Query 013478
Match_columns 442
No_of_seqs 260 out of 1620
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 04:15:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013478.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013478hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03036 glutamine synthetase; 100.0 2E-126 4E-131 986.4 42.4 432 1-442 1-432 (432)
2 PLN02284 glutamine synthetase 100.0 2.1E-99 5E-104 771.8 38.5 349 62-423 5-353 (354)
3 KOG0683 Glutamine synthetase [ 100.0 6.9E-94 1.5E-98 710.5 20.9 353 65-429 18-374 (380)
4 COG0174 GlnA Glutamine synthet 100.0 3.7E-83 7.9E-88 664.6 31.0 316 100-425 22-361 (443)
5 TIGR00653 GlnA glutamine synth 100.0 7.7E-78 1.7E-82 631.7 30.7 317 101-425 20-375 (460)
6 PRK09469 glnA glutamine synthe 100.0 5.3E-77 1.1E-81 626.4 30.4 319 100-425 22-383 (469)
7 TIGR03105 gln_synth_III glutam 100.0 6.1E-76 1.3E-80 613.8 28.8 310 101-425 18-354 (435)
8 PF00120 Gln-synt_C: Glutamine 100.0 3.3E-67 7.2E-72 514.4 17.2 240 173-421 1-259 (259)
9 COG3968 Uncharacterized protei 99.7 5.3E-17 1.1E-21 165.7 17.5 216 192-424 214-502 (724)
10 PF03951 Gln-synt_N: Glutamine 99.6 9E-15 1.9E-19 120.5 7.5 67 101-167 10-84 (84)
11 TIGR02050 gshA_cyan_rel unchar 98.6 2.9E-06 6.3E-11 85.1 18.4 183 195-421 1-248 (287)
12 PRK13517 carboxylate-amine lig 98.4 1.3E-05 2.8E-10 83.2 18.9 132 193-358 10-167 (373)
13 PRK13516 gamma-glutamyl:cystei 98.4 1.3E-05 2.9E-10 83.1 17.7 187 193-420 11-259 (373)
14 PRK13515 carboxylate-amine lig 98.2 4.6E-05 1E-09 79.0 15.7 131 193-358 5-161 (371)
15 PLN02611 glutamate--cysteine l 97.9 0.00019 4E-09 76.8 13.5 151 177-358 51-246 (482)
16 PRK13518 carboxylate-amine lig 97.5 0.00037 8E-09 72.1 9.6 131 194-358 13-169 (357)
17 TIGR01436 glu_cys_lig_pln glut 97.5 0.0029 6.4E-08 67.3 15.4 154 177-358 5-203 (446)
18 TIGR02048 gshA_cyano glutamate 97.3 0.0017 3.8E-08 67.6 11.4 93 258-357 31-149 (376)
19 PF04107 GCS2: Glutamate-cyste 97.3 0.001 2.2E-08 66.6 9.3 149 257-411 35-240 (288)
20 COG2170 Uncharacterized conser 97.0 0.0051 1.1E-07 62.9 10.4 187 194-423 3-253 (369)
21 TIGR03444 gshA_related glutama 95.1 0.13 2.8E-06 53.9 9.8 89 266-358 70-186 (390)
22 COG3572 GshA Gamma-glutamylcys 79.9 4.1 8.8E-05 42.8 6.2 45 259-304 91-136 (456)
23 cd04863 MtLigD_Pol_like MtLigD 76.7 9.1 0.0002 37.6 7.3 111 263-390 100-213 (231)
24 TIGR02778 ligD_pol DNA polymer 76.5 15 0.00033 36.4 8.8 110 264-390 113-225 (245)
25 KOG0683 Glutamine synthetase [ 76.4 0.91 2E-05 47.0 0.3 58 357-424 285-342 (380)
26 cd04869 ACT_GcvR_2 ACT domains 74.8 6.7 0.00015 30.9 4.9 65 240-306 11-81 (81)
27 cd04862 PaeLigD_Pol_like PaeLi 70.8 27 0.00059 34.2 8.9 116 261-390 94-209 (227)
28 PF13740 ACT_6: ACT domain; PD 70.7 9.5 0.00021 30.3 4.9 62 240-304 14-75 (76)
29 PF12224 Amidoligase_2: Putati 69.2 44 0.00095 32.2 10.2 22 396-417 224-245 (252)
30 cd04864 LigD_Pol_like_1 LigD_P 68.9 17 0.00038 35.6 7.1 111 262-390 97-210 (228)
31 cd04861 LigD_Pol_like LigD_Pol 66.1 38 0.00081 33.3 8.8 114 263-390 96-209 (227)
32 cd04870 ACT_PSP_1 CT domains f 65.7 14 0.00031 29.0 4.9 65 240-306 11-75 (75)
33 cd04872 ACT_1ZPV ACT domain pr 64.7 11 0.00023 30.7 4.1 67 240-307 13-79 (88)
34 cd04866 LigD_Pol_like_3 LigD_P 64.2 49 0.0011 32.4 9.2 111 263-390 91-205 (223)
35 PF06877 RraB: Regulator of ri 62.6 59 0.0013 27.1 8.5 94 177-301 3-98 (104)
36 PRK02471 bifunctional glutamat 62.3 8.7 0.00019 43.9 4.2 37 259-295 54-91 (752)
37 PRK00194 hypothetical protein; 57.6 18 0.00038 29.4 4.3 66 240-306 15-80 (90)
38 cd04865 LigD_Pol_like_2 LigD_P 55.0 45 0.00097 32.8 7.2 113 264-390 98-210 (228)
39 KOG0558 Dihydrolipoamide trans 50.4 15 0.00032 38.2 3.1 28 280-307 275-302 (474)
40 COG3285 Predicted eukaryotic-t 44.6 1.3E+02 0.0028 30.7 8.7 72 249-327 104-180 (299)
41 cd04893 ACT_GcvR_1 ACT domains 44.1 65 0.0014 25.5 5.5 64 239-305 12-75 (77)
42 TIGR02776 NHEJ_ligase_prk DNA 42.6 1E+02 0.0022 34.1 8.4 111 263-389 389-502 (552)
43 PRK05972 ligD ATP-dependent DN 41.9 2.2E+02 0.0047 33.4 11.1 123 250-389 665-794 (860)
44 PRK09633 ligD ATP-dependent DN 32.9 1.1E+02 0.0024 34.4 6.8 111 264-390 431-544 (610)
45 KOG0500 Cyclic nucleotide-gate 31.8 77 0.0017 34.6 5.1 82 56-144 318-412 (536)
46 PF14395 COOH-NH2_lig: Phage p 27.6 90 0.0019 31.2 4.5 52 273-326 56-108 (261)
47 PF00311 PEPcase: Phosphoenolp 27.2 1.1E+02 0.0025 35.3 5.9 62 238-305 415-482 (794)
48 PRK09632 ATP-dependent DNA lig 25.8 2.3E+02 0.0049 32.8 7.9 111 265-389 135-245 (764)
49 KOG0073 GTP-binding ADP-ribosy 25.0 69 0.0015 30.2 2.9 35 32-71 5-40 (185)
50 COG4519 Uncharacterized protei 23.7 2.6E+02 0.0056 23.3 5.7 25 174-204 33-57 (95)
51 PRK11589 gcvR glycine cleavage 22.9 73 0.0016 30.3 2.8 70 229-307 99-178 (190)
52 PF04468 PSP1: PSP1 C-terminal 22.9 1.1E+02 0.0023 25.3 3.5 60 239-303 25-84 (88)
53 PRK06027 purU formyltetrahydro 21.7 1.8E+02 0.0039 29.3 5.5 67 239-306 17-85 (286)
54 PF01921 tRNA-synt_1f: tRNA sy 21.4 3.8E+02 0.0083 28.1 7.9 141 157-311 23-178 (360)
55 smart00874 B5 tRNA synthetase 20.7 1.8E+02 0.0039 22.3 4.2 48 245-300 24-71 (71)
56 PF02042 RWP-RK: RWP-RK domain 20.7 82 0.0018 23.8 2.1 26 275-300 16-41 (52)
57 PRK11675 LexA regulated protei 20.6 95 0.0021 26.2 2.7 33 35-67 34-68 (90)
58 COG1384 LysS Lysyl-tRNA synthe 20.4 6.6E+02 0.014 27.8 9.6 91 158-261 20-128 (521)
59 cd04875 ACT_F4HF-DF N-terminal 20.2 1.2E+02 0.0025 23.5 3.1 60 240-301 11-73 (74)
No 1
>PLN03036 glutamine synthetase; Provisional
Probab=100.00 E-value=2e-126 Score=986.42 Aligned_cols=432 Identities=91% Similarity=1.475 Sum_probs=411.3
Q ss_pred CCccCCCCcceeeecccccCCCCCchhhhhhhHHHHHhhccCcccCcceEEEEeecchhHHHHHHHhhcCCCCCCCccee
Q 013478 1 MAQILAPSMQWQMRMPKYSNIASPMTTKMWSSLLMKQNKKGTNRSSAKFRVLALKSEDSTVNRLEDLLNLDITPYTDKII 80 (442)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (442)
|||||+||+||||||+|.++.+.|+++++|+|+++||+|++......+||++++........++++|++|+..++++||+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (432)
T PLN03036 1 MAQILAPSPQCQMRVPKNSAVAAPMTSKLWSSLVLKQKKKGTAKVSGKFRVLALQSENSTVNRVEDLLNLDTTPYTDRII 80 (432)
T ss_pred CCcccccccccccCCCCCCCcccccccceecccchhhhhhhhhhcccceeeeeccccchhhhhHHHHhhhcccccCCeEE
Confidence 99999999999999999999999999999999999999998877788999999776655578899999998888999999
Q ss_pred EEeecccCcceeeEeecccccCCCceeeeeeCCCCCCCCCCccccccCCCCCCCCCCccEEEEeEeeeecCCCCCCeEEE
Q 013478 81 AEYICQNNTISCWNRIGGTGIDMRSKSKTISKPVEHPSELPKWNYDGSSTGQAPGEDSEVILYPQAIFKDPFRGGNNILV 160 (442)
Q Consensus 81 ~~yi~~~~~i~~w~~idg~g~DlrGk~r~~~~p~~~~~~l~~~~fDGSs~g~a~~~~sD~~L~Pd~~~~~P~~~~~~a~V 160 (442)
|||| | |||+|+|||||+|++.+|+++++++|+|+|||||++|+++++||++|+||+++++||+++++++|
T Consensus 81 ~~yi--------w--~~g~~~dlrgk~r~~~~~~~~~~~~~~w~fDGSs~g~a~~~~sD~~l~PDTl~~~Pw~~~~~a~V 150 (432)
T PLN03036 81 AEYI--------W--IGGSGIDLRSKSRTISKPVEHPSELPKWNYDGSSTGQAPGEDSEVILYPQAIFKDPFRGGNNILV 150 (432)
T ss_pred EEEE--------E--eCCCCCCCCCCeEEeCccccccccCCceeeecCccCCCcCCCCCEEEEccEEEECCcCCCCeEEE
Confidence 9999 9 99999999999999999999999999999999999999999999999999999999987779999
Q ss_pred EEEeecCCCCCCCCCHHHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHH
Q 013478 161 ICDTYTPAGEPIPTNKRHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRD 240 (442)
Q Consensus 161 lcd~~~~dG~P~~~~pR~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~d 240 (442)
+||+|++||+|++.|||+.|++++++++..|+++|+|+|+|||||+.+..++.|||.+++|.++++|||+.+.+..+.++
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 99999999999999999999999999988999999999999999987544677898878999999999999998888899
Q ss_pred HHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeee
Q 013478 241 IADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHT 320 (442)
Q Consensus 241 i~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~ 320 (442)
|+++|+++|+++||+|+++|+|+|||||||+++|+++++|||++|++|++||+||++||++|||||||+.++|+|||||+
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 99999999999999999999999999999999999999999999999999999999999999999999987799999999
Q ss_pred eccccccccCCchhhHHHHHHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeecccCCCCCccEEE
Q 013478 321 NYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRETEKQGKGYLE 400 (442)
Q Consensus 321 h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~~~~~~~~r~E 400 (442)
|+||+++++++|.+.++++++||+|+|++||+||++||||||+|++|||+|++++||++||+++||||......+++|||
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 99999988767889999999998899999999999999999999999988889999999999999999877544578999
Q ss_pred ecCCCCCCCHHHHHHHHHHHhhcCCCCcHHHHHHHhhhhccC
Q 013478 401 DRRPASNMDPYVVTSLLAETTILWEPTLEAEALAAQKLALNV 442 (442)
Q Consensus 401 ~R~pda~aNPYLv~Aail~agl~G~~~~~~~~~~~~~~~~~~ 442 (442)
+|+||++||||||+|+|+.|+++.+|+||+|+||||||+|||
T Consensus 391 ~R~pda~aNPYLv~aai~~t~~~~~~~~~~~~~~~~~~~~~~ 432 (432)
T PLN03036 391 DRRPASNMDPYIVTSLLAETTILWEPTLEAEALAAQKLSLNV 432 (432)
T ss_pred EeCCCCCCCHHHHHHHHHHHHhcCCcchhHHHHHhhhhccCC
Confidence 999999999999999999999999999999999999999997
No 2
>PLN02284 glutamine synthetase
Probab=100.00 E-value=2.1e-99 Score=771.78 Aligned_cols=349 Identities=81% Similarity=1.394 Sum_probs=325.9
Q ss_pred HHHHHhhcCCCCCCCcceeEEeecccCcceeeEeecccccCCCceeeeeeCCCCCCCCCCccccccCCCCCCCCCCccEE
Q 013478 62 NRLEDLLNLDITPYTDKIIAEYICQNNTISCWNRIGGTGIDMRSKSKTISKPVEHPSELPKWNYDGSSTGQAPGEDSEVI 141 (442)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~yi~~~~~i~~w~~idg~g~DlrGk~r~~~~p~~~~~~l~~~~fDGSs~g~a~~~~sD~~ 141 (442)
..+.+|+.+ ++.++++|||| | ||+.++||+||+|++.+|++.++++++|+|||||+|++.+++||++
T Consensus 5 ~~~~~~~~~---~~~~~~~~~y~--------w--i~~~~~dl~g~~~~~~~~~~~~~~~~~~~fdGssi~~~~~~~sD~~ 71 (354)
T PLN02284 5 SDLINLNLS---DSTDKIIAEYI--------W--IGGSGMDLRSKARTLPGPVTDPSKLPKWNYDGSSTGQAPGEDSEVI 71 (354)
T ss_pred hhhHhhccc---CcCCeEEEEEE--------E--EEEEecCCCCceEEecccccccccCCceeecCCCCCCccCCCceEE
Confidence 346677666 67899999999 9 9999999999999999999999999999999999999999999999
Q ss_pred EEeEeeeecCCCCCCeEEEEEEeecCCCCCCCCCHHHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCC
Q 013478 142 LYPQAIFKDPFRGGNNILVICDTYTPAGEPIPTNKRHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYP 221 (442)
Q Consensus 142 L~Pd~~~~~P~~~~~~a~Vlcd~~~~dG~P~~~~pR~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p 221 (442)
|+||+++++||+++++++|+||++++||+|++.|||++|+++++++++.|+++++|+|+|||||+.+..++.|||.+++|
T Consensus 72 l~PDt~~~~Pw~~~~~~~vlcdv~~~dG~p~~~dPR~vL~r~~~~~~~~g~~~~~G~E~EF~lf~~~~~~~~g~~~~~~~ 151 (354)
T PLN02284 72 LYPQAIFKDPFRGGNNILVMCDAYTPAGEPIPTNKRAKAAKIFSHPDVAAEEPWYGIEQEYTLLQKDVKWPLGWPVGGYP 151 (354)
T ss_pred EEccEEEECCCCCCCeEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHhcCCceeEEeceEEEEEecCCcccCCCCCCCcc
Confidence 99999999999876689999999999999999999999999999999999999999999999998654446688877788
Q ss_pred CCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcE
Q 013478 222 GPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVV 301 (442)
Q Consensus 222 ~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~ 301 (442)
.++++||+..+.+..++++++++|+++|+++||+|+++|||++||||||+++|++++++||+++++|++||+||++||++
T Consensus 152 ~~~~~y~~~~~~~~~~~~~~~~~l~~~l~~~Gi~ve~~h~E~apGQ~Ei~l~~~d~l~aAD~~~~~K~vvk~vA~~~Gl~ 231 (354)
T PLN02284 152 GPQGPYYCGVGADKAFGRDIVDAHYKACLYAGINISGINGEVMPGQWEFQVGPVVGISAGDQLWVARYILERITEIAGVV 231 (354)
T ss_pred cCCCCcccCcchhhHHHHHHHHHHHHHHHHCCCCeEEEEcCcCCCceEEEecCCcHHHHHHHHHHHHHHHHHHHHHhCCE
Confidence 89999999988777778999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecccCCCCCCCCceeeeeccccccccCCchhhHHHHHHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCC
Q 013478 302 LSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANR 381 (442)
Q Consensus 302 aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR 381 (442)
|||||||+.++|+|||||+|+||+++++++|.+.++++++|+.|+|+++|+||++||||||+|++|||++.+++||.+||
T Consensus 232 ATFMPKP~~~~~~GSGmH~H~SL~~~~~~gg~~~~~~~l~~~~l~h~~~l~a~~~NSYkRL~p~~eap~~~~~~wg~~NR 311 (354)
T PLN02284 232 VSFDPKPIPGDWNGAGAHTNYSTKSMREDGGYEVIKKAIEKLGLRHKEHIAAYGEGNERRLTGKHETADINTFSWGVANR 311 (354)
T ss_pred EEEcCCCCCCCCccCcceeecChhhcccCCcHHHHHHHHHHHHHHHHHHhhhhhcCcHhhcCCCccCcccccceeecCCC
Confidence 99999999877899999999999997766788999999999889999999999999999999999999877999999999
Q ss_pred cceeeecccCCCCCccEEEecCCCCCCCHHHHHHHHHHHhhc
Q 013478 382 GCSIRVGRETEKQGKGYLEDRRPASNMDPYVVTSLLAETTIL 423 (442)
Q Consensus 382 ~a~IRIp~~~~~~~~~r~E~R~pda~aNPYLv~Aail~agl~ 423 (442)
+++||||......+++|||+|+||++|||||++|++|+|+++
T Consensus 312 sa~iRIP~~~~~~~~~riE~R~pd~~aNPYLa~aaila~~~~ 353 (354)
T PLN02284 312 GASIRVGRDTEKEGKGYFEDRRPASNMDPYVVTSMIAETTIL 353 (354)
T ss_pred ceeEEECCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHHHHhc
Confidence 999999987643346899999999999999999999999986
No 3
>KOG0683 consensus Glutamine synthetase [Amino acid transport and metabolism]
Probab=100.00 E-value=6.9e-94 Score=710.47 Aligned_cols=353 Identities=61% Similarity=1.101 Sum_probs=341.2
Q ss_pred HHhhcCCCCCCCcceeEEeecccCcceeeEeecccccCCCceeeeeeCCCCCCCCCCccccccCCCCCCCCCCccEEEEe
Q 013478 65 EDLLNLDITPYTDKIIAEYICQNNTISCWNRIGGTGIDMRSKSKTISKPVEHPSELPKWNYDGSSTGQAPGEDSEVILYP 144 (442)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~yi~~~~~i~~w~~idg~g~DlrGk~r~~~~p~~~~~~l~~~~fDGSs~g~a~~~~sD~~L~P 144 (442)
.+++.| ..+.+|++++|| | |||+|+++|+|+|++..+++.++++|.|+|||||++|+.+.+||++|+|
T Consensus 18 ~~~~~L--~~~~~kv~a~YV--------w--idg~ge~~rsk~rt~d~~~~~~~~lp~wnydgsst~QA~g~nSd~~l~P 85 (380)
T KOG0683|consen 18 LEYLYL--RAKRKKVQAEYV--------W--IDGTGENLRSKTRTLDAEPSSISELPIWNYDGSSTGQAPGENSDVYLRP 85 (380)
T ss_pred hhhccc--cccCceEEEEEE--------E--ecCccccchhhcccccCCccCcccCccccccCcccccccCCCCceEEee
Confidence 456666 244799999999 9 9999999999999999999999999999999999999999999999999
Q ss_pred EeeeecCCCCCCeEEEEEEeecCCCCCCCCCHHHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCCCCC
Q 013478 145 QAIFKDPFRGGNNILVICDTYTPAGEPIPTNKRHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQ 224 (442)
Q Consensus 145 d~~~~~P~~~~~~a~Vlcd~~~~dG~P~~~~pR~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~ 224 (442)
.+++++||+.|++.+|+|++|+.+|.|.++|.|..|.+++.....+..+||||+||||++++.+.++|+|||.+|||+||
T Consensus 86 va~~~dPfr~g~Nilv~c~~~~~~~~P~~tn~R~~c~~~~~~~~~~~~~PWfg~Eqeyt~l~~~~~~p~gwp~~GFp~Pq 165 (380)
T KOG0683|consen 86 VAIYPDPFRNGNNILVMCDTYDFDGKPTETNKRVACARIMPKLSTKDTEPWFGMEQEYTLLDALDGHPFGWPKGGFPGPQ 165 (380)
T ss_pred hhhcCCcccCCCCEEEEeeccCCCCCcccccchhhHHHHhccccccccCCchhhhHHHhhhccccCCcccCCccCCCCCC
Confidence 99999999999999999999999999999999999999999887789999999999999999966899999999999999
Q ss_pred CCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEe
Q 013478 225 GPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSL 304 (442)
Q Consensus 225 g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTF 304 (442)
|+|||+++.++.|+|||+++||++|+++||+|.++|.|+||||||||++||.||.|||++|++|++||||||++|+.|||
T Consensus 166 gpyyc~VGad~~~~rdiveahy~acLyaGl~i~G~N~EvmPgQwEfqvGp~~GI~~gD~lw~aR~il~rVae~~Gviasf 245 (380)
T KOG0683|consen 166 GPYYCGVGADRVFGRDIVEAHYRACLYAGLNISGINVEVMPGQWEFQVGPCEGISMGDQLWMARYILHRVAEKFGVIASF 245 (380)
T ss_pred CCceeeccccccccchhhhhhHHHHHhhheeeccccccccCceeEEeecchhcccchhhHHHHHHHHHHHHHHhCeeEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCceeeeeccccccccCCchhhHHHHHHhhHHHHHHHHhcc----cccccccCCCCCCCCCCCceeeccCC
Q 013478 305 DPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAY----GEGNERRLTGKHETASIDSFSWGVAN 380 (442)
Q Consensus 305 mPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~----~~nsYkRL~~~~eap~~~~~sWG~~N 380 (442)
+|||..|+|||+|||+|+|+.+||.++|++.|+.++.+|+++|..|+.+| +.+|.+||++.|||++++.|+||++|
T Consensus 246 ~pKp~~g~WngaG~Htn~ST~~mr~~~g~~~i~~a~~~ls~rh~~hi~~ydp~~G~dN~rrltg~hEt~~i~~Fs~GvAn 325 (380)
T KOG0683|consen 246 DPKPILGDWNGAGCHTNFSTKEMREAGGLKIIEEAIPKLSKRHREHIAAYDPKGGKDNERRLTGRHETGSIDNFSWGVAN 325 (380)
T ss_pred cCCCCCCcccCcccccccchhHHHhccCHHHHHHHhhhcchhhhhhhhhcCccCCccchhhhcCCCcccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999 78999999999999999999999999
Q ss_pred CcceeeecccCCCCCccEEEecCCCCCCCHHHHHHHHHHHhhcCCCCcH
Q 013478 381 RGCSIRVGRETEKQGKGYLEDRRPASNMDPYVVTSLLAETTILWEPTLE 429 (442)
Q Consensus 381 R~a~IRIp~~~~~~~~~r~E~R~pda~aNPYLv~Aail~agl~G~~~~~ 429 (442)
|+++||||+.+...+++|||+|+||+|+|||+|+.+++.++|+.++.++
T Consensus 326 r~~siri~r~va~~~~Gy~edrrP~sN~Dpy~Vt~~~~~t~l~~~~~~~ 374 (380)
T KOG0683|consen 326 RNPSIRIPRTVAAEGKGYFEDRRPSSNCDPYAVTLMIIPTTLLEAVELE 374 (380)
T ss_pred CCceeeechhhhcccccccccCCCcCCCCcceeeHHHhhHHHhcccchh
Confidence 9999999999998889999999999999999999999999999988844
No 4
>COG0174 GlnA Glutamine synthetase [Amino acid transport and metabolism]
Probab=100.00 E-value=3.7e-83 Score=664.63 Aligned_cols=316 Identities=28% Similarity=0.434 Sum_probs=279.3
Q ss_pred ccCCCceeeeeeCCCCC----CCCCC--ccccccCCC-CCCCCCCccEEEEeEe--eeecCCCCCCeEEEEEEeecCCCC
Q 013478 100 GIDMRSKSKTISKPVEH----PSELP--KWNYDGSST-GQAPGEDSEVILYPQA--IFKDPFRGGNNILVICDTYTPAGE 170 (442)
Q Consensus 100 g~DlrGk~r~~~~p~~~----~~~l~--~~~fDGSs~-g~a~~~~sD~~L~Pd~--~~~~P~~~~~~a~Vlcd~~~~dG~ 170 (442)
.+|+.|++|+|.+|+.+ ++... +..|||||+ |+...++||++|+||+ ++++||+++++++|+||+++++|+
T Consensus 22 f~D~~G~~r~k~ip~~~~~~~~~~~~~~g~~fdgss~~g~~~i~~sDm~l~Pd~~T~~~~Pw~~~~ta~v~cdv~~~~g~ 101 (443)
T COG0174 22 FTDLNGVLRGKTIPAEKPVSVLAQLFEGGVVFDGSSIAGFEGIGESDMVLKPDLSTLVVDPWREGPTARVLCDVYDPDGT 101 (443)
T ss_pred EECCCCCeeeEEEecccchhHHHhhhccCcCcCCccccccCCCCCCCEEEeeccCceeeCCCCCCCcEEEEEEEECCCCC
Confidence 35788899999999983 33332 467999999 6766699999999995 999999998899999999999999
Q ss_pred CCCCCHHHHHHHHHHhhhcCCccc-eEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHH
Q 013478 171 PIPTNKRHRAAEIFSNSKVSAEVP-WFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKAC 249 (442)
Q Consensus 171 P~~~~pR~~Lk~~~~~l~~~G~~~-~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al 249 (442)
|++.|||++|+|+++++++.|+.+ ++|+|+|||||+.+...+.+ +.|.++|+||+..+.++ ..+++.+++.+|
T Consensus 102 p~~~dPR~vlkr~~~~l~~~G~~~~~~g~E~EFfLfd~~~~~~~~----~~~~~~~~yf~~~~~~~--~~~~~~di~~~l 175 (443)
T COG0174 102 PYPRDPRSVLKRALARLKDEGLAPAVVGPELEFFLFDRDGRDPDG----GRPADKGGYFDVAPLDE--AEDFRRDIVEAL 175 (443)
T ss_pred cCCCChHHHHHHHHHHHHhcCCccceeecceeEEEeecccCCccc----CccCCCCcccCcccccc--HHHHHHHHHHHH
Confidence 999999999999999999999985 99999999999975332221 57889999999999988 578888888889
Q ss_pred HHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccc-
Q 013478 250 LYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMR- 328 (442)
Q Consensus 250 ~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~- 328 (442)
+++||+|+.+|||+|||||||++++.+++++||+++++|++||+||++||++|||||||+.|+ +|||||+|+|||+..
T Consensus 176 ~~~Gi~ie~~hhEva~gQ~EI~~~~~~~l~~AD~~~~~K~vvk~vA~~hG~~aTFMpKP~~g~-~GSGMH~H~Sl~~~dg 254 (443)
T COG0174 176 EAAGIEIEAIHHEVAPGQFEINLRFDDALKAADQIVIFKYVVKEVAEKHGLTATFMPKPFFGD-NGSGMHVHQSLWDKDG 254 (443)
T ss_pred HHCCCCcEeccccccCCceEEecCCCCHHHHHHHHHHHHHHHHHHHHHhCCeEEEeCCCCCCC-CCCceeEEEEEecCCC
Confidence 999999999999999999999999999999999999999999999999999999999999997 999999999999642
Q ss_pred -----cCC---chh-hHHHHHHhhHHHHHHHHhcccc---cccccC-CCCCCCCCCCceeeccCCCcceeeecccCCCCC
Q 013478 329 -----EEG---GYE-TIKKAILNLSLRHKEHISAYGE---GNERRL-TGKHETASIDSFSWGVANRGCSIRVGRETEKQG 395 (442)
Q Consensus 329 -----~~~---G~~-~~~~~iaGL~L~H~~al~a~~~---nsYkRL-~~~~eap~~~~~sWG~~NR~a~IRIp~~~~~~~ 395 (442)
+++ |++ .+++||+|| |+|+++++|+++ |||||| +|..|||+ +++||.+||+|+||||.+.....
T Consensus 255 ~nlF~d~~~~~~lS~~~~~~igGi-lkha~~~~ai~~PtvNSYkRl~vp~e~AP~--~~~wg~~NRsa~iRIP~~~~~~~ 331 (443)
T COG0174 255 GNLFADEDGYAGLSETALHFIGGI-LKHAPALTAITAPTVNSYKRLGVPYEWAPT--YIAWGVRNRSASVRIPASGANGK 331 (443)
T ss_pred CccccCCCCcccHHHHHHHHHHHH-HHHHHHHHhHhCCCcchhhhcCCCcccCcc--hhcccccCcceEEEeCCCCCCCC
Confidence 222 233 458999998 999999999986 999999 66234998 99999999999999999854334
Q ss_pred ccEEEecCCCCCCCHHHHHHHHHHHhhcCC
Q 013478 396 KGYLEDRRPASNMDPYVVTSLLAETTILWE 425 (442)
Q Consensus 396 ~~r~E~R~pda~aNPYLv~Aail~agl~G~ 425 (442)
++|||+|+||++|||||++||+|+|||+|+
T Consensus 332 ~~RiE~R~pd~~aNPYLa~AaiL~Agl~GI 361 (443)
T COG0174 332 ARRVEFRVPDPDANPYLAFAAILAAGLDGI 361 (443)
T ss_pred cceeEeeCCCCCCCHHHHHHHHHHHHHHHH
Confidence 679999999999999999999999999994
No 5
>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=7.7e-78 Score=631.72 Aligned_cols=317 Identities=25% Similarity=0.365 Sum_probs=278.3
Q ss_pred cCCCceeeeeeCCCCCCCC-C--CccccccCCC-CCCCCCCccEEEEeEe--eeecCCCCCCeEEEEEEeecC-CCCCCC
Q 013478 101 IDMRSKSKTISKPVEHPSE-L--PKWNYDGSST-GQAPGEDSEVILYPQA--IFKDPFRGGNNILVICDTYTP-AGEPIP 173 (442)
Q Consensus 101 ~DlrGk~r~~~~p~~~~~~-l--~~~~fDGSs~-g~a~~~~sD~~L~Pd~--~~~~P~~~~~~a~Vlcd~~~~-dG~P~~ 173 (442)
+|+.|++|+|.+|++.+++ + .|.+|||+++ |+...+++|++|+||+ ++++||.++++++|+||+++. ||+|++
T Consensus 20 ~Dl~G~~rgk~vp~~~~~~~~~~~G~~~~~~~~~~~~~~~~~D~~l~PD~~Tl~~~pw~~~~~a~v~~d~~~~~dg~p~~ 99 (460)
T TIGR00653 20 TDIKGKPQHVEIPASALDKEAFEEGIMFDGSSIRGFQGIEESDMLLKPDPSTAVIDPWRAEKTLRVICDVYEPFTGEPYE 99 (460)
T ss_pred ECCCCCEeeEEEeHHHhhHHHhcCCeecccccccccccCCCCcEEEeccCCcceeccCCCCCcEEEEEEEEECCCCCCCC
Confidence 4899999999999999864 3 5799999998 6667788999999997 899999776799999999998 999999
Q ss_pred CCHHHHHHHHHHhhh-cCCccceEeeeeeEEEecCCCCCCC-------------------CCCCCCCCCCCCCceeeccc
Q 013478 174 TNKRHRAAEIFSNSK-VSAEVPWFGIEQEYTLLQQNVKWPL-------------------GWPVGAYPGPQGPYYCGAGA 233 (442)
Q Consensus 174 ~~pR~~Lk~~~~~l~-~~G~~~~~G~E~EF~L~~~~~~~p~-------------------g~p~~~~p~~~g~yy~~~~~ 233 (442)
.|||++|++++++++ +.|+++++|+|+|||||+.+...+. +|. +..|.+++.||+..+.
T Consensus 100 ~~PR~~L~r~~~~l~~~~G~~~~~g~E~EF~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 178 (460)
T TIGR00653 100 RDPRSIAKRAEEYLKSGIGDTAYFGPEPEFFLFDSVEFGSLANGSFYEVDSEEGRWNEESGNR-GYKPRDKGGYFPVAPT 178 (460)
T ss_pred CCHHHHHHHHHHHHHhCCCCceeEEcceEEEEEecCccCcccccceeeeccccccccccCCcC-CCcccCCccccCCCCc
Confidence 999999999999999 8999999999999999986432210 111 2345566668887777
Q ss_pred ChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCC
Q 013478 234 DKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDW 313 (442)
Q Consensus 234 ~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~ 313 (442)
+. ..+++++++++|+.+||+|+++|+|+|||||||++.|++++++||+++++|++||+||++||++|||||||+.+ +
T Consensus 179 ~~--~~~~~~~i~~~l~~~Gi~v~~~~~E~gpGQ~Ei~l~~~~~l~aAD~~~~~k~~ik~vA~~~G~~ATFmpKP~~~-~ 255 (460)
T TIGR00653 179 DT--AVDIRREMVLYLEQLGFDVEVHHHEVATGQHEIDFKFDTLLKTADDIQTYKYVVKNVARKHGKTATFMPKPLFG-D 255 (460)
T ss_pred cc--HHHHHHHHHHHHHHcCCCceeeecCcCCCceeEecCCCCHHHHHHHHHHHHHHHHHHHHHhCCEEEEecccCCC-C
Confidence 65 46788888888999999999999999999999999999999999999999999999999999999999999998 5
Q ss_pred CCceeeeeccccccc-----cC---Cchh-hHHHHHHhhHHHHHHHHhcccc---cccccCCCCCCCCCCCceeeccCCC
Q 013478 314 NGAGCHTNYSTKSMR-----EE---GGYE-TIKKAILNLSLRHKEHISAYGE---GNERRLTGKHETASIDSFSWGVANR 381 (442)
Q Consensus 314 ~GSG~H~h~Sl~~~~-----~~---~G~~-~~~~~iaGL~L~H~~al~a~~~---nsYkRL~~~~eap~~~~~sWG~~NR 381 (442)
+|||+|+|+|||+.. ++ .|++ ..++||+|| |+|+++++||++ ||||||+|++|||+ +++||.+||
T Consensus 256 ~GSG~H~H~Sl~d~g~n~F~d~~~~~~lS~~~~~fiaGi-L~h~~~l~a~~~PtvNSYkRl~p~~~ap~--~~~WG~~NR 332 (460)
T TIGR00653 256 NGSGMHCHQSLWKDGENLFAGEEGYAGLSETALYYIGGI-LKHAKALAAFTNPTVNSYKRLVPGYEAPV--YLAYSARNR 332 (460)
T ss_pred CcCceeEEECccCCCeeccCCCCCCcccCHHHHHHHHHH-HHHHHHhhhHhcCCCcchhhcCCCCcCcc--eeecccCCC
Confidence 999999999999742 11 2344 457999998 999999999986 99999999999999 999999999
Q ss_pred cceeeecccCCCCCccEEEecCCCCCCCHHHHHHHHHHHhhcCC
Q 013478 382 GCSIRVGRETEKQGKGYLEDRRPASNMDPYVVTSLLAETTILWE 425 (442)
Q Consensus 382 ~a~IRIp~~~~~~~~~r~E~R~pda~aNPYLv~Aail~agl~G~ 425 (442)
+++||||.... ...+|||+|+||++|||||++||+|+||++|+
T Consensus 333 ~a~iRvp~~~~-~~~~riE~R~~da~aNPYLalAa~laAGl~Gi 375 (460)
T TIGR00653 333 SALIRIPASGN-PKAKRIEFRFPDPSANPYLAFAAMLMAGLDGI 375 (460)
T ss_pred CceEEecCCCC-CcCceEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 99999997642 24679999999999999999999999999993
No 6
>PRK09469 glnA glutamine synthetase; Provisional
Probab=100.00 E-value=5.3e-77 Score=626.39 Aligned_cols=319 Identities=23% Similarity=0.334 Sum_probs=276.5
Q ss_pred ccCCCceeeeeeCCCCCCCC-C--CccccccCCC-CCCCCCCccEEEEeEe--eeecCCCCCCeEEEEEEeecCC-CCCC
Q 013478 100 GIDMRSKSKTISKPVEHPSE-L--PKWNYDGSST-GQAPGEDSEVILYPQA--IFKDPFRGGNNILVICDTYTPA-GEPI 172 (442)
Q Consensus 100 g~DlrGk~r~~~~p~~~~~~-l--~~~~fDGSs~-g~a~~~~sD~~L~Pd~--~~~~P~~~~~~a~Vlcd~~~~d-G~P~ 172 (442)
.+|+.|+.|+|.+|++.+++ . .|..|||+++ |+...+++|++|+||+ ++++||.+.++++|+||+++.+ |+|+
T Consensus 22 ~~Dl~G~~rgk~ip~~~~~~~~~~~G~~f~~~~~~g~~~~~~~D~~l~PD~~Tl~~~Pw~~~~~a~v~~d~~~~~~g~p~ 101 (469)
T PRK09469 22 FTDTKGKEQHVTIPAHQVNADFFEEGKMFDGSSIGGWKGINESDMVLMPDASTAVLDPFFEDSTLIIRCDILEPGTMQGY 101 (469)
T ss_pred EECCCCCEeEEEEEHHHhhHHHhcCCceeccccccccCcCCCCCEEEEEcCCccEECCcCCCCcEEEEEEEEECCCCCcC
Confidence 35899999999999998874 3 6789999998 6667789999999996 8999997545999999999985 8999
Q ss_pred CCCHHHHHHHHHHhhhcCCc--cceEeeeeeEEEecCCCC--CC-----------CCCCC---------CCCCCCCCCce
Q 013478 173 PTNKRHRAAEIFSNSKVSAE--VPWFGIEQEYTLLQQNVK--WP-----------LGWPV---------GAYPGPQGPYY 228 (442)
Q Consensus 173 ~~~pR~~Lk~~~~~l~~~G~--~~~~G~E~EF~L~~~~~~--~p-----------~g~p~---------~~~p~~~g~yy 228 (442)
+.|||++|++++++++++|+ ++.+|+|+|||||+.+.. .+ ..|+. +..|..++.||
T Consensus 102 ~~~PR~iLkr~~~~l~~~G~~~~~~~g~ElEF~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y 181 (469)
T PRK09469 102 DRDPRSIAKRAEDYLRSTGIADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEAAWNSGTKYEGGNKGHRPGVKGGYF 181 (469)
T ss_pred CcCHHHHHHHHHHHHHHcCCCcceeEecceEEEEEeccccccCccccccccccchhcccccccccCCCCCCccCCCcccc
Confidence 99999999999999999999 999999999999985420 00 11211 11344555578
Q ss_pred eecccChhHHHHHHHHHHHHHHHcCCceeeecCCCC-CCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEeccc
Q 013478 229 CGAGADKSFGRDIADAHYKACLYAGINISGTNGEVM-PGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPK 307 (442)
Q Consensus 229 ~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~-pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPK 307 (442)
...+.+. ..+++++++++|+.+||+|+++|+|++ ||||||++.|.+++++||+++++|++||+||++||++||||||
T Consensus 182 ~~~~~~~--~~~~~~~i~~~l~~~Gi~v~~~h~E~g~~GQ~Ei~l~~~d~L~aaD~~~~~k~~vk~va~~~g~~atFmpK 259 (469)
T PRK09469 182 PVPPVDS--SQDIRSAMCLVMEEMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHNVAHAFGKTATFMPK 259 (469)
T ss_pred CCCcccc--hHHHHHHHHHHHHHCCCCcEEeeCCCCCCCeEEEeccCCCHHHHHHHHHHHHHHHHHHHHHhCCEEEEecc
Confidence 8777776 578888888899999999999999999 5999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceeeeeccccccc------c-CCchh-hHHHHHHhhHHHHHHHHhcccc---cccccCCCCCCCCCCCceee
Q 013478 308 PIEGDWNGAGCHTNYSTKSMR------E-EGGYE-TIKKAILNLSLRHKEHISAYGE---GNERRLTGKHETASIDSFSW 376 (442)
Q Consensus 308 P~~g~~~GSG~H~h~Sl~~~~------~-~~G~~-~~~~~iaGL~L~H~~al~a~~~---nsYkRL~~~~eap~~~~~sW 376 (442)
|+.+. +|||||+|+|||+.. + .+|++ ..++||+|| |+|+++++||++ ||||||+|++|||+ +++|
T Consensus 260 P~~~~-~GsG~H~H~Sl~~~g~N~F~~~~~~~ls~~~~~fiaGl-L~h~~~l~a~~~PtvNSYkRl~p~~~ap~--~~~W 335 (469)
T PRK09469 260 PMFGD-NGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGGI-IKHAKAINALANPTTNSYKRLVPGYEAPV--MLAY 335 (469)
T ss_pred ccCCC-CCceeEEEEeecCCCccccCCCCcCCcCHHHHHHHHHH-HHHHHHHHhhhcCCCchHhhcCCCCcCcC--ccee
Confidence 99984 999999999999852 1 13454 447999998 999999999976 99999999999999 9999
Q ss_pred ccCCCcceeeecccCCCCCccEEEecCCCCCCCHHHHHHHHHHHhhcCC
Q 013478 377 GVANRGCSIRVGRETEKQGKGYLEDRRPASNMDPYVVTSLLAETTILWE 425 (442)
Q Consensus 377 G~~NR~a~IRIp~~~~~~~~~r~E~R~pda~aNPYLv~Aail~agl~G~ 425 (442)
|.+||+++||||... .+..+|||+|.||++|||||++|++|+||++|+
T Consensus 336 G~~NR~a~iRvp~~~-~~~~~riE~R~~da~aNPYL~~AaiLaAGldGI 383 (469)
T PRK09469 336 SARNRSASIRIPVVA-SPKARRIEVRFPDPAANPYLCFAALLMAGLDGI 383 (469)
T ss_pred cCCCCcceEEeccCC-CCCCceEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 999999999999522 223679999999999999999999999999994
No 7
>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=6.1e-76 Score=613.80 Aligned_cols=310 Identities=20% Similarity=0.254 Sum_probs=268.3
Q ss_pred cCCCceeeeeeCCCCCCCCC--CccccccCCCC--CCCCCCccEEEEeEe--eeecCCCCCCeEEEEEEeecCCCCCCCC
Q 013478 101 IDMRSKSKTISKPVEHPSEL--PKWNYDGSSTG--QAPGEDSEVILYPQA--IFKDPFRGGNNILVICDTYTPAGEPIPT 174 (442)
Q Consensus 101 ~DlrGk~r~~~~p~~~~~~l--~~~~fDGSs~g--~a~~~~sD~~L~Pd~--~~~~P~~~~~~a~Vlcd~~~~dG~P~~~ 174 (442)
+|+.|++|+|.+|.++++++ .|..|+++++. ....+++|++|+||+ ++++||.++ +++|+||++. +|+|++.
T Consensus 18 ~D~~G~~r~k~vp~~~~~~~~~~G~~~~~~~~~~~~~~~~~~D~~l~PD~~Tl~~~pw~~~-~a~v~~d~~~-~G~p~~~ 95 (435)
T TIGR03105 18 VDLHGVQKAKLVPAEAIDHMATGGAGFAGFAAWGLGQSPADPDLMAIPDLDSLTQLPWQPG-VAWVAADLHV-NGKPYPQ 95 (435)
T ss_pred ECCCCCeeEEEEeHHHHHHHHcCCCcccchhhhccCCCCCCCCEEEEeccccceeCCCCCC-eEEEEEEEee-CCCcCCC
Confidence 37889999999999988775 67899998873 334467999999996 899999885 9999999976 8999999
Q ss_pred CHHHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCC
Q 013478 175 NKRHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGI 254 (442)
Q Consensus 175 ~pR~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI 254 (442)
|||++|+++++++++.|+.+++|+|+|||||+.+.++.. .+.+..+....+||+..+.+. ..+++++++++|+.+||
T Consensus 96 ~PR~vL~r~~~~~~~~G~~~~~g~E~EF~l~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~l~~~gi 172 (435)
T TIGR03105 96 APRVVLKRQLAEAAELGLTLNTGVECEFFLLRRDEDGSL-SIADRADTLAKPCYDQRGLMR--RYDVLTEISDAMNALGW 172 (435)
T ss_pred CHHHHHHHHHHHHHhcCCceeEEeceEEEEEecCCCCCc-ccCCCCCCCCccCCCCcchhh--hhHHHHHHHHHHHHCCC
Confidence 999999999999999999999999999999987532111 111111222344677666655 57899999999999999
Q ss_pred ceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeecccccccc-----
Q 013478 255 NISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMRE----- 329 (442)
Q Consensus 255 ~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~----- 329 (442)
+|+++|+|++||||||++.|++++++||+++++|++||+||++||++|||||||+.+ ++|||||+|+|||+...
T Consensus 173 ~ve~~~~E~gpGQ~Ei~l~~~~~l~aaD~~~~~k~~vk~vA~~~Gl~atFmpKP~~~-~~GsG~H~H~Sl~d~~g~n~f~ 251 (435)
T TIGR03105 173 DPYQNDHEDANGQFEMNFTYADALTTADRHAFFRYMVKEIAEKHGMRATFMPKPFAD-LTGNGCHFHLSLWDEDGRNLFA 251 (435)
T ss_pred CeEEeecCcCCCceEEecCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEecCccCCC-CCccceEEEEeeecCCCccccc
Confidence 999999999999999999999999999999999999999999999999999999998 69999999999996321
Q ss_pred ----C--Cchhh-HHHHHHhhHHHHHHHHhcccc---cccccCCCC------CCCCCCCceeeccCCCcceeeecccCCC
Q 013478 330 ----E--GGYET-IKKAILNLSLRHKEHISAYGE---GNERRLTGK------HETASIDSFSWGVANRGCSIRVGRETEK 393 (442)
Q Consensus 330 ----~--~G~~~-~~~~iaGL~L~H~~al~a~~~---nsYkRL~~~------~eap~~~~~sWG~~NR~a~IRIp~~~~~ 393 (442)
+ .|++. .++||+|| |+|++++++|++ ||||||+|+ +|||+ +++||.+||+++||||.
T Consensus 252 d~~~~~~~~lS~~~~~fiaGl-L~h~~~l~a~~~PtvNSYkRl~p~~~~~~~~~AP~--~~~WG~~NR~a~iRv~~---- 324 (435)
T TIGR03105 252 DDSDPNGLGLSKLAYHFIGGI-LHHAPALCAVLAPTVNSYKRLNAPRTTSGATWAPN--FISYGGNNRTHMVRIPD---- 324 (435)
T ss_pred CCCCCccccccHHHHHHHHHH-HHHHHHHHHHHCCCCccccccCCCcCCcCcccCCc--eeeccCCCCceeEeccC----
Confidence 1 12543 37999998 999999999976 999999995 78998 99999999999999992
Q ss_pred CCccEEEecCCCCCCCHHHHHHHHHHHhhcCC
Q 013478 394 QGKGYLEDRRPASNMDPYVVTSLLAETTILWE 425 (442)
Q Consensus 394 ~~~~r~E~R~pda~aNPYLv~Aail~agl~G~ 425 (442)
.+|||+|+||++|||||++||+|+||++|+
T Consensus 325 --~~riE~R~~da~aNPYL~lAailaAgl~Gi 354 (435)
T TIGR03105 325 --PGRFELRLADGAANPYLAQAAILAAGLDGI 354 (435)
T ss_pred --CCeeEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 469999999999999999999999999994
No 8
>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=3.3e-67 Score=514.37 Aligned_cols=240 Identities=25% Similarity=0.456 Sum_probs=202.3
Q ss_pred CCCHHHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCC-CCCC----CCCCCceeecccChhHHHHHHHHHHH
Q 013478 173 PTNKRHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPV-GAYP----GPQGPYYCGAGADKSFGRDIADAHYK 247 (442)
Q Consensus 173 ~~~pR~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~-~~~p----~~~g~yy~~~~~~~~~~~di~e~~~~ 247 (442)
+.|||++|+++++++++.|+++++|+|+|||||+.++. .++|. .+.+ ...++||.....+. .+++++++++
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 47999999999999999999999999999999998532 34441 2222 23566777776555 5889999999
Q ss_pred HHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeecccccc
Q 013478 248 ACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSM 327 (442)
Q Consensus 248 al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~ 327 (442)
+|+++||+|+++|+|++||||||++.|++++++||+++++|++||+||++||++|||||||+.++ +|||+|+|+|||+.
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 ALEQAGIPVEQIHHEVGPGQYEINLGPCDPLEAADNLVLFKEIIKEVARKHGLTATFMPKPFSGD-NGSGMHLHISLWDA 155 (259)
T ss_dssp HHHHCT--EEEEEEESSTTEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHTTEEEE-SSSSSTTS-S--BEEEEEEECHH
T ss_pred HHHHhhccccccccccchHhhccccccCcHHHHHHHHHHHHHHHHHHHHHcCCceeeeccccCCc-Cccchhhhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999996 89999999999974
Q ss_pred c-------cCC---chhh-HHHHHHhhHHHHHHHHhcccc---cccccCCCCCCCCCCCceeeccCCCcceeeecccCCC
Q 013478 328 R-------EEG---GYET-IKKAILNLSLRHKEHISAYGE---GNERRLTGKHETASIDSFSWGVANRGCSIRVGRETEK 393 (442)
Q Consensus 328 ~-------~~~---G~~~-~~~~iaGL~L~H~~al~a~~~---nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~~~~ 393 (442)
. +++ +++. .++||+|| |+|+++|++|++ ||||||+++.|+|+ +++||.+||+++||||... .
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-LKHAPALTAFTAPTVNSYKRLVPGSWAPT--YISWGYDNRSAAIRIPSGG-G 231 (259)
T ss_dssp HTTEETTBSTTSHGHHHHHHHHHHHHH-HCHHHHHHHCHSTSTTHHHHSSSTSSSSS--BEEEEESHTTSSEEE-HHH-H
T ss_pred cccccccccccccccccHHHHHHHHHH-HHHHHHHHhhhCccCcchhhCCCCcccee--ccchhhcccchhhheeccc-c
Confidence 1 122 3433 36899998 999999999964 99999999999998 9999999999999999871 1
Q ss_pred CCccEEEecCCCCCCCHHHHHHHHHHHh
Q 013478 394 QGKGYLEDRRPASNMDPYVVTSLLAETT 421 (442)
Q Consensus 394 ~~~~r~E~R~pda~aNPYLv~Aail~ag 421 (442)
++.+|||+|+||++|||||++|+||+||
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 2368999999999999999999999997
No 9
>COG3968 Uncharacterized protein related to glutamine synthetase [General function prediction only]
Probab=99.74 E-value=5.3e-17 Score=165.73 Aligned_cols=216 Identities=26% Similarity=0.344 Sum_probs=152.3
Q ss_pred ccceEeeeeeEEEecCCCC--CCC----CCCCCCCCCCCC-----Cceeeccc-ChhHHHHHHHHHHHHHHHcCCceeee
Q 013478 192 EVPWFGIEQEYTLLQQNVK--WPL----GWPVGAYPGPQG-----PYYCGAGA-DKSFGRDIADAHYKACLYAGINISGT 259 (442)
Q Consensus 192 ~~~~~G~E~EF~L~~~~~~--~p~----g~p~~~~p~~~g-----~yy~~~~~-~~~~~~di~e~~~~al~~aGI~i~~~ 259 (442)
.-..+|.||||||++.... +|. |.-.-|.|.+.| +||...+- -.+|+.|+-+++| ..||+...-
T Consensus 214 V~s~~GaEQEYFlvd~~~~~~RpDLi~tGRTLFGa~ppkGQEldDHYFGaipeRV~~FM~Dve~~Ly----aLGIpaKTr 289 (724)
T COG3968 214 VFSNVGAEQEYFLVDKKSYDERPDLIFTGRTLFGAPPPKGQELDDHYFGAIPERVSAFMKDVEKELY----ALGIPAKTR 289 (724)
T ss_pred hccCCCccceeEEechhhcccCcceeeechhhcCCCCCCCccccchhccccHHHHHHHHHHHHHHHH----HcCCccccc
Confidence 4578999999999987521 110 111123445555 46655553 2467888877755 599999999
Q ss_pred cCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhH---
Q 013478 260 NGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETI--- 336 (442)
Q Consensus 260 h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~--- 336 (442)
|.|++||||||.--+.++--|+||-.+.-.++|.+|.+||+++-.+-|||.|. ||||-|+|+|+-.. +|.|++
T Consensus 290 HNEVAPgQfEIApife~~N~A~DhqQL~M~vLk~tA~KhGlVCLLHEKPFAGi-NGSGKH~NWSmGtd---~g~NLLdPg 365 (724)
T COG3968 290 HNEVAPGQFEIAPIFESGNLATDHQQLVMEVLKKTALKHGLVCLLHEKPFAGI-NGSGKHNNWSMGTD---DGLNLLDPG 365 (724)
T ss_pred ccccCCCceeeeeeeccccccchHHHHHHHHHHHHHHhcceEEEeecCCccCc-CCCCCccccccccC---CCcccCCCC
Confidence 99999999999999999999999999999999999999999999999999996 99999999998653 222211
Q ss_pred -------------HHHHHhhHHHHHHHHhccc--ccccccCCCCCCCCC-CCce--------------------------
Q 013478 337 -------------KKAILNLSLRHKEHISAYG--EGNERRLTGKHETAS-IDSF-------------------------- 374 (442)
Q Consensus 337 -------------~~~iaGL~L~H~~al~a~~--~nsYkRL~~~~eap~-~~~~-------------------------- 374 (442)
..-|.++ -++.+-|.+-. +.|-.||.. .|+|. |-.+
T Consensus 366 D~PhdN~QFL~Fc~AvIkaV-dkY~~LlRa~~a~AsNDhRLGA-NEAPPAI~SVflGdqLedifEqi~~G~~~ssk~~g~ 443 (724)
T COG3968 366 DMPHDNKQFLLFCTAVIKAV-DKYADLLRASAANASNDHRLGA-NEAPPAIISVFLGDQLEDIFEQIEKGKATSSKGNGK 443 (724)
T ss_pred CCCCccceeehhhHHHHHHH-HHHHHHHHHHHhccCCcccccc-CCCCcceeEeeccchHHHHHHHHhcCCCcccccCcc
Confidence 1234453 55555554443 356788854 45543 2222
Q ss_pred -------------eeccCCCcceeeecccCCCCCccEEEecCCCCC---CCHHHHHHHHHHHhhcC
Q 013478 375 -------------SWGVANRGCSIRVGRETEKQGKGYLEDRRPASN---MDPYVVTSLLAETTILW 424 (442)
Q Consensus 375 -------------sWG~~NR~a~IRIp~~~~~~~~~r~E~R~pda~---aNPYLv~Aail~agl~G 424 (442)
--|..||+.+.-.. ..+||+|.++++ +-|-.|+-++++-.+..
T Consensus 444 mdLg~~vlP~v~kdAgDRNRTSPFAFT-------GNkFEFRavgSSqSvs~P~tVLN~~vAesl~~ 502 (724)
T COG3968 444 MDLGISVLPAVEKDAGDRNRTSPFAFT-------GNKFEFRAVGSSQSVSEPNTVLNVIVAESLSE 502 (724)
T ss_pred cccchhhccccccccccccCCCCceec-------cceeeEecCCcccccccchHHHHHHHHHHHHH
Confidence 12344444443332 358999999876 57999999888876654
No 10
>PF03951 Gln-synt_N: Glutamine synthetase, beta-Grasp domain; InterPro: IPR008147 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) has, currently, only been found in Bacteroides fragilis and in Butyrivibrio fibrisolvens. It is a hexamer of identical chains. 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, 0006542 glutamine biosynthetic process, 0006807 nitrogen compound metabolic process; PDB: 3NG0_A 2D3A_A 2D3C_E 2D3B_H 1LGR_C 2GLS_I 1F1H_B 1FPY_C 2LGS_D 1F52_A ....
Probab=99.55 E-value=9e-15 Score=120.51 Aligned_cols=67 Identities=34% Similarity=0.593 Sum_probs=58.5
Q ss_pred cCCCceeeeeeCCCCCC-CCC--CccccccCCC-CCCCCCCccEEEEeE--eeeecCCCCCC--eEEEEEEeecC
Q 013478 101 IDMRSKSKTISKPVEHP-SEL--PKWNYDGSST-GQAPGEDSEVILYPQ--AIFKDPFRGGN--NILVICDTYTP 167 (442)
Q Consensus 101 ~DlrGk~r~~~~p~~~~-~~l--~~~~fDGSs~-g~a~~~~sD~~L~Pd--~~~~~P~~~~~--~a~Vlcd~~~~ 167 (442)
+|+.|++|++.+|++.+ ++. .+++|||||+ ||+++++||++|+|| +++++||++++ +++|+||+|+|
T Consensus 10 ~D~~G~~~~~~i~~~~~~~~~~~~g~~fDGSSi~g~~~~~~SDm~l~Pd~~t~~~~P~~~~~~~~~~v~cdv~~P 84 (84)
T PF03951_consen 10 TDLFGRLKHVTIPASEFDEDALEDGIGFDGSSIRGFATIEESDMYLKPDPSTFFIDPWRPDPGKTARVICDVYDP 84 (84)
T ss_dssp E-TTSSEEEEEEEGCCESCSGGGS-EEEECCGTTTSSBSCCEEEEEEEEGGEEEESTTTSTT-TEEEEEEEEEST
T ss_pred EcCCCCcceEEEEHHHCCchHhhCCCCCCcccCcCcccCCCCCEEEecCcccEEECccCCCCceEEEEEEEeECc
Confidence 47778999999999888 554 4789999999 999999999999999 59999999865 99999999985
No 11
>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=98.60 E-value=2.9e-06 Score=85.06 Aligned_cols=183 Identities=19% Similarity=0.181 Sum_probs=112.9
Q ss_pred eEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCC
Q 013478 195 WFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGP 274 (442)
Q Consensus 195 ~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p 274 (442)
.+|+|.||+|.|..+. .+.+. .. .+++++.. ...| ..+.+|...+|.|++..|
T Consensus 1 t~GvE~E~~lvD~~t~---------~~~~~---------~~---~~~l~~~~---~~~~---~~~~~El~~~qiEi~t~p 53 (287)
T TIGR02050 1 TLGVEEELLLVDPHTY---------DLAAS---------AS---AVLIGACR---EKIG---AGFKHELFESQVELATPV 53 (287)
T ss_pred CceeeeeeeeEcCCcc---------CcCcc---------Ch---HHHHHhhh---hhcc---cccChhhhccEEEecCCC
Confidence 3799999999997632 11111 11 24444421 1122 348899999999999999
Q ss_pred Ch-hHHHHHHHHHHHHHHHHHHHHcCcEE---EecccCCCCCC-------------------------CCceeeeecccc
Q 013478 275 SV-GIDAGDHIWCSRYLLERITEQAGVVL---SLDPKPIEGDW-------------------------NGAGCHTNYSTK 325 (442)
Q Consensus 275 ~~-~i~aaD~l~~~R~iik~vA~~~Gl~a---TFmPKP~~g~~-------------------------~GSG~H~h~Sl~ 325 (442)
+. .-++.+.+.-.+..++++|+++|+.. .+.|. .+ | .-+|+|+|+++.
T Consensus 54 ~~~~~~l~~~l~~~~~~l~~~a~~~g~~l~~~G~hP~--~~-~~~~~~~~~~RY~~m~~~~g~~~~~~~~~g~hVhv~v~ 130 (287)
T TIGR02050 54 CTTLAEAAAQIRAVRARLVQAASDHGLRICGAGTHPF--AR-WRRQEVADNPRYQRLLERYGYVARQQLVFGLHVHVGVP 130 (287)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHcCCEEEeccCCCC--CC-CccCCCCcHHHHHHHHHHHHHHHHhHceeeEEEEeCCC
Confidence 84 66699999999999999999999753 33443 21 2 237899999996
Q ss_pred ccccCCchhhHHHHHHhhHHHHHHHHhcccccc------------cc-----cCCCCCCCCCCCceeec-----------
Q 013478 326 SMREEGGYETIKKAILNLSLRHKEHISAYGEGN------------ER-----RLTGKHETASIDSFSWG----------- 377 (442)
Q Consensus 326 ~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns------------Yk-----RL~~~~eap~~~~~sWG----------- 377 (442)
+. ...-..+..+ ..++|.+.|+++|| || ++ |..--| +..-+|.
T Consensus 131 d~------~~~i~~~n~l-~~~lP~llALsANSPf~~G~dtg~~s~R~~i~~~~-p~~G~p-~~f~~~~~y~~~~~~l~~ 201 (287)
T TIGR02050 131 SP------DDAVAVLNRL-LPWLPHLLALSASSPFWQGFDTGYASYRRNIFQAW-PTAGLP-PAFGSWDAFEAYFADLLE 201 (287)
T ss_pred CH------HHHHHHHHHH-HHHHHHHHHHHhCCccccCcCCchHHHHHHHHHhC-CCCCCC-CcCCCHHHHHHHHHHHHH
Confidence 42 1222334454 67788888887654 22 22 211112 1233452
Q ss_pred ---cCCCcce---eeecccCCCCCccEEEecCCCCCCCHHH--HHHHHHHHh
Q 013478 378 ---VANRGCS---IRVGRETEKQGKGYLEDRRPASNMDPYV--VTSLLAETT 421 (442)
Q Consensus 378 ---~~NR~a~---IRIp~~~~~~~~~r~E~R~pda~aNPYL--v~Aail~ag 421 (442)
..+++.. ||.. .+-+++|+|.+|+..++=- ++|+++.+-
T Consensus 202 ~g~i~~~~~iww~vRp~-----~~~~tvE~Rv~D~~~~~~~~~~~aal~~~L 248 (287)
T TIGR02050 202 TGVIDDDGDLWWDIRPS-----PHFGTVEVRVADTCLNLEHAVAIAALIRAL 248 (287)
T ss_pred cCCcCCCCeeEEEeccC-----CCCCCeeEEcCCCCCCHHHHHHHHHHHHHH
Confidence 2333333 3322 1357899999999887754 455554443
No 12
>PRK13517 carboxylate-amine ligase; Provisional
Probab=98.44 E-value=1.3e-05 Score=83.15 Aligned_cols=132 Identities=20% Similarity=0.158 Sum_probs=89.4
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEe
Q 013478 193 VPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQV 272 (442)
Q Consensus 193 ~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l 272 (442)
.+.+|+|.||+|+|..+. .+.+ + ..++++++ ... -.-..+..|..-+|.|++.
T Consensus 10 ~~tiGvE~E~~lVD~~t~---------~~~~---~----------~~~vl~~~----~~~-~~~~~i~~El~~~qiEi~t 62 (373)
T PRK13517 10 RPTLGVEWELLLVDPETG---------ELSP---R----------AAEVLAAA----GED-DEGPHLQKELLRNTVEVVT 62 (373)
T ss_pred CCeeEeeeeEeeECCCcC---------CcCc---c----------HHHHHHhc----ccc-cCCCcccccccCCEEEECC
Confidence 569999999999997532 1111 0 24454442 211 1124678899999999999
Q ss_pred CCCh-hHHHHHHHHHHHHHHHHHHHHcCcEE---EecccCCCCC----------------------CCCceeeeeccccc
Q 013478 273 GPSV-GIDAGDHIWCSRYLLERITEQAGVVL---SLDPKPIEGD----------------------WNGAGCHTNYSTKS 326 (442)
Q Consensus 273 ~p~~-~i~aaD~l~~~R~iik~vA~~~Gl~a---TFmPKP~~g~----------------------~~GSG~H~h~Sl~~ 326 (442)
+|+. .-++.+++.-.+..++++|+++|+.. ...|.....+ ..-+|+|+|+++.+
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 9984 66799999999999999999999653 3444421110 02579999999964
Q ss_pred cccCCchhhHHHHHHhhHHHHHHHHhcccccc
Q 013478 327 MREEGGYETIKKAILNLSLRHKEHISAYGEGN 358 (442)
Q Consensus 327 ~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns 358 (442)
. ...-..+..+ ..++|.+.|+++||
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 1122345565 77889999887654
No 13
>PRK13516 gamma-glutamyl:cysteine ligase; Provisional
Probab=98.40 E-value=1.3e-05 Score=83.14 Aligned_cols=187 Identities=16% Similarity=0.097 Sum_probs=113.1
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEe
Q 013478 193 VPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQV 272 (442)
Q Consensus 193 ~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l 272 (442)
.+.+|+|.||+|+|.++. .+.+. ..++++++ ..... -..+..|..-+|.|++.
T Consensus 11 ~~t~GvE~E~~LVD~~t~---------~~~~~-------------~~~vl~~~----~~~~~-~~~v~~El~~~qIEi~T 63 (373)
T PRK13516 11 PFTLGVELELQLVNPHDY---------DLTQD-------------SSDLLRAV----KNQPT-AGEIKPEITESMIEIAT 63 (373)
T ss_pred CCeeEEEEEEEeEcCCCc---------CcCcc-------------HHHHHHhc----ccccc-ccccChhhhCceEEEcC
Confidence 459999999999998632 12111 24555542 11100 12578899999999999
Q ss_pred CCC-hhHHHHHHHHHHHHHHHHHHHHcCcEEE---eccc------CCCCC----------------CCCceeeeeccccc
Q 013478 273 GPS-VGIDAGDHIWCSRYLLERITEQAGVVLS---LDPK------PIEGD----------------WNGAGCHTNYSTKS 326 (442)
Q Consensus 273 ~p~-~~i~aaD~l~~~R~iik~vA~~~Gl~aT---FmPK------P~~g~----------------~~GSG~H~h~Sl~~ 326 (442)
.|+ +.-++.+++.-.|..++++|+++|+..- .+|- +.... ..-.|||+|+.+.+
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 998 5666999999999999999999998642 3332 11110 02458999998854
Q ss_pred cccCCchhhHHHHHHhhHHHHHHHHhcccccc------------cc-----cCCCCCCCCCCCceeeccCC---------
Q 013478 327 MREEGGYETIKKAILNLSLRHKEHISAYGEGN------------ER-----RLTGKHETASIDSFSWGVAN--------- 380 (442)
Q Consensus 327 ~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns------------Yk-----RL~~~~eap~~~~~sWG~~N--------- 380 (442)
. -..+ ..+..+ ..++|++.|+.+|| || |+ |..--| +...+|..=.
T Consensus 144 ~-----~~av-~~~~~l-~~~lP~llALsAsSPf~~G~dTG~~S~R~~~~~~~-P~~G~p-p~~~~~~~y~~~~~~l~~~ 214 (373)
T PRK13516 144 G-----DDAL-YLLHGL-SRYVPHFIALSASSPYVQGVDTGFASARLNSVSAF-PLSGRA-PFVLNWQEFEAYFRKMSYT 214 (373)
T ss_pred H-----HHHH-HHHHHH-HhHhHHHHHHHhCCccccCcCCcchhHHHHHHhcC-CCCCCC-CCcCCHHHHHHHHHHHHHc
Confidence 2 1111 234444 66778888886543 33 32 322112 2244554100
Q ss_pred ----Ccc----eeeecccCCCCCccEEEecCCCCCCCHHHH--HHHHHHH
Q 013478 381 ----RGC----SIRVGRETEKQGKGYLEDRRPASNMDPYVV--TSLLAET 420 (442)
Q Consensus 381 ----R~a----~IRIp~~~~~~~~~r~E~R~pda~aNPYLv--~Aail~a 420 (442)
-.. -|| |. +.-+.+|.|.+|...++--+ +|+++.+
T Consensus 215 G~i~d~~~~~WdvR-p~----~~~~TvEiRv~D~~~~~~~~~~iaal~~a 259 (373)
T PRK13516 215 GVIDSMKDFYWDIR-PK----PEFGTVEVRVMDTPLTLERAAAIAAYIQA 259 (373)
T ss_pred CCcCCCCeeEEEec-cC----CCCCCeEEecCCCCCCHHHHHHHHHHHHH
Confidence 000 244 22 23578999999999999855 4444443
No 14
>PRK13515 carboxylate-amine ligase; Provisional
Probab=98.17 E-value=4.6e-05 Score=79.02 Aligned_cols=131 Identities=16% Similarity=0.096 Sum_probs=87.3
Q ss_pred cceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEe
Q 013478 193 VPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQV 272 (442)
Q Consensus 193 ~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l 272 (442)
.+.+|+|.||+|.|..+. .+.+. ..+++++ +... .-..+..|..-+|.|++.
T Consensus 5 ~~t~GvE~E~~lVD~~t~---------~l~~~-------------~~~~l~~----~~~~--~~~~i~~El~~~qiEi~T 56 (371)
T PRK13515 5 EFTLGIEEEYLLVDPETR---------DLRSY-------------PDALVEA----CRDT--LGEQVKPEMHQSQVEVGT 56 (371)
T ss_pred CCcceEeEeEEEecCCcc---------ccccc-------------HHHHHHh----chhh--cCCccCcchhccEEEECC
Confidence 568999999999998632 11111 1344433 1111 122688999999999999
Q ss_pred CCCh-hHHHHHHHHHHHHHHHHHHHHcCcEEE---ecccCCC------------------C----CCCCceeeeeccccc
Q 013478 273 GPSV-GIDAGDHIWCSRYLLERITEQAGVVLS---LDPKPIE------------------G----DWNGAGCHTNYSTKS 326 (442)
Q Consensus 273 ~p~~-~i~aaD~l~~~R~iik~vA~~~Gl~aT---FmPKP~~------------------g----~~~GSG~H~h~Sl~~ 326 (442)
.|+. .-++.+.+.-.+..+.++|+++|+... ..|.... + ...-+|+|+|+++.+
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 9985 556889999999999999999998763 3443110 0 012359999999964
Q ss_pred cccCCchhhHHHHHHhhHHHHHHHHhcccccc
Q 013478 327 MREEGGYETIKKAILNLSLRHKEHISAYGEGN 358 (442)
Q Consensus 327 ~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns 358 (442)
. ...-.++..+ ..++|.+.|+++||
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 1223344554 67788888887765
No 15
>PLN02611 glutamate--cysteine ligase
Probab=97.87 E-value=0.00019 Score=76.79 Aligned_cols=151 Identities=15% Similarity=0.112 Sum_probs=92.5
Q ss_pred HHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCc-
Q 013478 177 RHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGIN- 255 (442)
Q Consensus 177 R~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~- 255 (442)
+.-|-.-++.--..+-...+|+|+|.+.++.++.. |. +|+ -.+++++.+.. ..|.+
T Consensus 51 ~~~lv~~~~~gck~~~~~~iG~E~E~f~~~~~~~~---------pv---~y~--------~i~~lL~~l~~---~~gw~~ 107 (482)
T PLN02611 51 KEDLVAYLASGCKPKEKWRIGTEHEKFGFELATLR---------PM---KYD--------QIAQLLEGLAE---RFGWEK 107 (482)
T ss_pred HHHHHHHHHhcCCCCCCCeeEEeeeeeeccCCCCC---------CC---CHH--------HHHHHHHHHHH---hcCCce
Confidence 34444444432224556799999999999875321 11 222 13455554321 12210
Q ss_pred ------e-------eeecCCCCCCceEEEeCCC-hhHHHHHHHHHHHHHHHHHHHHcCcEE---EecccCCCCC------
Q 013478 256 ------I-------SGTNGEVMPGQWEYQVGPS-VGIDAGDHIWCSRYLLERITEQAGVVL---SLDPKPIEGD------ 312 (442)
Q Consensus 256 ------i-------~~~h~E~~pGQ~Ei~l~p~-~~i~aaD~l~~~R~iik~vA~~~Gl~a---TFmPKP~~g~------ 312 (442)
| ..+.-|-| ||+|++..|+ +.-++++.+...+..|+.+|+++|+.. -++|+....+
T Consensus 108 ~~e~g~iIgl~~~g~~ITlEPG-gQiElSt~p~~si~e~~~el~~~~~~l~~~a~~~Gl~l~g~G~hP~~~~~~~~i~pk 186 (482)
T PLN02611 108 IMEGDNIIGLKQDGQSVSLEPG-GQFELSGAPLETLHQTCAEVNSHLYQVKAVAEEMGIGFLGIGFQPKWSVADIPIMPK 186 (482)
T ss_pred eccCCceecccCCCCceEeccc-ceEEecccCcCCHHHHHHHHHHHHHHHHHHHHHcCCCeEccCCCCCCccccccCCCC
Confidence 0 24455777 9999999998 577799999999999999999999843 2344422110
Q ss_pred -------------------C--CCceeeeeccccccccCCchhhHHHHHHhhHHHHHHHHhcccccc
Q 013478 313 -------------------W--NGAGCHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEGN 358 (442)
Q Consensus 313 -------------------~--~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns 358 (442)
. .-+|+|+|+.+-+. -..++ -+.-+ +.+.|.++|+++||
T Consensus 187 ~RY~~M~~y~~~~g~~g~~MM~~t~g~QVhvd~~se-----ed~v~-~~~~~-~~l~Pvl~ALfANS 246 (482)
T PLN02611 187 GRYKIMRNYMPKVGSLGLDMMFRTCTVQVNLDFSSE-----QDMVR-KFRVG-LALQPIATALFANS 246 (482)
T ss_pred hHHHHHHHHHHHhhhhhhhhccceEEEEEEecCCCH-----HHHHH-HHHHH-HHHHHHHHHHHhCC
Confidence 0 35789999988541 11222 22233 77788888887654
No 16
>PRK13518 carboxylate-amine ligase; Provisional
Probab=97.55 E-value=0.00037 Score=72.08 Aligned_cols=131 Identities=17% Similarity=0.093 Sum_probs=85.1
Q ss_pred ceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeC
Q 013478 194 PWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPGQWEYQVG 273 (442)
Q Consensus 194 ~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~ 273 (442)
-.+|+|.||.|+|.. .. +.+. . ...++++ +..... -..+.+|...+|.||+.+
T Consensus 13 ~TlGvEeE~~lvD~~-~~---------~~~~--------~----~~~vl~~----~~~~~~-~~~~~~El~~~qvEi~T~ 65 (357)
T PRK13518 13 GTLGIEEEFFVVDEY-GR---------PTSG--------T----DELVYEH----EPPEIL-AGRLDHELFKFVIETQTP 65 (357)
T ss_pred CceEEEEEEEEECCC-CC---------cccc--------h----hHHHHHh----cccccC-CCcccccccCceEEEcCc
Confidence 379999999999975 31 1100 0 1233332 121111 235889999999999999
Q ss_pred CC-hhHHHHHHHHHHHHHHHHHHHHcCcEE---Eec-----------ccCC-------CCCC----CCceeeeecccccc
Q 013478 274 PS-VGIDAGDHIWCSRYLLERITEQAGVVL---SLD-----------PKPI-------EGDW----NGAGCHTNYSTKSM 327 (442)
Q Consensus 274 p~-~~i~aaD~l~~~R~iik~vA~~~Gl~a---TFm-----------PKP~-------~g~~----~GSG~H~h~Sl~~~ 327 (442)
+| +.-++.+++...|..+.++|+++|+.. -++ |||. .+.+ .=+|+|+|+.+.+.
T Consensus 66 ~~~~~~el~~~L~~~r~~l~~aa~~~g~~l~a~GthP~~~~~~~~~t~~~RY~~m~~~~~~~~~~~~~~G~HVHVg~~d~ 145 (357)
T PRK13518 66 LIEDPSEAGAALREVRDALVDHAAAHGYRIAAAGLHPAAKWRELEHAEKPRYRSQLDRIQYPQHRNTTAGLHVHVGVDDA 145 (357)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHcCCEEEecCCCCCCCccccCCCCCcHHHHHHHhcccchhcceeeEEEEEeCCCCH
Confidence 98 677799999999999999999999853 233 4441 0101 23689999988441
Q ss_pred ccCCchhhHHHHHHhhHHHHHHHHhcccccc
Q 013478 328 REEGGYETIKKAILNLSLRHKEHISAYGEGN 358 (442)
Q Consensus 328 ~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns 358 (442)
-..+ ..+..| ..++|++.|+.+||
T Consensus 146 -----d~av-~v~n~l-r~~LP~LlALsAnS 169 (357)
T PRK13518 146 -----DKAV-WIANEL-RWHLPILLALSANS 169 (357)
T ss_pred -----HHHH-HHHHHH-HhHHHHHHHHHcCC
Confidence 1111 123454 66779999987653
No 17
>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=97.47 E-value=0.0029 Score=67.29 Aligned_cols=154 Identities=19% Similarity=0.177 Sum_probs=92.2
Q ss_pred HHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCc-
Q 013478 177 RHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGIN- 255 (442)
Q Consensus 177 R~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~- 255 (442)
+.-|-+.++.-...+-...+|+|.|-|.|+.++..|. +|+.-.+ ..++++.+. ...|.+
T Consensus 5 ~~~l~~~~~~g~k~~~~~~iG~E~E~f~~~~~~~~~~------------~y~~~~g-----i~~~l~~l~---~~~g~~~ 64 (446)
T TIGR01436 5 RDDLIAYLAAGCKPKEQWRIGTEHEKFGFEKNTLRPM------------KYEQKGG-----IAELLNGIA---ERFGWQK 64 (446)
T ss_pred HHHHHHHHHhCCCcCCCCceEeeeeeeeeecCCCCCC------------CCCCchh-----HHHHHHHHH---hhcCCce
Confidence 4444455554333455679999999999987643222 2221111 245555432 122211
Q ss_pred ------e-------eeecCCCCCCceEEEeCCC-hhHHHHHHHHHHHHHHHHHHHHcCcEE---EecccCCCCC------
Q 013478 256 ------I-------SGTNGEVMPGQWEYQVGPS-VGIDAGDHIWCSRYLLERITEQAGVVL---SLDPKPIEGD------ 312 (442)
Q Consensus 256 ------i-------~~~h~E~~pGQ~Ei~l~p~-~~i~aaD~l~~~R~iik~vA~~~Gl~a---TFmPKP~~g~------ 312 (442)
| ..+.-|.| ||+|++..|+ +.-++++.+...+..++.+|+++|+.. -++|+....+
T Consensus 65 ~~e~g~~i~l~~~~~~itlEPg-gQlElS~~p~~~i~e~~~~l~~~~~~l~~~a~~~Gl~l~~~G~~P~~~~~~~~~~pk 143 (446)
T TIGR01436 65 VMEGDKIIGLKQDKQSISLEPG-GQFELSGAPLETIHETCDEINSHLYQVKEVAEEMGIGFLGLGFQPKWRREDIPLMPK 143 (446)
T ss_pred eccCCceeeecCCCCeEEEcCc-CeEEecccccCCHHHHHHHHHHHHHHHHHHHHhcCCCeEecCCCCCCCcccCCCCCc
Confidence 1 34445766 9999999998 567799999999999999999999853 2344422110
Q ss_pred -----------C----------CCceeeeeccccccccCCchhhHHHHHHhhHHHHHHHHhcccccc
Q 013478 313 -----------W----------NGAGCHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEGN 358 (442)
Q Consensus 313 -----------~----------~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns 358 (442)
+ .-+|+|+|+-.-+. ...++ -+.- .+...|.++|+++||
T Consensus 144 ~RY~~M~~~~~~~G~~g~~mm~~t~g~qVhld~~~e-----~d~v~-~~~~-~~~l~Pvl~ALfANS 203 (446)
T TIGR01436 144 GRYDIMRNYMPKVGKLGLDMMLRTCTVQVNLDFSSE-----ADMVR-KFRA-SLALQPLATALFANS 203 (446)
T ss_pred hHHHHHHHHHhhcchHHHHHhHhheeEEEeeCCCCH-----HHHHH-HHHH-HHHHHHHHHHHHhCC
Confidence 0 03677888776431 11121 2222 266788889887765
No 18
>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=97.33 E-value=0.0017 Score=67.63 Aligned_cols=93 Identities=17% Similarity=0.063 Sum_probs=65.2
Q ss_pred eecCCCCCCceEEEeCCC-hhHHHHHHHHHHHHHHHHHHHHcCc-E-EE-----ec-c-c--CCCC--------------
Q 013478 258 GTNGEVMPGQWEYQVGPS-VGIDAGDHIWCSRYLLERITEQAGV-V-LS-----LD-P-K--PIEG-------------- 311 (442)
Q Consensus 258 ~~h~E~~pGQ~Ei~l~p~-~~i~aaD~l~~~R~iik~vA~~~Gl-~-aT-----Fm-P-K--P~~g-------------- 311 (442)
++..|.-..|.|++.+|| +.-++.+++.-.|..+..+|+++|. . +. |+ | . |..+
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 456688899999999998 6677999999999999999999997 3 21 11 1 1 1111
Q ss_pred CCCCceeeeeccccccccCCchhhHHHHHHhhHHHHHHHHhccccc
Q 013478 312 DWNGAGCHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEG 357 (442)
Q Consensus 312 ~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~n 357 (442)
..+=+|||+|+.+-+. ...-..+..| ..++|+|.|+.+|
T Consensus 111 ~~~i~G~HVHVgv~d~------d~av~v~n~l-r~~LP~LlALSAs 149 (376)
T TIGR02048 111 QVVTASVHINIGIPDP------EELMRACRLV-RMEAPLFLALSAS 149 (376)
T ss_pred hheeeEEEEEcCCCCH------HHHHHHHHHH-HHHHHHHHHHhcC
Confidence 0134789999999652 1122345665 7788888888653
No 19
>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=97.32 E-value=0.001 Score=66.58 Aligned_cols=149 Identities=16% Similarity=0.070 Sum_probs=86.6
Q ss_pred eeecCCCCCCceEEEeCCC-hhHHHHHHHHHHHHHHHHHHHHcCcEEE---ecc-----------cC-------------
Q 013478 257 SGTNGEVMPGQWEYQVGPS-VGIDAGDHIWCSRYLLERITEQAGVVLS---LDP-----------KP------------- 308 (442)
Q Consensus 257 ~~~h~E~~pGQ~Ei~l~p~-~~i~aaD~l~~~R~iik~vA~~~Gl~aT---FmP-----------KP------------- 308 (442)
..+.+|..-+|.||+..|| +.-++.+.+.-.+..+..+|+++|+... +.| ||
T Consensus 35 ~~~~~E~~~~qvEi~t~p~~~~~el~~~l~~~~~~l~~~a~~~g~~l~~~G~~P~~~~~~~~~~~~~RY~~~~~~~~~~g 114 (288)
T PF04107_consen 35 GRVVTELPQSQVEISTPPCRSLAELREELRALRRALADAAAELGLRLVAAGTHPFARWRDQPITPKPRYRAMAEYFGRRG 114 (288)
T ss_dssp SEEEEESSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHCTTEEEE--SB-SS--GGGS---S-HHHHCHHHHHGGH-
T ss_pred CceeeccCCCEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEecCCCcCCCcccccCCCChhhhHHHHHHhhhh
Confidence 4788899999999999998 4556999999999999999999997643 344 21
Q ss_pred -CCCCCCCceeeeeccccccccCCchhhHHHHHHhhHHHHHHHHhccccc------------ccccCC-CCC--CCCCCC
Q 013478 309 -IEGDWNGAGCHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEG------------NERRLT-GKH--ETASID 372 (442)
Q Consensus 309 -~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~n------------sYkRL~-~~~--eap~~~ 372 (442)
+..+.--+|+|+|+++-+. -...-..+..+ ...+|.+.|+++| |||-.. ... .++.+.
T Consensus 115 ~~~~~~~~~g~hvhV~v~~~-----~e~~v~~~n~~-~~~~P~llALsANSP~~~G~~tg~~s~R~~~~~~~p~~~~~P~ 188 (288)
T PF04107_consen 115 VLARRMMTCGAHVHVGVDDG-----DEAAVRVMNAL-RPWLPVLLALSANSPFWEGRDTGYASYRSRIWERWPRCGGVPP 188 (288)
T ss_dssp SGCCSHHBHEEEEEEEESSS-----HHHHHHHHHHH-HTTHHHHHHHH--B-EETTEE-S-SBHGGGCCTTSTTECS-GG
T ss_pred hhhhhhhhcccceEEeCCCc-----cHHHHHHHHHH-HHHhHHHHHHHcCCccccCCcCCCcCcHHHHHHhCCCCCCCCC
Confidence 1111123489999999652 11222344454 6678888888654 343111 110 123333
Q ss_pred ceeecc--------CCCcceeeecccC-----CCCCccEEEecCCCCCCCHH
Q 013478 373 SFSWGV--------ANRGCSIRVGRET-----EKQGKGYLEDRRPASNMDPY 411 (442)
Q Consensus 373 ~~sWG~--------~NR~a~IRIp~~~-----~~~~~~r~E~R~pda~aNPY 411 (442)
.+.++. --++-+|...+.. .......+|.|..|+..+|=
T Consensus 189 ~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~r~~~~~~t~E~r~~d~~~~p~ 240 (288)
T PF04107_consen 189 AFDDWADYEEYVEYLLDTGVIFDRRMIWWDVRPSPRFPTVELRVHDSTLFPP 240 (288)
T ss_dssp GSSHHHCHHHHHHHHTTSTTESSGGGHHBSEEEETTTTEEEEEEEETT-EES
T ss_pred CCCchhHHHHHHHHHHhCCccccchhhHhhcCCCCCCChhHHHhhcCCCcHH
Confidence 555542 1122333322210 01123589999999999883
No 20
>COG2170 Uncharacterized conserved protein [Function unknown]
Probab=96.99 E-value=0.0051 Score=62.88 Aligned_cols=187 Identities=20% Similarity=0.247 Sum_probs=112.5
Q ss_pred ceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeec--CCCCCCceEEE
Q 013478 194 PWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTN--GEVMPGQWEYQ 271 (442)
Q Consensus 194 ~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h--~E~~pGQ~Ei~ 271 (442)
+.+|+|.||++.++.+ |+.++.. ..|++++ .=++...| +|.--.+-|+.
T Consensus 3 ltlGvE~E~~lvd~~g------------------~dl~~~s----~~ii~~~-------~~~~~~~~~~~e~~e~~vE~~ 53 (369)
T COG2170 3 LTLGVELEFQLVDPQG------------------YDLVGSS----DAIIEAL-------KGKVTAGHLKHEITESTVELA 53 (369)
T ss_pred cccceEEEEEecCCCC------------------ccccccc----HHHHHhc-------CCCCCCcchhHHHHHHhhccc
Confidence 6789999999998652 2223322 3444442 22333334 66666788888
Q ss_pred eCCChhHH-HHHHHHHHHHHHHHHHHHcCcEEE-ecccCCCCCC-------C------------------Cceeeeeccc
Q 013478 272 VGPSVGID-AGDHIWCSRYLLERITEQAGVVLS-LDPKPIEGDW-------N------------------GAGCHTNYST 324 (442)
Q Consensus 272 l~p~~~i~-aaD~l~~~R~iik~vA~~~Gl~aT-FmPKP~~g~~-------~------------------GSG~H~h~Sl 324 (442)
.+.|..+. |+=.+--.|..++++|.+||+... =-.-||.+ | | =.|.|+|+.+
T Consensus 54 t~vc~~~~eA~~~~r~~r~~l~q~a~d~gL~~~~~GtHPfad-w~~~~~~~~prY~~~ie~~~y~~~q~~v~G~HVHVGi 132 (369)
T COG2170 54 TGVCRLLAEAAAQLRALRDYLVQAASDHGLRICGGGTHPFAD-WRRQEVPDNPRYQRLIERTGYLGRQMTVAGQHVHVGI 132 (369)
T ss_pred chhhhhHHHHHHHHHHHHHHHHHHhhhcCceecccCCCchhh-hhhccCCCChhHHHHHHHhhhHHhheeeeeEEEEecC
Confidence 88886654 666777889999999999998742 12223322 2 1 2578888888
Q ss_pred cccccCCchhhHHHHHHhhHHHHHHHHhccccc------------ccccCCCCCCCC----CCCceeec-----------
Q 013478 325 KSMREEGGYETIKKAILNLSLRHKEHISAYGEG------------NERRLTGKHETA----SIDSFSWG----------- 377 (442)
Q Consensus 325 ~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~n------------sYkRL~~~~eap----~~~~~sWG----------- 377 (442)
-+. ...-..+-++ +.++|++.|+.++ |+|+-. -...| .+..-+|+
T Consensus 133 ~~~------d~~~~~l~~l-~~~~PhlLALSASSPf~~G~dTGyAS~R~~i-f~~~P~~g~pp~f~sw~~f~~~~~~~~~ 204 (369)
T COG2170 133 PSP------DDAMYLLHRL-LRYVPHLLALSASSPFWQGTDTGYASARANI-FSQLPTNGLPPAFQSWAAFEAFFRDQLE 204 (369)
T ss_pred CCH------HHHHHHHHHH-HhhhhHHHhhhcCCccccCccchhhhhhHhh-hhhCCcCCCCccccCHHHHHHHHHHHHH
Confidence 542 1122456777 9999999999652 343321 01111 11234554
Q ss_pred ---cCCCcc---eeeecccCCCCCccEEEecCCCCCCCHHHH--HHHHHHHhhc
Q 013478 378 ---VANRGC---SIRVGRETEKQGKGYLEDRRPASNMDPYVV--TSLLAETTIL 423 (442)
Q Consensus 378 ---~~NR~a---~IRIp~~~~~~~~~r~E~R~pda~aNPYLv--~Aail~agl~ 423 (442)
.+|..- .|| |. +.=+++|.|++|.-.||--+ +++++.|-+.
T Consensus 205 tG~I~~~~~lwwdIR-Ps----ph~gTlEvRi~D~~~~l~~~~aivaL~~Alv~ 253 (369)
T COG2170 205 TGTIDSMGDLWWDIR-PS----PHLGTLEVRICDTVLNLAELLAIVALIHALVV 253 (369)
T ss_pred hcccccccceEEecc-cC----CCCCceEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 233321 233 11 22479999999999999755 4556666543
No 21
>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=95.07 E-value=0.13 Score=53.92 Aligned_cols=89 Identities=15% Similarity=0.045 Sum_probs=58.1
Q ss_pred CceEEEeCCC-hhHHHHHHHHHHHHHHHHHHHHcCcEE---Eeccc---------C--------CC---CC----CCCce
Q 013478 266 GQWEYQVGPS-VGIDAGDHIWCSRYLLERITEQAGVVL---SLDPK---------P--------IE---GD----WNGAG 317 (442)
Q Consensus 266 GQ~Ei~l~p~-~~i~aaD~l~~~R~iik~vA~~~Gl~a---TFmPK---------P--------~~---g~----~~GSG 317 (442)
||+|++..|+ +.-++++.+.-.+..|+++|+++|+.. -+.|+ | +. |. .--+|
T Consensus 70 gQvELSt~P~~sl~el~~el~~~l~~l~~~a~~~Gl~lva~G~~P~~~~~~itpk~RY~~M~~~~~~~~G~~G~~MM~~t 149 (390)
T TIGR03444 70 GQLELSGPPADGLTAAVAALAADLAVLRAALAEDGLALVGLGADPLRPPRRVLPGPRYRAMEQFFATGIGPFGALMMCST 149 (390)
T ss_pred CEEEecCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEEeccCCCCCccCCCchHHHHHHHHHhhhccCchHHHHhhCc
Confidence 7999999998 666799999999999999999999853 34555 2 11 11 12577
Q ss_pred eeeeccccccccCCchhhHHHHHHhhHHHHHHHHhcccccc
Q 013478 318 CHTNYSTKSMREEGGYETIKKAILNLSLRHKEHISAYGEGN 358 (442)
Q Consensus 318 ~H~h~Sl~~~~~~~G~~~~~~~iaGL~L~H~~al~a~~~ns 358 (442)
||+|+++-... ....+.+.+.=. ..-.|.+.|+++||
T Consensus 150 asVQV~ld~~~---~e~D~~~k~rva-~aL~PvLlALfANS 186 (390)
T TIGR03444 150 ASVQVNLDAGT---DPAEWAERWRLA-HALGPVLIAAFANS 186 (390)
T ss_pred eeEEEccCCCC---CHHHHHHHHHHH-HHHHHHHHHHHhCC
Confidence 99999995421 012222211111 22267777776654
No 22
>COG3572 GshA Gamma-glutamylcysteine synthetase [Coenzyme metabolism]
Probab=79.88 E-value=4.1 Score=42.82 Aligned_cols=45 Identities=20% Similarity=0.146 Sum_probs=34.6
Q ss_pred ecCCCCCCceEEEeCCChhHH-HHHHHHHHHHHHHHHHHHcCcEEEe
Q 013478 259 TNGEVMPGQWEYQVGPSVGID-AGDHIWCSRYLLERITEQAGVVLSL 304 (442)
Q Consensus 259 ~h~E~~pGQ~Ei~l~p~~~i~-aaD~l~~~R~iik~vA~~~Gl~aTF 304 (442)
+.-|.+ ||+|+...|.+.|. ++-..----..||++|+..|+-..+
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 445777 99999999998776 5555555667899999999877553
No 23
>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=76.74 E-value=9.1 Score=37.60 Aligned_cols=111 Identities=13% Similarity=0.136 Sum_probs=69.0
Q ss_pred CCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHH---HH
Q 013478 263 VMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIK---KA 339 (442)
Q Consensus 263 ~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~---~~ 339 (442)
--|-+.=|.|.|.+++.-.|=+-.++ .+|++-++.|+.. | || .. -|.|+|+.+-+... -+....+ ++
T Consensus 100 e~PD~~vfDLDP~~~~~f~~v~~~A~-~~r~~L~~lgL~s-~-~K--TS--G~kGlHV~vPl~~~---~~~~~vr~fa~~ 169 (231)
T cd04863 100 GPPDRLVFDLDPGEPAGLVECARVAL-WLRDRLAALGLAS-F-PK--TS--GSKGLHLYVPLDGP---VSSDQTKEFAKA 169 (231)
T ss_pred CCCCEEEEECCCCCCCCHHHHHHHHH-HHHHHHHHcCCcc-c-eE--CC--CCCeEEEEEEcCCC---CCHHHHHHHHHH
Confidence 35999999999998876666555554 5899999999874 4 66 22 48899999999753 2333444 44
Q ss_pred HHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 340 ILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 340 iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
|+-...+..|.+.. ..-.|.-.++. . ++-|-.++|+..+=-|-+
T Consensus 170 ~A~~l~~~~P~~~t--~~~~k~~R~gr---v--fiDylqN~~g~T~vapYS 213 (231)
T cd04863 170 LARELEREHPDLVV--SRMTKSLRAGK---V--FVDWSQNDAAKTTIAPYS 213 (231)
T ss_pred HHHHHHHHCchhhh--hHhhHhhCCCc---E--EEECccCCCCCeEEeccc
Confidence 55432333344433 22112111221 2 788888888876655544
No 24
>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=76.53 E-value=15 Score=36.38 Aligned_cols=110 Identities=13% Similarity=0.166 Sum_probs=68.3
Q ss_pred CCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhH---HHHH
Q 013478 264 MPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETI---KKAI 340 (442)
Q Consensus 264 ~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~---~~~i 340 (442)
-|.+.=|.+.|.++..-.|=+-.+ ..+|++.++.|+.. | || .. -|.|+|+.+-+... -+.... .++|
T Consensus 113 ~PD~lvfDLDP~~~~~f~~v~~~A-~~~r~~L~~lgL~~-f-~K--TS--G~kGlHV~vPl~~~---~~~~~~r~fa~~i 182 (245)
T TIGR02778 113 KPDRIVFDLDPGPGVAWKLVVEAA-QLIRELLDELGLES-F-VK--TS--GGKGLHVYVPLRPT---LSWDEVKDFAKAL 182 (245)
T ss_pred CCCEEEEECCCCCCCCHHHHHHHH-HHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEECCCC---CCHHHHHHHHHHH
Confidence 589999999999987655555444 45899999999873 4 66 32 48899999999753 233333 3455
Q ss_pred HhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 341 LNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 341 aGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
+....+..|.+......--+| ++. . ++-|..++|+..+=-|-+
T Consensus 183 A~~l~~~~Pd~~t~~~~k~~R--~gk---v--fiDylqN~~g~T~vapYS 225 (245)
T TIGR02778 183 AQALAQQMPDRFTAEMSKKNR--VGK---I--FVDYLRNARGKTTVAPYS 225 (245)
T ss_pred HHHHHHHCchhhhhHhhHHhC--CCC---E--EEECccCCCCCeEEeccc
Confidence 554233334433221111122 221 2 788888888876655543
No 25
>KOG0683 consensus Glutamine synthetase [Amino acid transport and metabolism]
Probab=76.40 E-value=0.91 Score=46.96 Aligned_cols=58 Identities=10% Similarity=-0.124 Sum_probs=46.6
Q ss_pred cccccCCCCCCCCCCCceeeccCCCcceeeecccCCCCCccEEEecCCCCCCCHHHHHHHHHHHhhcC
Q 013478 357 GNERRLTGKHETASIDSFSWGVANRGCSIRVGRETEKQGKGYLEDRRPASNMDPYVVTSLLAETTILW 424 (442)
Q Consensus 357 nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~~~~~~~~r~E~R~pda~aNPYLv~Aail~agl~G 424 (442)
++++|.....+. .+||.+|+-...+ +.. .....++-...+|+|||+.++.+++++.+|
T Consensus 285 s~rh~~hi~~yd-----p~~G~dN~rrltg-~hE----t~~i~~Fs~GvAnr~~siri~r~va~~~~G 342 (380)
T KOG0683|consen 285 SKRHREHIAAYD-----PKGGKDNERRLTG-RHE----TGSIDNFSWGVANRNPSIRIPRTVAAEGKG 342 (380)
T ss_pred chhhhhhhhhcC-----ccCCccchhhhcC-CCc----cccccccccccccCCceeeechhhhccccc
Confidence 678888776553 5699999998888 221 245677777888899999999999999999
No 26
>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=74.76 E-value=6.7 Score=30.90 Aligned_cols=65 Identities=20% Similarity=0.194 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHcCCceeeecCCCCC------CceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecc
Q 013478 240 DIADAHYKACLYAGINISGTNGEVMP------GQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDP 306 (442)
Q Consensus 240 di~e~~~~al~~aGI~i~~~h~E~~p------GQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmP 306 (442)
.++..+.+.|...|++|..+..+..+ ++|.+.+.-.-+ .-. +.--++.-++++|+++|+.++|.|
T Consensus 11 Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p-~~~-~~~~l~~~l~~l~~~~~~~~~~~~ 81 (81)
T cd04869 11 GIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALP-AGT-DLDALREELEELCDDLNVDISLEP 81 (81)
T ss_pred CHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecC-CCC-CHHHHHHHHHHHHHHhcceEEecC
Confidence 34555666688899999999876655 777544332211 111 244678889999999999998864
No 27
>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=70.77 E-value=27 Score=34.24 Aligned_cols=116 Identities=12% Similarity=0.088 Sum_probs=69.5
Q ss_pred CCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHHHHH
Q 013478 261 GEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKAI 340 (442)
Q Consensus 261 ~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~i 340 (442)
..--|.+.=|.|.|.+++.-.|- +-+=..+|++.++.|+.. | || .. -|.|+|+.+-|....+-+....+.++|
T Consensus 94 ~~e~PD~lvfDLDP~~~~~f~~v-~~~A~~~r~~L~~lgL~~-~-~K--TS--G~kGlHV~vPl~~~~~~~~~r~fa~~l 166 (227)
T cd04862 94 RLERPDRIVFDLDPGPGVPWKAV-VEAALLVRELLDELGLES-F-VK--TS--GGKGLHVVVPLAPRAGWDEVKAFAKAL 166 (227)
T ss_pred CCCCCCEEEEECCCCCCCCHHHH-HHHHHHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEEcCCCCCHHHHHHHHHHH
Confidence 33469999999999988655444 445567888999999874 4 66 32 488999999997531111123334455
Q ss_pred HhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 341 LNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 341 aGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
+...-+..|.+.... -.|...++. . ++-|..++|+..+=-|.+
T Consensus 167 A~~l~~~~P~~~t~~--~~k~~R~gk---v--fiDylqN~~g~T~vapYS 209 (227)
T cd04862 167 AQHLARTNPDRFVAT--MGKAKRVGK---I--FIDYLRNGRGATAVAPYS 209 (227)
T ss_pred HHHHHHHCchhhhHH--hhHHhCCCc---E--EEECccCCCCCeEEeccc
Confidence 543223334433221 112222221 2 788888888876665544
No 28
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=70.72 E-value=9.5 Score=30.26 Aligned_cols=62 Identities=23% Similarity=0.244 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEe
Q 013478 240 DIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSL 304 (442)
Q Consensus 240 di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTF 304 (442)
.++.++.++|...|.+|..++.-...|+|-+.+.-.-+ .|+.-..+..+++++++.|+.+.|
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 45666777788999999999999999998777654433 567778899999999999999876
No 29
>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=69.19 E-value=44 Score=32.25 Aligned_cols=22 Identities=18% Similarity=0.394 Sum_probs=18.7
Q ss_pred ccEEEecCCCCCCCHHHHHHHH
Q 013478 396 KGYLEDRRPASNMDPYVVTSLL 417 (442)
Q Consensus 396 ~~r~E~R~pda~aNPYLv~Aai 417 (442)
.+.+|+|.|.++.|+--+.+.+
T Consensus 224 ~~TvEFR~~~~s~d~~~~~~wi 245 (252)
T PF12224_consen 224 RPTVEFRQPNGSLDAEEISAWI 245 (252)
T ss_pred CCeEEEecCCCCCCHHHHHHHH
Confidence 4589999999999998887655
No 30
>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=68.89 E-value=17 Score=35.59 Aligned_cols=111 Identities=10% Similarity=0.156 Sum_probs=69.1
Q ss_pred CCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhH---HH
Q 013478 262 EVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETI---KK 338 (442)
Q Consensus 262 E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~---~~ 338 (442)
.--|-+.=|.+.|. +. .=++++-+=..+|++-++.|+.+ | || .. -|.|+|+.+-|... -+.... .+
T Consensus 97 ~e~PD~~vfDLDP~-~~-~f~~v~~~A~~~r~~L~~~gL~~-f-~K--TS--G~kGlHv~vPl~~~---~~~~~~r~fa~ 165 (228)
T cd04864 97 LEHPDLMVFDLDPS-AD-DIEAVRTAALAVRELLDELGLPS-F-VK--TT--GSRGFHVVVPLDGR---GDFDDVRAFAA 165 (228)
T ss_pred CCCCCEEEEecCCC-CC-CHHHHHHHHHHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEEcCCC---CCHHHHHHHHH
Confidence 34589999999998 44 44555666678899999999874 4 66 32 48899999999763 233333 44
Q ss_pred HHHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 339 AILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 339 ~iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
+|+-..-+..|.+... .-.|...++. . ++-|..++|+..+=-|-+
T Consensus 166 ~lA~~l~~~~P~~~t~--~~~k~~R~gr---v--fiDylqN~~g~T~vapYS 210 (228)
T cd04864 166 EAADALAKRDPDLLTT--EARKAKRGDR---V--FLDIGRNAYGQTAVAPYA 210 (228)
T ss_pred HHHHHHHHHCchhhhH--HhhHHhCCCc---E--EEECccCCCCCeEEeccc
Confidence 5555423333443322 2222222221 2 788888888876655544
No 31
>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=66.10 E-value=38 Score=33.26 Aligned_cols=114 Identities=17% Similarity=0.208 Sum_probs=68.0
Q ss_pred CCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHHHHHHh
Q 013478 263 VMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKAILN 342 (442)
Q Consensus 263 ~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaG 342 (442)
--|-+.=|.+.|.+++.-.|= +-+=..+|++-++.|+.+ | || .. .|.|+|+.+-+....+-+....+.++|+-
T Consensus 96 e~PD~lvfDLDP~~~~~f~~v-~~~A~~vr~~L~~lgL~~-f-~K--TS--G~kGlHV~vPl~~~~~~~~~r~fa~~iA~ 168 (227)
T cd04861 96 ERPDRLVFDLDPGPGVPFEDV-VEAALLLRELLDELGLES-F-PK--TS--GGKGLHVYVPLAPRYTWDEVRAFAKALAR 168 (227)
T ss_pred CCCCEEEEECCCCCCCCHHHH-HHHHHHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 358999999999988755443 445567888889999874 4 66 32 48899999999753111112333445555
Q ss_pred hHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 343 LSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 343 L~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
...+..|.+......--+| ++. . ++-|..++|+..+=-|-+
T Consensus 169 ~l~~~~P~~~t~~~~k~~R--~gr---v--fiDy~qN~~g~T~vapYS 209 (227)
T cd04861 169 ELARRLPDLFTAEMAKAKR--GGK---I--FVDYLQNARGKTTVAPYS 209 (227)
T ss_pred HHHHHCchhhhhHhhHHhC--CCC---E--EEECccCCCCCeEEeccc
Confidence 4233334443322111122 221 2 778888888776655544
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=65.70 E-value=14 Score=29.04 Aligned_cols=65 Identities=12% Similarity=0.115 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecc
Q 013478 240 DIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDP 306 (442)
Q Consensus 240 di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmP 306 (442)
-|+.++.+.+...|++|...+.-...|+|-+.+.-.-+ ...++-.++..+..+|++.|+.+++.|
T Consensus 11 Giv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p--~~~~~~~l~~~l~~l~~~l~l~i~~~~ 75 (75)
T cd04870 11 GLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIP--DSADSEALLKDLLFKAHELGLQVRFEP 75 (75)
T ss_pred CHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcC--CCCCHHHHHHHHHHHHHHcCceEEEeC
Confidence 46677777788999999999877777777665532211 111345688999999999999998754
No 33
>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=64.75 E-value=11 Score=30.70 Aligned_cols=67 Identities=13% Similarity=0.148 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEeccc
Q 013478 240 DIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPK 307 (442)
Q Consensus 240 di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPK 307 (442)
.++.++.+.|...|++|...+..+..++|.+.+.-.-+ ...+++-.++.-++++|++.|+.+++-+.
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 45666666788899999999998888877665433211 11344667889999999999999998654
No 34
>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=64.25 E-value=49 Score=32.40 Aligned_cols=111 Identities=11% Similarity=0.079 Sum_probs=68.2
Q ss_pred CCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeecccc-ccccCCchhhHHH---
Q 013478 263 VMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTK-SMREEGGYETIKK--- 338 (442)
Q Consensus 263 ~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~-~~~~~~G~~~~~~--- 338 (442)
--|.+.=|.+.|.+++.-.| ++-+=..+|++.++.|+.. | || .. -|.|+|+.+-+. .. -.....+.
T Consensus 91 e~PD~lvfDLDP~~~~~f~~-v~~~A~~vr~~L~~lgL~~-f-~K--TS--G~kGlHV~vPl~~~~---~~~~~~r~fa~ 160 (223)
T cd04866 91 NKPSEIVFDLDPPSRDHFSL-AVEAANLLKEILDALGLTS-F-VK--TS--GNKGLQVYIPLPDNK---FTYDETRLFTE 160 (223)
T ss_pred CCCCeEEEECCCCCCCCHHH-HHHHHHHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEEcCCCC---CCHHHHHHHHH
Confidence 36999999999998865444 3455567899999999874 5 66 32 488999999997 32 23344444
Q ss_pred HHHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 339 AILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 339 ~iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
+|+-...+..|.+. +..-.|...++. . ++-|..++|+..+=-|-+
T Consensus 161 ~iA~~l~~~~P~~~--t~~~~k~~R~gk---V--fiDylqN~~g~T~vapYS 205 (223)
T cd04866 161 FIAEYLCQQFPELF--TTERLKKNRHNR---L--YLDYVQHAEGKTIIAPYS 205 (223)
T ss_pred HHHHHHHHHCchhh--hHHhhHHhCCCC---E--EEECccCCCCCeEEeccc
Confidence 44443222333332 222112222221 2 788888888877665544
No 35
>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=62.60 E-value=59 Score=27.12 Aligned_cols=94 Identities=12% Similarity=0.049 Sum_probs=54.0
Q ss_pred HHHHHHHHHhhhcCCccceEeeeeeEEEecCCCCCCCCCCCCCCCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCce
Q 013478 177 RHRAAEIFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLGWPVGAYPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINI 256 (442)
Q Consensus 177 R~~Lk~~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g~p~~~~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i 256 (442)
...-+++++.+++.|..+..-.+.||++.-.+. +-++.+...+...|..|
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 344567888888889999989999998875431 22333444567899999
Q ss_pred eeecC--CCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcE
Q 013478 257 SGTNG--EVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVV 301 (442)
Q Consensus 257 ~~~h~--E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~ 301 (442)
+.... |-+.+.|.+.+.....+.. +.+.-.-.-+-.+|+++|..
T Consensus 53 ~~~~~~~~d~~~~~~~~~~~~~~~~~-~~I~~~~~~l~~lA~~~~g~ 98 (104)
T PF06877_consen 53 ESAEEDEEDGDGPYCLDISREMVLDY-EDINAITQELEDLAKEFGGE 98 (104)
T ss_dssp B----B-SS-SSBEEEEEEEEE-S-H-HHHHHHHHHHHHHHHHHT-E
T ss_pred EEeecccCCCCceEEEEEEEecCCCH-HHHHHHHHHHHHHHHHhCcE
Confidence 88765 6678899999877655543 33334445566788888865
No 36
>PRK02471 bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional
Probab=62.26 E-value=8.7 Score=43.92 Aligned_cols=37 Identities=8% Similarity=-0.067 Sum_probs=22.4
Q ss_pred ecCCCCCCceEEEeCCChh-HHHHHHHHHHHHHHHHHH
Q 013478 259 TNGEVMPGQWEYQVGPSVG-IDAGDHIWCSRYLLERIT 295 (442)
Q Consensus 259 ~h~E~~pGQ~Ei~l~p~~~-i~aaD~l~~~R~iik~vA 295 (442)
+.+|..-.|.|+...++.- -++.+.|-..|..+.+.+
T Consensus 54 ittdfsesqlE~iTp~~~~~~~~~~~L~~l~~~~~~~~ 91 (752)
T PRK02471 54 IQTDFSESQLELITPVADSIEEVYRFLGALHDVASRSL 91 (752)
T ss_pred cCchhHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence 4455556666666666643 336666666666666665
No 37
>PRK00194 hypothetical protein; Validated
Probab=57.62 E-value=18 Score=29.36 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecc
Q 013478 240 DIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDP 306 (442)
Q Consensus 240 di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmP 306 (442)
-++.++.+.|...|++|..++.....|.+.+.+.-.-+ ...++.--.+.-+++++++.|+.++|-+
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 45566666788899999999998877777763221111 1122344577888999999999999854
No 38
>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=55.00 E-value=45 Score=32.76 Aligned_cols=113 Identities=12% Similarity=0.141 Sum_probs=67.6
Q ss_pred CCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHHHHHHhh
Q 013478 264 MPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKAILNL 343 (442)
Q Consensus 264 ~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL 343 (442)
-|.+.=|.|.|.+++.-.|- +-+=..+|++.++.|+.. | || .. -|.|+|+.+-+....+-+....+.++|+-.
T Consensus 98 ~PD~lvfDLDP~~~~~f~~v-~~~A~~vr~~L~~lgL~s-f-~K--TS--G~kGlHv~vPl~~~~~~~~~r~fa~~iA~~ 170 (228)
T cd04865 98 HPDELVIDLDPQPGTSFEDV-VEVALLVREVLDELGLRG-Y-PK--TS--GARGLHIYVPIAPRYTFEEVRRFAELLARE 170 (228)
T ss_pred CCCEEEEECCCCCCCCHHHH-HHHHHHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 58999999999988755544 445567899999999874 5 66 32 488999999996531111123334455553
Q ss_pred HHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 344 SLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 344 ~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
..+..|.+. +.+-.|.-.++. . ++-|..++|+..+=-|-+
T Consensus 171 l~~~~P~~~--t~~~~k~~R~gr---v--fiDylqN~~g~T~vapYS 210 (228)
T cd04865 171 VERRLPDLA--TTERWKKERGGR---V--YLDYLQNARGKTLAAPYS 210 (228)
T ss_pred HHHHCchhh--hhHhhHHhCCCC---E--EEECccCCCCCeEEeccc
Confidence 223334433 222112222221 2 788888888866655543
No 39
>KOG0558 consensus Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion]
Probab=50.36 E-value=15 Score=38.24 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHcCcEEEeccc
Q 013478 280 AGDHIWCSRYLLERITEQAGVVLSLDPK 307 (442)
Q Consensus 280 aaD~l~~~R~iik~vA~~~Gl~aTFmPK 307 (442)
-+|.++-+|.-+|.+|.+.|+..||||-
T Consensus 275 n~~sLvklr~elk~~a~e~~IKltfmPf 302 (474)
T KOG0558|consen 275 NCDSLVKLRQELKENAKERGIKLTFMPF 302 (474)
T ss_pred ChHHHHHHHHHHhhhhhhcCceeeehHH
Confidence 3699999999999999999999999985
No 40
>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]
Probab=44.61 E-value=1.3e+02 Score=30.72 Aligned_cols=72 Identities=17% Similarity=0.328 Sum_probs=50.4
Q ss_pred HHHcCCceeeecCCCC----CC-ceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeecc
Q 013478 249 CLYAGINISGTNGEVM----PG-QWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYS 323 (442)
Q Consensus 249 l~~aGI~i~~~h~E~~----pG-Q~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~S 323 (442)
++...|++.-.+++.. |+ |.-|.+.|.+++.-.--+-.++ .+|+.-++.|+. +| || .. .|.|.|+-.-
T Consensus 104 ~q~galE~H~w~~~~~~~e~pd~r~VfDLDP~~gv~~~~vveaA~-~lr~~Ld~lGL~-~f-~K--TS--GGKG~Hv~~P 176 (299)
T COG3285 104 AQQGALEFHPWGATIDDLEHPDERIVFDLDPGPGVAFAEVVEAAL-ELRDLLDELGLV-SF-PK--TS--GGKGLHVYVP 176 (299)
T ss_pred HHhceEEeecCCCcccccCCCCcceeEecCCCCCCCHHHHHHHHH-HHHHHHHHcCCc-cc-ee--cc--CCCeeEEEEe
Confidence 4445566655554443 67 8889999998886654444444 889999999986 56 66 32 4899999988
Q ss_pred cccc
Q 013478 324 TKSM 327 (442)
Q Consensus 324 l~~~ 327 (442)
|...
T Consensus 177 L~~~ 180 (299)
T COG3285 177 LAPK 180 (299)
T ss_pred cCCc
Confidence 8763
No 41
>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=44.09 E-value=65 Score=25.50 Aligned_cols=64 Identities=14% Similarity=0.103 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEec
Q 013478 239 RDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLD 305 (442)
Q Consensus 239 ~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFm 305 (442)
.-|+.++.+.|.+.|.+|...+.-...|+|-+-+.-... .+..--.+..++.+|+++|+.++..
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 356677777788999999999888888888654443322 1345567888899999999988753
No 42
>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=42.59 E-value=1e+02 Score=34.15 Aligned_cols=111 Identities=14% Similarity=0.134 Sum_probs=65.0
Q ss_pred CCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHHHH---
Q 013478 263 VMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKA--- 339 (442)
Q Consensus 263 ~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~--- 339 (442)
--|.+.=|.|.|.++..-.|-+- +=..+|++-++.|+.. | || .. -|.|+|+.+-|... .-+....+.|
T Consensus 389 ~~Pd~~v~DLDP~~~~~f~~v~~-~A~~~r~~L~~~gl~~-~-~K--tS--G~kGlhv~vPl~~~--~~~~~~~~~fa~~ 459 (552)
T TIGR02776 389 DKPDRIVFDLDPPPGVAFKLAVE-AAQLMKQLLDELGLVS-F-VK--TS--GGKGLHVVVPLRPN--TFTWDETKLFAKA 459 (552)
T ss_pred CCCCEEEEECCCCCCCCHHHHHH-HHHHHHHHHHHcCCcc-c-eE--cc--CCCeEEEEEEcCCC--CCCHHHHHHHHHH
Confidence 36899999999998865555444 4445899999999874 4 66 22 48899999999751 1234444444
Q ss_pred HHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeecc
Q 013478 340 ILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGR 389 (442)
Q Consensus 340 iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~ 389 (442)
|+-...+..|.+. +..-.+.-.++. . ++-|-.++|+..+=-|.
T Consensus 460 ~a~~~~~~~P~~~--t~~~~k~~R~gr---v--~iDy~qn~~~~T~~apY 502 (552)
T TIGR02776 460 IAEYLARQFPERF--TTEMGKKNRVGR---I--FIDYLRNARGKTTVAPY 502 (552)
T ss_pred HHHHHHHHCccee--hhhhhHhhCCCC---E--EEEcccCCCCCeEEecc
Confidence 4443222233332 221111111221 2 67777777775554443
No 43
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=41.87 E-value=2.2e+02 Score=33.42 Aligned_cols=123 Identities=13% Similarity=0.168 Sum_probs=70.7
Q ss_pred HHcCCceeeecCC----CCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeecccc
Q 013478 250 LYAGINISGTNGE----VMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTK 325 (442)
Q Consensus 250 ~~aGI~i~~~h~E----~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~ 325 (442)
+..-|++.-.++- --|.+.=|.|.|.+++.-.+- +-+=..+|++.++.|+. +| || .. -|.|+|+.+-|.
T Consensus 665 n~~~iE~H~w~~~~~~~~~Pd~lvfDLDP~~~~~f~~v-~~aA~~~r~~L~~lgL~-sf-~K--TS--G~kGlHv~vPl~ 737 (860)
T PRK05972 665 QMGAVELHTWNATPDRIEVPDRLVFDLDPGPGVPWKAV-VEAARLMRTRLDELGLE-SF-LK--TS--GGKGLHVVVPLA 737 (860)
T ss_pred HhCcEEeecCCCCCCCCCCCCEEEEECCCCCCCCHHHH-HHHHHHHHHHHHHcCCc-ee-eE--CC--CCCeEEEEEEcC
Confidence 3334555544432 258999999999988765444 44445689999999987 35 66 32 488999999997
Q ss_pred ccccCCchhhHH---HHHHhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeecc
Q 013478 326 SMREEGGYETIK---KAILNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGR 389 (442)
Q Consensus 326 ~~~~~~G~~~~~---~~iaGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~ 389 (442)
.. -++...+ ++|+-...+..|.+ |+....+...++. . ++-|-.++|+..+=-|.
T Consensus 738 ~~---~~~~~~~~fa~~ia~~l~~~~P~~--~t~~~~k~~R~gr---i--fiDylqN~~g~T~vapY 794 (860)
T PRK05972 738 RR---LDWDEVKAFAQAVCQHMARDLPER--FLAKMGKKNRVGK---I--FLDYLRNGRGATTVAAL 794 (860)
T ss_pred CC---CCHHHHHHHHHHHHHHHHHHCchh--ehhhhhHhhCCCc---E--EEEccccCCCCeEEecc
Confidence 53 2344444 44444322222333 3322222222221 2 66677666665554443
No 44
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=32.91 E-value=1.1e+02 Score=34.36 Aligned_cols=111 Identities=14% Similarity=0.137 Sum_probs=65.1
Q ss_pred CCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHH---HHH
Q 013478 264 MPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIK---KAI 340 (442)
Q Consensus 264 ~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~---~~i 340 (442)
-|.+.=|.+.|.+++.-.|- +-+=..+|++-++.|+. +| || .. -|.|+|+.+-|.... -.....+ ++|
T Consensus 431 ~pd~~v~DLDP~~~~~~~~v-~~~A~~~r~~L~~~gl~-~~-~k--tS--G~kGlhv~vPl~~~~--~~~~~~~~fa~~~ 501 (610)
T PRK09633 431 RPTEIVFDLDPPSRDEFPLA-VEAALELKRLFDQFGLT-SF-VK--TS--GNKGLQLYIPLSKNA--FTYEETRLFTEFI 501 (610)
T ss_pred CCCEEEEECCCCCCCCHHHH-HHHHHHHHHHHHHcCCc-cc-eE--cc--CCCeEEEEEEcCCCC--CCHHHHHHHHHHH
Confidence 58999999999988755443 34455778888999987 35 66 32 488999999996520 1233343 445
Q ss_pred HhhHHHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeeccc
Q 013478 341 LNLSLRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGRE 390 (442)
Q Consensus 341 aGL~L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~~ 390 (442)
|-...+..|.+ |+..-.+...++. . ++-|-.++|+..+=-|.+
T Consensus 502 a~~~~~~~P~~--~t~~~~k~~R~gr---v--fiDy~qN~~~~T~~apYS 544 (610)
T PRK09633 502 AEYLCSQFPEL--FTTERLKKNRGNR---L--YLDYVQHAEGKTIIAPYS 544 (610)
T ss_pred HHHHHHHCcce--ehhhhhHhhCCCC---E--EEEcccCCCCCeEEeccc
Confidence 44322222333 2322222222221 2 677777777765554433
No 45
>KOG0500 consensus Cyclic nucleotide-gated cation channel CNGA1-3 and related proteins [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=31.82 E-value=77 Score=34.56 Aligned_cols=82 Identities=16% Similarity=0.261 Sum_probs=49.0
Q ss_pred cchhHHHHHHHhhcCCCCCCCcceeEEeecccCcc--eeeEeecccc----cCCCceeeeeeCCCCC-CCCCCccccccC
Q 013478 56 SEDSTVNRLEDLLNLDITPYTDKIIAEYICQNNTI--SCWNRIGGTG----IDMRSKSKTISKPVEH-PSELPKWNYDGS 128 (442)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~yi~~~~~i--~~w~~idg~g----~DlrGk~r~~~~p~~~-~~~l~~~~fDGS 128 (442)
.+.+.+..|...|+...=. ++ .|||+++++ +|+ |=-.| ++=.|++--...+..+ |.|+...++.|+
T Consensus 318 ce~~lL~elVLklk~qvfS-Pg----DyICrKGdvgkEMy--IVk~G~L~Vv~dDg~t~~~~L~~G~~FGEisIlni~g~ 390 (536)
T KOG0500|consen 318 CEAGLLVELVLKLKPQVFS-PG----DYICRKGDVGKEMY--IVKEGKLAVVADDGVTVFVTLKAGSVFGEISILNIKGN 390 (536)
T ss_pred cchhHHHHHHHHhcceeeC-CC----CeEEecCcccceEE--EEEccEEEEEecCCcEEEEEecCCceeeeeEEEEEcCc
Confidence 4667788888777664311 22 388999999 898 64443 1112343333444333 456666788887
Q ss_pred CCCC------CCCCCccEEEEe
Q 013478 129 STGQ------APGEDSEVILYP 144 (442)
Q Consensus 129 s~g~------a~~~~sD~~L~P 144 (442)
-.|- .+.++||+++.-
T Consensus 391 ~~gNRRtanvrSvGYSDlfvLs 412 (536)
T KOG0500|consen 391 KNGNRRTANVRSVGYSDLFVLS 412 (536)
T ss_pred ccCCcceeeeeeeccceeeEee
Confidence 6542 356788877653
No 46
>PF14395 COOH-NH2_lig: Phage phiEco32-like COOH.NH2 ligase-type 2
Probab=27.58 E-value=90 Score=31.21 Aligned_cols=52 Identities=15% Similarity=0.121 Sum_probs=32.6
Q ss_pred CC-ChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccc
Q 013478 273 GP-SVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKS 326 (442)
Q Consensus 273 ~p-~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~ 326 (442)
.| .++.+..+++..+.....+.+...++.--==..|+.| ---|.|+|||-..
T Consensus 56 ~P~~~P~~L~~~i~~~l~~A~~~i~~~~l~W~AG~mP~~g--fp~GGHiHfsgv~ 108 (261)
T PF14395_consen 56 APSPDPAELFENIRRALREAARRIPDRSLEWLAGSMPFPG--FPLGGHIHFSGVP 108 (261)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHhCCCCCceEecCCCCCCC--CCcCCeEEecCCC
Confidence 34 3788888888766666666666666542222335555 3568999998543
No 47
>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=27.22 E-value=1.1e+02 Score=35.29 Aligned_cols=62 Identities=16% Similarity=0.106 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChh------HHHHHHHHHHHHHHHHHHHHcCcEEEec
Q 013478 238 GRDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVG------IDAGDHIWCSRYLLERITEQAGVVLSLD 305 (442)
Q Consensus 238 ~~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~------i~aaD~l~~~R~iik~vA~~~Gl~aTFm 305 (442)
..+|++++ ...++..-|-+.-.+..||-+||+|. +.+.=.+..++.-|.+||++||+.++|.
T Consensus 415 a~~im~~l------l~~p~yr~~l~~~~~~QeVMlGYSDS~KDgG~laa~w~ly~Aq~~L~~v~~~~gV~l~~F 482 (794)
T PF00311_consen 415 APDIMEEL------LSNPAYRAHLKARGNRQEVMLGYSDSNKDGGYLAANWALYKAQEALVAVARKHGVKLRFF 482 (794)
T ss_dssp HHHHHHHH------CCSHHHHHHCTT---EEEEEEECCCHHHHC-HHHHHHHHHHHHHHHHHHHHCCT-EEEEE
T ss_pred HHHHHHHH------HcCHHHHHHHhcCcceEEEEeccccccccccHHHHHHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 46666654 56677666666545678999999985 4577788899999999999999999985
No 48
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=25.79 E-value=2.3e+02 Score=32.79 Aligned_cols=111 Identities=10% Similarity=0.156 Sum_probs=63.8
Q ss_pred CCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecccCCCCCCCCceeeeeccccccccCCchhhHHHHHHhhH
Q 013478 265 PGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDPKPIEGDWNGAGCHTNYSTKSMREEGGYETIKKAILNLS 344 (442)
Q Consensus 265 pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmPKP~~g~~~GSG~H~h~Sl~~~~~~~G~~~~~~~iaGL~ 344 (442)
|.+.=|.|.|.+++.-.|-+ -+=..+|++-++.|+.. | || .. -|.|+|+.+-|....+-+....+.++||-..
T Consensus 135 PD~lv~DLDP~~~~~f~~v~-~~A~~~r~~L~~lgL~~-~-~K--TS--G~kGlHv~vPl~~~~~~~~~~~fa~~~A~~l 207 (764)
T PRK09632 135 ATRLVFDLDPGEGVGLAECA-EVARAVRDLLADIGLET-F-PV--TS--GSKGIHLYAPLDGPVSSEGASVVAKEVARAL 207 (764)
T ss_pred CCEEEEECCCCCCCCHHHHH-HHHHHHHHHHHHcCCce-e-eE--CC--CCCeEEEEEECCCCCCHHHHHHHHHHHHHHH
Confidence 56999999999887554444 44456788888999873 4 66 32 4889999999965311111233344555432
Q ss_pred HHHHHHHhcccccccccCCCCCCCCCCCceeeccCCCcceeeecc
Q 013478 345 LRHKEHISAYGEGNERRLTGKHETASIDSFSWGVANRGCSIRVGR 389 (442)
Q Consensus 345 L~H~~al~a~~~nsYkRL~~~~eap~~~~~sWG~~NR~a~IRIp~ 389 (442)
.+..|.+. +..-.|...++. . ++-|-.++|+..+=-|.
T Consensus 208 ~~~~P~~~--t~~~~k~~R~gk---v--fiDy~qN~~g~T~vapY 245 (764)
T PRK09632 208 EQDHPDLV--TSTMTKSLRAGK---V--FVDWSQNNGSKTTIAPY 245 (764)
T ss_pred HHHCccee--hhhhhHhhCCCC---E--EEECccCCCCCeEEecc
Confidence 23333332 222112222221 2 67777777776554443
No 49
>KOG0073 consensus GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=24.96 E-value=69 Score=30.24 Aligned_cols=35 Identities=34% Similarity=0.448 Sum_probs=23.8
Q ss_pred hHHHHHhhccCcccCcceEEEEeecchh-HHHHHHHhhcCC
Q 013478 32 SLLMKQNKKGTNRSSAKFRVLALKSEDS-TVNRLEDLLNLD 71 (442)
Q Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 71 (442)
|++-||+.| -+.+|++-|..|+| --..+.+|++.+
T Consensus 5 silrk~k~k-----erE~riLiLGLdNsGKTti~~kl~~~~ 40 (185)
T KOG0073|consen 5 SILRKQKLK-----EREVRILILGLDNSGKTTIVKKLLGED 40 (185)
T ss_pred HHHHHHHhh-----hheeEEEEEecCCCCchhHHHHhcCCC
Confidence 566777766 44899999998886 333455666664
No 50
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.74 E-value=2.6e+02 Score=23.28 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHhhhcCCccceEeeeeeEEE
Q 013478 174 TNKRHRAAEIFSNSKVSAEVPWFGIEQEYTL 204 (442)
Q Consensus 174 ~~pR~~Lk~~~~~l~~~G~~~~~G~E~EF~L 204 (442)
.=||..++.+++.+ |-.|+++||.-
T Consensus 33 GwPRRT~QDvikAl------pglgi~l~FvQ 57 (95)
T COG4519 33 GWPRRTAQDVIKAL------PGLGIVLEFVQ 57 (95)
T ss_pred CCchhHHHHHHHhC------cCCCeEEEeee
Confidence 34899999999866 45677788865
No 51
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=22.95 E-value=73 Score=30.25 Aligned_cols=70 Identities=11% Similarity=-0.016 Sum_probs=52.7
Q ss_pred eecccChhHHHHHHHHHHHHHHHcCCceeeecCCCCCC----------ceEEEeCCChhHHHHHHHHHHHHHHHHHHHHc
Q 013478 229 CGAGADKSFGRDIADAHYKACLYAGINISGTNGEVMPG----------QWEYQVGPSVGIDAGDHIWCSRYLLERITEQA 298 (442)
Q Consensus 229 ~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~E~~pG----------Q~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~ 298 (442)
...|.|+ --|+.++.+.+...||+|+..+++..+. ++|+.+.... ++--+|.-+.++|.+.
T Consensus 99 ~v~G~Dr---PGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~lP~~~------~~~~L~~~l~~l~~eL 169 (190)
T PRK11589 99 QVEVADS---PHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPASQ------DAANIEQAFKALCTEL 169 (190)
T ss_pred EEEECCC---CCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEEcCCCC------CHHHHHHHHHHHHHHh
Confidence 4556676 4677778888999999999999997764 3444454331 2345788999999999
Q ss_pred CcEEEeccc
Q 013478 299 GVVLSLDPK 307 (442)
Q Consensus 299 Gl~aTFmPK 307 (442)
++.+++-|.
T Consensus 170 ~vd~~l~~~ 178 (190)
T PRK11589 170 NAQGSINVV 178 (190)
T ss_pred CceEEEEEe
Confidence 999999875
No 52
>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=22.85 E-value=1.1e+02 Score=25.30 Aligned_cols=60 Identities=7% Similarity=-0.064 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEE
Q 013478 239 RDIADAHYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLS 303 (442)
Q Consensus 239 ~di~e~~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aT 303 (442)
.+.+....+.+...|++++-+..|+.-..--+.+-+. ||+-+=||.++|.++..++..+-
T Consensus 25 ~~al~~c~~~~~~~~L~m~lvd~e~~~D~~k~~fyy~-----a~~rvDFR~Lvr~L~~~f~~RIe 84 (88)
T PF04468_consen 25 EEALKFCRELVKELGLPMKLVDVEYQFDGSKLTFYYT-----AESRVDFRELVRDLAREFKTRIE 84 (88)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEEEEEcCCCEEEEEEE-----eCCcCcHHHHHHHHHHHhCceEE
Confidence 4445555556678999999999999877777777776 78888999999999999998764
No 53
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=21.73 E-value=1.8e+02 Score=29.32 Aligned_cols=67 Identities=16% Similarity=-0.027 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHcCCceeeecCCC--CCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEEEecc
Q 013478 239 RDIADAHYKACLYAGINISGTNGEV--MPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVLSLDP 306 (442)
Q Consensus 239 ~di~e~~~~al~~aGI~i~~~h~E~--~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~aTFmP 306 (442)
--|+.++.+.|...|++|+.+.... ..|+|.+.+.-.. -...+.+-..+..+..++++.|+.+++..
T Consensus 17 pGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~-~~~~~~~~~L~~~L~~l~~~l~l~i~l~~ 85 (286)
T PRK06027 17 PGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEG-DGLIFNLETLRADFAALAEEFEMDWRLLD 85 (286)
T ss_pred CcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEe-CCCCCCHHHHHHHHHHHHHHhCCEEEEcc
Confidence 3567777777899999999998888 7788776554221 01112255689999999999999988764
No 54
>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=21.39 E-value=3.8e+02 Score=28.14 Aligned_cols=141 Identities=17% Similarity=0.194 Sum_probs=66.9
Q ss_pred eEEEEEEeecCCCCCCCCCHHHHHHH--HHHhhhcCCccceEeeeeeEEEecCCCCCCCC-CCCCCCCCC-CCCc----e
Q 013478 157 NILVICDTYTPAGEPIPTNKRHRAAE--IFSNSKVSAEVPWFGIEQEYTLLQQNVKWPLG-WPVGAYPGP-QGPY----Y 228 (442)
Q Consensus 157 ~a~Vlcd~~~~dG~P~~~~pR~~Lk~--~~~~l~~~G~~~~~G~E~EF~L~~~~~~~p~g-~p~~~~p~~-~g~y----y 228 (442)
...|+..=+.|.|.|+-.|-|.++.- +.+.|+++|.. .+|+++-.+-+ ++. -|. ..|.. -..| +
T Consensus 23 ~~~v~~sG~sPSG~~HIGn~rEv~~~~~V~~al~~~g~~------~r~i~~~DD~D-~lRKvP~-~~p~~~~~~ylg~Pl 94 (360)
T PF01921_consen 23 EPYVFASGISPSGLPHIGNFREVLRADMVARALRDRGKD------VRLIYFSDDMD-PLRKVPP-NVPNPELEKYLGKPL 94 (360)
T ss_dssp SEEEEEEEE--SS---HHHHHHHHHHHHHHHHHHTTT-E------EEEEEEE-TTS-B-----T-TS-CC-CCCCTTSBT
T ss_pred ccEEEecCCCCCCCcccccccchhhHHHHHHHHHHcCCC------EEEEEEeecCC-cccCCCC-CCChHHHHHhcCCcc
Confidence 45677777889999999999998854 33334555655 67777765533 110 011 11211 1112 1
Q ss_pred eec----ccChhHHHHHHHHHHHHHHHcCCceeeecC--CCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCcEE
Q 013478 229 CGA----GADKSFGRDIADAHYKACLYAGINISGTNG--EVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGVVL 302 (442)
Q Consensus 229 ~~~----~~~~~~~~di~e~~~~al~~aGI~i~~~h~--E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl~a 302 (442)
+.+ +-..+|.+.....+.+.|...||+++-+.+ -+..|.|.=++ ..+-.+.-..+.||.++-.+- +..
T Consensus 95 t~VPdP~G~~~SyaeH~~~~~~~~L~~~gie~e~~s~te~Y~sG~y~~~i-----~~aL~~~~~I~~Il~~~~~~~-~~~ 168 (360)
T PF01921_consen 95 TRVPDPFGCHESYAEHFNAPFEEFLDEFGIEYEFISQTEMYRSGRYDEQI-----RTALENRDEIREILNEYRGRE-RPE 168 (360)
T ss_dssp TTSB-TTSSSSCHHHHHHHHHHHHHHTTT---EEEECCCCCCTTTTHHHH-----CHHHHTHHHHHHHHHHHHHHT---T
T ss_pred ccCCCCCCCCccHHHHHHHHHHHHHHHcCCceEEEeHHHhhhCCchHHHH-----HHHHHhHHHHHHHHHHhcCcC-CCC
Confidence 211 123466777777777889999998876543 34456553221 224444444566666664433 555
Q ss_pred Eecc-cCCCC
Q 013478 303 SLDP-KPIEG 311 (442)
Q Consensus 303 TFmP-KP~~g 311 (442)
++.| .|+-.
T Consensus 169 ~y~Pf~piC~ 178 (360)
T PF01921_consen 169 TYSPFLPICE 178 (360)
T ss_dssp T--SEEEEET
T ss_pred Ceeeeeeecc
Confidence 5555 34433
No 55
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=20.70 E-value=1.8e+02 Score=22.31 Aligned_cols=48 Identities=17% Similarity=0.129 Sum_probs=31.6
Q ss_pred HHHHHHHcCCceeeecCCCCCCceEEEeCCChhHHHHHHHHHHHHHHHHHHHHcCc
Q 013478 245 HYKACLYAGINISGTNGEVMPGQWEYQVGPSVGIDAGDHIWCSRYLLERITEQAGV 300 (442)
Q Consensus 245 ~~~al~~aGI~i~~~h~E~~pGQ~Ei~l~p~~~i~aaD~l~~~R~iik~vA~~~Gl 300 (442)
+.+.|..+|++++.. .+ .+++++.+.+-.. ++...--++.+||+-+|+
T Consensus 24 i~~~L~~lg~~~~~~-~~--~~~~~v~~P~~R~-----Di~~~~DliEei~r~~Gy 71 (71)
T smart00874 24 IEEILKRLGFEVEVS-GD--DDTLEVTVPSYRF-----DILIEADLIEEVARIYGY 71 (71)
T ss_pred HHHHHHHCCCeEEec-CC--CCeEEEECCCCcc-----ccCcccHHHHHHHHHhCC
Confidence 344578899998541 11 4578888876532 444555678888888885
No 56
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=20.69 E-value=82 Score=23.82 Aligned_cols=26 Identities=19% Similarity=0.120 Sum_probs=22.3
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHcCc
Q 013478 275 SVGIDAGDHIWCSRYLLERITEQAGV 300 (442)
Q Consensus 275 ~~~i~aaD~l~~~R~iik~vA~~~Gl 300 (442)
.+-.+||..+=+.-.++|++|+++|+
T Consensus 16 lp~~eAA~~Lgv~~T~LKr~CR~~GI 41 (52)
T PF02042_consen 16 LPIKEAAKELGVSVTTLKRRCRRLGI 41 (52)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 35567888888999999999999996
No 57
>PRK11675 LexA regulated protein; Provisional
Probab=20.56 E-value=95 Score=26.20 Aligned_cols=33 Identities=21% Similarity=0.329 Sum_probs=25.7
Q ss_pred HHHhhc--cCcccCcceEEEEeecchhHHHHHHHh
Q 013478 35 MKQNKK--GTNRSSAKFRVLALKSEDSTVNRLEDL 67 (442)
Q Consensus 35 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (442)
+|.||+ ..+-.+.+.+.+.|+-+.++++.|.+|
T Consensus 34 l~inkrnq~~rdk~~glKRveVKldedl~ekL~ey 68 (90)
T PRK11675 34 LRINKRNQLKRDKVRGLKRVELKLNADLVDALNEL 68 (90)
T ss_pred HHhhHHHHHHHHHHcCceeEEEEECHHHHHHHHHH
Confidence 444443 234467899999999999999999999
No 58
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=20.44 E-value=6.6e+02 Score=27.77 Aligned_cols=91 Identities=18% Similarity=0.185 Sum_probs=55.4
Q ss_pred EEEEEEeecCCCCCCCCCHHHHHHHH--HHhhhcCCccceEeeeeeEEEecCCCCC--------C--------CCCCCCC
Q 013478 158 ILVICDTYTPAGEPIPTNKRHRAAEI--FSNSKVSAEVPWFGIEQEYTLLQQNVKW--------P--------LGWPVGA 219 (442)
Q Consensus 158 a~Vlcd~~~~dG~P~~~~pR~~Lk~~--~~~l~~~G~~~~~G~E~EF~L~~~~~~~--------p--------~g~p~~~ 219 (442)
..|+..=+.|.|.|+-.|-|.++.-- -..+++.|. |..+..+-.+-+. | +|+|..-
T Consensus 20 ~~~v~tGisPSG~~HIGn~rEv~t~d~V~ralr~~g~------~~r~I~~~DD~D~lRkvp~~lp~~~~~e~Ylg~Plt~ 93 (521)
T COG1384 20 EYVVATGISPSGLIHIGNFREVLTADAVRRALRDRGD------EVRLIYISDDYDPLRKVPRNLPDPEELEQYLGMPLTE 93 (521)
T ss_pred cEEEecCcCCCCCcccccHHHHHHHHHHHHHHHHcCC------ceEEEEEccCCcccccCCCCCCChHHHHHHcCCcccc
Confidence 34555567889999999999988542 222345666 6677776654321 1 2344433
Q ss_pred CCCCCCCceeecccChhHHHHHHHHHHHHHHHcCCceeeecC
Q 013478 220 YPGPQGPYYCGAGADKSFGRDIADAHYKACLYAGINISGTNG 261 (442)
Q Consensus 220 ~p~~~g~yy~~~~~~~~~~~di~e~~~~al~~aGI~i~~~h~ 261 (442)
.|-|.|. ..+|.+.....+.+.|...||++|-+.+
T Consensus 94 IPdP~G~-------~~Sya~hf~~~f~~~l~~~Gi~~E~~s~ 128 (521)
T COG1384 94 IPDPFGC-------CDSYAEHFLRPFEEFLDEFGIEVEFVSA 128 (521)
T ss_pred CCCCccc-------cchHHHHHHHHHHHHHHhcCCceEEEEh
Confidence 4444441 1244555555566668899999987654
No 59
>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=20.23 E-value=1.2e+02 Score=23.49 Aligned_cols=60 Identities=12% Similarity=-0.068 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHcCCceeeecCC--CCCCceEEEeCCChhHHHH-HHHHHHHHHHHHHHHHcCcE
Q 013478 240 DIADAHYKACLYAGINISGTNGE--VMPGQWEYQVGPSVGIDAG-DHIWCSRYLLERITEQAGVV 301 (442)
Q Consensus 240 di~e~~~~al~~aGI~i~~~h~E--~~pGQ~Ei~l~p~~~i~aa-D~l~~~R~iik~vA~~~Gl~ 301 (442)
-|+..+.+.+...|++|..++.- ...+.|.+.+.-..+ .. .+.-.++..+..+|++.|+.
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 45666666788899999999776 355666554432211 11 13456788889999888753
Done!