Query 024513
Match_columns 266
No_of_seqs 160 out of 1261
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 05:09:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024513hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02284 glutamine synthetase 100.0 5.1E-81 1.1E-85 580.9 28.6 264 1-264 91-354 (354)
2 COG0174 GlnA Glutamine synthet 100.0 9.8E-79 2.1E-83 575.7 26.1 255 1-265 92-361 (443)
3 PLN03036 glutamine synthetase; 100.0 9.2E-78 2E-82 568.0 29.2 266 1-266 151-416 (432)
4 TIGR00653 GlnA glutamine synth 100.0 1E-77 2.2E-82 575.4 26.3 257 1-265 86-375 (460)
5 PRK09469 glnA glutamine synthe 100.0 4E-77 8.7E-82 572.2 26.2 257 1-265 89-383 (469)
6 TIGR03105 gln_synth_III glutam 100.0 6.2E-76 1.3E-80 559.9 25.9 251 1-265 83-354 (435)
7 PF00120 Gln-synt_C: Glutamine 100.0 2.1E-75 4.4E-80 523.3 16.8 240 13-261 1-259 (259)
8 KOG0683 Glutamine synthetase [ 100.0 8.5E-44 1.8E-48 322.1 14.3 265 1-265 102-370 (380)
9 COG3968 Uncharacterized protei 99.8 1.3E-18 2.8E-23 162.1 15.0 217 32-262 214-500 (724)
10 TIGR02050 gshA_cyan_rel unchar 98.9 1.1E-07 2.3E-12 86.8 17.9 187 35-261 1-248 (287)
11 PRK13517 carboxylate-amine lig 98.8 1.1E-07 2.4E-12 89.7 15.7 132 33-198 10-167 (373)
12 PRK13515 carboxylate-amine lig 98.7 4.2E-07 9.1E-12 85.7 16.5 131 33-198 5-161 (371)
13 PRK13516 gamma-glutamyl:cystei 98.7 8.2E-07 1.8E-11 83.8 15.6 188 33-260 11-259 (373)
14 PRK13518 carboxylate-amine lig 98.4 3.6E-06 7.8E-11 78.9 13.0 155 97-260 49-260 (357)
15 TIGR02048 gshA_cyano glutamate 98.3 1.5E-05 3.2E-10 75.4 13.8 92 98-196 31-148 (376)
16 PLN02611 glutamate--cysteine l 98.2 2.2E-05 4.8E-10 76.2 14.0 137 31-198 65-246 (482)
17 PF04107 GCS2: Glutamate-cyste 98.0 5.5E-05 1.2E-09 68.9 10.4 96 96-197 34-158 (288)
18 TIGR01436 glu_cys_lig_pln glut 97.8 0.00058 1.3E-08 66.0 14.1 140 31-198 19-203 (446)
19 COG2170 Uncharacterized conser 97.6 0.00044 9.5E-09 64.0 9.8 187 33-261 2-251 (369)
20 TIGR03444 gshA_related glutama 96.8 0.011 2.4E-07 56.1 10.7 95 99-198 64-186 (390)
21 KOG0683 Glutamine synthetase [ 94.8 0.0086 1.9E-07 55.7 0.2 58 197-264 285-342 (380)
22 cd04869 ACT_GcvR_2 ACT domains 90.4 0.76 1.7E-05 33.0 5.3 65 80-146 11-81 (81)
23 PF13740 ACT_6: ACT domain; PD 87.4 2 4.2E-05 30.9 5.6 62 80-144 14-75 (76)
24 PF12224 Amidoligase_2: Putati 86.0 14 0.0003 32.4 11.4 22 237-258 225-246 (252)
25 PF06877 RraB: Regulator of ri 85.8 3.9 8.5E-05 31.0 6.8 94 17-141 3-98 (104)
26 TIGR02778 ligD_pol DNA polymer 85.7 6.1 0.00013 35.3 8.9 126 91-230 95-225 (245)
27 PF14395 COOH-NH2_lig: Phage p 84.3 1.6 3.4E-05 39.2 4.4 52 109-165 52-107 (261)
28 cd04862 PaeLigD_Pol_like PaeLi 82.8 10 0.00022 33.6 8.9 127 90-230 78-209 (227)
29 cd04872 ACT_1ZPV ACT domain pr 82.6 2.4 5.1E-05 31.2 4.3 67 80-147 13-79 (88)
30 COG3572 GshA Gamma-glutamylcys 82.2 2.5 5.3E-05 40.3 5.0 45 99-144 91-136 (456)
31 PRK02471 bifunctional glutamat 81.5 5.5 0.00012 41.3 7.7 17 33-49 18-34 (752)
32 cd04870 ACT_PSP_1 CT domains f 81.4 4.1 9E-05 29.0 5.0 65 80-146 11-75 (75)
33 PRK00194 hypothetical protein; 81.3 3.1 6.8E-05 30.6 4.5 66 80-146 15-80 (90)
34 cd04861 LigD_Pol_like LigD_Pol 80.9 13 0.00028 32.9 8.8 126 91-230 79-209 (227)
35 cd04864 LigD_Pol_like_1 LigD_P 80.2 14 0.0003 32.8 8.8 112 104-230 99-210 (228)
36 cd04863 MtLigD_Pol_like MtLigD 80.0 15 0.00032 32.6 8.9 113 104-230 101-213 (231)
37 KOG0558 Dihydrolipoamide trans 79.9 1.7 3.7E-05 40.7 3.1 27 121-147 276-302 (474)
38 cd04866 LigD_Pol_like_3 LigD_P 78.2 18 0.00039 31.9 8.9 111 104-230 92-205 (223)
39 cd04865 LigD_Pol_like_2 LigD_P 78.0 18 0.00039 32.0 8.8 113 104-230 98-210 (228)
40 cd04893 ACT_GcvR_1 ACT domains 74.5 10 0.00022 27.2 5.4 64 79-145 12-75 (77)
41 PF04468 PSP1: PSP1 C-terminal 70.7 5.9 0.00013 29.6 3.5 59 79-142 25-83 (88)
42 PRK11191 RNase E inhibitor pro 65.6 42 0.00092 27.4 7.7 92 19-141 13-107 (138)
43 cd04875 ACT_F4HF-DF N-terminal 61.5 24 0.00051 24.8 5.0 60 80-141 11-73 (74)
44 COG3364 Zn-ribbon containing p 59.3 5.7 0.00012 30.7 1.4 24 90-114 55-78 (112)
45 PF03484 B5: tRNA synthetase B 58.4 33 0.0007 24.2 5.3 47 83-140 22-70 (70)
46 TIGR02776 NHEJ_ligase_prk DNA 55.9 57 0.0012 32.7 8.2 110 104-229 390-502 (552)
47 PRK05972 ligD ATP-dependent DN 54.4 2.1E+02 0.0045 30.5 12.3 123 90-229 664-794 (860)
48 PRK11589 gcvR glycine cleavage 54.2 30 0.00066 29.7 5.3 63 79-147 106-178 (190)
49 smart00874 B5 tRNA synthetase 53.3 32 0.00069 23.9 4.5 47 84-140 23-71 (71)
50 PF01921 tRNA-synt_1f: tRNA sy 52.9 57 0.0012 30.9 7.3 137 5-156 31-182 (360)
51 PF07574 SMC_Nse1: Nse1 non-SM 51.3 91 0.002 26.7 7.9 67 78-144 46-120 (200)
52 PRK09632 ATP-dependent DNA lig 51.2 68 0.0015 33.5 8.1 111 105-229 135-245 (764)
53 PRK13011 formyltetrahydrofolat 50.1 35 0.00075 31.2 5.3 65 79-145 18-84 (286)
54 PRK09633 ligD ATP-dependent DN 47.2 91 0.002 31.7 8.2 112 104-229 431-543 (610)
55 cd04882 ACT_Bt0572_2 C-termina 46.9 53 0.0012 21.7 4.7 49 82-141 13-63 (65)
56 cd04871 ACT_PSP_2 ACT domains 44.0 45 0.00097 24.4 4.2 61 79-144 11-82 (84)
57 cd02639 R3H_RRM R3H domain of 42.2 54 0.0012 22.8 4.1 33 106-145 16-48 (60)
58 COG4456 VagC Virulence-associa 41.8 18 0.0004 26.3 1.7 28 218-246 7-34 (74)
59 PF14528 LAGLIDADG_3: LAGLIDAD 41.7 50 0.0011 23.2 4.1 37 78-114 30-66 (77)
60 PRK06027 purU formyltetrahydro 40.8 71 0.0015 29.1 5.8 65 79-145 17-84 (286)
61 PRK10629 EnvZ/OmpR regulon mod 36.3 90 0.0019 25.0 5.1 56 80-144 50-105 (127)
62 PRK13895 conjugal transfer pro 35.7 26 0.00056 28.8 1.8 17 127-143 5-21 (144)
63 COG4326 Spo0M Sporulation cont 35.3 51 0.0011 29.0 3.7 39 79-117 154-199 (270)
64 PF11657 Activator-TraM: Trans 35.2 25 0.00055 28.9 1.8 17 127-143 5-21 (144)
65 PF09845 DUF2072: Zn-ribbon co 34.9 17 0.00037 29.3 0.7 21 92-113 82-102 (131)
66 PF13721 SecD-TM1: SecD export 31.8 1.3E+02 0.0028 23.0 5.1 45 83-135 49-93 (101)
67 PF04914 DltD_C: DltD C-termin 31.7 23 0.00051 28.5 1.0 68 20-109 38-106 (130)
68 cd04908 ACT_Bt0572_1 N-termina 31.2 1.7E+02 0.0036 19.8 5.7 21 81-101 14-34 (66)
69 PF10411 DsbC_N: Disulfide bon 29.8 37 0.0008 23.0 1.6 26 87-112 3-30 (57)
70 cd04888 ACT_PheB-BS C-terminal 29.7 1.1E+02 0.0024 21.0 4.2 31 81-111 13-44 (76)
71 PRK01060 endonuclease IV; Prov 28.7 2.9E+02 0.0062 24.3 7.7 95 15-140 9-103 (281)
72 PF00311 PEPcase: Phosphoenolp 28.4 80 0.0017 33.2 4.5 61 79-145 416-482 (794)
73 cd04889 ACT_PDH-BS-like C-term 28.2 1.4E+02 0.003 19.3 4.3 41 81-121 11-52 (56)
74 PRK13010 purU formyltetrahydro 26.3 1.3E+02 0.0028 27.5 5.0 68 79-147 20-90 (289)
75 PF13710 ACT_5: ACT domain; PD 25.7 80 0.0017 21.8 2.8 54 81-140 5-60 (63)
76 COG1384 LysS Lysyl-tRNA synthe 25.6 3.2E+02 0.0069 27.3 7.7 127 5-150 27-174 (521)
77 TIGR03884 sel_bind_Methan sele 25.5 67 0.0015 23.4 2.4 29 15-43 26-54 (74)
78 TIGR01619 hyp_HI0040 conserved 23.3 3.8E+02 0.0083 24.1 7.3 88 21-139 143-238 (249)
79 cd06007 R3H_DEXH_helicase R3H 23.2 1.2E+02 0.0026 20.9 3.2 28 107-142 16-44 (59)
80 cd04916 ACT_AKiii-YclM-BS_2 AC 22.9 1.6E+02 0.0034 19.4 3.9 37 80-116 16-52 (66)
81 COG1540 Uncharacterized protei 22.8 3E+02 0.0065 24.7 6.3 73 5-99 171-251 (252)
82 PLN00200 argininosuccinate syn 22.7 1.1E+02 0.0024 29.5 4.0 82 64-150 87-179 (404)
83 TIGR00629 uvde UV damage endon 21.8 6.5E+02 0.014 23.4 10.8 92 82-196 54-147 (312)
84 PRK14166 bifunctional 5,10-met 21.8 83 0.0018 28.8 2.8 64 8-102 5-68 (282)
85 PF09899 DUF2126: Putative ami 21.8 4.3E+02 0.0094 27.8 8.1 81 78-164 347-441 (819)
86 PF03851 UvdE: UV-endonuclease 21.7 3.3E+02 0.0071 24.8 6.6 62 81-150 46-111 (275)
87 cd02646 R3H_G-patch R3H domain 21.6 1.1E+02 0.0023 20.8 2.7 41 108-165 17-57 (58)
88 COG1671 Uncharacterized protei 21.4 89 0.0019 25.9 2.6 38 127-166 13-50 (150)
89 PF01261 AP_endonuc_2: Xylose 21.3 4.5E+02 0.0096 21.3 8.1 66 79-150 70-136 (213)
90 COG1943 Transposase and inacti 21.2 2.9E+02 0.0063 22.1 5.7 52 106-165 12-65 (136)
91 PF12116 SpoIIID: Stage III sp 21.1 1.2E+02 0.0026 22.5 2.9 26 116-141 7-32 (82)
92 cd02885 IPP_Isomerase Isopente 21.0 2.8E+02 0.0061 22.5 5.7 22 1-22 3-24 (165)
93 PRK14167 bifunctional 5,10-met 20.9 86 0.0019 28.9 2.7 64 8-102 6-69 (297)
94 PF09904 HTH_43: Winged helix- 20.7 82 0.0018 23.8 2.1 17 16-32 34-50 (90)
95 TIGR00655 PurU formyltetrahydr 20.4 1.8E+02 0.004 26.4 4.8 67 80-147 12-81 (280)
96 PRK11589 gcvR glycine cleavage 20.2 2.6E+02 0.0057 23.8 5.5 63 79-144 19-81 (190)
97 cd04933 ACT_AK1-AT_1 ACT domai 20.2 3.4E+02 0.0075 19.5 6.3 36 80-117 16-51 (78)
98 TIGR02432 lysidine_TilS_N tRNA 20.1 3.2E+02 0.0069 22.4 6.0 60 80-144 45-104 (189)
No 1
>PLN02284 glutamine synthetase
Probab=100.00 E-value=5.1e-81 Score=580.95 Aligned_cols=264 Identities=92% Similarity=1.544 Sum_probs=237.3
Q ss_pred CceeeCCCCCCCCCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHH
Q 024513 1 MCDAYTPAGEPIPTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRD 80 (266)
Q Consensus 1 ~~d~~~~~g~p~~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (266)
+||++++||+|++.|||.+|||+++++++.|+++++|+|+|||||+.+..++.|++..+.+.++++||+..+.+..+.++
T Consensus 91 lcdv~~~dG~p~~~dPR~vL~r~~~~~~~~g~~~~~G~E~EF~lf~~~~~~~~g~~~~~~~~~~~~y~~~~~~~~~~~~~ 170 (354)
T PLN02284 91 MCDAYTPAGEPIPTNKRAKAAKIFSHPDVAAEEPWYGIEQEYTLLQKDVKWPLGWPVGGYPGPQGPYYCGVGADKAFGRD 170 (354)
T ss_pred EEEEECCCCCCCCCCHHHHHHHHHHHHHhcCCceeEEeceEEEEEecCCcccCCCCCCCcccCCCCcccCcchhhHHHHH
Confidence 69999999999999999999999999999999999999999999986543334554434566778888777765556789
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeE
Q 024513 81 IVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHA 160 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~ 160 (266)
++++|+++|+++||+|+++|||+|||||||++.|+++|++||++++||++||+||++||++|||||||+.++++|||||+
T Consensus 171 ~~~~l~~~l~~~Gi~ve~~h~E~apGQ~Ei~l~~~d~l~aAD~~~~~K~vvk~vA~~~Gl~ATFMPKP~~~~~~GSGmH~ 250 (354)
T PLN02284 171 IVDAHYKACLYAGINISGINGEVMPGQWEFQVGPVVGISAGDQLWVARYILERITEIAGVVVSFDPKPIPGDWNGAGAHT 250 (354)
T ss_pred HHHHHHHHHHHCCCCeEEEEcCcCCCceEEEecCCcHHHHHHHHHHHHHHHHHHHHHhCCEEEEcCCCCCCCCccCccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999875579999999
Q ss_pred eEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcCCCCCCCceeE
Q 024513 161 NYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRDTEKEGKGYFE 240 (266)
Q Consensus 161 h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~~~~~~~~riE 240 (266)
|+|||+.++++|.+.++++++|+.|+|+++|+||++||||||+|++|||.+++++||.+||+++||||.....++++|||
T Consensus 251 H~SL~~~~~~gg~~~~~~~l~~~~l~h~~~l~a~~~NSYkRL~p~~eap~~~~~~wg~~NRsa~iRIP~~~~~~~~~riE 330 (354)
T PLN02284 251 NYSTKSMREDGGYEVIKKAIEKLGLRHKEHIAAYGEGNERRLTGKHETADINTFSWGVANRGASIRVGRDTEKEGKGYFE 330 (354)
T ss_pred ecChhhcccCCcHHHHHHHHHHHHHHHHHHhhhhhcCcHhhcCCCccCcccccceeecCCCceeEEECCCCCCCCCCEEE
Confidence 99999854346778889999999999999999999999999999999997679999999999999999765333467999
Q ss_pred eCCCCCCCCHHHHHHHHHHHhhcC
Q 024513 241 DRRPASNMDPYVVTSMIAETTILW 264 (266)
Q Consensus 241 ~R~~da~aNPYLalAailaAgl~g 264 (266)
+|+||++|||||++|++|++.+.+
T Consensus 331 ~R~pd~~aNPYLa~aaila~~~~~ 354 (354)
T PLN02284 331 DRRPASNMDPYVVTSMIAETTILW 354 (354)
T ss_pred EcCCCCCCCHHHHHHHHHHHHhcC
Confidence 999999999999999999998863
No 2
>COG0174 GlnA Glutamine synthetase [Amino acid transport and metabolism]
Probab=100.00 E-value=9.8e-79 Score=575.68 Aligned_cols=255 Identities=27% Similarity=0.425 Sum_probs=228.8
Q ss_pred CceeeCCCCCCCCCChHHHHHHHHccccccCCc-ceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHH
Q 024513 1 MCDAYTPAGEPIPTNKRFNAAKVFGHPDVVAEE-PWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGR 79 (266)
Q Consensus 1 ~~d~~~~~g~p~~~~pR~~L~~~~~~~~~~G~~-~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (266)
+||+++++|+|++.|||++|||+++++++.|+. +.+|+|+|||||+.+.....+ +.+.+.++||+..+.++ ..
T Consensus 92 ~cdv~~~~g~p~~~dPR~vlkr~~~~l~~~G~~~~~~g~E~EFfLfd~~~~~~~~----~~~~~~~~yf~~~~~~~--~~ 165 (443)
T COG0174 92 LCDVYDPDGTPYPRDPRSVLKRALARLKDEGLAPAVVGPELEFFLFDRDGRDPDG----GRPADKGGYFDVAPLDE--AE 165 (443)
T ss_pred EEEEECCCCCcCCCChHHHHHHHHHHHHhcCCccceeecceeEEEeecccCCccc----CccCCCCcccCcccccc--HH
Confidence 699999999999999999999999999999998 599999999999985531111 35678899999999887 57
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceee
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAH 159 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H 159 (266)
+++.+|+.+|+++||+||.+|||+|||||||++++.+++++||++++||++||+||++||++|||||||+.+ .+|||||
T Consensus 166 ~~~~di~~~l~~~Gi~ie~~hhEva~gQ~EI~~~~~~~l~~AD~~~~~K~vvk~vA~~hG~~aTFMpKP~~g-~~GSGMH 244 (443)
T COG0174 166 DFRRDIVEALEAAGIEIEAIHHEVAPGQFEINLRFDDALKAADQIVIFKYVVKEVAEKHGLTATFMPKPFFG-DNGSGMH 244 (443)
T ss_pred HHHHHHHHHHHHCCCCcEeccccccCCceEEecCCCCHHHHHHHHHHHHHHHHHHHHHhCCeEEEeCCCCCC-CCCCcee
Confidence 999999999999999999999999999999999999999999999999999999999999999999999995 8999999
Q ss_pred EeEeccccCC------CC---chH-HHHHHHHHHHHHHHHHHhhhhc---cccccC-CCCCCCCCccceeeccCCCCceE
Q 024513 160 ANYSTKSMRN------DG---GID-VIKKAIEKLGKRHGEHIAAYGE---GNERRL-TGRHETADINTFSWGVANRGASI 225 (266)
Q Consensus 160 ~h~Sl~~~~~------~~---g~~-~~~~~iaGl~L~h~~al~a~~~---nsYkRl-~~~~~a~~p~~~~WG~~NR~a~i 225 (266)
+|+|||+.++ ++ |++ .++|||+|| |+|+++++||++ |||||| +|..||| ++++||.+||||+|
T Consensus 245 ~H~Sl~~~dg~nlF~d~~~~~~lS~~~~~~igGi-lkha~~~~ai~~PtvNSYkRl~vp~e~AP--~~~~wg~~NRsa~i 321 (443)
T COG0174 245 VHQSLWDKDGGNLFADEDGYAGLSETALHFIGGI-LKHAPALTAITAPTVNSYKRLGVPYEWAP--TYIAWGVRNRSASV 321 (443)
T ss_pred EEEEEecCCCCccccCCCCcccHHHHHHHHHHHH-HHHHHHHHhHhCCCcchhhhcCCCcccCc--chhcccccCcceEE
Confidence 9999997541 22 353 679999999 999999999998 899999 6634577 89999999999999
Q ss_pred EeCcCCCCCCCceeEeCCCCCCCCHHHHHHHHHHHhhcCC
Q 024513 226 RVGRDTEKEGKGYFEDRRPASNMDPYVVTSMIAETTILWK 265 (266)
Q Consensus 226 Rvp~~~~~~~~~riE~R~~da~aNPYLalAailaAgl~g~ 265 (266)
|||.+.....++|||+|+||++|||||++||+|+|||+|+
T Consensus 322 RIP~~~~~~~~~RiE~R~pd~~aNPYLa~AaiL~Agl~GI 361 (443)
T COG0174 322 RIPASGANGKARRVEFRVPDPDANPYLAFAAILAAGLDGI 361 (443)
T ss_pred EeCCCCCCCCcceeEeeCCCCCCCHHHHHHHHHHHHHHHH
Confidence 9998743223579999999999999999999999999996
No 3
>PLN03036 glutamine synthetase; Provisional
Probab=100.00 E-value=9.2e-78 Score=568.05 Aligned_cols=266 Identities=78% Similarity=1.410 Sum_probs=241.7
Q ss_pred CceeeCCCCCCCCCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHH
Q 024513 1 MCDAYTPAGEPIPTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRD 80 (266)
Q Consensus 1 ~~d~~~~~g~p~~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (266)
+||+|++||+|++.|||.+|++++++++..|+++++|+|+|||||+.+..++.|++..+.|.++++||+..+.+..+.++
T Consensus 151 lcd~y~~dG~P~~~dpR~~L~~vl~~~~~~g~~p~~G~E~EF~Lf~~~~~~~~G~~~~~~p~p~g~yy~~~~~d~~~~~~ 230 (432)
T PLN03036 151 ICDTYTPAGEPIPTNKRHRAAEIFSNKKVVDEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRD 230 (432)
T ss_pred EEEEECCCCCCCCCCHHHHHHHHHHHhcccCCeEEEEeeeEEEEEEcccccccCCCCCCccCCCCCcCCCchhhhhhHHH
Confidence 69999999999999999999999999999999999999999999986543345666545677888988877777666789
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeE
Q 024513 81 IVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHA 160 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~ 160 (266)
++++++++|+.+||+|+++|+|++||||||++.|++++++||++++||+++|+||++||++|||||||+.+|++|||||+
T Consensus 231 i~~~i~~a~~~~GI~Ie~~~~E~gpGQ~Ei~l~~~d~L~aAD~~~l~R~ivk~VA~~~Gl~ATFMPKP~~gd~~GSGmHi 310 (432)
T PLN03036 231 ISDAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYILERITEQAGVVLTLDPKPIEGDWNGAGCHT 310 (432)
T ss_pred HHHHHHHHHHHCCCCeEEEEcCcCCCceEEecCCChHHHHHHHHHHHHHHHHHHHHHhCCEEEEcCCcCCCCcCCCCcee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999875689999999
Q ss_pred eEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcCCCCCCCceeE
Q 024513 161 NYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRDTEKEGKGYFE 240 (266)
Q Consensus 161 h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~~~~~~~~riE 240 (266)
|+|||+.++++|.+.++++++||+|+|+++++|+++||||||++++|||.|.+++||.+||+++||||......+++|||
T Consensus 311 H~Sl~d~r~~gg~~~~~~~i~gl~l~H~~~i~A~~~NsykRL~~~~ea~~p~~~swG~~NR~asIRIP~~~~~~~~~riE 390 (432)
T PLN03036 311 NYSTKSMREEGGFEVIKKAILNLSLRHKEHISAYGEGNERRLTGKHETASIDTFSWGVANRGCSIRVGRDTEKKGKGYLE 390 (432)
T ss_pred EechhhccccchHHHHHHHHhhHHHHHHHHHHhhhcChhhccCCCccccCCccceEeccCCcceEEECCCCCCCcccEEE
Confidence 99999854434778889999996699999999999999999999999987789999999999999999765333467999
Q ss_pred eCCCCCCCCHHHHHHHHHHHhhcCCC
Q 024513 241 DRRPASNMDPYVVTSMIAETTILWKP 266 (266)
Q Consensus 241 ~R~~da~aNPYLalAailaAgl~g~~ 266 (266)
+|.||++|||||++|+|+...++.+|
T Consensus 391 ~R~pda~aNPYLv~aai~~t~~~~~~ 416 (432)
T PLN03036 391 DRRPASNMDPYIVTSLLAETTILWEP 416 (432)
T ss_pred EeCCCCCCCHHHHHHHHHHHHhcCCc
Confidence 99999999999999999999998876
No 4
>TIGR00653 GlnA glutamine synthetase, type I. Alternate name: glutamate--ammonia ligase. This model represents the dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. E. coli, Synechocystis PCC6803, Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon Sulfolobus acidocaldarius differs from that in E. coli in that it is not regulated by adenylylation.
Probab=100.00 E-value=1e-77 Score=575.45 Aligned_cols=257 Identities=23% Similarity=0.315 Sum_probs=225.3
Q ss_pred CceeeCC-CCCCCCCChHHHHHHHHcccc-ccCCcceEeeeeeEEEecCCCCCCC-------------------CCCCCC
Q 024513 1 MCDAYTP-AGEPIPTNKRFNAAKVFGHPD-VVAEEPWYGIEQEYTLLQKDINWPL-------------------GWPVGG 59 (266)
Q Consensus 1 ~~d~~~~-~g~p~~~~pR~~L~~~~~~~~-~~G~~~~~g~E~EF~l~~~~~~~~~-------------------~~~~~~ 59 (266)
+||+++. ||+|++.|||++|||++++++ +.|+++++|+|+|||||+.+..... ++. ..
T Consensus 86 ~~d~~~~~dg~p~~~~PR~~L~r~~~~l~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 164 (460)
T TIGR00653 86 ICDVYEPFTGEPYERDPRSIAKRAEEYLKSGIGDTAYFGPEPEFFLFDSVEFGSLANGSFYEVDSEEGRWNEESGNR-GY 164 (460)
T ss_pred EEEEEECCCCCCCCCCHHHHHHHHHHHHHhCCCCceeEEcceEEEEEecCccCcccccceeeeccccccccccCCcC-CC
Confidence 5999998 999999999999999999999 8999999999999999986442100 110 11
Q ss_pred CCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcC
Q 024513 60 YPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAG 139 (266)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hG 139 (266)
.|.+.+.||+....+. ..+++++|+++|+++||+|+++|+|+|||||||++.|+++|++||++++||++||+||++||
T Consensus 165 ~~~~~~~~~~~~~~~~--~~~~~~~i~~~l~~~Gi~v~~~~~E~gpGQ~Ei~l~~~~~l~aAD~~~~~k~~ik~vA~~~G 242 (460)
T TIGR00653 165 KPRDKGGYFPVAPTDT--AVDIRREMVLYLEQLGFDVEVHHHEVATGQHEIDFKFDTLLKTADDIQTYKYVVKNVARKHG 242 (460)
T ss_pred cccCCccccCCCCccc--HHHHHHHHHHHHHHcCCCceeeecCcCCCceeEecCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 2445555677666654 57899999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEcccCCCCCCCCceeeEeEeccccCC--------CCchH-HHHHHHHHHHHHHHHHHhhhhc---cccccCCCCCC
Q 024513 140 VVLSFDPKPIKGDWNGAGAHANYSTKSMRN--------DGGID-VIKKAIEKLGKRHGEHIAAYGE---GNERRLTGRHE 207 (266)
Q Consensus 140 l~atFmpKP~~~d~~GsG~H~h~Sl~~~~~--------~~g~~-~~~~~iaGl~L~h~~al~a~~~---nsYkRl~~~~~ 207 (266)
++|||||||+. +.+|||+|+|+||||... +.|++ .+++||+|| |+|++++++|++ ||||||+|++|
T Consensus 243 ~~ATFmpKP~~-~~~GSG~H~H~Sl~d~g~n~F~d~~~~~~lS~~~~~fiaGi-L~h~~~l~a~~~PtvNSYkRl~p~~~ 320 (460)
T TIGR00653 243 KTATFMPKPLF-GDNGSGMHCHQSLWKDGENLFAGEEGYAGLSETALYYIGGI-LKHAKALAAFTNPTVNSYKRLVPGYE 320 (460)
T ss_pred CEEEEecccCC-CCCcCceeEEECccCCCeeccCCCCCCcccCHHHHHHHHHH-HHHHHHhhhHhcCCCcchhhcCCCCc
Confidence 99999999999 589999999999998431 12353 679999999 999999999997 89999999999
Q ss_pred CCCccceeeccCCCCceEEeCcCCCCCCCceeEeCCCCCCCCHHHHHHHHHHHhhcCC
Q 024513 208 TADINTFSWGVANRGASIRVGRDTEKEGKGYFEDRRPASNMDPYVVTSMIAETTILWK 265 (266)
Q Consensus 208 a~~p~~~~WG~~NR~a~iRvp~~~~~~~~~riE~R~~da~aNPYLalAailaAgl~g~ 265 (266)
|| ++++||.+||+++||||.... ...+|||+|++|++|||||++||+|+|||+|+
T Consensus 321 ap--~~~~WG~~NR~a~iRvp~~~~-~~~~riE~R~~da~aNPYLalAa~laAGl~Gi 375 (460)
T TIGR00653 321 AP--VYLAYSARNRSALIRIPASGN-PKAKRIEFRFPDPSANPYLAFAAMLMAGLDGI 375 (460)
T ss_pred Cc--ceeecccCCCCceEEecCCCC-CcCceEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 98 799999999999999997531 24679999999999999999999999999985
No 5
>PRK09469 glnA glutamine synthetase; Provisional
Probab=100.00 E-value=4e-77 Score=572.15 Aligned_cols=257 Identities=21% Similarity=0.257 Sum_probs=223.2
Q ss_pred CceeeCCC-CCCCCCChHHHHHHHHccccccCC--cceEeeeeeEEEecCCCC--CCC---------------------C
Q 024513 1 MCDAYTPA-GEPIPTNKRFNAAKVFGHPDVVAE--EPWYGIEQEYTLLQKDIN--WPL---------------------G 54 (266)
Q Consensus 1 ~~d~~~~~-g~p~~~~pR~~L~~~~~~~~~~G~--~~~~g~E~EF~l~~~~~~--~~~---------------------~ 54 (266)
+||+++.+ |+|++.|||++|||++++++++|+ ++++|+|+|||||+++.. .+. +
T Consensus 89 ~~d~~~~~~g~p~~~~PR~iLkr~~~~l~~~G~~~~~~~g~ElEF~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (469)
T PRK09469 89 RCDILEPGTMQGYDRDPRSIAKRAEDYLRSTGIADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEAAWNSGTKYEGG 168 (469)
T ss_pred EEEEEECCCCCcCCcCHHHHHHHHHHHHHHcCCCcceeEecceEEEEEeccccccCccccccccccchhcccccccccCC
Confidence 69999885 999999999999999999999999 999999999999985430 000 1
Q ss_pred CCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeeeCCCC-CCceeEecCCCchhHHHHHHHHHHHHHHH
Q 024513 55 WPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGINGEVM-PGQWEFQVGPCVGISSGDQLWMARYILER 133 (266)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E~g-pGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~ 133 (266)
+. ...+.+.+.||+....+. ..+++++|+++|+++||+|+++|+|+| ||||||+|.|.++|++||++++||++||+
T Consensus 169 ~~-~~~~~~~~~~y~~~~~~~--~~~~~~~i~~~l~~~Gi~v~~~h~E~g~~GQ~Ei~l~~~d~L~aaD~~~~~k~~vk~ 245 (469)
T PRK09469 169 NK-GHRPGVKGGYFPVPPVDS--SQDIRSAMCLVMEEMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHN 245 (469)
T ss_pred CC-CCccCCCccccCCCcccc--hHHHHHHHHHHHHHCCCCcEEeeCCCCCCCeEEEeccCCCHHHHHHHHHHHHHHHHH
Confidence 10 012333444667666665 579999999999999999999999999 59999999999999999999999999999
Q ss_pred HHHHcCceEEEcccCCCCCCCCceeeEeEeccccCC-------CCchH-HHHHHHHHHHHHHHHHHhhhhc---cccccC
Q 024513 134 ITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRN-------DGGID-VIKKAIEKLGKRHGEHIAAYGE---GNERRL 202 (266)
Q Consensus 134 vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~-------~~g~~-~~~~~iaGl~L~h~~al~a~~~---nsYkRl 202 (266)
||++||++|||||||+. +.+|||||+|+|||+... +.|++ .+++||+|| |+|++++++|++ ||||||
T Consensus 246 va~~~g~~atFmpKP~~-~~~GsG~H~H~Sl~~~g~N~F~~~~~~~ls~~~~~fiaGl-L~h~~~l~a~~~PtvNSYkRl 323 (469)
T PRK09469 246 VAHAFGKTATFMPKPMF-GDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGGI-IKHAKAINALANPTTNSYKRL 323 (469)
T ss_pred HHHHhCCEEEEeccccC-CCCCceeEEEEeecCCCccccCCCCcCCcCHHHHHHHHHH-HHHHHHHHhhhcCCCchHhhc
Confidence 99999999999999999 589999999999998531 13454 679999999 999999999997 899999
Q ss_pred CCCCCCCCccceeeccCCCCceEEeCcCCCCCCCceeEeCCCCCCCCHHHHHHHHHHHhhcCC
Q 024513 203 TGRHETADINTFSWGVANRGASIRVGRDTEKEGKGYFEDRRPASNMDPYVVTSMIAETTILWK 265 (266)
Q Consensus 203 ~~~~~a~~p~~~~WG~~NR~a~iRvp~~~~~~~~~riE~R~~da~aNPYLalAailaAgl~g~ 265 (266)
+|++||| ++++||++||+++||||... .+..+|||+|++|++|||||++||+|+|||+|+
T Consensus 324 ~p~~~ap--~~~~WG~~NR~a~iRvp~~~-~~~~~riE~R~~da~aNPYL~~AaiLaAGldGI 383 (469)
T PRK09469 324 VPGYEAP--VMLAYSARNRSASIRIPVVA-SPKARRIEVRFPDPAANPYLCFAALLMAGLDGI 383 (469)
T ss_pred CCCCcCc--CcceecCCCCcceEEeccCC-CCCCceEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 9999998 89999999999999999522 124679999999999999999999999999995
No 6
>TIGR03105 gln_synth_III glutamine synthetase, type III. This family consists of the type III isozyme of glutamine synthetase, originally described in Rhizobium meliloti, where types I and II also occur.
Probab=100.00 E-value=6.2e-76 Score=559.95 Aligned_cols=251 Identities=22% Similarity=0.286 Sum_probs=217.6
Q ss_pred CceeeCCCCCCCCCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHH
Q 024513 1 MCDAYTPAGEPIPTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRD 80 (266)
Q Consensus 1 ~~d~~~~~g~p~~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (266)
+||++. ||+|++.|||++|||++++++++|+++++|+|+|||||+.+.+.... +....+....++|+....+. ..+
T Consensus 83 ~~d~~~-~G~p~~~~PR~vL~r~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~ 158 (435)
T TIGR03105 83 AADLHV-NGKPYPQAPRVVLKRQLAEAAELGLTLNTGVECEFFLLRRDEDGSLS-IADRADTLAKPCYDQRGLMR--RYD 158 (435)
T ss_pred EEEEee-CCCcCCCCHHHHHHHHHHHHHhcCCceeEEeceEEEEEecCCCCCcc-cCCCCCCCCccCCCCcchhh--hhH
Confidence 589876 89999999999999999999999999999999999999975431111 10001111233455555443 579
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeE
Q 024513 81 IVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHA 160 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~ 160 (266)
++++|.++|+++||+|+++|+|+|||||||++.|.+++++||+++++|++||+||+|||++|||||||+. +.+|||+|+
T Consensus 159 ~~~~i~~~l~~~gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~k~~vk~vA~~~Gl~atFmpKP~~-~~~GsG~H~ 237 (435)
T TIGR03105 159 VLTEISDAMNALGWDPYQNDHEDANGQFEMNFTYADALTTADRHAFFRYMVKEIAEKHGMRATFMPKPFA-DLTGNGCHF 237 (435)
T ss_pred HHHHHHHHHHHCCCCeEEeecCcCCCceEEecCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEecCccCC-CCCccceEE
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999 589999999
Q ss_pred eEeccccCC---------C--CchH-HHHHHHHHHHHHHHHHHhhhhc---cccccCCCC------CCCCCccceeeccC
Q 024513 161 NYSTKSMRN---------D--GGID-VIKKAIEKLGKRHGEHIAAYGE---GNERRLTGR------HETADINTFSWGVA 219 (266)
Q Consensus 161 h~Sl~~~~~---------~--~g~~-~~~~~iaGl~L~h~~al~a~~~---nsYkRl~~~------~~a~~p~~~~WG~~ 219 (266)
|+|||+.++ + .+++ .+++||+|| |+|++++++|++ ||||||+|+ +||| ++++||.+
T Consensus 238 H~Sl~d~~g~n~f~d~~~~~~~~lS~~~~~fiaGl-L~h~~~l~a~~~PtvNSYkRl~p~~~~~~~~~AP--~~~~WG~~ 314 (435)
T TIGR03105 238 HLSLWDEDGRNLFADDSDPNGLGLSKLAYHFIGGI-LHHAPALCAVLAPTVNSYKRLNAPRTTSGATWAP--NFISYGGN 314 (435)
T ss_pred EEeeecCCCcccccCCCCCccccccHHHHHHHHHH-HHHHHHHHHHHCCCCccccccCCCcCCcCcccCC--ceeeccCC
Confidence 999996421 1 1254 679999999 999999999997 899999996 7887 89999999
Q ss_pred CCCceEEeCcCCCCCCCceeEeCCCCCCCCHHHHHHHHHHHhhcCC
Q 024513 220 NRGASIRVGRDTEKEGKGYFEDRRPASNMDPYVVTSMIAETTILWK 265 (266)
Q Consensus 220 NR~a~iRvp~~~~~~~~~riE~R~~da~aNPYLalAailaAgl~g~ 265 (266)
||+++||||. .+|||+|++|++|||||++||+|+|||+|+
T Consensus 315 NR~a~iRv~~------~~riE~R~~da~aNPYL~lAailaAgl~Gi 354 (435)
T TIGR03105 315 NRTHMVRIPD------PGRFELRLADGAANPYLAQAAILAAGLDGI 354 (435)
T ss_pred CCceeEeccC------CCeeEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 9999999992 469999999999999999999999999996
No 7
>PF00120 Gln-synt_C: Glutamine synthetase, catalytic domain; InterPro: IPR008146 Glutamine synthetase (6.3.1.2 from EC) (GS) [] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [, , ]: Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637 from INTERPRO). Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast. Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.; GO: 0004356 glutamate-ammonia ligase activity, 0006807 nitrogen compound metabolic process; PDB: 2J9I_E 3ZXV_D 1HTQ_D 1HTO_F 2BVC_F 2WGS_G 3ZXR_B 2WHI_D 3NG0_A 1LGR_C ....
Probab=100.00 E-value=2.1e-75 Score=523.28 Aligned_cols=240 Identities=28% Similarity=0.483 Sum_probs=201.2
Q ss_pred CCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCC-CCCC----CCCCCCccccccchhhHHHHHHHHHH
Q 024513 13 PTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPV-GGYP----GPQGPYYCGVGADKALGRDIVNSHYK 87 (266)
Q Consensus 13 ~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~-~~~~----~~~~~~~~~~~~~~~~~~~~~~~l~~ 87 (266)
+.|||.+|||+++++++.|+++++|+|+|||||+++.. .+++. .+.+ ...+.+|+....+. ..+++++|++
T Consensus 1 ~~~PR~~Lkr~~~~~~~~g~~~~~g~E~EF~l~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~ 76 (259)
T PF00120_consen 1 EACPRSILKRVLERLEEMGLSFKVGFELEFYLFDRDDD--GGWPRPSGYPDEPGQDYGGYYSLSPLDA--GEDFLEEIVD 76 (259)
T ss_dssp -T-HHHHHHHHHHHHHHTCCEEEEEEEEEEEEESTCEE--TTSSSTTSEESESSSTTTBSSTTTTTST--THHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHhCCceEEEEeEEEEEeccCcc--cccccccccccccccccCCcCCCchhhH--HHHHHHHHHH
Confidence 47999999999999999999999999999999998643 12221 0111 13455666665444 5799999999
Q ss_pred HHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEecccc
Q 024513 88 ACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSM 167 (266)
Q Consensus 88 ~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~ 167 (266)
+|+++||+|+++|+|+|||||||++.|.+++++||+++++|++||+||+|||++|||||||+. +.+|||+|+|+|||+.
T Consensus 77 ~l~~~Gi~ve~~h~E~gpgQ~Ei~~~~~~~l~aaD~~~~~k~~ik~vA~~~Gl~atFmpKP~~-~~~GsG~H~h~Sl~~~ 155 (259)
T PF00120_consen 77 ALEQAGIPVEQIHHEVGPGQYEINLGPCDPLEAADNLVLFKEIIKEVARKHGLTATFMPKPFS-GDNGSGMHLHISLWDA 155 (259)
T ss_dssp HHHHCT--EEEEEEESSTTEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHTTEEEE-SSSSST-TSS--BEEEEEEECHH
T ss_pred HHHHhhccccccccccchHhhccccccCcHHHHHHHHHHHHHHHHHHHHHcCCceeeeccccC-CcCccchhhhhhhhhc
Confidence 999999999999999999999999999999999999999999999999999999999999999 5899999999999974
Q ss_pred -CC------C-C--chH-HHHHHHHHHHHHHHHHHhhhhc---cccccCCCCCCCCCccceeeccCCCCceEEeCcCCCC
Q 024513 168 -RN------D-G--GID-VIKKAIEKLGKRHGEHIAAYGE---GNERRLTGRHETADINTFSWGVANRGASIRVGRDTEK 233 (266)
Q Consensus 168 -~~------~-~--g~~-~~~~~iaGl~L~h~~al~a~~~---nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~~~~ 233 (266)
++ + + +++ ..++||+|| |+|+++|++|++ ||||||+|++||| ++++||.+||+++||||... .
T Consensus 156 ~~g~n~f~~~~~~~~ls~~~~~flaGl-l~h~~~l~a~~~pt~nsykRl~~~~~ap--~~~~wG~~NR~a~iRi~~~~-~ 231 (259)
T PF00120_consen 156 KDGKNLFYDPDGPAGLSELARHFLAGL-LKHAPALTAFTAPTVNSYKRLVPGSWAP--TYISWGYDNRSAAIRIPSGG-G 231 (259)
T ss_dssp HTTEETTBSTTSHGHHHHHHHHHHHHH-HCHHHHHHHCHSTSTTHHHHSSSTSSSS--SBEEEEESHTTSSEEE-HHH-H
T ss_pred cccccccccccccccccHHHHHHHHHH-HHHHHHHHhhhCccCcchhhCCCCccce--eccchhhcccchhhheeccc-c
Confidence 21 2 1 453 578999999 999999999986 8999999999998 89999999999999999861 1
Q ss_pred CCCceeEeCCCCCCCCHHHHHHHHHHHh
Q 024513 234 EGKGYFEDRRPASNMDPYVVTSMIAETT 261 (266)
Q Consensus 234 ~~~~riE~R~~da~aNPYLalAailaAg 261 (266)
+.++|||+|++|++|||||++||||+||
T Consensus 232 ~~~~~~E~R~~da~aNPYL~laailaAG 259 (259)
T PF00120_consen 232 PKGTRIENRLPDADANPYLALAAILAAG 259 (259)
T ss_dssp HGGSEEEEESSBTTSSHHHHHHHHHHHH
T ss_pred ccccEEeccCCCCCcCHHHHHHHHHhcC
Confidence 1357999999999999999999999998
No 8
>KOG0683 consensus Glutamine synthetase [Amino acid transport and metabolism]
Probab=100.00 E-value=8.5e-44 Score=322.11 Aligned_cols=265 Identities=67% Similarity=1.197 Sum_probs=248.0
Q ss_pred CceeeCCCCCCCCCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHH
Q 024513 1 MCDAYTPAGEPIPTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRD 80 (266)
Q Consensus 1 ~~d~~~~~g~p~~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (266)
+|+.++.+|.|.+.+-|....+++...+-..-+|++|.|.||.+++....+++|||..++|.++++||+..+.++.+.++
T Consensus 102 ~c~~~~~~~~P~~tn~R~~c~~~~~~~~~~~~~PWfg~Eqeyt~l~~~~~~p~gwp~~GFp~Pqgpyyc~VGad~~~~rd 181 (380)
T KOG0683|consen 102 MCDTYDFDGKPTETNKRVACARIMPKLSTKDTEPWFGMEQEYTLLDALDGHPFGWPKGGFPGPQGPYYCGVGADRVFGRD 181 (380)
T ss_pred EeeccCCCCCcccccchhhHHHHhccccccccCCchhhhHHHhhhccccCCcccCCccCCCCCCCCceeeccccccccch
Confidence 59999999999999999999999999887888999999999999999655699999999999999999999988888899
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeE
Q 024513 81 IVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHA 160 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~ 160 (266)
+.+..+.++...||++..++.|+.|||||+.+.|+.++.++|+++.+|+++++||+++|+.|||.|||..++|+|+|+|.
T Consensus 182 iveahy~acLyaGl~i~G~N~EvmPgQwEfqvGp~~GI~~gD~lw~aR~il~rVae~~Gviasf~pKp~~g~WngaG~Ht 261 (380)
T KOG0683|consen 182 IVEAHYRACLYAGLNISGINVEVMPGQWEFQVGPCEGISMGDQLWMARYILHRVAEKFGVIASFDPKPILGDWNGAGCHT 261 (380)
T ss_pred hhhhhHHHHHhhheeeccccccccCceeEEeecchhcccchhhHHHHHHHHHHHHHHhCeeEEecCCCCCCcccCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhc----cccccCCCCCCCCCccceeeccCCCCceEEeCcCCCCCCC
Q 024513 161 NYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGE----GNERRLTGRHETADINTFSWGVANRGASIRVGRDTEKEGK 236 (266)
Q Consensus 161 h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~----nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~~~~~~~ 236 (266)
++|..+++.++|++.+..++..|..+|..++.+.-. .+-+||...+++...+..+||.-||.+.||||......++
T Consensus 262 n~ST~~mr~~~g~~~i~~a~~~ls~rh~~hi~~ydp~~G~dN~rrltg~hEt~~i~~Fs~GvAnr~~siri~r~va~~~~ 341 (380)
T KOG0683|consen 262 NFSTKEMREAGGLKIIEEAIPKLSKRHREHIAAYDPKGGKDNERRLTGRHETGSIDNFSWGVANRNPSIRIPRTVAAEGK 341 (380)
T ss_pred ccchhHHHhccCHHHHHHHhhhcchhhhhhhhhcCccCCccchhhhcCCCccccccccccccccCCceeeechhhhcccc
Confidence 999988777788999999999999999999999843 5788998777887778999999999999999998777678
Q ss_pred ceeEeCCCCCCCCHHHHHHHHHHHhhcCC
Q 024513 237 GYFEDRRPASNMDPYVVTSMIAETTILWK 265 (266)
Q Consensus 237 ~riE~R~~da~aNPYLalAailaAgl~g~ 265 (266)
+++|.|.||+++.||+|..+++-..|+..
T Consensus 342 Gy~edrrP~sN~Dpy~Vt~~~~~t~l~~~ 370 (380)
T KOG0683|consen 342 GYFEDRRPSSNCDPYAVTLMIIPTTLLEA 370 (380)
T ss_pred cccccCCCcCCCCcceeeHHHhhHHHhcc
Confidence 89999999999999999999998887764
No 9
>COG3968 Uncharacterized protein related to glutamine synthetase [General function prediction only]
Probab=99.79 E-value=1.3e-18 Score=162.06 Aligned_cols=217 Identities=25% Similarity=0.336 Sum_probs=153.1
Q ss_pred CcceEeeeeeEEEecCCCC--CC----CCCCCCCCCCCCC-----CCccccccchhhHHHHHHHHHHHHHHcCceeeeee
Q 024513 32 EEPWYGIEQEYTLLQKDIN--WP----LGWPVGGYPGPQG-----PYYCGVGADKALGRDIVNSHYKACLYAGINISGIN 100 (266)
Q Consensus 32 ~~~~~g~E~EF~l~~~~~~--~~----~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~ 100 (266)
+-..+|.|+||||+++... .+ .|....|.+.++| +||...+-+ ...++.++.+.|-++||+++.-|
T Consensus 214 V~s~~GaEQEYFlvd~~~~~~RpDLi~tGRTLFGa~ppkGQEldDHYFGaipeR---V~~FM~Dve~~LyaLGIpaKTrH 290 (724)
T COG3968 214 VFSNVGAEQEYFLVDKKSYDERPDLIFTGRTLFGAPPPKGQELDDHYFGAIPER---VSAFMKDVEKELYALGIPAKTRH 290 (724)
T ss_pred hccCCCccceeEEechhhcccCcceeeechhhcCCCCCCCccccchhccccHHH---HHHHHHHHHHHHHHcCCcccccc
Confidence 5678999999999987432 01 1111112344444 344444322 46788888888889999999999
Q ss_pred CCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCC-----CC----
Q 024513 101 GEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRN-----DG---- 171 (266)
Q Consensus 101 ~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~-----~~---- 171 (266)
.|++||||||..-+.++--|+|+-.+..+++|.+|+|||+.+-..-|||.| .+|||-|.|+|+-.+.+ ++
T Consensus 291 NEVAPgQfEIApife~~N~A~DhqQL~M~vLk~tA~KhGlVCLLHEKPFAG-iNGSGKH~NWSmGtd~g~NLLdPgD~Ph 369 (724)
T COG3968 291 NEVAPGQFEIAPIFESGNLATDHQQLVMEVLKKTALKHGLVCLLHEKPFAG-INGSGKHNNWSMGTDDGLNLLDPGDMPH 369 (724)
T ss_pred cccCCCceeeeeeeccccccchHHHHHHHHHHHHHHhcceEEEeecCCccC-cCCCCCccccccccCCCcccCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999996 99999999999965431 11
Q ss_pred -chH---HHHHHHHHHHHHHHHHHhhhhc--cccccCCCCCCCCCcccee------------------------------
Q 024513 172 -GID---VIKKAIEKLGKRHGEHIAAYGE--GNERRLTGRHETADINTFS------------------------------ 215 (266)
Q Consensus 172 -g~~---~~~~~iaGl~L~h~~al~a~~~--nsYkRl~~~~~a~~p~~~~------------------------------ 215 (266)
+.. .+...|-++ -++.+-|-+-.+ .+-.||..+ +|| |.-++
T Consensus 370 dN~QFL~Fc~AvIkaV-dkY~~LlRa~~a~AsNDhRLGAN-EAP-PAI~SVflGdqLedifEqi~~G~~~ssk~~g~mdL 446 (724)
T COG3968 370 DNKQFLLFCTAVIKAV-DKYADLLRASAANASNDHRLGAN-EAP-PAIISVFLGDQLEDIFEQIEKGKATSSKGNGKMDL 446 (724)
T ss_pred ccceeehhhHHHHHHH-HHHHHHHHHHHhccCCccccccC-CCC-cceeEeeccchHHHHHHHHhcCCCcccccCccccc
Confidence 111 123345555 566655555444 346778654 565 24333
Q ss_pred -----------eccCCCCceEEeCcCCCCCCCceeEeCCCCCC---CCHHHHHHHHHHHhh
Q 024513 216 -----------WGVANRGASIRVGRDTEKEGKGYFEDRRPASN---MDPYVVTSMIAETTI 262 (266)
Q Consensus 216 -----------WG~~NR~a~iRvp~~~~~~~~~riE~R~~da~---aNPYLalAailaAgl 262 (266)
-|..||+.+.-.. ..+||+|.++++ +-|-.++-+++|--|
T Consensus 447 g~~vlP~v~kdAgDRNRTSPFAFT-------GNkFEFRavgSSqSvs~P~tVLN~~vAesl 500 (724)
T COG3968 447 GISVLPAVEKDAGDRNRTSPFAFT-------GNKFEFRAVGSSQSVSEPNTVLNVIVAESL 500 (724)
T ss_pred chhhccccccccccccCCCCceec-------cceeeEecCCcccccccchHHHHHHHHHHH
Confidence 2344444433222 247999999876 568888888887554
No 10
>TIGR02050 gshA_cyan_rel uncharacterized enzyme. This family represents a division of a larger family, the other branch of which is predicted to act as glutamate--cysteine ligase (the first of two enzymes in glutathione biosynthesis) in the cyanobacteria. Species containing this protein, however, are generally not believe to make glutathione, and the function is unknown.
Probab=98.91 E-value=1.1e-07 Score=86.76 Aligned_cols=187 Identities=17% Similarity=0.152 Sum_probs=114.7
Q ss_pred eEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCC
Q 024513 35 WYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGP 114 (266)
Q Consensus 35 ~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~ 114 (266)
.+|+|.||+|++.... .+ .. ... .+++.++.+ ..+ ..+++|...+|.||+..|
T Consensus 1 t~GvE~E~~lvD~~t~----~~-----~~---------~~~---~~~l~~~~~---~~~---~~~~~El~~~qiEi~t~p 53 (287)
T TIGR02050 1 TLGVEEELLLVDPHTY----DL-----AA---------SAS---AVLIGACRE---KIG---AGFKHELFESQVELATPV 53 (287)
T ss_pred CceeeeeeeeEcCCcc----Cc-----Cc---------cCh---HHHHHhhhh---hcc---cccChhhhccEEEecCCC
Confidence 4799999999997542 11 00 000 145544322 222 348899999999999999
Q ss_pred -CchhHHHHHHHHHHHHHHHHHHHcCceEEEccc-CCCC------------------------CCCCceeeEeEeccccC
Q 024513 115 -CVGISSGDQLWMARYILERITEIAGVVLSFDPK-PIKG------------------------DWNGAGAHANYSTKSMR 168 (266)
Q Consensus 115 -~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpK-P~~~------------------------d~~GsG~H~h~Sl~~~~ 168 (266)
.+.-++.+.+...+..++++|+++|+...-..- |+.. +..-+|+|+|+++-+.
T Consensus 54 ~~~~~~l~~~l~~~~~~l~~~a~~~g~~l~~~G~hP~~~~~~~~~~~~~RY~~m~~~~g~~~~~~~~~g~hVhv~v~d~- 132 (287)
T TIGR02050 54 CTTLAEAAAQIRAVRARLVQAASDHGLRICGAGTHPFARWRRQEVADNPRYQRLLERYGYVARQQLVFGLHVHVGVPSP- 132 (287)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHcCCEEEeccCCCCCCCccCCCCcHHHHHHHHHHHHHHHHhHceeeEEEEeCCCCH-
Confidence 567779999999999999999999976543221 2220 0124799999999752
Q ss_pred CCCchHHHHHHHHHHHHHHHHHHhhhhccc------------cccCC----CCCCCCCccceeec--------------c
Q 024513 169 NDGGIDVIKKAIEKLGKRHGEHIAAYGEGN------------ERRLT----GRHETADINTFSWG--------------V 218 (266)
Q Consensus 169 ~~~g~~~~~~~iaGl~L~h~~al~a~~~ns------------YkRl~----~~~~a~~p~~~~WG--------------~ 218 (266)
...-..+..+ ...+|.+.|+++|| ||... |..- +.|..-+|. .
T Consensus 133 -----~~~i~~~n~l-~~~lP~llALsANSPf~~G~dtg~~s~R~~i~~~~p~~G-~p~~f~~~~~y~~~~~~l~~~g~i 205 (287)
T TIGR02050 133 -----DDAVAVLNRL-LPWLPHLLALSASSPFWQGFDTGYASYRRNIFQAWPTAG-LPPAFGSWDAFEAYFADLLETGVI 205 (287)
T ss_pred -----HHHHHHHHHH-HHHHHHHHHHHhCCccccCcCCchHHHHHHHHHhCCCCC-CCCcCCCHHHHHHHHHHHHHcCCc
Confidence 1223344455 67778888887643 33111 2211 223455563 2
Q ss_pred CCCCce---EEeCcCCCCCCCceeEeCCCCCCCCH--HHHHHHHHHHh
Q 024513 219 ANRGAS---IRVGRDTEKEGKGYFEDRRPASNMDP--YVVTSMIAETT 261 (266)
Q Consensus 219 ~NR~a~---iRvp~~~~~~~~~riE~R~~da~aNP--YLalAailaAg 261 (266)
.++... ||... .-.+||+|++|+..++ -+++||++.|-
T Consensus 206 ~~~~~iww~vRp~~-----~~~tvE~Rv~D~~~~~~~~~~~aal~~~L 248 (287)
T TIGR02050 206 DDDGDLWWDIRPSP-----HFGTVEVRVADTCLNLEHAVAIAALIRAL 248 (287)
T ss_pred CCCCeeEEEeccCC-----CCCCeeEEcCCCCCCHHHHHHHHHHHHHH
Confidence 222223 44321 3468999999998876 44566666553
No 11
>PRK13517 carboxylate-amine ligase; Provisional
Probab=98.84 E-value=1.1e-07 Score=89.72 Aligned_cols=132 Identities=17% Similarity=0.174 Sum_probs=88.8
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeeeCCCCCCceeEec
Q 024513 33 EPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGINGEVMPGQWEFQV 112 (266)
Q Consensus 33 ~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l 112 (266)
.+.+|+|.||+|++.... .+. +. ..++++.+ ... -.-..+..|...+|.||+.
T Consensus 10 ~~tiGvE~E~~lVD~~t~----~~~--------~~----------~~~vl~~~----~~~-~~~~~i~~El~~~qiEi~t 62 (373)
T PRK13517 10 RPTLGVEWELLLVDPETG----ELS--------PR----------AAEVLAAA----GED-DEGPHLQKELLRNTVEVVT 62 (373)
T ss_pred CCeeEeeeeEeeECCCcC----CcC--------cc----------HHHHHHhc----ccc-cCCCcccccccCCEEEECC
Confidence 569999999999997432 110 00 23444333 211 1124678899999999999
Q ss_pred CC-CchhHHHHHHHHHHHHHHHHHHHcCceEE---EcccCCCCC----------------------CCCceeeEeEeccc
Q 024513 113 GP-CVGISSGDQLWMARYILERITEIAGVVLS---FDPKPIKGD----------------------WNGAGAHANYSTKS 166 (266)
Q Consensus 113 ~~-~~~l~aaD~~~~~r~~ik~vA~~hGl~at---FmpKP~~~d----------------------~~GsG~H~h~Sl~~ 166 (266)
.| .+.-++.+++.-.+..++++|+++|+..- ..|.....+ ..-+|+|+|+++-+
T Consensus 63 ~p~~~~~el~~~L~~~~~~l~~~a~~~g~~l~~~G~~P~~~~~~~~~~~~~RY~~m~~~~~~~~~~~~~~g~hVhv~v~~ 142 (373)
T PRK13517 63 GVCDTVAEARADLRRTRALARRAAERRGARLAAAGTHPFSDWSEQPVTDKPRYAELIERTQWWARQQLICGVHVHVGVPS 142 (373)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEeeCCCCCCCCccCCCCCchHHHHHHHHHHHHHHhheeeeeEEEeCCCC
Confidence 99 56777999999999999999999996543 233311001 13579999999964
Q ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhhhhccc
Q 024513 167 MRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGN 198 (266)
Q Consensus 167 ~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ns 198 (266)
. ...-..+..+ ..++|.+.|+++||
T Consensus 143 ~------~~~i~~~n~l-~~~lP~llALsAnS 167 (373)
T PRK13517 143 R------EKVVPVINRL-RPWLPHLLALSANS 167 (373)
T ss_pred H------HHHHHHHHHH-HHHHHHHHHHHhCC
Confidence 2 1233455666 77888888888754
No 12
>PRK13515 carboxylate-amine ligase; Provisional
Probab=98.75 E-value=4.2e-07 Score=85.71 Aligned_cols=131 Identities=15% Similarity=0.071 Sum_probs=86.9
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeeeCCCCCCceeEec
Q 024513 33 EPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGINGEVMPGQWEFQV 112 (266)
Q Consensus 33 ~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l 112 (266)
.+.+|+|.||+|++.... .+. + . ..+++... ... .-..+.+|..-+|.||+.
T Consensus 5 ~~t~GvE~E~~lVD~~t~----~l~--------~--------~--~~~~l~~~----~~~--~~~~i~~El~~~qiEi~T 56 (371)
T PRK13515 5 EFTLGIEEEYLLVDPETR----DLR--------S--------Y--PDALVEAC----RDT--LGEQVKPEMHQSQVEVGT 56 (371)
T ss_pred CCcceEeEeEEEecCCcc----ccc--------c--------c--HHHHHHhc----hhh--cCCccCcchhccEEEECC
Confidence 468999999999997541 110 0 0 12344322 111 122688999999999999
Q ss_pred CC-CchhHHHHHHHHHHHHHHHHHHHcCceEE---EcccCCC------------------C----CCCCceeeEeEeccc
Q 024513 113 GP-CVGISSGDQLWMARYILERITEIAGVVLS---FDPKPIK------------------G----DWNGAGAHANYSTKS 166 (266)
Q Consensus 113 ~~-~~~l~aaD~~~~~r~~ik~vA~~hGl~at---FmpKP~~------------------~----d~~GsG~H~h~Sl~~ 166 (266)
.| .+.-++.+.+...+..+.++|+++|+... ..|.... + ...-+|+|+|+++-+
T Consensus 57 ~p~~~~~el~~~L~~~~~~l~~~a~~~g~~l~~~G~~P~~~~~~~~~t~~~RY~~m~~~~~~~~~~~~~~g~HVhv~~~d 136 (371)
T PRK13515 57 PVCATIAEAREELGRLRQRVAQLAAQFGLRIIAAGTHPFADWRRQEITPKERYAQLVEDLQDVARRNLICGLHVHVGIPD 136 (371)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHHHcCCEEEeccCCCCCCCccCCCCCchHHHHHHHHHHHHHHhhceeeeEEEeCCCC
Confidence 99 46666888999999999999999998763 2332100 0 112359999999864
Q ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhhhhccc
Q 024513 167 MRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGN 198 (266)
Q Consensus 167 ~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ns 198 (266)
. .....++..+ ...+|.|.|+++||
T Consensus 137 ~------e~~~~~~n~~-~~~lP~llALsanS 161 (371)
T PRK13515 137 R------EDRIDLMNQV-RYFLPHLLALSTSS 161 (371)
T ss_pred H------HHHHHHHHHH-HHHHHHHHHHHcCC
Confidence 2 1234455566 77788888888765
No 13
>PRK13516 gamma-glutamyl:cysteine ligase; Provisional
Probab=98.66 E-value=8.2e-07 Score=83.80 Aligned_cols=188 Identities=16% Similarity=0.108 Sum_probs=114.3
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeeeCCCCCCceeEec
Q 024513 33 EPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGINGEVMPGQWEFQV 112 (266)
Q Consensus 33 ~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l 112 (266)
.+.+|+|.||+|++.... .+ . +. ..++++.+. .-.. -+.+.+|..-+|.||+.
T Consensus 11 ~~t~GvE~E~~LVD~~t~----~~-----~---------~~----~~~vl~~~~----~~~~-~~~v~~El~~~qIEi~T 63 (373)
T PRK13516 11 PFTLGVELELQLVNPHDY----DL-----T---------QD----SSDLLRAVK----NQPT-AGEIKPEITESMIEIAT 63 (373)
T ss_pred CCeeEEEEEEEeEcCCCc----Cc-----C---------cc----HHHHHHhcc----cccc-ccccChhhhCceEEEcC
Confidence 459999999999997542 11 0 00 234554332 1000 22578899999999999
Q ss_pred CCC-chhHHHHHHHHHHHHHHHHHHHcCceEEE---cc-----------cC----------CCCC-CCCceeeEeEeccc
Q 024513 113 GPC-VGISSGDQLWMARYILERITEIAGVVLSF---DP-----------KP----------IKGD-WNGAGAHANYSTKS 166 (266)
Q Consensus 113 ~~~-~~l~aaD~~~~~r~~ik~vA~~hGl~atF---mp-----------KP----------~~~d-~~GsG~H~h~Sl~~ 166 (266)
.|. +.-++.+++...+..++++|+++|+...= .| || .... ..-+|+|+|+.+-+
T Consensus 64 ~p~~~~~el~~eL~~~r~~l~~~A~~~G~~lva~GthP~~~~~~~~it~~~RY~~l~~~~~~~~~~~~i~G~HVHvg~~d 143 (373)
T PRK13516 64 GVCRDIDQALGQLSAMRDVLVQAADKLNIGICGGGTHPFQQWQRQRICDNPRFQYLSELYGYLAKQFTVFGQHVHIGCPS 143 (373)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEeecCCCCCCccccCCCCcHHHHHHHHHhhhhhhhheeeeeEEEeCCCC
Confidence 995 67779999999999999999999975432 22 21 0000 02458999998854
Q ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhhhhcc------------ccccC----CCCCCCCCccceeecc------------
Q 024513 167 MRNDGGIDVIKKAIEKLGKRHGEHIAAYGEG------------NERRL----TGRHETADINTFSWGV------------ 218 (266)
Q Consensus 167 ~~~~~g~~~~~~~iaGl~L~h~~al~a~~~n------------sYkRl----~~~~~a~~p~~~~WG~------------ 218 (266)
. ...-..+..+ ..++|.+.|+++| |||-. .|.. .+.|..-+|..
T Consensus 144 ~------~~av~~~~~l-~~~lP~llALsAsSPf~~G~dTG~~S~R~~~~~~~P~~-G~pp~~~~~~~y~~~~~~l~~~G 215 (373)
T PRK13516 144 G------DDALYLLHGL-SRYVPHFIALSASSPYVQGVDTGFASARLNSVSAFPLS-GRAPFVLNWQEFEAYFRKMSYTG 215 (373)
T ss_pred H------HHHHHHHHHH-HhHhHHHHHHHhCCccccCcCCcchhHHHHHHhcCCCC-CCCCCcCCHHHHHHHHHHHHHcC
Confidence 2 1223345555 6677888888764 44322 1322 22234555540
Q ss_pred --CC-C--CceEEeCcCCCCCCCceeEeCCCCCCCCHHHH--HHHHHHH
Q 024513 219 --AN-R--GASIRVGRDTEKEGKGYFEDRRPASNMDPYVV--TSMIAET 260 (266)
Q Consensus 219 --~N-R--~a~iRvp~~~~~~~~~riE~R~~da~aNPYLa--lAailaA 260 (266)
.| + -=-|| |. +.-..||+|++|...++--+ +||++.|
T Consensus 216 ~i~d~~~~~WdvR-p~----~~~~TvEiRv~D~~~~~~~~~~iaal~~a 259 (373)
T PRK13516 216 VIDSMKDFYWDIR-PK----PEFGTVEVRVMDTPLTLERAAAIAAYIQA 259 (373)
T ss_pred CcCCCCeeEEEec-cC----CCCCCeEEecCCCCCCHHHHHHHHHHHHH
Confidence 00 0 00355 22 23467999999999999754 5555544
No 14
>PRK13518 carboxylate-amine ligase; Provisional
Probab=98.43 E-value=3.6e-06 Score=78.92 Aligned_cols=155 Identities=17% Similarity=0.124 Sum_probs=94.8
Q ss_pred eeeeCCCCCCceeEecCC-CchhHHHHHHHHHHHHHHHHHHHcCceE--------------EEcccCCCC----------
Q 024513 97 SGINGEVMPGQWEFQVGP-CVGISSGDQLWMARYILERITEIAGVVL--------------SFDPKPIKG---------- 151 (266)
Q Consensus 97 e~~~~E~gpGQ~Ei~l~~-~~~l~aaD~~~~~r~~ik~vA~~hGl~a--------------tFmpKP~~~---------- 151 (266)
+.+++|...+|.||+..+ .+.-++.+++...|..+.++|+++|+.. ..+|||...
T Consensus 49 ~~~~~El~~~qvEi~T~~~~~~~el~~~L~~~r~~l~~aa~~~g~~l~a~GthP~~~~~~~~~t~~~RY~~m~~~~~~~~ 128 (357)
T PRK13518 49 GRLDHELFKFVIETQTPLIEDPSEAGAALREVRDALVDHAAAHGYRIAAAGLHPAAKWRELEHAEKPRYRSQLDRIQYPQ 128 (357)
T ss_pred CcccccccCceEEEcCcCcCCHHHHHHHHHHHHHHHHHHHHHcCCEEEecCCCCCCCccccCCCCCcHHHHHHHhcccch
Confidence 468899999999999999 5788899999999999999999999853 234554210
Q ss_pred -CCCCceeeEeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhcc------------ccccCC----CCCCCCCccce
Q 024513 152 -DWNGAGAHANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEG------------NERRLT----GRHETADINTF 214 (266)
Q Consensus 152 -d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~n------------sYkRl~----~~~~a~~p~~~ 214 (266)
...-+|+|+|+.+-+. ...-..+..| ...+|.|.|+++| |||-.. |.. .+.|..-
T Consensus 129 ~~~~~~G~HVHVg~~d~------d~av~v~n~l-r~~LP~LlALsAnSPf~~G~dTG~aS~R~~iw~~~P~a-G~p~~f~ 200 (357)
T PRK13518 129 HRNTTAGLHVHVGVDDA------DKAVWIANEL-RWHLPILLALSANSPYWNGFDTGLASARAKIFEGLPNT-GMPTAFE 200 (357)
T ss_pred hcceeeEEEEEeCCCCH------HHHHHHHHHH-HhHHHHHHHHHcCCccccCcCCCcccHHHHHHHhCCCC-CCCcccC
Confidence 0013599999988442 1111234455 6677888888874 343221 221 1112444
Q ss_pred eec-cC------------CCCceEEeCcCCCCCCCceeEeCCCCCCCCHHHH--HHHHHHH
Q 024513 215 SWG-VA------------NRGASIRVGRDTEKEGKGYFEDRRPASNMDPYVV--TSMIAET 260 (266)
Q Consensus 215 ~WG-~~------------NR~a~iRvp~~~~~~~~~riE~R~~da~aNPYLa--lAailaA 260 (266)
+|. ++ .-.-+|--.- .+++.-..+|+|++|...++--+ +|+++.|
T Consensus 201 ~~~~ye~~v~~l~~~G~i~d~~~i~wdv-Rps~~~pTvEiRv~D~~~~~~~~~~lAal~ra 260 (357)
T PRK13518 201 DFEAFQRFERRMVETGSIEDRGELWYDV-RPHTGHGTVEVRTPDAQADPDVVLAFVEYVHA 260 (357)
T ss_pred CHHHHHHHHHHHHhcCCcCCCCceEEcc-CCCCCCCceeEecCCCCCCHHHHHHHHHHHHH
Confidence 553 11 1111111110 01223457999999999988754 4555544
No 15
>TIGR02048 gshA_cyano glutamate--cysteine ligase, cyanobacterial, putative. This family consists of proteins believed (see Copley SD, Dhillon JK, 2002) to be the glutamate--cysteine ligases of several cyanobacteria, which are known to make glutathione.
Probab=98.30 E-value=1.5e-05 Score=75.45 Aligned_cols=92 Identities=14% Similarity=0.049 Sum_probs=65.9
Q ss_pred eeeCCCCCCceeEecCC-CchhHHHHHHHHHHHHHHHHHHHcCc-e-EE-----Eccc-CCC--CC--------------
Q 024513 98 GINGEVMPGQWEFQVGP-CVGISSGDQLWMARYILERITEIAGV-V-LS-----FDPK-PIK--GD-------------- 152 (266)
Q Consensus 98 ~~~~E~gpGQ~Ei~l~~-~~~l~aaD~~~~~r~~ik~vA~~hGl-~-at-----FmpK-P~~--~d-------------- 152 (266)
.+..|.-..|.||+..+ .+.-++.+++.-.|..+.++|.++|. . +. ||.- ++. .+
T Consensus 31 ~~~~El~~~~IE~~T~~~~~~~el~~~L~~~r~~l~~~a~~~g~~~l~a~gthP~~~~~~~~~~t~~~rY~~~~~~~~~~ 110 (376)
T TIGR02048 31 GFVREPDSRNVEYTTPPLNSYDRLLCGLLRPRRQLRHYLSQLGDYTLIPGSTLSLGGTDRFYRSDPQNPYHTYIEQTYGT 110 (376)
T ss_pred CCccchhhcEEEecCCCcCCHHHHHHHHHHHHHHHHHHHHHcCCCeeeecccCCCCCCCccCcCCCcchHHHHHHHHhhh
Confidence 45668889999999999 57777999999999999999999997 3 21 2222 111 01
Q ss_pred -CCCceeeEeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhc
Q 024513 153 -WNGAGAHANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGE 196 (266)
Q Consensus 153 -~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ 196 (266)
..=+|+|||+.+-|. ...-..+..| .-++|.|.|+.+
T Consensus 111 ~~~i~G~HVHVgv~d~------d~av~v~n~l-r~~LP~LlALSA 148 (376)
T TIGR02048 111 QVVTASVHINIGIPDP------EELMRACRLV-RMEAPLFLALSA 148 (376)
T ss_pred hheeeEEEEEcCCCCH------HHHHHHHHHH-HHHHHHHHHHhc
Confidence 112489999999652 2344566777 778888888876
No 16
>PLN02611 glutamate--cysteine ligase
Probab=98.25 E-value=2.2e-05 Score=76.18 Aligned_cols=137 Identities=16% Similarity=0.078 Sum_probs=86.5
Q ss_pred CCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCce------------e--
Q 024513 31 AEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGIN------------I-- 96 (266)
Q Consensus 31 G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~------------v-- 96 (266)
+=...+|+|+|.++++.+.. .| . +| . -...+++.+.+ ..|++ -
T Consensus 65 ~~~~~iG~E~E~f~~~~~~~----~p-----v---~y-~-------~i~~lL~~l~~---~~gw~~~~e~g~iIgl~~~g 121 (482)
T PLN02611 65 KEKWRIGTEHEKFGFELATL----RP-----M---KY-D-------QIAQLLEGLAE---RFGWEKIMEGDNIIGLKQDG 121 (482)
T ss_pred CCCCeeEEeeeeeeccCCCC----CC-----C---CH-H-------HHHHHHHHHHH---hcCCceeccCCceecccCCC
Confidence 44679999999999986532 11 1 11 1 12445544422 12210 0
Q ss_pred eeeeCCCCCCceeEecCCC-chhHHHHHHHHHHHHHHHHHHHcCceEE--------------EcccCCC----------C
Q 024513 97 SGINGEVMPGQWEFQVGPC-VGISSGDQLWMARYILERITEIAGVVLS--------------FDPKPIK----------G 151 (266)
Q Consensus 97 e~~~~E~gpGQ~Ei~l~~~-~~l~aaD~~~~~r~~ik~vA~~hGl~at--------------FmpKP~~----------~ 151 (266)
..+.=|-| ||+|++..+. +.-++++.+...+..++++|+++|+... .||||-- +
T Consensus 122 ~~ITlEPG-gQiElSt~p~~si~e~~~el~~~~~~l~~~a~~~Gl~l~g~G~hP~~~~~~~~i~pk~RY~~M~~y~~~~g 200 (482)
T PLN02611 122 QSVSLEPG-GQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFLGIGFQPKWSVADIPIMPKGRYKIMRNYMPKVG 200 (482)
T ss_pred CceEeccc-ceEEecccCcCCHHHHHHHHHHHHHHHHHHHHHcCCCeEccCCCCCCccccccCCCChHHHHHHHHHHHhh
Confidence 24455777 9999999995 7888999999999999999999998432 2444420 0
Q ss_pred ----CC--CCceeeEeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhccc
Q 024513 152 ----DW--NGAGAHANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGN 198 (266)
Q Consensus 152 ----d~--~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ns 198 (266)
+. .-+|+|||+.+-+. + ..-.-+.-+ +...|.++|+++||
T Consensus 201 ~~g~~MM~~t~g~QVhvd~~se---e---d~v~~~~~~-~~l~Pvl~ALfANS 246 (482)
T PLN02611 201 SLGLDMMFRTCTVQVNLDFSSE---Q---DMVRKFRVG-LALQPIATALFANS 246 (482)
T ss_pred hhhhhhccceEEEEEEecCCCH---H---HHHHHHHHH-HHHHHHHHHHHhCC
Confidence 11 24689999988652 1 122233334 67778888888653
No 17
>PF04107 GCS2: Glutamate-cysteine ligase family 2(GCS2); InterPro: IPR006336 Also known as gamma-glutamylcysteine synthetase and gamma-ECS (6.3.2.2 from EC). This enzyme catalyses the first and rate limiting step in de novo glutathione biosynthesis. Members of this family are found in archaea, bacteria and plants. May and Leaver [] discuss the possible evolutionary origins of glutamate-cysteine ligase enzymes in different organisms and suggest that it evolved independently in different eukaryotes, from an ancestral bacterial enzyme. They also state that Arabidopsis thaliana (Mouse-ear cress) gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast and Escherichia coli homologues. In plants, there are separate cytosolic and chloroplast forms of the enzyme.; GO: 0004357 glutamate-cysteine ligase activity, 0006750 glutathione biosynthetic process; PDB: 1R8G_A 2GWC_E 2GWD_A 1TT4_B.
Probab=97.98 E-value=5.5e-05 Score=68.89 Aligned_cols=96 Identities=17% Similarity=0.126 Sum_probs=65.2
Q ss_pred eeeeeCCCCCCceeEecCC-CchhHHHHHHHHHHHHHHHHHHHcCceEEE--------------ccc-------------
Q 024513 96 ISGINGEVMPGQWEFQVGP-CVGISSGDQLWMARYILERITEIAGVVLSF--------------DPK------------- 147 (266)
Q Consensus 96 ve~~~~E~gpGQ~Ei~l~~-~~~l~aaD~~~~~r~~ik~vA~~hGl~atF--------------mpK------------- 147 (266)
-..+++|.--+|.||+..| .+.-++.+.+...+..+.++|+++|+...= .||
T Consensus 34 ~~~~~~E~~~~qvEi~t~p~~~~~el~~~l~~~~~~l~~~a~~~g~~l~~~G~~P~~~~~~~~~~~~~RY~~~~~~~~~~ 113 (288)
T PF04107_consen 34 GGRVVTELPQSQVEISTPPCRSLAELREELRALRRALADAAAELGLRLVAAGTHPFARWRDQPITPKPRYRAMAEYFGRR 113 (288)
T ss_dssp SSEEEEESSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHCTTEEEE--SB-SS--GGGS---S-HHHHCHHHHHGGH
T ss_pred CCceeeccCCCEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEecCCCcCCCcccccCCCChhhhHHHHHHhhh
Confidence 3477889999999999999 567779999999999999999999976532 222
Q ss_pred -CCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhcc
Q 024513 148 -PIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEG 197 (266)
Q Consensus 148 -P~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~n 197 (266)
++..+..-+|+|+|+++-+. -...-..+..+ ...+|.+.|+++|
T Consensus 114 g~~~~~~~~~g~hvhV~v~~~-----~e~~v~~~n~~-~~~~P~llALsAN 158 (288)
T PF04107_consen 114 GVLARRMMTCGAHVHVGVDDG-----DEAAVRVMNAL-RPWLPVLLALSAN 158 (288)
T ss_dssp -SGCCSHHBHEEEEEEEESSS-----HHHHHHHHHHH-HTTHHHHHHHH--
T ss_pred hhhhhhhhhcccceEEeCCCc-----cHHHHHHHHHH-HHHhHHHHHHHcC
Confidence 21112234599999999642 11222455555 7778888888764
No 18
>TIGR01436 glu_cys_lig_pln glutamate--cysteine ligase, plant type. This model represents one of two highly dissimilar forms of glutamate--cysteine ligase (gamma-glutamylcysteine synthetase), an enzyme of glutathione biosynthesis. The other type is modeled by TIGR01434. This type is found in plants (with a probable transit peptide), root nodule and other bacteria, but not E. coli and closely related species.
Probab=97.78 E-value=0.00058 Score=65.97 Aligned_cols=140 Identities=19% Similarity=0.139 Sum_probs=84.9
Q ss_pred CCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCce-------e-------
Q 024513 31 AEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGIN-------I------- 96 (266)
Q Consensus 31 G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~-------v------- 96 (266)
+=..++|+|+|-|.|+.++..++ +|....+ ..++++.+. ...|++ +
T Consensus 19 ~~~~~iG~E~E~f~~~~~~~~~~------------~y~~~~g-----i~~~l~~l~---~~~g~~~~~e~g~~i~l~~~~ 78 (446)
T TIGR01436 19 KEQWRIGTEHEKFGFEKNTLRPM------------KYEQKGG-----IAELLNGIA---ERFGWQKVMEGDKIIGLKQDK 78 (446)
T ss_pred CCCCceEeeeeeeeeecCCCCCC------------CCCCchh-----HHHHHHHHH---hhcCCceeccCCceeeecCCC
Confidence 44679999999999987553111 1211000 244555442 122211 0
Q ss_pred eeeeCCCCCCceeEecCCC-chhHHHHHHHHHHHHHHHHHHHcCceEE--------------EcccCCCC----------
Q 024513 97 SGINGEVMPGQWEFQVGPC-VGISSGDQLWMARYILERITEIAGVVLS--------------FDPKPIKG---------- 151 (266)
Q Consensus 97 e~~~~E~gpGQ~Ei~l~~~-~~l~aaD~~~~~r~~ik~vA~~hGl~at--------------FmpKP~~~---------- 151 (266)
..+.-|-| ||+|++..|. +.-++++.+...+..++++|+++|+... .||||.-.
T Consensus 79 ~~itlEPg-gQlElS~~p~~~i~e~~~~l~~~~~~l~~~a~~~Gl~l~~~G~~P~~~~~~~~~~pk~RY~~M~~~~~~~G 157 (446)
T TIGR01436 79 QSISLEPG-GQFELSGAPLETIHETCDEINSHLYQVKEVAEEMGIGFLGLGFQPKWRREDIPLMPKGRYDIMRNYMPKVG 157 (446)
T ss_pred CeEEEcCc-CeEEecccccCCHHHHHHHHHHHHHHHHHHHHhcCCCeEecCCCCCCCcccCCCCCchHHHHHHHHHhhcc
Confidence 24445766 9999999995 6778999999999999999999997533 24444210
Q ss_pred ----CCC--CceeeEeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhccc
Q 024513 152 ----DWN--GAGAHANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGN 198 (266)
Q Consensus 152 ----d~~--GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ns 198 (266)
+.. -+|+|+|+.+-+. - .+..-+.-+ +...|.++|+++||
T Consensus 158 ~~g~~mm~~t~g~qVhld~~~e-----~-d~v~~~~~~-~~l~Pvl~ALfANS 203 (446)
T TIGR01436 158 KLGLDMMLRTCTVQVNLDFSSE-----A-DMVRKFRAS-LALQPLATALFANS 203 (446)
T ss_pred hHHHHHhHhheeEEEeeCCCCH-----H-HHHHHHHHH-HHHHHHHHHHHhCC
Confidence 001 3678888876541 1 112222333 66778888887654
No 19
>COG2170 Uncharacterized conserved protein [Function unknown]
Probab=97.61 E-value=0.00044 Score=64.00 Aligned_cols=187 Identities=19% Similarity=0.206 Sum_probs=110.7
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeeee--CCCCCCceeE
Q 024513 33 EPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGIN--GEVMPGQWEF 110 (266)
Q Consensus 33 ~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~--~E~gpGQ~Ei 110 (266)
.+..|+|.|||+.++... +..... ..+++.+ .=++..-| +|.--.+.|+
T Consensus 2 ~ltlGvE~E~~lvd~~g~------------------dl~~~s----~~ii~~~-------~~~~~~~~~~~e~~e~~vE~ 52 (369)
T COG2170 2 RLTLGVELEFQLVDPQGY------------------DLVGSS----DAIIEAL-------KGKVTAGHLKHEITESTVEL 52 (369)
T ss_pred CcccceEEEEEecCCCCc------------------cccccc----HHHHHhc-------CCCCCCcchhHHHHHHhhcc
Confidence 367899999999986442 111111 2344322 22222223 6665667777
Q ss_pred ecCCCchhH-HHHHHHHHHHHHHHHHHHcCceEEE--------------cccC-CCC---C--CCC-----ceeeEeEec
Q 024513 111 QVGPCVGIS-SGDQLWMARYILERITEIAGVVLSF--------------DPKP-IKG---D--WNG-----AGAHANYST 164 (266)
Q Consensus 111 ~l~~~~~l~-aaD~~~~~r~~ik~vA~~hGl~atF--------------mpKP-~~~---d--~~G-----sG~H~h~Sl 164 (266)
....++.+. |+-..--.|..+++.|..|||...= -+|| +.. + ..| -|.|||+.+
T Consensus 53 ~t~vc~~~~eA~~~~r~~r~~l~q~a~d~gL~~~~~GtHPfadw~~~~~~~~prY~~~ie~~~y~~~q~~v~G~HVHVGi 132 (369)
T COG2170 53 ATGVCRLLAEAAAQLRALRDYLVQAASDHGLRICGGGTHPFADWRRQEVPDNPRYQRLIERTGYLGRQMTVAGQHVHVGI 132 (369)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHHhhhcCceecccCCCchhhhhhccCCCChhHHHHHHHhhhHHhheeeeeEEEEecC
Confidence 777765554 5555556788999999999987532 3444 000 0 012 389999998
Q ss_pred cccCCCCchHHHHHHHHHHHHHHHHHHhhhhcc------------ccccCC----CCCCCCCccceeec-----------
Q 024513 165 KSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEG------------NERRLT----GRHETADINTFSWG----------- 217 (266)
Q Consensus 165 ~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~n------------sYkRl~----~~~~a~~p~~~~WG----------- 217 (266)
-+. ...-..+-+| +.++|.+.|+.++ |+|+-. |.. .+.|..-+|.
T Consensus 133 ~~~------d~~~~~l~~l-~~~~PhlLALSASSPf~~G~dTGyAS~R~~if~~~P~~-g~pp~f~sw~~f~~~~~~~~~ 204 (369)
T COG2170 133 PSP------DDAMYLLHRL-LRYVPHLLALSASSPFWQGTDTGYASARANIFSQLPTN-GLPPAFQSWAAFEAFFRDQLE 204 (369)
T ss_pred CCH------HHHHHHHHHH-HhhhhHHHhhhcCCccccCccchhhhhhHhhhhhCCcC-CCCccccCHHHHHHHHHHHHH
Confidence 652 2345678888 9999999999862 554432 211 1223455665
Q ss_pred ---cCCCC---ceEEeCcCCCCCCCceeEeCCCCCCCCHHH--HHHHHHHHh
Q 024513 218 ---VANRG---ASIRVGRDTEKEGKGYFEDRRPASNMDPYV--VTSMIAETT 261 (266)
Q Consensus 218 ---~~NR~---a~iRvp~~~~~~~~~riE~R~~da~aNPYL--alAailaAg 261 (266)
.+|.- -.|| |. +.=+++|+|++|...||=- ++++++-|-
T Consensus 205 tG~I~~~~~lwwdIR-Ps----ph~gTlEvRi~D~~~~l~~~~aivaL~~Al 251 (369)
T COG2170 205 TGTIDSMGDLWWDIR-PS----PHLGTLEVRICDTVLNLAELLAIVALIHAL 251 (369)
T ss_pred hcccccccceEEecc-cC----CCCCceEEEecCCCCCHHHHHHHHHHHHHH
Confidence 12221 2344 21 1237899999999999964 466666554
No 20
>TIGR03444 gshA_related glutamate--cysteine ligase family protein. Members of this bacterial protein family bear homology to glutamate--cysteine ligase, an enzyme in the two-step pathway of glutathione (GSH) biosynthesis, but are distinctly different. Among the bacterial genomes that carry the uncharacterized methyltransferase (TIGR03438) and conserved hypothetical protein TIGR03440, this protein is found in a subset, always in the vicinity of these other genes. Conserved hypothetical protein TIGR03442 is found in these same genomes. The role of this cassette is probably biosynthetic, but the product is unknown.
Probab=96.84 E-value=0.011 Score=56.08 Aligned_cols=95 Identities=17% Similarity=0.052 Sum_probs=60.0
Q ss_pred eeCCCCCCceeEecCCC-chhHHHHHHHHHHHHHHHHHHHcCceEE---E---------cccCC-----------CC---
Q 024513 99 INGEVMPGQWEFQVGPC-VGISSGDQLWMARYILERITEIAGVVLS---F---------DPKPI-----------KG--- 151 (266)
Q Consensus 99 ~~~E~gpGQ~Ei~l~~~-~~l~aaD~~~~~r~~ik~vA~~hGl~at---F---------mpKP~-----------~~--- 151 (266)
+.-|= -||+|++..|. +.-++++.+...+..++++|+++|+..- + ||||- .|
T Consensus 64 iTlEP-GgQvELSt~P~~sl~el~~el~~~l~~l~~~a~~~Gl~lva~G~~P~~~~~~itpk~RY~~M~~~~~~~~G~~G 142 (390)
T TIGR03444 64 ITVEP-GGQLELSGPPADGLTAAVAALAADLAVLRAALAEDGLALVGLGADPLRPPRRVLPGPRYRAMEQFFATGIGPFG 142 (390)
T ss_pred EEeCC-CCEEEecCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEEeccCCCCCccCCCchHHHHHHHHHhhhccCchH
Confidence 33352 36999999995 7778999999999999999999997542 2 33331 01
Q ss_pred -CCCCceeeEeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhccc
Q 024513 152 -DWNGAGAHANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGN 198 (266)
Q Consensus 152 -d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ns 198 (266)
+...+|+|+|++|-...++. ...+.+-.. ..-.|.++|+++||
T Consensus 143 ~~MM~~tasVQV~ld~~~~e~--D~~~k~rva--~aL~PvLlALfANS 186 (390)
T TIGR03444 143 ALMMCSTASVQVNLDAGTDPA--EWAERWRLA--HALGPVLIAAFANS 186 (390)
T ss_pred HHHhhCceeEEEccCCCCCHH--HHHHHHHHH--HHHHHHHHHHHhCC
Confidence 11256899999995421111 122222221 12267777877653
No 21
>KOG0683 consensus Glutamine synthetase [Amino acid transport and metabolism]
Probab=94.80 E-value=0.0086 Score=55.74 Aligned_cols=58 Identities=10% Similarity=-0.112 Sum_probs=47.4
Q ss_pred cccccCCCCCCCCCccceeeccCCCCceEEeCcCCCCCCCceeEeCCCCCCCCHHHHHHHHHHHhhcC
Q 024513 197 GNERRLTGRHETADINTFSWGVANRGASIRVGRDTEKEGKGYFEDRRPASNMDPYVVTSMIAETTILW 264 (266)
Q Consensus 197 nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~~~~~~~~riE~R~~da~aNPYLalAailaAgl~g 264 (266)
++|+|.....|. -+||.+|+..+.+ +. +.+...+|....|++|||+.++.+.+++.+|
T Consensus 285 s~rh~~hi~~yd-----p~~G~dN~rrltg-~h----Et~~i~~Fs~GvAnr~~siri~r~va~~~~G 342 (380)
T KOG0683|consen 285 SKRHREHIAAYD-----PKGGKDNERRLTG-RH----ETGSIDNFSWGVANRNPSIRIPRTVAAEGKG 342 (380)
T ss_pred chhhhhhhhhcC-----ccCCccchhhhcC-CC----ccccccccccccccCCceeeechhhhccccc
Confidence 679999887554 5799999998888 22 2356777888888899999999999999988
No 22
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=90.44 E-value=0.76 Score=32.98 Aligned_cols=65 Identities=23% Similarity=0.223 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCC------CceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcc
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMP------GQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDP 146 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gp------GQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmp 146 (266)
.++.+|.+.|.+.|++|..+..+.-+ ++|.+.+.-.-+- ..| .-.++..++++|++.|+.++|-|
T Consensus 11 Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p~-~~~-~~~l~~~l~~l~~~~~~~~~~~~ 81 (81)
T cd04869 11 GIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPA-GTD-LDALREELEELCDDLNVDISLEP 81 (81)
T ss_pred CHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecCC-CCC-HHHHHHHHHHHHHHhcceEEecC
Confidence 46777888889999999999776544 7775554443331 112 45778999999999999988854
No 23
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=87.41 E-value=2 Score=30.92 Aligned_cols=62 Identities=23% Similarity=0.222 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
.++.++.+.|.+.|.+++.++.-.-.|+|-+.+.-+-+ .|+.-.++..+++++++.|+.+.|
T Consensus 14 Giv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~---~~~~~~l~~~L~~l~~~~~l~v~v 75 (76)
T PF13740_consen 14 GIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP---EDSLERLESALEELAEELGLDVSV 75 (76)
T ss_dssp THHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES---HHHHHHHHHHHHHHHHHTT-EEEE
T ss_pred cHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC---cccHHHHHHHHHHHHHHCCcEEEE
Confidence 47778888899999999999988888998776665444 456677899999999999999876
No 24
>PF12224 Amidoligase_2: Putative amidoligase enzyme; InterPro: IPR022025 This family of proteins are likely to act as amidoligase enzymes [] Protein in this family are found in conserved gene neighbourhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes) [].
Probab=85.96 E-value=14 Score=32.41 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=18.4
Q ss_pred ceeEeCCCCCCCCHHHHHHHHH
Q 024513 237 GYFEDRRPASNMDPYVVTSMIA 258 (266)
Q Consensus 237 ~riE~R~~da~aNPYLalAail 258 (266)
..||+|.+.++-++--+.+.+-
T Consensus 225 ~TvEFR~~~~s~d~~~~~~wi~ 246 (252)
T PF12224_consen 225 PTVEFRQPNGSLDAEEISAWIE 246 (252)
T ss_pred CeEEEecCCCCCCHHHHHHHHH
Confidence 4799999999999987766654
No 25
>PF06877 RraB: Regulator of ribonuclease activity B; InterPro: IPR009671 This entry occurs in several hypothetical bacterial proteins of around 120 residues in length. The function of these proteins is unknown. The protein structure has been determined for one member of this group, the hypothetical protein VCO424 from Vibrio cholerae; it has an alpha+beta sandwich fold.; PDB: 1NXI_A.
Probab=85.77 E-value=3.9 Score=31.05 Aligned_cols=94 Identities=11% Similarity=0.017 Sum_probs=56.0
Q ss_pred HHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCcee
Q 024513 17 RFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINI 96 (266)
Q Consensus 17 R~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~v 96 (266)
...-+++++.|++.|-.+..-.++||+++-.+. +-++.+...+.+.|..|
T Consensus 3 ~~~n~~vl~~L~~~Gddl~~~r~ieh~~~f~~~------------------------------~~~~~f~~~~~~~g~~v 52 (104)
T PF06877_consen 3 IIENREVLEALEEDGDDLSKPRPIEHWFYFEDE------------------------------EDAEKFAEELEKLGYEV 52 (104)
T ss_dssp HHHHHHHHHHHHHHT--TTS-EEEEEEEEES-H------------------------------HHHHHHHHHHHHHS---
T ss_pred HHHHHHHHHHHHhcCCCCCCCeEEEEEEEeCCH------------------------------HHHHHHHHHHHHCCCEE
Confidence 345577888889999999999999999875422 23344445667999999
Q ss_pred eeeeC--CCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCce
Q 024513 97 SGING--EVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVV 141 (266)
Q Consensus 97 e~~~~--E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~ 141 (266)
+.... |.+.+.|.+.+.....+...+ +.-.-.-+-.+|+++|..
T Consensus 53 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~-I~~~~~~l~~lA~~~~g~ 98 (104)
T PF06877_consen 53 ESAEEDEEDGDGPYCLDISREMVLDYED-INAITQELEDLAKEFGGE 98 (104)
T ss_dssp B----B-SS-SSBEEEEEEEEE-S-HHH-HHHHHHHHHHHHHHHT-E
T ss_pred EEeecccCCCCceEEEEEEEecCCCHHH-HHHHHHHHHHHHHHhCcE
Confidence 88775 678889999998876665433 333445566688887754
No 26
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=85.70 E-value=6.1 Score=35.35 Aligned_cols=126 Identities=12% Similarity=0.069 Sum_probs=75.6
Q ss_pred HcC-ceeeeeeCC----CCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEecc
Q 024513 91 YAG-INISGINGE----VMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTK 165 (266)
Q Consensus 91 ~~G-i~ve~~~~E----~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~ 165 (266)
++| |++..+.+- --|.+.=++|.|.++..-.| ++-+=..+|++-.+.|+.. .|| . ..|.|+|+.+-|.
T Consensus 95 n~~~lE~H~w~s~~~~~~~PD~lvfDLDP~~~~~f~~-v~~~A~~~r~~L~~lgL~~--f~K--T--SG~kGlHV~vPl~ 167 (245)
T TIGR02778 95 QQGALEFHIWGARIDAPEKPDRIVFDLDPGPGVAWKL-VVEAAQLIRELLDELGLES--FVK--T--SGGKGLHVYVPLR 167 (245)
T ss_pred HhCcEEeeCCCCCCCCCCCCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc--ceE--c--cCCCeEEEEEECC
Confidence 444 555444332 23889999999988765544 4455567999999999984 255 3 3578999999997
Q ss_pred ccCCCCchHHHHHHHHHHHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 166 SMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 166 ~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
...+-+....+-++||-.+-+..|.+.... -.|....| -.++.|..|+|...+=-|-+
T Consensus 168 ~~~~~~~~r~fa~~iA~~l~~~~Pd~~t~~--~~k~~R~g-----kvfiDylqN~~g~T~vapYS 225 (245)
T TIGR02778 168 PTLSWDEVKDFAKALAQALAQQMPDRFTAE--MSKKNRVG-----KIFVDYLRNARGKTTVAPYS 225 (245)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCchhhhhH--hhHHhCCC-----CEEEECccCCCCCeEEeccc
Confidence 531111122333445444222334443322 22222233 17999999999987766643
No 27
>PF14395 COOH-NH2_lig: Phage phiEco32-like COOH.NH2 ligase-type 2
Probab=84.27 E-value=1.6 Score=39.16 Aligned_cols=52 Identities=17% Similarity=0.173 Sum_probs=28.3
Q ss_pred eEecCC-CchhHHHHHHHHHHHHHHHHHHHcC-ceEEEc--ccCCCCCCCCceeeEeEecc
Q 024513 109 EFQVGP-CVGISSGDQLWMARYILERITEIAG-VVLSFD--PKPIKGDWNGAGAHANYSTK 165 (266)
Q Consensus 109 Ei~l~~-~~~l~aaD~~~~~r~~ik~vA~~hG-l~atFm--pKP~~~d~~GsG~H~h~Sl~ 165 (266)
||--.| .+|.+..+++.. ++++.+++-. -.+.|. ..|+.+ .--|.|||+|-.
T Consensus 52 ElRP~P~~~P~~L~~~i~~---~l~~A~~~i~~~~l~W~AG~mP~~g--fp~GGHiHfsgv 107 (261)
T PF14395_consen 52 ELRPAPSPDPAELFENIRR---ALREAARRIPDRSLEWLAGSMPFPG--FPLGGHIHFSGV 107 (261)
T ss_pred ecCCCCCCCHHHHHHHHHH---HHHHHHHhCCCCCceEecCCCCCCC--CCcCCeEEecCC
Confidence 666666 577777777644 4444333332 223332 123342 446789999854
No 28
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=82.80 E-value=10 Score=33.58 Aligned_cols=127 Identities=13% Similarity=0.099 Sum_probs=76.4
Q ss_pred HHcC-ceeeeeeC----CCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEec
Q 024513 90 LYAG-INISGING----EVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYST 164 (266)
Q Consensus 90 ~~~G-i~ve~~~~----E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl 164 (266)
.++| |++.-+.. .--|.+.=++|.|.+++.-.| ++-+=..+|++-.+.||.+ .|| . ..|.|+|+.+-|
T Consensus 78 an~g~iE~H~w~~r~~~~e~PD~lvfDLDP~~~~~f~~-v~~~A~~~r~~L~~lgL~~--~~K--T--SG~kGlHV~vPl 150 (227)
T cd04862 78 VQMGVLEFHTWGARIDRLERPDRIVFDLDPGPGVPWKA-VVEAALLVRELLDELGLES--FVK--T--SGGKGLHVVVPL 150 (227)
T ss_pred HHhCcEEeeCCCCCCCCCCCCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc--ceE--c--cCCCeEEEEEEc
Confidence 3444 55543333 224899999999988765544 4555678999999999984 255 3 257899999999
Q ss_pred cccCCCCchHHHHHHHHHHHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 165 KSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 165 ~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
....+-+....+-++||-.+-+..|.+.... -.|....|- .++.|..|+|...+=-|-+
T Consensus 151 ~~~~~~~~~r~fa~~lA~~l~~~~P~~~t~~--~~k~~R~gk-----vfiDylqN~~g~T~vapYS 209 (227)
T cd04862 151 APRAGWDEVKAFAKALAQHLARTNPDRFVAT--MGKAKRVGK-----IFIDYLRNGRGATAVAPYS 209 (227)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCchhhhHH--hhHHhCCCc-----EEEECccCCCCCeEEeccc
Confidence 7531111122333445544222234443322 222233331 7999999999987776643
No 29
>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=82.64 E-value=2.4 Score=31.24 Aligned_cols=67 Identities=18% Similarity=0.157 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEccc
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPK 147 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpK 147 (266)
.++.++.+.|.+.|++|..++...-.++|.+.+.-.-+ ...+++-.++..+++++.+.|+..++-+.
T Consensus 13 Giva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~-~~~~~~~~L~~~l~~l~~~~~l~~~i~~~ 79 (88)
T cd04872 13 GIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDIS-ESNLDFAELQEELEELGKELGVKIRIQHE 79 (88)
T ss_pred CHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeC-CCCCCHHHHHHHHHHHHHHcCCEEEEEhH
Confidence 47778888889999999999988878888766554432 11344667899999999999999998554
No 30
>COG3572 GshA Gamma-glutamylcysteine synthetase [Coenzyme metabolism]
Probab=82.24 E-value=2.5 Score=40.28 Aligned_cols=45 Identities=22% Similarity=0.190 Sum_probs=34.9
Q ss_pred eeCCCCCCceeEecCCCchhH-HHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 99 INGEVMPGQWEFQVGPCVGIS-SGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 99 ~~~E~gpGQ~Ei~l~~~~~l~-aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
+.-|-| ||||+...|.+.+. +|-..-.--.+||++|...|+-..+
T Consensus 91 IslEpg-gq~Elsgapletihq~~~e~n~hlavlr~~a~~~gl~fvG 136 (456)
T COG3572 91 ISLEPG-GQFELSGAPLETIHQTCGEMNQHLAVLREIAAELGLGFVG 136 (456)
T ss_pred EEeccC-ceEEecCCchHHHHHHHHHHHHHHHHHHHHHHhcCCceEe
Confidence 344777 99999999976665 5555555667899999999988776
No 31
>PRK02471 bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional
Probab=81.48 E-value=5.5 Score=41.34 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=14.8
Q ss_pred cceEeeeeeEEEecCCC
Q 024513 33 EPWYGIEQEYTLLQKDI 49 (266)
Q Consensus 33 ~~~~g~E~EF~l~~~~~ 49 (266)
...+|+|-|+.+++.+.
T Consensus 18 ~~~~GiE~E~lrVd~~g 34 (752)
T PRK02471 18 QANFGLEKESLRVDSDG 34 (752)
T ss_pred cCCcceEeeeeEECCCC
Confidence 67899999999999753
No 32
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=81.37 E-value=4.1 Score=28.98 Aligned_cols=65 Identities=12% Similarity=0.106 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcc
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDP 146 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmp 146 (266)
-++.++.+.|.+.|++++.++.-.-.|+|-+.+.-.-+- ..+.-.++..+..++++.|+.++.-|
T Consensus 11 Giv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p~--~~~~~~l~~~l~~l~~~l~l~i~~~~ 75 (75)
T cd04870 11 GLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIPD--SADSEALLKDLLFKAHELGLQVRFEP 75 (75)
T ss_pred CHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcCC--CCCHHHHHHHHHHHHHHcCceEEEeC
Confidence 477888888999999999997766667776554332221 11345679999999999999988643
No 33
>PRK00194 hypothetical protein; Validated
Probab=81.30 E-value=3.1 Score=30.59 Aligned_cols=66 Identities=17% Similarity=0.176 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcc
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDP 146 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmp 146 (266)
-++.++.+.|.+.|++|..++...-.|.|.+.+.-.-+ ...++.-.++..+++++.+.|+.++|-+
T Consensus 15 Giva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~-~~~~~~~~l~~~l~~l~~~~~~~~~~~~ 80 (90)
T PRK00194 15 GIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDIS-ESKKDFAELKEELEELGKELGVKIRIQH 80 (90)
T ss_pred CHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEec-CCCCCHHHHHHHHHHHHHHcCCEEEEEh
Confidence 47777888889999999999998877888774332211 1123345678889999999999999843
No 34
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=80.93 E-value=13 Score=32.94 Aligned_cols=126 Identities=17% Similarity=0.164 Sum_probs=76.0
Q ss_pred HcC-ceeeeeeCC----CCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEecc
Q 024513 91 YAG-INISGINGE----VMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTK 165 (266)
Q Consensus 91 ~~G-i~ve~~~~E----~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~ 165 (266)
++| |++..+.+- --|.+.=++|.|.+++.-.| ++-+=..+|++-.+.||.+ .|| . ..|.|+|+.+-|.
T Consensus 79 n~~~lE~H~w~sr~~~~e~PD~lvfDLDP~~~~~f~~-v~~~A~~vr~~L~~lgL~~--f~K--T--SG~kGlHV~vPl~ 151 (227)
T cd04861 79 NLGAIELHPWLSRADDLERPDRLVFDLDPGPGVPFED-VVEAALLLRELLDELGLES--FPK--T--SGGKGLHVYVPLA 151 (227)
T ss_pred HhCcEEeeCCCCCCCCCCCCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc--ceE--c--cCCCeEEEEEEcC
Confidence 444 555444432 23889999999998875544 4555678899999999984 255 3 2578999999997
Q ss_pred ccCCCCchHHHHHHHHHHHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 166 SMRNDGGIDVIKKAIEKLGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 166 ~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
...+-+....+-++||-.+-+..|.+.... -.|....+ -.++.|..|+|...+=-|-+
T Consensus 152 ~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~--~~k~~R~g-----rvfiDy~qN~~g~T~vapYS 209 (227)
T cd04861 152 PRYTWDEVRAFAKALARELARRLPDLFTAE--MAKAKRGG-----KIFVDYLQNARGKTTVAPYS 209 (227)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCchhhhhH--hhHHhCCC-----CEEEECccCCCCCeEEeccc
Confidence 531111222334455554222334443332 22222222 17899999999887766643
No 35
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=80.17 E-value=14 Score=32.75 Aligned_cols=112 Identities=10% Similarity=0.077 Sum_probs=70.7
Q ss_pred CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHH
Q 024513 104 MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKL 183 (266)
Q Consensus 104 gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl 183 (266)
-|.+.=|+|.|. +. .=++++-+=..+|++-.+.||.+ .|| . ..|.|+|+.+-|....+-+....+-++||-.
T Consensus 99 ~PD~~vfDLDP~-~~-~f~~v~~~A~~~r~~L~~~gL~~--f~K--T--SG~kGlHv~vPl~~~~~~~~~r~fa~~lA~~ 170 (228)
T cd04864 99 HPDLMVFDLDPS-AD-DIEAVRTAALAVRELLDELGLPS--FVK--T--TGSRGFHVVVPLDGRGDFDDVRAFAAEAADA 170 (228)
T ss_pred CCCEEEEecCCC-CC-CHHHHHHHHHHHHHHHHHcCCcc--ceE--c--cCCCeEEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 488999999997 33 44556677788999999999984 256 3 3578999999997531111122333445544
Q ss_pred HHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 184 GKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 184 ~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
+-+..|.+... .-.|....|- .++.|..|+|...+=-|-+
T Consensus 171 l~~~~P~~~t~--~~~k~~R~gr-----vfiDylqN~~g~T~vapYS 210 (228)
T cd04864 171 LAKRDPDLLTT--EARKAKRGDR-----VFLDIGRNAYGQTAVAPYA 210 (228)
T ss_pred HHHHCchhhhH--HhhHHhCCCc-----EEEECccCCCCCeEEeccc
Confidence 22233444332 2223333332 7999999999987776643
No 36
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=80.03 E-value=15 Score=32.64 Aligned_cols=113 Identities=13% Similarity=0.136 Sum_probs=69.6
Q ss_pred CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHH
Q 024513 104 MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKL 183 (266)
Q Consensus 104 gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl 183 (266)
-|.+.=|+|.|.+++.-.| ++-+=..+|++-.+.|+.. | || . ..|.|+|+.+-|....+-+....+-++||-.
T Consensus 101 ~PD~~vfDLDP~~~~~f~~-v~~~A~~~r~~L~~lgL~s-~-~K--T--SG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~ 173 (231)
T cd04863 101 PPDRLVFDLDPGEPAGLVE-CARVALWLRDRLAALGLAS-F-PK--T--SGSKGLHLYVPLDGPVSSDQTKEFAKALARE 173 (231)
T ss_pred CCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc-c-eE--C--CCCCeEEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 4899999999988765554 3445567999999999984 2 55 3 3579999999997531111122233444444
Q ss_pred HHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 184 GKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 184 ~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
+-+..|.+... +..|.-..+- .++.|..|+|...+=-|-+
T Consensus 174 l~~~~P~~~t~--~~~k~~R~gr-----vfiDylqN~~g~T~vapYS 213 (231)
T cd04863 174 LEREHPDLVVS--RMTKSLRAGK-----VFVDWSQNDAAKTTIAPYS 213 (231)
T ss_pred HHHHCchhhhh--HhhHhhCCCc-----EEEECccCCCCCeEEeccc
Confidence 22233444432 2222222221 6899999999887766643
No 37
>KOG0558 consensus Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion]
Probab=79.88 E-value=1.7 Score=40.71 Aligned_cols=27 Identities=30% Similarity=0.311 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEccc
Q 024513 121 GDQLWMARYILERITEIAGVVLSFDPK 147 (266)
Q Consensus 121 aD~~~~~r~~ik~vA~~hGl~atFmpK 147 (266)
+|.++.+|+-+|++|+..|++.||||-
T Consensus 276 ~~sLvklr~elk~~a~e~~IKltfmPf 302 (474)
T KOG0558|consen 276 CDSLVKLRQELKENAKERGIKLTFMPF 302 (474)
T ss_pred hHHHHHHHHHHhhhhhhcCceeeehHH
Confidence 699999999999999999999999995
No 38
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=78.21 E-value=18 Score=31.91 Aligned_cols=111 Identities=13% Similarity=0.040 Sum_probs=70.1
Q ss_pred CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHH
Q 024513 104 MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKL 183 (266)
Q Consensus 104 gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl 183 (266)
-|.+.=++|.|.+++.-.| ++-+=..+|++-.+.|+.. | || . ..|.|+|+.+-|.+.+ ......+.|...|
T Consensus 92 ~PD~lvfDLDP~~~~~f~~-v~~~A~~vr~~L~~lgL~~-f-~K--T--SG~kGlHV~vPl~~~~--~~~~~~r~fa~~i 162 (223)
T cd04866 92 KPSEIVFDLDPPSRDHFSL-AVEAANLLKEILDALGLTS-F-VK--T--SGNKGLQVYIPLPDNK--FTYDETRLFTEFI 162 (223)
T ss_pred CCCeEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc-c-eE--c--cCCCeEEEEEEcCCCC--CCHHHHHHHHHHH
Confidence 4899999999988765444 4566688999999999984 2 55 3 3578999999997211 2233344444444
Q ss_pred ---HHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 184 ---GKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 184 ---~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
+-+..|.+... +-.|....+ -.++.|..|+|...+=-|-+
T Consensus 163 A~~l~~~~P~~~t~--~~~k~~R~g-----kVfiDylqN~~g~T~vapYS 205 (223)
T cd04866 163 AEYLCQQFPELFTT--ERLKKNRHN-----RLYLDYVQHAEGKTIIAPYS 205 (223)
T ss_pred HHHHHHHCchhhhH--HhhHHhCCC-----CEEEECccCCCCCeEEeccc
Confidence 12222433322 222222233 17899999999988776643
No 39
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=77.99 E-value=18 Score=32.03 Aligned_cols=113 Identities=13% Similarity=0.161 Sum_probs=70.5
Q ss_pred CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHH
Q 024513 104 MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKL 183 (266)
Q Consensus 104 gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl 183 (266)
-|.+.=|+|.|.+++.-.| ++-+=..+|++..+.||.+ | || . ..|.|+|+.+-|....+-+....+-++||-.
T Consensus 98 ~PD~lvfDLDP~~~~~f~~-v~~~A~~vr~~L~~lgL~s-f-~K--T--SG~kGlHv~vPl~~~~~~~~~r~fa~~iA~~ 170 (228)
T cd04865 98 HPDELVIDLDPQPGTSFED-VVEVALLVREVLDELGLRG-Y-PK--T--SGARGLHIYVPIAPRYTFEEVRRFAELLARE 170 (228)
T ss_pred CCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc-c-eE--c--cCCCeEEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 3889999999998765544 4556678999999999984 2 55 3 2578999999996532111222334455554
Q ss_pred HHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCcC
Q 024513 184 GKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGRD 230 (266)
Q Consensus 184 ~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~~ 230 (266)
+-+..|.+... +-.|.-..+ -.++.|..|+|...+=-|-+
T Consensus 171 l~~~~P~~~t~--~~~k~~R~g-----rvfiDylqN~~g~T~vapYS 210 (228)
T cd04865 171 VERRLPDLATT--ERWKKERGG-----RVYLDYLQNARGKTLAAPYS 210 (228)
T ss_pred HHHHCchhhhh--HhhHHhCCC-----CEEEECccCCCCCeEEeccc
Confidence 22223444332 222222222 17899999999877766643
No 40
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=74.45 E-value=10 Score=27.24 Aligned_cols=64 Identities=14% Similarity=0.089 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEc
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFD 145 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFm 145 (266)
.-++..+.+.|.+.|++|..+..-.-.|+|-+.+....+ .+..--++..++++|++.|+.++.+
T Consensus 12 ~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~---~~~~~~l~~~l~~~~~~~~l~i~v~ 75 (77)
T cd04893 12 PGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS---WDAIAKLEAALPGLARRLDLTLMMK 75 (77)
T ss_pred ChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec---cccHHHHHHHHHHHHHHcCCEEEEE
Confidence 357888888899999999998887778888665555433 1345567888999999999988753
No 41
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=70.75 E-value=5.9 Score=29.59 Aligned_cols=59 Identities=5% Similarity=-0.057 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceE
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVL 142 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~a 142 (266)
.+.+....+.+.+.|++++-+..|+--..--+.+-++ ||.-+-||.++|++++.++..+
T Consensus 25 ~~al~~c~~~~~~~~L~m~lvd~e~~~D~~k~~fyy~-----a~~rvDFR~Lvr~L~~~f~~RI 83 (88)
T PF04468_consen 25 EEALKFCRELVKELGLPMKLVDVEYQFDGSKLTFYYT-----AESRVDFRELVRDLAREFKTRI 83 (88)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEEEEEcCCCEEEEEEE-----eCCcCcHHHHHHHHHHHhCceE
Confidence 5666667777889999999999999777777888887 7888999999999999998765
No 42
>PRK11191 RNase E inhibitor protein; Provisional
Probab=65.61 E-value=42 Score=27.37 Aligned_cols=92 Identities=11% Similarity=-0.032 Sum_probs=59.5
Q ss_pred HHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeee
Q 024513 19 NAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISG 98 (266)
Q Consensus 19 ~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~ 98 (266)
.=+++++.|.+.|-.+..-.++|+++.-.+. +-++++...+.++|..|..
T Consensus 13 ~~~eVi~~L~edGsd~~~~~~IEH~~~f~d~------------------------------~~lek~a~~a~klGyeV~~ 62 (138)
T PRK11191 13 ETREIIEELLEDGSDPDALYTIEHHFSADDF------------------------------DKLEKAAVEAFKLGYEVTD 62 (138)
T ss_pred HHHHHHHHHHHcCCCcCCCEEEEEEEecCCH------------------------------HHHHHHHHHHHHcCCeeec
Confidence 3456777788889999999999998764322 2334444556799999943
Q ss_pred ---eeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCce
Q 024513 99 ---INGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVV 141 (266)
Q Consensus 99 ---~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~ 141 (266)
+..|.+..-|-+.+.....+...+-- -.-.-+-.+|.++|..
T Consensus 63 ~ee~e~edg~~~~~~~~~~e~~l~~e~I~-~~~~~L~~LA~k~~g~ 107 (138)
T PRK11191 63 AEELELEDGDVIFCCDAVSEVALNAELID-AQVEQLLALAEKFDVE 107 (138)
T ss_pred ccccccCCCCeEEEEEEEecCCCCHHHHH-HHHHHHHHHHHHhCCC
Confidence 23455555677677766666654433 3334455688888864
No 43
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=61.52 E-value=24 Score=24.76 Aligned_cols=60 Identities=12% Similarity=-0.104 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHcCceeeeeeCC--CCCCceeEecCCCchhHHH-HHHHHHHHHHHHHHHHcCce
Q 024513 80 DIVNSHYKACLYAGINISGINGE--VMPGQWEFQVGPCVGISSG-DQLWMARYILERITEIAGVV 141 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E--~gpGQ~Ei~l~~~~~l~aa-D~~~~~r~~ik~vA~~hGl~ 141 (266)
-++.+|.+.+.+.|+++..++.- ...++|.+.+.-.-+ .. .+.-.++..+..++.+.++.
T Consensus 11 Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~~ 73 (74)
T cd04875 11 GIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFELE--GFDLSREALEAAFAPVAAEFDMD 73 (74)
T ss_pred CHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEEeC--CCCCCHHHHHHHHHHHHHHcCCc
Confidence 47788888899999999999776 456677665554322 11 13456788889999887753
No 44
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=59.31 E-value=5.7 Score=30.71 Aligned_cols=24 Identities=25% Similarity=0.253 Sum_probs=19.9
Q ss_pred HHcCceeeeeeCCCCCCceeEecCC
Q 024513 90 LYAGINISGINGEVMPGQWEFQVGP 114 (266)
Q Consensus 90 ~~~Gi~ve~~~~E~gpGQ~Ei~l~~ 114 (266)
-++|=++|++--+ +|||||||+.-
T Consensus 55 ~a~ge~ietIrI~-~pG~YeiNl~~ 78 (112)
T COG3364 55 GAQGEPIETIRIL-RPGVYEINLES 78 (112)
T ss_pred hcccCcceEEEEe-cCceEEEehhh
Confidence 4788888888876 79999999874
No 45
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=58.42 E-value=33 Score=24.19 Aligned_cols=47 Identities=21% Similarity=0.174 Sum_probs=32.9
Q ss_pred HHHHHHHHHcCceeeeeeCCCCCCceeEecCC--CchhHHHHHHHHHHHHHHHHHHHcCc
Q 024513 83 NSHYKACLYAGINISGINGEVMPGQWEFQVGP--CVGISSGDQLWMARYILERITEIAGV 140 (266)
Q Consensus 83 ~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~--~~~l~aaD~~~~~r~~ik~vA~~hGl 140 (266)
+++.+.|+.+|+.++.. ....+++...+ .|....+| ++-+||+-+|+
T Consensus 22 ~~i~~~L~~lg~~~~~~----~~~~~~v~vP~~R~Di~~~~D-------liEEiaR~yGY 70 (70)
T PF03484_consen 22 EEIIKILKRLGFKVEKI----DGDTLEVTVPSYRFDIEHEED-------LIEEIARIYGY 70 (70)
T ss_dssp HHHHHHHHHTT-EEEE-----CTTEEEEEEETTSTT-SSHHH-------HHHHHHHHHTG
T ss_pred HHHHHHHHHCCCEEEEC----CCCEEEEEcCCCcCCcCcccH-------HHHHHHHHhCC
Confidence 45567788999999875 56678887776 57776665 67788888775
No 46
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=55.91 E-value=57 Score=32.73 Aligned_cols=110 Identities=15% Similarity=0.056 Sum_probs=67.3
Q ss_pred CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHH
Q 024513 104 MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKL 183 (266)
Q Consensus 104 gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl 183 (266)
-|.+.=++|.|.+.+.-.| ++-+=..+|++-.+.||.. .|| . ..|.|+|+.+-|.... .+....+.|...|
T Consensus 390 ~Pd~~v~DLDP~~~~~f~~-v~~~A~~~r~~L~~~gl~~--~~K--t--SG~kGlhv~vPl~~~~--~~~~~~~~fa~~~ 460 (552)
T TIGR02776 390 KPDRIVFDLDPPPGVAFKL-AVEAAQLMKQLLDELGLVS--FVK--T--SGGKGLHVVVPLRPNT--FTWDETKLFAKAI 460 (552)
T ss_pred CCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc--ceE--c--cCCCeEEEEEEcCCCC--CCHHHHHHHHHHH
Confidence 4889999999987765444 4455567999999999984 256 3 3578999999997511 2233344444444
Q ss_pred ---HHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCc
Q 024513 184 ---GKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGR 229 (266)
Q Consensus 184 ---~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~ 229 (266)
+-+..|.+... .-.|.-..+ -.++.|..|+|...+=-|-
T Consensus 461 a~~~~~~~P~~~t~--~~~k~~R~g-----rv~iDy~qn~~~~T~~apY 502 (552)
T TIGR02776 461 AEYLARQFPERFTT--EMGKKNRVG-----RIFIDYLRNARGKTTVAPY 502 (552)
T ss_pred HHHHHHHCcceehh--hhhHhhCCC-----CEEEEcccCCCCCeEEecc
Confidence 12222333322 122222222 2688888888887766664
No 47
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=54.42 E-value=2.1e+02 Score=30.45 Aligned_cols=123 Identities=15% Similarity=0.128 Sum_probs=73.6
Q ss_pred HHcC-ceeeeeeCCC----CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEec
Q 024513 90 LYAG-INISGINGEV----MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYST 164 (266)
Q Consensus 90 ~~~G-i~ve~~~~E~----gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl 164 (266)
.++| |++..+.+-. -|.+.=++|.|.+++.-.+ ++-+=..+|++-.+.||.. | || . ..|.|+||.+-|
T Consensus 664 an~~~iE~H~w~~~~~~~~~Pd~lvfDLDP~~~~~f~~-v~~aA~~~r~~L~~lgL~s-f-~K--T--SG~kGlHv~vPl 736 (860)
T PRK05972 664 AQMGAVELHTWNATPDRIEVPDRLVFDLDPGPGVPWKA-VVEAARLMRTRLDELGLES-F-LK--T--SGGKGLHVVVPL 736 (860)
T ss_pred HHhCcEEeecCCCCCCCCCCCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCce-e-eE--C--CCCCeEEEEEEc
Confidence 3444 6655444322 3899999999988765443 4555577999999999983 2 45 3 257899999999
Q ss_pred cccCCCCchHHHHHH---HHHHHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCc
Q 024513 165 KSMRNDGGIDVIKKA---IEKLGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGR 229 (266)
Q Consensus 165 ~~~~~~~g~~~~~~~---iaGl~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~ 229 (266)
... ......+.| |+-.+-+..|.+.. .+..|....+- .++.|-.|+|...+=-|-
T Consensus 737 ~~~---~~~~~~~~fa~~ia~~l~~~~P~~~t--~~~~k~~R~gr-----ifiDylqN~~g~T~vapY 794 (860)
T PRK05972 737 ARR---LDWDEVKAFAQAVCQHMARDLPERFL--AKMGKKNRVGK-----IFLDYLRNGRGATTVAAL 794 (860)
T ss_pred CCC---CCHHHHHHHHHHHHHHHHHHCchheh--hhhhHhhCCCc-----EEEEccccCCCCeEEecc
Confidence 752 223333444 44431222233322 22333333331 678888888876665553
No 48
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=54.25 E-value=30 Score=29.65 Aligned_cols=63 Identities=8% Similarity=-0.007 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCC------ce----eEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEccc
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPG------QW----EFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPK 147 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpG------Q~----Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpK 147 (266)
--|+.++.+.|.+.||+|+.+.++..+. .| |+.+.... ++--+|..+.++|.+.++.+++-|.
T Consensus 106 PGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~lP~~~------~~~~L~~~l~~l~~eL~vd~~l~~~ 178 (190)
T PRK11589 106 PHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPASQ------DAANIEQAFKALCTELNAQGSINVV 178 (190)
T ss_pred CCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEEcCCCC------CHHHHHHHHHHHHHHhCceEEEEEe
Confidence 4688899999999999999999986553 44 44444321 2345688999999999999998775
No 49
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=53.27 E-value=32 Score=23.95 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=31.5
Q ss_pred HHHHHHHHcCceeeeeeCCCCCCceeEecCC--CchhHHHHHHHHHHHHHHHHHHHcCc
Q 024513 84 SHYKACLYAGINISGINGEVMPGQWEFQVGP--CVGISSGDQLWMARYILERITEIAGV 140 (266)
Q Consensus 84 ~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~--~~~l~aaD~~~~~r~~ik~vA~~hGl 140 (266)
++.+.|..+|++++. . + ..+++++...+ .|.+..+| ++-+||+-+|+
T Consensus 23 ei~~~L~~lg~~~~~-~-~-~~~~~~v~~P~~R~Di~~~~D-------liEei~r~~Gy 71 (71)
T smart00874 23 EIEEILKRLGFEVEV-S-G-DDDTLEVTVPSYRFDILIEAD-------LIEEVARIYGY 71 (71)
T ss_pred HHHHHHHHCCCeEEe-c-C-CCCeEEEECCCCccccCcccH-------HHHHHHHHhCC
Confidence 455677899999965 1 1 14567777666 45555554 67888888875
No 50
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=52.92 E-value=57 Score=30.91 Aligned_cols=137 Identities=18% Similarity=0.136 Sum_probs=64.5
Q ss_pred eCCCCCCCCCChHHHHHH--HHccccccCCcceEeeeeeEEEecCCCC----CCCCCCCC------CCCCCCCCCccccc
Q 024513 5 YTPAGEPIPTNKRFNAAK--VFGHPDVVAEEPWYGIEQEYTLLQKDIN----WPLGWPVG------GYPGPQGPYYCGVG 72 (266)
Q Consensus 5 ~~~~g~p~~~~pR~~L~~--~~~~~~~~G~~~~~g~E~EF~l~~~~~~----~~~~~~~~------~~~~~~~~~~~~~~ 72 (266)
+.+.|.|.-.+-|.++.- +...|+++|.. .+|.++-.+-+ .+.+.|.. +.|...-| +...
T Consensus 31 ~sPSG~~HIGn~rEv~~~~~V~~al~~~g~~------~r~i~~~DD~D~lRKvP~~~p~~~~~~ylg~Plt~VP--dP~G 102 (360)
T PF01921_consen 31 ISPSGLPHIGNFREVLRADMVARALRDRGKD------VRLIYFSDDMDPLRKVPPNVPNPELEKYLGKPLTRVP--DPFG 102 (360)
T ss_dssp E--SS---HHHHHHHHHHHHHHHHHHTTT-E------EEEEEEE-TTSB-----TTS-CC-CCCCTTSBTTTSB---TTS
T ss_pred CCCCCCcccccccchhhHHHHHHHHHHcCCC------EEEEEEeecCCcccCCCCCCChHHHHHhcCCccccCC--CCCC
Confidence 467788888888888764 23335666665 67777765543 11111110 00110000 0011
Q ss_pred cchhhHHHHHHHHHHHHHHcCceeeeeeC--CCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEccc-CC
Q 024513 73 ADKALGRDIVNSHYKACLYAGINISGING--EVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPK-PI 149 (266)
Q Consensus 73 ~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~--E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpK-P~ 149 (266)
..+++...+...+.+.|+..||++|-+.. -+-.|.|.=. ...+-.+.-.++.++.++-.+- +..++.|- |.
T Consensus 103 ~~~SyaeH~~~~~~~~L~~~gie~e~~s~te~Y~sG~y~~~-----i~~aL~~~~~I~~Il~~~~~~~-~~~~y~Pf~pi 176 (360)
T PF01921_consen 103 CHESYAEHFNAPFEEFLDEFGIEYEFISQTEMYRSGRYDEQ-----IRTALENRDEIREILNEYRGRE-RPETYSPFLPI 176 (360)
T ss_dssp SSSCHHHHHHHHHHHHHHTTT---EEEECCCCCCTTTTHHH-----HCHHHHTHHHHHHHHHHHHHHT---TT--SEEEE
T ss_pred CCccHHHHHHHHHHHHHHHcCCceEEEeHHHhhhCCchHHH-----HHHHHHhHHHHHHHHHHhcCcC-CCCCeeeeeee
Confidence 22456788888889999999999987654 3556766411 1223333334466666665444 67777663 55
Q ss_pred CCCCCCc
Q 024513 150 KGDWNGA 156 (266)
Q Consensus 150 ~~d~~Gs 156 (266)
. ..+|.
T Consensus 177 C-~~cGr 182 (360)
T PF01921_consen 177 C-EKCGR 182 (360)
T ss_dssp E-TTTEE
T ss_pred c-cccCC
Confidence 4 24444
No 51
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=51.28 E-value=91 Score=26.67 Aligned_cols=67 Identities=13% Similarity=0.036 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHcCceeeeeeC-CCCCCce--eEecCCCchhH-----HHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 78 GRDIVNSHYKACLYAGINISGING-EVMPGQW--EFQVGPCVGIS-----SGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 78 ~~~~~~~l~~~l~~~Gi~ve~~~~-E~gpGQ~--Ei~l~~~~~l~-----aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
..+++.+|-..|...+++|....+ |...-.| =||+..++..+ .++.+-+||.+|.+|+...+...+-
T Consensus 46 l~~~I~~IN~~L~~l~~~Ir~~~~~q~~g~~~y~lVN~~~D~~sklaT~ys~~Ei~ffK~lle~I~~~~~~~~~~ 120 (200)
T PF07574_consen 46 LDEFINEINSKLSPLDFEIRRIRDGQPDGERYYALVNTSSDEISKLATTYSPNEIAFFKKLLEEIVESENTSRSE 120 (200)
T ss_dssp HHHHHHHHHHHHGGGTEEEEEEE--TTT--EEEEEEESSS-TTHHHHTTS-HHHHHHHHHHHHHHHHSSSS-EEH
T ss_pred HHHHHHHHHHhhhhcCcEEEEEeccCCCCCEEEEEEeCCCCHHHHhcCCCCHHHHHHHHHHHHHHHhCCCCceeh
Confidence 579999999999999999999999 7544333 34566565555 6789999999999999999987663
No 52
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=51.24 E-value=68 Score=33.51 Aligned_cols=111 Identities=13% Similarity=0.171 Sum_probs=67.1
Q ss_pred CCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccccCCCCchHHHHHHHHHHH
Q 024513 105 PGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSMRNDGGIDVIKKAIEKLG 184 (266)
Q Consensus 105 pGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~~~~~g~~~~~~~iaGl~ 184 (266)
|.+.=+.|.|.+++.-.| ++-+=..+|++-...||.. | || . ..|.|+|+.+-|....+-+....+-++||-.+
T Consensus 135 PD~lv~DLDP~~~~~f~~-v~~~A~~~r~~L~~lgL~~-~-~K--T--SG~kGlHv~vPl~~~~~~~~~~~fa~~~A~~l 207 (764)
T PRK09632 135 ATRLVFDLDPGEGVGLAE-CAEVARAVRDLLADIGLET-F-PV--T--SGSKGIHLYAPLDGPVSSEGASVVAKEVARAL 207 (764)
T ss_pred CCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCce-e-eE--C--CCCCeEEEEEECCCCCCHHHHHHHHHHHHHHH
Confidence 458889999988765544 4455678899999999984 2 55 3 25789999999965311111223334444442
Q ss_pred HHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCc
Q 024513 185 KRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGR 229 (266)
Q Consensus 185 L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~ 229 (266)
-+..|.+.... -.|....+ -.++.|..|+|...+=-|-
T Consensus 208 ~~~~P~~~t~~--~~k~~R~g-----kvfiDy~qN~~g~T~vapY 245 (764)
T PRK09632 208 EQDHPDLVTST--MTKSLRAG-----KVFVDWSQNNGSKTTIAPY 245 (764)
T ss_pred HHHCcceehhh--hhHhhCCC-----CEEEECccCCCCCeEEecc
Confidence 22224333222 22222232 1788899888887766664
No 53
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=50.15 E-value=35 Score=31.17 Aligned_cols=65 Identities=15% Similarity=0.068 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCC--CCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEc
Q 024513 79 RDIVNSHYKACLYAGINISGINGE--VMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFD 145 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E--~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFm 145 (266)
--|+.++.+.|.+.|++|+.+... .+.++|.+.+.-..+ +..+.-.+|+.+.++|.+.|+.++.-
T Consensus 18 pGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p--~~~~~~~L~~~L~~l~~~l~l~i~i~ 84 (286)
T PRK13011 18 AGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSE--EGLDEDALRAGFAPIAARFGMQWELH 84 (286)
T ss_pred CCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecC--CCCCHHHHHHHHHHHHHHhCcEEEEe
Confidence 358888889999999999999984 678899876554322 11235678999999999999887765
No 54
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=47.21 E-value=91 Score=31.69 Aligned_cols=112 Identities=13% Similarity=0.041 Sum_probs=67.3
Q ss_pred CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEecccc-CCCCchHHHHHHHHH
Q 024513 104 MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKSM-RNDGGIDVIKKAIEK 182 (266)
Q Consensus 104 gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~~-~~~~g~~~~~~~iaG 182 (266)
-|.+.=+.|.|.+++.-.| ++-+=..+|++-.+.||.. | || . ..|.|+|+.+-|... .+-+....+-++||-
T Consensus 431 ~pd~~v~DLDP~~~~~~~~-v~~~A~~~r~~L~~~gl~~-~-~k--t--SG~kGlhv~vPl~~~~~~~~~~~~fa~~~a~ 503 (610)
T PRK09633 431 RPTEIVFDLDPPSRDEFPL-AVEAALELKRLFDQFGLTS-F-VK--T--SGNKGLQLYIPLSKNAFTYEETRLFTEFIAE 503 (610)
T ss_pred CCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc-c-eE--c--cCCCeEEEEEEcCCCCCCHHHHHHHHHHHHH
Confidence 3888999999988875544 4455578899999999983 2 55 3 257899999999652 110112233344444
Q ss_pred HHHHHHHHHhhhhccccccCCCCCCCCCccceeeccCCCCceEEeCc
Q 024513 183 LGKRHGEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASIRVGR 229 (266)
Q Consensus 183 l~L~h~~al~a~~~nsYkRl~~~~~a~~p~~~~WG~~NR~a~iRvp~ 229 (266)
.+-+..|.+... +-.|....|- .++.|..|+|...+=-|-
T Consensus 504 ~~~~~~P~~~t~--~~~k~~R~gr-----vfiDy~qN~~~~T~~apY 543 (610)
T PRK09633 504 YLCSQFPELFTT--ERLKKNRGNR-----LYLDYVQHAEGKTIIAPY 543 (610)
T ss_pred HHHHHCcceehh--hhhHhhCCCC-----EEEEcccCCCCCeEEecc
Confidence 412222333322 2223333331 688888888887766553
No 55
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=46.89 E-value=53 Score=21.70 Aligned_cols=49 Identities=16% Similarity=0.004 Sum_probs=27.3
Q ss_pred HHHHHHHHHHcCceeeeeeCCCC--CCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCce
Q 024513 82 VNSHYKACLYAGINISGINGEVM--PGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVV 141 (266)
Q Consensus 82 ~~~l~~~l~~~Gi~ve~~~~E~g--pGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~ 141 (266)
+.++.+.+.+.|++|.+++.... .|.-.+.+.-.+ ...++++-+++|+.
T Consensus 13 L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~-----------~~~~~~~L~~~G~~ 63 (65)
T cd04882 13 LHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTED-----------IEKAIEVLQERGVE 63 (65)
T ss_pred HHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCC-----------HHHHHHHHHHCCce
Confidence 34445667799999976654222 344445544433 23444555666764
No 56
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=43.99 E-value=45 Score=24.40 Aligned_cols=61 Identities=20% Similarity=0.137 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCC---------C--ceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMP---------G--QWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gp---------G--Q~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
..++..+.+.|.+.|++|+.++.-.+. . -.|+.+...+ . +.--+|..+.+++++.|+.++|
T Consensus 11 a~~ia~Vs~~lA~~~~NI~~I~~l~~~~~~~~~~~~~~~~~e~~v~~~~--~---~~~~lr~~L~~la~elgvDIav 82 (84)
T cd04871 11 AEQLAAVTRVVADQGLNIDRIRRLSGRVPLEEQDDSPKACVEFSVRGQP--A---DLEALRAALLELASELNVDIAF 82 (84)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHhhccccccccCCCCcEEEEEEEeCCC--C---CHHHHHHHHHHHhcccCceEEE
Confidence 468888899999999999988875332 2 1244444222 1 2335688888999999998887
No 57
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=42.17 E-value=54 Score=22.75 Aligned_cols=33 Identities=18% Similarity=0.183 Sum_probs=25.9
Q ss_pred CceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEc
Q 024513 106 GQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFD 145 (266)
Q Consensus 106 GQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFm 145 (266)
..+|+.|.+. +...+ |.+|..+|.+.|+..+..
T Consensus 16 ~~~eL~Fp~~--ls~~e-----Rriih~la~~lGL~~~s~ 48 (60)
T cd02639 16 MRDELAFPSS--LSPAE-----RRIVHLLASRLGLNHVSD 48 (60)
T ss_pred CceEEEcCCC--CCHHH-----HHHHHHHHHHcCCceEEe
Confidence 3889999765 55544 889999999999997743
No 58
>COG4456 VagC Virulence-associated protein and related proteins [Function unknown]
Probab=41.81 E-value=18 Score=26.30 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=19.9
Q ss_pred cCCCCceEEeCcCCCCCCCceeEeCCCCC
Q 024513 218 VANRGASIRVGRDTEKEGKGYFEDRRPAS 246 (266)
Q Consensus 218 ~~NR~a~iRvp~~~~~~~~~riE~R~~da 246 (266)
..|||-+||+|..-.-+ ..++|++.-+.
T Consensus 7 ~snrSQAVRLP~e~~f~-~~~VeI~r~G~ 34 (74)
T COG4456 7 RSNRSQAVRLPKEFRFP-EDRVEIIREGD 34 (74)
T ss_pred ecCCeeeEecchheecC-CcEEEEEEeCC
Confidence 47999999999754222 36888876554
No 59
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=41.71 E-value=50 Score=23.20 Aligned_cols=37 Identities=16% Similarity=0.280 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCC
Q 024513 78 GRDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGP 114 (266)
Q Consensus 78 ~~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~ 114 (266)
..++++++...|...||.-.-...+...+.|++.+.-
T Consensus 30 s~~ll~~v~~lL~~lGi~~~i~~~~~~~~~y~l~i~~ 66 (77)
T PF14528_consen 30 SKELLEDVQKLLLRLGIKASIYEKKRKKGSYRLRISG 66 (77)
T ss_dssp -HHHHHHHHHHHHHTT--EEEEEEECTTTEEEEEEEC
T ss_pred CHHHHHHHHHHHHHCCCeeEEEEEcCCCceEEEEECc
Confidence 3688999999999999999665455668889999865
No 60
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=40.77 E-value=71 Score=29.10 Aligned_cols=65 Identities=18% Similarity=0.020 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCC--CCCceeEecCCCc-hhHHHHHHHHHHHHHHHHHHHcCceEEEc
Q 024513 79 RDIVNSHYKACLYAGINISGINGEV--MPGQWEFQVGPCV-GISSGDQLWMARYILERITEIAGVVLSFD 145 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~--gpGQ~Ei~l~~~~-~l~aaD~~~~~r~~ik~vA~~hGl~atFm 145 (266)
--++.+|.+.|.+.|++++.+.... -.|+|.+.+.-.- +. .+++-.+++.+.+++.+.|+.++.-
T Consensus 17 pGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~--~~~~~~L~~~L~~l~~~l~l~i~l~ 84 (286)
T PRK06027 17 PGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGL--IFNLETLRADFAALAEEFEMDWRLL 84 (286)
T ss_pred CcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCC--CCCHHHHHHHHHHHHHHhCCEEEEc
Confidence 3588888899999999999998877 6778866544321 10 1125567999999999999998764
No 61
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=36.26 E-value=90 Score=25.01 Aligned_cols=56 Identities=20% Similarity=0.128 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
.....+++.|++.||.++++..|.+ +..|.|.-. |+-..+|.++++.-.. ++.+.+
T Consensus 50 ~~~~~v~~~L~~~gI~~ksi~~~~~--~~~irf~~~------~~Ql~Ak~vL~~~L~~-~y~VAl 105 (127)
T PRK10629 50 PDGFYVYQHLDANGIHIKSITPEND--SLLIRFDSP------EQSAAAKEVLDRTLPH-GYIIAQ 105 (127)
T ss_pred chHHHHHHHHHHCCCCcceEEeeCC--EEEEEECCH------HHHHHHHHHHHHHcCC-CCEEEE
Confidence 5667788999999999999988854 677777643 5667788888887644 455544
No 62
>PRK13895 conjugal transfer protein TraM; Provisional
Probab=35.71 E-value=26 Score=28.75 Aligned_cols=17 Identities=12% Similarity=0.350 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHcCceEE
Q 024513 127 ARYILERITEIAGVVLS 143 (266)
Q Consensus 127 ~r~~ik~vA~~hGl~at 143 (266)
+.++|++||.|||+..+
T Consensus 5 i~e~I~~IA~KHGIal~ 21 (144)
T PRK13895 5 IEELIKEIAAKHGIAVG 21 (144)
T ss_pred HHHHHHHHHHHcCcccC
Confidence 57899999999999865
No 63
>COG4326 Spo0M Sporulation control protein [General function prediction only]
Probab=35.28 E-value=51 Score=28.96 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCCc-------eeEecCCCch
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPGQ-------WEFQVGPCVG 117 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ-------~Ei~l~~~~~ 117 (266)
.++++.+..+++.+|+.+.+...|.+++- .|+.|.|+.+
T Consensus 154 hP~m~~vl~AiE~lGfrL~~vdCEqa~yF~~a~PFVQEfEFvPTtG 199 (270)
T COG4326 154 HPMMDGVLSAIEALGFRLRQVDCEQAKYFGGALPFVQEFEFVPTTG 199 (270)
T ss_pred chHHHHHHHHHHhhccEeeeccccccccccccccceeEEEEeccCC
Confidence 58889999999999999999999999863 4888888644
No 64
>PF11657 Activator-TraM: Transcriptional activator TraM
Probab=35.18 E-value=25 Score=28.88 Aligned_cols=17 Identities=29% Similarity=0.436 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHcCceEE
Q 024513 127 ARYILERITEIAGVVLS 143 (266)
Q Consensus 127 ~r~~ik~vA~~hGl~at 143 (266)
+.++|++||++||+..+
T Consensus 5 ~~eiI~~IA~khgI~L~ 21 (144)
T PF11657_consen 5 IEEIIAEIARKHGIALS 21 (144)
T ss_pred HHHHHHHHHHHcCCccC
Confidence 58999999999999865
No 65
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=34.89 E-value=17 Score=29.35 Aligned_cols=21 Identities=24% Similarity=0.336 Sum_probs=14.8
Q ss_pred cCceeeeeeCCCCCCceeEecC
Q 024513 92 AGINISGINGEVMPGQWEFQVG 113 (266)
Q Consensus 92 ~Gi~ve~~~~E~gpGQ~Ei~l~ 113 (266)
.+-.+|++--. +||||||||.
T Consensus 82 ~~~~iESIrI~-~pG~YElNL~ 102 (131)
T PF09845_consen 82 LNDRIESIRIL-EPGSYELNLE 102 (131)
T ss_pred cccCcceEEEe-cCceEEecHH
Confidence 44555555543 7999999986
No 66
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=31.79 E-value=1.3e+02 Score=22.99 Aligned_cols=45 Identities=22% Similarity=0.195 Sum_probs=34.4
Q ss_pred HHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHH
Q 024513 83 NSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERIT 135 (266)
Q Consensus 83 ~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA 135 (266)
..+.+.|++.||.++.+..| .++..|.|.-. |+-..+|.++++.-
T Consensus 49 ~~v~~~L~~~~I~~k~i~~~--~~~llirf~~~------~~Ql~Ak~~L~~~L 93 (101)
T PF13721_consen 49 FQVEQALKAAGIAVKSIEQE--GDSLLIRFDST------DQQLKAKDVLSKAL 93 (101)
T ss_pred HHHHHHHHHCCCCcceEEee--CCEEEEEECCH------HHHHHHHHHHHHHc
Confidence 47889999999999998876 47888888754 55556677777643
No 67
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=31.70 E-value=23 Score=28.49 Aligned_cols=68 Identities=12% Similarity=0.148 Sum_probs=42.1
Q ss_pred HHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCceeeee
Q 024513 20 AAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINISGI 99 (266)
Q Consensus 20 L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~ 99 (266)
|+-+|+.+++.|+.+. |.+. +..|..|+.++++...+..+...|...|++.|++|-.+
T Consensus 38 l~l~L~~~k~~g~~~l------fVi~----------------PvNg~wydytG~~~~~r~~~y~kI~~~~~~~gf~v~D~ 95 (130)
T PF04914_consen 38 LQLLLDVCKELGIDVL------FVIQ----------------PVNGKWYDYTGLSKEMRQEYYKKIKYQLKSQGFNVADF 95 (130)
T ss_dssp HHHHHHHHHHTT-EEE------EEE--------------------HHHHHHTT--HHHHHHHHHHHHHHHHTTT--EEE-
T ss_pred HHHHHHHHHHcCCceE------EEec----------------CCcHHHHHHhCCCHHHHHHHHHHHHHHHHHCCCEEEec
Confidence 6677777777777655 3332 12344567777776678999999999999999998776
Q ss_pred eC-CCCCCcee
Q 024513 100 NG-EVMPGQWE 109 (266)
Q Consensus 100 ~~-E~gpGQ~E 109 (266)
.. |+-|.-++
T Consensus 96 s~~~y~~yfm~ 106 (130)
T PF04914_consen 96 SDDEYEPYFMQ 106 (130)
T ss_dssp TTGTTSTTSBS
T ss_pred ccCCCCCceee
Confidence 54 56676443
No 68
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=31.22 E-value=1.7e+02 Score=19.75 Aligned_cols=21 Identities=24% Similarity=0.172 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHcCceeeeeeC
Q 024513 81 IVNSHYKACLYAGINISGING 101 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~ 101 (266)
.+.++.+.+.+.|++|+++..
T Consensus 14 ~La~v~~~l~~~~inI~~i~~ 34 (66)
T cd04908 14 RLAAVTEILSEAGINIRALSI 34 (66)
T ss_pred hHHHHHHHHHHCCCCEEEEEE
Confidence 455566777899999998875
No 69
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=29.76 E-value=37 Score=23.05 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=20.4
Q ss_pred HHHHHc--CceeeeeeCCCCCCceeEec
Q 024513 87 KACLYA--GINISGINGEVMPGQWEFQV 112 (266)
Q Consensus 87 ~~l~~~--Gi~ve~~~~E~gpGQ~Ei~l 112 (266)
++|++. |++|+++..---||-||+.+
T Consensus 3 ~~l~~~~p~~~v~~v~~spi~GlyeV~~ 30 (57)
T PF10411_consen 3 QALKKAFPGLKVESVSPSPIPGLYEVVL 30 (57)
T ss_dssp HHHHCT--T-TCEEEEE-SSTTEEEEEE
T ss_pred hHHHhhcCCCceeEEEcCCCCCeEEEEE
Confidence 455666 99999999888899999998
No 70
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.68 E-value=1.1e+02 Score=20.95 Aligned_cols=31 Identities=13% Similarity=0.119 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCC-CceeEe
Q 024513 81 IVNSHYKACLYAGINISGINGEVMP-GQWEFQ 111 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gp-GQ~Ei~ 111 (266)
++.+|.+.+.+.|+++..++....+ |+.++.
T Consensus 13 ~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~ 44 (76)
T cd04888 13 VLSKVLNTIAQVRGNVLTINQNIPIHGRANVT 44 (76)
T ss_pred hHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEE
Confidence 4555667778999999999875433 444443
No 71
>PRK01060 endonuclease IV; Provisional
Probab=28.75 E-value=2.9e+02 Score=24.29 Aligned_cols=95 Identities=8% Similarity=-0.048 Sum_probs=48.1
Q ss_pred ChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCc
Q 024513 15 NKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGI 94 (266)
Q Consensus 15 ~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi 94 (266)
+++.-++++++.+++.|+... |.++-... . +..... ..+-+.++.+.+++.|+
T Consensus 9 ~~~~~~~~~l~~~~~~G~d~v-----El~~~~p~-----~-------------~~~~~~----~~~~~~~lk~~~~~~gl 61 (281)
T PRK01060 9 SAAGGLEGAVAEAAEIGANAF-----MIFTGNPQ-----Q-------------WKRKPL----EELNIEAFKAACEKYGI 61 (281)
T ss_pred ecCCCHHHHHHHHHHcCCCEE-----EEECCCCC-----C-------------CcCCCC----CHHHHHHHHHHHHHcCC
Confidence 344448889999999999732 33321110 0 000011 13456667777788888
Q ss_pred eeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCc
Q 024513 95 NISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGV 140 (266)
Q Consensus 95 ~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl 140 (266)
.+..+.. .+.|-+++...++-.-...+-.+|..++ +|++.|.
T Consensus 62 ~~~~~~~---h~~~~~nl~~~d~~~r~~s~~~~~~~i~-~A~~lga 103 (281)
T PRK01060 62 SPEDILV---HAPYLINLGNPNKEILEKSRDFLIQEIE-RCAALGA 103 (281)
T ss_pred CCCceEE---ecceEecCCCCCHHHHHHHHHHHHHHHH-HHHHcCC
Confidence 7532221 1235566666555333333334444443 3666665
No 72
>PF00311 PEPcase: Phosphoenolpyruvate carboxylase; InterPro: IPR021135 Phosphoenolpyruvate carboxylase (PEPCase), an enzyme found in all multicellular plants, catalyses the formation of oxaloacetate from phosphoenolpyruvate (PEP) and a hydrocarbonate ion []. This reaction is harnessed by C4 plants to capture and concentrate carbon dioxide into the photosynthetic bundle sheath cells. It also plays a key role in the nitrogen fixation pathway in legume root nodules: here it functions in concert with glutamine, glutamate and asparagine synthetases and aspartate amido transferase, to synthesise aspartate and asparagine, the major nitrogen transport compounds in various amine-transporting plant species []. PEPCase also plays an antipleurotic role in bacteria and plant cells, supplying oxaloacetate to the TCA cycle, which requires continuous input of C4 molecules in order to replenish the intermediates removed for amino acid biosynthesis []. The C terminus of the enzyme contains the active site that includes a conserved lysine residue, involved in substrate binding, and other conserved residues important for the catalytic mechanism []. Based on sequence similarity, PEPCase enzymes can be grouped into two distinct families, one found primarily in bacteria and plants, and another found primarily in archaea.; GO: 0008964 phosphoenolpyruvate carboxylase activity, 0006099 tricarboxylic acid cycle, 0015977 carbon fixation; PDB: 1JQO_A 1QB4_A 1JQN_A 1FIY_A.
Probab=28.43 E-value=80 Score=33.16 Aligned_cols=61 Identities=18% Similarity=0.095 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhH------HHHHHHHHHHHHHHHHHHcCceEEEc
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGIS------SGDQLWMARYILERITEIAGVVLSFD 145 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~------aaD~~~~~r~~ik~vA~~hGl~atFm 145 (266)
.++++++ ...++..-|-+.-.+..||-++|+|.-+ +.=.+..+++-+.+||++||+.++|.
T Consensus 416 ~~im~~l------l~~p~yr~~l~~~~~~QeVMlGYSDS~KDgG~laa~w~ly~Aq~~L~~v~~~~gV~l~~F 482 (794)
T PF00311_consen 416 PDIMEEL------LSNPAYRAHLKARGNRQEVMLGYSDSNKDGGYLAANWALYKAQEALVAVARKHGVKLRFF 482 (794)
T ss_dssp HHHHHHH------CCSHHHHHHCTT---EEEEEEECCCHHHHC-HHHHHHHHHHHHHHHHHHHHCCT-EEEEE
T ss_pred HHHHHHH------HcCHHHHHHHhcCcceEEEEeccccccccccHHHHHHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 4555544 5566666666654467799999998755 56667778899999999999999985
No 73
>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A
Probab=28.20 E-value=1.4e+02 Score=19.32 Aligned_cols=41 Identities=15% Similarity=-0.091 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCC-CceeEecCCCchhHHH
Q 024513 81 IVNSHYKACLYAGINISGINGEVMP-GQWEFQVGPCVGISSG 121 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gp-GQ~Ei~l~~~~~l~aa 121 (266)
.+.++.+.+.+.|++++++...... ++-.+.+.-.+.-+|.
T Consensus 11 ~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~~~~~a~ 52 (56)
T cd04889 11 RLAEVTEILAEAGINIKAISIAETRGEFGILRLIFSDPERAK 52 (56)
T ss_pred hHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEECCHHHHH
Confidence 4445556778999999988865543 4555555555544433
No 74
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=26.34 E-value=1.3e+02 Score=27.52 Aligned_cols=68 Identities=13% Similarity=0.069 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCC--CCCCceeEecCCCchh-HHHHHHHHHHHHHHHHHHHcCceEEEccc
Q 024513 79 RDIVNSHYKACLYAGINISGINGE--VMPGQWEFQVGPCVGI-SSGDQLWMARYILERITEIAGVVLSFDPK 147 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E--~gpGQ~Ei~l~~~~~l-~aaD~~~~~r~~ik~vA~~hGl~atFmpK 147 (266)
--++..+.+.|.+.|++|..+..- ...|+|-+-+.-.+.. ...| .--+|..+.+++++.|+..+.-+.
T Consensus 20 ~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~~~~~~~-~~~l~~~l~~l~~~l~l~~~i~~~ 90 (289)
T PRK13010 20 PGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQSAEAAS-VDTFRQEFQPVAEKFDMQWAIHPD 90 (289)
T ss_pred CCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcCCCCCCC-HHHHHHHHHHHHHHhCCeEEEecC
Confidence 357788888899999999998874 4566775543322111 0112 346789999999999988777543
No 75
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=25.72 E-value=80 Score=21.76 Aligned_cols=54 Identities=13% Similarity=0.133 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHcCceeeeeeCCC--CCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCc
Q 024513 81 IVNSHYKACLYAGINISGINGEV--MPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGV 140 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~--gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl 140 (266)
++..+..-...-|+++++++.+. .+|...|++.....-+.. ..++|++.+..+.
T Consensus 5 vL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~~~~i------~~l~~Ql~KlidV 60 (63)
T PF13710_consen 5 VLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGDDREI------EQLVKQLEKLIDV 60 (63)
T ss_dssp HHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES-CCHH------HHHHHHHHCSTTE
T ss_pred HHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeCchhH------HHHHHHHhccCCe
Confidence 45566667789999999999887 799999988765433333 3466666665543
No 76
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=25.64 E-value=3.2e+02 Score=27.28 Aligned_cols=127 Identities=17% Similarity=0.139 Sum_probs=71.8
Q ss_pred eCCCCCCCCCChHHHHHHH-Hc-cccccCCcceEeeeeeEEEecCCCC----CC------------CCCCCCCCCCCCCC
Q 024513 5 YTPAGEPIPTNKRFNAAKV-FG-HPDVVAEEPWYGIEQEYTLLQKDIN----WP------------LGWPVGGYPGPQGP 66 (266)
Q Consensus 5 ~~~~g~p~~~~pR~~L~~~-~~-~~~~~G~~~~~g~E~EF~l~~~~~~----~~------------~~~~~~~~~~~~~~ 66 (266)
+.+.|.|.-.+-|.++.-- |. .|+++|. |..|..+-.+-+ .+ +|.|....|-+.|
T Consensus 27 isPSG~~HIGn~rEv~t~d~V~ralr~~g~------~~r~I~~~DD~D~lRkvp~~lp~~~~~e~Ylg~Plt~IPdP~G- 99 (521)
T COG1384 27 ISPSGLIHIGNFREVLTADAVRRALRDRGD------EVRLIYISDDYDPLRKVPRNLPDPEELEQYLGMPLTEIPDPFG- 99 (521)
T ss_pred cCCCCCcccccHHHHHHHHHHHHHHHHcCC------ceEEEEEccCCcccccCCCCCCChHHHHHHcCCccccCCCCcc-
Confidence 4678999999999888643 22 3566777 666766655433 00 2222211222222
Q ss_pred CccccccchhhHHHHHHHHHHHHHHcCceeeeeeCC--CCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 67 YYCGVGADKALGRDIVNSHYKACLYAGINISGINGE--VMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~~~E--~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
...++...+...+...|...||++|-+.+- +..|-|+- -...+.++.--.+.++-++-.+ -+..+|
T Consensus 100 ------~~~Sya~hf~~~f~~~l~~~Gi~~E~~s~se~Yk~G~~~~-----~i~~ale~rdeI~~il~~~~~~-~~~e~~ 167 (521)
T COG1384 100 ------CCDSYAEHFLRPFEEFLDEFGIEVEFVSATELYKSGLYDE-----AIRIALERRDEIMEILNEYRGR-ELEEDW 167 (521)
T ss_pred ------ccchHHHHHHHHHHHHHHhcCCceEEEEhHHhhhcccHHH-----HHHHHHhhHHHHHHHHHHhcCC-cccCCc
Confidence 123566778888888899999999988752 33555532 2223344443445555444443 356666
Q ss_pred ccc-CCC
Q 024513 145 DPK-PIK 150 (266)
Q Consensus 145 mpK-P~~ 150 (266)
.|- |+.
T Consensus 168 ~P~~piC 174 (521)
T COG1384 168 SPFMPIC 174 (521)
T ss_pred eeccccc
Confidence 554 444
No 77
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=25.54 E-value=67 Score=23.36 Aligned_cols=29 Identities=3% Similarity=-0.155 Sum_probs=27.1
Q ss_pred ChHHHHHHHHccccccCCcceEeeeeeEE
Q 024513 15 NKRFNAAKVFGHPDVVAEEPWYGIEQEYT 43 (266)
Q Consensus 15 ~pR~~L~~~~~~~~~~G~~~~~g~E~EF~ 43 (266)
||-..++++.++++++|-...+|+-+++-
T Consensus 26 d~d~Al~eM~e~A~~lGAnAVVGvr~d~s 54 (74)
T TIGR03884 26 NVDEIVENLREKVKAKGGMGLIAFRITCA 54 (74)
T ss_pred CHHHHHHHHHHHHHHcCCCEEEEEEEEcC
Confidence 89999999999999999999999988776
No 78
>TIGR01619 hyp_HI0040 conserved hypothetical protein, TIGR01619. This model represents a hypothetical equivalog of gamma proteobacteria, includes HI0040. These sequences do not have any similarity to known proteins by PSI-BLAST.
Probab=23.25 E-value=3.8e+02 Score=24.06 Aligned_cols=88 Identities=9% Similarity=-0.025 Sum_probs=52.4
Q ss_pred HHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHHHHHHcCcee----
Q 024513 21 AKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYKACLYAGINI---- 96 (266)
Q Consensus 21 ~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~v---- 96 (266)
+++++.|++.|=.+....++|-+++=+++ .-+..+++++ ++.|+.|
T Consensus 143 ~~Vl~~L~~~GD~l~~~R~IdHw~yF~~e--------------------------~d~~~F~e~~----~~~gy~v~~~~ 192 (249)
T TIGR01619 143 EELLDLLKKKGRDLAALYLIEHSFHFDEE--------------------------AKMFAFMDEL----HLGDISFTSLQ 192 (249)
T ss_pred HHHHHHHHHcCccccCceEeeeEEecCCH--------------------------HHHHHHHHHH----HhcCceeeeee
Confidence 45666666666665555555544432211 1134566554 5899988
Q ss_pred ---eeee-CCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcC
Q 024513 97 ---SGIN-GEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAG 139 (266)
Q Consensus 97 ---e~~~-~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hG 139 (266)
+.+. .|...+.|-+.+...+.+..+|- ...-.-+.++|+++|
T Consensus 193 ~~~~~~~~~~~~~~~y~v~l~re~~~~~~~I-~~~t~~l~~lA~~~~ 238 (249)
T TIGR01619 193 YSALAIMFEEDDEPVFLVKLEQEISLDNSEI-FEQVEQFEDIAEQFS 238 (249)
T ss_pred ecccccccCCCCCCceEEEEEecCCCchHHH-HHHHHHHHHHHHHhC
Confidence 2221 24446678999999888886553 333455667888876
No 79
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=23.20 E-value=1.2e+02 Score=20.92 Aligned_cols=28 Identities=14% Similarity=0.241 Sum_probs=22.3
Q ss_pred ceeEecCC-CchhHHHHHHHHHHHHHHHHHHHcCceE
Q 024513 107 QWEFQVGP-CVGISSGDQLWMARYILERITEIAGVVL 142 (266)
Q Consensus 107 Q~Ei~l~~-~~~l~aaD~~~~~r~~ik~vA~~hGl~a 142 (266)
+.++.|.| .+..+ |.+|.++|++.||..
T Consensus 16 ~~~l~Fpp~ls~~e--------R~~vH~~a~~~gL~s 44 (59)
T cd06007 16 NEEYEFPSSLTNHE--------RAVIHRLCRKLGLKS 44 (59)
T ss_pred ccEEEcCCCCCHHH--------HHHHHHHHHHcCCCc
Confidence 68888887 34433 889999999999984
No 80
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.87 E-value=1.6e+02 Score=19.41 Aligned_cols=37 Identities=24% Similarity=0.034 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCc
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCV 116 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~ 116 (266)
.+..++.+.|.+.||++..+.......++-+.+...|
T Consensus 16 ~~~~~i~~~L~~~~i~v~~i~~~~s~~~isf~v~~~d 52 (66)
T cd04916 16 GVSARATAALAKAGINIRMINQGSSEISIMIGVHNED 52 (66)
T ss_pred cHHHHHHHHHHHCCCCEEEEEecCcccEEEEEEeHHH
Confidence 3455566778899999999986543455555555544
No 81
>COG1540 Uncharacterized proteins, homologs of lactam utilization protein B [General function prediction only]
Probab=22.75 E-value=3e+02 Score=24.70 Aligned_cols=73 Identities=19% Similarity=0.228 Sum_probs=45.1
Q ss_pred eCCCCCCCC--------CChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchh
Q 024513 5 YTPAGEPIP--------TNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKA 76 (266)
Q Consensus 5 ~~~~g~p~~--------~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (266)
|++||+.++ .||-.+++++++-+++-.++..-|.++ -++.+. -|.-+ |..
T Consensus 171 Y~~dG~Lv~R~~pgA~i~d~~~a~~qvl~m~~~g~v~a~dG~~v---~v~ads------------------iCvHG-D~p 228 (252)
T COG1540 171 YQPDGTLVPRSLPGAVIHDEEEALAQVLQMVREGKVTAIDGEWV---AVEADS------------------ICVHG-DNP 228 (252)
T ss_pred cCCCCcEecCCCCCccccCHHHHHHHHHHHHhcCceEeeCCcEE---eeecce------------------EEEcC-CCH
Confidence 667777553 489999999999887655554433332 111111 01111 111
Q ss_pred hHHHHHHHHHHHHHHcCceeeee
Q 024513 77 LGRDIVNSHYKACLYAGINISGI 99 (266)
Q Consensus 77 ~~~~~~~~l~~~l~~~Gi~ve~~ 99 (266)
-.-.+...|++.|++.||.|...
T Consensus 229 ~Al~~~~riR~~l~~~gi~v~~~ 251 (252)
T COG1540 229 HALAFARRIRAALEAEGIKVAAL 251 (252)
T ss_pred HHHHHHHHHHHHHHHcCCeeecC
Confidence 13589999999999999999754
No 82
>PLN00200 argininosuccinate synthase; Provisional
Probab=22.70 E-value=1.1e+02 Score=29.46 Aligned_cols=82 Identities=13% Similarity=0.065 Sum_probs=48.0
Q ss_pred CCCCccccccchhhHHHHHHHHHHHHHHcCceeee-eeCCCCCCceeE-----ecCC----CchhHHHHHHHHHHHHHHH
Q 024513 64 QGPYYCGVGADKALGRDIVNSHYKACLYAGINISG-INGEVMPGQWEF-----QVGP----CVGISSGDQLWMARYILER 133 (266)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~-~~~E~gpGQ~Ei-----~l~~----~~~l~aaD~~~~~r~~ik~ 133 (266)
.+.|++..++.. --+...+.+.+++.|+++-. -+.-.|..|..+ .+.| -.|+.-. -+.-|.-+++
T Consensus 87 e~~Y~~~tsl~R---p~i~~~lv~~A~~~G~~~VahG~tgkGnDq~rf~~~~~al~pel~ViaPlre~--~~~~r~e~~~ 161 (404)
T PLN00200 87 EGKYLLGTSMAR---PLIAKAMVDIAKEVGADAVAHGATGKGNDQVRFELTFFALNPELKVVAPWREW--DIKGREDLIE 161 (404)
T ss_pred cceeccccchhh---HHHHHHHHHHHHHcCCCEEEeCCcCCCCcHHHHHHHHHHhCCCCeeeCchhhc--CCCCHHHHHH
Confidence 345666665543 34666777888899998643 222223556543 1222 1122221 1224999999
Q ss_pred HHHHcCceEEEccc-CCC
Q 024513 134 ITEIAGVVLSFDPK-PIK 150 (266)
Q Consensus 134 vA~~hGl~atFmpK-P~~ 150 (266)
+|++||+.+...|+ |+.
T Consensus 162 ~A~~~Gipv~~~~~~~yS 179 (404)
T PLN00200 162 YAKKHNIPVPVTKKSIYS 179 (404)
T ss_pred HHHHcCCCCCCCCCCCCc
Confidence 99999998776654 554
No 83
>TIGR00629 uvde UV damage endonuclease UvdE. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.82 E-value=6.5e+02 Score=23.36 Aligned_cols=92 Identities=16% Similarity=0.161 Sum_probs=59.6
Q ss_pred HHHHHHHHHHcCceeeeeeCCCCCC-ce-eEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceee
Q 024513 82 VNSHYKACLYAGINISGINGEVMPG-QW-EFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAH 159 (266)
Q Consensus 82 ~~~l~~~l~~~Gi~ve~~~~E~gpG-Q~-Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H 159 (266)
+..+.+...+.||..--+.++.-|- -+ |+...+.+ .+++ --.-|.++|+++|+..||.|-.|. .
T Consensus 54 l~~~L~~n~~~~I~f~RisS~l~P~ash~~~~~~~~~--~~~~----~l~~iG~~a~~~~iRLS~Hp~qfi-~------- 119 (312)
T TIGR00629 54 TMKTLHWNIGHGIPFYRFSSSIFPFASHPDVGYDLVT--FAQK----ELREIGELAKTHQHRLTFHPGQFT-Q------- 119 (312)
T ss_pred HHHHHHHHHHcCCcEEecCccccCcCcCchhhhhHHH--HHHH----HHHHHHHHHHHcCeEEEECCCccc-c-------
Confidence 3445577889999999999888762 12 22111111 1222 224578899999999999999887 3
Q ss_pred EeEeccccCCCCchHHHHHHHHHHHHHHHHHHhhhhc
Q 024513 160 ANYSTKSMRNDGGIDVIKKAIEKLGKRHGEHIAAYGE 196 (266)
Q Consensus 160 ~h~Sl~~~~~~~g~~~~~~~iaGl~L~h~~al~a~~~ 196 (266)
|.. ..-.+.+..+.-| ..|+.-+-++..
T Consensus 120 ----LnS----~~~evv~~Si~~L-~~ha~~l~~mg~ 147 (312)
T TIGR00629 120 ----FTS----PRESVVKSAIRDL-AYHDEMLSAMKL 147 (312)
T ss_pred ----CCC----CCHHHHHHHHHHH-HHHHHHHHHcCC
Confidence 322 1224567778888 888887777653
No 84
>PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.80 E-value=83 Score=28.79 Aligned_cols=64 Identities=16% Similarity=0.142 Sum_probs=43.3
Q ss_pred CCCCCCCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHH
Q 024513 8 AGEPIPTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYK 87 (266)
Q Consensus 8 ~g~p~~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 87 (266)
||+++...-+.-+++.++++++.|..|..+. .+...+.. ..-+.....+
T Consensus 5 ~Gk~~a~~i~~~l~~~v~~l~~~g~~P~Lai----i~vg~d~a---------------------------s~~Yv~~k~k 53 (282)
T PRK14166 5 DGKALSAKIKEELKEKNQFLKSKGIESCLAV----ILVGDNPA---------------------------SQTYVKSKAK 53 (282)
T ss_pred ehHHHHHHHHHHHHHHHHHHHhCCCCceEEE----EEeCCCHH---------------------------HHHHHHHHHH
Confidence 6777777777888888888877788776554 22221110 2345666678
Q ss_pred HHHHcCceeeeeeCC
Q 024513 88 ACLYAGINISGINGE 102 (266)
Q Consensus 88 ~l~~~Gi~ve~~~~E 102 (266)
.+++.||..+.++-.
T Consensus 54 ~a~~~Gi~~~~~~l~ 68 (282)
T PRK14166 54 ACEECGIKSLVYHLN 68 (282)
T ss_pred HHHHcCCEEEEEECC
Confidence 899999999887654
No 85
>PF09899 DUF2126: Putative amidoligase enzyme (DUF2126); InterPro: IPR018667 This domain is found in bacterial transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown.
Probab=21.75 E-value=4.3e+02 Score=27.79 Aligned_cols=81 Identities=17% Similarity=0.194 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHcCceee--eeeC-----------CCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceE-E
Q 024513 78 GRDIVNSHYKACLYAGINIS--GING-----------EVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVL-S 143 (266)
Q Consensus 78 ~~~~~~~l~~~l~~~Gi~ve--~~~~-----------E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~a-t 143 (266)
..+++..|..+.+++|++|- .+-. =-.||-.|||+.|+..- |.++-.-+.+.+-|++.+|.+ .
T Consensus 347 yL~LiaaiE~tA~~l~~pv~lEGY~PP~D~rl~~~~vTPDPGVIEVNi~Pa~sW---~e~v~~t~~LYe~Ar~~rL~teK 423 (819)
T PF09899_consen 347 YLDLIAAIEATAAELGMPVVLEGYPPPRDPRLEVLKVTPDPGVIEVNIHPAASW---DELVEITETLYEEARQSRLGTEK 423 (819)
T ss_pred HHHHHHHHHHHHHHcCCCEEEecCCcCCCCccceEEEeCCCceEEecCCCCcCH---HHHHHHHHHHHHHHHHhCcchhh
Confidence 36888999999999997752 1111 11359999999997655 555666788999999999875 4
Q ss_pred EcccCCCCCCCCceeeEeEec
Q 024513 144 FDPKPIKGDWNGAGAHANYST 164 (266)
Q Consensus 144 FmpKP~~~d~~GsG~H~h~Sl 164 (266)
||-. |...|+|.=-|+-|
T Consensus 424 Fm~D---GrhtGTGGGNHvtl 441 (819)
T PF09899_consen 424 FMLD---GRHTGTGGGNHVTL 441 (819)
T ss_pred hccC---CccccCCCCCeEec
Confidence 6654 23455554444444
No 86
>PF03851 UvdE: UV-endonuclease UvdE; InterPro: IPR004601 Schizosaccharomyces pombe ultraviolet damage endonuclease (UVDE or Uve1p) performs the initial step in an alternative excision repair pathway for UV-induced DNA damage. This DNA repair pathway was originally thought to be specific for UV damage, however Uve1p also recognises UV-induced bipyrimidine photoadducts and other non-UV-induced DNA adducts []. The Deinococcus radiodurans UVSE protein has also shown to be a UV DNA damage endonuclease that catalyzes repair of UV-induced DNA damage by a similar mechanism [].; GO: 0004519 endonuclease activity, 0006289 nucleotide-excision repair, 0009411 response to UV; PDB: 3BZG_A 3BZJ_A 3C0L_A 3C0S_A 3C0Q_A.
Probab=21.71 E-value=3.3e+02 Score=24.84 Aligned_cols=62 Identities=15% Similarity=0.131 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHcCceeeeeeCCCCC-CceeEecCCCchhHHHHHHHHHH---HHHHHHHHHcCceEEEcccCCC
Q 024513 81 IVNSHYKACLYAGINISGINGEVMP-GQWEFQVGPCVGISSGDQLWMAR---YILERITEIAGVVLSFDPKPIK 150 (266)
Q Consensus 81 ~~~~l~~~l~~~Gi~ve~~~~E~gp-GQ~Ei~l~~~~~l~aaD~~~~~r---~~ik~vA~~hGl~atFmpKP~~ 150 (266)
-+.++.+...+.||..--+.++.-| +-++ ....|..-.++ ..|.+.|+++|+..||.|-.|.
T Consensus 46 ~l~~~L~~n~~~~I~~yRisS~liP~ashp--------~~~~~~~~~~~~~l~~iG~~~~~~~iRls~HP~qf~ 111 (275)
T PF03851_consen 46 DLLRILEYNIAHGIRFYRISSDLIPLASHP--------EVGWDWEEEFAEELAEIGDLAKENGIRLSMHPDQFT 111 (275)
T ss_dssp HHHHHHHHHHHTT--EEE--TTSSTTTTST--------T--S-HHHHHHHHHHHHHHHHHHTT-EEEE---TT-
T ss_pred HHHHHHHHHHHcCCCEEecCcccCCCCCCc--------ccccchHHHHHHHHHHHHHHHHHcCCeEEecCCcce
Confidence 3445667888999999999988766 1121 11111111222 4566789999999999999887
No 87
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=21.62 E-value=1.1e+02 Score=20.76 Aligned_cols=41 Identities=10% Similarity=0.091 Sum_probs=28.0
Q ss_pred eeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEecc
Q 024513 108 WEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTK 165 (266)
Q Consensus 108 ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~ 165 (266)
-++.|.|.++- -|.+|+++|+.+||... ..|+|-+=|+.++
T Consensus 17 ~~~~fppm~~~--------~R~~vH~lA~~~~L~S~---------S~G~g~~R~v~v~ 57 (58)
T cd02646 17 DSLSFPPMDKH--------GRKTIHKLANCYNLKSK---------SRGKGKKRFVTVT 57 (58)
T ss_pred ceEecCCCCHH--------HHHHHHHHHHHcCCccc---------ccccCCceEEEEE
Confidence 46677775432 38899999999999832 3466766666554
No 88
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.37 E-value=89 Score=25.89 Aligned_cols=38 Identities=11% Similarity=0.073 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEeccc
Q 024513 127 ARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTKS 166 (266)
Q Consensus 127 ~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~~ 166 (266)
+|..|.++|.+||+.+||..-=+.. .+ .+-|+..-..+
T Consensus 13 Vk~~i~r~A~r~~~~v~~Van~~~~-~~-~~~~i~~v~V~ 50 (150)
T COG1671 13 VKDEIYRVAERMGLKVTFVANFPHR-VP-PSPEIRTVVVD 50 (150)
T ss_pred hHHHHHHHHHHhCCeEEEEeCCCcc-CC-CCCceeEEEec
Confidence 7999999999999999998753331 23 55666655554
No 89
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....
Probab=21.29 E-value=4.5e+02 Score=21.26 Aligned_cols=66 Identities=15% Similarity=0.127 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCC-CchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCC
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGP-CVGISSGDQLWMARYILERITEIAGVVLSFDPKPIK 150 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~-~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~ 150 (266)
.+.+.+..+.++.+|++.-.+|.=. + ...+ .+.-+.-|.++-.=.-+-++|+++|++..+-|.|..
T Consensus 70 ~~~~~~~i~~a~~lg~~~i~~~~g~----~--~~~~~~~~~~~~~~~~~~l~~l~~~a~~~gv~i~lE~~~~~ 136 (213)
T PF01261_consen 70 LEYLKKAIDLAKRLGAKYIVVHSGR----Y--PSGPEDDTEENWERLAENLRELAEIAEEYGVRIALENHPGP 136 (213)
T ss_dssp HHHHHHHHHHHHHHTBSEEEEECTT----E--SSSTTSSHHHHHHHHHHHHHHHHHHHHHHTSEEEEE-SSSS
T ss_pred HHHHHHHHHHHHHhCCCceeecCcc----c--ccccCCCHHHHHHHHHHHHHHHHhhhhhhcceEEEecccCc
Confidence 5677777888999999998888321 1 1111 122244455555446666788899999999998865
No 90
>COG1943 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.18 E-value=2.9e+02 Score=22.12 Aligned_cols=52 Identities=19% Similarity=0.229 Sum_probs=34.9
Q ss_pred CceeEecCC--CchhHHHHHHHHHHHHHHHHHHHcCceEEEcccCCCCCCCCceeeEeEecc
Q 024513 106 GQWEFQVGP--CVGISSGDQLWMARYILERITEIAGVVLSFDPKPIKGDWNGAGAHANYSTK 165 (266)
Q Consensus 106 GQ~Ei~l~~--~~~l~aaD~~~~~r~~ik~vA~~hGl~atFmpKP~~~d~~GsG~H~h~Sl~ 165 (266)
++|=|++.+ .-.+-..|..-.+|.+++++|++++..+.=|.= .+ | |+|+=+.
T Consensus 12 ~~yH~v~~~kyRr~vl~~~~~~~l~~~l~~~~~~~~~eI~a~~v-~p-d------HVHlli~ 65 (136)
T COG1943 12 LKYHFVWVPKYRRKVLTGEVLNLLRSILREVAEQKNFEILAMEV-MP-D------HVHLLIT 65 (136)
T ss_pred CcEEEEEeccCchHhhhHhHHHHHHHHHHHHHHhCCCEEEEEEe-cC-C------EEEEEEe
Confidence 445555544 444555567888999999999999987653322 22 3 9997654
No 91
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=21.08 E-value=1.2e+02 Score=22.52 Aligned_cols=26 Identities=12% Similarity=0.157 Sum_probs=19.5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHcCce
Q 024513 116 VGISSGDQLWMARYILERITEIAGVV 141 (266)
Q Consensus 116 ~~l~aaD~~~~~r~~ik~vA~~hGl~ 141 (266)
-+++.|..++--+.+||+.|+.+|+.
T Consensus 7 R~i~i~~yIi~~~aTVR~~Ak~FGvS 32 (82)
T PF12116_consen 7 RVIEIANYIIETKATVRQAAKVFGVS 32 (82)
T ss_dssp HHHHHHHHHHHH---HHHHHHHHTS-
T ss_pred HHHHHHHHHHHcccHHHHHHHHHCCc
Confidence 36788899999999999999999975
No 92
>cd02885 IPP_Isomerase Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mamm
Probab=20.97 E-value=2.8e+02 Score=22.46 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=18.3
Q ss_pred CceeeCCCCCCCCCChHHHHHH
Q 024513 1 MCDAYTPAGEPIPTNKRFNAAK 22 (266)
Q Consensus 1 ~~d~~~~~g~p~~~~pR~~L~~ 22 (266)
+.++||.+|++...++|....+
T Consensus 3 ~~~~~d~~~~~~g~~~r~~~~~ 24 (165)
T cd02885 3 LVILVDEDDNPIGTAEKLEAHL 24 (165)
T ss_pred EEEEECCCCCCccccCHHHHhh
Confidence 4689999999999999976643
No 93
>PRK14167 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.86 E-value=86 Score=28.92 Aligned_cols=64 Identities=14% Similarity=0.225 Sum_probs=43.1
Q ss_pred CCCCCCCChHHHHHHHHccccccCCcceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCCccccccchhhHHHHHHHHHH
Q 024513 8 AGEPIPTNKRFNAAKVFGHPDVVAEEPWYGIEQEYTLLQKDINWPLGWPVGGYPGPQGPYYCGVGADKALGRDIVNSHYK 87 (266)
Q Consensus 8 ~g~p~~~~pR~~L~~~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 87 (266)
||+++...-|.-|++.++++++.|++|..+. .+...+. . ..-+.....+
T Consensus 6 ~Gk~vA~~i~~~l~~~v~~l~~~g~~P~Lai----I~vg~d~-------------------------a--s~~Yv~~k~k 54 (297)
T PRK14167 6 DGNAVAAQIRDDLTDAIETLEDAGVTPGLAT----VLMSDDP-------------------------A--SETYVSMKQR 54 (297)
T ss_pred eHHHHHHHHHHHHHHHHHHHHhCCCCceEEE----EEeCCCH-------------------------H--HHHHHHHHHH
Confidence 6777777778888888888887788776543 1221111 0 2345666678
Q ss_pred HHHHcCceeeeeeCC
Q 024513 88 ACLYAGINISGINGE 102 (266)
Q Consensus 88 ~l~~~Gi~ve~~~~E 102 (266)
++++.||+.+.++=+
T Consensus 55 ~~~~~Gi~~~~~~l~ 69 (297)
T PRK14167 55 DCEEVGIEAIDVEID 69 (297)
T ss_pred HHHHcCCEEEEEECC
Confidence 899999999876643
No 94
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=20.72 E-value=82 Score=23.82 Aligned_cols=17 Identities=6% Similarity=-0.101 Sum_probs=13.4
Q ss_pred hHHHHHHHHccccccCC
Q 024513 16 KRFNAAKVFGHPDVVAE 32 (266)
Q Consensus 16 pR~~L~~~~~~~~~~G~ 32 (266)
||..++.++..|.+.|+
T Consensus 34 PrRT~Qd~i~aL~~~~I 50 (90)
T PF09904_consen 34 PRRTIQDTIKALPELGI 50 (90)
T ss_dssp -HHHHHHHHHGGGGGT-
T ss_pred CHhHHHHHHHHhhcCCe
Confidence 89999999999986655
No 95
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=20.36 E-value=1.8e+02 Score=26.38 Aligned_cols=67 Identities=10% Similarity=-0.023 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCC--CCCceeEecCCCchhHHHHHHHHHHHHHHH-HHHHcCceEEEccc
Q 024513 80 DIVNSHYKACLYAGINISGINGEV--MPGQWEFQVGPCVGISSGDQLWMARYILER-ITEIAGVVLSFDPK 147 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~--gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~-vA~~hGl~atFmpK 147 (266)
-++..+.+.|.+.|++|..+..-. ..|+|-+.+.-.-+ ...-..-.++..+++ ++++.|+..+.-..
T Consensus 12 GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~~~-~~~~~~~~l~~~l~~~~~~~~~l~i~l~~~ 81 (280)
T TIGR00655 12 GLVAAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQLE-GFRLEESSLLAAFKSALAEKFEMTWELILA 81 (280)
T ss_pred ChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEEeC-CCCCCHHHHHHHHHHHHHHHhCCEEEEecC
Confidence 477788888999999998887655 35888655444322 111124467889999 99999988877543
No 96
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=20.24 E-value=2.6e+02 Score=23.85 Aligned_cols=63 Identities=13% Similarity=0.103 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 79 RDIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 79 ~~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
--++.+|.+.|.+.|++++....-.--|+|-+-+--+.+- +.+..++..+..+.++.|+....
T Consensus 19 pGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lvs~~~---~~~~~le~~L~~l~~~~~L~i~v 81 (190)
T PRK11589 19 PGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSW---NAITLIESTLPLKGAELDLLIVM 81 (190)
T ss_pred ChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEEeCCh---hHHHHHHHHHHhhhhhcCeEEEE
Confidence 4588889999999999999999888889997766553332 36667789999999999999876
No 97
>cd04933 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.18 E-value=3.4e+02 Score=19.53 Aligned_cols=36 Identities=8% Similarity=0.102 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCch
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVG 117 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~ 117 (266)
.+..++.+.|++.||+|+.+.. +...+-+++...+.
T Consensus 16 g~~a~IF~~La~~~InVDmI~q--s~~sISftV~~sd~ 51 (78)
T cd04933 16 GFLAKVFSIFETLGISVDVVAT--SEVSISLTLDPSKL 51 (78)
T ss_pred CHHHHHHHHHHHcCCcEEEEEe--cCCEEEEEEEhhhh
Confidence 3455566777899999999975 23556666666554
No 98
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).
Probab=20.06 E-value=3.2e+02 Score=22.42 Aligned_cols=60 Identities=10% Similarity=-0.029 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHcCceeeeeeCCCCCCceeEecCCCchhHHHHHHHHHHHHHHHHHHHcCceEEE
Q 024513 80 DIVNSHYKACLYAGINISGINGEVMPGQWEFQVGPCVGISSGDQLWMARYILERITEIAGVVLSF 144 (266)
Q Consensus 80 ~~~~~l~~~l~~~Gi~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~r~~ik~vA~~hGl~atF 144 (266)
...+.+.+.++..||+...++-+...-|.+.... .-..|-+ .-+..+.++|+++|+..-+
T Consensus 45 ~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~---~~~~~r~--~R~~~l~~~a~~~g~~~i~ 104 (189)
T TIGR02432 45 EEAEFVQQFCKKLNIPLEIKKVDVKALAKGKKKN---LEEAARE--ARYDFFEEIAKKHGADYIL 104 (189)
T ss_pred HHHHHHHHHHHHcCCCEEEEEecchhhccccCCC---HHHHHHH--HHHHHHHHHHHHcCCCEEE
Confidence 3456666778899999988776543222222111 1112221 3446788899999986444
Done!