of unknown function (DUF493); InterPro: IPR007454 This family includes several proteins of uncharacterised function.; PDB: 1RWU_A 2JOQ_A 2H9Z_A.
Probab=32.10 E-value=1.4e+02 Score=19.90 Aligned_cols=60 Identities=8% Similarity=0.143 Sum_probs=38.3
Q ss_pred EEEE-ecCChhHHHHHHHhhhhhC----CCcEEEEeeecCCc--cEEEEEEecCHHHHHHHHHHHHH
Q 031335 91 KSLT-TNLSDLEAAQPLSKLCLEF----PDLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 91 ~~l~-~gi~ES~la~~L~~l~~~~----~~v~igsyp~~~~~--~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
..++ .|..+..+.+.+.++..++ .+..+..-++..+. .+.+++...+++.++++.+.|.+
T Consensus 11 y~~KvIg~~~~~~~~~v~~iv~~~~~~~~~~~~~~k~S~~GkY~Svtv~v~v~s~eq~~~iy~~L~~ 77 (85)
T PF04359_consen 11 YPFKVIGKAEEDFVEAVKEIVEKHAPEFDDEKVSSKPSSKGKYVSVTVSVTVESAEQVDAIYRELKA 77 (85)
T ss_dssp EEEEEEEC-STTHHHHHCCCCCCHSS--SSEEEEECCSTTSSEEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred ceEEEEEECcHhHHHHHHHHHHHhCCcCccCceEEecCCCCeEEEEEEEEEECCHHHHHHHHHHhcc
Confidence 3444 5776677777777654432 35566677655443 36677777888888887777764
No 44
>PRK10850 PTS system phosphohistidinoprotein-hexose phosphotransferase subunit Hpr; Provisional
Probab=31.40 E-value=98 Score=20.97 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=14.6
Q ss_pred ccEEEEEEecCHHHHHHHHHHH
Q 031335 127 GPLIISFEGKDQARIEAAIESL 148 (161)
Q Consensus 127 ~~v~lt~~g~d~~~~~~a~~~l 148 (161)
..|+|+++|.|++++-++...+
T Consensus 59 ~~v~i~~~G~De~~A~~~l~~l 80 (85)
T PRK10850 59 TVVTISAEGEDEQKAVEHLVKL 80 (85)
T ss_pred CEEEEEEeCcCHHHHHHHHHHH
Confidence 3599999999977543333333
No 45
>cd03084 phosphohexomutase The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=31.15 E-value=91 Score=26.30 Aligned_cols=32 Identities=13% Similarity=0.057 Sum_probs=24.8
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHH
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKK 151 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~ 151 (161)
..|+..+--+||.+++.+++.+++..+.+.+.
T Consensus 323 irps~tep~~ri~~Ea~~~e~a~~l~~~~~~~ 354 (355)
T cd03084 323 VRASGTEPAIRIYAEADTQEDVEQIKKEAREL 354 (355)
T ss_pred EecCCCCcEEEEEEeeCCHHHHHHHHHHHHhh
Confidence 34555455699999999999888888877764
No 46
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=31.01 E-value=62 Score=22.06 Aligned_cols=15 Identities=40% Similarity=0.479 Sum_probs=11.8
Q ss_pred ccEEEEEEecCHHHH
Q 031335 127 GPLIISFEGKDQARI 141 (161)
Q Consensus 127 ~~v~lt~~g~d~~~~ 141 (161)
..|.++++|.|++++
T Consensus 59 ~~v~i~a~G~De~~A 73 (88)
T PRK13780 59 ADITISAEGADAADA 73 (88)
T ss_pred CEEEEEEeCcCHHHH
Confidence 459999999997643
No 47
>cd03089 PMM_PGM The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other membe
Probab=30.87 E-value=1.1e+02 Score=26.68 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=24.0
Q ss_pred eeecCCccEEEEEEecCHHHHHHHHHHHHHH
Q 031335 121 YRKSRQGPLIISFEGKDQARIEAAIESLFKK 151 (161)
Q Consensus 121 yp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~ 151 (161)
.|+..+-.+||.++++|++.+++..+++.+.
T Consensus 412 RpSgtEP~iriy~Ea~~~~~a~~l~~~~~~~ 442 (443)
T cd03089 412 RASNTEPVLVLRFEADTEEGLEEIKAELRKL 442 (443)
T ss_pred eecCCCCEEEEEEEeCCHHHHHHHHHHHHhh
Confidence 3444444599999999999999888887764
No 48
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=30.46 E-value=1.5e+02 Score=18.96 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=26.0
Q ss_pred HHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHH
Q 031335 101 EAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQAR 140 (161)
Q Consensus 101 ~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~ 140 (161)
.+.+.|+.+.....++++..........+.+.+.++|...
T Consensus 3 ~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~ 42 (73)
T PF13083_consen 3 FLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGR 42 (73)
T ss_dssp --HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHH
T ss_pred hHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccce
Confidence 4567777776555577777775555667999999988654
No 49
>PF02391 MoaE: MoaE protein; InterPro: IPR003448 This family contains the MoaE protein that is involved in biosynthesis of molybdopterin []. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulphurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2WP4_B 2OMD_B 1NVJ_E 1FM0_E 3BII_E 1NVI_E 1FMA_E 2QIE_K 2Q5W_E 3RPF_A ....
Probab=28.31 E-value=2.2e+02 Score=20.27 Aligned_cols=57 Identities=9% Similarity=0.169 Sum_probs=36.1
Q ss_pred cCChhHHHHHHHhhhhhCCCcE------EEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 96 NLSDLEAAQPLSKLCLEFPDLH------IGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 96 gi~ES~la~~L~~l~~~~~~v~------igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
...|..+.+...++.++|+-.. +|..+ .++.-+.+.+.|....++=+|++.+.++++
T Consensus 52 ~ma~~~l~~I~~e~~~~~~~~~v~i~HR~G~l~-vGe~~v~V~vsa~hR~eaf~A~~~~id~iK 114 (117)
T PF02391_consen 52 EMAEKELEEIAEEARERFGIVDVAIVHRVGRLK-VGEPIVLVAVSAPHRKEAFEACEYIIDRIK 114 (117)
T ss_dssp HHHHHHHHHHHHHHHHHSTTCEEEEEEEEEEEE-TTSEEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCeEEEEEEeeCCCC-CCCeEEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 4556777777777777887544 44444 233447777888877766566666665554
No 50
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=27.94 E-value=1.8e+02 Score=19.07 Aligned_cols=40 Identities=23% Similarity=0.376 Sum_probs=28.7
Q ss_pred CCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 114 PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 114 ~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
-+|++-.+-....++..+.+.| |.+.++.+.+..++....
T Consensus 24 A~V~l~~~~~~~~g~~~~~v~G-dvs~V~~Av~a~~~~~~~ 63 (75)
T smart00877 24 ANVELVGYESIGGGKVTVIITG-DVAAVRAAVEAGLEAAER 63 (75)
T ss_pred cCcEEEEEEecCCCEEEEEEEE-cHHHHHHHHHHHHHHHhh
Confidence 3788888776666778888888 667777777766665543
No 51
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.87 E-value=3.4e+02 Score=22.15 Aligned_cols=56 Identities=14% Similarity=0.127 Sum_probs=32.0
Q ss_pred ecCChhHHHHHHHhhhhhCCC--cEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 95 TNLSDLEAAQPLSKLCLEFPD--LHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 95 ~gi~ES~la~~L~~l~~~~~~--v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
.|=.|+.+...=+.+.....+ |++..-. .....++++++|+|++ -|...|++.++.
T Consensus 8 yGd~~r~ld~L~~~v~n~lgdLdV~~~i~~-~~~~wv~vtl~GeD~e---va~Nll~eefGe 65 (225)
T PF09883_consen 8 YGDAERALDSLRSLVENDLGDLDVEWDIGI-TKDDWVKVTLEGEDEE---VAANLLREEFGE 65 (225)
T ss_pred eccHHHHHHHHHHHHHHhhcCeeEEEEecc-ccCCceEEEEecCcHH---HHHHHHHHHhCC
Confidence 343367755433344444444 4443322 2245699999999876 555667777764
No 52
>PRK14320 glmM phosphoglucosamine mutase; Provisional
Probab=27.73 E-value=91 Score=27.30 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=27.3
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
..|+..+--+|+.+++++++.+++..+.+.+.+..
T Consensus 406 iRpS~teP~~rv~~Ea~s~e~a~~l~~~~~~~i~~ 440 (443)
T PRK14320 406 LRPSGTEPVLRVMVEADDKSLATNEAEYLVEKVKQ 440 (443)
T ss_pred EecCCCCceEEEEEecCCHHHHHHHHHHHHHHHHh
Confidence 45655455699999999999998888888777654
No 53
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=27.59 E-value=1.8e+02 Score=18.92 Aligned_cols=63 Identities=27% Similarity=0.394 Sum_probs=36.1
Q ss_pred cEEEEEEE--ecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 87 PYTSKSLT--TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 87 ~~~~~~l~--~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
+..+..+. -...+..+.+.|.++.++-|.+.+..-.. .+.+.|+.-| +-.++-+.+.|+++++
T Consensus 4 Pv~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~~d~e--t~e~~l~g~G--elhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 4 PVLSVAIEPKNKEDEPKLSEALQKLSEEDPSLRVERDEE--TGELILSGMG--ELHLEVLLERLKRRFG 68 (75)
T ss_dssp -SEEEEEEESSHHHHHHHHHHHHHHHHH-TTSEEEEETT--TSEEEEEESS--HHHHHHHHHHHHHTTC
T ss_pred CeEEEEEEECCHhHHHHHHHHHHHHHhcCCeEEEEEcch--hceEEEEECC--HHHHHHHHHHHHHHHC
Confidence 34445554 24466677788888877767666554332 2344444443 4555677777777765
No 54
>PRK14318 glmM phosphoglucosamine mutase; Provisional
Probab=27.16 E-value=1e+02 Score=27.01 Aligned_cols=35 Identities=9% Similarity=0.026 Sum_probs=27.7
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
..|+..+--+|+.+++++++.+++..+++.+.+..
T Consensus 411 vRpS~teP~irv~~Ea~~~~~a~~l~~~~~~~v~~ 445 (448)
T PRK14318 411 LRPSGTEPLVRVMVEAADEETARRVAGRLADVVAE 445 (448)
T ss_pred EeeCCCCcEEEEEEeECCHHHHHHHHHHHHHHHHH
Confidence 55665556699999999999988888888777643
No 55
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=27.07 E-value=1.9e+02 Score=20.96 Aligned_cols=51 Identities=24% Similarity=0.334 Sum_probs=29.6
Q ss_pred EecCChhHHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHHH
Q 031335 94 TTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 94 ~~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
+.-=+|..+.. .++..+--+|++|+.-++ .+.+.++-+ -+.++.|.+.+.+
T Consensus 45 TiTP~E~aIIA--aDIA~Kaa~V~igF~DRF-sGslvitGd---vs~Ve~Al~~V~~ 95 (111)
T PRK15468 45 TLTPGETAMIA--GDLALKAADVHIGFLDRF-SGALVIYGS---VGAVEEALSQTVS 95 (111)
T ss_pred EeCcchHHHHH--HHhhhhccCcEEeeeecc-ceeEEEEcc---HHHHHHHHHHHHH
Confidence 34445655432 466666679999999877 455656543 3444444444333
No 56
>PLN02895 phosphoacetylglucosamine mutase
Probab=26.95 E-value=2.7e+02 Score=25.75 Aligned_cols=36 Identities=6% Similarity=-0.036 Sum_probs=27.6
Q ss_pred EEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 118 IGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 118 igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
+-..|+..+.-||+.+++++++.+++..+++.+.+.
T Consensus 517 ~lvRpSGTEp~vRv~~Ea~t~~~~~~l~~~v~~~v~ 552 (562)
T PLN02895 517 AFVRPSGTEDVVRVYAEASTQEAADSLAREVARLVY 552 (562)
T ss_pred EEEEcCCCCcEEEEEEEECCHHHHHHHHHHHHHHHH
Confidence 446676656679999999999888888777776654
No 57
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=26.83 E-value=2e+02 Score=19.15 Aligned_cols=46 Identities=11% Similarity=0.289 Sum_probs=30.1
Q ss_pred HHHHHHHhhhhhCCCcEEEEeeecCCccEEEEEEecCHHHHHHHHHHHH
Q 031335 101 EAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLF 149 (161)
Q Consensus 101 ~la~~L~~l~~~~~~v~igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~ 149 (161)
.+++..+.+ ...|++++--. ...+++.+++++.+...+.+....|.
T Consensus 16 ~~~~v~~~l-~~~~gvEVh~~--~~~GKiVVtiE~~~~~~~~~~~~~i~ 61 (79)
T PF03927_consen 16 RLEEVAEAL-AAIPGVEVHAV--DEDGKIVVTIEAESSEEEVDLIDAIN 61 (79)
T ss_dssp CHHHHHHHH-CCSTTEEEEEE--ETTTEEEEEEEESSHHHHHHHHHHHC
T ss_pred hHHHHHHHH-HcCCCcEEEee--CCCCeEEEEEEeCChHHHHHHHHHHH
Confidence 444444444 35688886433 33488999999999877666666654
No 58
>PRK14317 glmM phosphoglucosamine mutase; Provisional
Probab=26.56 E-value=90 Score=27.56 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=27.3
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
..|+..+--+|+.+++.+++.+++..+.+.+.+..
T Consensus 428 iRpS~TEP~irv~~Ea~~~~~~~~l~~~~~~~v~~ 462 (465)
T PRK14317 428 VRASGTEPLIRVMVEAEDAELVNHWTNHLVAVVQQ 462 (465)
T ss_pred EecCCCCCEEEEEEEeCCHHHHHHHHHHHHHHHHH
Confidence 45655555699999999999988888887776653
No 59
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 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. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=26.36 E-value=1.7e+02 Score=18.38 Aligned_cols=53 Identities=19% Similarity=0.214 Sum_probs=31.0
Q ss_pred hHHHHHHHhhhhhC-CCcEEEEeeecCCccEEEEEEec-C-HHHHHHHHHHHHHHc
Q 031335 100 LEAAQPLSKLCLEF-PDLHIGCYRKSRQGPLIISFEGK-D-QARIEAAIESLFKKF 152 (161)
Q Consensus 100 S~la~~L~~l~~~~-~~v~igsyp~~~~~~v~lt~~g~-d-~~~~~~a~~~l~~~l 152 (161)
-.++..|+...... |++.+...+......+++...|+ + .+.+.+|++.+.+++
T Consensus 10 ~tl~N~LRr~ll~~vp~~ai~~~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~ 65 (66)
T PF01193_consen 10 HTLGNALRRILLSEVPGVAIDGHPNEDKFVFRIETDGSLTPKEALLKAIKILKEKL 65 (66)
T ss_dssp HHHHHHHHHHHHSSSEEEEEEESSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHhcCCCceEEecCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhc
Confidence 44677777654444 77777775543223344444444 3 345688888887765
No 60
>PRK14324 glmM phosphoglucosamine mutase; Provisional
Probab=26.14 E-value=1.5e+02 Score=26.12 Aligned_cols=37 Identities=24% Similarity=0.321 Sum_probs=28.8
Q ss_pred EEEeeecCCccEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 118 IGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 118 igsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
+=..|+..+--+|+.+++++++.+++..+++.+.+..
T Consensus 406 ~lvR~SgTEp~irv~~Ea~~~~~~~~l~~~~~~~~~~ 442 (446)
T PRK14324 406 HLIRYSGTENKLRILLEGKDEKLLEKKMQELVEFFKK 442 (446)
T ss_pred EEEecCCCCceEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 3466766566799999999999988888887777643
No 61
>PRK14322 glmM phosphoglucosamine mutase; Provisional
Probab=25.72 E-value=1.2e+02 Score=26.35 Aligned_cols=34 Identities=24% Similarity=0.359 Sum_probs=27.7
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
..|+..+--+|+.+++.+++.+++..+.+.+.+.
T Consensus 395 vRpS~teP~irv~~Ea~~~~~a~~l~~~~~~~l~ 428 (429)
T PRK14322 395 IRPSGTEPVVRITVEGKDREEIEKIVEEISRVLE 428 (429)
T ss_pred EccCCCCcEEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 5566556669999999999999999888887763
No 62
>PRK14323 glmM phosphoglucosamine mutase; Provisional
Probab=25.58 E-value=1.2e+02 Score=26.42 Aligned_cols=34 Identities=21% Similarity=0.206 Sum_probs=26.5
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
..|+..+--+|+.+++++++.+++..+.+.+.+.
T Consensus 403 vRpS~TEP~irv~~Ea~s~~~~~~l~~~~~~~v~ 436 (440)
T PRK14323 403 LRPSGTEPLVRVMVEGPDEAEIEEVARELAGVVE 436 (440)
T ss_pred EecCCCccEeEEEEeeCCHHHHHHHHHHHHHHHH
Confidence 4565555569999999999998888888777653
No 63
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=25.42 E-value=1.2e+02 Score=26.59 Aligned_cols=34 Identities=18% Similarity=0.291 Sum_probs=27.5
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
..|+..+--+||.++++|++.+++..+++.+.+.
T Consensus 407 iRpS~tEP~iri~~Ea~s~e~a~~l~~~~~~~v~ 440 (443)
T PRK10887 407 LRKSGTEPLIRVMVEGEDEAQVTALAERIADAVK 440 (443)
T ss_pred EecCCCCeEEEEEEeeCCHHHHHHHHHHHHHHHH
Confidence 5565555569999999999999999888887764
No 64
>PRK14316 glmM phosphoglucosamine mutase; Provisional
Probab=24.93 E-value=1.3e+02 Score=26.28 Aligned_cols=35 Identities=6% Similarity=0.050 Sum_probs=27.5
Q ss_pred EEeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 119 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 119 gsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
=..|+..+--+|+.+++.+++.+++..+.+.+.+.
T Consensus 408 liRpS~TEP~irvy~Ea~~~e~~~~l~~~~~~~i~ 442 (448)
T PRK14316 408 LVRPSGTEPLVRVMAEAPTQEEVDKYVDRIADVVE 442 (448)
T ss_pred EEecCCCCcEEEEEEEeCCHHHHHHHHHHHHHHHH
Confidence 35676656679999999999988888887777664
No 65
>PRK09662 GspL-like protein; Provisional
Probab=24.23 E-value=4e+02 Score=22.41 Aligned_cols=54 Identities=13% Similarity=0.243 Sum_probs=37.1
Q ss_pred hhHHHHHHHhhhhhC-----CCcEEEEeeecCC-ccEEEEEEecCHHHHHHHHHHHHHHc
Q 031335 99 DLEAAQPLSKLCLEF-----PDLHIGCYRKSRQ-GPLIISFEGKDQARIEAAIESLFKKF 152 (161)
Q Consensus 99 ES~la~~L~~l~~~~-----~~v~igsyp~~~~-~~v~lt~~g~d~~~~~~a~~~l~~~l 152 (161)
.+.+-..|.++...+ +++++-++--+.. +.++|.+.++|=+.+|++.+.+.+.|
T Consensus 204 ~~~~l~~L~~l~~~l~~v~~~~l~~~sLryD~~R~ELrlq~~A~~F~~fEqlr~~l~~~f 263 (286)
T PRK09662 204 DTRLLAELSAIASTLKSASLSDIEMRGFTFDQKRQTLHLQLRAANFASFDKLRSALATDY 263 (286)
T ss_pred cchHHHHHHHHHHHhhccCCCCceEEEeeecCCCCeEEEEeecCCHHHHHHHHHHHhhcc
Confidence 455556665443322 5788888774432 46999999999888888888777754
No 66
>PRK04998 hypothetical protein; Provisional
Probab=24.20 E-value=2.3e+02 Score=19.12 Aligned_cols=56 Identities=16% Similarity=0.185 Sum_probs=34.8
Q ss_pred ecCChhHHHHHHHhhhhhC-CCc-EEEEeeecCCc--cEEEEEEecCHHHHHHHHHHHHH
Q 031335 95 TNLSDLEAAQPLSKLCLEF-PDL-HIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 95 ~gi~ES~la~~L~~l~~~~-~~v-~igsyp~~~~~--~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
.|-.+.++.+.+.++..++ |+. .+.+.++..+. .+.+++...+++.+++..+.|.+
T Consensus 21 ig~~~~~~~~~v~~v~~~~~~~~~~~~~r~S~~GkY~Svtv~v~v~s~eq~~~iY~~L~~ 80 (88)
T PRK04998 21 MGLARPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITITATSIEQVETLYEELAK 80 (88)
T ss_pred EEeCcHhHHHHHHHHHHHhCCCCCCceEccCCCCEEEEEEEEEEECCHHHHHHHHHHHhc
Confidence 4655556666666654443 432 25566765443 36777777888888887777764
No 67
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=24.19 E-value=1.9e+02 Score=25.37 Aligned_cols=32 Identities=9% Similarity=0.295 Sum_probs=24.9
Q ss_pred eecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 122 RKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 122 p~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
|+..+-.+|+.+++.+++.+++..+.+.+.+.
T Consensus 412 pSgTEP~lriy~Ea~~~e~~~~l~~~~~~~v~ 443 (445)
T PRK09542 412 ASNTEPLLRLNVEARTEEEVDALVDEVLAIIR 443 (445)
T ss_pred ecCCCcEEEEEEEeCCHHHHHHHHHHHHHHhh
Confidence 44334459999999999999888888887764
No 68
>COG3622 Hfi Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]
Probab=23.51 E-value=69 Score=26.57 Aligned_cols=65 Identities=9% Similarity=0.076 Sum_probs=42.0
Q ss_pred eEEEecCCCCch--hHHHHHHHHHHHHhCCCCCCCcEEEEEEE-ecCChhHHHHHHHhhhhhCCCcEEEEeeecCC
Q 031335 54 NVIILTATNVTE--LDKEWNCLIELLRSGGLSLMEPYTSKSLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ 126 (161)
Q Consensus 54 ~v~~LPG~~vP~--m~~m~~~v~p~L~~~~~~~~~~~~~~~l~-~gi~ES~la~~L~~l~~~~~~v~igsyp~~~~ 126 (161)
|.+-+|| +|- ...-+ .++..... ..-+..-.++ .-+.|.+++..|++......+|+|++-|...+
T Consensus 146 N~~d~PG--~~l~~~~~al-~li~~V~~-----~Nl~lq~D~YH~Q~~eGnL~~~lr~~~~~ighvQiAdvP~RhE 213 (260)
T COG3622 146 NLRDMPG--YFLTSQEQAL-ALIDEVGR-----PNLFLQLDLYHAQIMEGNLTRLLREYLPKIGHVQIADVPGRHE 213 (260)
T ss_pred CCCCCCC--cccccHHHHH-HHHHHhCC-----CCeEeehhHHHHHHhccHHHHHHHHhhhhhceeeecCCCCCCC
Confidence 4678999 883 33222 13323311 1122233333 68899999999999888888999999997654
No 69
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=23.51 E-value=3.5e+02 Score=20.82 Aligned_cols=28 Identities=25% Similarity=0.051 Sum_probs=24.1
Q ss_pred EecCChhHHHHHHHhhhhhCCCcEEEEe
Q 031335 94 TTNLSDLEAAQPLSKLCLEFPDLHIGCY 121 (161)
Q Consensus 94 ~~gi~ES~la~~L~~l~~~~~~v~igsy 121 (161)
.+|..+..+++..+.+.+++|++.+.-+
T Consensus 53 llG~~~~v~~~~~~~l~~~yP~l~i~g~ 80 (177)
T TIGR00696 53 LYGGKPDVLQQLKVKLIKEYPKLKIVGA 80 (177)
T ss_pred EECCCHHHHHHHHHHHHHHCCCCEEEEE
Confidence 3799999999999999999999987665
No 70
>TIGR01455 glmM phosphoglucosamine mutase. This model describes GlmM, phosphoglucosamine mutase, also designated in MrsA and YhbF E. coli, UreC in Helicobacter pylori, and femR315 or FemD in Staphlococcus aureus. It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides.
Probab=23.40 E-value=1.6e+02 Score=25.80 Aligned_cols=34 Identities=9% Similarity=0.112 Sum_probs=27.2
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
..|+..+--+++.+++++++.+++..+.+.+.+.
T Consensus 409 iRpS~teP~irv~~Ea~~~e~~~~l~~~~~~~v~ 442 (443)
T TIGR01455 409 LRPSGTEPLIRVMVEAADEELVQQLADTLADVVS 442 (443)
T ss_pred EecCCCCceEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 4565555569999999999999999888887763
No 71
>PRK14319 glmM phosphoglucosamine mutase; Provisional
Probab=23.26 E-value=1.3e+02 Score=26.23 Aligned_cols=34 Identities=12% Similarity=0.129 Sum_probs=26.9
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
..|+..+--+|+.+++++++.+++..+.+.+.+.
T Consensus 390 iRpS~TeP~irv~~Ea~~~~~a~~l~~~~~~~v~ 423 (430)
T PRK14319 390 VRPSGTEPVVRVLVEGPDEEYITNIANDIAGLIK 423 (430)
T ss_pred EecCCCccEEEEEEEeCCHHHHHHHHHHHHHHHH
Confidence 5566555669999999999998888887777654
No 72
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.14 E-value=2.5e+02 Score=19.13 Aligned_cols=55 Identities=16% Similarity=0.129 Sum_probs=36.3
Q ss_pred hHHHHHHHhhhhhCCC-cEEEEeeecCCc---cEEEEEEecCHHHHHHHHHHHHHHccC
Q 031335 100 LEAAQPLSKLCLEFPD-LHIGCYRKSRQG---PLIISFEGKDQARIEAAIESLFKKFHR 154 (161)
Q Consensus 100 S~la~~L~~l~~~~~~-v~igsyp~~~~~---~v~lt~~g~d~~~~~~a~~~l~~~l~~ 154 (161)
..+.+.|+.+....-+ .+|-|+|..... ...+-+++.+.+.++++.+.|++.++.
T Consensus 26 GsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~~~~~ 84 (90)
T cd04931 26 GALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDKKSAPALDPIIKSLRNDIGA 84 (90)
T ss_pred cHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCCCHHHHHHHHHHHHHhCC
Confidence 5688888877654323 568899965432 344666665346678888888887653
No 73
>PF06778 Chlor_dismutase: Chlorite dismutase; InterPro: IPR010644 This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyses the disproportionation of chlorite into chloride and oxygen [, ]. Note that many family members are hypothetical proteins.; PDB: 2VXH_B 3NN4_A 3NN2_A 3NN3_D 3NN1_E 3QPI_A 3Q08_Q 3Q09_B 1T0T_V 1VDH_E ....
Probab=22.37 E-value=3.9e+02 Score=21.02 Aligned_cols=53 Identities=17% Similarity=0.120 Sum_probs=36.0
Q ss_pred HHHHHhhhhhCCCcEEEEeeecCC---ccEEEEEEecCHHHHHHHHHHHHHH-ccCC
Q 031335 103 AQPLSKLCLEFPDLHIGCYRKSRQ---GPLIISFEGKDQARIEAAIESLFKK-FHRG 155 (161)
Q Consensus 103 a~~L~~l~~~~~~v~igsyp~~~~---~~v~lt~~g~d~~~~~~a~~~l~~~-l~~~ 155 (161)
.+.++++.........|+|--.+. .++-+...+.|.+.++++...|.+. ++++
T Consensus 11 ~~~~~~~~~~~~~~~~~~Y~~~G~radaDl~~w~~~~~~~~lq~~~~~l~~t~lg~~ 67 (193)
T PF06778_consen 11 EAFLEEWEEAGDGVLRGVYSVSGLRADADLMFWWHAPDLEDLQEAERRLRRTRLGRY 67 (193)
T ss_dssp HHHHHHHHHTTTTEEEEEEEETTTSTT-SEEEEEEESSHHHHHHHHHHHHHSTCGGG
T ss_pred HHHHHHHHhccCceEEEEEEeecccCCCcEEEEEeCCCHHHHHHHHHHHHhhhhhhh
Confidence 333444433333455899987663 3488999999999999999988765 6654
No 74
>PRK14434 acylphosphatase; Provisional
Probab=22.16 E-value=2.5e+02 Score=19.26 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=26.3
Q ss_pred EEeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 119 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 119 gsyp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
|+--....+.|.+.+.|++.+.+++..+.|++.-+
T Consensus 33 G~V~N~~dGsVei~~qG~~~~~l~~f~~~l~~g~p 67 (92)
T PRK14434 33 GRVWNNDDGTVEILAQSDDSAKLAKFIQEIRKGPS 67 (92)
T ss_pred EEEEECCCCCEEEEEEcCCHHHHHHHHHHHhcCCC
Confidence 55455556779999999876678899988887554
No 75
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=21.81 E-value=3.6e+02 Score=20.34 Aligned_cols=28 Identities=18% Similarity=0.222 Sum_probs=24.0
Q ss_pred EecCChhHHHHHHHhhhhhCCCcEEEEe
Q 031335 94 TTNLSDLEAAQPLSKLCLEFPDLHIGCY 121 (161)
Q Consensus 94 ~~gi~ES~la~~L~~l~~~~~~v~igsy 121 (161)
.+|..|..+++..+.+.+++|++.|..+
T Consensus 51 llG~~~~~~~~~~~~l~~~yp~l~i~g~ 78 (171)
T cd06533 51 LLGAKPEVLEKAAERLRARYPGLKIVGY 78 (171)
T ss_pred EECCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence 3799999999988899999999887664
No 76
>PRK14314 glmM phosphoglucosamine mutase; Provisional
Probab=21.78 E-value=1.3e+02 Score=26.46 Aligned_cols=34 Identities=9% Similarity=0.172 Sum_probs=26.0
Q ss_pred EeeecCCccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 120 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 120 syp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
..|+..+--+||.+++.|++.+++..+.+.+.+.
T Consensus 413 iRpS~tEP~iri~~Ea~~~~~a~~l~~~~~~~v~ 446 (450)
T PRK14314 413 LRYSGTENLCRVMVEGEDKHQVDSLAKEIADVVE 446 (450)
T ss_pred EecCCCCcEEEEEEeeCCHHHHHHHHHHHHHHHH
Confidence 4565555569999999999988888777776654
No 77
>cd05805 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily. This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional
Probab=21.04 E-value=2e+02 Score=25.08 Aligned_cols=31 Identities=29% Similarity=0.249 Sum_probs=23.1
Q ss_pred eeecCCccEEEEEEecCHHHHHHHHHHHHHH
Q 031335 121 YRKSRQGPLIISFEGKDQARIEAAIESLFKK 151 (161)
Q Consensus 121 yp~~~~~~v~lt~~g~d~~~~~~a~~~l~~~ 151 (161)
.|+..+-.+|+.+++.+++.+++..+.+.+.
T Consensus 410 RpS~TeP~iri~~Ea~~~~~~~~l~~~~~~~ 440 (441)
T cd05805 410 LPDADEPLCHIYAEGSDQERAEELTEFYVEK 440 (441)
T ss_pred ecCCCCCEEEEEEecCCHHHHHHHHHHHHhh
Confidence 3443344599999999999888888877654
No 78
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=20.60 E-value=2e+02 Score=17.04 Aligned_cols=23 Identities=35% Similarity=0.481 Sum_probs=15.5
Q ss_pred ccEEEEEEecCHHHHHHHHHHHHH
Q 031335 127 GPLIISFEGKDQARIEAAIESLFK 150 (161)
Q Consensus 127 ~~v~lt~~g~d~~~~~~a~~~l~~ 150 (161)
..+.+++...+ +.++++.+.|++
T Consensus 42 ~~~~~~~~~~~-~~~~~l~~~l~~ 64 (72)
T cd04878 42 SRITIVVEGDD-DVIEQIVKQLNK 64 (72)
T ss_pred EEEEEEEECCH-HHHHHHHHHHhC
Confidence 34667776655 777777777764
No 79
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=20.34 E-value=2.4e+02 Score=17.75 Aligned_cols=53 Identities=19% Similarity=0.224 Sum_probs=34.4
Q ss_pred hHHHHHHHhhhhhCCC-cEEEEeeecCC-c--cEEEEEEec-CHHHHHHHHHHHHHHc
Q 031335 100 LEAAQPLSKLCLEFPD-LHIGCYRKSRQ-G--PLIISFEGK-DQARIEAAIESLFKKF 152 (161)
Q Consensus 100 S~la~~L~~l~~~~~~-v~igsyp~~~~-~--~v~lt~~g~-d~~~~~~a~~~l~~~l 152 (161)
..+++.|+.+....-+ .+|-|+|.... . .+.+.+++. +...++++.+.+++..
T Consensus 11 G~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~~ 68 (75)
T cd04880 11 GALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRVT 68 (75)
T ss_pred CHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhC
Confidence 4578888877654323 56788886542 2 466666665 4566778888887754
No 80
>PRK14321 glmM phosphoglucosamine mutase; Provisional
Probab=20.19 E-value=2.1e+02 Score=25.10 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=22.0
Q ss_pred CccEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 126 QGPLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 126 ~~~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
+--+||.+++.+++.+++..+.+.+.+.
T Consensus 416 eP~~riy~Ea~s~e~~~~l~~~~~~~i~ 443 (449)
T PRK14321 416 EPIMRITLEAHTEEKAEELMEKAEKLVK 443 (449)
T ss_pred CceEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 3359999999999888888777776654
No 81
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=20.17 E-value=2.1e+02 Score=20.05 Aligned_cols=26 Identities=8% Similarity=0.074 Sum_probs=21.8
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHcc
Q 031335 128 PLIISFEGKDQARIEAAIESLFKKFH 153 (161)
Q Consensus 128 ~v~lt~~g~d~~~~~~a~~~l~~~l~ 153 (161)
.++|++.+-|...++++++.|.+...
T Consensus 2 ~irI~L~S~d~~~Ld~~~~~I~~~ak 27 (99)
T TIGR01046 2 KARIKLTSTNVRSLEKVCAQIKRIAE 27 (99)
T ss_pred cEEEEEEECCHHHHHHHHHHHHHHHH
Confidence 47899999999999999998887554
Done!