Query 021961
Match_columns 305
No_of_seqs 130 out of 1099
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:58:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021961.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021961hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0217 Uncharacterized conser 100.0 6.7E-76 1.5E-80 538.2 24.6 205 76-293 2-208 (241)
2 PRK12378 hypothetical protein; 100.0 2.1E-74 4.5E-79 530.8 24.7 206 76-296 1-209 (235)
3 PRK00110 hypothetical protein; 100.0 1.2E-73 2.6E-78 528.5 25.2 208 75-297 1-211 (245)
4 TIGR01033 DNA-binding regulato 100.0 5.9E-73 1.3E-77 522.0 25.4 210 75-297 1-213 (238)
5 PF01709 Transcrip_reg: Transc 100.0 3.3E-72 7.1E-77 515.7 17.9 203 78-293 1-204 (234)
6 KOG2972 Uncharacterized conser 100.0 4.6E-63 1E-67 454.3 20.8 226 63-293 17-244 (276)
7 PRK07562 ribonucleotide-diphos 98.7 2.7E-08 5.8E-13 109.1 7.2 131 12-149 222-371 (1220)
8 cd04882 ACT_Bt0572_2 C-termina 55.5 49 0.0011 23.0 5.8 59 171-233 2-62 (65)
9 PTZ00248 eukaryotic translatio 49.6 1.1E+02 0.0023 30.3 8.9 57 137-196 200-263 (319)
10 PF14257 DUF4349: Domain of un 48.9 46 0.00099 31.0 6.0 69 156-232 47-118 (262)
11 PF02662 FlpD: Methyl-viologen 47.5 68 0.0015 27.0 6.3 76 208-291 28-105 (124)
12 cd04879 ACT_3PGDH-like ACT_3PG 46.8 68 0.0015 22.1 5.4 28 171-198 2-29 (71)
13 cd04903 ACT_LSD C-terminal ACT 43.7 1.1E+02 0.0023 21.2 6.1 27 171-197 2-28 (71)
14 TIGR00341 conserved hypothetic 38.1 93 0.002 30.8 6.5 56 219-278 13-68 (325)
15 PF00392 GntR: Bacterial regul 36.5 95 0.0021 22.5 4.9 51 97-149 1-51 (64)
16 PF14502 HTH_41: Helix-turn-he 36.4 42 0.00092 24.4 2.9 43 121-168 5-47 (48)
17 PRK02472 murD UDP-N-acetylmura 36.4 84 0.0018 31.0 6.0 60 122-187 280-340 (447)
18 TIGR01143 murF UDP-N-acetylmur 35.7 1.2E+02 0.0026 29.9 7.0 61 122-188 259-319 (417)
19 PRK03803 murD UDP-N-acetylmura 35.4 1.2E+02 0.0025 30.3 6.8 61 122-188 278-339 (448)
20 cd04908 ACT_Bt0572_1 N-termina 35.1 1.5E+02 0.0032 21.3 5.8 59 171-233 4-62 (66)
21 TIGR01087 murD UDP-N-acetylmur 33.6 1.2E+02 0.0026 29.9 6.5 61 122-188 269-330 (433)
22 PRK01390 murD UDP-N-acetylmura 32.7 1.4E+02 0.003 29.8 6.9 60 122-187 292-352 (460)
23 PF08671 SinI: Anti-repressor 32.5 68 0.0015 21.1 3.1 25 121-145 4-28 (30)
24 TIGR01081 mpl UDP-N-acetylmura 32.2 1.7E+02 0.0038 29.1 7.5 60 122-188 283-343 (448)
25 PRK04663 murD UDP-N-acetylmura 32.1 1.2E+02 0.0027 30.1 6.4 61 122-188 274-335 (438)
26 PRK14106 murD UDP-N-acetylmura 32.0 1.3E+02 0.0028 29.7 6.5 61 122-188 284-345 (450)
27 PRK03806 murD UDP-N-acetylmura 31.9 1.5E+02 0.0032 29.4 6.9 61 122-188 273-334 (438)
28 PRK11930 putative bifunctional 31.3 1.4E+02 0.0031 32.4 7.2 61 122-188 291-352 (822)
29 PRK02705 murD UDP-N-acetylmura 31.2 1.4E+02 0.0031 29.6 6.7 61 122-188 286-347 (459)
30 COG3323 Uncharacterized protei 31.1 3E+02 0.0066 23.3 7.5 75 181-274 16-91 (109)
31 PRK10773 murF UDP-N-acetylmura 30.2 1.6E+02 0.0034 29.6 6.9 61 122-188 287-348 (453)
32 PF05225 HTH_psq: helix-turn-h 29.7 53 0.0011 22.9 2.4 22 125-146 19-40 (45)
33 PRK14022 UDP-N-acetylmuramoyla 29.4 1.7E+02 0.0037 29.5 7.0 59 122-188 301-360 (481)
34 PRK00139 murE UDP-N-acetylmura 28.1 2E+02 0.0043 28.9 7.1 60 122-188 283-343 (460)
35 PTZ00450 macrophage migration 27.9 29 0.00062 29.0 1.0 28 112-139 67-96 (113)
36 PRK12338 hypothetical protein; 27.3 1.5E+02 0.0032 29.2 5.9 132 123-280 172-315 (319)
37 TIGR00655 PurU formyltetrahydr 27.1 4.4E+02 0.0095 25.3 9.0 95 165-279 40-136 (280)
38 PRK13168 rumA 23S rRNA m(5)U19 27.0 1.4E+02 0.003 30.0 5.8 39 253-291 394-432 (443)
39 cd04925 ACT_ACR_2 ACT domain-c 26.5 84 0.0018 23.5 3.3 29 170-198 2-30 (74)
40 PF13740 ACT_6: ACT domain; PD 26.4 84 0.0018 23.6 3.3 31 169-199 3-33 (76)
41 PRK01710 murD UDP-N-acetylmura 26.4 1.6E+02 0.0035 29.5 6.1 58 123-187 289-347 (458)
42 PF14501 HATPase_c_5: GHKL dom 26.2 2.8E+02 0.0062 21.5 6.4 58 138-196 13-84 (100)
43 PF03698 UPF0180: Uncharacteri 25.4 55 0.0012 26.1 2.1 20 261-280 7-26 (80)
44 COG3636 Predicted transcriptio 24.8 1.2E+02 0.0027 25.2 4.1 40 90-134 44-90 (100)
45 PRK01368 murD UDP-N-acetylmura 24.7 2E+02 0.0043 29.1 6.5 61 122-188 280-341 (454)
46 TIGR00559 pdxJ pyridoxine 5'-p 24.4 1E+02 0.0022 29.3 4.0 89 169-278 38-126 (237)
47 cd00003 PNPsynthase Pyridoxine 24.1 1E+02 0.0022 29.3 3.9 56 220-278 71-126 (234)
48 PRK03094 hypothetical protein; 23.7 64 0.0014 25.8 2.2 20 261-280 7-26 (80)
49 TIGR01085 murE UDP-N-acetylmur 23.7 2.8E+02 0.0061 27.7 7.3 60 122-188 291-352 (464)
50 PF08438 MMR_HSR1_C: GTPase of 23.5 40 0.00087 28.3 1.0 52 136-195 30-85 (109)
51 smart00685 DM14 Repeats in fly 23.4 92 0.002 23.5 2.9 28 84-111 16-43 (59)
52 PRK05564 DNA polymerase III su 23.4 2.1E+02 0.0045 27.1 6.0 77 176-276 69-145 (313)
53 KOG3111 D-ribulose-5-phosphate 23.2 2.2E+02 0.0047 26.8 5.8 51 220-293 75-126 (224)
54 PRK05265 pyridoxine 5'-phospha 22.3 1.2E+02 0.0026 29.0 4.0 89 169-278 41-129 (239)
55 cd04909 ACT_PDH-BS C-terminal 22.0 3E+02 0.0065 19.5 5.6 60 171-233 4-67 (69)
56 TIGR03337 phnR transcriptional 21.9 2.3E+02 0.0049 25.2 5.7 52 97-150 2-53 (231)
57 TIGR00119 acolac_sm acetolacta 21.6 5.6E+02 0.012 22.6 9.2 107 170-279 3-112 (157)
58 PRK06027 purU formyltetrahydro 21.5 6.9E+02 0.015 23.9 9.2 93 167-279 48-141 (286)
59 PF07942 N2227: N2227-like pro 21.4 1.1E+02 0.0023 29.5 3.6 70 167-238 171-240 (270)
60 TIGR01082 murC UDP-N-acetylmur 21.2 2E+02 0.0043 28.7 5.6 52 122-180 278-330 (448)
61 TIGR00479 rumA 23S rRNA (uraci 21.1 86 0.0019 31.2 3.0 39 253-291 390-428 (431)
62 cd04906 ACT_ThrD-I_1 First of 21.0 3.8E+02 0.0083 20.5 6.1 55 219-280 13-71 (85)
63 KOG2121 Predicted metal-depend 20.8 43 0.00094 36.5 0.9 54 126-179 223-280 (746)
64 PF09682 Holin_LLH: Phage holi 20.8 4.7E+02 0.01 21.3 8.1 65 83-147 29-101 (108)
65 COG0347 GlnK Nitrogen regulato 20.3 1.1E+02 0.0025 25.9 3.1 24 254-277 3-26 (112)
66 PF02829 3H: 3H domain; Inter 20.3 3.5E+02 0.0076 22.1 5.9 86 177-276 6-96 (98)
67 PRK11929 putative bifunctional 20.2 2.6E+02 0.0057 30.8 6.8 61 122-188 796-857 (958)
68 PRK11589 gcvR glycine cleavage 20.1 3E+02 0.0065 25.0 6.1 110 168-280 8-125 (190)
No 1
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.7e-76 Score=538.18 Aligned_cols=205 Identities=40% Similarity=0.659 Sum_probs=196.1
Q ss_pred CCc-hhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccC-Cccc
Q 021961 76 MGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEA 153 (305)
Q Consensus 76 mG~-KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~-~~~~ 153 (305)
+|| ||+||||+|+++|++|+|+|+||+|+|++|+|.|||||+.||+||.+|++||++|||||+|||||+||+|. ++.+
T Consensus 2 aGHsKw~nIkhrK~a~Dakr~Kif~Kl~keI~vAaK~Gg~dP~~NprLr~aI~kAk~~nmPkd~IerAI~ka~G~~d~~~ 81 (241)
T COG0217 2 AGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGGPDPESNPRLRTAIEKAKAANMPKDNIERAIKKASGGKDGAN 81 (241)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHHHcCCCHHHHHHHHHhccCCCCccc
Confidence 465 99999999999999999999999999999999999999999999999999999999999999999999984 5579
Q ss_pred eeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCC
Q 021961 154 FIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA 233 (305)
Q Consensus 154 ~~e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGA 233 (305)
|+|++|||||||||+|||||||||+|||+++||++|+|+||+||++|||.|||+|||+|.+.+...|+|++||.|||+||
T Consensus 82 ~~ei~YEGygP~GvaiiVe~LTDN~NRTas~vR~~F~K~GG~lg~~GSV~~mF~~kGvi~~~~~~~~ed~l~e~~ieaga 161 (241)
T COG0217 82 YEEIRYEGYGPGGVAIIVEALTDNRNRTASNVRSAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIEAGA 161 (241)
T ss_pred eEEEEEEeECCCceEEEEEeccCCcchhHHHHHHHHHhcCCccCCCceEEEEEeccEEEEECCCCCCHHHHHHHHHHCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999877899999999999999
Q ss_pred ccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCCcc
Q 021961 234 EDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIE 293 (305)
Q Consensus 234 EDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve 293 (305)
|||+.. ++.|+|+|+|++|..|+++|+++|+++..+ ++.|+|+++|+
T Consensus 162 eDv~~~------------~~~~~V~t~p~~~~~V~~~L~~~g~~~~~a-el~~iP~~~v~ 208 (241)
T COG0217 162 EDVEED------------EGSIEVYTEPEDFNKVKEALEAAGYEIESA-ELTMIPQNTVE 208 (241)
T ss_pred hhhhcC------------CCeEEEEEChHHHHHHHHHHHHcCCceeee-eEEEecCCcee
Confidence 999851 247999999999999999999999999886 99999999998
No 2
>PRK12378 hypothetical protein; Provisional
Probab=100.00 E-value=2.1e-74 Score=530.81 Aligned_cols=206 Identities=38% Similarity=0.642 Sum_probs=194.2
Q ss_pred CCchhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccCCcccee
Q 021961 76 MGRRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFI 155 (305)
Q Consensus 76 mG~KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~ 155 (305)
|||||+||||+|+++|++|+|+|+||+|+|++|||+|||||+.|++||.+|++||+.|||||+||||||||+|.++.+|+
T Consensus 1 ~g~kW~~Ikh~K~~~Da~ksk~f~kl~reI~vA~k~GG~dP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~~~ 80 (235)
T PRK12378 1 MGRAWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGGPDPESNPALRFVIERAKKANVPKDVIERAIKKAKGGGGEDYE 80 (235)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHhccCCCCCceE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999987666899
Q ss_pred EEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCC--
Q 021961 156 EKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA-- 233 (305)
Q Consensus 156 e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGA-- 233 (305)
+++|||||||||+|||||||||+|||+++||++|+|+||+|+++|||.|+|+|+|+|.+... ++|++||+|||+||
T Consensus 81 e~~YEgygPgGvaiiVe~lTDN~nRt~~~vr~~f~K~gg~l~~~gsv~~~Fe~kG~i~i~~~--~~d~~~e~aieaGa~~ 158 (235)
T PRK12378 81 EVRYEGFGPNGVMVIVECLTDNVNRTVANVRSAFNKNGGNLGTSGSVAFMFDHKGVFVFEGD--DEDELLEALIDADVDV 158 (235)
T ss_pred EEEEEEEcCCCcEEEEEECCCCHHHHHHHHHHHHhhcCCeECCCCceeeeeecceEEEeCCC--CHHHHHHHHHhCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999854 79999999999999
Q ss_pred ccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCCcc-chh
Q 021961 234 EDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIE-DIH 296 (305)
Q Consensus 234 EDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve-~~~ 296 (305)
|||++ | ++.|+|+|+|++|.+|+++|++.||++.++ +++|+|+++|+ +++
T Consensus 159 edv~~-----~-------~~~~~i~t~p~~~~~v~~~L~~~g~~~~~s-ei~~~P~~~v~l~~e 209 (235)
T PRK12378 159 EDVEE-----E-------EGTITVYTDPTDFHKVKKALEAAGIEFLVA-ELEMIPQNPVELSGE 209 (235)
T ss_pred ccccc-----c-------CCeEEEEECHHHHHHHHHHHHHcCCCceee-EEEEecCCCccCCHH
Confidence 66632 1 136999999999999999999999999986 99999999999 544
No 3
>PRK00110 hypothetical protein; Validated
Probab=100.00 E-value=1.2e-73 Score=528.51 Aligned_cols=208 Identities=37% Similarity=0.636 Sum_probs=195.8
Q ss_pred cCCc-hhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccC-Ccc
Q 021961 75 CMGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQE 152 (305)
Q Consensus 75 ~mG~-KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~-~~~ 152 (305)
+||| ||+||||+|+++|++|+|+|+||+|+|++|||+|||||+.|++||++|++||+.|||||+||||||||+|. ++.
T Consensus 1 maGHskW~~Ikh~K~~~D~kksk~f~kl~reI~vAak~GG~DP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~ 80 (245)
T PRK00110 1 MAGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGGGDPEGNPRLRLAIDKAKAANMPKDNIERAIKKGTGELDGA 80 (245)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCcc
Confidence 4787 99999999999999999999999999999999999999999999999999999999999999999999986 667
Q ss_pred ceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCC
Q 021961 153 AFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAG 232 (305)
Q Consensus 153 ~~~e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaG 232 (305)
+|++++|||||||||+|||||||||+|||+++||++|+|+||+|+++|||.|+|+|+|+|.+... ++|++||+|||+|
T Consensus 81 ~~~e~~YEg~gP~GvaiiVe~lTDN~nRt~~~vR~~f~K~gG~l~~~Gsv~~~Fe~kG~i~~~~~--~~d~~~e~aieaG 158 (245)
T PRK00110 81 NYEEIRYEGYGPGGVAIIVEALTDNRNRTAAEVRHAFSKNGGNLGETGSVSYMFDRKGVIVIEPL--DEDELMEAALEAG 158 (245)
T ss_pred ceEEEEEEEEcCCCeEEEEEEecCCHHHHHHHHHHHHHhcCceeCCCcceEEEeccceEEEeCCC--CHHHHHHHHHhCC
Confidence 89999999999999999999999999999999999999999999999999999999999999743 7999999999999
Q ss_pred CccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCCcc-chhh
Q 021961 233 AEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIE-DIHQ 297 (305)
Q Consensus 233 AEDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve-~~~~ 297 (305)
||||++ || +.|+|+|+|++|.+|+++|++.||++.++ +++|+|+++|+ ++++
T Consensus 159 aeDv~~----e~--------~~~~i~~~p~~~~~v~~~L~~~g~~~~~s-ei~~~P~~~v~l~~e~ 211 (245)
T PRK00110 159 AEDVET----DD--------ESFEVITAPEDFEAVRDALEAAGLEAESA-EVTMIPQNTVELDEET 211 (245)
T ss_pred CCEeec----cC--------CeEEEEECHHHHHHHHHHHHHcCCCeeee-EEEEecCCCcccCHHH
Confidence 999953 11 35999999999999999999999999886 99999999999 5543
No 4
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=100.00 E-value=5.9e-73 Score=522.04 Aligned_cols=210 Identities=36% Similarity=0.633 Sum_probs=197.0
Q ss_pred cCCc-hhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccC-Ccc
Q 021961 75 CMGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQE 152 (305)
Q Consensus 75 ~mG~-KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~-~~~ 152 (305)
+||| ||+||||+|+++|++|+|+|+||+|+|++|||+|||||+.|++||++|++||++||||++||||||||+|. ++.
T Consensus 1 maGHskw~~Ikh~K~~~D~~ksk~f~kl~r~I~vA~k~GG~DP~~N~~L~~ai~~Ak~~~~Pkd~IerAIkr~~g~~~~~ 80 (238)
T TIGR01033 1 MAGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGGGDPESNPRLRTAIEKAKAANMPKDNIERAIKKGAGELDGS 80 (238)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCcc
Confidence 4787 99999999999999999999999999999999999999999999999999999999999999999999986 667
Q ss_pred ceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCC
Q 021961 153 AFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAG 232 (305)
Q Consensus 153 ~~~e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaG 232 (305)
+|++++|||||||||+|||||||||+|||+++||++|+|+||+|+++|+|.|+|+|+|+|.+..+..++|++||.|||+|
T Consensus 81 ~~~~~~YEg~gP~GvaiiVe~lTDN~nRt~~~ir~~f~K~gg~l~~~gsv~~~Fe~kG~i~~~~~~~~~d~~~e~aieaG 160 (238)
T TIGR01033 81 NYEEITYEGYAPGGVAIIVECLTDNKNRTASEVRSAFNKNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEAAIEAG 160 (238)
T ss_pred ceEEEEEEEEcCCceEEEEEEecCCHHhHHHHHHHHHHHcCCeeCCCCceeeeeecceEEEECCCCCCHHHHHHHHHhCC
Confidence 89999999999999999999999999999999999999999999999999999999999999865567999999999999
Q ss_pred CccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCCcc-chhh
Q 021961 233 AEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIE-DIHQ 297 (305)
Q Consensus 233 AEDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve-~~~~ 297 (305)
||||++. + +.|+|+|+|++|.+|+++|++.||++.++ +++|+|+++|+ ++++
T Consensus 161 Aedv~~~----~--------~~~~v~~~~~~~~~v~~~L~~~g~~i~~s-ei~~~P~~~v~l~~e~ 213 (238)
T TIGR01033 161 AEDIDVD----D--------DEFEVYTAPEELEKVKEALEAKGFPIESA-EITMIPLTTVDLDDEQ 213 (238)
T ss_pred Cceeecc----C--------CcEEEEECHHHHHHHHHHHHHcCCCceee-EEEEecCCCcccCHHH
Confidence 9999531 1 12999999999999999999999999986 99999999999 6554
No 5
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=100.00 E-value=3.3e-72 Score=515.67 Aligned_cols=203 Identities=39% Similarity=0.662 Sum_probs=180.1
Q ss_pred chhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccC-CccceeE
Q 021961 78 RRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEAFIE 156 (305)
Q Consensus 78 ~KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~-~~~~~~e 156 (305)
+||+||||+|+++|++|+++|+||+|+|++|||+|||||+.|++|+++|++||+.||||++||||||||++. ++.+|++
T Consensus 1 sKW~nIkh~K~~~D~~ksk~f~kl~reI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~IerAIkk~~~~~~~~~~~~ 80 (234)
T PF01709_consen 1 SKWSNIKHKKAAQDAKKSKLFTKLSREITVAVKEGGPDPDMNPRLRSAIEKAKKANMPKDNIERAIKKASGKSDGANYEE 80 (234)
T ss_dssp -SCGGTSSSTTTTTTSHHHHHHHHHHHHHHHHHCC-S-GGGSHHHHHHHHHHHHTT--HHHHHHHHHHCCSTSST---EE
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHHHHHhCCCHHHHHHHHHhcCcCCCCcCceE
Confidence 589999999999999999999999999999999999999999999999999999999999999999999987 7778999
Q ss_pred EEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCCccc
Q 021961 157 KVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDV 236 (305)
Q Consensus 157 ~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGAEDV 236 (305)
++|||||||||+|||||+|||+|||+++||++|+|+||+|+++|||.|||+|+|+|.+.....++|++||+|||+|||||
T Consensus 81 ~~yEg~gP~Gvaiive~lTDN~nRt~~~ir~~~~K~gg~l~~~gsv~~~F~~kG~i~~~~~~~~~d~~~e~aIe~GaeDv 160 (234)
T PF01709_consen 81 ITYEGYGPGGVAIIVECLTDNKNRTVSDIRSIFKKNGGSLGPSGSVSFMFERKGVIEVSKKDLDEDELMEDAIEAGAEDV 160 (234)
T ss_dssp EEEEEEETTTEEEEEEEEES-HHHHHHHHHHHHHTTT-EEE-TTSSGGGEEEEEEEEEEHCCS-HHHHHHHHHHHTESEE
T ss_pred EEEEEEcCCCcEEEEEEeCCCHhHHHHHHHHHHHHcCceeCCCCcceeeeeeeEEEEEEeCCCChHHHHHHHHhCCCcEe
Confidence 99999999999999999999999999999999999999999999999999999999998667899999999999999999
Q ss_pred cCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCCcc
Q 021961 237 IEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIE 293 (305)
Q Consensus 237 ee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve 293 (305)
++. ++.|+|+|+|.+|.+|+++|++.||++.++ +++|+|+++|+
T Consensus 161 e~~------------d~~~~~~c~p~~~~~v~~~L~~~g~~i~~~-e~~~~P~~~v~ 204 (234)
T PF01709_consen 161 EED------------DGEFEFICDPSDLSAVKKALEKKGYEIESA-ELEYIPNNPVE 204 (234)
T ss_dssp EEC------------TSEEEEEEEGGGHHHHHHHHHHTT---SEE-EEEEEESS-EE
T ss_pred eec------------CCeEEEEECHHHHHHHHHHHHHcCCCeeEE-EEEEeCCCCcc
Confidence 741 145999999999999999999999999986 99999999999
No 6
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=4.6e-63 Score=454.33 Aligned_cols=226 Identities=37% Similarity=0.571 Sum_probs=208.4
Q ss_pred ccccccccCCCccCCc-hhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHH
Q 021961 63 FQVRTIRTFAPVCMGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVER 141 (305)
Q Consensus 63 ~~~R~~~~~~~~~mG~-KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IEr 141 (305)
++.|++++++..+.|| ||+||||+|+++|++|+|++.||+++|..|||.||+||..|.+|+++++.||+.+||||.||+
T Consensus 17 s~s~sv~~s~~~~sgH~kwskIk~~Kg~nD~~rsk~~nkl~~~i~~aVk~gg~np~lN~~LAtlle~ak~~~vpkd~ien 96 (276)
T KOG2972|consen 17 SRSRSVTTSGWIMSGHNKWSKIKHKKGANDQARSKQINKLSQGIILAVKQGGANPELNMRLATLLESAKKISVPKDGIEN 96 (276)
T ss_pred CchhheecccceecccchhhhhcccccccHHHHHHHHHHHHHHHHHHHHhcCCCchhhhHHHHHHHHHHhcCCCHHHHHH
Confidence 3456777888888998 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCCccceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeE-EEEeeCCCCC
Q 021961 142 NIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRAR-VVNIKFTDAD 220 (305)
Q Consensus 142 AIkra~g~~~~~~~e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kG-vi~v~~~~~d 220 (305)
||+||+++++...+++.||+||||||+||||++|||+||+++.||++|+|+||.+. +++.|+|++|| ||.|+++..|
T Consensus 97 ~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~nk~GG~s~--~~~r~~FdkKG~Vv~V~~~~~d 174 (276)
T KOG2972|consen 97 AINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIFNKHGGASA--SGVRFLFDKKGVVVNVPPEKRD 174 (276)
T ss_pred HHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHHHHcCCccc--ccceeEEeccceEEecChhhcc
Confidence 99999998888888899999999999999999999999999999999999999766 46899999999 6778877788
Q ss_pred HHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCCcc
Q 021961 221 KDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIE 293 (305)
Q Consensus 221 ~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve 293 (305)
+|.+.-.+||+||+|+..+|+.|+|+||++ +.|+++|+|+++++|...|.+.||.+.. ++++|+|.++|+
T Consensus 175 k~vL~ie~ie~~A~d~~~~~~~e~d~eeer--~~fkiv~e~ssl~qV~~~Lr~~G~~i~d-~~le~~P~~~ve 244 (276)
T KOG2972|consen 175 KDVLNIEAIEAGAEDIVAEPVLEIDEEEER--EEFKIVTEPSSLNQVAHKLRSKGFEIKD-SGLEFIPLEEVE 244 (276)
T ss_pred hhhhhHHHHHhcccccccCccccccccccc--ceeEEEeccchHHHHHHHhhcCCceeec-cccccccCCccc
Confidence 888888889999999999888877655543 3499999999999999999999999996 599999999999
No 7
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.69 E-value=2.7e-08 Score=109.08 Aligned_cols=131 Identities=21% Similarity=0.188 Sum_probs=89.4
Q ss_pred HHHHhhccCCCcc-ccccccccccccc-cccccccccccccccccccccccc---ccc-ccccccCCCccCCc-------
Q 021961 12 AILHRISNGVSSK-WSPNSFALSKHGL-LSRNLFSSASSISSWIPLYEVKHC---NFQ-VRTIRTFAPVCMGR------- 78 (305)
Q Consensus 12 ~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~R~~~~~~~~~mG~------- 78 (305)
|+|++...|+... +.||. .+. |+..+ ..|...+|+.++..... +.. +|+=+.--.+-.=|
T Consensus 222 A~l~K~GGGtG~nfS~LR~-----~Ge~IsggG--~SSG~vsFmkifD~aa~aIkQGG~tRRGA~mv~LdvdHPDIeeFI 294 (1220)
T PRK07562 222 ARLFKYGSGTGSNFSNLRG-----EGEKLSGGG--KSSGLMSFLKIGDRAAGAIKSGGTTRRAAKMVIVDIDHPDIEEFI 294 (1220)
T ss_pred HHHHhcCCeEeecccccCC-----CCCcCCCCC--cCCChhhHHHHHHHHHHHHHhCCCCccCceEEEecCCcccHHHHH
Confidence 4556655555433 34444 333 44332 34466677777664332 222 24321111111113
Q ss_pred hhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhC------CCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccC
Q 021961 79 RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKG------GPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK 149 (305)
Q Consensus 79 KwsnIkh~K~a~DakKsklfsKl~keI~vAvk~G------G~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~ 149 (305)
.|-+.+..|.+.+..++|+++|+.++|..|+|.| |+||+.|++|+.+|++||+.+||++.|+|+|++|.+.
T Consensus 295 ~~K~~ee~Kvaalv~gski~~k~lk~I~~A~~~~~G~~~~~~DP~~NpaLk~aI~~Ak~~~vP~~~I~RvI~~A~qg 371 (1220)
T PRK07562 295 DWKVKEEQKVAALVTGSKIVSKHLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALVPENYIKRVIQFARQG 371 (1220)
T ss_pred HhccchhhhHHhhhhcchHHHHHHHHHHHHHHhccccccccCCccccHHHHHHHHHHHhccCCHHHHHHHHHHhhcc
Confidence 2333446899999999999999999999999998 6899999999999999999999999999999998764
No 8
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=55.52 E-value=49 Score=23.04 Aligned_cols=59 Identities=8% Similarity=0.149 Sum_probs=39.5
Q ss_pred EEEecCChhhHHHHHHHHHhhcCcccCCCccceecc--eeeEEEEeeCCCCCHHHHHHHHHHCCC
Q 021961 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKF--RRARVVNIKFTDADKDQLLDIALDAGA 233 (305)
Q Consensus 171 VE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F--~~kGvi~v~~~~~d~D~l~e~AIEaGA 233 (305)
+.+..+++....+++-.+|.++|+++..-.. +.. ...+.+.+..+ +.+++.+.--++|-
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~--~~~~~~~~~~v~~~ve--~~~~~~~~L~~~G~ 62 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYA--FVEKKGGKALLIFRTE--DIEKAIEVLQERGV 62 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEE--EccCCCCeEEEEEEeC--CHHHHHHHHHHCCc
Confidence 5667889999999999999999998753211 111 13455555543 36677776666664
No 9
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=49.59 E-value=1.1e+02 Score=30.30 Aligned_cols=57 Identities=19% Similarity=0.283 Sum_probs=33.7
Q ss_pred HHHHHHHHhhccCCccceeEEEEEEEecCCcEEEEEEecCChh-------hHHHHHHHHHhhcCccc
Q 021961 137 DIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT-------RSVAAVREVVKDCGGKM 196 (305)
Q Consensus 137 d~IErAIkra~g~~~~~~~e~~YE~~GPgGvaiIVE~lTDN~n-------Rt~s~ir~i~~K~gG~l 196 (305)
+.|.+||+.|.....+. ..+.....||.=..|- +.|.++. .++..+...++|+||.+
T Consensus 200 e~IK~aL~~~~~~~~~~-~~i~i~~igaP~Y~i~--~~~~d~k~g~~~l~~a~~~i~~~i~~~gG~~ 263 (319)
T PTZ00248 200 DAVKEALIAGQEVATDE-CKITIKLIAPPQYVIV--TTCSDKDKGMEIIGAALEAIKEVIKKKGGDF 263 (319)
T ss_pred HHHHHHHHHHHhcCCCc-CcEEEEEEcCCeEEEE--EEeCCHHHHHHHHHHHHHHHHHHHHHcCCeE
Confidence 56778887775433221 2455556677655544 4555544 56666677777877753
No 10
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=48.91 E-value=46 Score=30.97 Aligned_cols=69 Identities=16% Similarity=0.260 Sum_probs=50.6
Q ss_pred EEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccc---eecceeeEEEEeeCCCCCHHHHHHHHHHCC
Q 021961 156 EKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSV---MFKFRRARVVNIKFTDADKDQLLDIALDAG 232 (305)
Q Consensus 156 e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv---~f~F~~kGvi~v~~~~~d~D~l~e~AIEaG 232 (305)
.+.|.+. +...|++...+...|+.++.++||-+.....- .......+.+++..+...+|++++..-+.|
T Consensus 47 kii~~~~--------l~lev~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g 118 (262)
T PF14257_consen 47 KIIKTAD--------LSLEVKDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELG 118 (262)
T ss_pred eEEEEEE--------EEEEECCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccC
Confidence 3566665 77788999999999999999999987643221 233566777777665567888888777777
No 11
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=47.53 E-value=68 Score=27.01 Aligned_cols=76 Identities=14% Similarity=0.200 Sum_probs=42.9
Q ss_pred eeEEEEeeCCCCCHHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEE--EeCcccHHHHHHHHHHCCCCeeecccce
Q 021961 208 RARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKV--VSTSDNYTDITTKLREAGIPFETDNGSE 285 (305)
Q Consensus 208 ~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i--~~~p~d~~~V~~~L~~~G~~i~~s~ele 285 (305)
...+|.++-...-....+..|++.||+-|--.. . .. ++..|.- +-...-+..+++.|++.|++.+-- .+.
T Consensus 28 ~vriIrvpC~Grv~~~~il~Af~~GADGV~V~g---C-~~---g~Ch~~~Gn~~a~~Rv~~~k~~L~~~Gi~~eRv-~~~ 99 (124)
T PF02662_consen 28 NVRIIRVPCSGRVDPEFILRAFEKGADGVLVAG---C-HP---GDCHYREGNYRAEKRVERLKKLLEELGIEPERV-RLY 99 (124)
T ss_pred CeEEEEccCCCccCHHHHHHHHHcCCCEEEEeC---C-CC---CCCCcchhhHHHHHHHHHHHHHHHHcCCChhHe-EEE
Confidence 355777765443445677789999998875421 0 00 1122210 011233578888999999986443 344
Q ss_pred eecCCC
Q 021961 286 LLPITT 291 (305)
Q Consensus 286 ~iP~~~ 291 (305)
|+....
T Consensus 100 ~~~~~~ 105 (124)
T PF02662_consen 100 WISAPE 105 (124)
T ss_pred EeCccc
Confidence 454443
No 12
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=46.81 E-value=68 Score=22.06 Aligned_cols=28 Identities=11% Similarity=0.287 Sum_probs=24.0
Q ss_pred EEEecCChhhHHHHHHHHHhhcCcccCC
Q 021961 171 VEVLTDKITRSVAAVREVVKDCGGKMAD 198 (305)
Q Consensus 171 VE~lTDN~nRt~s~ir~i~~K~gG~l~~ 198 (305)
+.+..+|..+..++|-.+|.++|.++..
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~ 29 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAA 29 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeee
Confidence 3457889999999999999999998753
No 13
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=43.68 E-value=1.1e+02 Score=21.18 Aligned_cols=27 Identities=22% Similarity=0.251 Sum_probs=23.7
Q ss_pred EEEecCChhhHHHHHHHHHhhcCcccC
Q 021961 171 VEVLTDKITRSVAAVREVVKDCGGKMA 197 (305)
Q Consensus 171 VE~lTDN~nRt~s~ir~i~~K~gG~l~ 197 (305)
+.+.++|.....++|-.+|.++|.++.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~ 28 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIA 28 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCee
Confidence 456788999999999999999999875
No 14
>TIGR00341 conserved hypothetical protein TIGR00341. This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see model TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803.
Probab=38.07 E-value=93 Score=30.85 Aligned_cols=56 Identities=7% Similarity=0.057 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCe
Q 021961 219 ADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPF 278 (305)
Q Consensus 219 ~d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i 278 (305)
...|.+.+...+.+.|++.....+|+ ++ .+..+.++.+.++.+.|.++|++.|+.-
T Consensus 13 ~~~~~v~~~l~~~~~~~i~~~~~~~~--~~--~~~~i~~~v~~~~~e~vld~L~~lgl~~ 68 (325)
T TIGR00341 13 EGVVMRKEIVRGEDLEEIAIELGDKT--FI--YDDRIELYVQDSDTEKIVSRLKDKLLGY 68 (325)
T ss_pred chHHHHHHHHhccCcccceEEeccCC--CC--cceEEEEEcChhhHHHHHHHHHHcCCCC
Confidence 46788888777777744433211111 11 2367899999999999999999998764
No 15
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=36.54 E-value=95 Score=22.46 Aligned_cols=51 Identities=22% Similarity=0.346 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccC
Q 021961 97 LYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK 149 (305)
Q Consensus 97 lfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~ 149 (305)
++.++...|...+..|.--| +.+|-+.-+-|+..+++..++.+|+++-...
T Consensus 1 l~~~i~~~l~~~I~~g~~~~--g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGRLPP--GDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp HHHHHHHHHHHHHHTTSS-T--TSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHcCCCCC--CCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 45678888999999886443 3355556667899999999999999986643
No 16
>PF14502 HTH_41: Helix-turn-helix domain
Probab=36.38 E-value=42 Score=24.42 Aligned_cols=43 Identities=19% Similarity=0.265 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEecCCcE
Q 021961 121 VLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS 168 (305)
Q Consensus 121 ~La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~GPgGva 168 (305)
||..+-+-+.+.++..-+|++|||.-...+. +..|-.|--|.+
T Consensus 5 Ri~tI~e~~~~~~vs~GtiQ~Alk~Le~~ga-----I~Le~rGh~GTf 47 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSRGTIQNALKFLEENGA-----IKLESRGHLGTF 47 (48)
T ss_pred ccCCHHHHHHHhCcchhHHHHHHHHHHHCCc-----EEeeecCcCccc
Confidence 6677888999999999999999997554432 556777766654
No 17
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=36.36 E-value=84 Score=30.99 Aligned_cols=60 Identities=17% Similarity=0.163 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 187 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~ 187 (305)
+..+|.-|...++|.+.|.++|+.-.+-. -++|..+ .+|+.+|.|+.-.|+.-+..-++.
T Consensus 280 a~aAia~~~~lgi~~~~i~~~L~~f~~~~------~R~e~~~~~~g~~vi~D~~a~N~~s~~~al~~ 340 (447)
T PRK02472 280 ALAAIAAAKLLGVSNEAIREVLSTFSGVK------HRLQYVGTIDGRKFYNDSKATNILATQKALSG 340 (447)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CcceEEEEECCeEEEECCCCCCHHHHHHHHHh
Confidence 56677788899999999999998654322 3555544 468899999877788776665554
No 18
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ.
Probab=35.66 E-value=1.2e+02 Score=29.88 Aligned_cols=61 Identities=15% Similarity=0.199 Sum_probs=45.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..++.-|...++|.+.|.++|+.-.+-. -+.|....+|+.+|+++.-.|+.-..+-+..+
T Consensus 259 ~laAia~~~~lGi~~~~i~~~l~~~~~~~------gR~e~~~~~~~~vidDsya~np~s~~~al~~l 319 (417)
T TIGR01143 259 ALAAAALALELGIPLEEIAEGLAELKLVK------GRFEIQTKNGLTLIDDTYNANPDSMRAALDAL 319 (417)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceeEEcCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 55677788899999999999998754322 24453345789999998888888777666655
No 19
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=35.40 E-value=1.2e+02 Score=30.25 Aligned_cols=61 Identities=16% Similarity=0.176 Sum_probs=45.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...++|.+.|.++|+.-.+-. .++|..+ .+|+.+|.|.--.|+.-+.+-++.+
T Consensus 278 alaAia~a~~lgi~~~~i~~~L~~f~g~~------~R~e~v~~~~gv~~idDs~atN~~a~~~al~~l 339 (448)
T PRK03803 278 ALAALALGEAAGLPKEAMLEVLRTFTGLP------HRCEWVREVAGVDYYNDSKGTNVGATVAAIEGL 339 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCC------CceEEEEEeCCeEEEEcCCcCCHHHHHHHHHhh
Confidence 56788889999999999999998754422 3555544 3578788888677888887777765
No 20
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=35.11 E-value=1.5e+02 Score=21.31 Aligned_cols=59 Identities=17% Similarity=0.273 Sum_probs=40.5
Q ss_pred EEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCC
Q 021961 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA 233 (305)
Q Consensus 171 VE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGA 233 (305)
+.+..+|.....++|-.+|.++|.++-.-. .+.-..++++.+.. .|.|.+.+.--++|-
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i~--~~~~~~~~~~rl~~--~~~~~~~~~L~~~G~ 62 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRALS--IADTSEFGILRLIV--SDPDKAKEALKEAGF 62 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEEE--EEecCCCCEEEEEE--CCHHHHHHHHHHCCC
Confidence 445788999999999999999999874211 12222357777764 356677777666764
No 21
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase.
Probab=33.57 E-value=1.2e+02 Score=29.89 Aligned_cols=61 Identities=16% Similarity=0.219 Sum_probs=45.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.|..-.|+.-+..-++.+
T Consensus 269 a~aAia~a~~lgi~~~~i~~~L~~f~g~~------~R~e~v~~~~g~~~idD~~atn~~a~~~al~~~ 330 (433)
T TIGR01087 269 ILAAIALAKSLGLNLEAILEALRSFKGLP------HRLEYVGQKNGVHFYNDSKATNVHATLAALSAF 330 (433)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEEEECCEEEEEcCCCCCHHHHHHHHHhC
Confidence 56778889999999999999998765432 3555543 3688899997778888777777654
No 22
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=32.73 E-value=1.4e+02 Score=29.78 Aligned_cols=60 Identities=18% Similarity=0.226 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 187 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~ 187 (305)
+..|+.-|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.|+...|+.-+.+-|+.
T Consensus 292 a~aAiaa~~~lgi~~~~i~~gL~~~~~~~------gR~e~i~~~~g~~vIdDs~ahNp~s~~~aL~~ 352 (460)
T PRK01390 292 AAAAYAAARALGLSPEEIAAGLASFPGLA------HRMEQVGRRGGVLFVNDSKATNADAAAKALSS 352 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEeeeCCcEEEEcCCCCCHHHHHHHHHh
Confidence 45667778888999999999998754322 3555444 367888889888999888876663
No 23
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=32.47 E-value=68 Score=21.09 Aligned_cols=25 Identities=16% Similarity=0.251 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHh
Q 021961 121 VLAAVLEKAKELDVPKDIVERNIKR 145 (305)
Q Consensus 121 ~La~aI~~AK~~nmPKd~IErAIkr 145 (305)
-.-.+|.+|+..|++++-|..-++.
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4567899999999999999988864
No 24
>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase. Alternate name: murein tripeptide ligase
Probab=32.16 E-value=1.7e+02 Score=29.09 Aligned_cols=60 Identities=12% Similarity=0.173 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...+++.+.|.++++...+- +.++|..+ .+|+.+|.|+ ..|+.-+.+-++.+
T Consensus 283 a~~A~a~~~~lgi~~~~i~~~L~~~~~~------~~R~e~~~~~~g~~ii~D~-ahNp~s~~~~l~~l 343 (448)
T TIGR01081 283 ALMAIAAARHVGVAIEDACEALGSFVNA------KRRLELKGEANGITVYDDF-AHHPTAIEATLQGL 343 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCC------CcceEEEEecCCeEEEEeC-CCCHHHHHHHHHHH
Confidence 4567778888899999999999764432 23566554 4688999998 88888777666665
No 25
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=32.06 E-value=1.2e+02 Score=30.07 Aligned_cols=61 Identities=15% Similarity=0.135 Sum_probs=45.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
..+|+.-|...++|.+.|.++|+.-.+.. .++|..+ .+|+.+|-|+.--|+.-+.+-++.+
T Consensus 274 alaAia~a~~lGi~~~~i~~~L~~f~g~~------~R~e~v~~~~g~~~idDs~~tn~~s~~~Al~~~ 335 (438)
T PRK04663 274 VLVVLALLDAAGVDYRKALDALKSYTGLT------HRCQVVADNHGIKWVNDSKATNVASTLAALSGL 335 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEeeeeCCcEEEeCCCcCCHHHHHHHHHhc
Confidence 45677788999999999999998654432 3455443 3688899998877888887777764
No 26
>PRK14106 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=31.96 E-value=1.3e+02 Score=29.73 Aligned_cols=61 Identities=15% Similarity=0.171 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...++|.+.|..+|+...+-. -++|... .+|+.+|+|+.-.|+.-+.+-++.+
T Consensus 284 a~aAia~~~~lgi~~~~i~~~L~~~~~~~------gR~e~i~~~~~~~vi~D~~ahNP~s~~~~l~~l 345 (450)
T PRK14106 284 ALAATAAAYLLGISPDVIANTLKTFKGVE------HRIEFVAEINGVKFINDSKGTNPDAAIKALEAY 345 (450)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------cceEEEeeECCEEEEeCCCccCHHHHHHHHHhC
Confidence 66778889999999999999998754322 2444432 3567899998888997666555543
No 27
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=31.86 E-value=1.5e+02 Score=29.37 Aligned_cols=61 Identities=13% Similarity=0.183 Sum_probs=45.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...++|.+.|.++|+.-.+-. -++|..+ .+|+.+|.|+.-.|+.-+..-++.+
T Consensus 273 a~aAia~a~~lgi~~~~i~~~L~~f~~~~------gR~E~v~~~~~~~~i~Ds~a~n~~a~~~al~~l 334 (438)
T PRK03806 273 ALAALALADAVGIPRASSLKALTTFTGLP------HRFQLVLEHNGVRWINDSKATNVGSTEAALNGL 334 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CeEEEEEeeCCEEEEEcCCCCCHHHHHHHHHhC
Confidence 56778889999999999999998654322 3555554 3688888888888888777776664
No 28
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=31.29 E-value=1.4e+02 Score=32.37 Aligned_cols=61 Identities=11% Similarity=0.115 Sum_probs=47.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..++.-|...++|.+.|.++|+.-.+.. -++|..+ .+|+.+|.|+.-.|+.-+.+-|+.+
T Consensus 291 alaAia~a~~lGi~~~~i~~~L~~f~~~~------gR~e~~~~~~g~~vIdDSyn~nP~s~~aaL~~l 352 (822)
T PRK11930 291 LIHCIAVLLYLGYSADQIQERMARLEPVA------MRLEVKEGINNCTLINDSYNSDLQSLDIALDFL 352 (822)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CeeEEEEcCCCcEEEECCCCCCHHHHHHHHHHH
Confidence 44677789999999999999998654322 3566665 5789999998888888887777666
No 29
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=31.24 E-value=1.4e+02 Score=29.56 Aligned_cols=61 Identities=10% Similarity=0.198 Sum_probs=43.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...++|.+.|.++|+.-.+-. -++|..+ .+|+.+|.|+.-.|+.-+.+-++.+
T Consensus 286 alaAia~a~~lgv~~~~i~~~L~~f~~~~------gR~e~~~~~~~~~ii~Ds~a~N~~s~~~al~~l 347 (459)
T PRK02705 286 LLLAVAAARLAGLSAEAIAEALRSFPGVP------HRLERIGTINGIDFINDSKATNYDAAEVGLKAV 347 (459)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEEeeCCcEEEEeCCCCCHHHHHHHHHhC
Confidence 55677888889999999999998754322 3455444 2578899998778887666666554
No 30
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.07 E-value=3e+02 Score=23.29 Aligned_cols=75 Identities=16% Similarity=0.223 Sum_probs=51.8
Q ss_pred HHHHHHHHHhhcC-cccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEEEe
Q 021961 181 SVAAVREVVKDCG-GKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVS 259 (305)
Q Consensus 181 t~s~ir~i~~K~g-G~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i~~ 259 (305)
=+..||..|..+| |..|+-..+.|.=+..|.+..-.. .+. .-=|.|..+.. .+..++++|
T Consensus 16 ~~e~vr~aL~~aGag~iG~Y~~C~~~~~g~G~frP~eg-AnP-----~iGevgk~e~v-------------~E~kiE~v~ 76 (109)
T COG3323 16 YVEQVRDALFEAGAGHIGNYDHCTFSSEGTGQFRPLEG-ANP-----FIGEVGKLEFV-------------AEVKIEFVV 76 (109)
T ss_pred HHHHHHHHHHhcCCcceeccceEEEEeeeeEEEeecCC-CCC-----cccccceEEee-------------eeeEEEEEc
Confidence 4678999999998 689988888887788888775321 110 00022322211 135699999
Q ss_pred CcccHHHHHHHHHHC
Q 021961 260 TSDNYTDITTKLREA 274 (305)
Q Consensus 260 ~p~d~~~V~~~L~~~ 274 (305)
+.+..+.+.+.+.+.
T Consensus 77 ~~~~~~~v~~~ik~a 91 (109)
T COG3323 77 PAELRAAVLSAIKKA 91 (109)
T ss_pred CHHHHHHHHHHHHHh
Confidence 999999999999887
No 31
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=30.17 E-value=1.6e+02 Score=29.58 Aligned_cols=61 Identities=11% Similarity=0.031 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..||.-|...++|.+.|.++|+.-.+-. -++|... ++|+.+|-|+.-.|+.-..+-+..+
T Consensus 287 alaAia~a~~lGi~~~~i~~~L~~~~~~~------gR~e~v~~~~g~~iIDDsYn~nP~s~~aaL~~l 348 (453)
T PRK10773 287 ALAAAALAMSVGATLDAVKAGLANLKAVP------GRLFPIQLAEGQLLLDDSYNANVGSMTAAAQVL 348 (453)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceeEEECCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence 45677889999999999999998755422 2344332 5788777788888887666666555
No 32
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=29.73 E-value=53 Score=22.94 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=15.9
Q ss_pred HHHHHHhcCCCHHHHHHHHHhh
Q 021961 125 VLEKAKELDVPKDIVERNIKRA 146 (305)
Q Consensus 125 aI~~AK~~nmPKd~IErAIkra 146 (305)
.-+.|+..|||+.+|.+-++..
T Consensus 19 ~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 19 IRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp HHHHHHHHT--HHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHcCC
Confidence 4456899999999999888753
No 33
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=29.37 E-value=1.7e+02 Score=29.53 Aligned_cols=59 Identities=12% Similarity=0.094 Sum_probs=43.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...++|.+.|.++|+. .+-. -+.|..+ .+|+.+|+| ...|+.-..+-+..+
T Consensus 301 alaAia~a~~lgi~~~~i~~~L~~-~~~~------gR~e~i~~~~g~~vi~D-yahNP~s~~aal~~l 360 (481)
T PRK14022 301 AMAAGLACLRLGASLEDIQKGIAQ-TPVP------GRMEVLTQSNGAKVFID-YAHNGDSLNKLIDVV 360 (481)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcc-CCCC------CCeEEEECCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 556777888899999999999976 3322 3555555 368889999 788887766666655
No 34
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=28.07 E-value=2e+02 Score=28.90 Aligned_cols=60 Identities=15% Similarity=0.107 Sum_probs=45.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
...|+.-|...++|.+.|..+|+.-.+-. -++|... .+|+.+|+| .-.|+.-..+-+..+
T Consensus 283 alaAia~a~~lgi~~~~i~~~L~~~~~~~------gR~e~~~~~~~~~iI~D-yahNP~s~~aal~~l 343 (460)
T PRK00139 283 LLAALAALLALGVPLEDALAALAKLQGVP------GRMERVDAGQGPLVIVD-YAHTPDALEKVLEAL 343 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CCcEEEEcCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 45677788889999999999998765322 2455554 378999999 888888777777766
No 35
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=27.94 E-value=29 Score=28.97 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=18.5
Q ss_pred CCCCCCCCHHHHHHHHHH--HhcCCCHHHH
Q 021961 112 GGPNPTSNTVLAAVLEKA--KELDVPKDIV 139 (305)
Q Consensus 112 GG~DP~~N~~La~aI~~A--K~~nmPKd~I 139 (305)
|+.+|+.|..+.+.|-+. ++.++|+|.|
T Consensus 67 G~~~~~~n~~~s~~i~~~l~~~LgIp~dRi 96 (113)
T PTZ00450 67 GEYAPSKPKMMTPRITAAITKECGIPAERI 96 (113)
T ss_pred cCcCHHHHHHHHHHHHHHHHHHcCCCcccE
Confidence 456777777777777654 5567776654
No 36
>PRK12338 hypothetical protein; Provisional
Probab=27.28 E-value=1.5e+02 Score=29.24 Aligned_cols=132 Identities=17% Similarity=0.277 Sum_probs=78.8
Q ss_pred HHHHHHHHhcCCC---HHHHHHHHHhhccCCccceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCcccCCC
Q 021961 123 AAVLEKAKELDVP---KDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADP 199 (305)
Q Consensus 123 a~aI~~AK~~nmP---Kd~IErAIkra~g~~~~~~~e~~YE~~GPgGvaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~ 199 (305)
..+++.|++.++| ..++++++++.-..=. +... +=+.-.....+..++..++-++||.+-+-
T Consensus 172 ~~l~~~A~e~~VpvI~N~did~Tv~~ile~I~----e~s~-----------~i~~~H~~~~~~~El~~I~vd~Gg~v~dV 236 (319)
T PRK12338 172 DHLVEQAREHNVPVIKNDDIDCTVKKMLSYIR----EVCV-----------TVTLQHSVDDLDEVIEIIIKRHGGRITDI 236 (319)
T ss_pred HHHHHhHhhCCCceeCCCcHHHHHHHHHHHHH----hheE-----------EEEEeCCHHHHHHHHHeEEecCCCEEEEe
Confidence 3466789999999 6777888776643211 1111 23344567888888888889999998764
Q ss_pred ccceecc--eeeEEEEeeCCCCCHHHHHHHHHHCC-----CccccCCCCCCCCCcccccCce-EEEEe-CcccHHHHHHH
Q 021961 200 GSVMFKF--RRARVVNIKFTDADKDQLLDIALDAG-----AEDVIEPPVNEDDTDEDRAERY-YKVVS-TSDNYTDITTK 270 (305)
Q Consensus 200 gsv~f~F--~~kGvi~v~~~~~d~D~l~e~AIEaG-----AEDVee~~~~Ed~~~ed~~~~~-~~i~~-~p~d~~~V~~~ 270 (305)
..--|=| .=+|-+.+.. ..|-+..++..=+.. ++-+-+. +++-. ..|.+ +.++|..+.++
T Consensus 237 ~h~iyG~~~~i~~~l~i~s-~~dv~~Fi~~~~~~~~~~~~~~~L~~l----------T~gvH~Hti~a~~~e~l~~i~~~ 305 (319)
T PRK12338 237 SYPIPGFKDPLKREVNVSD-PDEAEKFIKRLNENPKKKEDLKRLYSL----------SNNVHSHRICAPDEESLNRIIEE 305 (319)
T ss_pred cccCCCCCceeEEEEccCC-HHHHHHHHHHHhhCCccccchhhHHHH----------hCCeeEEEEEeCCHHHHHHHHHH
Confidence 3112223 2233344432 234566666554444 3433322 01233 45555 55678999999
Q ss_pred HHHCCCCeee
Q 021961 271 LREAGIPFET 280 (305)
Q Consensus 271 L~~~G~~i~~ 280 (305)
|+++||=++.
T Consensus 306 L~~~G~L~~~ 315 (319)
T PRK12338 306 LEEEGLLYEE 315 (319)
T ss_pred HHHCCccccC
Confidence 9999997743
No 37
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=27.12 E-value=4.4e+02 Score=25.29 Aligned_cols=95 Identities=17% Similarity=0.197 Sum_probs=58.4
Q ss_pred CCcEEEEEEecCChhhHHHHHHHHHhh-cCcccCCCccceecce-eeEEEEeeCCCCCHHHHHHHHHHCCCccccCCCCC
Q 021961 165 GGVSIVVEVLTDKITRSVAAVREVVKD-CGGKMADPGSVMFKFR-RARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVN 242 (305)
Q Consensus 165 gGvaiIVE~lTDN~nRt~s~ir~i~~K-~gG~l~~~gsv~f~F~-~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~ 242 (305)
|=..|++++-.++.+....+++..|.. .+-.++-.-++.+.=+ .+-.|.+.+.+.++.++++ ++..|--+.+
T Consensus 40 ~~F~mr~~v~~~~~~~~~~~l~~~l~~~~~~~~~l~i~l~~~~~~~ki~vl~Sg~g~nl~~l~~-~~~~g~l~~~----- 113 (280)
T TIGR00655 40 GRFFMRVEFQLEGFRLEESSLLAAFKSALAEKFEMTWELILADKLKRVAILVSKEDHCLGDLLW-RWYSGELDAE----- 113 (280)
T ss_pred CeEEEEEEEEeCCCCCCHHHHHHHHHHHHHHHhCCEEEEecCCCCcEEEEEEcCCChhHHHHHH-HHHcCCCCcE-----
Confidence 445667787777766778899999999 7777763333333212 2334566666778888877 4666643322
Q ss_pred CCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCee
Q 021961 243 EDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 279 (305)
Q Consensus 243 Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~ 279 (305)
..-|+++..++..+ .++.|+++.
T Consensus 114 -----------i~~visn~~~~~~~---A~~~gIp~~ 136 (280)
T TIGR00655 114 -----------IALVISNHEDLRSL---VERFGIPFH 136 (280)
T ss_pred -----------EEEEEEcChhHHHH---HHHhCCCEE
Confidence 23566666655442 455677653
No 38
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=27.02 E-value=1.4e+02 Score=30.03 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=32.8
Q ss_pred ceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCC
Q 021961 253 RYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITT 291 (305)
Q Consensus 253 ~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~ 291 (305)
..+.|-|+|..|..=.+.|.+.||.++...-+.|.|.|+
T Consensus 394 ~ivyvSCnp~tlaRDl~~L~~~gY~l~~i~~~DmFP~T~ 432 (443)
T PRK13168 394 RIVYVSCNPATLARDAGVLVEAGYRLKRAGMLDMFPHTG 432 (443)
T ss_pred eEEEEEeChHHhhccHHHHhhCCcEEEEEEEeccCCCCC
Confidence 467899999999888889989999997766688889764
No 39
>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.47 E-value=84 Score=23.54 Aligned_cols=29 Identities=14% Similarity=0.165 Sum_probs=26.9
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCcccCC
Q 021961 170 VVEVLTDKITRSVAAVREVVKDCGGKMAD 198 (305)
Q Consensus 170 IVE~lTDN~nRt~s~ir~i~~K~gG~l~~ 198 (305)
++|+.+.++....++|-.+|..+|.++-+
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~ 30 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVE 30 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEE
Confidence 68999999999999999999999998763
No 40
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=26.44 E-value=84 Score=23.61 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=25.2
Q ss_pred EEEEEecCChhhHHHHHHHHHhhcCcccCCC
Q 021961 169 IVVEVLTDKITRSVAAVREVVKDCGGKMADP 199 (305)
Q Consensus 169 iIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~ 199 (305)
+||-++-.++...++.|-.++.++||++.+.
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~ 33 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDS 33 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEE
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEE
Confidence 6788888999999999999999999998764
No 41
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=26.39 E-value=1.6e+02 Score=29.54 Aligned_cols=58 Identities=16% Similarity=0.161 Sum_probs=42.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHH
Q 021961 123 AAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 187 (305)
Q Consensus 123 a~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~ 187 (305)
..|+.-|... +|.+.|.++|+.-.+.. .+.|..+ .+|+-+|.|+.--|+..+.+-|+.
T Consensus 289 laA~a~a~~~-i~~~~i~~~L~~f~~~~------~R~e~~~~~~g~~~i~Dsy~~np~s~~~al~~ 347 (458)
T PRK01710 289 LAAFCAVNDD-VSIESMKKVATTFSGVE------HRCEFVREINGVKYYNDSIASSPTRTLAGLKA 347 (458)
T ss_pred HHHHHHHHhC-CCHHHHHHHHHhCCCCC------cceEEEEEECCEEEecccccCCHHHHHHHHHh
Confidence 3445556666 99999999998755432 3555544 589999999999999977776653
No 42
>PF14501 HATPase_c_5: GHKL domain
Probab=26.21 E-value=2.8e+02 Score=21.46 Aligned_cols=58 Identities=16% Similarity=0.301 Sum_probs=34.0
Q ss_pred HHHHHHHhhccCCccceeEEEEEEEecCCcEEEEEEecCChh--------------hHHHHHHHHHhhcCccc
Q 021961 138 IVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT--------------RSVAAVREVVKDCGGKM 196 (305)
Q Consensus 138 ~IErAIkra~g~~~~~~~e~~YE~~GPgGvaiIVE~lTDN~n--------------Rt~s~ir~i~~K~gG~l 196 (305)
.||+||+-+.......+.++.+...+ +-+.|.|+=-+++.. ==...|+.+++|++|.+
T Consensus 13 lldNAiea~~~~~~~~~I~i~~~~~~-~~~~i~i~N~~~~~~~~~~~~~~~~~~~G~GL~~v~~i~~~y~g~~ 84 (100)
T PF14501_consen 13 LLDNAIEACKKYEDKRFISISIREEN-GFLVIIIENSCEKEIEKLESSSSKKKGHGIGLKNVKKILEKYNGSL 84 (100)
T ss_pred HHHHHHHHHHhcCCCcEEEEEEEecC-CEEEEEEEECCCCccccccccccCCCCCCcCHHHHHHHHHHCCCEE
Confidence 46778876655432556665444333 555555554443321 12467889999998865
No 43
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=25.44 E-value=55 Score=26.10 Aligned_cols=20 Identities=20% Similarity=0.421 Sum_probs=17.1
Q ss_pred cccHHHHHHHHHHCCCCeee
Q 021961 261 SDNYTDITTKLREAGIPFET 280 (305)
Q Consensus 261 p~d~~~V~~~L~~~G~~i~~ 280 (305)
-+.|+.|++.|++.||++..
T Consensus 7 E~~Ls~v~~~L~~~GyeVv~ 26 (80)
T PF03698_consen 7 EEGLSNVKEALREKGYEVVD 26 (80)
T ss_pred cCCchHHHHHHHHCCCEEEe
Confidence 35689999999999999854
No 44
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=24.77 E-value=1.2e+02 Score=25.22 Aligned_cols=40 Identities=15% Similarity=0.261 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHH-------HHHHHHhCCCCCCCCHHHHHHHHHHHhcCC
Q 021961 90 QDAKKAKLYSRMGKE-------VISAVKKGGPNPTSNTVLAAVLEKAKELDV 134 (305)
Q Consensus 90 ~DakKsklfsKl~ke-------I~vAvk~GG~DP~~N~~La~aI~~AK~~nm 134 (305)
.+.+|++=.++++++ ++.|... ..||++.+++.-.|..|+
T Consensus 44 g~var~~GMsqvA~~aGlsRe~LYkaLS~-----~GNPtf~Til~V~kAlG~ 90 (100)
T COG3636 44 GVVARSRGMSQVARKAGLSREGLYKALSP-----GGNPTFDTILAVLKALGL 90 (100)
T ss_pred HHHHHhcCHHHHHHHhCccHHHHHHHhCC-----CCCCcHHHHHHHHHHcCc
Confidence 344555556666554 4445544 458999999988888876
No 45
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=24.75 E-value=2e+02 Score=29.13 Aligned_cols=61 Identities=15% Similarity=0.169 Sum_probs=46.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEec-CCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGY-GGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~GP-gGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..++.-|...++|.+.|.++|+.-.+-. .++|..+- +|+.+|.|+-..|+.-+.+-++.+
T Consensus 280 a~aAia~~~~lgi~~~~i~~~L~~F~~~~------~Rle~v~~~~gv~~i~DS~atN~~a~~~al~~~ 341 (454)
T PRK01368 280 IAASYAVAKIIGVEPKKILESISSFQSLP------HRMQYIGSINNISFYNDSKATNAISAVQSIKAL 341 (454)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------cceEEEEEECCeEEEECCCCCCHHHHHHHHHhc
Confidence 45677778888999999999998744322 34554443 789999998888999888877776
No 46
>TIGR00559 pdxJ pyridoxine 5'-phosphate synthase. PdxJ is required in the biosynthesis of pyridoxine (vitamin B6), a precursor to the enzyme cofactor pyridoxal phosphate. ECOCYC describes the predicted reaction equation as 1-amino-propan-2-one-3-phosphate + deoxyxylulose-5-phosphate = pyridoxine-5'-phosphate. The product of that reaction is oxidized by PdxH to pyridoxal 5'-phosphate.
Probab=24.40 E-value=1e+02 Score=29.34 Aligned_cols=89 Identities=22% Similarity=0.288 Sum_probs=62.0
Q ss_pred EEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCCccccCCCCCCCCCcc
Q 021961 169 IVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDE 248 (305)
Q Consensus 169 iIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~Ed~~~e 248 (305)
|.|----|-+.=.-.||+.+-.-... .|+++ ....++++++|++.--+.|...| | ..+|
T Consensus 38 ITvHlReDrRHI~d~Dv~~l~~~~~~--------~lNlE----------~a~~~emi~ia~~vkP~~vtLVP--E-kr~E 96 (237)
T TIGR00559 38 ITVHLREDRRHIQDRDVYDLKEALTT--------PFNIE----------MAPTEEMIRIAEEIKPEQVTLVP--E-ARDE 96 (237)
T ss_pred EEecCCCCcCcCCHHHHHHHHHHcCC--------CEEec----------cCCCHHHHHHHHHcCCCEEEECC--C-CCCC
Confidence 34555566666666666666443221 22222 23357999999999999998876 2 2344
Q ss_pred cccCceEEEEeCcccHHHHHHHHHHCCCCe
Q 021961 249 DRAERYYKVVSTSDNYTDITTKLREAGIPF 278 (305)
Q Consensus 249 d~~~~~~~i~~~p~d~~~V~~~L~~~G~~i 278 (305)
-+.++.+-+....+.+..+-+.|.+.||.+
T Consensus 97 lTTegGldv~~~~~~l~~~i~~l~~~gI~V 126 (237)
T TIGR00559 97 VTTEGGLDVARLKDKLCELVKRFHAAGIEV 126 (237)
T ss_pred ccCCcCchhhhCHHHHHHHHHHHHHCCCEE
Confidence 456678999999999999999999999875
No 47
>cd00003 PNPsynthase Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites; the open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state; a hydrophilic channel running through the center of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed,
Probab=24.11 E-value=1e+02 Score=29.30 Aligned_cols=56 Identities=27% Similarity=0.442 Sum_probs=46.8
Q ss_pred CHHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHHCCCCe
Q 021961 220 DKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPF 278 (305)
Q Consensus 220 d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i 278 (305)
..++.+++|++.--+.|...| | ..+|-+.++.+-+....+.+..+-+.|.+.|+.+
T Consensus 71 ~t~em~~ia~~~kP~~vtLVP--E-kr~E~TTegGldv~~~~~~l~~~i~~l~~~gI~V 126 (234)
T cd00003 71 PTEEMLEIALEVKPHQVTLVP--E-KREELTTEGGLDVAGQAEKLKPIIERLKDAGIRV 126 (234)
T ss_pred CCHHHHHHHHHCCCCEEEECC--C-CCCCccCCccchhhcCHHHHHHHHHHHHHCCCEE
Confidence 358999999999999998876 2 2344456778999999999999999999999975
No 48
>PRK03094 hypothetical protein; Provisional
Probab=23.68 E-value=64 Score=25.81 Aligned_cols=20 Identities=20% Similarity=0.393 Sum_probs=17.0
Q ss_pred cccHHHHHHHHHHCCCCeee
Q 021961 261 SDNYTDITTKLREAGIPFET 280 (305)
Q Consensus 261 p~d~~~V~~~L~~~G~~i~~ 280 (305)
-+.|+.|++.|++.||++..
T Consensus 7 E~~Ls~i~~~L~~~GYeVv~ 26 (80)
T PRK03094 7 EQSLTDVQQALKQKGYEVVQ 26 (80)
T ss_pred ecCcHHHHHHHHHCCCEEEe
Confidence 35689999999999999853
No 49
>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetase. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown.
Probab=23.67 E-value=2.8e+02 Score=27.69 Aligned_cols=60 Identities=13% Similarity=0.111 Sum_probs=44.0
Q ss_pred HHHHHHHHHhcC-CCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELD-VPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~n-mPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+..|+.-|...+ +|.+.|..+|+.-.+.. -++|... .+|+.+|.| ...|+.-..+-+..+
T Consensus 291 alaAia~a~~lg~i~~e~i~~~L~~~~~~~------gR~e~~~~~~g~~vi~D-y~~NP~s~~aal~~l 352 (464)
T TIGR01085 291 LLAALATLLHLGGIDLEDIVAALEKFRGVP------GRMELVDGGQKFLVIVD-YAHTPDALEKALRTL 352 (464)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHhCCCCC------CCcEEEEcCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 456777788888 99999999998765432 2344333 368899999 888888777777766
No 50
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=23.51 E-value=40 Score=28.28 Aligned_cols=52 Identities=25% Similarity=0.448 Sum_probs=22.4
Q ss_pred HHHHHHHHHhhccCCccceeEEEEEEEecCCcE--EEEEE-ecCChhhHHHHHHH-HHhhcCcc
Q 021961 136 KDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS--IVVEV-LTDKITRSVAAVRE-VVKDCGGK 195 (305)
Q Consensus 136 Kd~IErAIkra~g~~~~~~~e~~YE~~GPgGva--iIVE~-lTDN~nRt~s~ir~-i~~K~gG~ 195 (305)
-+..|-+++|+...+ +. -|-||.-. ++-+. +++........||. ++.++||+
T Consensus 30 SA~aEl~Lr~a~k~g---~I-----~Y~pGd~~F~i~~~~~l~~~q~~~Le~I~~~vl~~~g~T 85 (109)
T PF08438_consen 30 SAAAELALRKAAKAG---LI-----DYIPGDSDFEITDDDKLSDKQKKALEKIRDNVLERYGST 85 (109)
T ss_dssp -HHHHHHHHS-SSS------------S----------------------TTHHHHHHTSSSSS-
T ss_pred cHHHHHHHHHHHHCC---CE-----EeCCCCCceEeecccccCHHHHHHHHHHHHHHHHhcCCc
Confidence 567888999887554 22 25666432 22333 89999999999999 99999983
No 51
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=23.42 E-value=92 Score=23.49 Aligned_cols=28 Identities=32% Similarity=0.313 Sum_probs=23.5
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 021961 84 AGRKGAQDAKKAKLYSRMGKEVISAVKK 111 (305)
Q Consensus 84 kh~K~a~DakKsklfsKl~keI~vAvk~ 111 (305)
-+-|.+.|..+++.|.|++|.+..+++.
T Consensus 16 ~~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 16 LQAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 3568889999999999999988777764
No 52
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=23.38 E-value=2.1e+02 Score=27.13 Aligned_cols=77 Identities=16% Similarity=0.292 Sum_probs=37.5
Q ss_pred CChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCCccccCCCCCCCCCcccccCceE
Q 021961 176 DKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYY 255 (305)
Q Consensus 176 DN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~ 255 (305)
+...-.+.+||.+..+..- . .+ +.+..|+.+... |.+.+.|.++=..-+|++| ....|
T Consensus 69 ~~~~i~v~~ir~~~~~~~~--~-----p~-~~~~kv~iI~~a----d~m~~~a~naLLK~LEepp----------~~t~~ 126 (313)
T PRK05564 69 NKKSIGVDDIRNIIEEVNK--K-----PY-EGDKKVIIIYNS----EKMTEQAQNAFLKTIEEPP----------KGVFI 126 (313)
T ss_pred cCCCCCHHHHHHHHHHHhc--C-----cc-cCCceEEEEech----hhcCHHHHHHHHHHhcCCC----------CCeEE
Confidence 4455567789988876421 1 11 234445555431 2222222221112345543 11345
Q ss_pred EEEeCcccHHHHHHHHHHCCC
Q 021961 256 KVVSTSDNYTDITTKLREAGI 276 (305)
Q Consensus 256 ~i~~~p~d~~~V~~~L~~~G~ 276 (305)
-++| ++.+.+...+.++..
T Consensus 127 il~~--~~~~~ll~TI~SRc~ 145 (313)
T PRK05564 127 ILLC--ENLEQILDTIKSRCQ 145 (313)
T ss_pred EEEe--CChHhCcHHHHhhce
Confidence 5555 456688778877754
No 53
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=23.20 E-value=2.2e+02 Score=26.82 Aligned_cols=51 Identities=27% Similarity=0.429 Sum_probs=41.1
Q ss_pred CHHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEEEeCc-ccHHHHHHHHHHCCCCeeecccceeecCCCcc
Q 021961 220 DKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTS-DNYTDITTKLREAGIPFETDNGSELLPITTIE 293 (305)
Q Consensus 220 d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i~~~p-~d~~~V~~~L~~~G~~i~~s~ele~iP~~~Ve 293 (305)
+.++..+.-..+||.- |.|.+++ .+...+-+.+++.|..+ ++..-|-|+|+
T Consensus 75 ~Peq~V~~~a~agas~-------------------~tfH~E~~q~~~~lv~~ir~~Gmk~----G~alkPgT~Ve 126 (224)
T KOG3111|consen 75 NPEQWVDQMAKAGASL-------------------FTFHYEATQKPAELVEKIREKGMKV----GLALKPGTPVE 126 (224)
T ss_pred CHHHHHHHHHhcCcce-------------------EEEEEeeccCHHHHHHHHHHcCCee----eEEeCCCCcHH
Confidence 4578888888999853 6676666 55789999999999875 57788999998
No 54
>PRK05265 pyridoxine 5'-phosphate synthase; Provisional
Probab=22.32 E-value=1.2e+02 Score=28.96 Aligned_cols=89 Identities=25% Similarity=0.306 Sum_probs=61.9
Q ss_pred EEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCCccccCCCCCCCCCcc
Q 021961 169 IVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDE 248 (305)
Q Consensus 169 iIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~Ed~~~e 248 (305)
|.|----|-+.=.-.||+.+-+-... .|+++ ....++++++|++.-.+.|...| | ..+|
T Consensus 41 ITvHlReDrRHI~d~Dv~~L~~~~~~--------~lNlE----------~a~~~em~~ia~~~kP~~vtLVP--E-~r~E 99 (239)
T PRK05265 41 ITVHLREDRRHIRDRDVRLLRETLKT--------ELNLE----------MAATEEMLDIALEVKPHQVTLVP--E-KREE 99 (239)
T ss_pred EEecCCCCcccCCHHHHHHHHHhcCC--------CEEec----------cCCCHHHHHHHHHCCCCEEEECC--C-CCCC
Confidence 34555566665556666665544321 22222 22347899999999999998876 2 2344
Q ss_pred cccCceEEEEeCcccHHHHHHHHHHCCCCe
Q 021961 249 DRAERYYKVVSTSDNYTDITTKLREAGIPF 278 (305)
Q Consensus 249 d~~~~~~~i~~~p~d~~~V~~~L~~~G~~i 278 (305)
-+.++.+-+....+.+..+.+.|.+.||.+
T Consensus 100 ~TTegGldv~~~~~~l~~~i~~L~~~gIrV 129 (239)
T PRK05265 100 LTTEGGLDVAGQFDKLKPAIARLKDAGIRV 129 (239)
T ss_pred ccCCccchhhcCHHHHHHHHHHHHHCCCEE
Confidence 456678999999999999999999999875
No 55
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.96 E-value=3e+02 Score=19.53 Aligned_cols=60 Identities=17% Similarity=0.291 Sum_probs=36.7
Q ss_pred EEEecCChhhHHHHHHHHHhhcCcccCCCccceecc-ee-eEE--EEeeCCCCCHHHHHHHHHHCCC
Q 021961 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKF-RR-ARV--VNIKFTDADKDQLLDIALDAGA 233 (305)
Q Consensus 171 VE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F-~~-kGv--i~v~~~~~d~D~l~e~AIEaGA 233 (305)
+.+..++.......|-.+|.++|.++-.-. .+.. .. .+. +.+... .+.+.+.+.--++|-
T Consensus 4 ~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~--~~~~~~~~~~~~~i~v~~~-~~~~~~~~~L~~~G~ 67 (69)
T cd04909 4 LYVDVPDEPGVIAEVTQILGDAGISIKNIE--ILEIREGIGGILRISFKTQ-EDRERAKEILKEAGY 67 (69)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCceeeE--eEEeecCCcEEEEEEECCH-HHHHHHHHHHHHcCC
Confidence 456678888899999999999999885321 1111 01 343 334322 245666666555664
No 56
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=21.87 E-value=2.3e+02 Score=25.19 Aligned_cols=52 Identities=10% Similarity=0.256 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHhhccCC
Q 021961 97 LYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKG 150 (305)
Q Consensus 97 lfsKl~keI~vAvk~GG~DP~~N~~La~aI~~AK~~nmPKd~IErAIkra~g~~ 150 (305)
+|.++...|+-.++.|+-.| +.+|-+--+-|+..+|+.-++-+||....+.+
T Consensus 2 ~y~qi~~~l~~~I~~g~~~~--g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eG 53 (231)
T TIGR03337 2 QYLYIKDHLSYQIRAGALLP--GDKLPSERDLGERFNTTRVTIREALQQLEAEG 53 (231)
T ss_pred HHHHHHHHHHHHHHcCCCCC--CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 46788889999999988544 33576777889999999999999999876544
No 57
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=21.61 E-value=5.6e+02 Score=22.57 Aligned_cols=107 Identities=14% Similarity=0.069 Sum_probs=58.1
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCcccCCCccceecc-eeeEEEEeeCCCCCHHHHHHHHHH--CCCccccCCCCCCCCC
Q 021961 170 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKF-RRARVVNIKFTDADKDQLLDIALD--AGAEDVIEPPVNEDDT 246 (305)
Q Consensus 170 IVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F-~~kGvi~v~~~~~d~D~l~e~AIE--aGAEDVee~~~~Ed~~ 246 (305)
++.++.+|.....+.|-.+|.+.|.++-. -.+...= ...-.+++.... |+ +.++.... .-..||.......+++
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~S-l~v~~t~~~~~sriti~V~~-d~-~~i~qi~kQl~Kli~V~~V~~~~~~~ 79 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIES-LTVGPTEDPDLSRMTIVVVG-DD-KVLEQITKQLNKLVDVIKVSDLTESA 79 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEE-EEEeecCCCCEEEEEEEEEC-CH-HHHHHHHHHHhcCccEEEEEecCCCc
Confidence 46789999999999999999999998731 1222211 112223222222 33 22222221 2223332210001110
Q ss_pred cccccCceEEEEeCcccHHHHHHHHHHCCCCee
Q 021961 247 DEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 279 (305)
Q Consensus 247 ~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~ 279 (305)
--..+=-.++|-+++++-..+.+-.+..+..+.
T Consensus 80 ~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~iv 112 (157)
T TIGR00119 80 IVERELCLVKVSAPGEGRDEIIRLTNIFRGRIV 112 (157)
T ss_pred ceeeEEEEEEEECCccCHHHHHHHHHHhCCEEE
Confidence 011222368999999988888888887766654
No 58
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=21.52 E-value=6.9e+02 Score=23.92 Aligned_cols=93 Identities=20% Similarity=0.231 Sum_probs=54.2
Q ss_pred cEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeE-EEEeeCCCCCHHHHHHHHHHCCCccccCCCCCCCC
Q 021961 167 VSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRAR-VVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDD 245 (305)
Q Consensus 167 vaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kG-vi~v~~~~~d~D~l~e~AIEaGAEDVee~~~~Ed~ 245 (305)
..+++++-.+...-...+++..|.+.+..++-..++...=.++. +|.+.+...+++.+++ +++.|--..
T Consensus 48 F~m~i~v~~~~~~~~~~~L~~~L~~l~~~l~l~i~l~~~~~~~ri~vl~Sg~gsnl~al~~-~~~~~~~~~--------- 117 (286)
T PRK06027 48 FFMRVEFEGDGLIFNLETLRADFAALAEEFEMDWRLLDSAERKRVVILVSKEDHCLGDLLW-RWRSGELPV--------- 117 (286)
T ss_pred EEEEEEEEeCCCCCCHHHHHHHHHHHHHHhCCEEEEcccccCcEEEEEEcCCCCCHHHHHH-HHHcCCCCc---------
Confidence 45556666633333477888888887776653333333223333 4556666778888877 466553221
Q ss_pred CcccccCceEEEEeCcccHHHHHHHHHHCCCCee
Q 021961 246 TDEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 279 (305)
Q Consensus 246 ~~ed~~~~~~~i~~~p~d~~~V~~~L~~~G~~i~ 279 (305)
+..-|+|++.+...+ .++.|+++.
T Consensus 118 -------~i~~visn~~~~~~l---A~~~gIp~~ 141 (286)
T PRK06027 118 -------EIAAVISNHDDLRSL---VERFGIPFH 141 (286)
T ss_pred -------EEEEEEEcChhHHHH---HHHhCCCEE
Confidence 134677777766554 556677754
No 59
>PF07942 N2227: N2227-like protein; InterPro: IPR012901 This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (P53934 from SWISSPROT). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions [].
Probab=21.43 E-value=1.1e+02 Score=29.54 Aligned_cols=70 Identities=14% Similarity=0.313 Sum_probs=49.8
Q ss_pred cEEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCCccccC
Q 021961 167 VSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIE 238 (305)
Q Consensus 167 vaiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGAEDVee 238 (305)
+.+.||+ ..|.-.-+..|.++++. ||-.-.-|.+.|-|...+.-.-..-+++.|++..++...|=+++.+
T Consensus 171 T~FFIDT-A~Ni~~Yi~tI~~lLkp-gG~WIN~GPLlyh~~~~~~~~~~sveLs~eEi~~l~~~~GF~~~~~ 240 (270)
T PF07942_consen 171 TCFFIDT-AENIIEYIETIEHLLKP-GGYWINFGPLLYHFEPMSIPNEMSVELSLEEIKELIEKLGFEIEKE 240 (270)
T ss_pred EEEEeec-hHHHHHHHHHHHHHhcc-CCEEEecCCccccCCCCCCCCCcccCCCHHHHHHHHHHCCCEEEEE
Confidence 3466666 67888899999999866 5544445679999986541000001468999999999999999865
No 60
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (murein tripeptide ligase) is described by TIGR01081.
Probab=21.16 E-value=2e+02 Score=28.70 Aligned_cols=52 Identities=21% Similarity=0.374 Sum_probs=35.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhh
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITR 180 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nR 180 (305)
+..|+.-|...++|.+.|..+|+...+.. .++|..+ .+|+.+|.| .-.|..-
T Consensus 278 ~~aA~a~~~~lgi~~~~i~~~l~~f~~~~------~R~e~~~~~~gv~~i~D-~ahn~~~ 330 (448)
T TIGR01082 278 ALAAIAVALELGIDFEAILRALANFQGVK------RRFEILGEFGGVLLIDD-YAHHPTE 330 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------ccceEEEEeCCeEEEEc-CCCCHHH
Confidence 45677778889999999999998765422 2444442 357888887 3334443
No 61
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=21.13 E-value=86 Score=31.18 Aligned_cols=39 Identities=15% Similarity=0.106 Sum_probs=30.5
Q ss_pred ceEEEEeCcccHHHHHHHHHHCCCCeeecccceeecCCC
Q 021961 253 RYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITT 291 (305)
Q Consensus 253 ~~~~i~~~p~d~~~V~~~L~~~G~~i~~s~ele~iP~~~ 291 (305)
..+-|.|+|..+..-.+.|.+.||.++...-+.|.|.|+
T Consensus 390 ~ivyvsc~p~tlard~~~l~~~gy~~~~~~~~DmFP~T~ 428 (431)
T TIGR00479 390 RIVYVSCNPATLARDLEFLCKEGYGITWVQPVDMFPHTA 428 (431)
T ss_pred EEEEEcCCHHHHHHHHHHHHHCCeeEEEEEEeccCCCCC
Confidence 455678899988888888888899876665677888764
No 62
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.97 E-value=3.8e+02 Score=20.47 Aligned_cols=55 Identities=7% Similarity=0.083 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHCCCccccCCCCCCCCCcccccCceEEEEeC----cccHHHHHHHHHHCCCCeee
Q 021961 219 ADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVST----SDNYTDITTKLREAGIPFET 280 (305)
Q Consensus 219 ~d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~~~~i~~~----p~d~~~V~~~L~~~G~~i~~ 280 (305)
-.+-.+++..-.+++.++.-.- ... +...+.|..+ ++++..+.+.|++.||.+..
T Consensus 13 G~L~~ll~~l~~anI~~~~y~~----~~~---~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~ 71 (85)
T cd04906 13 GSFKKFCELIGPRNITEFNYRY----ADE---KDAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71 (85)
T ss_pred cHHHHHHHHhCCCceeEEEEEc----cCC---CeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEE
Confidence 3456666644445445443210 000 1234555455 46699999999999998743
No 63
>KOG2121 consensus Predicted metal-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]
Probab=20.83 E-value=43 Score=36.53 Aligned_cols=54 Identities=28% Similarity=0.303 Sum_probs=38.7
Q ss_pred HHHHHhcCCCHHHHHHHHHhhccCCccceeEEEE-EEEec---CCcEEEEEEecCChh
Q 021961 126 LEKAKELDVPKDIVERNIKRASEKGQEAFIEKVY-EVYGY---GGVSIVVEVLTDKIT 179 (305)
Q Consensus 126 I~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~Y-E~~GP---gGvaiIVE~lTDN~n 179 (305)
+++|++.++|+.-+-..+++|..-.-++-+-.++ |+.|| |-+.+|++|-+++.-
T Consensus 223 ~~kA~~lGvp~Gp~~~~L~~G~~vt~~~g~i~~~~ev~gp~~~~~~f~il~cp~e~~l 280 (746)
T KOG2121|consen 223 VEKAKELGVPKGPLIGKLKSGESVTLDDGTIVVPSEVVGPSRPGASFLILDCPDESYL 280 (746)
T ss_pred HHHHHHhCCCCCcchhhhcCCCceeccCCcEEehhhhcCCCCCccEEEEecCCcHHHH
Confidence 6788999999998888898876532111122344 89998 668889999887743
No 64
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=20.81 E-value=4.7e+02 Score=21.33 Aligned_cols=65 Identities=22% Similarity=0.201 Sum_probs=39.2
Q ss_pred HhhhhhH-HHHHHHHHHHHHHHHHHHHHHh-CCCCCCCCHHHHHHHHHHHhc------CCCHHHHHHHHHhhc
Q 021961 83 IAGRKGA-QDAKKAKLYSRMGKEVISAVKK-GGPNPTSNTVLAAVLEKAKEL------DVPKDIVERNIKRAS 147 (305)
Q Consensus 83 Ikh~K~a-~DakKsklfsKl~keI~vAvk~-GG~DP~~N~~La~aI~~AK~~------nmPKd~IErAIkra~ 147 (305)
++.-|.+ +.-+..+++.-+++.-..||-+ .+.+.+..-++..|++..+.. +++.+.|+.+|..|-
T Consensus 29 ~~~l~~k~~~e~~~~~~~~vak~Av~aveq~~~~~~~G~~K~~~A~~~v~~~L~~~gi~~t~~~i~~~IEaAV 101 (108)
T PF09682_consen 29 IKYLKKKAGGEKLVKILEIVAKIAVNAVEQVAKEGGKGEEKKAEAVQYVKERLKKKGIKVTDEQIEGAIEAAV 101 (108)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 3333444 3334445555567766666654 333335666777776665554 778889999998764
No 65
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=20.31 E-value=1.1e+02 Score=25.86 Aligned_cols=24 Identities=21% Similarity=0.404 Sum_probs=21.9
Q ss_pred eEEEEeCcccHHHHHHHHHHCCCC
Q 021961 254 YYKVVSTSDNYTDITTKLREAGIP 277 (305)
Q Consensus 254 ~~~i~~~p~d~~~V~~~L~~~G~~ 277 (305)
.++.+.-|..|..|+++|++.|+.
T Consensus 3 ~I~aIiRP~kl~~vkeaL~~~G~~ 26 (112)
T COG0347 3 KIEAIIRPFKLDDVKEALEKAGVP 26 (112)
T ss_pred EEEEEeCHHHhHHHHHHHHHcCCC
Confidence 478899999999999999999976
No 66
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=20.30 E-value=3.5e+02 Score=22.15 Aligned_cols=86 Identities=15% Similarity=0.257 Sum_probs=48.9
Q ss_pred ChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeC---CCCCHHHHHHHHHHCCCccccCCCCCCCCCcccccCc
Q 021961 177 KITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKF---TDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAER 253 (305)
Q Consensus 177 N~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~---~~~d~D~l~e~AIEaGAEDVee~~~~Ed~~~ed~~~~ 253 (305)
...++..++..++. +||.+-+ |.+...--|.|...- +..|.+..++..=+..+.-+-.. + ++-
T Consensus 6 ~~~~~~~EL~~IVd-~Gg~V~D---V~veHp~YG~i~~~L~i~sr~Dv~~Fi~~l~~~~~~~Ls~L------T----~Gv 71 (98)
T PF02829_consen 6 TPDEIEDELEIIVD-NGGRVLD---VIVEHPVYGEITGNLNISSRRDVDKFIEKLEKSKAKPLSSL------T----GGV 71 (98)
T ss_dssp -GGGHHHHHHHHHH-TT-EEEE---EEEEETTTEEEEEEEEE-SHHHHHHHHHHHHH--S--STTG------G----GGE
T ss_pred CHHHHHHHHHHHHH-CCCEEEE---EEEeCCCCcEEEEEEecCCHHHHHHHHHHHhccCCcchHHh------c----CCE
Confidence 45667778888877 9998864 566554445444321 22355666666666677655432 1 122
Q ss_pred -eEEEEeCc-ccHHHHHHHHHHCCC
Q 021961 254 -YYKVVSTS-DNYTDITTKLREAGI 276 (305)
Q Consensus 254 -~~~i~~~p-~d~~~V~~~L~~~G~ 276 (305)
+.+|.|+. +.|..+.++|+++||
T Consensus 72 H~HtI~a~~~e~l~~I~~~L~~~G~ 96 (98)
T PF02829_consen 72 HYHTIEAPDEEDLDKIEEALKKKGF 96 (98)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHTT-
T ss_pred eeEEEEECCHHHHHHHHHHHHHCCC
Confidence 34555544 478999999999997
No 67
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=20.21 E-value=2.6e+02 Score=30.82 Aligned_cols=61 Identities=11% Similarity=0.056 Sum_probs=44.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 021961 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (305)
Q Consensus 122 La~aI~~AK~~nmPKd~IErAIkra~g~~~~~~~e~~YE~~G-PgGvaiIVE~lTDN~nRt~s~ir~i 188 (305)
+.+|+.-|...++|.+.|.++|+.-.+-. -+.|.+. .+|+.+|.|+.-.|+.-+.+-+..+
T Consensus 796 alaAia~a~~lGi~~~~i~~~L~~f~~~~------gR~e~~~~~~~~~iidDsya~np~s~~aaL~~l 857 (958)
T PRK11929 796 ALAAIACALAAGASLKQIRAGLERFQPVA------GRMQRRRLSCGTRIIDDTYNANPDSMRAAIDVL 857 (958)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCC------CCceEEEcCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 56677889999999999999998755422 2344433 4789999999888887666666554
No 68
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=20.13 E-value=3e+02 Score=24.96 Aligned_cols=110 Identities=13% Similarity=0.114 Sum_probs=63.8
Q ss_pred EEEEEEecCChhhHHHHHHHHHhhcCcccCCCccceecceeeEEEEeeCCCCCHHHHHHHHHHCCC-c-cccC--CCCCC
Q 021961 168 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA-E-DVIE--PPVNE 243 (305)
Q Consensus 168 aiIVE~lTDN~nRt~s~ir~i~~K~gG~l~~~gsv~f~F~~kGvi~v~~~~~d~D~l~e~AIEaGA-E-DVee--~~~~E 243 (305)
.+||-++-..+...++.|-.++.++||++.+......-=+-.+++.+..+.... +.++.++.... + ++.. .+...
T Consensus 8 ~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lvs~~~~~~-~~le~~L~~l~~~~~L~i~v~~~~~ 86 (190)
T PRK11589 8 YLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAI-TLIESTLPLKGAELDLLIVMKRTTA 86 (190)
T ss_pred EEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEEeCChhHH-HHHHHHHHhhhhhcCeEEEEEeccc
Confidence 478889999999999999999999999998754332211234455565443233 34444554332 2 1111 00001
Q ss_pred CCCcccccCceEEEEe----CcccHHHHHHHHHHCCCCeee
Q 021961 244 DDTDEDRAERYYKVVS----TSDNYTDITTKLREAGIPFET 280 (305)
Q Consensus 244 d~~~ed~~~~~~~i~~----~p~d~~~V~~~L~~~G~~i~~ 280 (305)
.. .......|.|.. .|.=+..|.+.|.+.|+++..
T Consensus 87 ~~--~~~~~~~~~v~v~G~DrPGIV~~vT~~la~~~iNI~~ 125 (190)
T PRK11589 87 RP--RPAMPATVWVQVEVADSPHLIERFTALFDSHHMNIAE 125 (190)
T ss_pred cc--cccCCceEEEEEEECCCCCHHHHHHHHHHHcCCChhh
Confidence 00 100111244433 355579999999999999854
Done!