Query 034019
Match_columns 106
No_of_seqs 113 out of 1043
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:53:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034019.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034019hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0384 Predicted epimerase, P 100.0 3.6E-36 7.8E-41 237.9 11.8 80 3-86 1-80 (291)
2 PRK10281 hypothetical protein; 100.0 7E-36 1.5E-40 235.2 10.9 78 6-86 3-80 (299)
3 PF02567 PhzC-PhzF: Phenazine 100.0 9.3E-34 2E-38 217.0 10.3 73 11-86 1-73 (281)
4 KOG3033 Predicted PhzC/PhzF-ty 100.0 2.2E-29 4.8E-34 196.9 9.9 98 1-101 1-106 (286)
5 TIGR00654 PhzF_family phenazin 100.0 3.6E-28 7.7E-33 188.5 11.7 77 6-85 3-79 (297)
6 PRK13971 hydroxyproline-2-epim 99.7 1.2E-17 2.5E-22 134.6 9.1 74 5-85 3-95 (333)
7 PRK13970 hydroxyproline-2-epim 99.6 1.2E-14 2.6E-19 116.4 8.3 76 7-86 4-95 (311)
8 PRK13577 diaminopimelate epime 99.5 5.7E-14 1.2E-18 109.4 8.1 68 14-84 3-76 (281)
9 PRK00450 dapF diaminopimelate 99.4 2.5E-12 5.3E-17 98.9 8.5 85 14-101 5-101 (274)
10 TIGR00652 DapF diaminopimelate 98.9 6.7E-09 1.5E-13 80.2 8.0 48 34-85 26-77 (268)
11 PLN02536 diaminopimelate epime 97.6 0.00024 5.3E-09 55.5 7.3 49 33-85 11-63 (267)
12 PRK13969 proline racemase; Pro 96.3 0.012 2.5E-07 48.0 6.0 88 7-101 6-123 (334)
13 PF05544 Pro_racemase: Proline 93.5 0.17 3.6E-06 41.2 5.1 81 18-101 5-115 (325)
14 COG0253 DapF Diaminopimelate e 92.3 1.4 3.1E-05 35.1 8.8 85 14-101 3-101 (272)
15 TIGR00654 PhzF_family phenazin 91.7 1.8 3.9E-05 33.6 8.6 65 19-84 160-234 (297)
16 PF01678 DAP_epimerase: Diamin 86.8 4.3 9.3E-05 27.4 6.7 77 19-100 4-96 (121)
17 COG4840 Uncharacterized protei 82.2 1.1 2.3E-05 29.2 1.8 17 31-47 52-68 (71)
18 COG3938 Proline racemase [Amin 81.9 8.5 0.00018 31.7 7.3 73 6-85 5-96 (341)
19 KOG3033 Predicted PhzC/PhzF-ty 79.4 1.8 4E-05 34.8 2.7 32 62-93 205-243 (286)
20 PRK10281 hypothetical protein; 79.2 18 0.0004 28.6 8.4 64 19-84 160-233 (299)
21 PF06569 DUF1128: Protein of u 70.4 3.7 8.1E-05 26.7 2.0 18 30-47 51-68 (71)
22 TIGR01565 homeo_ZF_HD homeobox 67.9 4.4 9.5E-05 25.2 1.9 21 33-53 30-50 (58)
23 cd00086 homeodomain Homeodomai 67.3 4 8.7E-05 23.5 1.6 19 32-50 24-42 (59)
24 smart00389 HOX Homeodomain. DN 64.1 5.1 0.00011 23.0 1.6 19 32-50 24-42 (56)
25 PRK13577 diaminopimelate epime 60.8 42 0.00091 26.0 6.6 60 20-85 156-223 (281)
26 PRK00450 dapF diaminopimelate 60.2 26 0.00057 26.7 5.3 60 19-84 153-220 (274)
27 TIGR00652 DapF diaminopimelate 58.9 23 0.00051 27.2 4.8 64 19-85 149-217 (268)
28 COG2355 Zn-dependent dipeptida 56.1 7.7 0.00017 31.6 1.8 31 19-49 189-219 (313)
29 PF00046 Homeobox: Homeobox do 55.8 7.3 0.00016 22.6 1.3 19 31-49 23-41 (57)
30 PF05920 Homeobox_KN: Homeobox 54.2 8.7 0.00019 21.9 1.3 17 33-49 11-27 (40)
31 KOG0491 Transcription factor B 53.9 4.3 9.4E-05 30.8 0.0 39 12-51 105-143 (194)
32 PF02567 PhzC-PhzF: Phenazine 53.3 59 0.0013 24.6 6.2 63 19-84 150-220 (281)
33 PF07040 DUF1326: Protein of u 51.9 48 0.001 24.8 5.4 41 5-45 43-83 (184)
34 PLN02536 diaminopimelate epime 51.6 39 0.00084 26.3 5.0 61 19-84 144-214 (267)
35 PRK14980 DNA-directed RNA poly 49.6 2.5 5.5E-05 30.4 -1.7 14 75-88 67-80 (127)
36 PF11548 Receptor_IA-2: Protei 44.2 22 0.00047 24.2 2.3 43 25-69 6-52 (91)
37 PF02603 Hpr_kinase_N: HPr Ser 42.9 30 0.00066 23.9 2.9 30 19-48 78-107 (127)
38 PRK00745 4-oxalocrotonate taut 42.8 44 0.00095 19.6 3.3 22 25-46 4-25 (62)
39 COG0253 DapF Diaminopimelate e 40.2 1.6E+02 0.0035 23.5 7.0 61 19-85 152-220 (272)
40 cd02252 nylC_like nylC-like fa 40.0 49 0.0011 26.4 4.0 37 10-46 169-206 (260)
41 PF01361 Tautomerase: Tautomer 38.9 41 0.00088 19.7 2.7 20 26-45 4-23 (60)
42 PRK02289 4-oxalocrotonate taut 38.4 56 0.0012 19.4 3.3 19 27-45 6-24 (60)
43 PF13596 PAS_10: PAS domain; P 37.9 65 0.0014 20.4 3.8 28 39-76 2-29 (106)
44 PF02812 ELFV_dehydrog_N: Glu/ 36.7 24 0.00052 25.0 1.6 33 15-47 64-96 (131)
45 PF04977 DivIC: Septum formati 36.6 45 0.00098 20.3 2.8 22 34-55 53-78 (80)
46 cd00491 4Oxalocrotonate_Tautom 35.9 67 0.0015 18.3 3.3 21 27-47 5-25 (58)
47 TIGR01958 nuoE_fam NADH-quinon 33.9 32 0.00068 24.5 1.9 19 31-49 30-48 (148)
48 PF15646 Tox-REase-2: Restrict 33.8 5.2 0.00011 28.7 -2.2 28 64-91 3-31 (125)
49 PF11869 DUF3389: Protein of u 33.7 75 0.0016 20.9 3.5 15 34-48 59-73 (75)
50 TIGR00013 taut 4-oxalocrotonat 33.0 79 0.0017 18.5 3.3 16 31-46 10-25 (63)
51 PRK09414 glutamate dehydrogena 30.4 64 0.0014 27.5 3.4 32 15-46 120-151 (445)
52 cd08313 Death_TNFR1 Death doma 30.0 35 0.00077 22.3 1.5 20 31-50 7-26 (80)
53 PRK11675 LexA regulated protei 29.4 15 0.00032 25.0 -0.4 39 1-44 1-39 (90)
54 PF04218 CENP-B_N: CENP-B N-te 29.0 36 0.00078 20.2 1.3 15 37-51 24-38 (53)
55 PRK01964 4-oxalocrotonate taut 28.8 92 0.002 18.5 3.2 23 25-47 4-26 (64)
56 cd08316 Death_FAS_TNFRSF6 Deat 28.1 28 0.00062 23.5 0.8 21 31-51 16-36 (97)
57 PRK11669 pbpG D-alanyl-D-alani 27.9 15 0.00033 29.6 -0.7 37 20-56 125-166 (306)
58 PRK02220 4-oxalocrotonate taut 27.8 1.1E+02 0.0023 17.8 3.3 16 31-46 10-25 (61)
59 PF07498 Rho_N: Rho terminatio 27.5 49 0.0011 18.9 1.6 16 33-48 5-20 (43)
60 COG3191 DmpA L-aminopeptidase/ 27.0 1.2E+02 0.0025 25.4 4.3 36 16-51 228-265 (348)
61 cd05568 PTS_IIB_bgl_like PTS_I 26.3 1.2E+02 0.0026 18.3 3.5 34 14-47 51-84 (85)
62 PF10588 NADH-G_4Fe-4S_3: NADH 26.3 50 0.0011 18.7 1.5 18 35-52 24-41 (41)
63 COG2150 Predicted regulator of 26.1 1.2E+02 0.0027 22.8 3.9 39 6-44 119-158 (167)
64 PRK05988 formate dehydrogenase 25.7 53 0.0011 23.8 1.9 20 31-50 37-56 (156)
65 PLN02477 glutamate dehydrogena 25.2 87 0.0019 26.3 3.3 33 15-47 94-126 (410)
66 PRK01271 4-oxalocrotonate taut 24.8 1.2E+02 0.0026 19.5 3.3 14 32-45 12-25 (76)
67 cd01777 SNX27_RA Ubiquitin dom 24.8 1.2E+02 0.0026 20.4 3.4 29 21-49 11-39 (87)
68 PF01244 Peptidase_M19: Membra 24.5 20 0.00044 28.7 -0.5 29 19-47 200-228 (320)
69 cd08315 Death_TRAILR_DR4_DR5 D 24.4 41 0.00089 22.5 1.1 20 31-50 15-34 (96)
70 PF13542 HTH_Tnp_ISL3: Helix-t 24.1 41 0.00088 19.0 0.9 14 37-50 29-42 (52)
71 KOG2882 p-Nitrophenyl phosphat 24.0 2.6E+02 0.0056 22.9 5.7 73 23-104 154-229 (306)
72 PRK07571 bidirectional hydroge 23.9 59 0.0013 24.1 1.9 19 31-49 50-68 (169)
73 cd01301 rDP_like renal dipepti 23.9 52 0.0011 26.3 1.7 35 19-53 194-228 (309)
74 PRK07539 NADH dehydrogenase su 23.8 60 0.0013 23.2 1.9 20 31-50 36-55 (154)
75 cd08784 Death_DRs Death Domain 23.3 49 0.0011 21.1 1.2 21 31-51 7-27 (79)
76 PF01257 2Fe-2S_thioredx: Thio 22.4 57 0.0012 23.0 1.5 19 32-50 28-46 (145)
77 PF00356 LacI: Bacterial regul 22.0 67 0.0015 18.7 1.5 14 38-51 2-15 (46)
78 PF02796 HTH_7: Helix-turn-hel 21.7 66 0.0014 18.1 1.4 15 37-51 23-37 (45)
79 PF08671 SinI: Anti-repressor 21.3 92 0.002 16.9 1.9 16 33-48 1-18 (30)
80 PRK14031 glutamate dehydrogena 20.9 1.2E+02 0.0027 25.8 3.5 32 15-46 116-147 (444)
81 KOG4449 Translocase of outer m 20.8 93 0.002 19.2 2.0 19 33-51 3-21 (53)
82 PF07085 DRTGG: DRTGG domain; 20.3 1.2E+02 0.0027 19.6 2.8 31 23-55 62-92 (105)
No 1
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=100.00 E-value=3.6e-36 Score=237.87 Aligned_cols=80 Identities=38% Similarity=0.502 Sum_probs=74.8
Q ss_pred CcceeEEEEeeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCCccCCCCc
Q 034019 3 KKLVQYSVVDAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVAEVSFSFY 82 (106)
Q Consensus 3 ~~~~~~~~vdvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~Ei~~cGH 82 (106)
|..++|++|||||+++|+|||+|||.++++|++++||+||+|+|+|||+||.+++ ++ .+++||||||+.|+|||||
T Consensus 1 ~~~~~~~~vDvFt~~~~~GNp~aVv~~a~~Lsd~~MQ~IA~e~n~SET~Fv~~~~---~~-~~~rlR~FTP~~Evpf~GH 76 (291)
T COG0384 1 MMTIPVYQVDVFTSKPFGGNPLAVVLDADGLSDEQMQAIAREFNLSETAFVLPPD---DP-ADARLRIFTPTTEVPFAGH 76 (291)
T ss_pred CCccceEEEEEecCCCCCCCceEEEeCCCCCCHHHHHHHHHHhCCceeEEEcCCC---Cc-CceEEEEeCCCcccccCCC
Confidence 4568899999999999999999999999999999999999999999999999983 33 6899999999999999999
Q ss_pred hHHH
Q 034019 83 NYKL 86 (106)
Q Consensus 83 atva 86 (106)
+|++
T Consensus 77 aTlg 80 (291)
T COG0384 77 ATLG 80 (291)
T ss_pred HHHH
Confidence 9986
No 2
>PRK10281 hypothetical protein; Provisional
Probab=100.00 E-value=7e-36 Score=235.16 Aligned_cols=78 Identities=35% Similarity=0.442 Sum_probs=72.4
Q ss_pred eeEEEEeeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCCccCCCCchHH
Q 034019 6 VQYSVVDAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVAEVSFSFYNYK 85 (106)
Q Consensus 6 ~~~~~vdvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~Ei~~cGHatv 85 (106)
++|++|||||+++|+|||+|||+++++|++++||+||||+|+|||+||.++. ++.++|+||||||..|||||||||+
T Consensus 3 ~~~~~vDaFt~~~f~GNpaaVv~~a~~L~~~~Mq~IAre~n~SETaFv~~~~---~~~~~~~lR~FTP~~Ev~fcGHaTl 79 (299)
T PRK10281 3 PQIYHVDAFTSQPFRGNSAGVVLNADGLSEAQMQLIARELNHSETAFLLSSD---DSSYDVRVRYFTPTVEVPICGHATV 79 (299)
T ss_pred ceEEEEEeccCCCCCCCceEEEcCCCCCCHHHHHHHHHHhCCceEEEEccCC---CCCCceEEEEECCCcccccCCcHHH
Confidence 6899999999999999999999999999999999999999999999999762 2245799999999999999999998
Q ss_pred H
Q 034019 86 L 86 (106)
Q Consensus 86 a 86 (106)
+
T Consensus 80 a 80 (299)
T PRK10281 80 A 80 (299)
T ss_pred H
Confidence 4
No 3
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=100.00 E-value=9.3e-34 Score=216.99 Aligned_cols=73 Identities=44% Similarity=0.632 Sum_probs=66.8
Q ss_pred EeeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCCccCCCCchHHH
Q 034019 11 VDAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVAEVSFSFYNYKL 86 (106)
Q Consensus 11 vdvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~Ei~~cGHatva 86 (106)
|||||+++|+|||+|||+++++|++++||+||+|+|+|||+||.+++ ++.++|+||||||.+|+|||||+|++
T Consensus 1 vdaFt~~~f~GNp~aVv~~~~~l~~~~mq~iA~e~n~sET~Fv~~~~---~~~~~~~vR~FTp~~Ev~fcGH~tla 73 (281)
T PF02567_consen 1 VDAFTDRPFGGNPAAVVLDADGLSDEQMQAIAREFNLSETAFVLPST---DDEADYRVRIFTPTGEVPFCGHATLA 73 (281)
T ss_dssp EEET-SSTTSSEEEEEEESSTTS-HHHHHHHHHHHTSSEEEEEEEES---SSTTSEEEEEEESSSEESSSHHHHHH
T ss_pred CccccCCCCCCCeEEEEEcCCCCCHHHHHHHHHHcCCCeeEEEEecc---CCCceeEEEEEeccCCCCCCCcHHHH
Confidence 79999999999999999999999999999999999999999999983 34678999999999999999999984
No 4
>KOG3033 consensus Predicted PhzC/PhzF-type epimerase [General function prediction only]
Probab=99.96 E-value=2.2e-29 Score=196.90 Aligned_cols=98 Identities=50% Similarity=0.808 Sum_probs=82.9
Q ss_pred CCCcceeEEEEeeccCCCCCCCeeEEEEcCC-CCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCCccCC
Q 034019 1 MAKKLVQYSVVDAFTDSAFKGNPAAVCLLEE-DRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVAEVSF 79 (106)
Q Consensus 1 m~~~~~~~~~vdvFt~~~f~GNPaaVv~~~~-~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~Ei~~ 79 (106)
|.. +.+|++||+|++.+|.|||++|+.+++ ..|++++|+||+|+|+|||+|+.|.. -....+|.||||||..|+||
T Consensus 1 m~~-~~~~~ivd~ft~~~f~gnpaav~~l~ene~d~e~Lq~iA~efNlSET~Fl~pi~--~~~~~~f~LRwFTp~aEvpl 77 (286)
T KOG3033|consen 1 MTE-KKPYFIVDAFTEKAFKGNPAAVCFLEENERDDEYLQSIAAEFNLSETAFLIPIG--GKKCSRFSLRWFTPTAEVPL 77 (286)
T ss_pred CCc-ccceeeeeeeecccccCCcceeeecccccccHHHHHHHHHhhCcccceeeecCC--CCcccceeEEEecccccCcc
Confidence 443 467999999999999999999999886 46899999999999999999999983 12356899999999999999
Q ss_pred CCchHHHHH-HHc------CCeEEEeeec
Q 034019 80 SFYNYKLWM-KLF------GSVLELDDLS 101 (106)
Q Consensus 80 cGHatvaw~-~~~------~~~~~~~~~~ 101 (106)
|||||+|-. .++ .+.+.++|+|
T Consensus 78 cGHaTLasahvlf~~~~n~n~~l~f~t~s 106 (286)
T KOG3033|consen 78 CGHATLASAHVLFNEIGNVNKELKFDTLS 106 (286)
T ss_pred cCcchhhHHHHHHHhccCCcceEEEEeec
Confidence 999998633 222 7788888887
No 5
>TIGR00654 PhzF_family phenazine biosynthesis protein PhzF family. Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear.
Probab=99.95 E-value=3.6e-28 Score=188.50 Aligned_cols=77 Identities=42% Similarity=0.535 Sum_probs=71.3
Q ss_pred eeEEEEeeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCCccCCCCchHH
Q 034019 6 VQYSVVDAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVAEVSFSFYNYK 85 (106)
Q Consensus 6 ~~~~~vdvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~Ei~~cGHatv 85 (106)
++|++|||||+.+++|||++||.+.++|++++||+||+|+|+|||+||.++. ++.++|++|||||..|++||||+++
T Consensus 3 ~~~~~vd~Ft~~~~~GN~~~Vv~~~~~l~~~~mq~iA~~~~~~et~Fv~~~~---~~~~~~~~R~Fnpg~E~~~CGh~tl 79 (297)
T TIGR00654 3 VPFYQVDVFTSQPFMGNPAAVVNFAEILSEEEMQAIANETNYSETTFLLKPS---SEKYDYRLRIFTPRSELPFAGHPTI 79 (297)
T ss_pred ceEEEEEeccCCCCCCCceEEEcCCCCCCHHHHHHHHHHhCCCceEEEcCCC---CCCCceEEEEECCCCccCcCCchHH
Confidence 7899999999999999999999998899999999999999999999999752 2346799999999999999999987
No 6
>PRK13971 hydroxyproline-2-epimerase; Provisional
Probab=99.73 E-value=1.2e-17 Score=134.62 Aligned_cols=74 Identities=16% Similarity=0.138 Sum_probs=66.5
Q ss_pred ceeEEEEeeccCCCCCCCeeEEEEcCC-CCCHHHH----HHHHHHhCCcee--------------EEEecCCCCCCCCCc
Q 034019 5 LVQYSVVDAFTDSAFKGNPAAVCLLEE-DRDEEWL----QAVASEFNISQT--------------CYLTRLTAADSPNPR 65 (106)
Q Consensus 5 ~~~~~~vdvFt~~~f~GNPaaVv~~~~-~l~~~~m----q~IA~e~n~sET--------------aFv~~~~~~~~~~~~ 65 (106)
...|.+||+|+ +|||+.||.+.. .|+.+.| |.|++|++++++ +||.||. ++.++
T Consensus 3 ~~~~~~VD~ht----~Gep~rVV~~g~p~l~g~tm~ek~~~~~~e~d~~r~~L~~EPRGh~~m~g~~l~pp~---~~~Ad 75 (333)
T PRK13971 3 RHTFFCIDAHT----CGNPVRLVAGGGPLLQGATMSEKRAHFLREYDWIRTGLMFEPRGHDMMSGSILYPPT---RPDCD 75 (333)
T ss_pred cceEEEEEecC----CCcceeEEECCCCCCCCcCHHHHHHHHHHHHHHHHHHhhcCCCCCccceEEEEECCC---CCCCC
Confidence 45699999995 999999999977 5888777 999999999998 9999984 45678
Q ss_pred eEEEEecCCCccCCCCchHH
Q 034019 66 FRLRWFTPVAEVSFSFYNYK 85 (106)
Q Consensus 66 ~~vR~FTp~~Ei~~cGHatv 85 (106)
+++|||||.+|+|||||+|+
T Consensus 76 ~gvrfFtp~~e~~mcGH~TI 95 (333)
T PRK13971 76 FAILFIETSGCLPMCGHGTI 95 (333)
T ss_pred EEEEEECCCcccCcCccHHH
Confidence 99999999999999999997
No 7
>PRK13970 hydroxyproline-2-epimerase; Provisional
Probab=99.56 E-value=1.2e-14 Score=116.41 Aligned_cols=76 Identities=13% Similarity=0.128 Sum_probs=66.9
Q ss_pred eEEEEeeccCCCCCCCeeEEEEcCC-----CCCHHHHHHHHHHhCCceeEEEecCC-----------CCCCCCCceEEEE
Q 034019 7 QYSVVDAFTDSAFKGNPAAVCLLEE-----DRDEEWLQAVASEFNISQTCYLTRLT-----------AADSPNPRFRLRW 70 (106)
Q Consensus 7 ~~~~vdvFt~~~f~GNPaaVv~~~~-----~l~~~~mq~IA~e~n~sETaFv~~~~-----------~~~~~~~~~~vR~ 70 (106)
++.+||+| .+|||+.||.... ++..++||.|+++++.++|+|+..|. ++.++.+++.++|
T Consensus 4 ~i~~VDaH----t~GeP~rVV~~G~p~l~G~t~~Ek~~~~~~~~d~~R~~l~~EPRG~~~M~gall~pP~~p~Ad~gvif 79 (311)
T PRK13970 4 RIQIIDSH----TGGEPTRLVVSGFPSLGGGTMAERRDVLAREHDRYRTACILEPRGSDVLVGALLCEPVSPDAAAGVIF 79 (311)
T ss_pred EEEEEEec----CCCCceEEEecCCCCCCCCCHHHHHHHHHHhhChhhheeeeCCCCCccceeeeecCCCCcccCEEEEE
Confidence 79999999 8999999999876 56899999999999999999999774 1123567889999
Q ss_pred ecCCCccCCCCchHHH
Q 034019 71 FTPVAEVSFSFYNYKL 86 (106)
Q Consensus 71 FTp~~Ei~~cGHatva 86 (106)
|+|.+|+++|||+|++
T Consensus 80 ~~~~g~~~mCGH~TIa 95 (311)
T PRK13970 80 FNNSGYLGMCGHGTIG 95 (311)
T ss_pred EcCCCcccccccchhe
Confidence 9999999999999984
No 8
>PRK13577 diaminopimelate epimerase; Provisional
Probab=99.51 E-value=5.7e-14 Score=109.36 Aligned_cols=68 Identities=24% Similarity=0.259 Sum_probs=58.7
Q ss_pred ccCCCCCCCeeEEEEcCC---CCCHHHHHHHH-HHhCCceeEEEe-cCCCCCCCCCceEEEEecCCC-ccCCCCchH
Q 034019 14 FTDSAFKGNPAAVCLLEE---DRDEEWLQAVA-SEFNISQTCYLT-RLTAADSPNPRFRLRWFTPVA-EVSFSFYNY 84 (106)
Q Consensus 14 Ft~~~f~GNPaaVv~~~~---~l~~~~mq~IA-~e~n~sETaFv~-~~~~~~~~~~~~~vR~FTp~~-Ei~~cGHat 84 (106)
|++=...||+..||.+.+ ++++++||+|| |++|++|+.||. ++. ++.++|++|||+|.+ |.+||||++
T Consensus 3 f~K~~g~GNdfvVvd~~~~~~~~~~~~~~~i~~R~~gig~Dg~i~~~~~---~~~~d~~mrifn~DGseaemCGNg~ 76 (281)
T PRK13577 3 FYKYHALGNDYLVIDPRDAPFDPSADAIRRICHRHFGVGSDGILFGPLP---SEGADFGLRIFNPDGSEAEKSGNGL 76 (281)
T ss_pred EEEecCCCCCEEEEECCCCCCCCCHHHHHHhhccccCcCCCEEEEEecC---CCCCCEEEEEEcCCCCHHHhccccH
Confidence 666778999999998755 67899999999 999999999998 331 235689999999996 999999998
No 9
>PRK00450 dapF diaminopimelate epimerase; Provisional
Probab=99.37 E-value=2.5e-12 Score=98.91 Aligned_cols=85 Identities=16% Similarity=0.175 Sum_probs=55.5
Q ss_pred ccCCCCCCCeeEEEEcCCC-CCHHHHHHHHH-H--hCCceeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHHH--
Q 034019 14 FTDSAFKGNPAAVCLLEED-RDEEWLQAVAS-E--FNISQTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYKL-- 86 (106)
Q Consensus 14 Ft~~~f~GNPaaVv~~~~~-l~~~~mq~IA~-e--~n~sETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatva-- 86 (106)
|.+=.-.||=--+|..... ...+.-+++.. . +|+|||+||.++. ++.++|++|||||. .|+|||||||++
T Consensus 5 f~k~~~~gNdf~~~~~~~~~~~~~~~~~~~~r~~gig~det~Fv~~~~---~~~ad~~~R~Ftp~gsEv~~CGHat~~~a 81 (274)
T PRK00450 5 FTKMHGLGNDFVVIDARTQELTPELARKLCDRHFGIGADGLLLVEPPS---SPGADFRMRIFNADGSEAEMCGNGARCFA 81 (274)
T ss_pred EEEEecCCCCEEEEeCCCCcCcHHHHHHhhccCCccCCCeEEEEccCC---CCCCCEEEEEEECCCCHHHcCcchHHHHH
Confidence 5555667888777765433 22333334433 2 6889999999752 23568999999999 599999999873
Q ss_pred HHHHc-----CCeEEEeeec
Q 034019 87 WMKLF-----GSVLELDDLS 101 (106)
Q Consensus 87 w~~~~-----~~~~~~~~~~ 101 (106)
|.... .+.+.+++.+
T Consensus 82 ~~L~~~g~~~~~~~~~~t~~ 101 (274)
T PRK00450 82 RFLYEKGLTNKTEIRVETLA 101 (274)
T ss_pred HHHHHcCCCCCCeEEEEeCC
Confidence 33221 2356666543
No 10
>TIGR00652 DapF diaminopimelate epimerase.
Probab=98.90 E-value=6.7e-09 Score=80.22 Aligned_cols=48 Identities=15% Similarity=0.334 Sum_probs=38.6
Q ss_pred CHHHHHHHHH---HhCCceeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH
Q 034019 34 DEEWLQAVAS---EFNISQTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK 85 (106)
Q Consensus 34 ~~~~mq~IA~---e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv 85 (106)
+.+.++++.. ++|.+||+||.+. ++.++|++|||||. .|++||||+++
T Consensus 26 ~~~~~~~l~~r~~~ig~d~~~fv~~~----~~~ad~~~r~Fnpdg~e~~~CGh~t~ 77 (268)
T TIGR00652 26 EPEFVRQVCDRHFGIGADGVLFVEPG----SPEADYKMRIFNSDGSEAEMCGNGIR 77 (268)
T ss_pred CHHHHHHhcccCccccccEEEEEcCC----CCCccEEEEEEeCCCCHHHhCcCcHH
Confidence 4566777773 4689999999863 23568999999999 49999999986
No 11
>PLN02536 diaminopimelate epimerase
Probab=97.62 E-value=0.00024 Score=55.49 Aligned_cols=49 Identities=10% Similarity=0.110 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHH-hC--CceeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH
Q 034019 33 RDEEWLQAVASE-FN--ISQTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK 85 (106)
Q Consensus 33 l~~~~mq~IA~e-~n--~sETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv 85 (106)
++.++.++++.+ ++ ----+||.++ ...++|++|||+|. .|.++|||++.
T Consensus 11 ~~~~~~~~lc~R~~GiGaDgli~i~~~----~~~ad~~mrifN~DGSea~mCGNg~R 63 (267)
T PLN02536 11 LTPEQAVKLCDRNFGIGADGVIFAMPG----VNGTDYTMRIFNSDGSEPEMCGNGIR 63 (267)
T ss_pred CCHHHHHHhcccCCCcCCCEEEEEecC----CCCccEEEEEEcCCCChhhhCccHHH
Confidence 467778888874 43 3567898865 22467999999999 69999999975
No 12
>PRK13969 proline racemase; Provisional
Probab=96.28 E-value=0.012 Score=47.96 Aligned_cols=88 Identities=9% Similarity=0.041 Sum_probs=56.3
Q ss_pred eEEEEeeccCCCCCCCeeEEEEcCC-CC---C-HHHHHHHHHHhC------------Cc--eeEEEecCCCCCCCCCceE
Q 034019 7 QYSVVDAFTDSAFKGNPAAVCLLEE-DR---D-EEWLQAVASEFN------------IS--QTCYLTRLTAADSPNPRFR 67 (106)
Q Consensus 7 ~~~~vdvFt~~~f~GNPaaVv~~~~-~l---~-~~~mq~IA~e~n------------~s--ETaFv~~~~~~~~~~~~~~ 67 (106)
.+.+||+ ...|+|.=||...- ++ + .++|+.+.+++. .. =-+++.||. ++.+++.
T Consensus 6 ~~~~id~----Ht~GEp~Riv~~G~p~l~g~t~~ek~~~~~~~~D~lR~~L~~EPRGh~~m~g~ll~pp~---~~~Ad~g 78 (334)
T PRK13969 6 SIQTIDS----HTMGEPTRIVVGGLPKIPGKTMAEKKEYLEENNDSLRTALMSEPRGHNDMFGSIYTEPA---DETADFG 78 (334)
T ss_pred eEEEEEc----cCCCCCEEEEecCCCCCCCCCHHHHHHHHHHhHHHHHHHhhcCCCCCCccEEEEEeCCC---CCCCCEE
Confidence 3666664 67899999998532 12 2 234444444311 11 235787773 4568999
Q ss_pred EEEecCCCccCCCCchHHH---HHHHcC--------CeEEEeeec
Q 034019 68 LRWFTPVAEVSFSFYNYKL---WMKLFG--------SVLELDDLS 101 (106)
Q Consensus 68 vR~FTp~~Ei~~cGHatva---w~~~~~--------~~~~~~~~~ 101 (106)
++||-..++.++|||++++ |+...| ..+.+||++
T Consensus 79 vif~~~~gy~~MCGhgtI~vat~l~e~G~v~~~~~~~~v~ieTPa 123 (334)
T PRK13969 79 IIFMDGGGYLNMCGHGSIGAATCAVETGIVKVEEPYTHIKLEAPA 123 (334)
T ss_pred EEEEeCCcccccccChHHHHHHHHHHcCCcCCCCCceeEEEECCc
Confidence 9999999999999999873 443222 146777764
No 13
>PF05544 Pro_racemase: Proline racemase; InterPro: IPR008794 This family consists of proline racemase (5.1.1.4 from EC) proteins which catalyse the interconversion of L- and D-proline in bacteria []. This family also contains several similar eukaryotic proteins including Q9NCP4 from SWISSPROT a sequence with B-cell mitogenic properties which has been characterised as a co-factor-independent proline racemase [].; GO: 0018112 proline racemase activity; PDB: 1TM0_A 2AZP_A 1W61_B 1W62_A.
Probab=93.49 E-value=0.17 Score=41.23 Aligned_cols=81 Identities=10% Similarity=0.018 Sum_probs=50.2
Q ss_pred CCCCCeeEEEEcCC-CC---C-HHHHHHHHHHhC------------Cc--eeEEEecCCCCCCCCCceEEEEecCCCccC
Q 034019 18 AFKGNPAAVCLLEE-DR---D-EEWLQAVASEFN------------IS--QTCYLTRLTAADSPNPRFRLRWFTPVAEVS 78 (106)
Q Consensus 18 ~f~GNPaaVv~~~~-~l---~-~~~mq~IA~e~n------------~s--ETaFv~~~~~~~~~~~~~~vR~FTp~~Ei~ 78 (106)
...|+|.=||...- .+ + .+.|+.+.++.. .. =-+++.||. ++++++.+=|+-+.+=.+
T Consensus 5 Ht~GEp~RIV~~G~p~l~G~T~~Ek~~~~~~~~D~lR~~Lm~EPRGh~~M~Gall~pp~---~~~Ad~Gvif~~~~gy~~ 81 (325)
T PF05544_consen 5 HTGGEPTRIVTGGIPDLPGNTMLEKREYFRENHDHLRRLLMFEPRGHADMYGALLVPPC---DPEADFGVIFMHNEGYSP 81 (325)
T ss_dssp EETTEEEEEEEESS---SSSSHHHHHHHHHHH-HHHHHHHHSTTTS-TT-EEEEEE--S---STTSSEEEEEEESSSC-S
T ss_pred cCCCCCeEEEeCCcCCCCCCCHHHHHHHHHHhHHHHHHhheeCCCCCCceEEEEEcCCC---CCCCCEEEEEEcCCCCCC
Confidence 35799999998642 22 2 244555544421 11 246888884 467899999999999999
Q ss_pred CCCchHHH---HHHHc--------CCeEEEeeec
Q 034019 79 FSFYNYKL---WMKLF--------GSVLELDDLS 101 (106)
Q Consensus 79 ~cGHatva---w~~~~--------~~~~~~~~~~ 101 (106)
+|||+|++ |+... ...++||+++
T Consensus 82 McGh~tI~~~t~lve~G~v~~~~~~t~v~letPa 115 (325)
T PF05544_consen 82 MCGHGTIAVATALVETGLVPMKEPETEVRLETPA 115 (325)
T ss_dssp STHHHHHHHHHHHHHTTSS-SECCECEEEEEETT
T ss_pred CcccHHHHHHHHHHHCCcccCCCCCEEEEEECCC
Confidence 99999873 55433 2356677654
No 14
>COG0253 DapF Diaminopimelate epimerase [Amino acid transport and metabolism]
Probab=92.31 E-value=1.4 Score=35.12 Aligned_cols=85 Identities=16% Similarity=0.180 Sum_probs=55.7
Q ss_pred ccCCCCCCCeeEEEEcCCC---CCHHHHHHHHHHh---CCceeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH-
Q 034019 14 FTDSAFKGNPAAVCLLEED---RDEEWLQAVASEF---NISQTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK- 85 (106)
Q Consensus 14 Ft~~~f~GNPaaVv~~~~~---l~~~~mq~IA~e~---n~sETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv- 85 (106)
|+.=.-.||---||..-+. ..++.-.+|+.+- +.---.||.+|. ++..++++|+|+.. .|..+||-++-
T Consensus 3 F~KmhG~GNdfivvd~~~~~~~~~~~~a~~l~~r~~giGaDgvl~i~~p~---s~~~d~~~rifN~DGS~ae~CGNG~Rc 79 (272)
T COG0253 3 FSKMHGLGNDFIVVDEFDKKDEETPELARALCDRHFGIGADGVLFVEPPR---SPGADFHLRIFNSDGSEAEMCGNGARC 79 (272)
T ss_pred eEEEcCCCCcEEEEeccccccccCHHHHHHHHhcccCcCCceEEEEecCC---CCCCCEEEEEEeCCCCHHhhcccHHHH
Confidence 4445567777776654332 3566666777665 355567998763 34678999999997 59999999953
Q ss_pred -H---HHHHc--CCeEEEeeec
Q 034019 86 -L---WMKLF--GSVLELDDLS 101 (106)
Q Consensus 86 -a---w~~~~--~~~~~~~~~~ 101 (106)
| +.... .+.+.+.|++
T Consensus 80 ~a~~l~~~~~~~~~~~~v~T~~ 101 (272)
T COG0253 80 FARFLAERGLVKKKEISVETLA 101 (272)
T ss_pred HHHHHHHhcCCcCccEEEEecc
Confidence 2 33322 2336776654
No 15
>TIGR00654 PhzF_family phenazine biosynthesis protein PhzF family. Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear.
Probab=91.66 E-value=1.8 Score=33.56 Aligned_cols=65 Identities=14% Similarity=0.045 Sum_probs=43.4
Q ss_pred CCCCeeEEEEcCCC-------CCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCC---ccCCCCchH
Q 034019 19 FKGNPAAVCLLEED-------RDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVA---EVSFSFYNY 84 (106)
Q Consensus 19 f~GNPaaVv~~~~~-------l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~---Ei~~cGHat 84 (106)
..|||-.||..++. ++.+.+.++.++++. ..+|+...+.+.....++++|.|.|.. |=|-||-|.
T Consensus 160 ~~G~ph~vv~v~~~~~l~~~~~d~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~R~f~p~~g~~EDpatGSa~ 234 (297)
T TIGR00654 160 STGPEWIVIPLKDEEACFNASPNFAMLAHQLKQNDH-VGVIPFGPKKEAAGKNDYHGRMFAPVIGIYEDPVTGSGS 234 (297)
T ss_pred ecCCCeEEEEeCCHHHHHhCCCCHHHHHHHHhhcCc-cEEEEEecCCCCCCCceEEEEeCCCCCCCcCCCcccHHH
Confidence 46999999886541 134455666666764 466776653211123469999999973 999999984
No 16
>PF01678 DAP_epimerase: Diaminopimelate epimerase; InterPro: IPR001653 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways []. There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different []. The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria. The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified. The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana. The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum. Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways. This entry represents diaminopimelate epimerase (5.1.1.7 from EC), which catalyses the isomerisation of L,L-dimaminopimelate to meso-DAP in the biosynthetic pathway leading from aspartate to lysine. It is a member of the broader family of PLP-independent amino acid racemases. This enzyme is a monomeric protein of about 30 kDa consisting of two domains which are homologus in structure though they share little sequence similarity []. Each domain consists of mixed beta-sheets which fold into a barrel around the central helix. The active site cleft is formed from both domains and contains two conserved cysteines thought to function as the acid and base in the catalytic reaction []. Other PLP-independent racemases such as glutamate racemase have been shown to share a similar structure and mechanism of catalysis.; GO: 0008837 diaminopimelate epimerase activity, 0009089 lysine biosynthetic process via diaminopimelate; PDB: 2OTN_A 3FVE_A 2Q9J_A 2GKJ_A 1GQZ_A 2Q9H_A 1BWZ_A 2GKE_A 3EKM_C 3EJX_D ....
Probab=86.82 E-value=4.3 Score=27.41 Aligned_cols=77 Identities=14% Similarity=0.234 Sum_probs=45.9
Q ss_pred CCCCeeEEEEcCC-C----CCHHHHHHHHHHh---CCceeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH--H-
Q 034019 19 FKGNPAAVCLLEE-D----RDEEWLQAVASEF---NISQTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK--L- 86 (106)
Q Consensus 19 f~GNPaaVv~~~~-~----l~~~~mq~IA~e~---n~sETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv--a- 86 (106)
..|||=.|++.++ . ++++.-++|...- +-.-..|+... +..++++|+|.+. .|-..||-++. +
T Consensus 4 ~~G~ph~vi~vd~~~~~~~~~~~~~~~~~~~~~~~~~dnv~fv~~~-----~~~~~~~r~~n~~g~et~aCGnG~~~~a~ 78 (121)
T PF01678_consen 4 MHGNPHDVIFVDDREEEDDLDSELARAICDRHFFPGGDNVNFVEIS-----DDADIRMRIFNRDGSETLACGNGCRCAAA 78 (121)
T ss_dssp ECSSEEEEEEEETTTCSSTCCHHHHHHHHTTTTSTT-SEEEEEEEE-----CTTEEEEEEEETTSBEESTTHHHHHHHHH
T ss_pred EeCCCcEEEEEcCcccccccchhhhhhhhccccCCcccceEEEEEe-----cCCcEEEEEEECCCCeeeecCcHHHHHHH
Confidence 4689988887543 1 1222333333221 12234588754 3578999999996 79999999842 2
Q ss_pred HHHHc----CCeEEEeee
Q 034019 87 WMKLF----GSVLELDDL 100 (106)
Q Consensus 87 w~~~~----~~~~~~~~~ 100 (106)
|+... .+.+.++++
T Consensus 79 ~~~~~~~~~~~~v~v~t~ 96 (121)
T PF01678_consen 79 YLLEGGIVGKDEVTVETP 96 (121)
T ss_dssp HHHHTTSSSSSEEEEEET
T ss_pred HHHHCCCCcceEEEEEeC
Confidence 33322 467776654
No 17
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.15 E-value=1.1 Score=29.21 Aligned_cols=17 Identities=29% Similarity=0.315 Sum_probs=14.3
Q ss_pred CCCCHHHHHHHHHHhCC
Q 034019 31 EDRDEEWLQAVASEFNI 47 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~ 47 (106)
+..|+.+||+||.|++.
T Consensus 52 enfSpsEmqaiA~eL~r 68 (71)
T COG4840 52 ENFSPSEMQAIADELGR 68 (71)
T ss_pred ccCCHHHHHHHHHHHHH
Confidence 45689999999999873
No 18
>COG3938 Proline racemase [Amino acid transport and metabolism]
Probab=81.86 E-value=8.5 Score=31.73 Aligned_cols=73 Identities=15% Similarity=0.081 Sum_probs=51.3
Q ss_pred eeEEEEeeccCCCCCCCeeEEEEcCCC-C----CHHHHHHHHHHhC-C-----c--------eeEEEecCCCCCCCCCce
Q 034019 6 VQYSVVDAFTDSAFKGNPAAVCLLEED-R----DEEWLQAVASEFN-I-----S--------QTCYLTRLTAADSPNPRF 66 (106)
Q Consensus 6 ~~~~~vdvFt~~~f~GNPaaVv~~~~~-l----~~~~mq~IA~e~n-~-----s--------ETaFv~~~~~~~~~~~~~ 66 (106)
..+++||+ ...|||-=||...-. + =.|++.-++++.. + - --.-++|+. .+.++.
T Consensus 5 ~ti~~id~----HteGe~grvV~GG~p~~pg~tm~Eq~~~~~~d~d~lR~~l~~EPRG~~~~~~~lL~Pp~---~pda~a 77 (341)
T COG3938 5 KTIHCIDC----HTEGEPGRVVVGGVPPLPGATMWEQRRWFARDHDWLRNFLMFEPRGHDFRSGNLLVPPK---RPDADA 77 (341)
T ss_pred eEEEEEcc----ccCCcceeEEEcCCCCCCCCcHHHHHHHHhcchHHHHHhheeCCCCCcceeeeEecCCC---CCCccE
Confidence 45788876 567999999986542 2 2466777777643 0 0 122445553 456789
Q ss_pred EEEEecCCCccCCCCchHH
Q 034019 67 RLRWFTPVAEVSFSFYNYK 85 (106)
Q Consensus 67 ~vR~FTp~~Ei~~cGHatv 85 (106)
.+=|+-|+.=.|+|||+|+
T Consensus 78 a~ii~eps~~~pMsGsntI 96 (341)
T COG3938 78 AVIIMEPSGCLPMSGSNTI 96 (341)
T ss_pred EEEEEccCCCCCcCCCCch
Confidence 9999999999999999976
No 19
>KOG3033 consensus Predicted PhzC/PhzF-type epimerase [General function prediction only]
Probab=79.41 E-value=1.8 Score=34.78 Aligned_cols=32 Identities=19% Similarity=0.346 Sum_probs=25.2
Q ss_pred CCCceEEEEecCC---CccCCCCchHH----HHHHHcCC
Q 034019 62 PNPRFRLRWFTPV---AEVSFSFYNYK----LWMKLFGS 93 (106)
Q Consensus 62 ~~~~~~vR~FTp~---~Ei~~cGHatv----aw~~~~~~ 93 (106)
...+|..|+|.|. .|=|-||+|.. -|.+-.|+
T Consensus 205 ~~~dy~~RyFAP~~GVnEDPvtGSa~caL~~yws~~~~k 243 (286)
T KOG3033|consen 205 SPYDYESRYFAPWVGVNEDPVTGSAHCALGPYWSLILGK 243 (286)
T ss_pred CCCceEeeeccccccccCCCCCCceeeehHHHHHHHcCc
Confidence 4568999999995 79999999953 38776544
No 20
>PRK10281 hypothetical protein; Provisional
Probab=79.21 E-value=18 Score=28.57 Aligned_cols=64 Identities=13% Similarity=0.118 Sum_probs=43.1
Q ss_pred CCCCeeEEEEcCC-------CCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCC---CccCCCCchH
Q 034019 19 FKGNPAAVCLLEE-------DRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPV---AEVSFSFYNY 84 (106)
Q Consensus 19 f~GNPaaVv~~~~-------~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~---~Ei~~cGHat 84 (106)
..|++--+|...+ .++.+.+.+++++.+.. .+++.-... .++..+++.|.|.|. .|=|-||.|.
T Consensus 160 ~~G~~~liv~l~~~~~l~~~~pd~~~l~~l~~~~~~~-g~~v~~~~~-~~~~~~~~~R~FaP~~Gi~EDPaTGSA~ 233 (299)
T PRK10281 160 STGHSKVMIPLKPEVDLDALSPNLAALTAISKQIGCN-GFFPFQIRP-GKNEILTDGRMFAPAIGIVEDPVTGNAN 233 (299)
T ss_pred ecCCceEEEEeCCHHHHHhCCCCHHHHHHHHHhcCCc-EEEEEEecC-CCCCceEEEeeCCCCCCCccCcccchhh
Confidence 4688766666554 23667888888887753 455543311 112345899999997 7999999984
No 21
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=70.45 E-value=3.7 Score=26.74 Aligned_cols=18 Identities=22% Similarity=0.276 Sum_probs=15.3
Q ss_pred CCCCCHHHHHHHHHHhCC
Q 034019 30 EEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 30 ~~~l~~~~mq~IA~e~n~ 47 (106)
.+..|..+||+||.|||.
T Consensus 51 K~~fS~sEm~aI~~ELG~ 68 (71)
T PF06569_consen 51 KDSFSPSEMQAIAEELGQ 68 (71)
T ss_pred ccCCCHHHHHHHHHHHHh
Confidence 456799999999999984
No 22
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=67.88 E-value=4.4 Score=25.18 Aligned_cols=21 Identities=10% Similarity=0.325 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHHhCCceeEEE
Q 034019 33 RDEEWLQAVASEFNISQTCYL 53 (106)
Q Consensus 33 l~~~~mq~IA~e~n~sETaFv 53 (106)
++.+..+.||.++|++|.+|=
T Consensus 30 ~~~~~r~~la~~lgl~~~vvK 50 (58)
T TIGR01565 30 KRREEVREFCEEIGVTRKVFK 50 (58)
T ss_pred CCHHHHHHHHHHhCCCHHHee
Confidence 789999999999999988763
No 23
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=67.34 E-value=4 Score=23.53 Aligned_cols=19 Identities=16% Similarity=0.214 Sum_probs=16.5
Q ss_pred CCCHHHHHHHHHHhCCcee
Q 034019 32 DRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 32 ~l~~~~mq~IA~e~n~sET 50 (106)
-++.++++.||+++|+++.
T Consensus 24 ~P~~~~~~~la~~~~l~~~ 42 (59)
T cd00086 24 YPSREEREELAKELGLTER 42 (59)
T ss_pred CCCHHHHHHHHHHHCcCHH
Confidence 4689999999999998764
No 24
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=64.13 E-value=5.1 Score=23.02 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=16.4
Q ss_pred CCCHHHHHHHHHHhCCcee
Q 034019 32 DRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 32 ~l~~~~mq~IA~e~n~sET 50 (106)
-++.++++.||+++|++++
T Consensus 24 ~P~~~~~~~la~~~~l~~~ 42 (56)
T smart00389 24 YPSREEREELAAKLGLSER 42 (56)
T ss_pred CCCHHHHHHHHHHHCcCHH
Confidence 4689999999999999853
No 25
>PRK13577 diaminopimelate epimerase; Provisional
Probab=60.81 E-value=42 Score=26.03 Aligned_cols=60 Identities=20% Similarity=0.209 Sum_probs=40.2
Q ss_pred CCCeeEEEEcCCCCCHHHHHHHHHHhC----Cc---eeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH
Q 034019 20 KGNPAAVCLLEEDRDEEWLQAVASEFN----IS---QTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK 85 (106)
Q Consensus 20 ~GNPaaVv~~~~~l~~~~mq~IA~e~n----~s---ETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv 85 (106)
.|||=.|+..++ +++.....++..+. +| ..-|+... ....+++|.|-+. +|=+=||.+..
T Consensus 156 ~G~PH~Vv~V~~-~~~~~~~~~g~~~~~~~~fp~~~Nv~f~~~~-----~~~~i~~R~~ErG~g~T~AcGTga~ 223 (281)
T PRK13577 156 IGNPHCVVLLDE-ISEELARELGPLIETHPRFPNRTNVQFLKVL-----DRNTIQIEIWERGAGYTLASGSSSC 223 (281)
T ss_pred CCCCcEEEEeCC-cchhhHHhhCccccccCCCCCCceEEEEEEc-----cCCeEEEEEECCCCCCCccCHHHHH
Confidence 699999998765 34444555555443 23 23356544 1347999999996 78889999843
No 26
>PRK00450 dapF diaminopimelate epimerase; Provisional
Probab=60.24 E-value=26 Score=26.70 Aligned_cols=60 Identities=17% Similarity=0.233 Sum_probs=34.7
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhC----Cce---eEEEecCCCCCCCCCceEEEEecCC-CccCCCCchH
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFN----ISQ---TCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNY 84 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n----~sE---TaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHat 84 (106)
..|||-.||..++ ++.+.+.++...+. +++ ..|+... ...+++.|.|.|. .|-|-||-++
T Consensus 153 ~~G~~~lvv~v~~-~~~~~l~~l~pd~~~~~~~~~~~nv~~~~~~-----~~~~~~~R~F~~gv~Ed~a~GTg~ 220 (274)
T PRK00450 153 SMGNPHAVIFVDD-VDAADVEELGPLLENHPRFPEGVNVNFVQVV-----DRDHIRLRVYERGVGETLACGTGA 220 (274)
T ss_pred ECCCCcEEEEeCC-CCcCchhHhchhcccCCCCCCCeEEEEEEEc-----cCCEEEEEEecCCCCcccccccch
Confidence 5788877777655 12333333333322 222 1233322 1246899999997 8999999875
No 27
>TIGR00652 DapF diaminopimelate epimerase.
Probab=58.89 E-value=23 Score=27.16 Aligned_cols=64 Identities=13% Similarity=0.117 Sum_probs=39.7
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhC----CceeEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFN----ISQTCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK 85 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n----~sETaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv 85 (106)
..|||=.||...+ ++.-..++++..++ +++.++|.-... .+...+++|.|-|. +|-+=||-+..
T Consensus 149 stG~ph~vv~v~~-~~~l~~~~~~~~~~~~~~fp~~~nV~~~~~--~~~~~i~~R~ferg~get~acGTGa~ 217 (268)
T TIGR00652 149 DTGNPHLVVFVDD-VEGLNLLILGPLLEYHERFPEGVNVNFVQV--KNDDTIKLRTYERGAGETLACGTGAC 217 (268)
T ss_pred ecCCCcEEEEeCC-cCcccHHHhccccccCCCCCCCeEEEEEEE--CcCCEEEEEEecCCCCcccccHHHHH
Confidence 3499999988764 22233344444433 355555443210 12457999999996 89999999853
No 28
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=56.09 E-value=7.7 Score=31.61 Aligned_cols=31 Identities=19% Similarity=0.142 Sum_probs=26.4
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhCCce
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFNISQ 49 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sE 49 (106)
..-|+.++|..+.+|+|+|+++|+..=|+=-
T Consensus 189 SHSN~~al~~h~RNl~D~qlkaI~~~gGvIg 219 (313)
T COG2355 189 SHSNARALVDHPRNLSDEQLKAIAETGGVIG 219 (313)
T ss_pred ecCCchhccCCCCCCCHHHHHHHHhcCCEEE
Confidence 3679999999999999999999998866433
No 29
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=55.80 E-value=7.3 Score=22.64 Aligned_cols=19 Identities=16% Similarity=0.223 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHHhCCce
Q 034019 31 EDRDEEWLQAVASEFNISQ 49 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sE 49 (106)
.-++.++++.||+++|+++
T Consensus 23 ~~p~~~~~~~la~~l~l~~ 41 (57)
T PF00046_consen 23 PYPSKEEREELAKELGLTE 41 (57)
T ss_dssp SSCHHHHHHHHHHHHTSSH
T ss_pred ccccccccccccccccccc
Confidence 3468899999999999975
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=54.17 E-value=8.7 Score=21.92 Aligned_cols=17 Identities=18% Similarity=0.206 Sum_probs=13.1
Q ss_pred CCHHHHHHHHHHhCCce
Q 034019 33 RDEEWLQAVASEFNISQ 49 (106)
Q Consensus 33 l~~~~mq~IA~e~n~sE 49 (106)
+++++++.||++.|+|.
T Consensus 11 Ps~~ek~~L~~~tgls~ 27 (40)
T PF05920_consen 11 PSKEEKEELAKQTGLSR 27 (40)
T ss_dssp --HHHHHHHHHHHTS-H
T ss_pred CCHHHHHHHHHHcCCCH
Confidence 48999999999999875
No 31
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=53.91 E-value=4.3 Score=30.84 Aligned_cols=39 Identities=18% Similarity=0.172 Sum_probs=28.1
Q ss_pred eeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCCceeE
Q 034019 12 DAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNISQTC 51 (106)
Q Consensus 12 dvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sETa 51 (106)
.||++....|++-- +-...-|+..+||.+|.-+|+|||-
T Consensus 105 tvfs~~ql~~l~~r-Fe~QrYLS~~e~~ELan~L~LS~~Q 143 (194)
T KOG0491|consen 105 TVFSDPQLSGLEKR-FERQRYLSTPERQELANALSLSETQ 143 (194)
T ss_pred ccccCccccccHHH-HhhhhhcccHHHHHHHHHhhhhHHH
Confidence 36777777666543 1112347999999999999999985
No 32
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=53.33 E-value=59 Score=24.64 Aligned_cols=63 Identities=21% Similarity=0.222 Sum_probs=35.6
Q ss_pred CCCCeeEEEEcCCC-----CCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCC---CccCCCCchH
Q 034019 19 FKGNPAAVCLLEED-----RDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPV---AEVSFSFYNY 84 (106)
Q Consensus 19 f~GNPaaVv~~~~~-----l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~---~Ei~~cGHat 84 (106)
..|++--+|.+.+. +..+. .++.+.............. +....+++.|+|.|. .|=|-||-|.
T Consensus 150 ~tg~~~llv~l~~~~~l~~l~pd~-~~~~~~~~~~~~~~~~~~~--~~~~~~~~~R~FaP~~Gi~EDpaTGSA~ 220 (281)
T PF02567_consen 150 STGNPWLLVPLKSAEALAALKPDF-AALLALCDRNGVHVFTFFT--DDEDSDFHSRMFAPGIGIPEDPATGSAA 220 (281)
T ss_dssp ESSSEEEEEEBSCHHHHHH---SH-HHHHHHHTTCEEEEEEEEE--ESSTTEEEEEEEEGGGTEEEESS-HHHH
T ss_pred ECCCCcEEEEEecccccccceech-hhhcccccccccccccccc--cCCCceEEEeeeecccCCCCCCCchhhH
Confidence 46788877776652 12222 4455555443322221111 123568999999996 4999999984
No 33
>PF07040 DUF1326: Protein of unknown function (DUF1326); InterPro: IPR009758 This family consists of several hypothetical bacterial proteins, which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N terminus. The function of this family is unknown.
Probab=51.90 E-value=48 Score=24.82 Aligned_cols=41 Identities=12% Similarity=0.208 Sum_probs=34.2
Q ss_pred ceeEEEEeeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHh
Q 034019 5 LVQYSVVDAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASEF 45 (106)
Q Consensus 5 ~~~~~~vdvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~ 45 (106)
.+++..+--|...-..||..++++.++.-|++|.++|.+=|
T Consensus 43 GL~va~~~~~PG~~~eG~~~~~~~IDerAs~~QreAL~~I~ 83 (184)
T PF07040_consen 43 GLNVAMAAHWPGNMHEGNWKVALYIDERASDAQREALEAIF 83 (184)
T ss_pred CCEEEEEEecCCCcccCceEEEEEECCCCCHHHHHHHHHHh
Confidence 46677777777777999999999999999999999996544
No 34
>PLN02536 diaminopimelate epimerase
Probab=51.63 E-value=39 Score=26.34 Aligned_cols=61 Identities=15% Similarity=0.217 Sum_probs=44.5
Q ss_pred CCCCeeEEEEcCCC--CCHHHHHHHHHHhCC----ceeE---EEecCCCCCCCCCceEEEEecCC-CccCCCCchH
Q 034019 19 FKGNPAAVCLLEED--RDEEWLQAVASEFNI----SQTC---YLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNY 84 (106)
Q Consensus 19 f~GNPaaVv~~~~~--l~~~~mq~IA~e~n~----sETa---Fv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHat 84 (106)
.-|||=+|+..++. +++.+.+.+++.+.. ||-+ |+... +....++|.|=-. +|-.=||-+.
T Consensus 144 s~GnPH~VifV~~~~~~~~~~~~~~g~~i~~~~~FP~~~NV~f~~v~-----~~~~i~~rt~ERGvg~TlACGTGa 214 (267)
T PLN02536 144 SMGNPHCVTFGEKELKVDDLPLEKIGPKFEHHEMFPARTNTEFVQVV-----SRSHLKMRVWERGAGATLACGTGA 214 (267)
T ss_pred ECCCCCEEEEECCccccCcCChHHhChhccccCCCCCCcEEEEEEEc-----CCCEEEEEEeccCCchhhccCccH
Confidence 45999999998764 778888888888873 3322 55433 2356899999664 8999999974
No 35
>PRK14980 DNA-directed RNA polymerase subunit G; Provisional
Probab=49.65 E-value=2.5 Score=30.38 Aligned_cols=14 Identities=14% Similarity=0.100 Sum_probs=10.7
Q ss_pred CccCCCCchHHHHH
Q 034019 75 AEVSFSFYNYKLWM 88 (106)
Q Consensus 75 ~Ei~~cGHatvaw~ 88 (106)
.|.+||||+++.-.
T Consensus 67 ~~~dFCghGyvV~~ 80 (127)
T PRK14980 67 TNDDFCAHGYIVTE 80 (127)
T ss_pred ccceeecCcEEEEE
Confidence 57899999976543
No 36
>PF11548 Receptor_IA-2: Protein-tyrosine phosphatase receptor IA-2; InterPro: IPR021613 IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. ; PDB: 2QT7_B 3N01_B 3N4W_B 3NG8_A.
Probab=44.15 E-value=22 Score=24.18 Aligned_cols=43 Identities=12% Similarity=0.262 Sum_probs=25.9
Q ss_pred EEEEcCCCCCH----HHHHHHHHHhCCceeEEEecCCCCCCCCCceEEE
Q 034019 25 AVCLLEEDRDE----EWLQAVASEFNISQTCYLTRLTAADSPNPRFRLR 69 (106)
Q Consensus 25 aVv~~~~~l~~----~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR 69 (106)
-|+...+.++. ..|..+|+-+++|-+.|...+.. .+.-+|+||
T Consensus 6 YIvt~nd~ls~~~G~~l~~~la~~l~l~s~~F~~i~V~--g~avTFrv~ 52 (91)
T PF11548_consen 6 YIVTGNDPLSWDEGSRLMEKLAELLHLPSSSFINISVV--GPAVTFRVR 52 (91)
T ss_dssp EEEES-TT--HHHHHHHHHHHHHHHTS-GGGEEEEEEE--TTEEEEEE-
T ss_pred EEEeCCCCCCHHHHHHHHHHHHHHhCCCcccceeeeec--CceEEEEec
Confidence 35566677764 45999999999999999876531 222356655
No 37
>PF02603 Hpr_kinase_N: HPr Serine kinase N terminus; InterPro: IPR011126 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria []. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes []. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains []. ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1KNX_B 1KO7_A.
Probab=42.91 E-value=30 Score=23.91 Aligned_cols=30 Identities=23% Similarity=0.322 Sum_probs=19.4
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhCCc
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFNIS 48 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n~s 48 (106)
+..+|.+||+-.+...++++..+|++.|.|
T Consensus 78 ~~~~~P~iIvt~~~~~p~~l~e~a~~~~ip 107 (127)
T PF02603_consen 78 FSYNPPCIIVTRGLEPPPELIELAEKYNIP 107 (127)
T ss_dssp CTTT-S-EEEETTT---HHHHHHHHHCT--
T ss_pred hCCCCCEEEEECcCCCCHHHHHHHHHhCCc
Confidence 667888888876666789999999998864
No 38
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=42.76 E-value=44 Score=19.61 Aligned_cols=22 Identities=23% Similarity=0.086 Sum_probs=16.0
Q ss_pred EEEEcCCCCCHHHHHHHHHHhC
Q 034019 25 AVCLLEEDRDEEWLQAVASEFN 46 (106)
Q Consensus 25 aVv~~~~~l~~~~mq~IA~e~n 46 (106)
.-|....+.+++++++|++++-
T Consensus 4 i~I~~~~grs~eqk~~l~~~it 25 (62)
T PRK00745 4 FHIELFEGRTVEQKRKLVEEIT 25 (62)
T ss_pred EEEEEcCCCCHHHHHHHHHHHH
Confidence 3344455679999999998864
No 39
>COG0253 DapF Diaminopimelate epimerase [Amino acid transport and metabolism]
Probab=40.19 E-value=1.6e+02 Score=23.50 Aligned_cols=61 Identities=18% Similarity=0.207 Sum_probs=42.7
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhCCce-------eEEEecCCCCCCCCCceEEEEecCC-CccCCCCchHH
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFNISQ-------TCYLTRLTAADSPNPRFRLRWFTPV-AEVSFSFYNYK 85 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sE-------TaFv~~~~~~~~~~~~~~vR~FTp~-~Ei~~cGHatv 85 (106)
.-|||=+|+..+ +.+.+..+.++.-+...| .-|+... .....+||.|=-. +|-.=||-++.
T Consensus 152 s~GnPH~V~~Vd-dv~~~~~~~~g~~l~~h~~Fp~~vNV~F~~v~-----~~~~i~vrv~ERG~G~T~ACGTGa~ 220 (272)
T COG0253 152 SMGNPHLVIFVD-DVETANLEELGPLLESHELFPEGVNVGFVQVL-----SRDAIRLRVYERGAGETLACGTGAC 220 (272)
T ss_pred ecCCCeEEEEeC-CcccchhhhhhhhhhcCccCCCceEEEEEEeC-----CCCcEEEEEeecCCcccccchhHHH
Confidence 569999999988 666788888888876532 2366554 1244667766443 68888999843
No 40
>cd02252 nylC_like nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly-polymerized 6-aminohexanoate oligomers. Together with other nylon degradation enzymes, such as 6-aminohexanoate cyclic dimer hydrolase (EI) and 6-aminohexanoate dimer hydrolase (EII), EIII plays a role in the detoxification and biological removal of the synthetic by-products of nylon manufacture. EIII shows sequence similarity to L-aminopeptidase D-amidase/D-esterase (DmpA), an aminopeptidase that releases N-terminal D and L amino acids from peptide substrates. Like DmpA, EIII undergoes autocatalytic cleavage in front of a nucleophile to form a heterodimer. DmpA shows similarity in catalytic mechanism to N-terminal nucleophile (Ntn) hydrolases, which are enzymes that catalyze the cleavage of amide bonds through the nucl
Probab=40.02 E-value=49 Score=26.40 Aligned_cols=37 Identities=16% Similarity=0.083 Sum_probs=28.7
Q ss_pred EEeeccC-CCCCCCeeEEEEcCCCCCHHHHHHHHHHhC
Q 034019 10 VVDAFTD-SAFKGNPAAVCLLEEDRDEEWLQAVASEFN 46 (106)
Q Consensus 10 ~vdvFt~-~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n 46 (106)
.|-|... ++++|.=++||..+.+|++.|+++||+.-.
T Consensus 169 tVgalV~vN~~GnTtI~vVaTdapL~~~ql~RlA~~A~ 206 (260)
T cd02252 169 TVGALVVVNAVGNTTIGVVATDAALTKAEAKRLASMAH 206 (260)
T ss_pred EEEEEEEEECCCCcEEEEEEeCCcCCHHHHHHHHHHhh
Confidence 3444433 457788999999899999999999999843
No 41
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=38.89 E-value=41 Score=19.72 Aligned_cols=20 Identities=20% Similarity=0.222 Sum_probs=13.9
Q ss_pred EEEcCCCCCHHHHHHHHHHh
Q 034019 26 VCLLEEDRDEEWLQAVASEF 45 (106)
Q Consensus 26 Vv~~~~~l~~~~mq~IA~e~ 45 (106)
-|-...+.+++++++|++++
T Consensus 4 ~i~~~~g~~~e~K~~l~~~i 23 (60)
T PF01361_consen 4 TIKIPEGRTAEQKRELAEAI 23 (60)
T ss_dssp EEEEESTS-HHHHHHHHHHH
T ss_pred EEEECCCCCHHHHHHHHHHH
Confidence 34444556999999999885
No 42
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=38.44 E-value=56 Score=19.43 Aligned_cols=19 Identities=37% Similarity=0.268 Sum_probs=13.4
Q ss_pred EEcCCCCCHHHHHHHHHHh
Q 034019 27 CLLEEDRDEEWLQAVASEF 45 (106)
Q Consensus 27 v~~~~~l~~~~mq~IA~e~ 45 (106)
|..-.+.|++|+++|++++
T Consensus 6 i~~~~Grs~EqK~~L~~~i 24 (60)
T PRK02289 6 IDLFEGRSQEQKNALAREV 24 (60)
T ss_pred EEECCCCCHHHHHHHHHHH
Confidence 3344467899988888775
No 43
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=37.88 E-value=65 Score=20.44 Aligned_cols=28 Identities=25% Similarity=0.590 Sum_probs=19.1
Q ss_pred HHHHHHhCCceeEEEecCCCCCCCCCceEEEEecCCCc
Q 034019 39 QAVASEFNISQTCYLTRLTAADSPNPRFRLRWFTPVAE 76 (106)
Q Consensus 39 q~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~FTp~~E 76 (106)
.+|=..++. +++|+.+. .+||+|+|..+
T Consensus 2 ~~il~s~~~-~i~~vD~~---------~~I~~~n~~a~ 29 (106)
T PF13596_consen 2 NNILDSMPI-GIIFVDRN---------LRIRYFNPAAA 29 (106)
T ss_dssp HHHHHHSSS-EEEEEETT---------SBEEEE-SCGC
T ss_pred hHHHhcCCC-CEEEEcCC---------CeEEEeChhHh
Confidence 345556665 77888643 69999999855
No 44
>PF02812 ELFV_dehydrog_N: Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; InterPro: IPR006097 Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases (1.4.1.2 from EC, 1.4.1.3 from EC, and 1.4.1.4 from EC) (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate [, ]. GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids []. Leucine dehydrogenase (1.4.1.9 from EC) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues []. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. Phenylalanine dehydrogenase (1.4.1.20 from EC) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate []. Valine dehydrogenase (1.4.1.8 from EC) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate []. This entry represents the dimerisation region of these enzymes.; GO: 0016491 oxidoreductase activity, 0006520 cellular amino acid metabolic process, 0055114 oxidation-reduction process; PDB: 2BMA_C 1C1D_B 1BXG_A 1BW9_B 1C1X_A 2YFQ_B 3R3J_D 1V9L_C 1B26_C 2TMG_B ....
Probab=36.66 E-value=24 Score=24.96 Aligned_cols=33 Identities=12% Similarity=0.205 Sum_probs=26.3
Q ss_pred cCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCC
Q 034019 15 TDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 15 t~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~ 47 (106)
++-|++|--.+|..++..+++.++++|.+.+..
T Consensus 64 ~~lp~GGaKggI~~dp~~~s~~e~e~l~r~f~~ 96 (131)
T PF02812_consen 64 AGLPFGGAKGGIKIDPKDLSDNERERLTRRFGR 96 (131)
T ss_dssp TTSS-EEEEEEEESSGGGS-HHHHHHHHHHHHH
T ss_pred ccCCCCceeEEeecCcccccHHHHHHHHHHHHH
Confidence 567899999999888888999999998888764
No 45
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=36.64 E-value=45 Score=20.32 Aligned_cols=22 Identities=14% Similarity=0.431 Sum_probs=17.3
Q ss_pred CHHHHHHHHH-HhCCc---eeEEEec
Q 034019 34 DEEWLQAVAS-EFNIS---QTCYLTR 55 (106)
Q Consensus 34 ~~~~mq~IA~-e~n~s---ETaFv~~ 55 (106)
|++...++|| ++|++ |++|..+
T Consensus 53 ~~~~ie~~AR~~lgm~~~~E~v~~~~ 78 (80)
T PF04977_consen 53 DPDYIEKVAREKLGMVKPGEIVFKIP 78 (80)
T ss_pred CHHHHHHHHHHHcCCcCCCCEEEeCC
Confidence 7889999999 78875 6776654
No 46
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=35.86 E-value=67 Score=18.34 Aligned_cols=21 Identities=14% Similarity=0.158 Sum_probs=15.3
Q ss_pred EEcCCCCCHHHHHHHHHHhCC
Q 034019 27 CLLEEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 27 v~~~~~l~~~~mq~IA~e~n~ 47 (106)
|....+.+.++++++++++-.
T Consensus 5 i~~~~grt~eqk~~l~~~i~~ 25 (58)
T cd00491 5 IYILEGRTDEQKRELIERVTE 25 (58)
T ss_pred EEEcCCCCHHHHHHHHHHHHH
Confidence 334445689999999998753
No 47
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=33.85 E-value=32 Score=24.46 Aligned_cols=19 Identities=26% Similarity=0.127 Sum_probs=17.1
Q ss_pred CCCCHHHHHHHHHHhCCce
Q 034019 31 EDRDEEWLQAVASEFNISQ 49 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sE 49 (106)
..++++.++.||+.+|+|.
T Consensus 30 G~i~~~~~~~iA~~l~~~~ 48 (148)
T TIGR01958 30 GWVTPEAIAAVAEMLGIPP 48 (148)
T ss_pred CCCCHHHHHHHHHHhCcCH
Confidence 3679999999999999986
No 48
>PF15646 Tox-REase-2: Restriction endonuclease fold toxin 2
Probab=33.76 E-value=5.2 Score=28.74 Aligned_cols=28 Identities=14% Similarity=0.062 Sum_probs=22.8
Q ss_pred CceEEEEe-cCCCccCCCCchHHHHHHHc
Q 034019 64 PRFRLRWF-TPVAEVSFSFYNYKLWMKLF 91 (106)
Q Consensus 64 ~~~~vR~F-Tp~~Ei~~cGHatvaw~~~~ 91 (106)
..|.+|++ .|+.|||+.||...+|..++
T Consensus 3 ~aYQ~rvAGypE~~v~lp~~~~~~~vDG~ 31 (125)
T PF15646_consen 3 NAYQKRVAGYPEYEVPLPGQKSVIMVDGI 31 (125)
T ss_pred hhhhHHhcCCCceEeecCCCCCceeeccc
Confidence 45899999 56799999999887777666
No 49
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=33.70 E-value=75 Score=20.91 Aligned_cols=15 Identities=53% Similarity=0.711 Sum_probs=13.5
Q ss_pred CHHHHHHHHHHhCCc
Q 034019 34 DEEWLQAVASEFNIS 48 (106)
Q Consensus 34 ~~~~mq~IA~e~n~s 48 (106)
+++|++.||.++|..
T Consensus 59 ~eeQL~~ia~~lGi~ 73 (75)
T PF11869_consen 59 NEEQLQAIAEELGID 73 (75)
T ss_pred CHHHHHHHHHHhCcc
Confidence 799999999999864
No 50
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=32.96 E-value=79 Score=18.47 Aligned_cols=16 Identities=19% Similarity=0.256 Sum_probs=13.7
Q ss_pred CCCCHHHHHHHHHHhC
Q 034019 31 EDRDEEWLQAVASEFN 46 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n 46 (106)
.+.+.+++++|++++-
T Consensus 10 ~grt~eqK~~l~~~it 25 (63)
T TIGR00013 10 EGRTDEQKRQLIEGVT 25 (63)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 5689999999999874
No 51
>PRK09414 glutamate dehydrogenase; Provisional
Probab=30.44 E-value=64 Score=27.45 Aligned_cols=32 Identities=9% Similarity=0.120 Sum_probs=27.5
Q ss_pred cCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhC
Q 034019 15 TDSAFKGNPAAVCLLEEDRDEEWLQAVASEFN 46 (106)
Q Consensus 15 t~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n 46 (106)
++=|++|--.+|..++..+++.++++|.|.+.
T Consensus 120 ~~lP~GGgKggI~~dP~~~s~~Eler~~r~~~ 151 (445)
T PRK09414 120 TGLPIGGGKGGSDFDPKGKSDAEIMRFCQSFM 151 (445)
T ss_pred cCCCCCCceeeeecCCccCCHHHHHHHHHHHH
Confidence 45689999999999999999999888888764
No 52
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=29.95 E-value=35 Score=22.28 Aligned_cols=20 Identities=5% Similarity=0.185 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHHHHhCCcee
Q 034019 31 EDRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sET 50 (106)
+..+..+...+||.+|+||+
T Consensus 7 d~v~~~~wk~~~R~LGlse~ 26 (80)
T cd08313 7 DEVPPRRWKEFVRRLGLSDN 26 (80)
T ss_pred HhCCHHHHHHHHHHcCCCHH
Confidence 45667777789999999984
No 53
>PRK11675 LexA regulated protein; Provisional
Probab=29.41 E-value=15 Score=24.96 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=27.6
Q ss_pred CCCcceeEEEEeeccCCCCCCCeeEEEEcCCCCCHHHHHHHHHH
Q 034019 1 MAKKLVQYSVVDAFTDSAFKGNPAAVCLLEEDRDEEWLQAVASE 44 (106)
Q Consensus 1 m~~~~~~~~~vdvFt~~~f~GNPaaVv~~~~~l~~~~mq~IA~e 44 (106)
||.......++|-|++++.-|-|-. .+|+-++-.+|=+.
T Consensus 1 mak~~~d~~t~dlf~~~~~~grp~t-----npl~r~~ql~inkr 39 (90)
T PRK11675 1 MAKEQTDRTTLDLFADERRPGRPKT-----NPLSRDEQLRINKR 39 (90)
T ss_pred CccccccchHHHHhccCCCCCCCCC-----CCCChHHHHHhhHH
Confidence 7888888899999999999887753 34554444444433
No 54
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=29.01 E-value=36 Score=20.18 Aligned_cols=15 Identities=27% Similarity=0.443 Sum_probs=10.2
Q ss_pred HHHHHHHHhCCceeE
Q 034019 37 WLQAVASEFNISQTC 51 (106)
Q Consensus 37 ~mq~IA~e~n~sETa 51 (106)
-+..||++||++.+.
T Consensus 24 s~~~ia~~fgv~~sT 38 (53)
T PF04218_consen 24 SKRDIAREFGVSRST 38 (53)
T ss_dssp -HHHHHHHHT--CCH
T ss_pred CHHHHHHHhCCCHHH
Confidence 578999999998764
No 55
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=28.79 E-value=92 Score=18.48 Aligned_cols=23 Identities=26% Similarity=0.216 Sum_probs=16.7
Q ss_pred EEEEcCCCCCHHHHHHHHHHhCC
Q 034019 25 AVCLLEEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 25 aVv~~~~~l~~~~mq~IA~e~n~ 47 (106)
.-|....+.+.+++++|++++..
T Consensus 4 v~i~l~~grt~eqk~~l~~~it~ 26 (64)
T PRK01964 4 VQIQLLEGRPEEKIKNLIREVTE 26 (64)
T ss_pred EEEEEeCCCCHHHHHHHHHHHHH
Confidence 33444556799999999988754
No 56
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=28.08 E-value=28 Score=23.52 Aligned_cols=21 Identities=5% Similarity=-0.045 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHhCCceeE
Q 034019 31 EDRDEEWLQAVASEFNISQTC 51 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sETa 51 (106)
+.++..++.++||++|+||+.
T Consensus 16 ~~~~~~~wK~faR~lglse~~ 36 (97)
T cd08316 16 DVMTLKDVKKFVRKSGLSEPK 36 (97)
T ss_pred HHcCHHHHHHHHHHcCCCHHH
Confidence 456777788899999999864
No 57
>PRK11669 pbpG D-alanyl-D-alanine endopeptidase; Provisional
Probab=27.89 E-value=15 Score=29.61 Aligned_cols=37 Identities=22% Similarity=0.232 Sum_probs=26.0
Q ss_pred CCCeeEEEEcCC-CCC----HHHHHHHHHHhCCceeEEEecC
Q 034019 20 KGNPAAVCLLEE-DRD----EEWLQAVASEFNISQTCYLTRL 56 (106)
Q Consensus 20 ~GNPaaVv~~~~-~l~----~~~mq~IA~e~n~sETaFv~~~ 56 (106)
+||-+|+.+-.. .-+ -+.|.+-|+|+|+..|-|..|.
T Consensus 125 S~NDAA~aLAe~v~Gs~~~Fv~~MN~kAkeLGm~~T~F~np~ 166 (306)
T PRK11669 125 SENRAAASLAHHYPGGYKAFIKAMNAKAKALGMTNTRYVEPT 166 (306)
T ss_pred CcHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCCEEeCCC
Confidence 567777654221 112 2559999999999999999875
No 58
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=27.84 E-value=1.1e+02 Score=17.79 Aligned_cols=16 Identities=38% Similarity=0.545 Sum_probs=12.8
Q ss_pred CCCCHHHHHHHHHHhC
Q 034019 31 EDRDEEWLQAVASEFN 46 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n 46 (106)
.+.|++|+++|++++-
T Consensus 10 ~Grs~eqk~~l~~~it 25 (61)
T PRK02220 10 EGRTEEQLKALVKDVT 25 (61)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 4579999999888864
No 59
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=27.54 E-value=49 Score=18.85 Aligned_cols=16 Identities=25% Similarity=0.266 Sum_probs=12.5
Q ss_pred CCHHHHHHHHHHhCCc
Q 034019 33 RDEEWLQAVASEFNIS 48 (106)
Q Consensus 33 l~~~~mq~IA~e~n~s 48 (106)
++-.+++.||+++|++
T Consensus 5 ~~~~eL~~iAk~lgI~ 20 (43)
T PF07498_consen 5 MTLSELREIAKELGIE 20 (43)
T ss_dssp S-HHHHHHHHHCTT-T
T ss_pred CCHHHHHHHHHHcCCC
Confidence 5678999999999985
No 60
>COG3191 DmpA L-aminopeptidase/D-esterase [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=26.98 E-value=1.2e+02 Score=25.37 Aligned_cols=36 Identities=17% Similarity=0.157 Sum_probs=28.7
Q ss_pred CCCCCCCeeEEEEcCCCCCHHHHHHHHHH--hCCceeE
Q 034019 16 DSAFKGNPAAVCLLEEDRDEEWLQAVASE--FNISQTC 51 (106)
Q Consensus 16 ~~~f~GNPaaVv~~~~~l~~~~mq~IA~e--~n~sETa 51 (106)
..+-.|.-++||..+.+|+..|+|++|+. -++.-|.
T Consensus 228 ~~~~~gTtI~vvATDapL~~aq~~RlA~rA~~GlARtg 265 (348)
T COG3191 228 GGDEKGTTIGVVATDAPLTKAQLKRLARRAHDGLARTG 265 (348)
T ss_pred CCCCCCCEEEEEEcCCcCCHHHHHHHHHHhhcchheec
Confidence 45567788899998999999999999987 4555554
No 61
>cd05568 PTS_IIB_bgl_like PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved in sugar utilization. The domain architecture of the IIB-containing protein includes a region N-terminal to the IIB domain which is homologous to the BglG transcription antiterminator with an RNA-binding domain followed by two homologous domains, PRD1 and PRD2 (PTS Regulation Domains). C-terminal to the IIB domain is a domain similar to the PTS IIA domain. In this system, the BglG-like region and the IIB and IIA-like domains are all expressed together as a single multidomain protein. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include this sensory system with similarity to the bacterial
Probab=26.28 E-value=1.2e+02 Score=18.34 Aligned_cols=34 Identities=9% Similarity=0.088 Sum_probs=23.8
Q ss_pred ccCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCC
Q 034019 14 FTDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 14 Ft~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~ 47 (106)
||+.+....+..|+....-++++++++|-+.++.
T Consensus 51 itT~~l~~~~~pvi~i~~~l~~~d~~~i~~~i~~ 84 (85)
T cd05568 51 ISTVPLEDTDKPVIVVSPILTEEDIKKIRKFIKK 84 (85)
T ss_pred EEccccCCCCCCEEEECCCCCHHHHHHHHHHHhc
Confidence 4554544334567777777899999999888754
No 62
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=26.27 E-value=50 Score=18.73 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=9.8
Q ss_pred HHHHHHHHHHhCCceeEE
Q 034019 35 EEWLQAVASEFNISQTCY 52 (106)
Q Consensus 35 ~~~mq~IA~e~n~sETaF 52 (106)
+=++|.+|.++|..+.-|
T Consensus 24 ~CeLQ~~~~~~gv~~~~f 41 (41)
T PF10588_consen 24 NCELQDLAYEYGVDEQRF 41 (41)
T ss_dssp G-HHHHHHHHH-S-----
T ss_pred CCHHHHHHHHhCCCcCCC
Confidence 447999999999876543
No 63
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=26.13 E-value=1.2e+02 Score=22.75 Aligned_cols=39 Identities=8% Similarity=0.161 Sum_probs=32.3
Q ss_pred eeEEEEeeccCCC-CCCCeeEEEEcCCCCCHHHHHHHHHH
Q 034019 6 VQYSVVDAFTDSA-FKGNPAAVCLLEEDRDEEWLQAVASE 44 (106)
Q Consensus 6 ~~~~~vdvFt~~~-f~GNPaaVv~~~~~l~~~~mq~IA~e 44 (106)
..+.+..+|+++| +.++|-..|.....++.+-.-.|.+.
T Consensus 119 ~gi~Irqi~~~dpe~~~e~~l~IVte~~iP~~li~el~~i 158 (167)
T COG2150 119 RGISIRQIISEDPELQEEPKLTIVTERPIPGDLIDELKKI 158 (167)
T ss_pred cCceEEEEecCCcccCCCceEEEEEeccCCHHHHHHHhcc
Confidence 4567888999999 99999999999998888776666543
No 64
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=25.71 E-value=53 Score=23.83 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHHhCCcee
Q 034019 31 EDRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sET 50 (106)
..++++.|+.||+.+|+|.+
T Consensus 37 G~Ip~e~~~~iA~~l~v~~~ 56 (156)
T PRK05988 37 GYVPEDAVPVIAEALNLSRA 56 (156)
T ss_pred CCCCHHHHHHHHHHhCCCHH
Confidence 46799999999999999864
No 65
>PLN02477 glutamate dehydrogenase
Probab=25.18 E-value=87 Score=26.30 Aligned_cols=33 Identities=15% Similarity=0.214 Sum_probs=28.1
Q ss_pred cCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhCC
Q 034019 15 TDSAFKGNPAAVCLLEEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 15 t~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n~ 47 (106)
++=|++|--.+|+.++..+|+.++.++.|.+..
T Consensus 94 ~~lP~GGgKggI~~dP~~~s~~e~e~l~r~f~~ 126 (410)
T PLN02477 94 ANIPYGGAKGGIGCDPRDLSESELERLTRVFTQ 126 (410)
T ss_pred cCCCCcCceeeeccCCccCCHHHHHHHHHHHHH
Confidence 446899999999999999999999888888764
No 66
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=24.85 E-value=1.2e+02 Score=19.50 Aligned_cols=14 Identities=36% Similarity=0.449 Sum_probs=11.9
Q ss_pred CCCHHHHHHHHHHh
Q 034019 32 DRDEEWLQAVASEF 45 (106)
Q Consensus 32 ~l~~~~mq~IA~e~ 45 (106)
.++.+|+++||+++
T Consensus 12 ~~s~EqK~~La~~i 25 (76)
T PRK01271 12 ELDEEQKAALAADI 25 (76)
T ss_pred CCCHHHHHHHHHHH
Confidence 47999999999885
No 67
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=24.84 E-value=1.2e+02 Score=20.40 Aligned_cols=29 Identities=10% Similarity=0.165 Sum_probs=25.1
Q ss_pred CCeeEEEEcCCCCCHHHHHHHHHHhCCce
Q 034019 21 GNPAAVCLLEEDRDEEWLQAVASEFNISQ 49 (106)
Q Consensus 21 GNPaaVv~~~~~l~~~~mq~IA~e~n~sE 49 (106)
|....|-.....-+++-.|++++++++|+
T Consensus 11 g~~i~V~v~~s~~a~~Vleav~~kl~L~~ 39 (87)
T cd01777 11 KATVTVRVRKNATTDQVYQALVAKAGMDS 39 (87)
T ss_pred CCEEEEEEEEcccHHHHHHHHHHHhCCCH
Confidence 88888887777778999999999999984
No 68
>PF01244 Peptidase_M19: Membrane dipeptidase (Peptidase family M19); InterPro: IPR008257 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ. Renal dipeptidase (rDP) (3.4.13.19 from EC), also known as microsomal dipeptidase, is a zinc-dependent metalloenzyme that hydrolyzes a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown [,] to be important for the catalytic activity of rDP. rDP seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae.; GO: 0008235 metalloexopeptidase activity, 0008239 dipeptidyl-peptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis; PDB: 3NEH_B 2RAG_D 3LU2_A 3B40_A 3LY0_A 3FDG_B 2I5G_B 3S2J_A 3S2N_A 3S2L_A ....
Probab=24.50 E-value=20 Score=28.71 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=21.4
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhCC
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFNI 47 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n~ 47 (106)
.-.|..+++..+.+|+|+++++||+.=|+
T Consensus 200 SHSn~ral~~h~RNltDe~iraia~~GGv 228 (320)
T PF01244_consen 200 SHSNARALCPHPRNLTDEQIRAIAERGGV 228 (320)
T ss_dssp CCEEBTTTS--TTSB-HHHHHHHHHTT-E
T ss_pred eccChHhhCCCCCCCCHHHHHHHHHCCcE
Confidence 45678888888999999999999998665
No 69
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=24.37 E-value=41 Score=22.46 Aligned_cols=20 Identities=5% Similarity=0.140 Sum_probs=15.9
Q ss_pred CCCCHHHHHHHHHHhCCcee
Q 034019 31 EDRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sET 50 (106)
+.++..+...+||++|+||+
T Consensus 15 ~~V~~~~Wk~laR~LGLse~ 34 (96)
T cd08315 15 KEVPFDSWNRLMRQLGLSEN 34 (96)
T ss_pred HHCCHHHHHHHHHHcCCCHH
Confidence 45676777789999999885
No 70
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.11 E-value=41 Score=19.01 Aligned_cols=14 Identities=29% Similarity=0.373 Sum_probs=11.5
Q ss_pred HHHHHHHHhCCcee
Q 034019 37 WLQAVASEFNISQT 50 (106)
Q Consensus 37 ~mq~IA~e~n~sET 50 (106)
-++.||+++|+|.+
T Consensus 29 s~~~vA~~~~vs~~ 42 (52)
T PF13542_consen 29 SFKDVARELGVSWS 42 (52)
T ss_pred CHHHHHHHHCCCHH
Confidence 57889999998864
No 71
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=23.96 E-value=2.6e+02 Score=22.94 Aligned_cols=73 Identities=16% Similarity=-0.036 Sum_probs=47.9
Q ss_pred eeEEEEc-CCCCCHHHHHHHHHHhCCceeEEEecCCCCCCCCCceEEEEe-cCCCccCCCCchHHHHH-HHcCCeEEEee
Q 034019 23 PAAVCLL-EEDRDEEWLQAVASEFNISQTCYLTRLTAADSPNPRFRLRWF-TPVAEVSFSFYNYKLWM-KLFGSVLELDD 99 (106)
Q Consensus 23 PaaVv~~-~~~l~~~~mq~IA~e~n~sETaFv~~~~~~~~~~~~~~vR~F-Tp~~Ei~~cGHatvaw~-~~~~~~~~~~~ 99 (106)
+-|||.. +...+.-.|+.-.+-+.-|+..||.-.. .-..+ +|..++|-+|-=..|-. ...-.++.+.+
T Consensus 154 VgAVvvg~D~hfsy~KL~kA~~yLqnP~clflatn~---------D~~~p~~~~~~ipG~G~~v~av~~~t~R~P~v~GK 224 (306)
T KOG2882|consen 154 VGAVVVGYDEHFSYPKLMKALNYLQNPGCLFLATNR---------DATTPPTPGVEIPGAGSFVAAVKFATGRQPIVLGK 224 (306)
T ss_pred CCEEEEecccccCHHHHHHHHHHhCCCCcEEEeccC---------ccccCCCCCeeccCCccHHHHHHHHhcCCCeecCC
Confidence 4566654 5678999999999999999999997431 11223 55778887765322222 11246788888
Q ss_pred eceee
Q 034019 100 LSFFM 104 (106)
Q Consensus 100 ~~~~~ 104 (106)
+|=+|
T Consensus 225 P~~~m 229 (306)
T KOG2882|consen 225 PSTFM 229 (306)
T ss_pred CCHHH
Confidence 77665
No 72
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=23.92 E-value=59 Score=24.06 Aligned_cols=19 Identities=16% Similarity=0.198 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHHHhCCce
Q 034019 31 EDRDEEWLQAVASEFNISQ 49 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sE 49 (106)
..++++.++.||+.+|+|.
T Consensus 50 GyIp~e~~~~iA~~l~v~~ 68 (169)
T PRK07571 50 GYLERDLLLYVARQLKLPL 68 (169)
T ss_pred CCCCHHHHHHHHHHhCcCH
Confidence 4579999999999999986
No 73
>cd01301 rDP_like renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism.
Probab=23.89 E-value=52 Score=26.32 Aligned_cols=35 Identities=17% Similarity=0.227 Sum_probs=28.6
Q ss_pred CCCCeeEEEEcCCCCCHHHHHHHHHHhCCceeEEE
Q 034019 19 FKGNPAAVCLLEEDRDEEWLQAVASEFNISQTCYL 53 (106)
Q Consensus 19 f~GNPaaVv~~~~~l~~~~mq~IA~e~n~sETaFv 53 (106)
...|+.+++..+.+++++++++||+.=|+=.-.|.
T Consensus 194 SHsn~ral~~h~RNltD~~i~~ia~~GGvigi~~~ 228 (309)
T cd01301 194 SHSNARALCDHPRNLTDAQLKAIAETGGVIGVNFY 228 (309)
T ss_pred eccChHHhcCCCCCCCHHHHHHHHHcCCEEEEeee
Confidence 45678888888899999999999998777665554
No 74
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=23.83 E-value=60 Score=23.21 Aligned_cols=20 Identities=20% Similarity=0.152 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHHHhCCcee
Q 034019 31 EDRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sET 50 (106)
..++++.|+.||+.+|+|.+
T Consensus 36 g~ip~~~~~~iA~~l~v~~~ 55 (154)
T PRK07539 36 GWVPDEAIEAVADYLGMPAI 55 (154)
T ss_pred CCCCHHHHHHHHHHhCcCHH
Confidence 35799999999999999863
No 75
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.34 E-value=49 Score=21.12 Aligned_cols=21 Identities=10% Similarity=0.055 Sum_probs=16.6
Q ss_pred CCCCHHHHHHHHHHhCCceeE
Q 034019 31 EDRDEEWLQAVASEFNISQTC 51 (106)
Q Consensus 31 ~~l~~~~mq~IA~e~n~sETa 51 (106)
+.++..+...+||.+|+||+.
T Consensus 7 ~~v~~~~Wk~laR~LGls~~~ 27 (79)
T cd08784 7 EEVPFDQHKRFFRKLGLSDNE 27 (79)
T ss_pred HHCCHHHHHHHHHHcCCCHHH
Confidence 446777888899999998753
No 76
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=22.40 E-value=57 Score=23.03 Aligned_cols=19 Identities=26% Similarity=0.288 Sum_probs=14.3
Q ss_pred CCCHHHHHHHHHHhCCcee
Q 034019 32 DRDEEWLQAVASEFNISQT 50 (106)
Q Consensus 32 ~l~~~~mq~IA~e~n~sET 50 (106)
.++++.++.||+.+|++.+
T Consensus 28 ~i~~~~~~~iA~~l~i~~~ 46 (145)
T PF01257_consen 28 YIPEEALEEIAEALGIPPA 46 (145)
T ss_dssp S--HHHHHHHHHHHTS-HH
T ss_pred CCCHHHHHHHHHHHCCCHH
Confidence 5799999999999999864
No 77
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=22.05 E-value=67 Score=18.68 Aligned_cols=14 Identities=21% Similarity=0.449 Sum_probs=11.0
Q ss_pred HHHHHHHhCCceeE
Q 034019 38 LQAVASEFNISQTC 51 (106)
Q Consensus 38 mq~IA~e~n~sETa 51 (106)
|+.||++.|+|-++
T Consensus 2 i~dIA~~agvS~~T 15 (46)
T PF00356_consen 2 IKDIAREAGVSKST 15 (46)
T ss_dssp HHHHHHHHTSSHHH
T ss_pred HHHHHHHHCcCHHH
Confidence 67899999988654
No 78
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.69 E-value=66 Score=18.14 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=10.6
Q ss_pred HHHHHHHHhCCceeE
Q 034019 37 WLQAVASEFNISQTC 51 (106)
Q Consensus 37 ~mq~IA~e~n~sETa 51 (106)
-...||+++|+|-++
T Consensus 23 si~~IA~~~gvsr~T 37 (45)
T PF02796_consen 23 SIAEIAKQFGVSRST 37 (45)
T ss_dssp -HHHHHHHTTS-HHH
T ss_pred CHHHHHHHHCcCHHH
Confidence 467899999998654
No 79
>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=21.28 E-value=92 Score=16.88 Aligned_cols=16 Identities=44% Similarity=0.792 Sum_probs=7.5
Q ss_pred CCHHHHHHH--HHHhCCc
Q 034019 33 RDEEWLQAV--ASEFNIS 48 (106)
Q Consensus 33 l~~~~mq~I--A~e~n~s 48 (106)
|++++++.| |+++|+|
T Consensus 1 LD~EW~~Li~eA~~~Gls 18 (30)
T PF08671_consen 1 LDEEWVELIKEAKESGLS 18 (30)
T ss_dssp --HHHHHHHHHHHHTT--
T ss_pred CCHHHHHHHHHHHHcCCC
Confidence 355665554 6777765
No 80
>PRK14031 glutamate dehydrogenase; Provisional
Probab=20.95 E-value=1.2e+02 Score=25.79 Aligned_cols=32 Identities=9% Similarity=0.105 Sum_probs=27.8
Q ss_pred cCCCCCCCeeEEEEcCCCCCHHHHHHHHHHhC
Q 034019 15 TDSAFKGNPAAVCLLEEDRDEEWLQAVASEFN 46 (106)
Q Consensus 15 t~~~f~GNPaaVv~~~~~l~~~~mq~IA~e~n 46 (106)
++=|++|--.+|..++..+++.++.++.+.+-
T Consensus 116 ~~lP~GGgKggi~~dP~~~s~~Eler~~r~f~ 147 (444)
T PRK14031 116 TTLPMGGGKGGSDFSPRGKSNAEVMRFCQAFM 147 (444)
T ss_pred cCCCCCCceeeeeCCCCCCCHHHHHHHHHHHH
Confidence 45699999999999999999999998888764
No 81
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.79 E-value=93 Score=19.17 Aligned_cols=19 Identities=32% Similarity=0.310 Sum_probs=16.8
Q ss_pred CCHHHHHHHHHHhCCceeE
Q 034019 33 RDEEWLQAVASEFNISQTC 51 (106)
Q Consensus 33 l~~~~mq~IA~e~n~sETa 51 (106)
||++.+++|.+-++.|.++
T Consensus 3 lS~esKerl~k~~~is~~v 21 (53)
T KOG4449|consen 3 LSEESKERLVKVFNISKFV 21 (53)
T ss_pred cCHHHHHHHHHHeechhee
Confidence 7899999999999988765
No 82
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=20.27 E-value=1.2e+02 Score=19.61 Aligned_cols=31 Identities=23% Similarity=0.131 Sum_probs=18.7
Q ss_pred eeEEEEcCCCCCHHHHHHHHHHhCCceeEEEec
Q 034019 23 PAAVCLLEEDRDEEWLQAVASEFNISQTCYLTR 55 (106)
Q Consensus 23 PaaVv~~~~~l~~~~mq~IA~e~n~sETaFv~~ 55 (106)
.+++++......+++...+|++.+. +++..+
T Consensus 62 i~~iIltg~~~~~~~v~~la~~~~i--~vi~t~ 92 (105)
T PF07085_consen 62 IACIILTGGLEPSEEVLELAKELGI--PVISTP 92 (105)
T ss_dssp ECEEEEETT----HHHHHHHHHHT---EEEE-S
T ss_pred CCEEEEeCCCCCCHHHHHHHHHCCC--EEEEEC
Confidence 5677776666678899999999994 344443
Done!