Query psy13610
Match_columns 123
No_of_seqs 106 out of 724
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 15:31:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13610.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13610hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0100 RpsK Ribosomal protein 100.0 3.2E-36 6.8E-41 220.4 12.1 92 23-114 16-108 (129)
2 TIGR03632 bact_S11 30S ribosom 100.0 1.7E-35 3.8E-40 210.5 12.4 89 26-114 1-90 (108)
3 CHL00041 rps11 ribosomal prote 100.0 1.7E-35 3.7E-40 213.1 12.2 92 23-114 11-103 (116)
4 TIGR03628 arch_S11P archaeal r 100.0 1.5E-35 3.3E-40 213.2 11.7 90 25-114 2-101 (114)
5 PRK05309 30S ribosomal protein 100.0 4.5E-35 9.7E-40 214.2 12.3 92 23-114 15-107 (128)
6 PTZ00129 40S ribosomal protein 100.0 5E-35 1.1E-39 218.6 11.7 91 24-114 27-127 (149)
7 PRK09607 rps11p 30S ribosomal 100.0 6.3E-35 1.4E-39 214.6 12.0 91 24-114 8-108 (132)
8 KOG0408|consensus 100.0 8.7E-35 1.9E-39 220.6 11.6 106 8-113 62-168 (190)
9 PF00411 Ribosomal_S11: Riboso 100.0 9.4E-35 2E-39 207.0 10.6 89 26-114 1-90 (110)
10 PTZ00090 40S ribosomal protein 100.0 2.5E-29 5.3E-34 197.5 12.4 90 24-114 117-209 (233)
11 KOG0407|consensus 99.9 1.4E-24 3E-29 156.8 11.2 91 24-114 15-115 (139)
12 cd00432 Ribosomal_L18_L5e Ribo 97.7 0.00086 1.9E-08 46.7 9.9 86 24-109 10-100 (103)
13 TIGR00060 L18_bact ribosomal p 97.2 0.0093 2E-07 43.1 10.3 87 24-112 23-113 (114)
14 CHL00139 rpl18 ribosomal prote 96.9 0.019 4.1E-07 41.1 10.1 90 23-112 13-108 (109)
15 PF00861 Ribosomal_L18p: Ribos 96.9 0.015 3.3E-07 41.8 9.4 91 23-113 21-119 (119)
16 PRK05593 rplR 50S ribosomal pr 96.9 0.02 4.3E-07 41.4 9.8 90 23-112 22-116 (117)
17 PRK08569 rpl18p 50S ribosomal 96.7 0.032 7E-07 43.7 10.4 93 23-115 30-132 (193)
18 PTZ00032 60S ribosomal protein 95.9 0.096 2.1E-06 41.6 9.4 94 16-112 99-210 (211)
19 COG0256 RplR Ribosomal protein 94.2 0.99 2.2E-05 33.2 9.8 89 24-112 28-124 (125)
20 cd01076 NAD_bind_1_Glu_DH NAD( 74.7 6.6 0.00014 30.9 4.7 55 59-114 3-58 (227)
21 cd05313 NAD_bind_2_Glu_DH NAD( 68.0 11 0.00023 30.6 4.6 54 60-114 11-65 (254)
22 PRK14030 glutamate dehydrogena 65.9 15 0.00032 32.2 5.3 64 46-115 192-256 (445)
23 COG2099 CobK Precorrin-6x redu 61.9 13 0.00029 30.4 4.1 30 65-95 74-103 (257)
24 KOG0408|consensus 61.7 3.6 7.9E-05 32.0 0.8 14 110-123 142-155 (190)
25 PTZ00079 NADP-specific glutama 60.6 17 0.00038 31.9 4.8 64 45-114 200-264 (454)
26 PLN02477 glutamate dehydrogena 57.4 24 0.00052 30.5 5.1 53 61-114 180-233 (410)
27 COG4782 Uncharacterized protei 56.5 37 0.0008 29.4 6.0 51 48-98 151-202 (377)
28 cd07996 WGR_MMR_like WGR domai 55.4 46 0.00099 21.1 5.1 45 43-87 24-72 (74)
29 cd05211 NAD_bind_Glu_Leu_Phe_V 49.9 29 0.00064 27.1 4.1 46 66-112 2-48 (217)
30 PF00208 ELFV_dehydrog: Glutam 46.1 19 0.00041 28.7 2.6 50 64-113 8-58 (244)
31 PRK09414 glutamate dehydrogena 45.4 42 0.00092 29.3 4.8 53 61-114 206-259 (445)
32 PRK14031 glutamate dehydrogena 45.4 51 0.0011 28.9 5.3 55 60-115 201-256 (444)
33 PRK14444 acylphosphatase; Prov 42.9 79 0.0017 21.4 5.0 37 85-122 2-43 (92)
34 COG0334 GdhA Glutamate dehydro 42.6 39 0.00084 29.5 4.1 66 45-116 170-236 (411)
35 TIGR00715 precor6x_red precorr 41.7 45 0.00098 26.8 4.2 27 65-92 73-99 (256)
36 PTZ00069 60S ribosomal protein 40.1 2E+02 0.0044 24.2 7.7 68 16-84 37-112 (300)
37 PF10670 DUF4198: Domain of un 39.8 54 0.0012 24.2 4.1 37 16-52 158-199 (215)
38 KOG2299|consensus 39.0 87 0.0019 26.2 5.4 62 53-116 106-169 (301)
39 KOG0747|consensus 38.1 56 0.0012 27.8 4.2 55 64-118 153-216 (331)
40 PRK13260 2,3-diketo-L-gulonate 37.6 1.3E+02 0.0028 25.2 6.3 69 43-111 62-132 (332)
41 COG3981 Predicted acetyltransf 37.3 1.1E+02 0.0023 23.9 5.4 70 23-105 79-150 (174)
42 PF02571 CbiJ: Precorrin-6x re 36.7 48 0.001 26.5 3.6 30 65-95 74-103 (249)
43 TIGR01139 cysK cysteine syntha 36.4 98 0.0021 24.6 5.3 45 45-105 56-100 (298)
44 PRK08057 cobalt-precorrin-6x r 35.7 50 0.0011 26.4 3.5 27 65-92 73-99 (248)
45 TIGR00829 FRU PTS system, fruc 35.3 75 0.0016 21.3 3.8 28 69-97 12-39 (85)
46 COG1060 ThiH Thiamine biosynth 34.0 48 0.001 28.3 3.3 44 48-92 67-113 (370)
47 cd01075 NAD_bind_Leu_Phe_Val_D 31.8 96 0.0021 23.6 4.4 52 66-117 5-58 (200)
48 PRK14447 acylphosphatase; Prov 31.5 1.4E+02 0.0031 20.2 4.9 35 86-121 3-42 (95)
49 PRK14743 thrL thr operon leade 31.2 27 0.00058 18.9 0.9 15 33-47 5-19 (26)
50 PRK14742 thrL thr operon leade 30.6 28 0.00061 19.1 0.9 16 32-47 10-25 (28)
51 PF11589 DUF3244: Domain of un 30.5 63 0.0014 22.1 2.9 29 28-56 41-69 (106)
52 PF02615 Ldh_2: Malate/L-lacta 29.7 2.4E+02 0.0052 23.6 6.8 69 43-111 62-132 (335)
53 COG2840 Uncharacterized protei 29.3 1.1E+02 0.0025 23.8 4.4 39 66-105 105-145 (184)
54 PLN00105 malate/L-lactate dehy 29.0 2.2E+02 0.0047 23.8 6.4 59 54-112 63-123 (330)
55 COG1980 Archaeal fructose 1,6- 28.8 67 0.0014 27.2 3.2 16 106-121 96-111 (369)
56 PRK15025 ureidoglycolate dehyd 28.4 2.3E+02 0.005 24.0 6.4 58 54-111 74-132 (349)
57 COG1710 Uncharacterized protei 28.2 90 0.002 23.2 3.5 29 72-100 64-92 (139)
58 cd01853 Toc34_like Toc34-like 27.7 1.9E+02 0.0042 22.8 5.6 45 64-108 7-52 (249)
59 PF05990 DUF900: Alpha/beta hy 27.6 1.1E+02 0.0023 23.9 4.1 54 44-98 47-104 (233)
60 PRK10646 ADP-binding protein; 27.4 95 0.0021 23.2 3.6 44 66-113 10-54 (153)
61 TIGR01136 cysKM cysteine synth 27.3 1.6E+02 0.0035 23.4 5.2 43 45-103 57-99 (299)
62 cd04518 TBP_archaea archaeal T 27.3 1.4E+02 0.003 22.8 4.5 49 37-88 39-87 (174)
63 PRK14450 acylphosphatase; Prov 27.3 2E+02 0.0042 19.3 5.0 34 88-122 3-41 (91)
64 PF03123 CAT_RBD: CAT RNA bind 27.0 95 0.0021 19.7 3.1 31 31-62 4-34 (59)
65 PRK11761 cysM cysteine synthas 26.5 1.6E+02 0.0034 23.7 5.0 45 46-106 63-107 (296)
66 PRK14430 acylphosphatase; Prov 26.5 1.6E+02 0.0034 20.0 4.3 35 87-122 4-43 (92)
67 PRK14420 acylphosphatase; Prov 26.2 1.8E+02 0.0039 19.4 4.5 22 100-121 18-40 (91)
68 PF06289 FlbD: Flagellar prote 26.2 79 0.0017 20.3 2.6 26 17-43 7-34 (60)
69 TIGR00732 dprA DNA protecting 26.0 2.8E+02 0.0061 21.6 6.2 55 57-116 47-104 (220)
70 TIGR03175 AllD ureidoglycolate 26.0 2.5E+02 0.0055 23.7 6.3 57 55-111 75-132 (349)
71 COG1763 MobB Molybdopterin-gua 25.9 89 0.0019 23.6 3.2 42 55-102 6-52 (161)
72 PRK14436 acylphosphatase; Prov 25.9 1.9E+02 0.004 19.5 4.6 35 87-122 4-43 (91)
73 PRK10098 putative dehydrogenas 25.8 2.8E+02 0.006 23.4 6.5 69 43-111 66-136 (350)
74 cd05569 PTS_IIB_fructose PTS_I 24.7 1.6E+02 0.0034 19.9 4.1 27 69-96 13-39 (96)
75 PRK14441 acylphosphatase; Prov 23.9 1.7E+02 0.0038 19.7 4.1 36 86-122 4-44 (93)
76 PRK10427 putative PTS system f 23.8 1.4E+02 0.0031 21.1 3.8 28 69-97 17-44 (114)
77 smart00773 WGR Proposed nuclei 23.3 1.4E+02 0.003 19.4 3.5 39 42-80 29-67 (84)
78 TIGR00150 HI0065_YjeE ATPase, 23.0 1.4E+02 0.003 21.7 3.7 43 67-113 5-48 (133)
79 TIGR01138 cysM cysteine syntha 23.0 2.2E+02 0.0048 22.8 5.2 40 46-101 59-98 (290)
80 PRK00394 transcription factor; 22.9 2.3E+02 0.0049 21.6 5.0 48 38-88 39-86 (179)
81 cd01561 CBS_like CBS_like: Thi 22.6 2.3E+02 0.0049 22.4 5.2 51 46-114 53-103 (291)
82 cd04516 TBP_eukaryotes eukaryo 22.4 2E+02 0.0044 21.8 4.7 44 41-87 43-86 (174)
83 PRK14426 acylphosphatase; Prov 22.0 2.5E+02 0.0053 18.9 4.6 34 88-122 5-43 (92)
84 PRK13678 hypothetical protein; 21.8 1.1E+02 0.0023 21.1 2.7 25 30-54 2-26 (95)
85 PF02481 DNA_processg_A: DNA r 21.7 2.6E+02 0.0057 21.6 5.2 53 58-115 48-103 (212)
86 PRK14424 acylphosphatase; Prov 21.4 2.4E+02 0.0052 19.2 4.5 36 86-122 6-46 (94)
87 PRK14422 acylphosphatase; Prov 21.3 2.7E+02 0.0059 18.8 4.7 36 86-122 5-45 (93)
88 PF00150 Cellulase: Cellulase 21.2 1.7E+02 0.0037 22.1 4.1 43 42-94 1-43 (281)
89 PRK14429 acylphosphatase; Prov 21.2 2.1E+02 0.0046 19.1 4.1 26 96-122 15-41 (90)
90 PLN00062 TATA-box-binding prot 21.0 2.2E+02 0.0047 21.8 4.6 43 41-86 43-85 (179)
91 PRK14423 acylphosphatase; Prov 20.8 2.2E+02 0.0048 19.1 4.2 35 87-122 5-44 (92)
92 TIGR00055 uppS undecaprenyl di 20.7 1.7E+02 0.0037 23.4 4.0 30 66-95 24-53 (226)
93 COG5436 Predicted integral mem 20.7 1.7E+02 0.0038 22.7 3.9 40 13-52 64-106 (182)
94 PRK14428 acylphosphatase; Prov 20.7 2.2E+02 0.0048 19.6 4.2 37 85-122 6-47 (97)
95 PRK06552 keto-hydroxyglutarate 20.6 1.8E+02 0.004 22.6 4.2 34 74-109 27-60 (213)
96 PF09741 DUF2045: Uncharacteri 20.4 2E+02 0.0044 23.3 4.5 54 38-97 161-223 (237)
97 PRK14435 acylphosphatase; Prov 20.3 2.8E+02 0.0061 18.6 4.6 16 106-121 25-40 (90)
98 cd06562 GH20_HexA_HexB-like Be 20.3 1.9E+02 0.0042 23.9 4.5 64 33-98 31-95 (348)
99 TIGR02530 flg_new flagellar op 20.2 1.2E+02 0.0027 21.3 2.8 20 26-45 61-80 (96)
100 PF10708 DUF2510: Protein of u 20.1 66 0.0014 18.7 1.2 16 6-21 3-20 (36)
101 cd00652 TBP_TLF TATA box bindi 20.1 2.3E+02 0.005 21.4 4.5 48 38-88 40-87 (174)
102 TIGR01911 HesB_rel_seleno HesB 20.1 1.9E+02 0.0042 19.4 3.8 23 75-97 12-36 (92)
103 PF13590 DUF4136: Domain of un 20.0 2.8E+02 0.0062 19.1 4.8 30 35-64 103-132 (151)
No 1
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-36 Score=220.41 Aligned_cols=92 Identities=38% Similarity=0.507 Sum_probs=89.2
Q ss_pred ccccEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHH
Q psy13610 23 KNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLK 102 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~ 102 (123)
...+++||++||||||||+||++||+++|.|+|.+|||++||+||||||+||+++++.++|+||+.|||+|||||+|||+
T Consensus 16 i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkgpG~Grea 95 (129)
T COG0100 16 IADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKGPGPGREA 95 (129)
T ss_pred cccceEEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCCCCCHHHHHHHHHHHHHHHHHhCccEEEEEEECCCCcHHH
Confidence 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh-hcCceee
Q psy13610 103 ALEIG-VSSVRIN 114 (123)
Q Consensus 103 alkal-~~g~~i~ 114 (123)
|||+| ++|++|+
T Consensus 96 AiraL~~ag~~i~ 108 (129)
T COG0100 96 AIRALAAAGLKIT 108 (129)
T ss_pred HHHHHHHccceEE
Confidence 99987 8899986
No 2
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=100.00 E-value=1.7e-35 Score=210.54 Aligned_cols=89 Identities=36% Similarity=0.504 Sum_probs=86.2
Q ss_pred cEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHH
Q psy13610 26 PIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKALE 105 (123)
Q Consensus 26 ~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alk 105 (123)
+++||++|+||||||+||++|++++|.|+|++||||+||+||||||.+|++++++++++||+.|+|++||+|+||+++||
T Consensus 1 gi~hI~~s~NNT~itlTd~~g~~~~~~S~G~~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~kG~G~gr~~~ir 80 (108)
T TIGR03632 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGAGRESAIR 80 (108)
T ss_pred CEEEEEccCCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hh-hcCceee
Q psy13610 106 IG-VSSVRIN 114 (123)
Q Consensus 106 al-~~g~~i~ 114 (123)
+| ++|++|.
T Consensus 81 ~l~~~glkI~ 90 (108)
T TIGR03632 81 ALQAAGLEVT 90 (108)
T ss_pred HHHHCCCEEE
Confidence 86 6788875
No 3
>CHL00041 rps11 ribosomal protein S11
Probab=100.00 E-value=1.7e-35 Score=213.10 Aligned_cols=92 Identities=33% Similarity=0.468 Sum_probs=88.9
Q ss_pred ccccEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHH
Q psy13610 23 KNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLK 102 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~ 102 (123)
...+++||++|+||||||+||++|++++|.|+|++||||+||+||||||++|++++++|+++|++.|+|++||+|+||++
T Consensus 11 ~~~gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG~G~Gr~~ 90 (116)
T CHL00041 11 IPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKGPGLGRDT 90 (116)
T ss_pred ceeEEEEEEcccCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh-hcCceee
Q psy13610 103 ALEIG-VSSVRIN 114 (123)
Q Consensus 103 alkal-~~g~~i~ 114 (123)
+||+| ++|++|.
T Consensus 91 ~ir~l~~~glkI~ 103 (116)
T CHL00041 91 ALRAIRRSGLKLS 103 (116)
T ss_pred HHHHHHHCCCEEE
Confidence 99987 7799886
No 4
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=100.00 E-value=1.5e-35 Score=213.23 Aligned_cols=90 Identities=30% Similarity=0.356 Sum_probs=87.0
Q ss_pred ccEEEEEecCCCceEEEeCCCCC-EEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc--------
Q psy13610 25 LPIMNIRVTKNNTILSLSDAKGV-VKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG-------- 95 (123)
Q Consensus 25 ~~i~hI~st~NNTiitlTD~~G~-~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-------- 95 (123)
.+|+||++|+||||||+||.+|+ +++|+|+|++|||++||+||||||.|+|+++++|+++||+.|+|+|||
T Consensus 2 ~gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~~ 81 (114)
T TIGR03628 2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS 81 (114)
T ss_pred cEEEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCCC
Confidence 68999999999999999999995 699999999999999999999999999999999999999999999999
Q ss_pred CCcCHHHHHHhh-hcCceee
Q psy13610 96 LGPGRLKALEIG-VSSVRIN 114 (123)
Q Consensus 96 ~G~GR~~alkal-~~g~~i~ 114 (123)
+|+||++|||+| ++|++|.
T Consensus 82 ~G~Gr~~air~l~~~glkI~ 101 (114)
T TIGR03628 82 PGPGAQAAIRALARAGLRIG 101 (114)
T ss_pred CCCcHHHHHHHHHHCCCEEE
Confidence 999999999987 8899986
No 5
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00 E-value=4.5e-35 Score=214.16 Aligned_cols=92 Identities=36% Similarity=0.450 Sum_probs=88.2
Q ss_pred ccccEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHH
Q psy13610 23 KNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLK 102 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~ 102 (123)
...+|+||++|+||||||+||++|++++|.|||++||||+||+||||||++|++++++|+++||+.|+|++||+|+||++
T Consensus 15 ~~~gi~hI~~t~NNTiitlTd~~G~~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr~~ 94 (128)
T PRK05309 15 IPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKGPGSGRES 94 (128)
T ss_pred cceeEEEEEccCCCEEEEEEcCCCCEEEEEecCccEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcHHH
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh-hcCceee
Q psy13610 103 ALEIG-VSSVRIN 114 (123)
Q Consensus 103 alkal-~~g~~i~ 114 (123)
+||+| ++|++|.
T Consensus 95 air~L~~~glkI~ 107 (128)
T PRK05309 95 AIRALQAAGLEVT 107 (128)
T ss_pred HHHHHHHCCCEEE
Confidence 99987 6788775
No 6
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00 E-value=5e-35 Score=218.63 Aligned_cols=91 Identities=24% Similarity=0.381 Sum_probs=88.2
Q ss_pred cccEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCC-CCChHHHHHHHHHHHHHHHHcCCeEEEEEE--------E
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNAR-KGTNIAAQAAGITIGKKALEIGVSSVRINV--------R 94 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~r-K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~i--------k 94 (123)
..+|+||++|+|||||||||++|++++|.|+|.+|||++| |+||||||.||++++++|+++||+.|+|+| +
T Consensus 27 ~~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~gg~~~k 106 (149)
T PTZ00129 27 VFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGINALHIKLRATGGVRTK 106 (149)
T ss_pred eEEEEEEEcccCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCCCCCC
Confidence 5799999999999999999999999999999999999999 999999999999999999999999999999 8
Q ss_pred cCCcCHHHHHHhh-hcCceee
Q psy13610 95 GLGPGRLKALEIG-VSSVRIN 114 (123)
Q Consensus 95 G~G~GR~~alkal-~~g~~i~ 114 (123)
|+|+||++|||+| ++|++|.
T Consensus 107 g~GpGr~~airaL~~~glkI~ 127 (149)
T PTZ00129 107 TPGPGAQAALRALARAGLKIG 127 (149)
T ss_pred CCCCCHHHHHHHHHHCCCEEE
Confidence 8999999999987 8899986
No 7
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00 E-value=6.3e-35 Score=214.59 Aligned_cols=91 Identities=30% Similarity=0.363 Sum_probs=88.3
Q ss_pred cccEEEEEecCCCceEEEeCCCCC-EEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-------
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAKGV-VKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG------- 95 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~G~-~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG------- 95 (123)
..+|+||++|+|||||||||++|+ +++|+|+|++|||+++|+||||||.|||+++++|+++||+.|+|+|||
T Consensus 8 ~~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~~~ 87 (132)
T PRK09607 8 KWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQK 87 (132)
T ss_pred eeeEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCc
Confidence 579999999999999999999996 999999999999999999999999999999999999999999999999
Q ss_pred -CCcCHHHHHHhh-hcCceee
Q psy13610 96 -LGPGRLKALEIG-VSSVRIN 114 (123)
Q Consensus 96 -~G~GR~~alkal-~~g~~i~ 114 (123)
+|+||++|||+| ++|++|.
T Consensus 88 ~~G~Gr~~airal~~~glkI~ 108 (132)
T PRK09607 88 SPGPGAQAAIRALARAGLRIG 108 (132)
T ss_pred CCCCcHHHHHHHHHHCCCEEE
Confidence 999999999987 8899986
No 8
>KOG0408|consensus
Probab=100.00 E-value=8.7e-35 Score=220.62 Aligned_cols=106 Identities=43% Similarity=0.757 Sum_probs=103.0
Q ss_pred CCCCCCccccCCeecccccEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCe
Q psy13610 8 PDENTPDLIFDGLKFKNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVS 87 (123)
Q Consensus 8 p~~~~~~~~~~g~~~~~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~ 87 (123)
|++++-+.+|+|++|.+++|+||++|+|||||++||.+|.++.|+|||.+||||+||+|++|||.|+..++.++.++|++
T Consensus 62 p~aet~~r~~~g~~f~eiPi~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrntrkgT~iAaQtaavaa~~r~v~~G~~ 141 (190)
T KOG0408|consen 62 PGAETNTRSFSGKNFREIPIIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNTRKGTPIAAQTAAVAAIRRAVDQGMQ 141 (190)
T ss_pred CChhhhhcccCCccccccceEEEEecCCCeEEEEEccCCcEEEEeecccccccccccCCchhHHHHHHHHHHHHHHhcce
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEcCCcCHHHHHHhh-hcCcee
Q psy13610 88 SVRINVRGLGPGRLKALEIG-VSSVRI 113 (123)
Q Consensus 88 ~i~V~ikG~G~GR~~alkal-~~g~~i 113 (123)
.++|+|||+||||.+|+|.| |+|+.+
T Consensus 142 ~vrV~VkGlGpGRmsa~kgl~m~Gl~v 168 (190)
T KOG0408|consen 142 TVRVRVKGLGPGRMSALKGLRMGGLLV 168 (190)
T ss_pred EEEEEEecCCccHHHHHhhhhhcceEE
Confidence 99999999999999999976 888875
No 9
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=100.00 E-value=9.4e-35 Score=206.99 Aligned_cols=89 Identities=46% Similarity=0.656 Sum_probs=86.3
Q ss_pred cEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHH
Q psy13610 26 PIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKALE 105 (123)
Q Consensus 26 ~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alk 105 (123)
||+||++|+||||||+||.+|++++|.|+|++|||++||+||||||+++++++++|+++|++.|+|+|||+|+||+++||
T Consensus 1 giihI~~s~NNt~vtlTd~~G~~~~~~S~G~~gfK~~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~g~gr~~~lk 80 (110)
T PF00411_consen 1 GIIHIKSSFNNTIVTLTDLKGNVLFWSSAGSLGFKGARKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKGFGPGREAALK 80 (110)
T ss_dssp EEEEEEEESSEEEEEEEETTSEEEEEEETTTSSTTTTCGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEESSSTTHHHHHH
T ss_pred CEEEEEecCCCEEEEEECCCCCEEEEEeccccccccccccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcCCCccHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hh-hcCceee
Q psy13610 106 IG-VSSVRIN 114 (123)
Q Consensus 106 al-~~g~~i~ 114 (123)
+| ++|++|.
T Consensus 81 ~l~~~gl~I~ 90 (110)
T PF00411_consen 81 ALKKSGLKIV 90 (110)
T ss_dssp HHHHTTSEEE
T ss_pred HHHhcCCEEE
Confidence 87 5798875
No 10
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=99.96 E-value=2.5e-29 Score=197.51 Aligned_cols=90 Identities=19% Similarity=0.222 Sum_probs=84.6
Q ss_pred cccEEEEEecCCCceEEEeCCCCCE--EEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHH
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAKGVV--KLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRL 101 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~G~~--l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~ 101 (123)
+.-.+-|++|+||||||+||.+||+ ++|+|+|.|||||+||+||||||.||++++++|+++||+.|+|+|||+| |||
T Consensus 117 ~~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGsKKsTpfAAQ~aae~aakka~~~GIk~V~V~vKGpG-gRE 195 (233)
T PTZ00090 117 DRFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKLQQSERCAYRIGENIAKKCRRLGIFAVDIKFRRIM-RVE 195 (233)
T ss_pred CcEEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccCccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeCCC-hHH
Confidence 4445669999999999999999995 9999999999999999999999999999999999999999999999999 699
Q ss_pred HHHHhh-hcCceee
Q psy13610 102 KALEIG-VSSVRIN 114 (123)
Q Consensus 102 ~alkal-~~g~~i~ 114 (123)
+|||++ .+|++|+
T Consensus 196 tALRaL~~~GLkIt 209 (233)
T PTZ00090 196 TVLQAFYANGLQVT 209 (233)
T ss_pred HHHHHHHHCCCEEE
Confidence 999987 7799986
No 11
>KOG0407|consensus
Probab=99.92 E-value=1.4e-24 Score=156.77 Aligned_cols=91 Identities=27% Similarity=0.402 Sum_probs=87.5
Q ss_pred cccEEEEEecCCCceEEEeCCCCCEEEEEeecccccccCC-CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-------
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNAR-KGTNIAAQAAGITIGKKALEIGVSSVRINVRG------- 95 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~r-K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG------- 95 (123)
..++.||++|||+|||++||++|++....-.|.+..|..| .+|||||++||++++.+|+++||+.+||++|+
T Consensus 15 vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh~klratgg~ktk 94 (139)
T KOG0407|consen 15 VFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTKTK 94 (139)
T ss_pred eeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEecCCcccC
Confidence 6789999999999999999999999999999999999999 89999999999999999999999999999998
Q ss_pred -CCcCHHHHHHhh-hcCceee
Q psy13610 96 -LGPGRLKALEIG-VSSVRIN 114 (123)
Q Consensus 96 -~G~GR~~alkal-~~g~~i~ 114 (123)
+|||.+++||+| |+|++|+
T Consensus 95 tpgpgaqsalralar~gmrig 115 (139)
T KOG0407|consen 95 TPGPGAQSALRALARSGMRIG 115 (139)
T ss_pred CCCccHHHHHHHHHHhcceee
Confidence 889999999976 9999996
No 12
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=97.67 E-value=0.00086 Score=46.74 Aligned_cols=86 Identities=22% Similarity=0.214 Sum_probs=71.5
Q ss_pred cccEEEEEecCCCceEEEeCCC-CCEEEEEeecccccccCC--CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCC-cC
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAK-GVVKLLRSCGMEGFKNAR--KGTNIAAQAAGITIGKKALEIGVSSVRINVRGLG-PG 99 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~-G~~l~~~S~G~~GfK~~r--K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G-~G 99 (123)
..+.+.|+.|.+|....+.|.. +++++..|+-...+++.. .....||+.+++.++++|+++|+..+.+-..|+- -|
T Consensus 10 ~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~~~~~~~g 89 (103)
T cd00432 10 ERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRYHG 89 (103)
T ss_pred CCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeCCCccccc
Confidence 6788999999999999999997 889999999998888753 6778899999999999999999999998876655 35
Q ss_pred HHHH-HHhhhc
Q psy13610 100 RLKA-LEIGVS 109 (123)
Q Consensus 100 R~~a-lkal~~ 109 (123)
|-.+ +++++.
T Consensus 90 rv~a~~~~~r~ 100 (103)
T cd00432 90 RVKALAKGARE 100 (103)
T ss_pred HHHHHHHHHHH
Confidence 6443 345544
No 13
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=97.15 E-value=0.0093 Score=43.10 Aligned_cols=87 Identities=21% Similarity=0.233 Sum_probs=65.0
Q ss_pred cccEEEEEecCCCceEEEeCCCCC-EEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCC-cCHH
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAKGV-VKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLG-PGRL 101 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~G~-~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G-~GR~ 101 (123)
+.|.+.|+-|.++....+.|..+. +++..|+=...++ ...+-.||..+++.++++|++.||..+..--.|+= -||-
T Consensus 23 ~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~--~~~n~~aA~~vG~~la~ra~~~gi~~vvfDrgg~~YhGrv 100 (114)
T TIGR00060 23 NRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK--YTGNKDAAKKVGKLVAERLKEKGIKDVVFDRGGYKYHGRV 100 (114)
T ss_pred CCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc--CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCcchHHH
Confidence 577899999999999999877555 6777666444565 56667899999999999999999999977744433 2675
Q ss_pred HHHH-hhhc-Cce
Q psy13610 102 KALE-IGVS-SVR 112 (123)
Q Consensus 102 ~alk-al~~-g~~ 112 (123)
.++- ++|+ |++
T Consensus 101 ~A~a~~aRe~Gl~ 113 (114)
T TIGR00060 101 AALAEAAREAGLN 113 (114)
T ss_pred HHHHHHHHHhCCC
Confidence 5554 5544 554
No 14
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=96.94 E-value=0.019 Score=41.12 Aligned_cols=90 Identities=22% Similarity=0.269 Sum_probs=66.8
Q ss_pred ccccEEEEEecCCCceEEEe-CCCCCEEEEEeecccccccCC--CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-
Q psy13610 23 KNLPIMNIRVTKNNTILSLS-DAKGVVKLLRSCGMEGFKNAR--KGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP- 98 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlT-D~~G~~l~~~S~G~~GfK~~r--K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~- 98 (123)
...|.+-|+-|.++....+. |.+|++++..|+=...+++.. ...-.||+.+++-++++|++.||..+..--.|+=+
T Consensus 13 ~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDrgg~~yh 92 (109)
T CHL00139 13 AERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDRGGKLYH 92 (109)
T ss_pred CCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCCccc
Confidence 35678899999999988776 568899999998666666543 56677899999999999999999998777444333
Q ss_pred CHHHHH-Hhhhc-Cce
Q psy13610 99 GRLKAL-EIGVS-SVR 112 (123)
Q Consensus 99 GR~~al-kal~~-g~~ 112 (123)
||-.++ .++|+ |++
T Consensus 93 GrV~a~a~~are~GL~ 108 (109)
T CHL00139 93 GRIKALAEAAREAGLQ 108 (109)
T ss_pred hHHHHHHHHHHHhCCC
Confidence 564444 35544 554
No 15
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=96.88 E-value=0.015 Score=41.75 Aligned_cols=91 Identities=20% Similarity=0.194 Sum_probs=69.8
Q ss_pred ccccEEEEEecCCCceEEEeCCC-CCEEEEEeecccccccC----CCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCC
Q psy13610 23 KNLPIMNIRVTKNNTILSLSDAK-GVVKLLRSCGMEGFKNA----RKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLG 97 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlTD~~-G~~l~~~S~G~~GfK~~----rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G 97 (123)
...+.+-|+.|..++...+.|.. +.++...|+=..-++.. ....-.||+.+++.++++|++.||..+..-..|+-
T Consensus 21 ~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr~~~~ 100 (119)
T PF00861_consen 21 AERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDRGGYK 100 (119)
T ss_dssp TSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECTSTSS
T ss_pred CCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcCCCCc
Confidence 35678889999999999886655 88888888888888863 23467799999999999999999999888877765
Q ss_pred c-CHHH-HHHhhh-cCcee
Q psy13610 98 P-GRLK-ALEIGV-SSVRI 113 (123)
Q Consensus 98 ~-GR~~-alkal~-~g~~i 113 (123)
. ||-. ++++++ .|+++
T Consensus 101 y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 101 YHGRVKALADGAREGGLEF 119 (119)
T ss_dssp SSSHHHHHHHHHHHTTCB-
T ss_pred ccHHHHHHHHHHHHcCCCC
Confidence 5 5644 444554 47653
No 16
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=96.86 E-value=0.02 Score=41.43 Aligned_cols=90 Identities=19% Similarity=0.221 Sum_probs=65.9
Q ss_pred ccccEEEEEecCCCceEEEeCCCCC-EEEEEeecccccccCC-CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-C
Q psy13610 23 KNLPIMNIRVTKNNTILSLSDAKGV-VKLLRSCGMEGFKNAR-KGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-G 99 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlTD~~G~-~l~~~S~G~~GfK~~r-K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-G 99 (123)
.+.|.+-|+.|.++....+.|..+. +++..|+=...++..- ...-.||+.+++.++++|++.||..+..--.|+=+ |
T Consensus 22 ~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~vvfDrg~~~yhG 101 (117)
T PRK05593 22 AERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQVVFDRGGYKYHG 101 (117)
T ss_pred CCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccccCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCCcccH
Confidence 4678899999999999999977666 6677776555554433 66678999999999999999999998777444333 5
Q ss_pred HHHHH-Hhhh-cCce
Q psy13610 100 RLKAL-EIGV-SSVR 112 (123)
Q Consensus 100 R~~al-kal~-~g~~ 112 (123)
|-.++ .++| .|++
T Consensus 102 rV~a~a~~are~Gl~ 116 (117)
T PRK05593 102 RVKALADAAREAGLK 116 (117)
T ss_pred HHHHHHHHHHHhCCC
Confidence 54443 3554 4654
No 17
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=96.68 E-value=0.032 Score=43.74 Aligned_cols=93 Identities=23% Similarity=0.234 Sum_probs=69.4
Q ss_pred ccccEEEEEecCCCceEEEe--CC-CCCEEEEEeecccccccCC--CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCC
Q psy13610 23 KNLPIMNIRVTKNNTILSLS--DA-KGVVKLLRSCGMEGFKNAR--KGTNIAAQAAGITIGKKALEIGVSSVRINVRGLG 97 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlT--D~-~G~~l~~~S~G~~GfK~~r--K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G 97 (123)
.+.+.+-|+-|.+|.++-+. |. .+.+++..|+=....++-. ....-||+.++.-++++|++.||+.+.+=.-|.=
T Consensus 30 ~~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~~~N~~AAy~vG~llA~ral~kGi~~vvfDrGg~~ 109 (193)
T PRK08569 30 SGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEAVLDIGLHR 109 (193)
T ss_pred cCCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEecCCcc
Confidence 34578889999999999999 44 5557777777666555533 5667789999999999999999999888876644
Q ss_pred c---CHHH-HHHhh-hcCceeee
Q psy13610 98 P---GRLK-ALEIG-VSSVRINV 115 (123)
Q Consensus 98 ~---GR~~-alkal-~~g~~i~~ 115 (123)
+ ||-. +++++ -+|++|-.
T Consensus 110 yh~gGRV~A~akgArd~GL~fPh 132 (193)
T PRK08569 110 PTKGSRVFAALKGAIDAGLEIPH 132 (193)
T ss_pred ccCCccHHHHHHHHHHcCCcCCC
Confidence 3 6744 55555 55888754
No 18
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=95.92 E-value=0.096 Score=41.58 Aligned_cols=94 Identities=26% Similarity=0.332 Sum_probs=68.7
Q ss_pred ccCCeecccccEEEEEecCCCceEEEeC-CCCCEEEEEeecccccccC--------------CCCChHHHHHHHHHHHHH
Q psy13610 16 IFDGLKFKNLPIMNIRVTKNNTILSLSD-AKGVVKLLRSCGMEGFKNA--------------RKGTNIAAQAAGITIGKK 80 (123)
Q Consensus 16 ~~~g~~~~~~~i~hI~st~NNTiitlTD-~~G~~l~~~S~G~~GfK~~--------------rK~T~~Aa~~aa~~v~~~ 80 (123)
+.+|+ ..+.+-|+-|.++.-..+.| .+|.++++.|+=.-.+++. ..++-.||..+++.++++
T Consensus 99 i~~gk---rrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAer 175 (211)
T PTZ00032 99 IIKGK---RRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRK 175 (211)
T ss_pred HHcCC---CcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHH
Confidence 44555 46777888898888888866 4788888888755555442 356788999999999999
Q ss_pred HHHcCCeEEEEEEEcCCc-CHHHHHH-hhhc-Cce
Q psy13610 81 ALEIGVSSVRINVRGLGP-GRLKALE-IGVS-SVR 112 (123)
Q Consensus 81 a~~~Gi~~i~V~ikG~G~-GR~~alk-al~~-g~~ 112 (123)
|+++||..|..==.|+=. ||-.||- ++|+ |++
T Consensus 176 Al~kGI~kVvFDRgGy~YHGRVkALAdaARe~GLk 210 (211)
T PTZ00032 176 ALSKGISKVRFDRAHYKYAGKVEALAEGARAVGLQ 210 (211)
T ss_pred HHHCCCCEEEEeCCCCeehhHHHHHHHHHHHcCCC
Confidence 999999998776444433 7877776 4544 553
No 19
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=94.16 E-value=0.99 Score=33.20 Aligned_cols=89 Identities=21% Similarity=0.256 Sum_probs=60.8
Q ss_pred cccEEEEEecCCCceEEEeCCC-CCEEEEEeeccccccc--C--CCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc
Q psy13610 24 NLPIMNIRVTKNNTILSLSDAK-GVVKLLRSCGMEGFKN--A--RKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP 98 (123)
Q Consensus 24 ~~~i~hI~st~NNTiitlTD~~-G~~l~~~S~G~~GfK~--~--rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~ 98 (123)
..+.+-|+-|.+|.+.-+.|.. +.++...|+=.--.++ . ....-.||..+++.++++|++.||+.+.+=..|+=.
T Consensus 28 ~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr~g~~y 107 (125)
T COG0256 28 GRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGGYKY 107 (125)
T ss_pred CCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEcCCCCCc
Confidence 5566778888888888876654 5567766654433321 1 133467899999999999999999999877777665
Q ss_pred -CHHHHH-Hhhh-cCce
Q psy13610 99 -GRLKAL-EIGV-SSVR 112 (123)
Q Consensus 99 -GR~~al-kal~-~g~~ 112 (123)
||=.++ ++++ .|++
T Consensus 108 hgRV~Ala~~AreaGL~ 124 (125)
T COG0256 108 HGRVAALADGAREAGLE 124 (125)
T ss_pred chHHHHHHHHHHHcCcC
Confidence 454443 4544 4665
No 20
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. 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-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=74.65 E-value=6.6 Score=30.87 Aligned_cols=55 Identities=20% Similarity=0.218 Sum_probs=41.2
Q ss_pred cccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceee
Q psy13610 59 FKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRIN 114 (123)
Q Consensus 59 fK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~ 114 (123)
..+....|.|....+.+.+.+... ..++..+|.|.|+|. |+..+-...+.|+++.
T Consensus 3 ~~~~~~~Tg~Gv~~~~~~~~~~~~-~~l~~~~v~I~G~G~VG~~~a~~L~~~g~~vv 58 (227)
T cd01076 3 SLGREEATGRGVAYATREALKKLG-IGLAGARVAIQGFGNVGSHAARFLHEAGAKVV 58 (227)
T ss_pred CCCCCccchHHHHHHHHHHHHhcC-CCccCCEEEEECCCHHHHHHHHHHHHCCCEEE
Confidence 345556788887777776665543 457889999999995 8888877778888876
No 21
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. 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-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=67.98 E-value=11 Score=30.56 Aligned_cols=54 Identities=11% Similarity=0.034 Sum_probs=38.3
Q ss_pred ccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceee
Q psy13610 60 KNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRIN 114 (123)
Q Consensus 60 K~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~ 114 (123)
.+....|-|....+.+.+.+.. ...++..+|.|.|||- |+.++-.....|.++.
T Consensus 11 ~gR~~aTg~Gv~~~~~~~~~~~-~~~l~g~~vaIqGfGnVG~~~a~~L~e~Gakvv 65 (254)
T cd05313 11 LIRPEATGYGLVYFVEEMLKDR-NETLKGKRVAISGSGNVAQYAAEKLLELGAKVV 65 (254)
T ss_pred CCCCchhHHHHHHHHHHHHHhc-CCCcCCCEEEEECCCHHHHHHHHHHHHCCCEEE
Confidence 4445677777777766655544 4567789999999996 6766665667787775
No 22
>PRK14030 glutamate dehydrogenase; Provisional
Probab=65.88 E-value=15 Score=32.22 Aligned_cols=64 Identities=13% Similarity=0.047 Sum_probs=45.2
Q ss_pred CCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceeee
Q psy13610 46 GVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRINV 115 (123)
Q Consensus 46 G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~~ 115 (123)
|+++.| .|+.| ....|-|....+++.+.+.. ...++..+|.|.|||- |..+|.+....|.++-.
T Consensus 192 Gkp~~~--gGs~g---r~~ATg~Gv~~~~~~~~~~~-g~~l~g~~vaIQGfGnVG~~aA~~L~e~GakvVa 256 (445)
T PRK14030 192 GKGLEF--GGSLI---RPEATGFGALYFVHQMLETK-GIDIKGKTVAISGFGNVAWGAATKATELGAKVVT 256 (445)
T ss_pred cccccc--CCCCC---CCCccHHHHHHHHHHHHHHc-CCCcCCCEEEEECCCHHHHHHHHHHHHCCCEEEE
Confidence 666654 44433 44678888877777665544 2347789999999995 88888877788888755
No 23
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=61.85 E-value=13 Score=30.43 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=24.3
Q ss_pred CChHHHHHHHHHHHHHHHHcCCeEEEEEEEc
Q psy13610 65 GTNIAAQAAGITIGKKALEIGVSSVRINVRG 95 (123)
Q Consensus 65 ~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG 95 (123)
+-|||++. .+++.+.|++.||..++..=-+
T Consensus 74 THPyAa~i-S~Na~~aake~gipy~r~eRP~ 103 (257)
T COG2099 74 THPYAARI-SQNAARAAKETGIPYLRLERPP 103 (257)
T ss_pred CChHHHHH-HHHHHHHHHHhCCcEEEEECCc
Confidence 45999995 5788999999999998876443
No 24
>KOG0408|consensus
Probab=61.75 E-value=3.6 Score=31.99 Aligned_cols=14 Identities=64% Similarity=1.379 Sum_probs=11.9
Q ss_pred CceeeeeccCCCCC
Q psy13610 110 SVRINVRGLGPGRL 123 (123)
Q Consensus 110 g~~i~~~~~~~~~~ 123 (123)
-+++-||||||||+
T Consensus 142 ~vrV~VkGlGpGRm 155 (190)
T KOG0408|consen 142 TVRVRVKGLGPGRM 155 (190)
T ss_pred EEEEEEecCCccHH
Confidence 45789999999985
No 25
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=60.55 E-value=17 Score=31.91 Aligned_cols=64 Identities=13% Similarity=0.049 Sum_probs=46.1
Q ss_pred CCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceee
Q psy13610 45 KGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRIN 114 (123)
Q Consensus 45 ~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~ 114 (123)
+|+.+.| .|+ .+....|-|....+++.+.+.. ...++..+|.|.|+|- |..+|.++...|.++-
T Consensus 200 TGK~~~~--GGs---~~r~eATG~Gv~~~~~~~l~~~-~~~l~Gk~VaVqG~GnVg~~aa~~L~e~GakVV 264 (454)
T PTZ00079 200 TGKNVKW--GGS---NIRPEATGYGLVYFVLEVLKKL-NDSLEGKTVVVSGSGNVAQYAVEKLLQLGAKVL 264 (454)
T ss_pred CCCCCCC--CCC---CCCCcccHHHHHHHHHHHHHHc-CCCcCCCEEEEECCCHHHHHHHHHHHHCCCEEE
Confidence 5666655 333 3445788888888877766544 4557889999999995 7777777777788775
No 26
>PLN02477 glutamate dehydrogenase
Probab=57.43 E-value=24 Score=30.46 Aligned_cols=53 Identities=15% Similarity=0.115 Sum_probs=39.0
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceee
Q psy13610 61 NARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRIN 114 (123)
Q Consensus 61 ~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~ 114 (123)
+....|-|....+++.+++. ....++..+|.|.|||. |+.++-.....|.+|.
T Consensus 180 ~r~~aTg~Gv~~~~~~~~~~-~g~~l~g~~VaIqGfGnVG~~~A~~L~e~GakVV 233 (410)
T PLN02477 180 GREAATGRGVVFATEALLAE-HGKSIAGQTFVIQGFGNVGSWAAQLIHEKGGKIV 233 (410)
T ss_pred CCCccchHHHHHHHHHHHHH-cCCCccCCEEEEECCCHHHHHHHHHHHHcCCEEE
Confidence 44477888887777766655 23346778999999996 8888766667788876
No 27
>COG4782 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.54 E-value=37 Score=29.35 Aligned_cols=51 Identities=22% Similarity=0.206 Sum_probs=40.4
Q ss_pred EEEEEeeccc-ccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc
Q psy13610 48 VKLLRSCGME-GFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP 98 (123)
Q Consensus 48 ~l~~~S~G~~-GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~ 98 (123)
+..|.|.|++ ||--.|.++.|+.-..+.-+-.-+.+...+.|+|.=.-.|-
T Consensus 151 vFSWPS~g~l~~Yn~DreS~~~Sr~aLe~~lr~La~~~~~~~I~ilAHSMGt 202 (377)
T COG4782 151 VFSWPSRGSLLGYNYDRESTNYSRPALERLLRYLATDKPVKRIYLLAHSMGT 202 (377)
T ss_pred EEEcCCCCeeeecccchhhhhhhHHHHHHHHHHHHhCCCCceEEEEEecchH
Confidence 5789999987 89999999999888775555555666779999998887663
No 28
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=55.35 E-value=46 Score=21.08 Aligned_cols=45 Identities=24% Similarity=0.249 Sum_probs=29.9
Q ss_pred CCCCCEEEEEeecccccccCCCC----ChHHHHHHHHHHHHHHHHcCCe
Q psy13610 43 DAKGVVKLLRSCGMEGFKNARKG----TNIAAQAAGITIGKKALEIGVS 87 (123)
Q Consensus 43 D~~G~~l~~~S~G~~GfK~~rK~----T~~Aa~~aa~~v~~~a~~~Gi~ 87 (123)
|+.|....+..-|-+|-.|..+. ++..|..+.+++.+.-...|+.
T Consensus 24 ~lfg~~~v~~~wGRiG~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 24 DLFGEWSLVRRWGRIGTKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred cCCCCEEEEEEECCCCCCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 55677888888999997777764 4455555555555555555653
No 29
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=49.91 E-value=29 Score=27.06 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=30.1
Q ss_pred ChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCce
Q psy13610 66 TNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVR 112 (123)
Q Consensus 66 T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~ 112 (123)
|-|....+.+.+.+... ..+...+|.|.|||. |+..+-...+.|.+
T Consensus 2 Tg~Gv~~~~~~~~~~~~-~~l~g~~vaIqGfGnVG~~~a~~L~~~G~~ 48 (217)
T cd05211 2 TGYGVVVAMKAAMKHLG-DSLEGLTVAVQGLGNVGWGLAKKLAEEGGK 48 (217)
T ss_pred chhHHHHHHHHHHHHcC-CCcCCCEEEEECCCHHHHHHHHHHHHcCCE
Confidence 34444444444443332 457788999999995 88888777777663
No 30
>PF00208 ELFV_dehydrog: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; InterPro: IPR006096 Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases (1.4.1.2 from EC, 1.4.1.3 from EC, and 1.4.1.4 from EC) (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate [, ]. GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids []. Leucine dehydrogenase (1.4.1.9 from EC) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues []. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. Phenylalanine dehydrogenase (1.4.1.20 from EC) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate []. Valine dehydrogenase (1.4.1.8 from EC) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate []. This entry represents the C-terminal domain of these proteins.; GO: 0016491 oxidoreductase activity, 0006520 cellular amino acid metabolic process, 0055114 oxidation-reduction process; PDB: 1LEH_A 3AOG_D 3AOE_A 2YFQ_B 2YFH_B 1HRD_A 1K89_A 1AUP_A 1BGV_A 1B26_C ....
Probab=46.15 E-value=19 Score=28.70 Aligned_cols=50 Identities=14% Similarity=0.121 Sum_probs=33.4
Q ss_pred CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCcee
Q psy13610 64 KGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRI 113 (123)
Q Consensus 64 K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i 113 (123)
..|-|....+.+.+.+......++..+|.|.|||. |+..+......|.+|
T Consensus 8 ~aTg~GV~~~~~~~~~~~~~~~l~g~~v~IqGfG~VG~~~a~~l~~~Ga~v 58 (244)
T PF00208_consen 8 EATGYGVAYAIEAALEHLGGDSLEGKRVAIQGFGNVGSHAARFLAELGAKV 58 (244)
T ss_dssp THHHHHHHHHHHHHHHHTTCHSSTTCEEEEEESSHHHHHHHHHHHHTTEEE
T ss_pred cchHHHHHHHHHHHHHHcCCCCcCCCEEEEECCCHHHHHHHHHHHHcCCEE
Confidence 45555555555555554222236789999999996 777777777778766
No 31
>PRK09414 glutamate dehydrogenase; Provisional
Probab=45.44 E-value=42 Score=29.35 Aligned_cols=53 Identities=11% Similarity=-0.001 Sum_probs=39.5
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceee
Q psy13610 61 NARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRIN 114 (123)
Q Consensus 61 ~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~ 114 (123)
+....|-|....+++.+.+.. ...++..+|.|.|||- |+.+|......|.+|.
T Consensus 206 gr~~aTg~Gv~~~~~~~~~~~-~~~l~g~rVaIqGfGnVG~~~A~~L~~~GakVV 259 (445)
T PRK09414 206 IRTEATGYGLVYFAEEMLKAR-GDSFEGKRVVVSGSGNVAIYAIEKAQQLGAKVV 259 (445)
T ss_pred CCCCcccHHHHHHHHHHHHhc-CCCcCCCEEEEECCCHHHHHHHHHHHHCCCEEE
Confidence 345788888887777666553 4457889999999995 7877776767787764
No 32
>PRK14031 glutamate dehydrogenase; Provisional
Probab=45.39 E-value=51 Score=28.87 Aligned_cols=55 Identities=11% Similarity=-0.026 Sum_probs=40.6
Q ss_pred ccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceeee
Q psy13610 60 KNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRINV 115 (123)
Q Consensus 60 K~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~~ 115 (123)
.+....|-|....+.+.+.+.. ...++..+|.|.|+|. |..+|-+++..|.++.+
T Consensus 201 ~~r~~aTg~Gv~~~~~~~~~~~-g~~l~g~rVaVQGfGNVG~~aA~~L~e~GAkVVa 256 (444)
T PRK14031 201 LIRPEATGYGNIYFLMEMLKTK-GTDLKGKVCLVSGSGNVAQYTAEKVLELGGKVVT 256 (444)
T ss_pred CCCCcccHHHHHHHHHHHHHhc-CCCcCCCEEEEECCCHHHHHHHHHHHHCCCEEEE
Confidence 4445788888877776665544 2347889999999996 77777777788988875
No 33
>PRK14444 acylphosphatase; Provisional
Probab=42.86 E-value=79 Score=21.41 Aligned_cols=37 Identities=22% Similarity=0.280 Sum_probs=23.6
Q ss_pred CCeEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 85 GVSSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 85 Gi~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
+++..++.++| -|. |..+.+ |.+-|+.=-|||+..|+
T Consensus 2 ~m~~~~i~v~G~VQGVGF-R~~v~~~A~~lgl~G~V~N~~dG~ 43 (92)
T PRK14444 2 DMVRAHVFISGRVQGVNF-RAYTRDRAREAGVKGWVRNLSDGR 43 (92)
T ss_pred CcEEEEEEEEEeeCCcCc-HHHHHHHHHHhCCEEEEEECCCCc
Confidence 45566666666 444 555555 55667777778877764
No 34
>COG0334 GdhA Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]
Probab=42.60 E-value=39 Score=29.50 Aligned_cols=66 Identities=20% Similarity=0.168 Sum_probs=43.2
Q ss_pred CCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceeeee
Q psy13610 45 KGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP-GRLKALEIGVSSVRINVR 116 (123)
Q Consensus 45 ~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~~~ 116 (123)
+|+++.+--++ +....|-|......+. +.+....+++..+|-|.|+|- |+.+|.++...|-++-+=
T Consensus 170 TGKp~~~GGS~-----~r~~aTg~Gv~~~~~~-a~~~~g~~l~G~rVaVQG~GNVg~~aa~~l~~~GAkvva~ 236 (411)
T COG0334 170 TGKPLELGGSL-----GRSEATGYGVFYAIRE-ALKALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAV 236 (411)
T ss_pred cCCcccccCCC-----CCCcccceehHHHHHH-HHHHcCCCcCCCEEEEECccHHHHHHHHHHHHcCCEEEEE
Confidence 46666553222 2335777777666663 334444458999999999995 777777776778887553
No 35
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=41.74 E-value=45 Score=26.77 Aligned_cols=27 Identities=26% Similarity=0.288 Sum_probs=22.7
Q ss_pred CChHHHHHHHHHHHHHHHHcCCeEEEEE
Q psy13610 65 GTNIAAQAAGITIGKKALEIGVSSVRIN 92 (123)
Q Consensus 65 ~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ 92 (123)
..|||.+ +.+.+.+.|+++|+.++++.
T Consensus 73 tHPfA~~-is~~a~~a~~~~~ipylR~e 99 (256)
T TIGR00715 73 THPFAAQ-ITTNATAVCKELGIPYVRFE 99 (256)
T ss_pred CCHHHHH-HHHHHHHHHHHhCCcEEEEE
Confidence 4688886 55778999999999999985
No 36
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=40.07 E-value=2e+02 Score=24.20 Aligned_cols=68 Identities=19% Similarity=0.253 Sum_probs=47.3
Q ss_pred ccCCe-ecc-cccEEEEEecCCCceEEE--eCCCCCEEEEEeecc----cccccCCCCChHHHHHHHHHHHHHHHHc
Q psy13610 16 IFDGL-KFK-NLPIMNIRVTKNNTILSL--SDAKGVVKLLRSCGM----EGFKNARKGTNIAAQAAGITIGKKALEI 84 (123)
Q Consensus 16 ~~~g~-~~~-~~~i~hI~st~NNTiitl--TD~~G~~l~~~S~G~----~GfK~~rK~T~~Aa~~aa~~v~~~a~~~ 84 (123)
|.+++ +|. +.+.+-|..|..|+|+-+ .++.|+.+.++.... .|+|++....| ||+.++.-++.++.+.
T Consensus 37 i~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k~gl~N~~-AAY~TGlL~arR~L~k 112 (300)
T PTZ00069 37 ILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIPVGLTNYA-AAYATGLLLARRLLKK 112 (300)
T ss_pred HHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCCccHH-HHHHHHHHHHHHHHHh
Confidence 45554 232 456677889999998777 468888766654432 48888877666 7788888888777665
No 37
>PF10670 DUF4198: Domain of unknown function (DUF4198)
Probab=39.82 E-value=54 Score=24.21 Aligned_cols=37 Identities=16% Similarity=0.155 Sum_probs=25.5
Q ss_pred ccCCeecccccEEEEEecCCC-----ceEEEeCCCCCEEEEE
Q psy13610 16 IFDGLKFKNLPIMNIRVTKNN-----TILSLSDAKGVVKLLR 52 (123)
Q Consensus 16 ~~~g~~~~~~~i~hI~st~NN-----TiitlTD~~G~~l~~~ 52 (123)
||||+|.....|--..-.... ....-||.+|.+.+..
T Consensus 158 l~~GkPl~~a~V~~~~~~~~~~~~~~~~~~~TD~~G~~~~~~ 199 (215)
T PF10670_consen 158 LFDGKPLAGAEVEAFSPGGWYDVEHEAKTLKTDANGRATFTL 199 (215)
T ss_pred EECCeEcccEEEEEEECCCccccccceEEEEECCCCEEEEec
Confidence 699999876444333333222 7889999999987764
No 38
>KOG2299|consensus
Probab=38.98 E-value=87 Score=26.16 Aligned_cols=62 Identities=18% Similarity=0.254 Sum_probs=50.1
Q ss_pred eecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHHhh--hcCceeeee
Q psy13610 53 SCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKALEIG--VSSVRINVR 116 (123)
Q Consensus 53 S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alkal--~~g~~i~~~ 116 (123)
|++|+++ .+=+-..-+.-+|-.+++.+.+.|++-.+|++--.|+-+..=.|.. =.|++++|.
T Consensus 106 S~~Ml~r--~kynLNevshdsam~LI~~v~~~gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~ 169 (301)
T KOG2299|consen 106 SASMLRR--NKYNLNEVSHDSAMGLIDEVLDQGVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVT 169 (301)
T ss_pred HHHHHHH--hcCCchhhhhHHHHHHHHHHHHhCCceEEEEEecCCChHHHHHHHHhhCCCeEEEEe
Confidence 6778777 3445677788888889999999999999999999999887766654 448999885
No 39
>KOG0747|consensus
Probab=38.10 E-value=56 Score=27.75 Aligned_cols=55 Identities=15% Similarity=0.222 Sum_probs=34.7
Q ss_pred CCChHHHHHHHHHHHHHH--HHcCCeEEEEEEEc-CCcCHHH---HH---HhhhcCceeeeecc
Q psy13610 64 KGTNIAAQAAGITIGKKA--LEIGVSSVRINVRG-LGPGRLK---AL---EIGVSSVRINVRGL 118 (123)
Q Consensus 64 K~T~~Aa~~aa~~v~~~a--~~~Gi~~i~V~ikG-~G~GR~~---al---kal~~g~~i~~~~~ 118 (123)
-.+||||..||..+.=.+ .+.|+..+.++..+ .||++-. .. +..+-+=+..++|=
T Consensus 153 PtnpyAasKaAaE~~v~Sy~~sy~lpvv~~R~nnVYGP~q~~~klipkFi~l~~~~~~~~i~g~ 216 (331)
T KOG0747|consen 153 PTNPYAASKAAAEMLVRSYGRSYGLPVVTTRMNNVYGPNQYPEKLIPKFIKLAMRGKEYPIHGD 216 (331)
T ss_pred CCCchHHHHHHHHHHHHHHhhccCCcEEEEeccCccCCCcChHHHhHHHHHHHHhCCCcceecC
Confidence 478999987775443333 46888888888887 7886632 22 23344555555553
No 40
>PRK13260 2,3-diketo-L-gulonate reductase; Provisional
Probab=37.55 E-value=1.3e+02 Score=25.25 Aligned_cols=69 Identities=12% Similarity=0.019 Sum_probs=48.9
Q ss_pred CCCCCEE-EEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCc
Q psy13610 43 DAKGVVK-LLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSV 111 (123)
Q Consensus 43 D~~G~~l-~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~ 111 (123)
|++.++. ...+..+.-+.+.+--.++++..|.+.+.++|++.|+-.|-|+=.- +|.....+.++...|+
T Consensus 62 ~~~~~~~v~~~~~a~a~~Dg~~g~G~~~~~~am~~aiekAr~~Gi~~v~vrns~H~G~~g~y~~~aa~~G~ 132 (332)
T PRK13260 62 IPDAQPQRVTSLGAIEQWDAQRAIGNLTAKKMMDRAIELARDHGIGLVALRNANHWMRGGSYGWQAAEKGY 132 (332)
T ss_pred CCCCCeEEEecCCcEEEEECCCCchHHHHHHHHHHHHHHHHHhCEEEEEEcCCCchhhHHHHHHHHHHCCC
Confidence 4444443 3333444456667778899999999999999999999887765443 6776667777776665
No 41
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=37.31 E-value=1.1e+02 Score=23.87 Aligned_cols=70 Identities=20% Similarity=0.260 Sum_probs=50.0
Q ss_pred ccccEEEEEecCCCceEEEeCCCCCEEEEEeecccccc--cCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCH
Q psy13610 23 KNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFK--NARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGR 100 (123)
Q Consensus 23 ~~~~i~hI~st~NNTiitlTD~~G~~l~~~S~G~~GfK--~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR 100 (123)
+-.|.++|.=+.|+-+.. .+|..||- -+.|.--||-+.. ..+.++|+++||+.|-|.-..=++..
T Consensus 79 ~ivG~i~lRh~Ln~~ll~------------~gGHIGY~VrPseR~KGYA~emL-kl~L~~ar~lgi~~Vlvtcd~dN~AS 145 (174)
T COG3981 79 QIVGFINLRHQLNDFLLE------------EGGHIGYSVRPSERRKGYAKEML-KLALEKARELGIKKVLVTCDKDNIAS 145 (174)
T ss_pred cEEEEEEeeeecchHHHh------------cCCcccceeChhhhccCHHHHHH-HHHHHHHHHcCCCeEEEEeCCCCchh
Confidence 456667766666554332 37888875 3446677888765 66789999999999999998877765
Q ss_pred HHHHH
Q psy13610 101 LKALE 105 (123)
Q Consensus 101 ~~alk 105 (123)
..+|.
T Consensus 146 rkvI~ 150 (174)
T COG3981 146 RKVIE 150 (174)
T ss_pred hHHHH
Confidence 55554
No 42
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=36.74 E-value=48 Score=26.51 Aligned_cols=30 Identities=17% Similarity=0.199 Sum_probs=23.8
Q ss_pred CChHHHHHHHHHHHHHHHHcCCeEEEEEEEc
Q psy13610 65 GTNIAAQAAGITIGKKALEIGVSSVRINVRG 95 (123)
Q Consensus 65 ~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG 95 (123)
+-|||.+. .+.+.+.|+++||..+++.=..
T Consensus 74 THPfA~~i-s~na~~a~~~~~ipylR~eRp~ 103 (249)
T PF02571_consen 74 THPFAAEI-SQNAIEACRELGIPYLRFERPS 103 (249)
T ss_pred CCchHHHH-HHHHHHHHhhcCcceEEEEcCC
Confidence 34999884 4778999999999999876433
No 43
>TIGR01139 cysK cysteine synthase A. This model distinguishes cysteine synthase A (CysK) from cysteine synthase B (CysM). CysM differs in having a broader specificity that also allows the use of thiosulfate to produce cysteine thiosulfonate.
Probab=36.38 E-value=98 Score=24.64 Aligned_cols=45 Identities=20% Similarity=0.192 Sum_probs=29.8
Q ss_pred CCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHH
Q psy13610 45 KGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKALE 105 (123)
Q Consensus 45 ~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alk 105 (123)
.|.++...|+|+ .+..++..|+.+|++..-+.=++..+.+...++
T Consensus 56 ~g~~vv~aSsGN----------------~g~alA~~a~~~Gl~~~i~vp~~~~~~k~~~~~ 100 (298)
T TIGR01139 56 PGKTIVEPTSGN----------------TGIALAMVAAARGYKLILTMPETMSIERRKLLK 100 (298)
T ss_pred CCCEEEEeCCCh----------------hHHHHHHHHHHcCCeEEEEeCCccCHHHHHHHH
Confidence 446788999998 555566677888998666655565555443433
No 44
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=35.70 E-value=50 Score=26.42 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=22.7
Q ss_pred CChHHHHHHHHHHHHHHHHcCCeEEEEE
Q psy13610 65 GTNIAAQAAGITIGKKALEIGVSSVRIN 92 (123)
Q Consensus 65 ~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ 92 (123)
+-|||.+.. +.+.+.|.++||.+++..
T Consensus 73 THPfA~~is-~~a~~ac~~~~ipyiR~e 99 (248)
T PRK08057 73 THPYAAQIS-ANAAAACRALGIPYLRLE 99 (248)
T ss_pred CCccHHHHH-HHHHHHHHHhCCcEEEEe
Confidence 349999854 778899999999999886
No 45
>TIGR00829 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters.
Probab=35.32 E-value=75 Score=21.28 Aligned_cols=28 Identities=21% Similarity=0.219 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHcCCeEEEEEEEcCC
Q psy13610 69 AAQAAGITIGKKALEIGVSSVRINVRGLG 97 (123)
Q Consensus 69 Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G 97 (123)
.+++|++.+.+.++++|+. +.|..+|..
T Consensus 12 ht~lAae~L~~aA~~~G~~-i~VE~qg~~ 39 (85)
T TIGR00829 12 HTFMAAEALEKAAKKRGWE-VKVETQGSV 39 (85)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEecCCc
Confidence 4678889889999999987 888888843
No 46
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=34.01 E-value=48 Score=28.25 Aligned_cols=44 Identities=20% Similarity=0.221 Sum_probs=30.6
Q ss_pred EEEEEeecccccccCCCCChHHHHHHHHHHHHH---HHHcCCeEEEEE
Q psy13610 48 VKLLRSCGMEGFKNARKGTNIAAQAAGITIGKK---ALEIGVSSVRIN 92 (123)
Q Consensus 48 ~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~---a~~~Gi~~i~V~ 92 (123)
-+|...|.-|+|.-.. +.+-|....-+.|.++ +.++|++.|.+.
T Consensus 67 N~C~~~C~fCaF~~~~-~~~~~y~Ls~eeI~~~~~~~~~~G~~Evli~ 113 (370)
T COG1060 67 NICVNDCTFCAFYRKP-GDPKAYTLSPEEILEEVREAVKRGITEVLIV 113 (370)
T ss_pred hhhcCCCCccccccCC-CCccccccCHHHHHHHHHHHHHcCCeEEEEe
Confidence 3678899999999776 4445555555555554 456899988765
No 47
>cd01075 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. 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-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily inc
Probab=31.79 E-value=96 Score=23.59 Aligned_cols=52 Identities=15% Similarity=0.095 Sum_probs=32.9
Q ss_pred ChHHHHHHHHHHHHHH-HHcCCeEEEEEEEcCCc-CHHHHHHhhhcCceeeeec
Q psy13610 66 TNIAAQAAGITIGKKA-LEIGVSSVRINVRGLGP-GRLKALEIGVSSVRINVRG 117 (123)
Q Consensus 66 T~~Aa~~aa~~v~~~a-~~~Gi~~i~V~ikG~G~-GR~~alkal~~g~~i~~~~ 117 (123)
|-|....+.+.+.+.. ....++.-+|-|-|+|. |+..+.+....|.++.+=.
T Consensus 5 Tg~Gv~~~~~~~~~~~~~~~~l~gk~v~I~G~G~vG~~~A~~L~~~G~~Vvv~D 58 (200)
T cd01075 5 TAYGVFLGMKAAAEHLLGTDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVAD 58 (200)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEc
Confidence 3444444444444443 12346667899999995 7777777778898887643
No 48
>PRK14447 acylphosphatase; Provisional
Probab=31.49 E-value=1.4e+02 Score=20.20 Aligned_cols=35 Identities=26% Similarity=0.226 Sum_probs=23.4
Q ss_pred CeEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCC
Q psy13610 86 VSSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPG 121 (123)
Q Consensus 86 i~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~ 121 (123)
+..+++.++| -|. |..+.+ |.+.|+.=.|||+..|
T Consensus 3 ~~~~~~~v~G~VQGVGF-R~~~~~~A~~~gl~G~V~N~~dG 42 (95)
T PRK14447 3 MVRAHLFIRGKVQGVFF-RQSMKEVANRNGVRGWVRNRSDG 42 (95)
T ss_pred cEEEEEEEEEecCCccc-hHHHHHHHhhcCeEEEEEECCCC
Confidence 4556666666 444 555555 5677888888888777
No 49
>PRK14743 thrL thr operon leader peptide; Provisional
Probab=31.17 E-value=27 Score=18.88 Aligned_cols=15 Identities=20% Similarity=0.169 Sum_probs=12.0
Q ss_pred cCCCceEEEeCCCCC
Q psy13610 33 TKNNTILSLSDAKGV 47 (123)
Q Consensus 33 t~NNTiitlTD~~G~ 47 (123)
+.+-||+|.|+-.|+
T Consensus 5 s~~ttiit~t~ttgn 19 (26)
T PRK14743 5 GMITTIITTTITTGN 19 (26)
T ss_pred eeEEEEEEEEEecCC
Confidence 456789999988876
No 50
>PRK14742 thrL thr operon leader peptide; Provisional
Probab=30.64 E-value=28 Score=19.06 Aligned_cols=16 Identities=25% Similarity=0.557 Sum_probs=12.9
Q ss_pred ecCCCceEEEeCCCCC
Q psy13610 32 VTKNNTILSLSDAKGV 47 (123)
Q Consensus 32 st~NNTiitlTD~~G~ 47 (123)
-+.+-||||-|+-.|+
T Consensus 10 i~l~ttiittt~ttg~ 25 (28)
T PRK14742 10 ISLNTTIITTTETTGY 25 (28)
T ss_pred EEeEEEEEEEEEeccc
Confidence 4567899999998876
No 51
>PF11589 DUF3244: Domain of unknown function (DUF3244); InterPro: IPR021638 This family of proteins with unknown function appear to be restricted to Bacteroidetes. The protein may have an immunoglobulin-like beta-sandwich fold however this cannot be confirmed. ; PDB: 3D33_B 3SD2_A.
Probab=30.48 E-value=63 Score=22.09 Aligned_cols=29 Identities=10% Similarity=0.243 Sum_probs=19.0
Q ss_pred EEEEecCCCceEEEeCCCCCEEEEEeecc
Q psy13610 28 MNIRVTKNNTILSLSDAKGVVKLLRSCGM 56 (123)
Q Consensus 28 ~hI~st~NNTiitlTD~~G~~l~~~S~G~ 56 (123)
++......+.-|+++|.+|+++...+-..
T Consensus 41 I~F~~~~~~vtI~I~d~~G~vVy~~~~~~ 69 (106)
T PF11589_consen 41 IEFESPIGDVTITIKDSTGNVVYSETVSN 69 (106)
T ss_dssp EEESS--SEEEEEEEETT--EEEEEEESC
T ss_pred EEEcCCCCCEEEEEEeCCCCEEEEEEccC
Confidence 34455667888999999999998876544
No 52
>PF02615 Ldh_2: Malate/L-lactate dehydrogenase; InterPro: IPR003767 The malate dehydrogenase (MDH) of some extremophilies is more similar to the L-lactate dehydrogenases (L-LDH) 1.1.1.27 from EC from various sources than to other MDHs []. This family consists of bacterial and archaeal malate/L-lactate dehydrogenases. The archaebacterial malate dehydrogenase 1.1.1.37 from EC, 1.1.1.82 from EC deviates from the eubacterial and eukaryotic enzymes having a low selectivity for the coenzyme (NAD(H) or NADP(H)) and catalyzing the reduction of oxalacetate to malate more efficiently than the reverse reaction [].; GO: 0016491 oxidoreductase activity, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 1VBI_A 2G8Y_B 2X06_H 1Z2I_B 1X0A_A 1V9N_A 1XRH_G 3I0P_A 2CWH_B 2CWF_B ....
Probab=29.68 E-value=2.4e+02 Score=23.61 Aligned_cols=69 Identities=17% Similarity=0.099 Sum_probs=46.8
Q ss_pred CCCCCEEEEEeec-ccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCc
Q psy13610 43 DAKGVVKLLRSCG-MEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSV 111 (123)
Q Consensus 43 D~~G~~l~~~S~G-~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~ 111 (123)
|++.++..-...+ +.-+.+..--.++++..|.+.+.++|++.|+-.+-|+=.. +|.....+.++.+.|+
T Consensus 62 ~~~~~~~i~~~~~a~~~vDg~~g~G~~~~~~A~~~aiekA~~~Gia~v~vrns~H~G~~g~y~~~aa~~G~ 132 (335)
T PF02615_consen 62 NPRAEPKIVRETPASAVVDGDNGFGQVAAKFAMELAIEKAKEHGIAAVAVRNSNHFGALGYYAEMAAEQGM 132 (335)
T ss_dssp BSS---EEEEEETTEEEEEETTBBHHHHHHHHHHHHHHHHHHHSEEEEEEEEEE--S-THHHHHHHHHTTS
T ss_pred cCCCCeEEEeccCeEEEEECCCCccHHHHHHHHHHHHHHHHHcCEEEEEEecCCCCCccHHHHHHHHHCCC
Confidence 3444443333333 3355666667789999999999999999999887776555 8888888888887775
No 53
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.27 E-value=1.1e+02 Score=23.76 Aligned_cols=39 Identities=23% Similarity=0.241 Sum_probs=30.1
Q ss_pred ChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCC--cCHHHHHH
Q psy13610 66 TNIAAQAAGITIGKKALEIGVSSVRINVRGLG--PGRLKALE 105 (123)
Q Consensus 66 T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G--~GR~~alk 105 (123)
|-.=|+++-.+....|.+.|+..+.| |.|-| .|...+||
T Consensus 105 tq~eAr~~L~~Fi~~a~~~~~rcv~V-ihGkG~s~g~~~vLK 145 (184)
T COG2840 105 TQEEARQELGAFIARARAEGLRCVLV-IHGKGRSKGSKPVLK 145 (184)
T ss_pred CHHHHHHHHHHHHHHHHHhCCcEEEE-EeCCCcCCCCchhHH
Confidence 44456677777888999999999987 46766 67788887
No 54
>PLN00105 malate/L-lactate dehydrogenase; Provisional
Probab=28.99 E-value=2.2e+02 Score=23.85 Aligned_cols=59 Identities=14% Similarity=-0.022 Sum_probs=46.0
Q ss_pred ecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEE-Ec-CCcCHHHHHHhhhcCce
Q psy13610 54 CGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINV-RG-LGPGRLKALEIGVSSVR 112 (123)
Q Consensus 54 ~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~i-kG-~G~GR~~alkal~~g~~ 112 (123)
....-+.+..--.++++..|.+.+.++|++.||-.|-|+= .. +|..-..+.++...|+-
T Consensus 63 ~a~a~vDg~~g~G~~~~~~am~~aiekAr~~Gi~~v~vrn~S~H~G~~g~y~~~aa~~Gli 123 (330)
T PLN00105 63 KTSAAVDGNKNAGMLVLHHAMDMAIDKAKTHGVGIVGTCNTSTSTGALGYYAEKVAQQGLI 123 (330)
T ss_pred CcEEEEECCCCccHHHHHHHHHHHHHHHHHhCEEEEEEeCCcCCccchHHHHHHHHHCCCe
Confidence 3344456666677899999999999999999999888876 33 88777778888877763
No 55
>COG1980 Archaeal fructose 1,6-bisphosphatase [Carbohydrate transport and metabolism]
Probab=28.79 E-value=67 Score=27.23 Aligned_cols=16 Identities=44% Similarity=0.746 Sum_probs=13.1
Q ss_pred hhhcCceeeeeccCCC
Q psy13610 106 IGVSSVRINVRGLGPG 121 (123)
Q Consensus 106 al~~g~~i~~~~~~~~ 121 (123)
.|...++=||||+|||
T Consensus 96 LL~DaFSGNvrGmGPg 111 (369)
T COG1980 96 LLKDAFSGNVRGMGPG 111 (369)
T ss_pred hhhhhhccccccCCCc
Confidence 4566777899999998
No 56
>PRK15025 ureidoglycolate dehydrogenase; Provisional
Probab=28.36 E-value=2.3e+02 Score=23.98 Aligned_cols=58 Identities=16% Similarity=0.044 Sum_probs=44.0
Q ss_pred ecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCc
Q psy13610 54 CGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSV 111 (123)
Q Consensus 54 ~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~ 111 (123)
..+.-..+..--.++++..|.+.+.++|++.|+-.+-|+=.. +|.....+.++.+.|+
T Consensus 74 ~a~a~vDg~~g~G~~a~~~Am~~aiekA~~~Gi~~v~vrnS~H~G~~g~y~~~aa~~Gl 132 (349)
T PRK15025 74 PCSAILHADNAAGQVAAKMGMEHAIETAKQNGVAVVGISRMGHSGAISYFVQQAARAGL 132 (349)
T ss_pred CcEEEEECCCCchHHHHHHHHHHHHHHHHHhCEEEEEEeCCCccccHHHHHHHHHHCCC
Confidence 333345666677899999999999999999999877665433 7777777777777765
No 57
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.16 E-value=90 Score=23.21 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHcCCeEEEEEEEcCCcCH
Q psy13610 72 AAGITIGKKALEIGVSSVRINVRGLGPGR 100 (123)
Q Consensus 72 ~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR 100 (123)
...+++.+...++||+.|.|++||-|.-|
T Consensus 64 k~skkvlkaleq~gI~vIPvk~KgrGrpr 92 (139)
T COG1710 64 KVSKKVLKALEQMGIKVIPVKLKGRGRPR 92 (139)
T ss_pred HHHHHHHHHHHhCCceEeeeeecCCCCCc
Confidence 46677888888899999999999977544
No 58
>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts). This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.
Probab=27.65 E-value=1.9e+02 Score=22.83 Aligned_cols=45 Identities=24% Similarity=0.119 Sum_probs=38.3
Q ss_pred CCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhh
Q psy13610 64 KGTNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGV 108 (123)
Q Consensus 64 K~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~ 108 (123)
...|.|+|..+.++..+.++..-..+.|.|=| .|.|+-+.+.++.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IllvG~tGvGKSSliNaLl 52 (249)
T cd01853 7 QFFPDAAQTKALELEAKGKEELDFSLTILVLGKTGVGKSSTINSIF 52 (249)
T ss_pred ccCcHHHHHHHHHHHHHhhhhccCCeEEEEECCCCCcHHHHHHHHh
Confidence 56789999999988888888888889999988 8899999988653
No 59
>PF05990 DUF900: Alpha/beta hydrolase of unknown function (DUF900); InterPro: IPR010297 This domain is associated with proteins of unknown function, which are hydrolase-like.
Probab=27.59 E-value=1.1e+02 Score=23.91 Aligned_cols=54 Identities=20% Similarity=0.260 Sum_probs=32.9
Q ss_pred CCCCE--EEEEeeccc-ccccCCCCChHHHHHHHHHHHHHHHH-cCCeEEEEEEEcCCc
Q psy13610 44 AKGVV--KLLRSCGME-GFKNARKGTNIAAQAAGITIGKKALE-IGVSSVRINVRGLGP 98 (123)
Q Consensus 44 ~~G~~--l~~~S~G~~-GfK~~rK~T~~Aa~~aa~~v~~~a~~-~Gi~~i~V~ikG~G~ 98 (123)
..|.+ ..|.|.|.. +|...+.+..+++...+ ++.+...+ .+.+.|+|.-...|-
T Consensus 47 ~~~~~i~FsWPS~g~~~~Y~~d~~~a~~s~~~l~-~~L~~L~~~~~~~~I~ilaHSMG~ 104 (233)
T PF05990_consen 47 FPGVVILFSWPSDGSLLGYFYDRESARFSGPALA-RFLRDLARAPGIKRIHILAHSMGN 104 (233)
T ss_pred CCceEEEEEcCCCCChhhhhhhhhhHHHHHHHHH-HHHHHHHhccCCceEEEEEeCchH
Confidence 34444 467787765 67766665555544443 34444444 488889988887663
No 60
>PRK10646 ADP-binding protein; Provisional
Probab=27.43 E-value=95 Score=23.23 Aligned_cols=44 Identities=18% Similarity=0.168 Sum_probs=30.2
Q ss_pred ChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCcee
Q psy13610 66 TNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSVRI 113 (123)
Q Consensus 66 T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~~i 113 (123)
++.+.+..|+.+++.++. . --|.+.| .|.|+-+..|++..++.+
T Consensus 10 s~~~t~~l~~~la~~l~~---g-~vi~L~GdLGaGKTtf~rgl~~~Lg~ 54 (153)
T PRK10646 10 DEQATLDLGARVAKACDG---A-TVIYLYGDLGAGKTTFSRGFLQALGH 54 (153)
T ss_pred CHHHHHHHHHHHHHhCCC---C-cEEEEECCCCCCHHHHHHHHHHHcCC
Confidence 455666666666654432 2 2478999 999999999987666544
No 61
>TIGR01136 cysKM cysteine synthases. This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff.
Probab=27.33 E-value=1.6e+02 Score=23.44 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=25.6
Q ss_pred CCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHH
Q psy13610 45 KGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKA 103 (123)
Q Consensus 45 ~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~a 103 (123)
.|+++.+.|+|+ .+..++-.|+.+|++..-+.=++..+.+...
T Consensus 57 ~g~~vv~aSsGN----------------~g~alA~~a~~~G~~~~i~vp~~~~~~k~~~ 99 (299)
T TIGR01136 57 PGDTIIEATSGN----------------TGIALAMVAAAKGYKLILTMPETMSLERRKL 99 (299)
T ss_pred CCCEEEEeCCCh----------------HHHHHHHHHHHcCCcEEEEECCCCCHHHHHH
Confidence 346788889988 3444556677788875544434433333333
No 62
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=27.30 E-value=1.4e+02 Score=22.76 Aligned_cols=49 Identities=20% Similarity=0.158 Sum_probs=31.6
Q ss_pred ceEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeE
Q psy13610 37 TILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSS 88 (123)
Q Consensus 37 TiitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~ 88 (123)
-++-+.|++-.++.| ++|.+-..|++ |...+..|++++++..+++|+..
T Consensus 39 li~Rl~~Pk~t~lIF-~SGKiv~tGak--s~~~a~~a~~~~~~~L~~~g~~~ 87 (174)
T cd04518 39 LVYRLEDPKIAALIF-RSGKMVCTGAK--SVEDLHRAVKEIIKKLKDYGIKV 87 (174)
T ss_pred EEEEccCCcEEEEEE-CCCeEEEEccC--CHHHHHHHHHHHHHHHHhcCCCc
Confidence 344455565555555 44555555544 45677778899999999999653
No 63
>PRK14450 acylphosphatase; Provisional
Probab=27.30 E-value=2e+02 Score=19.27 Aligned_cols=34 Identities=15% Similarity=0.053 Sum_probs=21.3
Q ss_pred EEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 88 SVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 88 ~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
.+++.++| -|. |..+.+ |.+.|+.=.|||+..|+
T Consensus 3 ~~~~~v~G~VQGVGF-R~~v~~~A~~~~l~G~V~N~~dG~ 41 (91)
T PRK14450 3 CLKAIVKGKVQGVYF-RDFTRTQATRLGLCGYAKNLANGN 41 (91)
T ss_pred EEEEEEEEEecCcCc-HHHHHHHHHHcCCEEEEEECCCCC
Confidence 44555555 555 555555 56778877788887663
No 64
>PF03123 CAT_RBD: CAT RNA binding domain; InterPro: IPR004341 The CAT RNA-binding domain is found at the amino terminus of a family of transcriptional antiterminator proteins, the Co-AntiTerminator (CAT) domain. This domain forms a dimer in the crystal structure []. Transcriptional antiterminators of the BglG/SacY family are regulatory proteins that mediate the induction of sugar metabolizing operons in Gram-positive and Gram-negative bacteria. Upon activation, these proteins bind to specific targets in nascent mRNAs, thereby preventing abortive dissociation of the RNA polymerase from the DNA template [].; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1AUU_B 1TLV_A 1L1C_A 1H99_A 3RIO_A.
Probab=26.96 E-value=95 Score=19.66 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=19.0
Q ss_pred EecCCCceEEEeCCCCCEEEEEeecccccccC
Q psy13610 31 RVTKNNTILSLSDAKGVVKLLRSCGMEGFKNA 62 (123)
Q Consensus 31 ~st~NNTiitlTD~~G~~l~~~S~G~~GfK~~ 62 (123)
.-.+||-.|-+.|.+|+++...--| +||...
T Consensus 4 ~KvlNNNvvl~~~~~~~E~Iv~GkG-IGF~kk 34 (59)
T PF03123_consen 4 KKVLNNNVVLAKDDNGQEVIVMGKG-IGFGKK 34 (59)
T ss_dssp EEEEETTEEEEE-CCSSEEEEE-TT-SSTT--
T ss_pred EEEccCeEEEEEeCCCCEEEEEeec-ceeccC
Confidence 3345655566679999998886655 599643
No 65
>PRK11761 cysM cysteine synthase B; Provisional
Probab=26.50 E-value=1.6e+02 Score=23.72 Aligned_cols=45 Identities=20% Similarity=0.186 Sum_probs=29.3
Q ss_pred CCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHHh
Q psy13610 46 GVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKALEI 106 (123)
Q Consensus 46 G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alka 106 (123)
|+.+.+.|+|+ .+..++-.|..+|++.+-+.=....+.+...+++
T Consensus 63 g~~vv~aSsGN----------------~g~alA~~a~~~G~~~~i~~p~~~~~~k~~~~~~ 107 (296)
T PRK11761 63 GDTLIEATSGN----------------TGIALAMIAAIKGYRMKLIMPENMSQERRAAMRA 107 (296)
T ss_pred CCEEEEeCCCh----------------HHHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHH
Confidence 46788889998 4455566777888886666655555444444443
No 66
>PRK14430 acylphosphatase; Provisional
Probab=26.48 E-value=1.6e+02 Score=19.99 Aligned_cols=35 Identities=20% Similarity=0.211 Sum_probs=21.9
Q ss_pred eEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 87 SSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 87 ~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
..+++.+.| -|. |..+.+ |.+-|+.=.|||+..|+
T Consensus 4 ~~~~i~v~G~VQGVGF-R~~~~~~A~~lgl~G~VrN~~dGs 43 (92)
T PRK14430 4 ETWRLVAHGRVQGVGY-RAACADAADDLGLGGWVRNRADGT 43 (92)
T ss_pred EEEEEEEEEeecceee-HHHHHHHHHHhCCEEEEEECCCCc
Confidence 344555554 555 555555 56777777778877764
No 67
>PRK14420 acylphosphatase; Provisional
Probab=26.19 E-value=1.8e+02 Score=19.36 Aligned_cols=22 Identities=14% Similarity=-0.009 Sum_probs=10.8
Q ss_pred HHHHHH-hhhcCceeeeeccCCC
Q psy13610 100 RLKALE-IGVSSVRINVRGLGPG 121 (123)
Q Consensus 100 R~~alk-al~~g~~i~~~~~~~~ 121 (123)
|..+.+ |.+-|++=.|||+.-|
T Consensus 18 R~~~~~~A~~~gl~G~V~N~~dG 40 (91)
T PRK14420 18 RYFVQMEADKRKLTGWVKNRDDG 40 (91)
T ss_pred hHHHHHHHHHcCCEEEEEECCCC
Confidence 333333 4445555555555554
No 68
>PF06289 FlbD: Flagellar protein (FlbD); InterPro: IPR009384 This family consists of several bacterial FlbD flagellar proteins. The exact function of this family is unknown [].
Probab=26.17 E-value=79 Score=20.31 Aligned_cols=26 Identities=27% Similarity=0.446 Sum_probs=20.4
Q ss_pred cCCeec--ccccEEEEEecCCCceEEEeC
Q psy13610 17 FDGLKF--KNLPIMNIRVTKNNTILSLSD 43 (123)
Q Consensus 17 ~~g~~~--~~~~i~hI~st~NNTiitlTD 43 (123)
+||.+| ...-|-.|.++.. |.||+++
T Consensus 7 lng~~f~lN~d~IE~ie~~PD-TvItL~~ 34 (60)
T PF06289_consen 7 LNGEPFYLNPDLIETIEETPD-TVITLTN 34 (60)
T ss_pred eCCCEEEEChHHEEEEEEcCC-eEEEEeC
Confidence 578886 4666888999885 9999985
No 69
>TIGR00732 dprA DNA protecting protein DprA. Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function.
Probab=26.02 E-value=2.8e+02 Score=21.61 Aligned_cols=55 Identities=22% Similarity=0.157 Sum_probs=36.8
Q ss_pred cccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHH-HHH-hh-hcCceeeee
Q psy13610 57 EGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLK-ALE-IG-VSSVRINVR 116 (123)
Q Consensus 57 ~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~-alk-al-~~g~~i~~~ 116 (123)
+..=|+|+.|+|+-. .++++++.+.+.|+ +.+.|...|=++ |.+ ++ ..|-.|.|=
T Consensus 47 iaIvGsR~~s~~~~~-~a~~l~~~l~~~g~----~IVSG~A~GiD~~ah~~al~~~g~tIaVl 104 (220)
T TIGR00732 47 VAIVGTRRPTKYGER-WTRKLAEELAKNGV----TIVSGLALGIDGIAHKAALKVNGRTIAVL 104 (220)
T ss_pred EEEEcCCCCCHHHHH-HHHHHHHHHHhCCC----EEEcCchhhHHHHHHHHHHHcCCCEEEEE
Confidence 344567889998755 45678888877777 477898888877 444 44 335555553
No 70
>TIGR03175 AllD ureidoglycolate dehydrogenase. This enzyme converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (GenProp0687). The pathway has been characterized in E. coli and is observed in the genomes of Entercoccus faecalis and Bacillus licheniformis.
Probab=26.01 E-value=2.5e+02 Score=23.73 Aligned_cols=57 Identities=18% Similarity=0.053 Sum_probs=43.3
Q ss_pred cccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCc
Q psy13610 55 GMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSV 111 (123)
Q Consensus 55 G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~ 111 (123)
...-+.+..--.++++..|.+.+.++|++.|+-.+-|+=.. +|.....+.++...|+
T Consensus 75 a~a~vDg~~g~G~~a~~~Am~~aiekAr~~Gi~~v~v~ns~H~G~~g~Y~~~aa~~G~ 132 (349)
T TIGR03175 75 CTAIFHGDNGAGQVAAKMAMEHAIEIAKKSGVAVVGISRMSHSGALSYFVRQAAEQGM 132 (349)
T ss_pred cEEEEECCCCchHHHHHHHHHHHHHHHHHhCEEEEEecCCCccccHHHHHHHHHHCCC
Confidence 33345566667789999999999999999999877765443 7776777777777765
No 71
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=25.92 E-value=89 Score=23.56 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=32.6
Q ss_pred cccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCC-----cCHHH
Q psy13610 55 GMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLG-----PGRLK 102 (123)
Q Consensus 55 G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G-----~GR~~ 102 (123)
|.+|||++-|.| ..+++..+.++.|++---|+--+=+ +|+++
T Consensus 6 ~ivG~k~SGKTT------Lie~lv~~L~~~G~rVa~iKH~hh~~~~D~~GkDs 52 (161)
T COG1763 6 GIVGYKNSGKTT------LIEKLVRKLKARGYRVATVKHAHHDFDLDKPGKDT 52 (161)
T ss_pred EEEecCCCChhh------HHHHHHHHHHhCCcEEEEEEecCCCCCCCCCCCcc
Confidence 457999999877 4688999999999988877776644 45555
No 72
>PRK14436 acylphosphatase; Provisional
Probab=25.87 E-value=1.9e+02 Score=19.52 Aligned_cols=35 Identities=23% Similarity=0.233 Sum_probs=18.9
Q ss_pred eEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 87 SSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 87 ~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
..+++.+.| -|. |..+.+ |.+-|+.=-|||+..|+
T Consensus 4 ~~~~i~v~G~VQGVGF-R~~v~~~A~~l~l~G~V~N~~dG~ 43 (91)
T PRK14436 4 VRAHLRIYGRVQGVGF-RWSMQREARKLGVNGWVRNLPDGS 43 (91)
T ss_pred EEEEEEEEEeeCCcCc-HHHHHHHHHHcCCEEEEEECCCCc
Confidence 344454444 444 444444 45666666667766654
No 73
>PRK10098 putative dehydrogenase; Provisional
Probab=25.79 E-value=2.8e+02 Score=23.45 Aligned_cols=69 Identities=13% Similarity=0.092 Sum_probs=48.3
Q ss_pred CCCCCEEEEE-eecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCc
Q psy13610 43 DAKGVVKLLR-SCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSV 111 (123)
Q Consensus 43 D~~G~~l~~~-S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~ 111 (123)
|++.++..-. +..+.-..+..--.++++..|.+.+.++|++.||-.+-|+=.. +|..-..+.++...|+
T Consensus 66 ~~~~~~~v~~~~~a~~~vDg~~g~G~~a~~~Am~~aie~Ar~~Gi~~v~vrnS~H~G~~g~y~~~aa~~G~ 136 (350)
T PRK10098 66 QLNHHAKIVKDAGAVLTLDGDRGFGQVVAHEAMALGIERARQHGICAVALRNSHHIGRIGHWAEQCAAAGL 136 (350)
T ss_pred CCCCCeEEEecCCcEEEEECCCCccHHHHHHHHHHHHHHHHHhCEEEEEEecCCCccchHHHHHHHHHCCC
Confidence 3444443333 2333345555667789999999999999999999877766544 7777777888877765
No 74
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=24.73 E-value=1.6e+02 Score=19.86 Aligned_cols=27 Identities=19% Similarity=0.338 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHcCCeEEEEEEEcC
Q psy13610 69 AAQAAGITIGKKALEIGVSSVRINVRGL 96 (123)
Q Consensus 69 Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~ 96 (123)
.++.+++.+.+.++++|+. +.|..+|.
T Consensus 13 ~s~laa~~L~~aa~~~g~~-~~ve~~~~ 39 (96)
T cd05569 13 HTYMAAEALEKAAKKLGWE-IKVETQGS 39 (96)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEEecC
Confidence 4567888889999999998 88887774
No 75
>PRK14441 acylphosphatase; Provisional
Probab=23.89 E-value=1.7e+02 Score=19.73 Aligned_cols=36 Identities=33% Similarity=0.284 Sum_probs=21.8
Q ss_pred CeEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 86 VSSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 86 i~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
+..+++.++| -|. |..+.+ |.+.|+.=-|||+..|+
T Consensus 4 ~~~~~i~v~G~VQGVGF-R~~v~~~A~~lgL~G~V~N~~dG~ 44 (93)
T PRK14441 4 RVRARIVVSGRVQGVAF-RQSAADEARRLGVEGWVRNLPDGR 44 (93)
T ss_pred cEEEEEEEEEecCCccc-hHHHHHHHhhcCcEEEEEECCCCE
Confidence 4555666665 444 555555 45667777777777663
No 76
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=23.82 E-value=1.4e+02 Score=21.09 Aligned_cols=28 Identities=18% Similarity=0.051 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHcCCeEEEEEEEcCC
Q psy13610 69 AAQAAGITIGKKALEIGVSSVRINVRGLG 97 (123)
Q Consensus 69 Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G 97 (123)
.++.|++.+.+.++++|+. +.|..+|..
T Consensus 17 ht~lAAeaL~kAA~~~G~~-i~VE~qg~~ 44 (114)
T PRK10427 17 HTYMAAERLEKLCQLEKWG-VKIETQGAL 44 (114)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEecCCc
Confidence 4678888888899999987 888888843
No 77
>smart00773 WGR Proposed nucleic acid binding domain. This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.
Probab=23.29 E-value=1.4e+02 Score=19.39 Aligned_cols=39 Identities=21% Similarity=0.137 Sum_probs=25.9
Q ss_pred eCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHH
Q psy13610 42 SDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKK 80 (123)
Q Consensus 42 TD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~ 80 (123)
.|..|....+..-|-+|.++..+..+|.....|.+.+++
T Consensus 29 ~~~~~~~~v~~~wGRiG~~g~~~~~~~~s~~~A~~~f~k 67 (84)
T smart00773 29 EDDFGGYSVWRRWGRIGTNGQTKLETFDSLEDAIKEFEK 67 (84)
T ss_pred EcCCCCEEEEEEeeecCCCCceeeEcCCCHHHHHHHHHH
Confidence 355567788888999999877776666544444444433
No 78
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=22.98 E-value=1.4e+02 Score=21.71 Aligned_cols=43 Identities=19% Similarity=0.219 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHHHHHcCCeEEEEEEEc-CCcCHHHHHHhhhcCcee
Q psy13610 67 NIAAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVSSVRI 113 (123)
Q Consensus 67 ~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG-~G~GR~~alkal~~g~~i 113 (123)
+.+.+..|+.+++.+.. .-.|.+.| .|.|+-+.+|.+..++.+
T Consensus 5 ~~~t~~l~~~l~~~l~~----~~~i~l~G~lGaGKTtl~~~l~~~lg~ 48 (133)
T TIGR00150 5 EKAMDKFGKAFAKPLDF----GTVVLLKGDLGAGKTTLVQGLLQGLGI 48 (133)
T ss_pred HHHHHHHHHHHHHhCCC----CCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence 44445555555544422 22477888 899999999987666543
No 79
>TIGR01138 cysM cysteine synthase B. Alternate name: O-acetylserine (thiol)-lyase
Probab=22.97 E-value=2.2e+02 Score=22.78 Aligned_cols=40 Identities=20% Similarity=0.185 Sum_probs=25.3
Q ss_pred CCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHH
Q psy13610 46 GVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRL 101 (123)
Q Consensus 46 G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~ 101 (123)
|+.+.+.|+|+ .+..++-.|..+|++.+-+.=....+.+.
T Consensus 59 g~~vv~aSsGN----------------~g~alA~~a~~~G~~~~i~~p~~~~~~k~ 98 (290)
T TIGR01138 59 GDVLIEATSGN----------------TGIALAMIAALKGYRMKLLMPDNMSQERK 98 (290)
T ss_pred CCEEEEECCCh----------------HHHHHHHHHHHcCCeEEEEECCCCCHHHH
Confidence 46788889998 44555667777888755554444333333
No 80
>PRK00394 transcription factor; Reviewed
Probab=22.87 E-value=2.3e+02 Score=21.62 Aligned_cols=48 Identities=23% Similarity=0.203 Sum_probs=31.6
Q ss_pred eEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeE
Q psy13610 38 ILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSS 88 (123)
Q Consensus 38 iitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~ 88 (123)
++-+.+|+--.+.| ++|.+--.|++ |...+..|++++++..+++|+..
T Consensus 39 i~Rl~~Pk~t~lIf-~sGKiv~tGa~--S~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 39 VYRLEDPKIAALIF-RSGKVVCTGAK--SVEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred EEEecCCceEEEEE-cCCcEEEEccC--CHHHHHHHHHHHHHHHHHcCCCc
Confidence 44555665555555 45555555554 44577888899999999999654
No 81
>cd01561 CBS_like CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine.
Probab=22.63 E-value=2.3e+02 Score=22.38 Aligned_cols=51 Identities=16% Similarity=0.183 Sum_probs=30.0
Q ss_pred CCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHHhhhcCceee
Q psy13610 46 GVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLKALEIGVSSVRIN 114 (123)
Q Consensus 46 G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alkal~~g~~i~ 114 (123)
|..+...|+|+ .+..++-.|..+|++.+-+.=++..+.+...++. -|.++-
T Consensus 53 ~~~vv~~SsGN----------------~g~alA~~a~~~G~~~~i~vp~~~~~~k~~~~~~--~Ga~v~ 103 (291)
T cd01561 53 GTTIIEPTSGN----------------TGIGLAMVAAAKGYRFIIVMPETMSEEKRKLLRA--LGAEVI 103 (291)
T ss_pred CCEEEEeCCCh----------------HHHHHHHHHHHcCCeEEEEECCCCCHHHHHHHHH--cCCEEE
Confidence 46677888888 4445566778889985555544444433333332 255444
No 82
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=22.45 E-value=2e+02 Score=21.79 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=28.3
Q ss_pred EeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCe
Q psy13610 41 LSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVS 87 (123)
Q Consensus 41 lTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~ 87 (123)
+.|++--.+.| |+|.+-..|++ |...+..|++++++..+++|++
T Consensus 43 l~~Pk~t~lIF-~SGKiviTGak--s~e~a~~a~~~i~~~L~~~g~~ 86 (174)
T cd04516 43 IREPKTTALIF-SSGKMVCTGAK--SEDDSKLAARKYARIIQKLGFP 86 (174)
T ss_pred eCCCcEEEEEE-CCCeEEEEecC--CHHHHHHHHHHHHHHHHHcCCC
Confidence 34554444555 55555555554 4456777888888888888864
No 83
>PRK14426 acylphosphatase; Provisional
Probab=22.04 E-value=2.5e+02 Score=18.88 Aligned_cols=34 Identities=18% Similarity=0.139 Sum_probs=19.0
Q ss_pred EEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 88 SVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 88 ~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
.+++.+.| -|. |..+.+ |.+.|+.=.|||+..|+
T Consensus 5 ~~~~~v~G~VQGVGF-R~~v~~~A~~~gl~G~V~N~~dG~ 43 (92)
T PRK14426 5 CIIAWVYGRVQGVGF-RYHTQHEALKLGLTGYAKNLDDGS 43 (92)
T ss_pred EEEEEEEEeeCCcCc-hHHHHHHHHHhCCEEEEEECCCCc
Confidence 34454444 444 444444 55667776677766653
No 84
>PRK13678 hypothetical protein; Provisional
Probab=21.82 E-value=1.1e+02 Score=21.11 Aligned_cols=25 Identities=16% Similarity=0.254 Sum_probs=17.3
Q ss_pred EEecCCCceEEEeCCCCCEEEEEee
Q psy13610 30 IRVTKNNTILSLSDAKGVVKLLRSC 54 (123)
Q Consensus 30 I~st~NNTiitlTD~~G~~l~~~S~ 54 (123)
|+.....-+|+|+|-+|+..-+.--
T Consensus 2 ~~~~~~~~~i~l~DEdG~E~ef~vl 26 (95)
T PRK13678 2 NHNNEEEELITLVDEEGNEVLFEIL 26 (95)
T ss_pred CcccCCCcEEEEECCCCCEEEEEEE
Confidence 3445566789999999997655443
No 85
>PF02481 DNA_processg_A: DNA recombination-mediator protein A; InterPro: IPR003488 The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In Helicobacter pylori, dprA is required for natural chromosomal and plasmid transformation []. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the Escherichia coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [].; GO: 0009294 DNA mediated transformation; PDB: 3MAJ_A.
Probab=21.72 E-value=2.6e+02 Score=21.58 Aligned_cols=53 Identities=17% Similarity=0.207 Sum_probs=28.4
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCcCHHH-HHH-hhhc-Cceeee
Q psy13610 58 GFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLK-ALE-IGVS-SVRINV 115 (123)
Q Consensus 58 GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~GR~~-alk-al~~-g~~i~~ 115 (123)
..=|+|+.|+|+-+ .++++++.+.+.|+ +.+.|.-.|=+. |.+ ++.. |-.|.|
T Consensus 48 aIvGsR~~s~~g~~-~a~~l~~~l~~~g~----~vvSGlA~GiD~~ah~~al~~~g~tIaV 103 (212)
T PF02481_consen 48 AIVGSRNPSEYGLK-FAKKLARELAKAGI----VVVSGLAKGIDAAAHRGALDAGGPTIAV 103 (212)
T ss_dssp EEE--SS--HHHHH-HHHHHHHHHHHHT-----EEEE---TTHHHHHHHHHTTT---EEEE
T ss_pred EEEcCCCCCHHHHH-HHHHHHHHHhhCCE----EEEcCCCCCHHHHHHHHHHHccCCEEEE
Confidence 34468899998855 55777788777776 678887777766 445 4543 555554
No 86
>PRK14424 acylphosphatase; Provisional
Probab=21.37 E-value=2.4e+02 Score=19.25 Aligned_cols=36 Identities=25% Similarity=0.339 Sum_probs=22.4
Q ss_pred CeEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 86 VSSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 86 i~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
+..+++.+.| -|. |..+.+ |.+.|++=-|||+..|+
T Consensus 6 m~~~~~~v~G~VQGVGF-R~~v~~~A~~~gl~G~V~N~~dG~ 46 (94)
T PRK14424 6 IETYYVRVRGVVQGVGF-RHATVREAHALGLRGWVANLEDGT 46 (94)
T ss_pred cEEEEEEEEEeecCCch-HHHHHHHHHHcCCeEEEEECCCCC
Confidence 4456666666 444 444444 56777777778777664
No 87
>PRK14422 acylphosphatase; Provisional
Probab=21.26 E-value=2.7e+02 Score=18.78 Aligned_cols=36 Identities=19% Similarity=0.089 Sum_probs=21.5
Q ss_pred CeEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 86 VSSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 86 i~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
+..+++.++| -|. |..+.+ |.+-|++=-|||+..|+
T Consensus 5 ~~~~~~~v~G~VQGVGF-R~~v~~~A~~~gl~G~V~N~~dG~ 45 (93)
T PRK14422 5 DVRLTAWVHGHVQGVGF-RWWTRSRALELGLTGYAANLADGR 45 (93)
T ss_pred cEEEEEEEEEeeCCcCc-HHHHHHHHHHcCCEEEEEECCCCC
Confidence 3455666655 444 555555 45667777777777664
No 88
>PF00150 Cellulase: Cellulase (glycosyl hydrolase family 5); InterPro: IPR001547 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 5 GH5 from CAZY comprises enzymes with several known activities; endoglucanase (3.2.1.4 from EC); beta-mannanase (3.2.1.78 from EC); exo-1,3-glucanase (3.2.1.58 from EC); endo-1,6-glucanase (3.2.1.75 from EC); xylanase (3.2.1.8 from EC); endoglycoceramidase (3.2.1.123 from EC). The microbial degradation of cellulose and xylans requires several types of enzymes. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family A [] or as the glycosyl hydrolases family 5 []. One of the conserved regions in this family contains a conserved glutamic acid residue which is potentially involved [] in the catalytic mechanism.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3NDY_A 3NDZ_B 1LF1_A 1TVP_B 1TVN_A 3AYR_A 3AYS_A 1QI0_A 1W3K_A 1OCQ_A ....
Probab=21.25 E-value=1.7e+02 Score=22.07 Aligned_cols=43 Identities=19% Similarity=0.119 Sum_probs=29.7
Q ss_pred eCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeEEEEEEE
Q psy13610 42 SDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVR 94 (123)
Q Consensus 42 TD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ik 94 (123)
.|.+|+++.|.---+. + ..++ ..++..+.++++|+..|||-+-
T Consensus 1 ~~~~G~~v~~~G~n~~-w-----~~~~----~~~~~~~~~~~~G~n~VRi~v~ 43 (281)
T PF00150_consen 1 VDQNGKPVNWRGFNTH-W-----YNPS----ITEADFDQLKALGFNTVRIPVG 43 (281)
T ss_dssp ECTTSEBEEEEEEEET-T-----SGGG----SHHHHHHHHHHTTESEEEEEEE
T ss_pred CCCCCCeEEeeeeecc-c-----CCCC----CHHHHHHHHHHCCCCEEEeCCC
Confidence 3788888877433222 1 1111 5567788999999999999998
No 89
>PRK14429 acylphosphatase; Provisional
Probab=21.25 E-value=2.1e+02 Score=19.10 Aligned_cols=26 Identities=23% Similarity=0.166 Sum_probs=13.8
Q ss_pred CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 96 LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 96 ~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
-|. |..+.+ |.+-|++=.|||+..|+
T Consensus 15 VGF-R~~v~~~A~~~gl~G~V~N~~dG~ 41 (90)
T PRK14429 15 VGC-RRATLTKARALGVTGYVTNCEDGS 41 (90)
T ss_pred eee-HHHHHHHHHHhCCEEEEEECCCCe
Confidence 444 444444 44556666666666553
No 90
>PLN00062 TATA-box-binding protein; Provisional
Probab=20.98 E-value=2.2e+02 Score=21.84 Aligned_cols=43 Identities=12% Similarity=0.211 Sum_probs=27.5
Q ss_pred EeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCC
Q psy13610 41 LSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGV 86 (123)
Q Consensus 41 lTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi 86 (123)
+.|++-.++.| ++|.+-..|++ |...+..|+.++++..+++|+
T Consensus 43 l~~Pk~t~lIF-~SGKiviTGak--s~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 43 IREPKTTALIF-ASGKMVCTGAK--SEHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred eCCCcEEEEEE-CCCeEEEEecC--CHHHHHHHHHHHHHHHHHcCC
Confidence 34554444444 55555555554 446677788888888888887
No 91
>PRK14423 acylphosphatase; Provisional
Probab=20.84 E-value=2.2e+02 Score=19.12 Aligned_cols=35 Identities=26% Similarity=0.230 Sum_probs=18.6
Q ss_pred eEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 87 SSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 87 ~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
..+++.+.| -|. |..+.+ |.+-|+.=-|||+..|+
T Consensus 5 ~~~~i~v~G~VQGVGF-R~~v~~~A~~lgl~G~V~N~~dG~ 44 (92)
T PRK14423 5 TRAHVFVSGRVQGVYY-RASTRDTARELGVDGWVRNLDDGR 44 (92)
T ss_pred EEEEEEEEEecCCeee-hHHHHHHHHHcCCEEEEEECCCCe
Confidence 344555555 333 444444 44556666666666653
No 92
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=20.72 E-value=1.7e+02 Score=23.36 Aligned_cols=30 Identities=13% Similarity=0.064 Sum_probs=23.8
Q ss_pred ChHHHHHHHHHHHHHHHHcCCeEEEEEEEc
Q psy13610 66 TNIAAQAAGITIGKKALEIGVSSVRINVRG 95 (123)
Q Consensus 66 T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG 95 (123)
...++..+..++.+.|.++||+.|.|+.=.
T Consensus 24 GH~~G~~~~~~v~~~c~~~GI~~lT~yaFS 53 (226)
T TIGR00055 24 GHKAGVKSLRRILRWCANLGVECLTLYAFS 53 (226)
T ss_pred hHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 455666677888899999999999998633
No 93
>COG5436 Predicted integral membrane protein [Function unknown]
Probab=20.66 E-value=1.7e+02 Score=22.69 Aligned_cols=40 Identities=20% Similarity=0.248 Sum_probs=28.8
Q ss_pred CccccCCeecc-cccEEEEEecCCCceEEE--eCCCCCEEEEE
Q psy13610 13 PDLIFDGLKFK-NLPIMNIRVTKNNTILSL--SDAKGVVKLLR 52 (123)
Q Consensus 13 ~~~~~~g~~~~-~~~i~hI~st~NNTiitl--TD~~G~~l~~~ 52 (123)
|+++.---+|. ..|-+||.+..|+++.++ .|.+|+.+++.
T Consensus 64 P~l~~a~C~fdvsegpvri~a~~nvpyWSvsiyds~~nn~fS~ 106 (182)
T COG5436 64 PNLLYAFCRFDVSEGPVRIEAKGNVPYWSVSIYDSNGNNFFSI 106 (182)
T ss_pred chhhhheeEeeccCCcEEEEecCCCceEEEEEEcCCCCceEEe
Confidence 44433333453 567889999999999765 79999988764
No 94
>PRK14428 acylphosphatase; Provisional
Probab=20.66 E-value=2.2e+02 Score=19.58 Aligned_cols=37 Identities=24% Similarity=0.207 Sum_probs=22.8
Q ss_pred CCeEEEEEEEc----CCcCHHHHHH-hhhcCceeeeeccCCCC
Q psy13610 85 GVSSVRINVRG----LGPGRLKALE-IGVSSVRINVRGLGPGR 122 (123)
Q Consensus 85 Gi~~i~V~ikG----~G~GR~~alk-al~~g~~i~~~~~~~~~ 122 (123)
++...++.++| -|. |..+.+ |..-|++=-|||+..|+
T Consensus 6 ~~~~~~i~v~G~VQGVGF-R~fv~~~A~~lgL~G~V~N~~dGs 47 (97)
T PRK14428 6 NLVRKHIVVTGLVQGVGF-RYFTVTQARRLGVQGWVRNCRDGS 47 (97)
T ss_pred heEEEEEEEEEecCCccc-hHHHHHHHHHcCCEEEEEECCCCE
Confidence 45556666666 444 444444 55667777788877664
No 95
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=20.58 E-value=1.8e+02 Score=22.62 Aligned_cols=34 Identities=12% Similarity=0.232 Sum_probs=26.3
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcCHHHHHHhhhc
Q psy13610 74 GITIGKKALEIGVSSVRINVRGLGPGRLKALEIGVS 109 (123)
Q Consensus 74 a~~v~~~a~~~Gi~~i~V~ikG~G~GR~~alkal~~ 109 (123)
+..+++.+.+-|++.+||-++. ++...+|+.++.
T Consensus 27 a~~~~~al~~~Gi~~iEit~~~--~~a~~~i~~l~~ 60 (213)
T PRK06552 27 ALKISLAVIKGGIKAIEVTYTN--PFASEVIKELVE 60 (213)
T ss_pred HHHHHHHHHHCCCCEEEEECCC--ccHHHHHHHHHH
Confidence 4567788899999999999995 556667776643
No 96
>PF09741 DUF2045: Uncharacterized conserved protein (DUF2045); InterPro: IPR019141 This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif. The function is unknown.
Probab=20.41 E-value=2e+02 Score=23.29 Aligned_cols=54 Identities=19% Similarity=0.229 Sum_probs=32.7
Q ss_pred eEEEeCCCCCEEEEEeecccccccCCC-----CChHHHHHHHHHHHHHHHHcCC----eEEEEEEEcCC
Q psy13610 38 ILSLSDAKGVVKLLRSCGMEGFKNARK-----GTNIAAQAAGITIGKKALEIGV----SSVRINVRGLG 97 (123)
Q Consensus 38 iitlTD~~G~~l~~~S~G~~GfK~~rK-----~T~~Aa~~aa~~v~~~a~~~Gi----~~i~V~ikG~G 97 (123)
.++.+|..|......=.|++.|..-++ .+.++ .+++++.. +|. +.-.|++||||
T Consensus 161 eL~A~~~~~~~~~vlF~Gsv~y~~l~~~yd~~~s~~~-----s~~~q~ls-~~~~~~~~~efv~M~GP~ 223 (237)
T PF09741_consen 161 ELVAHDRSGPFKGVLFLGSVRYEVLKKVYDSRVSETG-----SKMAQRLS-FGHYSQGRTEFVRMRGPG 223 (237)
T ss_pred EEEEecCCCCeeEEEEEeeeeHHHHHHHHhccchhhh-----HHHHHHhh-cCcccCCceEEEEEECCC
Confidence 466688888887777788888876552 22222 22333332 232 55678899986
No 97
>PRK14435 acylphosphatase; Provisional
Probab=20.33 E-value=2.8e+02 Score=18.57 Aligned_cols=16 Identities=19% Similarity=0.138 Sum_probs=7.9
Q ss_pred hhhcCceeeeeccCCC
Q psy13610 106 IGVSSVRINVRGLGPG 121 (123)
Q Consensus 106 al~~g~~i~~~~~~~~ 121 (123)
|.+-|+.=-|||+..|
T Consensus 25 A~~~gl~G~V~N~~dG 40 (90)
T PRK14435 25 AKSLGVKGYVMNMDDG 40 (90)
T ss_pred HHHhCCEEEEEECCCC
Confidence 3444555555555444
No 98
>cd06562 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in
Probab=20.32 E-value=1.9e+02 Score=23.93 Aligned_cols=64 Identities=16% Similarity=0.005 Sum_probs=40.4
Q ss_pred cCCCceEEEeCCCCCEEEEEeecccccccCCC-CChHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCc
Q psy13610 33 TKNNTILSLSDAKGVVKLLRSCGMEGFKNARK-GTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP 98 (123)
Q Consensus 33 t~NNTiitlTD~~G~~l~~~S~G~~GfK~~rK-~T~~Aa~~aa~~v~~~a~~~Gi~~i~V~ikG~G~ 98 (123)
.+|--++||||-.|=.+-..+--.+.-+|+.. +..|.-+.. ..+.+.|++.||. |.-.|--||-
T Consensus 31 KlN~lh~HltDd~~~rle~~~~P~Lt~~ga~~~~~~YT~~di-~eiv~yA~~rgI~-vIPEID~PGH 95 (348)
T cd06562 31 KLNVLHWHITDSQSFPLESPSYPELSKKGAYSPSEVYTPEDV-KEIVEYARLRGIR-VIPEIDTPGH 95 (348)
T ss_pred CCcEEEEeEEcCCCceEeeCCCchhhhccCcCCCceECHHHH-HHHHHHHHHcCCE-EEEeccCchh
Confidence 34555689999888776655444444444442 345555544 5588899999987 4445566665
No 99
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=20.25 E-value=1.2e+02 Score=21.29 Aligned_cols=20 Identities=20% Similarity=0.219 Sum_probs=16.1
Q ss_pred cEEEEEecCCCceEEEeCCC
Q psy13610 26 PIMNIRVTKNNTILSLSDAK 45 (123)
Q Consensus 26 ~i~hI~st~NNTiitlTD~~ 45 (123)
....|-+-.|+|+||.-|.+
T Consensus 61 d~AlVvsv~NrTVITAmd~~ 80 (96)
T TIGR02530 61 DAALVVSLKNRTVITAMDKD 80 (96)
T ss_pred CEEEEEEcCCCeEEEEeCch
Confidence 34678899999999998744
No 100
>PF10708 DUF2510: Protein of unknown function (DUF2510); InterPro: IPR018929 This domain of unknown function is found in a family of proteins conserved in Actinobacteria. Many members are annotated as putative membrane proteins but this could not be confirmed.
Probab=20.11 E-value=66 Score=18.66 Aligned_cols=16 Identities=31% Similarity=0.773 Sum_probs=12.7
Q ss_pred CCCCCCCCccc--cCCee
Q psy13610 6 IFPDENTPDLI--FDGLK 21 (123)
Q Consensus 6 ~~p~~~~~~~~--~~g~~ 21 (123)
-|||+..|.++ |||..
T Consensus 3 WYpDP~~~~~~R~WDG~~ 20 (36)
T PF10708_consen 3 WYPDPSGPGQLRYWDGAA 20 (36)
T ss_pred cCcCCCCCCceeEeCCCc
Confidence 38999888776 88876
No 101
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=20.10 E-value=2.3e+02 Score=21.35 Aligned_cols=48 Identities=19% Similarity=0.262 Sum_probs=31.1
Q ss_pred eEEEeCCCCCEEEEEeecccccccCCCCChHHHHHHHHHHHHHHHHcCCeE
Q psy13610 38 ILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSS 88 (123)
Q Consensus 38 iitlTD~~G~~l~~~S~G~~GfK~~rK~T~~Aa~~aa~~v~~~a~~~Gi~~ 88 (123)
++-+.|++.-++.| |+|.+--.|++ |...+..|++++.+..+++|+..
T Consensus 40 i~R~~~P~~t~lIf-~sGKivitGak--s~~~~~~a~~~~~~~L~~~g~~~ 87 (174)
T cd00652 40 IMRLREPKTTALIF-SSGKMVITGAK--SEEDAKLAARKYARILQKLGFPV 87 (174)
T ss_pred EEEcCCCcEEEEEE-CCCEEEEEecC--CHHHHHHHHHHHHHHHHHcCCCc
Confidence 34445566555555 45555555543 45667778888999999888665
No 102
>TIGR01911 HesB_rel_seleno HesB-like selenoprotein. This model represents a family of small proteins related to HesB and its close homologs, which are likely to be invovlved in iron-sulfur cluster assembly (See TIGR00049 and pfam01521). Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain. A variable Cys/Ser/Gly-rich C-terminal region is not included in the seed alignment and model.
Probab=20.07 E-value=1.9e+02 Score=19.44 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=13.3
Q ss_pred HHHHHHHHHcCCe--EEEEEEEcCC
Q psy13610 75 ITIGKKALEIGVS--SVRINVRGLG 97 (123)
Q Consensus 75 ~~v~~~a~~~Gi~--~i~V~ikG~G 97 (123)
+++.+...+.+-. .|+|.|+|-|
T Consensus 12 ~~i~~ll~~~~~~~~~LRi~v~~gG 36 (92)
T TIGR01911 12 EEFKDFLKENDIDNDVIRIHFAGMG 36 (92)
T ss_pred HHHHHHHHhCCCCCceEEEEEeCCC
Confidence 3333333344443 4999999866
No 103
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=20.04 E-value=2.8e+02 Score=19.09 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=23.2
Q ss_pred CCceEEEeCCCCCEEEEEeecccccccCCC
Q psy13610 35 NNTILSLSDAKGVVKLLRSCGMEGFKNARK 64 (123)
Q Consensus 35 NNTiitlTD~~G~~l~~~S~G~~GfK~~rK 64 (123)
..-+|.+.|.+-+.+.|.......++....
T Consensus 103 g~L~i~i~D~~~~~~vW~g~a~~~~~~~~~ 132 (151)
T PF13590_consen 103 GTLVIDIIDAKTNKVVWRGTASGRLSDNAD 132 (151)
T ss_pred EEEEEEEEeCCCCCEEEEEEEEeccCCCcC
Confidence 345788999988999999988776665444
Done!