Query 032821
Match_columns 133
No_of_seqs 138 out of 1031
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 06:21:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032821hhsearch_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 2.7E-29 5.8E-34 193.1 13.2 122 1-127 118-249 (255)
2 PRK00549 competence damage-ind 100.0 2.5E-28 5.5E-33 199.6 13.8 126 1-130 117-253 (414)
3 PRK03670 competence damage-ind 100.0 6.5E-28 1.4E-32 186.0 13.6 114 1-124 125-245 (252)
4 PRK03673 hypothetical protein; 99.9 2.8E-27 6E-32 192.3 13.7 126 1-131 118-250 (396)
5 TIGR00200 cinA_nterm competenc 99.9 7.3E-24 1.6E-28 173.2 14.1 126 1-130 117-254 (413)
6 PRK01215 competence damage-ind 99.9 8.5E-24 1.8E-28 164.1 13.3 120 1-126 120-255 (264)
7 cd00885 cinA Competence-damage 99.5 2.2E-14 4.8E-19 105.0 4.9 48 1-51 116-169 (170)
8 PF00994 MoCF_biosynth: Probab 94.4 0.017 3.8E-07 40.5 0.9 34 15-50 103-143 (144)
9 COG2921 Uncharacterized conser 91.3 1.9 4.1E-05 28.3 7.0 60 63-122 16-82 (90)
10 TIGR00177 molyb_syn molybdenum 86.9 0.82 1.8E-05 32.2 3.2 32 11-44 106-140 (144)
11 PRK00907 hypothetical protein; 85.3 8.1 0.00018 25.5 7.1 60 63-122 18-84 (92)
12 cd07027 RNAP_RPB11_like RPB11 80.1 8.5 0.00019 24.8 5.6 54 72-125 20-79 (83)
13 PF00408 PGM_PMM_IV: Phosphogl 78.3 7 0.00015 24.0 4.7 37 88-124 36-72 (73)
14 PRK02047 hypothetical protein; 76.5 18 0.0004 23.6 7.1 60 63-122 17-83 (91)
15 cd07029 RNAP_I_III_AC19 AC19 s 76.0 14 0.0003 23.9 5.7 53 72-124 20-78 (85)
16 PRK00341 hypothetical protein; 75.9 19 0.00042 23.5 6.7 59 64-122 19-83 (91)
17 cd06927 RNAP_L L subunit of Ar 70.3 25 0.00053 22.6 5.8 54 72-125 20-79 (83)
18 PRK01146 DNA-directed RNA poly 69.3 28 0.0006 22.5 6.3 54 72-125 22-81 (85)
19 PF00936 BMC: BMC domain; Int 66.0 30 0.00064 21.6 6.4 43 86-129 25-67 (75)
20 PRK04998 hypothetical protein; 65.4 34 0.00074 22.0 6.6 60 63-122 16-80 (88)
21 PF13656 RNA_pol_L_2: RNA poly 64.7 20 0.00043 22.6 4.5 53 72-124 12-70 (77)
22 PF04359 DUF493: Protein of un 62.0 21 0.00046 22.6 4.4 60 63-122 11-77 (85)
23 cd06926 RNAP_II_RPB11 RPB11 su 61.9 42 0.00092 21.9 5.9 54 72-125 28-87 (93)
24 cd07049 BMC_EutL_repeat1 ethan 60.9 36 0.00078 23.0 5.4 58 67-127 32-100 (103)
25 PF05036 SPOR: Sporulation rel 59.9 24 0.00053 20.9 4.2 52 69-121 13-65 (76)
26 PF03135 CagE_TrbE_VirB: CagE, 58.4 40 0.00086 24.7 5.9 38 87-130 143-180 (205)
27 PF03808 Glyco_tran_WecB: Glyc 57.2 49 0.0011 23.8 6.0 30 64-93 50-80 (172)
28 PTZ00302 N-acetylglucosamine-p 55.9 42 0.0009 29.4 6.3 53 74-126 527-580 (585)
29 PRK09417 mogA molybdenum cofac 54.8 12 0.00025 28.0 2.4 15 27-43 129-144 (193)
30 COG1925 FruB Phosphotransferas 54.6 20 0.00044 23.3 3.3 24 99-125 59-82 (88)
31 cd03086 PGM3 PGM3 (phosphogluc 54.4 57 0.0012 27.9 6.8 47 77-123 466-512 (513)
32 PF09883 DUF2110: Uncharacteri 54.3 31 0.00067 26.5 4.6 53 71-127 12-66 (225)
33 KOG0071 GTP-binding ADP-ribosy 54.2 38 0.00082 24.6 4.8 56 63-127 59-114 (180)
34 PF14492 EFG_II: Elongation Fa 51.6 56 0.0012 20.2 6.5 64 58-125 3-68 (75)
35 TIGR02667 moaB_proteo molybden 50.4 16 0.00035 26.3 2.5 24 27-52 127-152 (163)
36 COG1761 RPB11 DNA-directed RNA 49.0 79 0.0017 21.1 5.8 54 72-125 26-85 (99)
37 cd00758 MoCF_BD MoCF_BD: molyb 48.9 8.1 0.00018 26.6 0.8 20 27-48 111-132 (133)
38 PF12687 DUF3801: Protein of u 48.3 1.1E+02 0.0025 22.8 7.0 55 67-123 37-93 (204)
39 cd07053 BMC_PduT_repeat1 1,2-p 48.1 68 0.0015 20.2 6.7 44 86-130 24-67 (76)
40 PRK13780 phosphocarrier protei 46.0 36 0.00077 22.0 3.4 14 99-112 59-72 (88)
41 PRK10897 phosphohistidinoprote 43.6 47 0.001 21.5 3.8 25 100-124 62-87 (90)
42 cd00886 MogA_MoaB MogA_MoaB fa 42.4 26 0.00056 24.6 2.6 24 26-51 123-147 (152)
43 KOG3445 Mitochondrial/chloropl 42.3 1.3E+02 0.0027 21.6 8.2 67 60-126 23-107 (145)
44 PLN02895 phosphoacetylglucosam 41.5 1.2E+02 0.0026 26.5 6.9 51 75-125 502-552 (562)
45 KOG1794 N-Acetylglucosamine ki 40.5 42 0.00091 27.1 3.6 61 65-126 36-97 (336)
46 PRK03604 moaC bifunctional mol 39.2 28 0.0006 28.0 2.5 22 27-50 278-300 (312)
47 KOG3179 Predicted glutamine sy 39.1 63 0.0014 24.8 4.2 44 3-49 160-206 (245)
48 PF02391 MoaE: MoaE protein; 38.8 1.2E+02 0.0027 20.4 6.3 59 68-126 52-115 (117)
49 PRK14434 acylphosphatase; Prov 38.7 83 0.0018 20.4 4.4 50 75-125 18-67 (92)
50 PRK10850 PTS system phosphohis 37.8 64 0.0014 20.6 3.7 14 100-113 60-73 (85)
51 cd03084 phosphohexomutase The 37.6 66 0.0014 25.7 4.5 32 92-123 323-354 (355)
52 PRK14322 glmM phosphoglucosami 37.6 72 0.0016 26.3 4.8 34 92-125 395-428 (429)
53 PF09904 HTH_43: Winged helix- 37.5 1.2E+02 0.0026 20.0 5.3 54 67-122 31-88 (90)
54 PRK10597 DNA damage-inducible 37.0 83 0.0018 20.2 4.0 43 79-122 27-72 (81)
55 cd03089 PMM_PGM The phosphoman 36.4 84 0.0018 26.0 5.0 31 93-123 412-442 (443)
56 PRK14324 glmM phosphoglucosami 35.9 92 0.002 25.9 5.2 37 90-126 406-442 (446)
57 PRK14320 glmM phosphoglucosami 35.3 68 0.0015 26.6 4.4 35 92-126 406-440 (443)
58 PRK14323 glmM phosphoglucosami 35.1 68 0.0015 26.5 4.3 35 91-125 402-436 (440)
59 COG4810 EutS Ethanolamine util 34.9 87 0.0019 21.2 4.0 55 68-125 57-112 (121)
60 PRK10887 glmM phosphoglucosami 34.6 75 0.0016 26.3 4.5 36 91-126 406-441 (443)
61 PRK14316 glmM phosphoglucosami 34.1 75 0.0016 26.3 4.4 36 90-125 407-442 (448)
62 cd04905 ACT_CM-PDT C-terminal 33.9 1.1E+02 0.0025 18.6 6.2 52 72-123 13-69 (80)
63 PRK14318 glmM phosphoglucosami 33.7 78 0.0017 26.3 4.5 36 91-126 410-445 (448)
64 PRK14319 glmM phosphoglucosami 33.4 78 0.0017 26.1 4.4 35 91-125 389-423 (430)
65 PRK14317 glmM phosphoglucosami 33.3 69 0.0015 26.7 4.1 35 92-126 428-462 (465)
66 COG3622 Hfi Hydroxypyruvate is 33.1 41 0.0009 26.3 2.5 65 26-98 146-213 (260)
67 TIGR01046 S10_Arc_S20_Euk ribo 33.0 85 0.0018 20.8 3.7 26 100-125 2-27 (99)
68 PF00013 KH_1: KH domain syndr 32.9 1E+02 0.0022 17.7 5.4 40 77-120 21-60 (60)
69 cd04931 ACT_PAH ACT domain of 32.1 1.4E+02 0.0031 19.2 6.2 55 72-126 26-84 (90)
70 PRK09542 manB phosphomannomuta 31.7 1.2E+02 0.0027 25.1 5.3 33 93-125 411-443 (445)
71 TIGR01455 glmM phosphoglucosam 31.7 1E+02 0.0022 25.5 4.9 34 92-125 409-442 (443)
72 PRK12271 rps10p 30S ribosomal 31.2 94 0.002 20.8 3.7 26 100-125 3-28 (102)
73 PTZ00039 40S ribosomal protein 31.2 93 0.002 21.3 3.8 27 100-126 18-44 (115)
74 COG1254 AcyP Acylphosphatases 30.9 1.1E+02 0.0024 20.0 4.0 47 74-123 19-65 (92)
75 PF00708 Acylphosphatase: Acyl 30.2 1.5E+02 0.0032 18.8 4.6 49 74-125 19-67 (91)
76 cd02394 vigilin_like_KH K homo 29.3 1.2E+02 0.0026 17.4 4.5 40 78-120 22-61 (62)
77 cd00756 MoaE MoaE family. Memb 29.1 1.9E+02 0.0042 19.8 7.9 59 68-126 44-107 (124)
78 PRK14314 glmM phosphoglucosami 28.8 96 0.0021 25.8 4.2 34 92-125 413-446 (450)
79 PF01193 RNA_pol_L: RNA polyme 28.3 1.4E+02 0.003 17.8 4.0 51 72-124 10-65 (66)
80 cd05805 MPG1_transferase GTP-m 28.2 1.3E+02 0.0028 24.8 4.9 31 93-123 410-440 (441)
81 PRK15468 carboxysome structura 27.8 1.7E+02 0.0036 20.0 4.4 55 67-124 46-101 (111)
82 PRK14424 acylphosphatase; Prov 27.5 1.5E+02 0.0032 19.4 4.1 46 74-122 22-67 (94)
83 PF11211 DUF2997: Protein of u 27.4 1.3E+02 0.0028 17.2 4.5 36 89-127 2-37 (48)
84 PRK14321 glmM phosphoglucosami 27.2 1.5E+02 0.0031 24.7 5.0 27 99-125 417-443 (449)
85 PF12693 GspL_C: GspL periplas 26.8 2.2E+02 0.0048 19.7 5.3 56 68-123 74-133 (157)
86 PF06183 DinI: DinI-like famil 26.7 1.6E+02 0.0034 18.0 6.0 17 79-95 15-31 (65)
87 COG1839 Uncharacterized conser 26.6 2.5E+02 0.0054 20.3 6.6 50 81-130 36-85 (162)
88 PRK09662 GspL-like protein; Pr 26.5 2.6E+02 0.0057 22.2 6.1 54 71-124 204-263 (286)
89 PRK14449 acylphosphatase; Prov 26.3 1.7E+02 0.0037 18.7 4.2 47 74-123 18-64 (90)
90 PRK14315 glmM phosphoglucosami 26.1 1.3E+02 0.0027 25.1 4.4 35 91-125 410-444 (448)
91 smart00877 BMC Bacterial micro 25.8 1.7E+02 0.0037 18.1 6.8 40 86-126 24-63 (75)
92 PF09840 DUF2067: Uncharacteri 25.6 2.4E+02 0.0052 20.9 5.5 48 72-122 9-56 (190)
93 TIGR00696 wecB_tagA_cpsF bacte 25.6 2.7E+02 0.0058 20.2 6.5 27 67-93 54-80 (177)
94 cd05311 NAD_bind_2_malic_enz N 25.1 49 0.0011 25.0 1.7 9 25-33 159-167 (226)
95 PRK14420 acylphosphatase; Prov 24.7 2E+02 0.0042 18.4 4.5 47 74-123 17-63 (91)
96 PLN02390 molybdopterin synthas 24.6 2.3E+02 0.005 19.2 7.7 59 68-126 33-96 (111)
97 PRK14448 acylphosphatase; Prov 24.2 1.8E+02 0.0039 18.7 4.1 46 74-122 17-62 (90)
98 PF09383 NIL: NIL domain; Int 24.1 86 0.0019 19.0 2.5 49 73-123 14-69 (76)
99 PRK14429 acylphosphatase; Prov 24.0 1.7E+02 0.0038 18.7 4.0 47 74-123 17-63 (90)
100 PRK10678 moaE molybdopterin gu 23.8 2.8E+02 0.0061 19.8 7.9 59 68-126 57-120 (150)
101 PF02829 3H: 3H domain; Inter 23.7 1.3E+02 0.0027 20.0 3.3 49 70-123 45-94 (98)
102 PRK11169 leucine-responsive tr 23.6 2.2E+02 0.0047 20.1 4.8 18 67-84 38-55 (164)
103 cd05800 PGM_like2 This PGM-lik 23.5 1.8E+02 0.0038 24.2 4.9 25 99-123 436-460 (461)
104 PF00381 PTS-HPr: PTS HPr comp 23.4 1.7E+02 0.0037 18.2 3.8 14 100-113 60-73 (84)
105 PRK14435 acylphosphatase; Prov 23.0 2E+02 0.0044 18.4 4.2 46 74-122 17-62 (90)
106 cd04880 ACT_AAAH-PDT-like ACT 22.9 1.8E+02 0.0039 17.3 6.0 53 72-124 11-68 (75)
107 PF04008 Adenosine_kin: Adenos 22.9 3E+02 0.0065 19.9 6.3 49 81-129 29-77 (155)
108 cd04910 ACT_AK-Ectoine_1 ACT d 22.6 2E+02 0.0044 17.8 7.2 56 70-128 13-68 (71)
109 cd04884 ACT_CBS C-terminal ACT 22.4 1.8E+02 0.0039 17.1 5.6 51 72-122 11-65 (72)
110 PRK10503 multidrug efflux syst 22.2 3.4E+02 0.0073 25.4 6.8 54 73-126 639-700 (1040)
111 PF04319 NifZ: NifZ domain; I 22.1 45 0.00098 21.2 0.8 22 11-33 16-37 (75)
112 COG4044 Uncharacterized protei 22.0 2.2E+02 0.0047 22.0 4.6 26 98-126 41-66 (247)
113 KOG0132 RNA polymerase II C-te 21.7 3.5E+02 0.0075 24.9 6.4 32 58-89 417-449 (894)
114 cd06533 Glyco_transf_WecG_TagA 21.2 3.1E+02 0.0068 19.5 8.0 27 67-93 52-78 (171)
115 PRK14426 acylphosphatase; Prov 21.2 2.4E+02 0.0052 18.1 4.2 50 74-126 19-68 (92)
116 PF03927 NapD: NapD protein; 21.1 2.2E+02 0.0049 17.8 6.0 46 73-121 16-61 (79)
117 KOG3964 Phosphatidylglycerolph 21.1 3.1E+02 0.0068 23.2 5.7 71 16-96 18-91 (469)
118 PRK10614 multidrug efflux syst 20.7 3.9E+02 0.0085 24.9 6.9 27 100-126 660-686 (1025)
119 PRK00596 rpsJ 30S ribosomal pr 20.6 2E+02 0.0042 19.0 3.8 26 100-125 5-30 (102)
120 PRK14440 acylphosphatase; Prov 20.6 2.2E+02 0.0047 18.3 3.9 46 74-122 18-63 (90)
121 TIGR01132 pgm phosphoglucomuta 20.5 2.3E+02 0.005 24.3 5.1 33 93-125 506-539 (543)
122 cd03087 PGM_like1 This archaea 20.5 2.3E+02 0.0049 23.4 4.9 32 92-123 407-438 (439)
123 PLN02371 phosphoglucosamine mu 20.5 2E+02 0.0042 25.0 4.7 26 100-125 542-567 (583)
124 PRK14427 acylphosphatase; Prov 20.4 2.3E+02 0.005 18.4 4.0 47 74-123 21-67 (94)
No 1
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=99.96 E-value=2.7e-29 Score=193.12 Aligned_cols=122 Identities=25% Similarity=0.338 Sum_probs=106.3
Q ss_pred CccCCCCCceeeeCCCCcccEEEec----eEEEeeCCCCCc-hHHHHHH-HHHHHhhCCCCCCCCeEEEEEE-ecCChhh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSKSLT-TNLSDLE 73 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i~----~v~~LPGv~~P~-m~~m~~~-v~p~l~~~~~~~~~~~~~~~l~-~g~~Es~ 73 (133)
||++|+||+ +|+||+|+|||+.++ ++|+|||| |+ |++||++ +.|+++++ + ....+++++++ +|++||.
T Consensus 118 ~A~~P~Ga~-~l~NpvG~APG~~v~~~~~~v~~lPGv--P~Em~~M~e~~~~~~l~~~-~-~~~~~~~~~~~~~gi~ES~ 192 (255)
T COG1058 118 QAMLPEGAE-VLDNPVGTAPGFVVEGNGKNVYVLPGV--PSEMKPMFENVLLPLLTGR-F-PSTKYYSRVLRVFGIGESS 192 (255)
T ss_pred hccCCCCCE-eCCCCCCCCCeeEEecCCeEEEEeCCC--CHHHHHHHHHHHHHHhhcc-C-CCCceEEEEEEEcCCChHH
Confidence 899999997 999999999999998 79999999 99 9999986 57777665 2 22678999999 5999999
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEE---EEEEecCHHHHHHHHHHHHHHhcCC
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLI---ISFEGKDQARIEAAIESLFKKFHRG 127 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~---l~~~~~~~~~~~~~~~~l~~~l~~~ 127 (133)
|++.|++++.++++++|+|||+.+....+ |+.+++|++.++++.+++..++.+.
T Consensus 193 la~~L~~i~~~~~~~~i~s~p~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~i~~~ 249 (255)
T COG1058 193 LAPTLKDLQDEQPNVTIASYPKDGEVRLRELVIRAEARDEEEADALLRWLEGRLRAR 249 (255)
T ss_pred HHHHHHHHHhcCCCCEEEecCCCCceeccceEEEEecCCHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999998777444 8888899999888888888776543
No 2
>PRK00549 competence damage-inducible protein A; Provisional
Probab=99.96 E-value=2.5e-28 Score=199.61 Aligned_cols=126 Identities=20% Similarity=0.231 Sum_probs=109.2
Q ss_pred CccCCCCCceeeeCCCCcccEEEec----eEEEeeCCCCCc-hHHHHHH-HHHHHhhCCCCCCCCeEEEEEE-ecCChhh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSKSLT-TNLSDLE 73 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i~----~v~~LPGv~~P~-m~~m~~~-v~p~l~~~~~~~~~~~~~~~l~-~g~~Es~ 73 (133)
||++|+||+ +|+||+||||||+++ .+|+|||| |+ |++||++ ++|+|++. +.....+++++++ +|++||+
T Consensus 117 qA~~P~ga~-~l~N~~GtApG~~~~~~~~~i~~lPGv--P~Em~~m~~~~v~p~l~~~-~~~~~~~~~~~l~~~gi~Es~ 192 (414)
T PRK00549 117 QALIPEGAT-VLPNPVGTAPGMIIEVDGKTYIVLPGP--PSELKPMFEEYVVPYLSSA-KGTGEVLYSRVLRFFGIGESQ 192 (414)
T ss_pred hhcCCCCCE-ECcCCCCcCCeEEEEECCEEEEEeCCC--cHHHHHHHHHHhHHHHHhh-cCCCceEEEEEEEEcCCCHHH
Confidence 899999998 999999999999997 49999999 98 9999975 89999754 2222467889998 5999999
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHH----HHHHHHHHHhcCCCee
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIE----AAIESLFKKFHRGAFS 130 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~----~~~~~l~~~l~~~~~~ 130 (133)
+++.|.++..+++++++|+||+.+..+++|++++.|++.++ ++.++|++++++++|+
T Consensus 193 l~~~L~~l~~~~~~v~ig~~~~~~~~~vrl~~~~~~~~~~~~~~~~~~~~i~~~lg~~~~~ 253 (414)
T PRK00549 193 LATTLRDLIDNQTNPTIAPYAKDGEVTLRLTAKARSEEEAEKLIDPLEEEIRDRVGDYFYG 253 (414)
T ss_pred HHHHHHHHHhcCCCCEEEECccCCEEEEEEEEecCCHHHHHHHHHHHHHHHHHHhccceec
Confidence 99999999888899999999987667899999999876544 5778888999999986
No 3
>PRK03670 competence damage-inducible protein A; Provisional
Probab=99.95 E-value=6.5e-28 Score=186.00 Aligned_cols=114 Identities=19% Similarity=0.207 Sum_probs=100.3
Q ss_pred CccCCCCCceeeeCCCCcccEEEec----eEEEeeCCCCCc-hHHHHHH-HHHHHhhCCCCCCCCeEEEEEE-ecCChhh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSKSLT-TNLSDLE 73 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i~----~v~~LPGv~~P~-m~~m~~~-v~p~l~~~~~~~~~~~~~~~l~-~g~~Es~ 73 (133)
||++|+||+ +|+|++|+||||+++ ++|+|||| |+ |++||++ ++|+|.. ..++++++. ++.+||+
T Consensus 125 mA~~P~ga~-~l~N~~g~ApG~~~~~~~~~v~~lPGv--P~e~~~M~~~~v~p~l~~------~~~~~~~~~~~~~~Es~ 195 (252)
T PRK03670 125 MAYLPEGAE-PLENTEGAAPGAYIEHKGTKIFVLPGM--PREMKAMLEKEVLPRLGE------RKFVQKKFLAEITDESK 195 (252)
T ss_pred eeCCCCCCE-ECCCCCCcCceEEEEECCeEEEEeCCC--hHHHHHHHHHHHHHhhcc------CCeEEEEEEeCCCCHHH
Confidence 899999998 999999999999997 79999999 99 8999986 8998843 346677777 5899999
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHh
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 124 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l 124 (133)
+++.|++++++++ |+|||||+..+..++|+++|.|++.++++.+++++..
T Consensus 196 la~~l~~~~~~~~-v~igSyP~~~~~~~~l~~~g~~~~~~~~a~~~l~~~~ 245 (252)
T PRK03670 196 LAPILEEALERFN-VKIHSSPKGFGKYIGIIIFAEDEEEIEKAVEFMEERG 245 (252)
T ss_pred HHHHHHHHHHHCC-ceEecCCCCCCCcEEEEEEECCHHHHHHHHHHHHHhC
Confidence 9999999999995 9999999833347899999999999999999987543
No 4
>PRK03673 hypothetical protein; Provisional
Probab=99.95 E-value=2.8e-27 Score=192.28 Aligned_cols=126 Identities=18% Similarity=0.130 Sum_probs=108.1
Q ss_pred CccCCCCCceeeeCCCCcccEEEec----eEEEeeCCCCCc-hHHHHH-HHHHHHhhCCCCCCCCeEEEEEE-ecCChhh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWN-CLIELLRSGGLSLMEPYTSKSLT-TNLSDLE 73 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i~----~v~~LPGv~~P~-m~~m~~-~v~p~l~~~~~~~~~~~~~~~l~-~g~~Es~ 73 (133)
||++|+||+ +|+||+|||||++++ .+|+|||| |+ |++||+ .++|+|++. +.....++++.++ +|++||+
T Consensus 118 QA~~P~ga~-~l~N~~GtApG~~~~~~~~~i~~LPGv--P~Emk~M~~~~v~p~L~~~-~~~~~~~~~~~l~~~Gi~ES~ 193 (396)
T PRK03673 118 QAELPASAE-MIDNPVGTACGFALQLNRCLMFFTPGV--PSEFKVMVEQEILPRLRER-FSLPEPPLCLRLTTFGRSESD 193 (396)
T ss_pred hccCCCCCe-eccCCCccCCcEEEEECCEEEEEECCC--hHHHHHHHHHHHHHHHHhh-cCCCCceEEEEEEECCCCHHH
Confidence 899999998 999999999999996 39999999 98 999997 589999765 2221356678888 5999999
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCCeee
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFSE 131 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~ 131 (133)
+++.|.++.. .+++++|+|++.+..+++++.++.+.+.++++.+++++++++++|+.
T Consensus 194 l~~~l~~l~~-~~~~~i~~~~~~~~v~vrlt~~~~~~~~~~~~~~~i~~~lg~~v~~~ 250 (396)
T PRK03673 194 LAQSLDPLPL-PPGVVMGYRSSMPIIELKLTGPASQRQAMEQLWQQVRRVAGQSVIFE 250 (396)
T ss_pred HHHHHHHHhc-CCCCEEeecCCCCeEEEEEEEccCCHHHHHHHHHHHHHHhCCcEEEe
Confidence 9999999952 34899999999877889999998887667889999999999999963
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=99.91 E-value=7.3e-24 Score=173.25 Aligned_cols=126 Identities=15% Similarity=0.084 Sum_probs=106.5
Q ss_pred CccCCCCCceeeeCCCCcccEEEe-c----eEEEeeCCCCCc-hHHHHHH-HHHHHhhCCCCCCCCeEEEEEE-ecCChh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKC-Q----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSKSLT-TNLSDL 72 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i-~----~v~~LPGv~~P~-m~~m~~~-v~p~l~~~~~~~~~~~~~~~l~-~g~~Es 72 (133)
||++|+||+ +|+|++|||||+++ . .+++|||| |. |++||+. +.|+|+.. +.....+++++++ +|++||
T Consensus 117 qA~~p~ga~-~l~N~~G~APG~~~~~~~~~~i~~LPG~--P~e~~~m~~~~v~p~l~~~-~~~~~~~~~~~~~~~Gi~ES 192 (413)
T TIGR00200 117 QALLPAGAE-FLANPVGTAPGMFAVQLNRCLMLFTPGV--PSEFRVMVEHEALPRLRER-FSLPQPIVSLVLRFFGIGES 192 (413)
T ss_pred hcCCCCCCE-ECCCCCCCCCeeEEEecCCEEEEEeCCC--cHHHHHHHHHHhhHHHHHh-cCCCceEEEEEEEECCCCHH
Confidence 899999997 99999999999655 2 27889999 98 9999975 89999764 2222457889999 599999
Q ss_pred hhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHH----HHHHHHHHHHhcCCCee
Q 032821 73 EAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARI----EAAIESLFKKFHRGAFS 130 (133)
Q Consensus 73 ~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~----~~~~~~l~~~l~~~~~~ 130 (133)
++++.|.++...++++++++|++.+..+++++.++.+.+.. +++.++|++++++++|+
T Consensus 193 ~l~~~l~~~~~~~~~~~~~~~~~~~~v~vrl~~~~~~~~~a~~~~~~~~~~i~~~lg~~~~~ 254 (413)
T TIGR00200 193 QLEADLADSLDTLTNPTGAPMAYRGEVPLRELKLTGPESEQQRAMEKLWLDIKRVAGQSVIG 254 (413)
T ss_pred HHHHHHHHHHhcCCCCeEEEecCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHhCcceec
Confidence 99999999987778899999998777889999999876543 45888999999999996
No 6
>PRK01215 competence damage-inducible protein A; Provisional
Probab=99.91 E-value=8.5e-24 Score=164.13 Aligned_cols=120 Identities=15% Similarity=0.221 Sum_probs=97.5
Q ss_pred CccCCCCCceeeeCCCCcccEEEec----eEEEeeCCCCCc-hHHHHHH-HHHHHhhCCCCCCCCeEEEEEE-ecCChhh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWNC-LIELLRSGGLSLMEPYTSKSLT-TNLSDLE 73 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i~----~v~~LPGv~~P~-m~~m~~~-v~p~l~~~~~~~~~~~~~~~l~-~g~~Es~ 73 (133)
||++|+||+ +++|+.|||||+++. .+|+|||+ |. |+.||+. +.|+|++. ....+++++++ +|++||+
T Consensus 120 ~A~~P~ga~-~l~N~~Gtapg~~~~~~~~~i~~LPG~--P~e~~~m~~~~v~p~l~~~---~~~~~~~~~~~~~Gi~Es~ 193 (264)
T PRK01215 120 MAMMPPGAV-PLENPVGTAPGILIEHGGKDIVALPGV--PREMEAIFENFVEPLLKNR---PPLKYYEDSILVEGVMESD 193 (264)
T ss_pred eeeCCCCCE-ecCCCCCcCCeEEEEECCEEEEEeCCC--hHHHHHHHHHHHHHHHhcc---CCCcEEEEEEEECCCCHHH
Confidence 799999998 999999999999985 49999999 98 9999985 89999753 12467889999 5999999
Q ss_pred hhHHHHHHhhhCCCceEEEc-----cccCCCcEEEEEEecCHHHHH----HHHHHHHHHhcC
Q 032821 74 AAQPLSKLCLEFPDLHIGCY-----RKSRQGPLIISFEGKDQARIE----AAIESLFKKFHR 126 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsy-----p~~~~~~v~l~~~~~~~~~~~----~~~~~l~~~l~~ 126 (133)
+++.|.++..+++++++||+ ++.+.+.+++++++.+.+..+ ++.+.+++.+..
T Consensus 194 l~~~l~~l~~~~~~~~~~s~p~~~~~~~~~v~vrl~~~~~~~~~~~~~~~~~~~~i~~~~~~ 255 (264)
T PRK01215 194 LAPYVKELVKKYDRVYVKSHPKGYEVSKPILEIQIAGSGEREEEAKVKVEKVLEELKELIKK 255 (264)
T ss_pred HHHHHHHHHHhCCCCEEecCccceecCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999888999999555 554456688888888765543 466666666653
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=99.50 E-value=2.2e-14 Score=104.97 Aligned_cols=48 Identities=29% Similarity=0.407 Sum_probs=44.2
Q ss_pred CccCCCCCceeeeCCCCcccEEEec----eEEEeeCCCCCc-hHHHHH-HHHHHHhh
Q 032821 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTE-LDKEWN-CLIELLRS 51 (133)
Q Consensus 1 mA~vPega~~~l~N~~gtAPg~~i~----~v~~LPGv~~P~-m~~m~~-~v~p~l~~ 51 (133)
||++|+||+ +|.|+.|+|||++++ ++|+|||| |+ |++||+ .+.|+|++
T Consensus 116 ~a~~p~ga~-~i~N~~G~apg~~~~~~~~~i~~lPG~--P~e~~~m~~~~~~~~l~~ 169 (170)
T cd00885 116 QAMLPEGAT-LLPNPVGTAPGFSVEHNGKNVFLLPGV--PSEMKPMLEEEVLPRLRE 169 (170)
T ss_pred eecCCCCCE-ECcCCCCEeeEEEEEeCCeEEEEECCC--hHHHHHHHHHHHHHHHhc
Confidence 799999998 999999999999997 69999999 98 999998 58998854
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=94.36 E-value=0.017 Score=40.52 Aligned_cols=34 Identities=24% Similarity=0.138 Sum_probs=25.4
Q ss_pred CCCcccEEEec-----eEEEeeCCCCCc-hHHHHHHH-HHHHh
Q 032821 15 DKLLLPLIKCQ-----NVIILTATNVTE-LDKEWNCL-IELLR 50 (133)
Q Consensus 15 ~~gtAPg~~i~-----~v~~LPGv~~P~-m~~m~~~v-~p~l~ 50 (133)
|.++++++.++ .+|.|||. |. ++.+|+.+ .|.|+
T Consensus 103 p~~~~~~~~~~~~~~~~v~~LPG~--P~~~~~~~~~~v~P~L~ 143 (144)
T PF00994_consen 103 PTGLAPGAYLSRKGGKPVFGLPGN--PVAAKVMLEVLVLPLLR 143 (144)
T ss_dssp TCETEGGGGGTSSETTEEEEE-SS--HHHHHHHHHHHHHHHHH
T ss_pred ccceeeEEEeeCCCCcEEEEcCCC--HHHHHHHHHHHHHHhcC
Confidence 45677776654 49999999 98 89999864 59885
No 9
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=91.33 E-value=1.9 Score=28.35 Aligned_cols=60 Identities=13% Similarity=0.184 Sum_probs=43.8
Q ss_pred EEEE-ecCChhhhhHHHHHHhhhC-C---CceEEEccccCCC--cEEEEEEecCHHHHHHHHHHHHH
Q 032821 63 KSLT-TNLSDLEAAQPLSKLCLEF-P---DLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 63 ~~l~-~g~~Es~l~~~L~~l~~~~-~---~v~igsyp~~~~~--~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
-+++ .|...-++++.+-++.+++ | ..++...|+..++ .|.|+++++|.+.++.+.++|.+
T Consensus 16 F~~KVmG~a~~~l~~~vv~vvqr~ap~~~~~~~~~k~SSkGnY~svsI~i~A~~~EQ~e~ly~eL~~ 82 (90)
T COG2921 16 FTYKVMGAAGPELEDQVVEVVQRHAPGDYTPRVSWKPSSKGNYLSVSITIRATNIEQVEALYRELRK 82 (90)
T ss_pred ceeeehcccchhHHHHHHHHHHHHCCcccCceeeeccCCCCceEEEEEEEEECCHHHHHHHHHHHhh
Confidence 3455 4887778888887776665 4 3456666765554 48999999999999988888765
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=86.89 E-value=0.82 Score=32.15 Aligned_cols=32 Identities=6% Similarity=-0.111 Sum_probs=24.7
Q ss_pred eeeCCCCcccEEEece--EEEeeCCCCCc-hHHHHHH
Q 032821 11 LLHHDKLLLPLIKCQN--VIILTATNVTE-LDKEWNC 44 (133)
Q Consensus 11 ~l~N~~gtAPg~~i~~--v~~LPGv~~P~-m~~m~~~ 44 (133)
+.-+|-+++.+..+++ ++.|||. |. .+.+|+.
T Consensus 106 ~~~~PG~~~~~~~~~~~~v~~LPG~--P~aa~~~~~~ 140 (144)
T TIGR00177 106 VLSRPGKPATAGVRGGTLIFGLPGN--PVSALVTFEV 140 (144)
T ss_pred hhCCCCCceEEEEECCEEEEECCCC--HHHHHHHHHH
Confidence 4557777777777763 9999999 98 7888864
No 11
>PRK00907 hypothetical protein; Provisional
Probab=85.33 E-value=8.1 Score=25.48 Aligned_cols=60 Identities=17% Similarity=0.171 Sum_probs=43.6
Q ss_pred EEEE-ecCChhhhhHHHHHHhhhC-C---CceEEEccccCCC--cEEEEEEecCHHHHHHHHHHHHH
Q 032821 63 KSLT-TNLSDLEAAQPLSKLCLEF-P---DLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 63 ~~l~-~g~~Es~l~~~L~~l~~~~-~---~v~igsyp~~~~~--~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
-.++ .|....++.+.+.++..++ | +-.+...++..+. .+++++..++++.++++.++|.+
T Consensus 18 fpiKVmG~a~~~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~GkY~Svtv~i~ats~eQld~iY~~L~~ 84 (92)
T PRK00907 18 FELSAMGTAERGLETELPRLLAATGVELLQERISWKHSSSGKYVSVRIGFRAESREQYDAAHQALRD 84 (92)
T ss_pred CeEEEEEcCchhHHHHHHHHHHHhCCCCCcCcEEeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 4456 4888788888888876554 4 4556777765443 37888889999999988888765
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=80.09 E-value=8.5 Score=24.76 Aligned_cols=54 Identities=13% Similarity=0.149 Sum_probs=37.5
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--C--cEEEEEEe-cC-HHHHHHHHHHHHHHhc
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--G--PLIISFEG-KD-QARIEAAIESLFKKFH 125 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~--~v~l~~~~-~~-~~~~~~~~~~l~~~l~ 125 (133)
-.+...|+....+.|+|.++.|--.++ . .++|..++ .+ .+.+++|.+.+.+.+.
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 457888888777789999999865333 2 35666665 23 4567788888877664
No 13
>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=78.34 E-value=7 Score=24.05 Aligned_cols=37 Identities=11% Similarity=0.167 Sum_probs=29.2
Q ss_pred ceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHh
Q 032821 88 LHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 124 (133)
Q Consensus 88 v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l 124 (133)
..+-..|+..+.-+|+.+++.+.+.+++..+.+.+.+
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 3344888866667999999999998888888877654
No 14
>PRK02047 hypothetical protein; Provisional
Probab=76.52 E-value=18 Score=23.57 Aligned_cols=60 Identities=15% Similarity=0.150 Sum_probs=42.5
Q ss_pred EEEE-ecCChhhhhHHHHHHhhhC-CC---ceEEEccccCCC--cEEEEEEecCHHHHHHHHHHHHH
Q 032821 63 KSLT-TNLSDLEAAQPLSKLCLEF-PD---LHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 63 ~~l~-~g~~Es~l~~~L~~l~~~~-~~---v~igsyp~~~~~--~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
..++ .|-.+.++.+.+.++..++ |+ -.+.+.++..+. .+.+++...++++++++.++|.+
T Consensus 17 ~~~KvIG~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~GkY~Svtv~v~v~s~eq~~~iY~~L~~ 83 (91)
T PRK02047 17 FPIKVMGKAHPEFADTIFKVVSVHDPEFDLEKIEERPSSGGNYTGLTITVRATSREQLDNIYRALTG 83 (91)
T ss_pred CeEEEEEeCcHhHHHHHHHHHHHhCCCCccCceEEccCCCCeEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 3455 4777777888888876655 33 447777865443 36888888899988888887765
No 15
>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=76.03 E-value=14 Score=23.90 Aligned_cols=53 Identities=15% Similarity=0.223 Sum_probs=36.2
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--Cc--EEEEEEe-cC-HHHHHHHHHHHHHHh
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--GP--LIISFEG-KD-QARIEAAIESLFKKF 124 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~~--v~l~~~~-~~-~~~~~~~~~~l~~~l 124 (133)
-.+...|+....+.|+|.++.|--.++ .. ++|..++ .+ .+.+++|.+.|.+.+
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 558888888877889999999965333 23 5666665 34 345677777776654
No 16
>PRK00341 hypothetical protein; Provisional
Probab=75.89 E-value=19 Score=23.51 Aligned_cols=59 Identities=5% Similarity=0.037 Sum_probs=41.1
Q ss_pred EEE-ecCChhhhhHHHHHHhhhCC---CceEEEccccCCC--cEEEEEEecCHHHHHHHHHHHHH
Q 032821 64 SLT-TNLSDLEAAQPLSKLCLEFP---DLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 64 ~l~-~g~~Es~l~~~L~~l~~~~~---~v~igsyp~~~~~--~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
.++ .|....++.+.+.++..++- .-.+.+.++.++. .+.+++...+++.++++.++|.+
T Consensus 19 ~~KViG~~~~~~~~~V~~iv~~~~~~~~~~~~~k~Ss~GkY~S~tv~i~~~s~~q~~~iy~~L~~ 83 (91)
T PRK00341 19 PIKVIGDTGVGFKDLVIEILQKHADVDLSTLAERQSSNGKYTTVQLHIVATDEDQLQDINSALRA 83 (91)
T ss_pred cEEEEEcCchhHHHHHHHHHHHhCCCcccceeeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 345 48777888888888765542 3445556664443 37888888999988888888765
No 17
>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=70.26 E-value=25 Score=22.59 Aligned_cols=54 Identities=19% Similarity=0.234 Sum_probs=37.3
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--Cc--EEEEEEe-cC-HHHHHHHHHHHHHHhc
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--GP--LIISFEG-KD-QARIEAAIESLFKKFH 125 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~~--v~l~~~~-~~-~~~~~~~~~~l~~~l~ 125 (133)
-.+...|+....+.|+|.++.|--.++ .. ++|...+ .+ .+.+++|.+.+.+.++
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 457888888777789999999975443 23 5666655 23 4557788888877664
No 18
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=69.32 E-value=28 Score=22.47 Aligned_cols=54 Identities=19% Similarity=0.224 Sum_probs=37.3
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--Cc--EEEEEEe-cC-HHHHHHHHHHHHHHhc
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--GP--LIISFEG-KD-QARIEAAIESLFKKFH 125 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~~--v~l~~~~-~~-~~~~~~~~~~l~~~l~ 125 (133)
-.+...|+....+.|+|.++.|-..++ .. ++|..++ .+ .+.+.+|.+.|.+.+.
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 457888888777789999999975444 23 5666553 24 4456788888777664
No 19
>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=65.99 E-value=30 Score=21.58 Aligned_cols=43 Identities=12% Similarity=0.173 Sum_probs=32.7
Q ss_pred CCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCCe
Q 032821 86 PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAF 129 (133)
Q Consensus 86 ~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~~ 129 (133)
-+|++..+-....+.+.+.+.| |.+.++++.+..++..+..++
T Consensus 25 a~V~l~~~~~~~~g~~~~~i~G-~vs~V~~Av~a~~~~~~~~~v 67 (75)
T PF00936_consen 25 ANVELVEIELICGGKVTVIITG-DVSAVKAAVDAAEEAAGKKLV 67 (75)
T ss_dssp SSEEEEEEEEESTTEEEEEEEE-SHHHHHHHHHHHHHHHHHTEE
T ss_pred CCEEEEEEEecCCCeEEEEEEE-CHHHHHHHHHHHHHHHhhcee
Confidence 4899888776666778888888 777788888888777766533
No 20
>PRK04998 hypothetical protein; Provisional
Probab=65.37 E-value=34 Score=22.04 Aligned_cols=60 Identities=15% Similarity=0.163 Sum_probs=39.0
Q ss_pred EEEE-ecCChhhhhHHHHHHhhhC-CCc-eEEEccccCCC--cEEEEEEecCHHHHHHHHHHHHH
Q 032821 63 KSLT-TNLSDLEAAQPLSKLCLEF-PDL-HIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 63 ~~l~-~g~~Es~l~~~L~~l~~~~-~~v-~igsyp~~~~~--~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
..++ +|-.+.++.+.+..+..++ |+. .+.+.++..+. .+.+++...+++.+++..++|.+
T Consensus 16 ~~~Kvig~~~~~~~~~v~~v~~~~~~~~~~~~~r~S~~GkY~Svtv~v~v~s~eq~~~iY~~L~~ 80 (88)
T PRK04998 16 FTYKVMGLARPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITITATSIEQVETLYEELAK 80 (88)
T ss_pred ceEEEEEeCcHhHHHHHHHHHHHhCCCCCCceEccCCCCEEEEEEEEEEECCHHHHHHHHHHHhc
Confidence 3455 4766667777777765443 432 25667764443 36777888899888888877765
No 21
>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=64.67 E-value=20 Score=22.61 Aligned_cols=53 Identities=21% Similarity=0.289 Sum_probs=33.5
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--CcEEEEEE--ec-C-HHHHHHHHHHHHHHh
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--GPLIISFE--GK-D-QARIEAAIESLFKKF 124 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~~v~l~~~--~~-~-~~~~~~~~~~l~~~l 124 (133)
-.+...|+....+.|+|.++.|-...+ ..+.|++. |. + .+.++++.+.+.+.+
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 457777887766779999998865333 34545554 43 3 344667777766654
No 22
>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=62.05 E-value=21 Score=22.64 Aligned_cols=60 Identities=8% Similarity=0.143 Sum_probs=40.3
Q ss_pred EEEE-ecCChhhhhHHHHHHhhhC----CCceEEEccccCCC--cEEEEEEecCHHHHHHHHHHHHH
Q 032821 63 KSLT-TNLSDLEAAQPLSKLCLEF----PDLHIGCYRKSRQG--PLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 63 ~~l~-~g~~Es~l~~~L~~l~~~~----~~v~igsyp~~~~~--~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
..++ +|..+.++.+.+.++..++ .+..+...++.++. .+.+++.-.+++.++++.++|.+
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 4456 4887777777777764432 35667777754443 36777788899988888877765
No 23
>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=61.87 E-value=42 Score=21.95 Aligned_cols=54 Identities=19% Similarity=0.266 Sum_probs=36.2
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--Cc--EEEEEEe-cC-HHHHHHHHHHHHHHhc
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--GP--LIISFEG-KD-QARIEAAIESLFKKFH 125 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~~--v~l~~~~-~~-~~~~~~~~~~l~~~l~ 125 (133)
-.|...|+....+.|+|.++.|.-.++ .. ++|..++ .+ .+.+++|.+.+.+.+.
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 458888888777789999999975433 23 4555554 23 4456777777776654
No 24
>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=60.89 E-value=36 Score=22.99 Aligned_cols=58 Identities=12% Similarity=0.218 Sum_probs=38.4
Q ss_pred ecCChhhhhHHHHHHhhhCCCceEEEccccC-----------CCcEEEEEEecCHHHHHHHHHHHHHHhcCC
Q 032821 67 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR-----------QGPLIISFEGKDQARIEAAIESLFKKFHRG 127 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~~~~v~igsyp~~~-----------~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~ 127 (133)
...+|..+-. .|...+..+|+++ |++.. .+.+.+.+.|.|.++++.+.+...+.+...
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 3566655322 3444444599999 56544 345677788889998888888887776643
No 25
>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=59.93 E-value=24 Score=20.89 Aligned_cols=52 Identities=21% Similarity=0.118 Sum_probs=31.1
Q ss_pred CChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEe-cCHHHHHHHHHHHH
Q 032821 69 LSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEG-KDQARIEAAIESLF 121 (133)
Q Consensus 69 ~~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~-~~~~~~~~~~~~l~ 121 (133)
-.++.....+.++....++..+ .....+....++.+-. .+.++++++.+.|.
T Consensus 13 ~~~~~A~~~~~~l~~~g~~~~~-~~~~~~~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 13 SSEENAERLLAKLKKKGPDAYV-VQVSKGGPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp S-HHHHHHHHHHHHHHT------EEEEEETTCEEEEECCECTCCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhcCCCcce-EEEecCCceEEEEECCCCCHHHHHHHHHHHh
Confidence 4667778888888877766554 3333334456676643 56677788888888
No 26
>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=58.40 E-value=40 Score=24.72 Aligned_cols=38 Identities=13% Similarity=0.300 Sum_probs=29.7
Q ss_pred CceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCCee
Q 032821 87 DLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFS 130 (133)
Q Consensus 87 ~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~~~ 130 (133)
.+..|.| +..|.+.++|.+.+++..+.+...+...-|.
T Consensus 143 ~~~~G~~------~~~i~v~~~~~~~l~~~~~~v~~~l~~~G~~ 180 (205)
T PF03135_consen 143 RVSFGYY------HFTIVVFADDPEELDDKVAEVSSALNNLGFV 180 (205)
T ss_pred Ceeeeee------EEEEEEEcCCHHHHHHHHHHHHHHHHHCCCE
Confidence 5556655 4778899999999999988888888766554
No 27
>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=57.20 E-value=49 Score=23.78 Aligned_cols=30 Identities=20% Similarity=0.230 Sum_probs=24.0
Q ss_pred EEE-ecCChhhhhHHHHHHhhhCCCceEEEc
Q 032821 64 SLT-TNLSDLEAAQPLSKLCLEFPDLHIGCY 93 (133)
Q Consensus 64 ~l~-~g~~Es~l~~~L~~l~~~~~~v~igsy 93 (133)
.++ +|-.|..+++..+.+...||++.|.-+
T Consensus 50 ~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~ 80 (172)
T PF03808_consen 50 RIFLLGGSEEVLEKAAANLRRRYPGLRIVGY 80 (172)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence 344 698888889888999999999887643
No 28
>PTZ00302 N-acetylglucosamine-phosphate mutase; Provisional
Probab=55.89 E-value=42 Score=29.36 Aligned_cols=53 Identities=4% Similarity=-0.018 Sum_probs=36.3
Q ss_pred hhHHHHHHhhhC-CCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 74 AAQPLSKLCLEF-PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 74 l~~~L~~l~~~~-~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
+++.+..+...+ ++=.+-.+|+..+.-+||.+++++++.+++..+++.+.+.+
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 455555554444 43334567765566699999999999888888777776653
No 29
>PRK09417 mogA molybdenum cofactor biosynthesis protein MogA; Provisional
Probab=54.83 E-value=12 Score=27.99 Aligned_cols=15 Identities=13% Similarity=0.330 Sum_probs=13.8
Q ss_pred EEEeeCCCCCc-hHHHHH
Q 032821 27 VIILTATNVTE-LDKEWN 43 (133)
Q Consensus 27 v~~LPGv~~P~-m~~m~~ 43 (133)
++.|||. |. .+.+|+
T Consensus 129 I~nLPGS--p~a~~~~le 144 (193)
T PRK09417 129 IINLPGQ--PKSIKETLE 144 (193)
T ss_pred EEECCCC--HHHHHHHHH
Confidence 8999999 98 888888
No 30
>COG1925 FruB Phosphotransferase system, HPr-related proteins [Carbohydrate transport and metabolism]
Probab=54.60 E-value=20 Score=23.34 Aligned_cols=24 Identities=29% Similarity=0.443 Sum_probs=15.4
Q ss_pred CcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 99 GPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 99 ~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
..++|+++|+|++ +|.+.|.+.+.
T Consensus 59 ~~i~i~a~G~de~---~Al~aL~~li~ 82 (88)
T COG1925 59 DEIELSAEGEDEE---EALEALSELIE 82 (88)
T ss_pred CEEEEEEeCccHH---HHHHHHHHHHH
Confidence 3589999999986 34444444443
No 31
>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=54.40 E-value=57 Score=27.95 Aligned_cols=47 Identities=4% Similarity=0.031 Sum_probs=32.6
Q ss_pred HHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 77 PLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 77 ~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
.++.+...+.+=.+=.+|+..+.-+||.+++++++.+++..+++.+.
T Consensus 466 ~iDG~~~~~~~gr~lVRpSGTEp~iRvyaEA~t~~~~~~l~~~i~~~ 512 (513)
T cd03086 466 KIDAIVAKYNNGRAFVRPSGTEDVVRVYAEAATQEEADELANEVAEL 512 (513)
T ss_pred HHHHHHhcCCCeeEEEecCCCCcEEEEEEEeCCHHHHHHHHHHHHhh
Confidence 33334334444345567776666699999999999988888887664
No 32
>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=54.30 E-value=31 Score=26.45 Aligned_cols=53 Identities=15% Similarity=0.125 Sum_probs=31.3
Q ss_pred hhhhhHHHHHHhhhCC--CceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCC
Q 032821 71 DLEAAQPLSKLCLEFP--DLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRG 127 (133)
Q Consensus 71 Es~l~~~L~~l~~~~~--~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~ 127 (133)
|+.++..=+.+..... +|++..-.. ....++++++|+|++ -|.+.|++.++.-
T Consensus 12 ~r~ld~L~~~v~n~lgdLdV~~~i~~~-~~~wv~vtl~GeD~e---va~Nll~eefGei 66 (225)
T PF09883_consen 12 ERALDSLRSLVENDLGDLDVEWDIGIT-KDDWVKVTLEGEDEE---VAANLLREEFGEI 66 (225)
T ss_pred HHHHHHHHHHHHHhhcCeeEEEEeccc-cCCceEEEEecCcHH---HHHHHHHHHhCCC
Confidence 6664432223333333 444433321 245799999999986 6777888888753
No 33
>KOG0071 consensus GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]
Probab=54.18 E-value=38 Score=24.63 Aligned_cols=56 Identities=23% Similarity=0.359 Sum_probs=39.4
Q ss_pred EEEEecCChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCC
Q 032821 63 KSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRG 127 (133)
Q Consensus 63 ~~l~~g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~ 127 (133)
+.+.+++-|--=++.++++...| |+. ...+...+++.+.+++++|.+++...+++.
T Consensus 59 kN~kfNvwdvGGqd~iRplWrhY-------y~g--tqglIFV~Dsa~~dr~eeAr~ELh~ii~~~ 114 (180)
T KOG0071|consen 59 KNVKFNVWDVGGQDKIRPLWRHY-------YTG--TQGLIFVVDSADRDRIEEARNELHRIINDR 114 (180)
T ss_pred eeeEEeeeeccCchhhhHHHHhh-------ccC--CceEEEEEeccchhhHHHHHHHHHHHhCCH
Confidence 44445555555577788876654 442 224778888888899999999999888754
No 34
>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=51.57 E-value=56 Score=20.18 Aligned_cols=64 Identities=22% Similarity=0.363 Sum_probs=39.2
Q ss_pred CCeEEEEEE-e-cCChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 58 EPYTSKSLT-T-NLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 58 ~~~~~~~l~-~-g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.+.++..+. . .-.+..+.+.|..+..+-|.+++..-.. .+. +.+.|--+-.++-+.+.++++++
T Consensus 3 ~Pv~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~~d~e--t~e--~~l~g~Gelhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 3 PPVLSVAIEPKNKEDEPKLSEALQKLSEEDPSLRVERDEE--TGE--LILSGMGELHLEVLLERLKRRFG 68 (75)
T ss_dssp S-SEEEEEEESSHHHHHHHHHHHHHHHHH-TTSEEEEETT--TSE--EEEEESSHHHHHHHHHHHHHTTC
T ss_pred CCeEEEEEEECCHhHHHHHHHHHHHHHhcCCeEEEEEcch--hce--EEEEECCHHHHHHHHHHHHHHHC
Confidence 355566666 2 4567778888888888777776665543 233 34444455556677777777765
No 35
>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=50.37 E-value=16 Score=26.26 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=19.3
Q ss_pred EEEeeCCCCCc-hHHHHHH-HHHHHhhC
Q 032821 27 VIILTATNVTE-LDKEWNC-LIELLRSG 52 (133)
Q Consensus 27 v~~LPGv~~P~-m~~m~~~-v~p~l~~~ 52 (133)
+|.|||. |. ...+|+. +.|.|...
T Consensus 127 v~~LPG~--P~aa~~~~~~~v~P~l~~~ 152 (163)
T TIGR02667 127 VFCLPGS--TGACRTAWDKIIAAQLDAR 152 (163)
T ss_pred EEECCCC--HHHHHHHHHHHHHHHHHHH
Confidence 9999999 97 7788864 78888543
No 36
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=49.00 E-value=79 Score=21.13 Aligned_cols=54 Identities=17% Similarity=0.263 Sum_probs=34.9
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCC--C--cEEEEEEec-C-HHHHHHHHHHHHHHhc
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQ--G--PLIISFEGK-D-QARIEAAIESLFKKFH 125 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~--~--~v~l~~~~~-~-~~~~~~~~~~l~~~l~ 125 (133)
-.+...|.....+.++|.+++|--.++ . .++|...+. | .+.+++|...+.+.+.
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 457788887776778999998864333 2 356666655 4 3456666666665544
No 37
>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=48.87 E-value=8.1 Score=26.56 Aligned_cols=20 Identities=10% Similarity=0.242 Sum_probs=15.8
Q ss_pred EEEeeCCCCCc-hHHHHHH-HHHH
Q 032821 27 VIILTATNVTE-LDKEWNC-LIEL 48 (133)
Q Consensus 27 v~~LPGv~~P~-m~~m~~~-v~p~ 48 (133)
++.|||. |. .+.+|.. +.|.
T Consensus 111 i~~LPG~--p~a~~~~~~~~v~p~ 132 (133)
T cd00758 111 IINLPGS--PKSALTTFEALVLPA 132 (133)
T ss_pred EEECCCC--HHHHHHHHHHhheec
Confidence 9999999 97 7777764 5654
No 38
>PF12687 DUF3801: Protein of unknown function (DUF3801); InterPro: IPR024234 This functionally uncharacterised protein family is found in bacteria. Proteins found in this family are typically between 158 and 187 amino acids in length and include the PcfB protein.
Probab=48.28 E-value=1.1e+02 Score=22.82 Aligned_cols=55 Identities=16% Similarity=0.287 Sum_probs=39.8
Q ss_pred ecCChhhhhHHHHHHhhhCCCceEEEccccC--CCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 67 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR--QGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~~~~v~igsyp~~~--~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+.+++++|.+ +.....+| +|.++...... ++.+.|.+.+.|.+.+++|.+.+...
T Consensus 37 i~i~~~~lk~-F~k~AkKy-GV~yav~kdk~~~~~~~~V~FkA~Da~~i~~af~~~~~~ 93 (204)
T PF12687_consen 37 IEITDEDLKE-FKKEAKKY-GVDYAVKKDKSTGPGKYDVFFKAKDADVINRAFKEFSAK 93 (204)
T ss_pred EecCHhhHHH-HHHHHHHc-CCceEEeeccCCCCCcEEEEEEcCcHHHHHHHHHHHHHH
Confidence 6788887554 45555667 88888888433 23689999999999888887776543
No 39
>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=48.13 E-value=68 Score=20.17 Aligned_cols=44 Identities=14% Similarity=0.137 Sum_probs=30.3
Q ss_pred CCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCCee
Q 032821 86 PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFS 130 (133)
Q Consensus 86 ~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~~~ 130 (133)
-+|++..|-....+++.+.++|+ -+.++++.+.-++..+..++.
T Consensus 24 a~V~l~~~~~~~~Gk~~vii~Gd-vsaV~~Av~a~~~~~~~~~v~ 67 (76)
T cd07053 24 ANVELVLAKTICPGKYIIIVSGD-VGAVQAAVDAGKEIGGKYVVD 67 (76)
T ss_pred CceEEEEEEeecCCEEEEEEEEc-HHHHHHHHHHHHHHhCCcEEE
Confidence 48999888766667777777774 445677777777766655444
No 40
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=46.04 E-value=36 Score=21.97 Aligned_cols=14 Identities=43% Similarity=0.532 Sum_probs=11.3
Q ss_pred CcEEEEEEecCHHH
Q 032821 99 GPLIISFEGKDQAR 112 (133)
Q Consensus 99 ~~v~l~~~~~~~~~ 112 (133)
..+.++++|.|+++
T Consensus 59 ~~v~i~a~G~De~~ 72 (88)
T PRK13780 59 ADITISAEGADAAD 72 (88)
T ss_pred CEEEEEEeCcCHHH
Confidence 35899999999864
No 41
>PRK10897 phosphohistidinoprotein-hexose phosphotransferase component of N-regulated PTS system (Npr); Provisional
Probab=43.60 E-value=47 Score=21.53 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=15.5
Q ss_pred cEEEEEEecCHHH-HHHHHHHHHHHh
Q 032821 100 PLIISFEGKDQAR-IEAAIESLFKKF 124 (133)
Q Consensus 100 ~v~l~~~~~~~~~-~~~~~~~l~~~l 124 (133)
.++++++|.|+++ ++++.+.+.+.|
T Consensus 62 ~i~v~~~G~De~~A~~~l~~~~~~~~ 87 (90)
T PRK10897 62 QIEVEATGPQEEEALAAVIALFNSGF 87 (90)
T ss_pred EEEEEEECcCHHHHHHHHHHHHHhcc
Confidence 5899999999864 334443333333
No 42
>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=42.39 E-value=26 Score=24.65 Aligned_cols=24 Identities=8% Similarity=0.194 Sum_probs=17.2
Q ss_pred eEEEeeCCCCCc-hHHHHHHHHHHHhh
Q 032821 26 NVIILTATNVTE-LDKEWNCLIELLRS 51 (133)
Q Consensus 26 ~v~~LPGv~~P~-m~~m~~~v~p~l~~ 51 (133)
-++.|||. |. -...|+.+.|.|+.
T Consensus 123 ~v~~LPG~--P~aa~~~~~~v~P~l~~ 147 (152)
T cd00886 123 LIFNLPGS--PKAVREALEVILPELPH 147 (152)
T ss_pred EEEECCCC--HHHHHHHHHHHHHHHHH
Confidence 38999999 96 44555448888854
No 43
>KOG3445 consensus Mitochondrial/chloroplast ribosomal protein 36a [Translation, ribosomal structure and biogenesis]
Probab=42.33 E-value=1.3e+02 Score=21.55 Aligned_cols=67 Identities=15% Similarity=0.081 Sum_probs=44.8
Q ss_pred eEEEEEEe-cCChhh------hhHHHHHHhhhCCCceEEEccccCCC----------cE-EEEEEecCHHHHHHHHHHHH
Q 032821 60 YTSKSLTT-NLSDLE------AAQPLSKLCLEFPDLHIGCYRKSRQG----------PL-IISFEGKDQARIEAAIESLF 121 (133)
Q Consensus 60 ~~~~~l~~-g~~Es~------l~~~L~~l~~~~~~v~igsyp~~~~~----------~v-~l~~~~~~~~~~~~~~~~l~ 121 (133)
..+-++.+ +.++|. ++..|.++.+++|+|.|-.-++.+.. .. .+.++-.+++++.+.+..|+
T Consensus 23 l~rit~sfCnwggSSrGmR~Fle~~L~~~a~enP~v~i~v~~rrg~hP~lraeY~NGre~vicvrnms~eevs~~~~lL~ 102 (145)
T KOG3445|consen 23 LRRITVSFCNWGGSSRGMREFLESELPDLARENPGVVIYVEPRRGQHPLLRAEYLNGRERVICVRNMSQEEVSKKATLLR 102 (145)
T ss_pred eeEEEEEEecCCCccHHHHHHHHHHHHHHHhhCCCeEEEEeccCCCCceEEEEecCCceEEEeeccCCHHHHHHHHHHHh
Confidence 33445554 677665 56677888889998887666654421 22 35557778888888888888
Q ss_pred HHhcC
Q 032821 122 KKFHR 126 (133)
Q Consensus 122 ~~l~~ 126 (133)
+..|.
T Consensus 103 ds~Gl 107 (145)
T KOG3445|consen 103 DSSGL 107 (145)
T ss_pred ccCCC
Confidence 77663
No 44
>PLN02895 phosphoacetylglucosamine mutase
Probab=41.48 E-value=1.2e+02 Score=26.46 Aligned_cols=51 Identities=6% Similarity=0.038 Sum_probs=33.3
Q ss_pred hHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 75 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 75 ~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.+.++.....+++=.+-.+|+..+.-+|+.+++++++.+++..+++.+.+.
T Consensus 502 q~~ID~~v~~~~~Gr~lvRpSGTEp~vRv~~Ea~t~~~~~~l~~~v~~~v~ 552 (562)
T PLN02895 502 QDAIDAEVAKYPRGRAFVRPSGTEDVVRVYAEASTQEAADSLAREVARLVY 552 (562)
T ss_pred HHHHHHHhcccCCceEEEEcCCCCcEEEEEEEECCHHHHHHHHHHHHHHHH
Confidence 334443222344333456776556669999999999988877777776654
No 45
>KOG1794 consensus N-Acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=40.53 E-value=42 Score=27.12 Aligned_cols=61 Identities=16% Similarity=0.173 Sum_probs=37.0
Q ss_pred EEecCChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCH-HHHHHHHHHHHHHhcC
Q 032821 65 LTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQ-ARIEAAIESLFKKFHR 126 (133)
Q Consensus 65 l~~g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~-~~~~~~~~~l~~~l~~ 126 (133)
.++.+++...++.++++..+- ..+-|.-++..-..+-+.++|.|+ +..++.+++++.+++.
T Consensus 36 nh~~ig~~~~~~rie~~i~~A-~~k~g~d~~~~lr~lgL~lSg~d~e~~~~~lv~~~R~~fps 97 (336)
T KOG1794|consen 36 NHWLIGSTTCASRIEDMIREA-KEKAGWDKKGPLRSLGLGLSGTDQEDKNRKLVTEFRDKFPS 97 (336)
T ss_pred ccccCCchHHHHHHHHHHHHH-HhhcCCCccCccceeeeecccCCchhHHHHHHHHHHHhccc
Confidence 345677777777777764432 222233333212346788887764 4567888888888874
No 46
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional
Probab=39.23 E-value=28 Score=27.99 Aligned_cols=22 Identities=18% Similarity=0.241 Sum_probs=17.8
Q ss_pred EEEeeCCCCCc-hHHHHHHHHHHHh
Q 032821 27 VIILTATNVTE-LDKEWNCLIELLR 50 (133)
Q Consensus 27 v~~LPGv~~P~-m~~m~~~v~p~l~ 50 (133)
+|.|||. |. ....|+.++|.|.
T Consensus 278 I~~LPG~--P~aa~~~~~~llp~l~ 300 (312)
T PRK03604 278 VVALPGS--PGGASDALAVLLPALF 300 (312)
T ss_pred EEECCCC--HHHHHHHHHHHHHHHH
Confidence 9999999 97 6677777777773
No 47
>KOG3179 consensus Predicted glutamine synthetase [Nucleotide transport and metabolism]
Probab=39.05 E-value=63 Score=24.83 Aligned_cols=44 Identities=18% Similarity=0.342 Sum_probs=30.5
Q ss_pred cCCCCCceeeeC-CCCcccEEEec-eEEEeeCCCCCch-HHHHHHHHHHH
Q 032821 3 LLPEGTTELLHH-DKLLLPLIKCQ-NVIILTATNVTEL-DKEWNCLIELL 49 (133)
Q Consensus 3 ~vPega~~~l~N-~~gtAPg~~i~-~v~~LPGv~~P~m-~~m~~~v~p~l 49 (133)
.+||||+ ++.- ..=..-+|+++ +++++-|- |++ +..+..++.++
T Consensus 160 e~PE~a~-llasSe~ceve~fs~~~~~l~fQGH--PEyn~eil~~ivdrv 206 (245)
T KOG3179|consen 160 ELPEGAE-LLASSEKCEVEMFSIEDHLLCFQGH--PEYNKEILFEIVDRV 206 (245)
T ss_pred cCCchhh-hhccccccceEEEEecceEEEecCC--chhhHHHHHHHHHHH
Confidence 4799998 7752 23345567776 69999999 996 66665555444
No 48
>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=38.79 E-value=1.2e+02 Score=20.43 Aligned_cols=59 Identities=7% Similarity=0.148 Sum_probs=39.8
Q ss_pred cCChhhhhHHHHHHhhhCCCceEEEccccC-----CCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 68 NLSDLEAAQPLSKLCLEFPDLHIGCYRKSR-----QGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 68 g~~Es~l~~~L~~l~~~~~~v~igsyp~~~-----~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
.+.|..+.+..+++.++|+...+..+=+.+ +..+-+.+.|.....+=+|++.+.+.++.
T Consensus 52 ~ma~~~l~~I~~e~~~~~~~~~v~i~HR~G~l~vGe~~v~V~vsa~hR~eaf~A~~~~id~iK~ 115 (117)
T PF02391_consen 52 EMAEKELEEIAEEARERFGIVDVAIVHRVGRLKVGEPIVLVAVSAPHRKEAFEACEYIIDRIKK 115 (117)
T ss_dssp HHHHHHHHHHHHHHHHHSTTCEEEEEEEEEEEETTSEEEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCeEEEEEEeeCCCCCCCeEEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 577788888888888888755544443322 22367778888877766777777776653
No 49
>PRK14434 acylphosphatase; Provisional
Probab=38.68 E-value=83 Score=20.41 Aligned_cols=50 Identities=22% Similarity=0.282 Sum_probs=32.4
Q ss_pred hHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 75 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 75 ~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
-.....+..++.++ .|+--+...+.|.+.++|++.+.+++..++|.+.-+
T Consensus 18 R~fv~~~A~~lg~l-~G~V~N~~dGsVei~~qG~~~~~l~~f~~~l~~g~p 67 (92)
T PRK14434 18 RYSVYSLALEIGDI-YGRVWNNDDGTVEILAQSDDSAKLAKFIQEIRKGPS 67 (92)
T ss_pred hHHHHHHHHHcCCc-EEEEEECCCCCEEEEEEcCCHHHHHHHHHHHhcCCC
Confidence 34444555544224 355445556779999999876678888888877543
No 50
>PRK10850 PTS system phosphohistidinoprotein-hexose phosphotransferase subunit Hpr; Provisional
Probab=37.78 E-value=64 Score=20.62 Aligned_cols=14 Identities=36% Similarity=0.544 Sum_probs=11.4
Q ss_pred cEEEEEEecCHHHH
Q 032821 100 PLIISFEGKDQARI 113 (133)
Q Consensus 100 ~v~l~~~~~~~~~~ 113 (133)
.++|+++|.|++++
T Consensus 60 ~v~i~~~G~De~~A 73 (85)
T PRK10850 60 VVTISAEGEDEQKA 73 (85)
T ss_pred EEEEEEeCcCHHHH
Confidence 58999999998643
No 51
>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=37.63 E-value=66 Score=25.68 Aligned_cols=32 Identities=13% Similarity=0.057 Sum_probs=24.4
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
.+|+..+.-+||.+++.|++.+++..+.+.+.
T Consensus 323 irps~tep~~ri~~Ea~~~e~a~~l~~~~~~~ 354 (355)
T cd03084 323 VRASGTEPAIRIYAEADTQEDVEQIKKEAREL 354 (355)
T ss_pred EecCCCCcEEEEEEeeCCHHHHHHHHHHHHhh
Confidence 45654455689999999999888887777654
No 52
>PRK14322 glmM phosphoglucosamine mutase; Provisional
Probab=37.57 E-value=72 Score=26.32 Aligned_cols=34 Identities=24% Similarity=0.359 Sum_probs=27.7
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.+|+..+.-+++.+++.|++.+++..+.+.+.+.
T Consensus 395 vRpS~teP~irv~~Ea~~~~~a~~l~~~~~~~l~ 428 (429)
T PRK14322 395 IRPSGTEPVVRITVEGKDREEIEKIVEEISRVLE 428 (429)
T ss_pred EccCCCCcEEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 5676555568999999999999998888888764
No 53
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=37.50 E-value=1.2e+02 Score=19.96 Aligned_cols=54 Identities=17% Similarity=0.190 Sum_probs=28.0
Q ss_pred ecCChhhhhHHHHHHhhhCCCceEEEccc---cCCCcEEEEEEec-CHHHHHHHHHHHHH
Q 032821 67 TNLSDLEAAQPLSKLCLEFPDLHIGCYRK---SRQGPLIISFEGK-DQARIEAAIESLFK 122 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~~~~v~igsyp~---~~~~~v~l~~~~~-~~~~~~~~~~~l~~ 122 (133)
+|+|+..+.+.|..+. +. ++++-+--. ...|..+|+--|. |.+-++.=.+.+++
T Consensus 31 TGmPrRT~Qd~i~aL~-~~-~I~~~Fvq~G~R~~~GyY~i~~WG~id~~wi~~~~~~i~~ 88 (90)
T PF09904_consen 31 TGMPRRTIQDTIKALP-EL-GIECEFVQDGERNNAGYYRISDWGPIDRKWIADHLQEIKA 88 (90)
T ss_dssp H---HHHHHHHHHGGG-GG-T-EEEEE--TTS-S--EEEEEE-TTB-HHHHHHHHHHHHH
T ss_pred hCCCHhHHHHHHHHhh-cC-CeEEEEEecCccCCCCcEEeeecCCCCHHHHHHHHHHHHh
Confidence 7999999999999986 33 666665531 1124578887775 45444444444443
No 54
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=37.02 E-value=83 Score=20.24 Aligned_cols=43 Identities=16% Similarity=0.312 Sum_probs=20.1
Q ss_pred HHHhhhCCCce--EEEccccCCCcEEEEE-EecCHHHHHHHHHHHHH
Q 032821 79 SKLCLEFPDLH--IGCYRKSRQGPLIISF-EGKDQARIEAAIESLFK 122 (133)
Q Consensus 79 ~~l~~~~~~v~--igsyp~~~~~~v~l~~-~~~~~~~~~~~~~~l~~ 122 (133)
+.+...||+.. +-..+.. ...+.++- ...|.+.++++.++.-+
T Consensus 27 kRl~~~fPd~~~~v~Vr~~s-~n~lsv~g~~k~dK~~i~eiLqE~we 72 (81)
T PRK10597 27 RRIQYAFPDNEGHVSVRYAA-ANNLSVIGATKEDKDRISEILQETWE 72 (81)
T ss_pred HHHHhhCCCCCccEEEeecC-CCceEecCCCcchHHHHHHHHHHHHh
Confidence 34566788765 5554432 22344322 22344445555554443
No 55
>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=36.38 E-value=84 Score=25.98 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=23.2
Q ss_pred ccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 93 YRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 93 yp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+|+..+.-+||.++++|++.+++..+++.+.
T Consensus 412 RpSgtEP~iriy~Ea~~~~~a~~l~~~~~~~ 442 (443)
T cd03089 412 RASNTEPVLVLRFEADTEEGLEEIKAELRKL 442 (443)
T ss_pred eecCCCCEEEEEEEeCCHHHHHHHHHHHHhh
Confidence 4443344589999999999888888877664
No 56
>PRK14324 glmM phosphoglucosamine mutase; Provisional
Probab=35.94 E-value=92 Score=25.88 Aligned_cols=37 Identities=24% Similarity=0.321 Sum_probs=28.9
Q ss_pred EEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 90 IGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 90 igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
+=.+|+..+.-+|+.+++++++.+++..+++.+.+..
T Consensus 406 ~lvR~SgTEp~irv~~Ea~~~~~~~~l~~~~~~~~~~ 442 (446)
T PRK14324 406 HLIRYSGTENKLRILLEGKDEKLLEKKMQELVEFFKK 442 (446)
T ss_pred EEEecCCCCceEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 4567776566699999999999988888887777643
No 57
>PRK14320 glmM phosphoglucosamine mutase; Provisional
Probab=35.35 E-value=68 Score=26.57 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=27.2
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
.+|+..+.-+|+.+++++++.+++..+.+.+.+..
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 45654445589999999999988888888877754
No 58
>PRK14323 glmM phosphoglucosamine mutase; Provisional
Probab=35.10 E-value=68 Score=26.51 Aligned_cols=35 Identities=20% Similarity=0.204 Sum_probs=26.7
Q ss_pred EEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 91 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 91 gsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
=.+|+..+.-+||.+++.+++.+++..+++.+.+.
T Consensus 402 LvRpS~TEP~irv~~Ea~s~~~~~~l~~~~~~~v~ 436 (440)
T PRK14323 402 NLRPSGTEPLVRVMVEGPDEAEIEEVARELAGVVE 436 (440)
T ss_pred EEecCCCccEeEEEEeeCCHHHHHHHHHHHHHHHH
Confidence 35565445558999999999998888888777664
No 59
>COG4810 EutS Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=34.91 E-value=87 Score=21.24 Aligned_cols=55 Identities=13% Similarity=0.218 Sum_probs=32.2
Q ss_pred cCChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEec-CHHHHHHHHHHHHHHhc
Q 032821 68 NLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGK-DQARIEAAIESLFKKFH 125 (133)
Q Consensus 68 g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~-~~~~~~~~~~~l~~~l~ 125 (133)
.-+|..+ .-.++..+..+|+||++-++ .+.+-++.+-. -++.+++....+.+.+.
T Consensus 57 TP~Eaai--Ia~DiA~Ksg~v~iGFlDRF-sGalvltGdv~aVE~aLkqv~~~L~e~l~ 112 (121)
T COG4810 57 TPGEAAI--IAGDIATKSGDVHIGFLDRF-SGALVLTGDVGAVEEALKQVVSGLGELLN 112 (121)
T ss_pred cCchhhh--hhhhhhcccCceEEeeeecc-cceEEEEcchHHHHHHHHHHHHHHHHHhc
Confidence 4455443 23577777789999999875 34455665422 23345555555555543
No 60
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=34.62 E-value=75 Score=26.33 Aligned_cols=36 Identities=17% Similarity=0.229 Sum_probs=28.1
Q ss_pred EEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 91 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 91 gsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
=.+|+..+.-++|.++++|++.+++..+++.+.+..
T Consensus 406 LiRpS~tEP~iri~~Ea~s~e~a~~l~~~~~~~v~~ 441 (443)
T PRK10887 406 LLRKSGTEPLIRVMVEGEDEAQVTALAERIADAVKA 441 (443)
T ss_pred EEecCCCCeEEEEEEeeCCHHHHHHHHHHHHHHHHh
Confidence 355655455589999999999999888888887753
No 61
>PRK14316 glmM phosphoglucosamine mutase; Provisional
Probab=34.08 E-value=75 Score=26.30 Aligned_cols=36 Identities=6% Similarity=0.077 Sum_probs=27.9
Q ss_pred EEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 90 IGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 90 igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
+=.+|+..+.-+||.+++.+++.+++..+.+.+.+.
T Consensus 407 ~liRpS~TEP~irvy~Ea~~~e~~~~l~~~~~~~i~ 442 (448)
T PRK14316 407 VLVRPSGTEPLVRVMAEAPTQEEVDKYVDRIADVVE 442 (448)
T ss_pred EEEecCCCCcEEEEEEEeCCHHHHHHHHHHHHHHHH
Confidence 346676555568999999999988888887777665
No 62
>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=33.87 E-value=1.1e+02 Score=18.58 Aligned_cols=52 Identities=17% Similarity=0.162 Sum_probs=31.1
Q ss_pred hhhhHHHHHHhhhCCC-ceEEEccccCC-Cc--EEEEEEec-CHHHHHHHHHHHHHH
Q 032821 72 LEAAQPLSKLCLEFPD-LHIGCYRKSRQ-GP--LIISFEGK-DQARIEAAIESLFKK 123 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~-v~igsyp~~~~-~~--v~l~~~~~-~~~~~~~~~~~l~~~ 123 (133)
..+++.++.+.+..=+ .++.++|.... .. +++.+++. +.+.++++.+.+.+.
T Consensus 13 G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~ 69 (80)
T cd04905 13 GALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRL 69 (80)
T ss_pred CHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHh
Confidence 3467777776543324 37889996332 22 45666665 355566777777664
No 63
>PRK14318 glmM phosphoglucosamine mutase; Provisional
Probab=33.68 E-value=78 Score=26.28 Aligned_cols=36 Identities=8% Similarity=-0.015 Sum_probs=27.8
Q ss_pred EEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 91 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 91 gsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
=.+|+..+.-+||.+++++++.+++..+++.+.+..
T Consensus 410 lvRpS~teP~irv~~Ea~~~~~a~~l~~~~~~~v~~ 445 (448)
T PRK14318 410 LLRPSGTEPLVRVMVEAADEETARRVAGRLADVVAE 445 (448)
T ss_pred EEeeCCCCcEEEEEEeECCHHHHHHHHHHHHHHHHH
Confidence 356765555689999999999988888888777653
No 64
>PRK14319 glmM phosphoglucosamine mutase; Provisional
Probab=33.40 E-value=78 Score=26.12 Aligned_cols=35 Identities=11% Similarity=0.082 Sum_probs=27.4
Q ss_pred EEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 91 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 91 gsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
=.+|+..+.-+||.+++++++.+++..+.+.+.+.
T Consensus 389 LiRpS~TeP~irv~~Ea~~~~~a~~l~~~~~~~v~ 423 (430)
T PRK14319 389 IVRPSGTEPVVRVLVEGPDEEYITNIANDIAGLIK 423 (430)
T ss_pred EEecCCCccEEEEEEEeCCHHHHHHHHHHHHHHHH
Confidence 35676555568999999999998888888877764
No 65
>PRK14317 glmM phosphoglucosamine mutase; Provisional
Probab=33.30 E-value=69 Score=26.75 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=27.3
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
.+|+..+.-+||.+++.|++.+++..+.+.+.+..
T Consensus 428 iRpS~TEP~irv~~Ea~~~~~~~~l~~~~~~~v~~ 462 (465)
T PRK14317 428 VRASGTEPLIRVMVEAEDAELVNHWTNHLVAVVQQ 462 (465)
T ss_pred EecCCCCCEEEEEEEeCCHHHHHHHHHHHHHHHHH
Confidence 55655455589999999999988888888777653
No 66
>COG3622 Hfi Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]
Probab=33.09 E-value=41 Score=26.30 Aligned_cols=65 Identities=9% Similarity=0.061 Sum_probs=42.8
Q ss_pred eEEEeeCCCCCc--hHHHHHHHHHHHhhCCCCCCCCeEEEEEE-ecCChhhhhHHHHHHhhhCCCceEEEccccCC
Q 032821 26 NVIILTATNVTE--LDKEWNCLIELLRSGGLSLMEPYTSKSLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ 98 (133)
Q Consensus 26 ~v~~LPGv~~P~--m~~m~~~v~p~l~~~~~~~~~~~~~~~l~-~g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~ 98 (133)
|.+-+||. |- ...-+ .++.... ..+-+....++ .-+.|.++...|++.......|+|++-|...+
T Consensus 146 N~~d~PG~--~l~~~~~al-~li~~V~-----~~Nl~lq~D~YH~Q~~eGnL~~~lr~~~~~ighvQiAdvP~RhE 213 (260)
T COG3622 146 NLRDMPGY--FLTSQEQAL-ALIDEVG-----RPNLFLQLDLYHAQIMEGNLTRLLREYLPKIGHVQIADVPGRHE 213 (260)
T ss_pred CCCCCCCc--ccccHHHHH-HHHHHhC-----CCCeEeehhHHHHHHhccHHHHHHHHhhhhhceeeecCCCCCCC
Confidence 56889999 73 32211 1333331 11334444444 68899999999999887778999999996543
No 67
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=33.04 E-value=85 Score=20.81 Aligned_cols=26 Identities=8% Similarity=0.074 Sum_probs=22.4
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 100 PLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 100 ~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.++|+++|-|...++++++.+.+...
T Consensus 2 ~irI~L~S~d~~~Ld~~~~~I~~~ak 27 (99)
T TIGR01046 2 KARIKLTSTNVRSLEKVCAQIKRIAE 27 (99)
T ss_pred cEEEEEEECCHHHHHHHHHHHHHHHH
Confidence 47899999999999999999887664
No 68
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=32.85 E-value=1e+02 Score=17.65 Aligned_cols=40 Identities=15% Similarity=0.206 Sum_probs=25.6
Q ss_pred HHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHH
Q 032821 77 PLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESL 120 (133)
Q Consensus 77 ~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l 120 (133)
.+.++..++ +++|-+-.+ + ....+++.| +.+.+++|.+.+
T Consensus 21 ~i~~I~~~t-~~~I~i~~~-~-~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 21 NIKEIEEET-GVKIQIPDD-D-ERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHHH-TSEEEEEST-T-EEEEEEEEE-SHHHHHHHHHHH
T ss_pred cHHHhhhhc-CeEEEEcCC-C-CcEEEEEEe-CHHHHHHHHhhC
Confidence 346666665 677666433 2 445788888 777777776643
No 69
>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=32.12 E-value=1.4e+02 Score=19.22 Aligned_cols=55 Identities=16% Similarity=0.102 Sum_probs=36.4
Q ss_pred hhhhHHHHHHhhhC-CCceEEEccccCCC---cEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 72 LEAAQPLSKLCLEF-PDLHIGCYRKSRQG---PLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 72 s~l~~~L~~l~~~~-~~v~igsyp~~~~~---~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
..|...|..+.... .=.+|-|+|..... .+-|-+++.+...++++.+.+.+.++.
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 56888888876543 34679999964432 244666665445677888888877653
No 70
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=31.73 E-value=1.2e+02 Score=25.09 Aligned_cols=33 Identities=9% Similarity=0.268 Sum_probs=24.7
Q ss_pred ccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 93 YRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 93 yp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
+|+..+..+|+.+++.+++.+++..+.+.+.+.
T Consensus 411 RpSgTEP~lriy~Ea~~~e~~~~l~~~~~~~v~ 443 (445)
T PRK09542 411 RASNTEPLLRLNVEARTEEEVDALVDEVLAIIR 443 (445)
T ss_pred EecCCCcEEEEEEEeCCHHHHHHHHHHHHHHhh
Confidence 343333448999999999998888888887764
No 71
>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=31.70 E-value=1e+02 Score=25.47 Aligned_cols=34 Identities=9% Similarity=0.112 Sum_probs=26.9
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.+|+..+.-++|.+++.+++.+++..+.+.+.+.
T Consensus 409 iRpS~teP~irv~~Ea~~~e~~~~l~~~~~~~v~ 442 (443)
T TIGR01455 409 LRPSGTEPLIRVMVEAADEELVQQLADTLADVVS 442 (443)
T ss_pred EecCCCCceEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 5566545558999999999999988888887763
No 72
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=31.20 E-value=94 Score=20.75 Aligned_cols=26 Identities=4% Similarity=0.106 Sum_probs=22.4
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 100 PLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 100 ~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.++|++.|-|...++++++.+.+...
T Consensus 3 ~irI~L~S~d~~~Ld~~~~~I~~~~k 28 (102)
T PRK12271 3 KARIRLSSTNPEDLDEVCDQIKEIAE 28 (102)
T ss_pred eEEEEEEeCCHHHHHHHHHHHHHHHH
Confidence 47999999999999999999887655
No 73
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=31.16 E-value=93 Score=21.31 Aligned_cols=27 Identities=15% Similarity=0.236 Sum_probs=23.2
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 100 PLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 100 ~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
.++|++.|.|...++++++.+.+...+
T Consensus 18 kirI~L~S~d~~~Ld~~~~~Ii~~ak~ 44 (115)
T PTZ00039 18 KIRITLTSKNLKSIEKVCADIITGAKE 44 (115)
T ss_pred EEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 589999999999999999998876653
No 74
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=30.94 E-value=1.1e+02 Score=20.04 Aligned_cols=47 Identities=30% Similarity=0.290 Sum_probs=30.0
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+-..+.....+. ++ -|+--+.+++.|.+.+.|++++ +++..++|.+-
T Consensus 19 FR~~~~~~A~~l-gl-~G~V~N~~DGsVeiva~G~~~~-v~~~~~~l~~g 65 (92)
T COG1254 19 FRYFTRSEALRL-GL-TGWVKNLDDGSVEIVAEGPDEA-VEKFIEWLRKG 65 (92)
T ss_pred HHHHHHHHHHHC-CC-EEEEEECCCCeEEEEEEcCHHH-HHHHHHHHHhC
Confidence 344445554444 33 2332334467899999999888 88888888854
No 75
>PF00708 Acylphosphatase: Acylphosphatase; InterPro: IPR001792 Acylphosphatase (3.6.1.7 from EC) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates [], its substrates including 1,3-diphosphoglycerate and carbamyl phosphate []. The enzyme has a mainly beta-sheet structure with 2 short alpha-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown []: it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis []. There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. While bacterial and archebacterial hypothetical proteins that are highly similar to that enzyme and that probably possess the same activity. These proteins include: Escherichia coli putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yccX). Bacillus subtilis putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yflL). Archaeoglobus fulgidus putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (O29440 from SWISSPROT). An acylphosphatase-like domain is also found in some prokaryotic hydrogenase maturation HypF carbamoyltransferases [, ].; PDB: 1APS_A 1GXT_A 1GXU_A 2HLT_A 2FHM_A 2HLU_A 3BR8_A 1ULR_A 3TRG_A 2BJD_A ....
Probab=30.24 E-value=1.5e+02 Score=18.78 Aligned_cols=49 Identities=22% Similarity=0.283 Sum_probs=30.1
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
+-..+..+..++ ++ -|+--+...+.|.+.++| +++.+++..+.|.+.-+
T Consensus 19 FR~~v~~~A~~~-gl-~G~V~N~~dg~V~i~~~G-~~~~l~~f~~~l~~g~p 67 (91)
T PF00708_consen 19 FRPFVKRIARKL-GL-TGWVRNLPDGSVEIEAEG-EEEQLEEFIKWLKKGPP 67 (91)
T ss_dssp HHHHHHHHHHHT-T--EEEEEE-TTSEEEEEEEE-EHHHHHHHHHHHHHSST
T ss_pred hhHHHHHHHHHh-CC-ceEEEECCCCEEEEEEEe-CHHHHHHHHHHHHhCCC
Confidence 455555655555 33 344334445679999998 55557888888887544
No 76
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=29.33 E-value=1.2e+02 Score=17.44 Aligned_cols=40 Identities=20% Similarity=0.249 Sum_probs=22.7
Q ss_pred HHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHH
Q 032821 78 LSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESL 120 (133)
Q Consensus 78 L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l 120 (133)
++++.+++ +++|-+.... ...-.+++.|. .+.+++|.+.+
T Consensus 22 i~~i~~~~-g~~I~i~~~~-~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 22 IRKIMEET-GVKIRFPDPG-SKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred HHHHHHHh-CCEEEcCCCC-CCCCEEEEEcC-HHHHHHHHHHh
Confidence 45665555 6666665532 22345677776 44566666554
No 77
>cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits.
Probab=29.08 E-value=1.9e+02 Score=19.79 Aligned_cols=59 Identities=10% Similarity=0.173 Sum_probs=38.7
Q ss_pred cCChhhhhHHHHHHhhhCCCceEEEccccCC---C--cEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 68 NLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ---G--PLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 68 g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~---~--~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
++.|..+.+..+++.++++-..+..+=+.+. + .+-+.+.+....++=+|++.+.++++.
T Consensus 44 ~ma~~~l~~I~~e~~~k~~~~~v~v~HR~G~l~vGe~~v~i~v~a~hR~~af~A~~~~id~lK~ 107 (124)
T cd00756 44 PMAEKELEEIAEEARERWGLLRVAIIHRVGRLPPGEAIVLVAVSSPHRKEAFEACEFLIDRLKH 107 (124)
T ss_pred hHHHHHHHHHHHHHHHhCCCceEEEEEEEcccCCCCEEEEEEEecCCHHHHHHHHHHHHHHHHh
Confidence 5677888888888888887555554443332 2 256777777777666777777776654
No 78
>PRK14314 glmM phosphoglucosamine mutase; Provisional
Probab=28.77 E-value=96 Score=25.76 Aligned_cols=34 Identities=9% Similarity=0.172 Sum_probs=25.9
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.+|+..+.-+||.+++.|++.+++..+.+.+.+.
T Consensus 413 iRpS~tEP~iri~~Ea~~~~~a~~l~~~~~~~v~ 446 (450)
T PRK14314 413 LRYSGTENLCRVMVEGEDKHQVDSLAKEIADVVE 446 (450)
T ss_pred EecCCCCcEEEEEEeeCCHHHHHHHHHHHHHHHH
Confidence 4565445558999999999988887777776664
No 79
>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=28.31 E-value=1.4e+02 Score=17.80 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=30.5
Q ss_pred hhhhHHHHHHhhhC-CCceEEEccccCCCcEEEEEE--ec-C-HHHHHHHHHHHHHHh
Q 032821 72 LEAAQPLSKLCLEF-PDLHIGCYRKSRQGPLIISFE--GK-D-QARIEAAIESLFKKF 124 (133)
Q Consensus 72 s~l~~~L~~l~~~~-~~v~igsyp~~~~~~v~l~~~--~~-~-~~~~~~~~~~l~~~l 124 (133)
..++..|+...... |++.|...+. ...+.++++ |. + .+.+.+|.+.+.+++
T Consensus 10 ~tl~N~LRr~ll~~vp~~ai~~~~~--~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~ 65 (66)
T PF01193_consen 10 HTLGNALRRILLSEVPGVAIDGHPN--EDKFVFRIETDGSLTPKEALLKAIKILKEKL 65 (66)
T ss_dssp HHHHHHHHHHHHSSSEEEEEEESSE--EEEEEEEEEEBSSS-HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHhcCCCceEEecCC--CCEEEEEEEECCCCCHHHHHHHHHHHHHHhc
Confidence 34667777765444 7777777553 334444444 43 3 345678888887765
No 80
>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=28.20 E-value=1.3e+02 Score=24.84 Aligned_cols=31 Identities=29% Similarity=0.249 Sum_probs=22.6
Q ss_pred ccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 93 YRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 93 yp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+|+..+.-+||.+++.+++.+++..+.+.++
T Consensus 410 RpS~TeP~iri~~Ea~~~~~~~~l~~~~~~~ 440 (441)
T cd05805 410 LPDADEPLCHIYAEGSDQERAEELTEFYVEK 440 (441)
T ss_pred ecCCCCCEEEEEEecCCHHHHHHHHHHHHhh
Confidence 3443333489999999999888888777654
No 81
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=27.75 E-value=1.7e+02 Score=20.04 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=31.6
Q ss_pred ecCChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecC-HHHHHHHHHHHHHHh
Q 032821 67 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKD-QARIEAAIESLFKKF 124 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~-~~~~~~~~~~l~~~l 124 (133)
+.=+|..+- -.|+..+..+|++|+.=++ .+.+.++.+-.+ +..++++.+.+.+.|
T Consensus 46 iTP~E~aII--AaDIA~Kaa~V~igF~DRF-sGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 46 LTPGETAMI--AGDLALKAADVHIGFLDRF-SGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eCcchHHHH--HHHhhhhccCcEEeeeecc-ceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 344565543 3677777779999998765 445656553222 223444444454444
No 82
>PRK14424 acylphosphatase; Provisional
Probab=27.51 E-value=1.5e+02 Score=19.38 Aligned_cols=46 Identities=13% Similarity=0.171 Sum_probs=31.6
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
+-.....+..+. +++ |+--+...+.|.|.+.|++++ +++..+.|++
T Consensus 22 FR~~v~~~A~~~-gl~-G~V~N~~dG~Vei~~qG~~~~-v~~f~~~l~~ 67 (94)
T PRK14424 22 FRHATVREAHAL-GLR-GWVANLEDGTVEAMIQGPAAQ-IDRMLAWLRH 67 (94)
T ss_pred hHHHHHHHHHHc-CCe-EEEEECCCCCEEEEEEECHHH-HHHHHHHHHh
Confidence 555566665555 443 665555567899999997655 7888888874
No 83
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=27.43 E-value=1.3e+02 Score=17.24 Aligned_cols=36 Identities=17% Similarity=0.129 Sum_probs=24.5
Q ss_pred eEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCC
Q 032821 89 HIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRG 127 (133)
Q Consensus 89 ~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~ 127 (133)
++-.+| .++|+..++|-.-..-.++.+.|.+.|+.-
T Consensus 2 ~~~I~~---dG~V~~~v~G~~G~~C~~~t~~lE~~LG~v 37 (48)
T PF11211_consen 2 EFTIYP---DGRVEEEVEGFKGSSCLEATAALEEALGTV 37 (48)
T ss_pred EEEECC---CcEEEEEEEeccChhHHHHHHHHHHHhCce
Confidence 445566 678888888765555567777777777743
No 84
>PRK14321 glmM phosphoglucosamine mutase; Provisional
Probab=27.21 E-value=1.5e+02 Score=24.71 Aligned_cols=27 Identities=19% Similarity=0.215 Sum_probs=21.5
Q ss_pred CcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 99 GPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 99 ~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.-+||.+++.+++.+++..+.+.+.+.
T Consensus 417 P~~riy~Ea~s~e~~~~l~~~~~~~i~ 443 (449)
T PRK14321 417 PIMRITLEAHTEEKAEELMEKAEKLVK 443 (449)
T ss_pred ceEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 348999999999988887777777654
No 85
>PF12693 GspL_C: GspL periplasmic domain; PDB: 2W7V_A.
Probab=26.79 E-value=2.2e+02 Score=19.68 Aligned_cols=56 Identities=16% Similarity=0.189 Sum_probs=36.2
Q ss_pred cCChhhhhHHHHHH---hhhCCCceEEEccccCC-CcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 68 NLSDLEAAQPLSKL---CLEFPDLHIGCYRKSRQ-GPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 68 g~~Es~l~~~L~~l---~~~~~~v~igsyp~~~~-~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+-+...+.+.|..+ ....+++++-+.-.... +.+++.+.+.+.+.++++.+.+.+.
T Consensus 74 ~~~~~~~~~ll~~l~~~~~~~~~~~l~~l~y~~~~~~L~l~~~a~~~~~le~l~~~l~~~ 133 (157)
T PF12693_consen 74 GGAGAGFLPLLAALAPALQQVPGIQLQSLRYDAGRGELRLQLEAPSFQALEQLRAALAAQ 133 (157)
T ss_dssp ----HHHHHHGGGHHHHHHTSTT-EEEEEEEETTTTEEEEEEEESSSHHHHHHHHHHHTT
T ss_pred CCCCccHHHHHHHHHHHhccCCCCceEEEEEcCCCcEEEEEeccCCHHHHHHHHHHHHhh
Confidence 33556666666554 33456888888775433 4699999999998888887777765
No 86
>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=26.72 E-value=1.6e+02 Score=17.98 Aligned_cols=17 Identities=18% Similarity=0.391 Sum_probs=9.8
Q ss_pred HHHhhhCCCceEEEccc
Q 032821 79 SKLCLEFPDLHIGCYRK 95 (133)
Q Consensus 79 ~~l~~~~~~v~igsyp~ 95 (133)
+.+...||+..+-..+.
T Consensus 15 kRl~~~yPd~~v~Vr~~ 31 (65)
T PF06183_consen 15 KRLHRQYPDAEVRVRPG 31 (65)
T ss_dssp HHHHHH-SS-EEEEEEE
T ss_pred HHHHHHCCCceEeeeec
Confidence 45667789877766653
No 87
>COG1839 Uncharacterized conserved protein [Function unknown]
Probab=26.58 E-value=2.5e+02 Score=20.27 Aligned_cols=50 Identities=26% Similarity=0.432 Sum_probs=32.8
Q ss_pred HhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCCee
Q 032821 81 LCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFS 130 (133)
Q Consensus 81 l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~~~ 130 (133)
+....|++++|.--.-..+.--++-+|.|++..+.|.+-.++.-..+.|.
T Consensus 36 lvt~vP~~kfgiAf~EAsg~rLvR~~GND~eL~~lA~ena~~I~AGHvFV 85 (162)
T COG1839 36 LVTAVPGLKFGIAFNEASGPRLVRYTGNDEELVKLAIENALKIGAGHVFV 85 (162)
T ss_pred HHhcCCCceEEEEeecccCCeeEEecCCcHHHHHHHHHHHHHhcCCcEEE
Confidence 34445888888766433444446677888887777777776655556654
No 88
>PRK09662 GspL-like protein; Provisional
Probab=26.49 E-value=2.6e+02 Score=22.18 Aligned_cols=54 Identities=13% Similarity=0.243 Sum_probs=38.0
Q ss_pred hhhhhHHHHHHhhhC-----CCceEEEccccCC-CcEEEEEEecCHHHHHHHHHHHHHHh
Q 032821 71 DLEAAQPLSKLCLEF-----PDLHIGCYRKSRQ-GPLIISFEGKDQARIEAAIESLFKKF 124 (133)
Q Consensus 71 Es~l~~~L~~l~~~~-----~~v~igsyp~~~~-~~v~l~~~~~~~~~~~~~~~~l~~~l 124 (133)
.+.+-..|.++...+ |++++-+.-.+.. +++++.++++|-+.+|++.+.+.+.|
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 345666665543222 5788888775443 57999999999988888888887754
No 89
>PRK14449 acylphosphatase; Provisional
Probab=26.28 E-value=1.7e+02 Score=18.73 Aligned_cols=47 Identities=13% Similarity=0.212 Sum_probs=30.4
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+-..+..+..++ +++ |+--+..++.|.+.++|++ +.+++..+.|.+.
T Consensus 18 FR~fv~~~A~~l-gl~-G~V~N~~dG~Vei~~~G~~-~~v~~f~~~l~~~ 64 (90)
T PRK14449 18 LRYSVYQKAVSL-GIT-GYAENLYDGSVEVVAEGDE-ENIKELINFIKTG 64 (90)
T ss_pred hHHHHHHHHHHc-CCE-EEEEECCCCeEEEEEEeCH-HHHHHHHHHHhhC
Confidence 455555665555 443 5544555667999999855 4477888888764
No 90
>PRK14315 glmM phosphoglucosamine mutase; Provisional
Probab=26.11 E-value=1.3e+02 Score=25.05 Aligned_cols=35 Identities=14% Similarity=0.216 Sum_probs=27.2
Q ss_pred EEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 91 GCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 91 gsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
=.+|+..+.-+||.++++|++.+++..+.+.+.+.
T Consensus 410 LiRpS~teP~iri~~Ea~s~~~~~~l~~~~~~~i~ 444 (448)
T PRK14315 410 LIRPSGTEPLIRVMAEGDDRALVEEVVDEIVDAVS 444 (448)
T ss_pred EEecCCCCcEEEEEEeeCCHHHHHHHHHHHHHHHH
Confidence 35666555558999999999998888888877765
No 91
>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=25.80 E-value=1.7e+02 Score=18.08 Aligned_cols=40 Identities=23% Similarity=0.376 Sum_probs=28.6
Q ss_pred CCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 86 PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 86 ~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
-+|++-.+-....+...+.+.| |.+.++.+.+..++....
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 3888888776556778888888 666677777776666543
No 92
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=25.62 E-value=2.4e+02 Score=20.94 Aligned_cols=48 Identities=23% Similarity=0.346 Sum_probs=28.6
Q ss_pred hhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHH
Q 032821 72 LEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
-++.+.|+.+++......+ |.+...+.++|.+.|.+. .++++...+++
T Consensus 9 ~E~~~fle~l~~~~~~~~~--~v~~k~n~l~I~i~G~~~-eike~~~~Ik~ 56 (190)
T PF09840_consen 9 EECEEFLERLSKMVKSIYI--YVEVKGNSLKIEIQGYEK-EIKEAIRRIKE 56 (190)
T ss_pred HHHHHHHHHHHhhccCcEE--EEEEeCCEEEEEEecChH-HHHHHHHHHHH
Confidence 4557777777665433333 333345789999999876 44444444443
No 93
>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=25.56 E-value=2.7e+02 Score=20.25 Aligned_cols=27 Identities=26% Similarity=0.069 Sum_probs=23.5
Q ss_pred ecCChhhhhHHHHHHhhhCCCceEEEc
Q 032821 67 TNLSDLEAAQPLSKLCLEFPDLHIGCY 93 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~~~~v~igsy 93 (133)
+|-.+..+++..+.+.++||++.|.-+
T Consensus 54 lG~~~~v~~~~~~~l~~~yP~l~i~g~ 80 (177)
T TIGR00696 54 YGGKPDVLQQLKVKLIKEYPKLKIVGA 80 (177)
T ss_pred ECCCHHHHHHHHHHHHHHCCCCEEEEE
Confidence 699988989988999999999987765
No 94
>cd05311 NAD_bind_2_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydroph
Probab=25.09 E-value=49 Score=24.99 Aligned_cols=9 Identities=22% Similarity=0.305 Sum_probs=8.1
Q ss_pred ceEEEeeCC
Q 032821 25 QNVIILTAT 33 (133)
Q Consensus 25 ~~v~~LPGv 33 (133)
+|.|++||+
T Consensus 159 nn~~~fPg~ 167 (226)
T cd05311 159 NNVLGFPGI 167 (226)
T ss_pred ceeeecchh
Confidence 589999998
No 95
>PRK14420 acylphosphatase; Provisional
Probab=24.71 E-value=2e+02 Score=18.38 Aligned_cols=47 Identities=15% Similarity=0.173 Sum_probs=28.2
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+-..+..+..++ ++ -|+--+...+.|.+.++|++ +.+++..++|++.
T Consensus 17 FR~~~~~~A~~~-gl-~G~V~N~~dG~Vei~~qG~~-~~i~~f~~~l~~~ 63 (91)
T PRK14420 17 FRYFVQMEADKR-KL-TGWVKNRDDGTVEIEAEGPE-EALQLFLDAIEKG 63 (91)
T ss_pred ChHHHHHHHHHc-CC-EEEEEECCCCcEEEEEEECH-HHHHHHHHHHHhC
Confidence 334444544444 33 24444444567889998864 5577888887765
No 96
>PLN02390 molybdopterin synthase catalytic subunit
Probab=24.65 E-value=2.3e+02 Score=19.15 Aligned_cols=59 Identities=10% Similarity=0.088 Sum_probs=38.5
Q ss_pred cCChhhhhHHHHHHhhhCCCceEEEccccCC---C--cEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 68 NLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ---G--PLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 68 g~~Es~l~~~L~~l~~~~~~v~igsyp~~~~---~--~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
++.|..+.+..+++.++|+...+..+=+.+. + .+-+.+.+......=+|++.+.+.++.
T Consensus 33 ~ma~~~l~~I~~e~~~~~~~~~v~i~HR~G~l~vge~~v~v~v~s~HR~~Af~A~~~~id~lK~ 96 (111)
T PLN02390 33 PMALRELRKICDEARSRWSLHKIAVAHRLGPVPVGETSVFVAVSSVHRADALDACKFLIDELKA 96 (111)
T ss_pred HHHHHHHHHHHHHHHHhCCCceEEEEEeeecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhh
Confidence 6778888888888888886544444433222 2 356777777776656677777776664
No 97
>PRK14448 acylphosphatase; Provisional
Probab=24.20 E-value=1.8e+02 Score=18.66 Aligned_cols=46 Identities=15% Similarity=0.125 Sum_probs=28.9
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
+-..+..+..++ +++ |+--+..++.|.+.++|++++ +++..+.|.+
T Consensus 17 FR~~v~~~A~~l-gl~-G~V~N~~dG~Vei~~~G~~~~-v~~f~~~l~~ 62 (90)
T PRK14448 17 FRYFTWQEATKI-GIK-GYVKNRPDGSVEVVAVGSDAQ-IAAFRDWLQH 62 (90)
T ss_pred hHHHHHHHHHHh-CCE-EEEEECCCCCEEEEEEeCHHH-HHHHHHHHHh
Confidence 344455555444 332 554445567799999996644 7888888864
No 98
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=24.08 E-value=86 Score=19.04 Aligned_cols=49 Identities=29% Similarity=0.447 Sum_probs=25.5
Q ss_pred hhhHHHHHHhhhCCCceEEEcc----ccCC---CcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 73 EAAQPLSKLCLEFPDLHIGCYR----KSRQ---GPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 73 ~l~~~L~~l~~~~~~v~igsyp----~~~~---~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
.-.+.|+++..++ ++.+..+- +... +.+.+.+.|+++ .++++.+.|++.
T Consensus 14 ~~~piis~l~~~~-~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~-~~~~a~~~L~~~ 69 (76)
T PF09383_consen 14 AQEPIISQLIREF-GVDVNILHGNIEEIQGTPFGILILELPGDDE-EIEKAIAYLREQ 69 (76)
T ss_dssp SSSCHHHHHHHHH-T-EEEEEEEEEEEETTEEEEEEEEEEES-HH-HHHHHHHHHHHT
T ss_pred cCchHHHHHHHHh-CCCEEEEEEEeEEcCCeeEEEEEEEEECCHH-HHHHHHHHHHHC
Confidence 3355566666666 44443332 1111 335666665444 467888888763
No 99
>PRK14429 acylphosphatase; Provisional
Probab=24.03 E-value=1.7e+02 Score=18.66 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=29.3
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+-..+..+..++ ++ -|+--+...++|.+.++|+++ .+++..++|.+.
T Consensus 17 FR~~v~~~A~~~-gl-~G~V~N~~dG~Vei~~qG~~~-~i~~f~~~l~~g 63 (90)
T PRK14429 17 CRRATLTKARAL-GV-TGYVTNCEDGSVEILAQGSDP-AVDNLIAWCEVG 63 (90)
T ss_pred eHHHHHHHHHHh-CC-EEEEEECCCCeEEEEEEeCHH-HHHHHHHHHhhC
Confidence 344455555544 33 354445556779999998554 478888888764
No 100
>PRK10678 moaE molybdopterin guanine dinucleotide biosynthesis protein MoaE; Provisional
Probab=23.76 E-value=2.8e+02 Score=19.83 Aligned_cols=59 Identities=5% Similarity=0.081 Sum_probs=38.2
Q ss_pred cCChhhhhHHHHHHhhhCCCceEEEccccC-----CCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 68 NLSDLEAAQPLSKLCLEFPDLHIGCYRKSR-----QGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 68 g~~Es~l~~~L~~l~~~~~~v~igsyp~~~-----~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
++.|..+.+..+++..+|+...+..+=+.+ +..+-+.+.+......=+|++.+.+.++.
T Consensus 57 ~ma~k~l~~I~~ea~~~~~~~~v~i~HR~G~l~~Ge~~v~Vav~s~HR~~Af~A~~~~id~lK~ 120 (150)
T PRK10678 57 GMTEKALAEIVDEARSRWPLGRVTVIHRVGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKT 120 (150)
T ss_pred cHHHHHHHHHHHHHHHhCCCCcEEEEEeEecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhh
Confidence 777888888888888888754443333222 22356667777776655676777776664
No 101
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=23.67 E-value=1.3e+02 Score=20.01 Aligned_cols=49 Identities=20% Similarity=0.165 Sum_probs=30.2
Q ss_pred ChhhhhHHHHHHhhhCCCceEEEccccCCCcE-EEEEEecCHHHHHHHHHHHHHH
Q 032821 70 SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL-IISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 70 ~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v-~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+..+++..++.+.+.. .- .+-...++ + -=|+++.|++.++++.++|+++
T Consensus 45 sr~Dv~~Fi~~l~~~~-~~---~Ls~LT~G-vH~HtI~a~~~e~l~~I~~~L~~~ 94 (98)
T PF02829_consen 45 SRRDVDKFIEKLEKSK-AK---PLSSLTGG-VHYHTIEAPDEEDLDKIEEALKKK 94 (98)
T ss_dssp SHHHHHHHHHHHHH---S-----STTGGGG-EEEEEEEESSHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHhccC-Cc---chHHhcCC-EeeEEEEECCHHHHHHHHHHHHHC
Confidence 5567888888886542 11 11111122 3 3567788999999999888874
No 102
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=23.63 E-value=2.2e+02 Score=20.12 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=16.4
Q ss_pred ecCChhhhhHHHHHHhhh
Q 032821 67 TNLSDLEAAQPLSKLCLE 84 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~ 84 (133)
+|++++.+..+++.|.+.
T Consensus 38 lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 38 VGLSPTPCLERVRRLERQ 55 (164)
T ss_pred HCcCHHHHHHHHHHHHHC
Confidence 699999999999999765
No 103
>cd05800 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model.
Probab=23.54 E-value=1.8e+02 Score=24.17 Aligned_cols=25 Identities=24% Similarity=0.161 Sum_probs=19.6
Q ss_pred CcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 99 GPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 99 ~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
..+|+.+++++++.+++..+.+.+.
T Consensus 436 p~iriy~Ea~~~~~a~~l~~~~~~~ 460 (461)
T cd05800 436 PLLRIYAEAPSPEKVEALLDAGKKL 460 (461)
T ss_pred ceEEEEEecCCHHHHHHHHHHHHhh
Confidence 3489999999998888877776653
No 104
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=23.38 E-value=1.7e+02 Score=18.17 Aligned_cols=14 Identities=29% Similarity=0.451 Sum_probs=11.0
Q ss_pred cEEEEEEecCHHHH
Q 032821 100 PLIISFEGKDQARI 113 (133)
Q Consensus 100 ~v~l~~~~~~~~~~ 113 (133)
.++|.++|+|++++
T Consensus 60 ~i~i~~~G~de~~a 73 (84)
T PF00381_consen 60 EIEIEAEGEDEEEA 73 (84)
T ss_dssp EEEEEEESTTHHHH
T ss_pred EEEEEEECcCHHHH
Confidence 47899999998643
No 105
>PRK14435 acylphosphatase; Provisional
Probab=23.04 E-value=2e+02 Score=18.41 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=29.6
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
+-..+..+..++ +++ |+--+...+.|.+.+.|++ +.+++..+.|.+
T Consensus 17 FR~~v~~~A~~~-gl~-G~V~N~~dG~Vei~~~G~~-~~i~~f~~~l~~ 62 (90)
T PRK14435 17 FRYFTRRVAKSL-GVK-GYVMNMDDGSVFIHAEGDE-NALRRFLNEVAK 62 (90)
T ss_pred ChHHHHHHHHHh-CCE-EEEEECCCCCEEEEEEECH-HHHHHHHHHHhh
Confidence 444455555554 443 5555555678999999955 447888888874
No 106
>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=22.86 E-value=1.8e+02 Score=17.30 Aligned_cols=53 Identities=19% Similarity=0.192 Sum_probs=33.6
Q ss_pred hhhhHHHHHHhhhC-CCceEEEccccC-CCc--EEEEEEec-CHHHHHHHHHHHHHHh
Q 032821 72 LEAAQPLSKLCLEF-PDLHIGCYRKSR-QGP--LIISFEGK-DQARIEAAIESLFKKF 124 (133)
Q Consensus 72 s~l~~~L~~l~~~~-~~v~igsyp~~~-~~~--v~l~~~~~-~~~~~~~~~~~l~~~l 124 (133)
..|++.|+.+.... .=.+|-|+|... ... +.+.+++. +...++++.+.+.+..
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 45788888876543 346688888644 233 45666665 4566677777776643
No 107
>PF04008 Adenosine_kin: Adenosine specific kinase; InterPro: IPR007153 The structure of a member of this family from the hyperthermophilic archaeon Pyrobaculum aerophilum contains a modified histidine residue which is interpreted as stable phosphorylation. In vitro binding studies confirmed that adenosine and AMP but not ADP or ATP bind to the protein [].; PDB: 1VGG_A 1RLH_A 1WVQ_A 2GL0_F 2JB7_B 2EKM_C 2D16_D.
Probab=22.85 E-value=3e+02 Score=19.88 Aligned_cols=49 Identities=22% Similarity=0.401 Sum_probs=31.1
Q ss_pred HhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCCe
Q 032821 81 LCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAF 129 (133)
Q Consensus 81 l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~~ 129 (133)
+....|++++|.--.-..+.--++.+|.|++..+.|.+-..+.--.+.|
T Consensus 29 lv~svp~ikFGiAFcEASG~~LvR~~GnD~eL~~~A~~na~~IgAGH~F 77 (155)
T PF04008_consen 29 LVTSVPGIKFGIAFCEASGPRLVRYSGNDEELIELAVKNALAIGAGHSF 77 (155)
T ss_dssp HHCCSTTSEEEEEEEETSTTTEEEEEESSHHHHHHHHHHHHHH--TTEE
T ss_pred HhhcCCCCeEEEEEeccCCceEEEecCCcHHHHHHHHHHHHHhcCCcEE
Confidence 3444588998876643445656888999998877666655554334444
No 108
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=22.63 E-value=2e+02 Score=17.81 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=36.6
Q ss_pred ChhhhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcCCC
Q 032821 70 SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGA 128 (133)
Q Consensus 70 ~Es~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~~~ 128 (133)
|+...+..|-++..++ ++++=+-.. .-+.+.+.+.+.. ..++++.++|++++++..
T Consensus 13 G~~g~d~~i~~~l~~~-~v~ii~K~~-nANtit~yl~~~~-k~~~r~~~~Le~~~p~a~ 68 (71)
T cd04910 13 GEVGYDLEILELLQRF-KVSIIAKDT-NANTITHYLAGSL-KTIKRLTEDLENRFPNAE 68 (71)
T ss_pred CChhHHHHHHHHHHHc-CCeEEEEec-CCCeEEEEEEcCH-HHHHHHHHHHHHhCccCc
Confidence 6666777777777666 666555432 2345666666543 356788888888887654
No 109
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.35 E-value=1.8e+02 Score=17.13 Aligned_cols=51 Identities=14% Similarity=-0.003 Sum_probs=24.1
Q ss_pred hhhhHHHHHHhhhCCCc-eEEEcccc---CCCcEEEEEEecCHHHHHHHHHHHHH
Q 032821 72 LEAAQPLSKLCLEFPDL-HIGCYRKS---RQGPLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 72 s~l~~~L~~l~~~~~~v-~igsyp~~---~~~~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
..|++.++-+.+..-++ ++..++.. +...+.+++..++.+.+++..+.|.+
T Consensus 11 G~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~e~~~~~~~i~~~L~~ 65 (72)
T cd04884 11 GTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTPMDRSKENELIEELKA 65 (72)
T ss_pred ccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEEecchHHHHHHHHHhC
Confidence 45666666554432233 44545531 12235555555544444455555544
No 110
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=22.17 E-value=3.4e+02 Score=25.41 Aligned_cols=54 Identities=7% Similarity=0.174 Sum_probs=34.6
Q ss_pred hhhHHHHHHhhhCCCceEEEcccc--------CCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 73 EAAQPLSKLCLEFPDLHIGCYRKS--------RQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 73 ~l~~~L~~l~~~~~~v~igsyp~~--------~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
++.+.+++-..+.|++++...|-. ....+.+++.|.|.+.++++.+++++.+..
T Consensus 639 ~v~~~lr~~l~~~p~~~~~~~~~~~~~~~~~~~~~~v~i~l~G~d~~~L~~~a~~l~~~l~~ 700 (1040)
T PRK10503 639 KVIARLQTAVAKVPGVDLYLQPTQDLTIDTQVSRTQYQFTLQATSLDALSTWVPKLMEKLQQ 700 (1040)
T ss_pred HHHHHHHHHHhcCCCcEEeccCCccccccCCCCCCCeEEEEECCCHHHHHHHHHHHHHHHhc
Confidence 445555544444677764332210 112588899999999998888888887764
No 111
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=22.08 E-value=45 Score=21.17 Aligned_cols=22 Identities=9% Similarity=0.135 Sum_probs=18.0
Q ss_pred eeeCCCCcccEEEeceEEEeeCC
Q 032821 11 LLHHDKLLLPLIKCQNVIILTAT 33 (133)
Q Consensus 11 ~l~N~~gtAPg~~i~~v~~LPGv 33 (133)
-|.|+ ||.||.....+.+=+|-
T Consensus 16 ~irND-Gt~Pg~~~g~lLv~~G~ 37 (75)
T PF04319_consen 16 DIRND-GTFPGKEIGELLVRKGD 37 (75)
T ss_pred EeEcC-CCCCCCCCCCEEEcCCC
Confidence 56787 99999887778888886
No 112
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.02 E-value=2.2e+02 Score=21.96 Aligned_cols=26 Identities=19% Similarity=0.360 Sum_probs=19.2
Q ss_pred CCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 98 QGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 98 ~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
....+++++|.|.+ .+.+.|.+.++.
T Consensus 41 ~~w~~itleGed~e---~sanli~eefge 66 (247)
T COG4044 41 KQWAKITLEGEDEE---VSANLIVEEFGE 66 (247)
T ss_pred ccceEEEEECccHH---HHHHHHHHHhCC
Confidence 44689999999885 566677777763
No 113
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=21.69 E-value=3.5e+02 Score=24.92 Aligned_cols=32 Identities=22% Similarity=0.281 Sum_probs=26.0
Q ss_pred CCeEEEEEEe-cCChhhhhHHHHHHhhhCCCce
Q 032821 58 EPYTSKSLTT-NLSDLEAAQPLSKLCLEFPDLH 89 (133)
Q Consensus 58 ~~~~~~~l~~-g~~Es~l~~~L~~l~~~~~~v~ 89 (133)
-.++++||++ +++-+.-++.|+.+.++|.+|+
T Consensus 417 isV~SrTLwvG~i~k~v~e~dL~~~feefGeiq 449 (894)
T KOG0132|consen 417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQ 449 (894)
T ss_pred eeEeeeeeeeccccchhhHHHHHHHHHhcccce
Confidence 4578999997 8998888888999888886543
No 114
>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=21.23 E-value=3.1e+02 Score=19.49 Aligned_cols=27 Identities=19% Similarity=0.246 Sum_probs=23.5
Q ss_pred ecCChhhhhHHHHHHhhhCCCceEEEc
Q 032821 67 TNLSDLEAAQPLSKLCLEFPDLHIGCY 93 (133)
Q Consensus 67 ~g~~Es~l~~~L~~l~~~~~~v~igsy 93 (133)
+|-.|..+++..+.+.+++|++.|..+
T Consensus 52 lG~~~~~~~~~~~~l~~~yp~l~i~g~ 78 (171)
T cd06533 52 LGAKPEVLEKAAERLRARYPGLKIVGY 78 (171)
T ss_pred ECCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence 699999999988899999999997764
No 115
>PRK14426 acylphosphatase; Provisional
Probab=21.23 E-value=2.4e+02 Score=18.12 Aligned_cols=50 Identities=18% Similarity=0.216 Sum_probs=30.6
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
+-..+..+..++ +++ |+--+...+.|.+.++|+++ .+++..+.|.+-.+.
T Consensus 19 FR~~v~~~A~~~-gl~-G~V~N~~dG~Vei~~~G~~~-~i~~f~~~l~~g~P~ 68 (92)
T PRK14426 19 FRYHTQHEALKL-GLT-GYAKNLDDGSVEVVACGEEE-QVEKLMEWLKEGGPR 68 (92)
T ss_pred chHHHHHHHHHh-CCE-EEEEECCCCcEEEEEEeCHH-HHHHHHHHHhcCCCC
Confidence 455555655554 342 54444456678999988544 477888888764343
No 116
>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=21.14 E-value=2.2e+02 Score=17.77 Aligned_cols=46 Identities=11% Similarity=0.283 Sum_probs=30.9
Q ss_pred hhhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHH
Q 032821 73 EAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLF 121 (133)
Q Consensus 73 ~l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~ 121 (133)
.+++..+.+ ...|+++|-..- ..+++.+++++++...+.+....|.
T Consensus 16 ~~~~v~~~l-~~~~gvEVh~~~--~~GKiVVtiE~~~~~~~~~~~~~i~ 61 (79)
T PF03927_consen 16 RLEEVAEAL-AAIPGVEVHAVD--EDGKIVVTIEAESSEEEVDLIDAIN 61 (79)
T ss_dssp CHHHHHHHH-CCSTTEEEEEEE--TTTEEEEEEEESSHHHHHHHHHHHC
T ss_pred hHHHHHHHH-HcCCCcEEEeeC--CCCeEEEEEEeCChHHHHHHHHHHH
Confidence 445545554 346888885443 2488999999999877666666554
No 117
>KOG3964 consensus Phosphatidylglycerolphosphate synthase [Lipid transport and metabolism]
Probab=21.06 E-value=3.1e+02 Score=23.22 Aligned_cols=71 Identities=18% Similarity=0.188 Sum_probs=51.5
Q ss_pred CCcccEEEec--eEEEeeCCCCCch-HHHHHHHHHHHhhCCCCCCCCeEEEEEEecCChhhhhHHHHHHhhhCCCceEEE
Q 032821 16 KLLLPLIKCQ--NVIILTATNVTEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (133)
Q Consensus 16 ~gtAPg~~i~--~v~~LPGv~~P~m-~~m~~~v~p~l~~~~~~~~~~~~~~~l~~g~~Es~l~~~L~~l~~~~~~v~igs 92 (133)
.|.+|.|.++ .+=+.--| |++ +. ++..++.. +..++-.+++.|--|-++.+-|+...++.|.+++.+
T Consensus 18 ~nl~pcf~~~~d~idiihep--~~fy~~----lk~~I~~a----q~Ri~lasLYlG~~E~elv~cl~~aL~~~~~L~v~i 87 (469)
T KOG3964|consen 18 DNLCPCFYVNGDDIDIIHEP--PEFYQR----LKKLIKKA----QRRIFLASLYLGKLERELVDCLSNALEKNPSLKVSI 87 (469)
T ss_pred hCcCcceeeccccceeecCC--HHHHHH----HHHHHHHh----hheeeeeeeccchhHHHHHHHHHHHhccCCCcEEEe
Confidence 4778999886 46666777 764 44 33333321 256777888889999999999999877788888888
Q ss_pred cccc
Q 032821 93 YRKS 96 (133)
Q Consensus 93 yp~~ 96 (133)
+..+
T Consensus 88 LlD~ 91 (469)
T KOG3964|consen 88 LLDF 91 (469)
T ss_pred ehhh
Confidence 8754
No 118
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=20.69 E-value=3.9e+02 Score=24.91 Aligned_cols=27 Identities=11% Similarity=0.049 Sum_probs=23.6
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHhcC
Q 032821 100 PLIISFEGKDQARIEAAIESLFKKFHR 126 (133)
Q Consensus 100 ~v~l~~~~~~~~~~~~~~~~l~~~l~~ 126 (133)
.+.+.+.|+|.+.++++.+++++++.+
T Consensus 660 ~i~i~l~G~d~~~L~~~a~~i~~~L~~ 686 (1025)
T PRK10614 660 SYQYTLLSDDLAALREWEPKIRKALAA 686 (1025)
T ss_pred CEEEEEECCCHHHHHHHHHHHHHHHhc
Confidence 488899999999999999999988864
No 119
>PRK00596 rpsJ 30S ribosomal protein S10; Reviewed
Probab=20.63 E-value=2e+02 Score=19.04 Aligned_cols=26 Identities=8% Similarity=0.213 Sum_probs=21.6
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 100 PLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 100 ~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
.++|+++|-|...++.+++.+.+...
T Consensus 5 ~irI~l~S~d~~~L~~~~~~i~~~a~ 30 (102)
T PRK00596 5 KIRIRLKAFDHRLLDQSAKKIVETAK 30 (102)
T ss_pred EEEEEEEECCHHHHHHHHHHHHHHHH
Confidence 58999999999999988888877544
No 120
>PRK14440 acylphosphatase; Provisional
Probab=20.58 E-value=2.2e+02 Score=18.28 Aligned_cols=46 Identities=11% Similarity=0.214 Sum_probs=29.3
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 122 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~ 122 (133)
+-..+.....+. ++ -|+--+...+.|.+.+.|++ +.+++..++|++
T Consensus 18 FR~~v~~~A~~~-gl-~G~V~N~~dG~Vei~~~G~~-~~v~~f~~~l~~ 63 (90)
T PRK14440 18 FRKFVQIHAIRL-GI-KGYAKNLPDGSVEVVAEGYE-EALSKLLERIKQ 63 (90)
T ss_pred chHHHHHHHHHc-CC-EEEEEECCCCCEEEEEEcCH-HHHHHHHHHHhh
Confidence 444555555544 34 35444444667999999855 557888888874
No 121
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific. This enzyme interconverts alpha-D-glucose-1-P and alpha-D-glucose-6-P.
Probab=20.54 E-value=2.3e+02 Score=24.27 Aligned_cols=33 Identities=9% Similarity=0.063 Sum_probs=24.4
Q ss_pred ccccCCCcEEEEEEe-cCHHHHHHHHHHHHHHhc
Q 032821 93 YRKSRQGPLIISFEG-KDQARIEAAIESLFKKFH 125 (133)
Q Consensus 93 yp~~~~~~v~l~~~~-~~~~~~~~~~~~l~~~l~ 125 (133)
+|+..+..+|+.+++ ++++.+++..+++.+.+.
T Consensus 506 RpSgTEP~irvy~Ea~~~~~~~~~l~~~~~~~v~ 539 (543)
T TIGR01132 506 RPSGTEDVYKIYCESFKGEEHLKQIEKEAVEIVS 539 (543)
T ss_pred ecCCCCceEEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 344334458999999 588888888888877765
No 122
>cd03087 PGM_like1 This archaeal PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. 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 phosphomannomutase/phosphoglucomutase (PMM/PGM). 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=20.53 E-value=2.3e+02 Score=23.37 Aligned_cols=32 Identities=19% Similarity=0.156 Sum_probs=23.0
Q ss_pred EccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 92 CYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 92 syp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
.+|+..+..+|+.+++.+++.+++..+.+.+.
T Consensus 407 iRpS~tep~~rvy~Ea~~~~~a~~l~~~~~~~ 438 (439)
T cd03087 407 IRPSGTEPKIRITAEAKTEERAKELLEEGRSK 438 (439)
T ss_pred EeccCCccEEEEEEeeCCHHHHHHHHHHHHhh
Confidence 34544444589999999998888877776654
No 123
>PLN02371 phosphoglucosamine mutase family protein
Probab=20.45 E-value=2e+02 Score=25.03 Aligned_cols=26 Identities=4% Similarity=0.069 Sum_probs=21.7
Q ss_pred cEEEEEEecCHHHHHHHHHHHHHHhc
Q 032821 100 PLIISFEGKDQARIEAAIESLFKKFH 125 (133)
Q Consensus 100 ~v~l~~~~~~~~~~~~~~~~l~~~l~ 125 (133)
-++|.+++++++.+++..+.+.+.+.
T Consensus 542 ~iri~~Ea~s~e~a~~l~~~~~~~v~ 567 (583)
T PLN02371 542 VIPLNIESSSPGGAQKMALVVLTWLK 567 (583)
T ss_pred eEEEEEeECCHHHHHHHHHHHHHHHh
Confidence 37999999999988888888777764
No 124
>PRK14427 acylphosphatase; Provisional
Probab=20.38 E-value=2.3e+02 Score=18.35 Aligned_cols=47 Identities=19% Similarity=0.243 Sum_probs=30.4
Q ss_pred hhHHHHHHhhhCCCceEEEccccCCCcEEEEEEecCHHHHHHHHHHHHHH
Q 032821 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 123 (133)
Q Consensus 74 l~~~L~~l~~~~~~v~igsyp~~~~~~v~l~~~~~~~~~~~~~~~~l~~~ 123 (133)
+-.....+..++ ++ -|+--+...+.|.+.++|+++ .+++..++|.+-
T Consensus 21 FR~fv~~~A~~l-gl-~G~V~N~~dGsVei~~qG~~~-~i~~f~~~l~~~ 67 (94)
T PRK14427 21 FRYWTMRKAEEL-GL-TGTVRNLDDGSVALVAEGTGE-QVEKLLDWLNSD 67 (94)
T ss_pred ChHHHHHHHHHc-CC-EEEEEECCCCeEEEEEEECHH-HHHHHHHHHhhC
Confidence 445555555554 34 255445556779999999654 478888888764
Done!