Query psy2327
Match_columns 97
No_of_seqs 141 out of 1049
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 21:46:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2327hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0325 Predicted enzyme with 100.0 1.7E-35 3.8E-40 222.5 7.1 87 1-92 3-89 (228)
2 cd06822 PLPDE_III_YBL036c_euk 100.0 5.6E-33 1.2E-37 208.2 8.1 82 2-92 2-83 (227)
3 KOG3157|consensus 100.0 1.1E-31 2.4E-36 200.8 7.6 81 4-91 10-90 (244)
4 TIGR00044 pyridoxal phosphate 99.9 4.4E-22 9.6E-27 147.9 8.3 86 1-91 4-89 (229)
5 cd06824 PLPDE_III_Yggs_like Py 99.7 4.8E-17 1E-21 120.1 8.4 84 1-89 2-85 (224)
6 cd00635 PLPDE_III_YBL036c_like 99.0 4.7E-09 1E-13 77.1 9.1 84 1-90 1-84 (222)
7 cd06815 PLPDE_III_AR_like_1 Ty 98.1 5.4E-06 1.2E-10 64.9 6.1 76 4-89 7-84 (353)
8 cd00430 PLPDE_III_AR Type III 97.6 0.00021 4.5E-09 55.7 6.7 74 5-89 8-86 (367)
9 PF01168 Ala_racemase_N: Alani 97.3 0.00039 8.4E-09 50.1 4.8 72 5-89 3-78 (218)
10 TIGR00492 alr alanine racemase 96.8 0.0082 1.8E-07 47.0 7.8 71 5-86 9-84 (367)
11 PRK00053 alr alanine racemase; 96.5 0.0082 1.8E-07 47.0 6.4 58 5-67 10-72 (363)
12 cd07376 PLPDE_III_DSD_D-TA_lik 95.6 0.016 3.6E-07 44.7 3.9 41 27-67 17-58 (345)
13 cd06811 PLPDE_III_yhfX_like Ty 95.3 0.054 1.2E-06 43.2 6.0 70 5-86 35-106 (382)
14 cd06821 PLPDE_III_D-TA Type II 93.5 0.11 2.3E-06 40.5 4.0 75 5-87 16-91 (361)
15 cd06808 PLPDE_III Type III Pyr 93.5 0.17 3.8E-06 35.6 4.7 55 27-87 15-70 (211)
16 cd06825 PLPDE_III_VanT Type II 91.3 0.75 1.6E-05 36.5 6.2 55 4-63 7-66 (368)
17 cd06820 PLPDE_III_LS_D-TA_like 90.6 0.29 6.2E-06 38.0 3.3 40 27-66 28-68 (353)
18 cd06826 PLPDE_III_AR2 Type III 88.1 1.7 3.8E-05 34.2 6.0 55 5-64 8-67 (365)
19 TIGR03619 F420_Rv2161c probabl 86.0 2 4.4E-05 32.1 5.1 48 4-53 189-242 (246)
20 COG3457 Predicted amino acid r 83.8 4.1 8.9E-05 33.0 6.1 39 27-65 28-68 (353)
21 cd06819 PLPDE_III_LS_D-TA Type 80.5 1.7 3.8E-05 33.6 2.9 37 27-63 32-69 (358)
22 PRK03646 dadX alanine racemase 78.6 7.2 0.00016 30.9 5.9 52 5-63 10-65 (355)
23 PRK11930 putative bifunctional 76.0 10 0.00022 33.0 6.5 55 4-63 465-524 (822)
24 PRK13340 alanine racemase; Rev 69.4 19 0.0004 28.9 6.2 56 5-65 47-107 (406)
25 PF00072 Response_reg: Respons 66.1 9.9 0.00021 23.3 3.3 27 27-53 71-97 (112)
26 TIGR03856 F420_MSMEG_2906 prob 65.3 22 0.00048 26.8 5.6 45 4-52 182-226 (249)
27 cd06827 PLPDE_III_AR_proteobac 64.9 23 0.0005 27.9 5.8 53 5-64 8-64 (354)
28 cd06817 PLPDE_III_DSD Type III 62.3 14 0.0003 29.8 4.2 39 27-65 31-72 (389)
29 cd06812 PLPDE_III_DSD_D-TA_lik 53.3 30 0.00065 26.9 4.6 37 27-63 31-68 (374)
30 cd06818 PLPDE_III_cryptic_DSD 47.4 49 0.0011 26.1 5.1 37 27-63 28-65 (382)
31 cd06814 PLPDE_III_DSD_D-TA_lik 45.6 68 0.0015 25.6 5.6 54 5-63 16-71 (379)
32 COG0787 Alr Alanine racemase [ 43.0 81 0.0018 25.6 5.7 55 4-64 10-69 (360)
33 PF12826 HHH_2: Helix-hairpin- 40.0 19 0.00042 21.6 1.4 24 45-68 3-26 (64)
34 TIGR03044 PS_II_psb27 photosys 39.0 75 0.0016 22.6 4.4 53 4-65 64-121 (135)
35 COG0484 DnaJ DnaJ-class molecu 36.3 22 0.00048 29.0 1.6 38 29-66 8-48 (371)
36 PLN00064 photosystem II protei 34.4 96 0.0021 22.8 4.4 55 3-65 92-151 (166)
37 cd06810 PLPDE_III_ODC_DapDC_li 30.4 1.8E+02 0.004 22.3 5.8 53 5-63 8-61 (368)
38 COG1031 Uncharacterized Fe-S o 29.6 34 0.00074 29.3 1.7 23 32-54 210-236 (560)
39 PF01645 Glu_synthase: Conserv 29.6 1.9E+02 0.0041 23.5 5.9 44 9-55 259-302 (368)
40 PF07386 DUF1499: Protein of u 29.4 11 0.00024 25.2 -1.1 23 42-64 92-116 (118)
41 cd06843 PLPDE_III_PvsE_like Ty 27.1 2.2E+02 0.0048 22.2 5.8 54 5-63 9-62 (377)
42 PF06755 DUF1219: Protein of u 27.1 59 0.0013 22.5 2.2 42 34-79 41-82 (114)
43 PF08799 PRP4: pre-mRNA proces 26.2 28 0.0006 18.6 0.4 15 46-60 6-22 (30)
44 KOG0713|consensus 26.1 34 0.00075 27.7 1.1 20 28-47 19-38 (336)
45 cd06813 PLPDE_III_DSD_D-TA_lik 25.8 2.3E+02 0.0051 22.4 5.8 53 5-63 18-72 (388)
46 PF12327 FtsZ_C: FtsZ family, 25.6 34 0.00073 22.1 0.8 19 53-71 11-29 (95)
47 KOG0871|consensus 25.3 69 0.0015 23.3 2.4 29 34-66 64-93 (156)
48 PLN00035 histone H4; Provision 25.3 2.2E+02 0.0048 19.2 4.9 20 35-54 80-100 (103)
49 PTZ00015 histone H4; Provision 24.6 2.3E+02 0.0049 19.1 4.9 21 34-54 80-101 (102)
50 cd06828 PLPDE_III_DapDC Type I 23.6 3E+02 0.0065 21.1 5.8 54 5-63 10-64 (373)
51 COG4565 CitB Response regulato 23.1 95 0.0021 23.8 2.9 41 27-67 74-119 (224)
52 smart00500 SFM Splicing Factor 22.1 88 0.0019 17.9 2.0 20 40-59 5-26 (44)
53 COG0074 SucD Succinyl-CoA synt 22.0 1.6E+02 0.0035 23.4 4.1 45 8-57 53-100 (293)
54 cd00076 H4 Histone H4, one of 22.0 2.3E+02 0.005 18.3 5.0 21 34-54 63-84 (85)
55 PLN02923 xylose isomerase 21.6 1.4E+02 0.003 25.4 3.8 49 3-58 159-228 (478)
56 PF12684 DUF3799: PDDEXK-like 21.3 45 0.00098 25.2 0.8 33 27-66 177-209 (237)
57 COG2115 XylA Xylose isomerase 21.1 1.8E+02 0.0039 24.1 4.3 20 39-58 168-187 (438)
58 cd06555 ASCH_PF0470_like ASC-1 20.9 1.3E+02 0.0029 20.3 3.0 40 27-66 50-89 (109)
59 PRK12465 xylose isomerase; Pro 20.7 1.5E+02 0.0032 25.0 3.8 49 3-58 125-194 (445)
60 PF05384 DegS: Sensor protein 20.7 21 0.00046 25.7 -1.0 21 28-48 62-85 (159)
61 PF14658 EF-hand_9: EF-hand do 20.6 88 0.0019 19.5 1.9 32 34-65 12-44 (66)
62 PRK10840 transcriptional regul 20.5 1.4E+02 0.003 20.8 3.2 27 27-53 80-106 (216)
63 TIGR01387 cztR_silR_copR heavy 20.4 1.6E+02 0.0035 19.7 3.4 27 27-53 70-96 (218)
64 PF13653 GDPD_2: Glycerophosph 20.4 1E+02 0.0022 16.2 1.9 20 39-58 10-29 (30)
65 smart00271 DnaJ DnaJ molecular 20.2 69 0.0015 17.9 1.3 20 29-48 5-24 (60)
No 1
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only]
Probab=100.00 E-value=1.7e-35 Score=222.46 Aligned_cols=87 Identities=34% Similarity=0.403 Sum_probs=80.9
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEE
Q psy2327 1 MEAAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKT 80 (97)
Q Consensus 1 i~~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh 80 (97)
|.+||+.|+++|.++|.++||++. +|+|||||||+|++.|+++|++|+++||||||||+.+|++.++. .+||+||
T Consensus 3 i~~nl~~v~~~I~~a~~~a~R~~~--~V~LvAVSK~~~~~~I~~~~~aG~r~fGENrvQe~~~K~~~l~~---~~~i~WH 77 (228)
T COG0325 3 IKENLAAVRERIAAAAERAGRNPG--SVTLVAVSKTVPAEDIREAYEAGQRHFGENRVQEALDKIEALKD---LPDIEWH 77 (228)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCC--cEEEEEEeCCCCHHHHHHHHHcCChhhcchHHHHHHHHHHhcCc---CCCeEEE
Confidence 578999999999999999999875 89999999999999999999999999999999999999999744 4589999
Q ss_pred EeeecccCCCCC
Q psy2327 81 AVKEVVDERAPS 92 (97)
Q Consensus 81 ~IG~lq~~~~~~ 92 (97)
|||+|||||++.
T Consensus 78 fIG~LQsNK~k~ 89 (228)
T COG0325 78 FIGPLQSNKVKL 89 (228)
T ss_pred EechhhhhHHHH
Confidence 999999999864
No 2
>cd06822 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins. This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog)
Probab=99.98 E-value=5.6e-33 Score=208.16 Aligned_cols=82 Identities=48% Similarity=0.650 Sum_probs=74.5
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEEE
Q psy2327 2 EAAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTA 81 (97)
Q Consensus 2 ~~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh~ 81 (97)
.+||+.|+++|..+|.+ |++ ++|+|||||||+|+++|+++|++|+++||||||||+.+|++.++. +|+|||
T Consensus 2 ~~~l~~i~~~i~~a~~~--r~~--~~v~LvaVsK~~~~~~i~~~~~~G~~~fGENrvQe~~~K~~~l~~-----~i~wHf 72 (227)
T cd06822 2 IANLKRIRQAVKRASKK--LPA--SKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHF 72 (227)
T ss_pred hHHHHHHHHHHHHHHHh--CCC--CCcEEEEEECCCCHHHHHHHHHcCCccccCcHHHHHHHHHHhccC-----CceEEE
Confidence 68999999999999988 554 379999999999999999999999999999999999999987522 699999
Q ss_pred eeecccCCCCC
Q psy2327 82 VKEVVDERAPS 92 (97)
Q Consensus 82 IG~lq~~~~~~ 92 (97)
|||||+||++.
T Consensus 73 IG~LQ~NK~k~ 83 (227)
T cd06822 73 IGHLQSNKVKK 83 (227)
T ss_pred ECCCchhhHHH
Confidence 99999999875
No 3
>KOG3157|consensus
Probab=99.97 E-value=1.1e-31 Score=200.81 Aligned_cols=81 Identities=47% Similarity=0.694 Sum_probs=75.0
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEEEee
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTAVK 83 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh~IG 83 (97)
.|..|.+||++++.+++|+.+ .++|||||||.|++.|.++|++|+|+||||||||+.+|++.++ +||+|||||
T Consensus 10 ~L~~v~~rv~qa~~~~~r~~~--~~rlvaVSKtKPa~~i~~~Y~~GqR~FGENYVQEl~eKap~lp-----~DI~WHFIG 82 (244)
T KOG3157|consen 10 ALRAVIERVQQAVNQRPRDEN--AVRLVAVSKTKPASLIIEAYDAGQRHFGENYVQELIEKAPLLP-----DDIKWHFIG 82 (244)
T ss_pred HHHHHHHHHHHHHHhcccccc--ceEEEEeecCCcHHHHHHHHHcCcChhhHHHHHHHHHhcccCc-----ccceeeeec
Confidence 578999999999999988865 7999999999999999999999999999999999999997653 599999999
Q ss_pred ecccCCCC
Q psy2327 84 EVVDERAP 91 (97)
Q Consensus 84 ~lq~~~~~ 91 (97)
|||+||..
T Consensus 83 ~lQsnK~k 90 (244)
T KOG3157|consen 83 HLQSNKCK 90 (244)
T ss_pred hhhhcccc
Confidence 99999964
No 4
>TIGR00044 pyridoxal phosphate enzyme, YggS family. Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae.
Probab=99.87 E-value=4.4e-22 Score=147.90 Aligned_cols=86 Identities=35% Similarity=0.424 Sum_probs=77.5
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEE
Q psy2327 1 MEAAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKT 80 (97)
Q Consensus 1 i~~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh 80 (97)
|.+||+.|+++|..+|++++|+++ +++|+||||+.+++.|..++++|+++|||||+||+.+|+..+. +..++.||
T Consensus 4 ~~~~~~~i~~~i~~~~~~~~~~~~--~~~l~aV~K~~~~~~i~~l~~~G~~~fg~~~~~Ea~~k~~~lr---~~~~~~~~ 78 (229)
T TIGR00044 4 IIHYLEDIKTKIEAANTHVNRNPS--KVKLLAVSKTKPASAIQIAYDAGQRAFGENYVQELVEKIKLLE---DLGKLEWH 78 (229)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCcC--CeEEEEEECCCCHHHHHHHHHcCCccccEEcHHHHHHHHHHhc---ccCCceEE
Confidence 468999999999999999999764 7999999999999999999999999999999999999997752 22379999
Q ss_pred EeeecccCCCC
Q psy2327 81 AVKEVVDERAP 91 (97)
Q Consensus 81 ~IG~lq~~~~~ 91 (97)
|||++|+|+..
T Consensus 79 ~ig~~q~~~~~ 89 (229)
T TIGR00044 79 FIGPLQSNKDR 89 (229)
T ss_pred EECCCcchHHH
Confidence 99999999864
No 5
>cd06824 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins. This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn.
Probab=99.70 E-value=4.8e-17 Score=120.13 Aligned_cols=84 Identities=36% Similarity=0.512 Sum_probs=74.6
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEE
Q psy2327 1 MEAAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKT 80 (97)
Q Consensus 1 i~~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh 80 (97)
+.+|+..|.++|..+|.++||++. +++|+||+|+++.+.|..++++|++.||+|++||+.+|+..+. +.+.+.||
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~i~aVvKahG~~~v~~~~~~G~~~fgva~~~Ea~~k~~~Lr---~~g~~~~~ 76 (224)
T cd06824 2 IAENLAQVKQRIAQAAKQAGRDPS--SVQLLAVSKTKPADAIREAYAAGQRHFGENYVQEALEKIEALR---DLQDIEWH 76 (224)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCcC--CeEEEEEECCCCHHHHHHHHHcCCcccCcChHHHHHHHHHHhc---cCCCeeEE
Confidence 467999999999999999998764 6899999999999999999999999999999999999997652 22259999
Q ss_pred EeeecccCC
Q psy2327 81 AVKEVVDER 89 (97)
Q Consensus 81 ~IG~lq~~~ 89 (97)
|||.+|.|+
T Consensus 77 ~lg~~~~~~ 85 (224)
T cd06824 77 FIGPIQSNK 85 (224)
T ss_pred EEcCchhhh
Confidence 999999875
No 6
>cd00635 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins. This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity.
Probab=98.97 E-value=4.7e-09 Score=77.10 Aligned_cols=84 Identities=32% Similarity=0.398 Sum_probs=70.7
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEE
Q psy2327 1 MEAAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKT 80 (97)
Q Consensus 1 i~~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh 80 (97)
|.+|++.++..|+...+.++|++. .++|+||+|++.+..|..++++|++.||.++++|+....+.+ . .+.+.|+
T Consensus 1 ~~~~~~~l~~Ni~~~~~~~~~~~~--~~~l~avvK~hg~~~va~~~~~G~~~f~va~l~Ea~~lr~~~---~-~~~~~~~ 74 (222)
T cd00635 1 IAENLEEVRERIAAAAERAGRDPD--EVTLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKAEEL---P-DPDIEWH 74 (222)
T ss_pred ChHHHHHHHHHHHHHHHHcCCCcC--CeEEEEEECCCCHHHHHHHHHcCCcccCCCcHHHHHHHHHHc---c-CCCceEE
Confidence 578999999999999888764432 689999999999999999999999999999999999876542 1 1468999
Q ss_pred EeeecccCCC
Q psy2327 81 AVKEVVDERA 90 (97)
Q Consensus 81 ~IG~lq~~~~ 90 (97)
|||.++.++.
T Consensus 75 llg~~~~~~~ 84 (222)
T cd00635 75 FIGHLQTNKV 84 (222)
T ss_pred EECccccccH
Confidence 9999887653
No 7
>cd06815 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=98.14 E-value=5.4e-06 Score=64.91 Aligned_cols=76 Identities=13% Similarity=0.100 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCC-C-HHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEEE
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKTK-P-KELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTA 81 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~-~-~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh~ 81 (97)
+++.++..++...+.++.. +++|+||+|+. . ++.++.++++|++.||.++++|+.. +.+ ..-...|++
T Consensus 7 dl~al~~Ni~~i~~~~~~~----~~~l~~vvKa~hg~~~va~~l~~~G~~~f~va~i~EA~~-lr~-----~G~~~~ill 76 (353)
T cd06815 7 NLSKIRHNAKVLVELCKSR----GIEVTGVTKVVCGDPEIAEALLEGGITHLADSRIENLKK-LKD-----LGISGPKML 76 (353)
T ss_pred eHHHHHHHHHHHHHHHhhc----CCEEEEEEcccCCCHHHHHHHHHcCCCEEEeccHHHHHH-HHh-----cCCCCCEEE
Confidence 3555666666555544311 57999999997 3 6777778899999999999999974 332 112348999
Q ss_pred eeecccCC
Q psy2327 82 VKEVVDER 89 (97)
Q Consensus 82 IG~lq~~~ 89 (97)
+|.++.++
T Consensus 77 lg~~~~~~ 84 (353)
T cd06815 77 LRIPMLSE 84 (353)
T ss_pred ECCCCHHH
Confidence 99988654
No 8
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with activ
Probab=97.61 E-value=0.00021 Score=55.70 Aligned_cols=74 Identities=12% Similarity=0.052 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCC----CHHHH-HHHHHcCCccccccchHHHHhhcCCcccccccCCceE
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTK----PKELI-IEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGK 79 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~----~~e~I-~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~w 79 (97)
++.++++++...+..+. .++|.+|+|+. +...| +.+.++|+..||.++++|+....... .+..|
T Consensus 8 ~~~i~~N~~~l~~~~~~-----~~~l~~vvKan~yGhg~~~i~~~l~~~G~~~~~vas~~Ea~~~~~~g------~~~~i 76 (367)
T cd00430 8 LDALRHNLRVIRRLLGP-----GTKIMAVVKADAYGHGAVEVAKALEEAGADYFAVATLEEALELREAG------ITAPI 76 (367)
T ss_pred HHHHHHHHHHHHHhCCC-----CCEEEEEEeeccccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcC------CCCCE
Confidence 34455555544443321 47999999994 45665 56778999999999999999887542 24679
Q ss_pred EEeeecccCC
Q psy2327 80 TAVKEVVDER 89 (97)
Q Consensus 80 h~IG~lq~~~ 89 (97)
+++|+++.++
T Consensus 77 ~~~~~~~~~~ 86 (367)
T cd00430 77 LVLGGTPPEE 86 (367)
T ss_pred EEEeCCCHHH
Confidence 9999987544
No 9
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel. This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alanine racemase activity.; PDB: 3KW3_A 1B54_A 1CT5_A 2ODO_B 2RJG_A 3B8V_D 2RJH_D 3B8T_D 3B8W_B 3B8U_A ....
Probab=97.34 E-value=0.00039 Score=50.08 Aligned_cols=72 Identities=15% Similarity=0.075 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC--CCHHHHHHHH-Hc-CCccccccchHHHHhhcCCcccccccCCceEE
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKT--KPKELIIEAY-NG-GQRHFGENYVQELLEKGHDPEISIQLKSRGKT 80 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~--~~~e~I~~a~-~~-G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh 80 (97)
++.++.+|+...+.. +. ..+|++|+|+ .+.+.+..+. .. |++.||+++++|+..=. ..+ ..+.
T Consensus 3 l~al~~Ni~~~~~~~-~~----~~~l~~vvK~~ayg~~~~~~~~~~~~g~~~~~va~~~Ea~~lr------~~g--~~il 69 (218)
T PF01168_consen 3 LDALRHNIRKIRQRA-GP----GTKLRAVVKANAYGHGIVRVAKALAEGIDGFAVATLEEAEELR------EAG--APIL 69 (218)
T ss_dssp HHHHHHHHHHHHHHH-CT----TSEEEEE-HHHHHTTHHHHHHHHHHHTCSEEEESSHHHHHHHH------HTT--SEEE
T ss_pred HHHHHHHHHHHHHHc-CC----CCEEEEEEcCCCcCccHHHHHHHHhcCCCEEEEeeHHHhhhHH------hcC--CceE
Confidence 566677776666665 32 3589999999 7777766666 55 89999999999999422 222 5677
Q ss_pred EeeecccCC
Q psy2327 81 AVKEVVDER 89 (97)
Q Consensus 81 ~IG~lq~~~ 89 (97)
+++.++.++
T Consensus 70 ~l~~~~~~~ 78 (218)
T PF01168_consen 70 VLGPIPPEE 78 (218)
T ss_dssp EESESTGGG
T ss_pred EEcCCChhh
Confidence 777755543
No 10
>TIGR00492 alr alanine racemase. This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or L-alanine and is involved in catabolism.
Probab=96.77 E-value=0.0082 Score=47.02 Aligned_cols=71 Identities=10% Similarity=0.084 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCC----HH-HHHHHHHcCCccccccchHHHHhhcCCcccccccCCceE
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKP----KE-LIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGK 79 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~----~e-~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~w 79 (97)
+..++++++...+..+. .++|++|+|.-+ .. .++.+.++|++.|+.++++|+..-.+. ..+..|
T Consensus 9 l~~l~~N~~~i~~~~~~-----~~~i~~vvKAnaYGhg~~~i~~~l~~~G~~~~~vas~~Ea~~lr~~------G~~~~i 77 (367)
T TIGR00492 9 LAALKHNLSAIRNHIGP-----KSKIMAVVKANAYGHGLIEVAKTLLQAGADYFGVANLEEAITLRKA------GITAPI 77 (367)
T ss_pred HHHHHHHHHHHHHhcCC-----CCEEEEEEEcCCccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhc------CCCCCE
Confidence 45555555554444321 468999999954 44 456668899999999999998875432 235678
Q ss_pred EEeeecc
Q psy2327 80 TAVKEVV 86 (97)
Q Consensus 80 h~IG~lq 86 (97)
+++|.++
T Consensus 78 lvl~~~~ 84 (367)
T TIGR00492 78 LLLGGFF 84 (367)
T ss_pred EEEeCCC
Confidence 9998875
No 11
>PRK00053 alr alanine racemase; Reviewed
Probab=96.55 E-value=0.0082 Score=47.02 Aligned_cols=58 Identities=21% Similarity=0.315 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC----CCHHHHHHHH-HcCCccccccchHHHHhhcCC
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKT----KPKELIIEAY-NGGQRHFGENYVQELLEKGHD 67 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~----~~~e~I~~a~-~~G~~~fGENrvQEl~~K~~~ 67 (97)
+..++++++...+..+. .++|++|+|. +....|..++ ++|++.||.++++|+......
T Consensus 10 l~~l~~N~~~i~~~~~~-----~~~i~~vvKanaYghg~~~i~~~l~~~G~~~~~vas~~Ea~~l~~~ 72 (363)
T PRK00053 10 LDALRHNLRQIRKHAPP-----KSKLMAVVKANAYGHGAVEVAKTLLEAGADGFGVATLEEALELREA 72 (363)
T ss_pred HHHHHHHHHHHHHhCCC-----CCEEEEEEeeccccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhc
Confidence 44555555554444321 4799999996 7788888776 689999999999999988754
No 12
>cd07376 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase. This family includes eukaryotic D-serine dehydratases (DSD), cryptic DSDs from bacteria, D-threonine aldolases (D-TA), low specificity D-TAs, and similar uncharacterized proteins. DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Members of this family are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity to AR, it is poss
Probab=95.60 E-value=0.016 Score=44.74 Aligned_cols=41 Identities=17% Similarity=0.087 Sum_probs=34.8
Q ss_pred CcEEEEeccCCCHHHHHH-HHHcCCccccccchHHHHhhcCC
Q psy2327 27 RPRLVAVSKTKPKELIIE-AYNGGQRHFGENYVQELLEKGHD 67 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~-a~~~G~~~fGENrvQEl~~K~~~ 67 (97)
+++|.+|+|++...+|.. +.++|...|+.++++|+......
T Consensus 17 ~~~l~~vvKah~~~~v~~~l~~~G~~~~~vat~~Ea~~l~~~ 58 (345)
T cd07376 17 GVRLRPHVKTHKSPELAQRQLAAGARGVTVATLAEAETFAEA 58 (345)
T ss_pred CCccccccchhcCHHHHHHHHhCCCCcEEEecHHHHHHHHHc
Confidence 478999999999877555 66889999999999999987643
No 13
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=95.28 E-value=0.054 Score=43.22 Aligned_cols=70 Identities=11% Similarity=-0.066 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCC--CHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceEEEe
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTK--PKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTAV 82 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~--~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh~I 82 (97)
++.|+++++...+..+.. +++|.+|+|.. .++.++.+.++|.+.|+-..+.|+..=.+ .++.|+.|
T Consensus 35 l~~I~~N~~~l~~~~~~~----~~~l~~vvKAna~~~~ia~~l~~~G~~g~~vas~~Ea~~lr~--------aGi~~~~I 102 (382)
T cd06811 35 LDQIEENARLLAETAEKY----GIELYFMTKQFGRNPFLARALLEAGIPGAVAVDFKEARALHE--------AGLPLGHV 102 (382)
T ss_pred HHHHHHHHHHHHHHHhhC----CCEEEEEEccCCCCHHHHHHHHHcCCCeEeEecHHHHHHHHH--------cCCCHHhE
Confidence 445555555444443221 47899999997 77777778899998888888888864221 15778888
Q ss_pred eecc
Q psy2327 83 KEVV 86 (97)
Q Consensus 83 G~lq 86 (97)
|+++
T Consensus 103 ~~l~ 106 (382)
T cd06811 103 GHLV 106 (382)
T ss_pred EEcc
Confidence 8776
No 14
>cd06821 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme D-Threonine Aldolase. D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Its activity is present in several genera of bacteria but not in fungi. It requires PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or Mg2+ as cofactors for catalytic activity and thermal stability. Members of this subfamily show similarity to bacterial alanine racemase (AR), a fold type III PLP-dependent enzyme which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that
Probab=93.54 E-value=0.11 Score=40.50 Aligned_cols=75 Identities=13% Similarity=0.016 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHH-HHHcCCccccccchHHHHhhcCCcccccccCCceEEEee
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIE-AYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTAVK 83 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~-a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh~IG 83 (97)
++.+.++|+...+..+. .++|.+|.|+++..+|.. ++++|...|+.++++|+......- . . ..-+.|+++|
T Consensus 16 ~~~l~~Ni~~~~~~~~~-----~~~l~~~vKah~~~~i~~~~~~~G~~~~~vas~~Ea~~~~~~G-~-~-~ill~~~~~~ 87 (361)
T cd06821 16 PDRIEENIRRMIRMAGD-----PQRLRPHVKTHKMAEIVRLQLEAGITKFKCATIAEAEMLAEAG-A-P-DVLLAYPLVG 87 (361)
T ss_pred HHHHHHHHHHHHHHHhc-----CCCccccchhhcCHHHHHHHHhcCCCcEEEecHHHHHHHHHcC-C-C-eEEEeCCCCH
Confidence 45566666655555432 247999999988777555 568999999999999999876531 0 1 0115577777
Q ss_pred eccc
Q psy2327 84 EVVD 87 (97)
Q Consensus 84 ~lq~ 87 (97)
..+.
T Consensus 88 ~~~~ 91 (361)
T cd06821 88 PNIE 91 (361)
T ss_pred HHHH
Confidence 6543
No 15
>cd06808 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these p
Probab=93.45 E-value=0.17 Score=35.63 Aligned_cols=55 Identities=13% Similarity=-0.020 Sum_probs=40.8
Q ss_pred CcEEEEeccCCCHHHHHH-HHHcCCccccccchHHHHhhcCCcccccccCCceEEEeeeccc
Q psy2327 27 RPRLVAVSKTKPKELIIE-AYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTAVKEVVD 87 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~-a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~wh~IG~lq~ 87 (97)
++++.+|+|..+...|.. +.++ ...|+.+.++|+..-.... .++..|+|.|++.+
T Consensus 15 ~~~i~~~vKan~~~~i~~~~~~~-~~~~~v~s~~E~~~~~~~g-----~~~~~I~~~~~~~~ 70 (211)
T cd06808 15 GITLFAVVKANANPEVARTLAAL-GTGFDVASLGEALLLRAAG-----IPPEPILFLGPCKQ 70 (211)
T ss_pred CCEEEEEEecCCCHHHHHHHHHc-CCcEEEcCHHHHHHHHHcC-----CCHHHEEEcCCCCC
Confidence 478999999999555544 4555 7889999999999765331 23467999998874
No 16
>cd06825 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins. This subfamily is composed of Enterococcus gallinarum VanT and similar proteins. VanT is a membrane-bound serine racemase (EC 5.1.1.18) that is essential for vancomycin resistance in Enterococcus gallinarum. It converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. The C-terminal region of this protein contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, which is homologous to the fold type III PLP-dependent enzyme, bacterial alanine racemase (AR). AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. On the basis of this similarity, it has been suggested that dimer formation of VanT is required for its catalytic activity, and that it catalyzes the racemization of serine in a mechanistically similar manner to that of alanine by
Probab=91.29 E-value=0.75 Score=36.46 Aligned_cols=55 Identities=16% Similarity=0.167 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC----CCHHHHHHHH-HcCCccccccchHHHHh
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKT----KPKELIIEAY-NGGQRHFGENYVQELLE 63 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~----~~~e~I~~a~-~~G~~~fGENrvQEl~~ 63 (97)
++..++..++...+..+. .++|++|.|. +...+|..++ ++|++.||-.++.|+..
T Consensus 7 dl~al~~N~~~i~~~~~~-----~~~i~~VVKanAYGhG~~~va~~l~~~G~~~faVa~~~EA~~ 66 (368)
T cd06825 7 DLSALEHNVKEIKRLLPS-----TCKLMAVVKANAYGHGDVEVARVLEQIGIDFFAVATIDEGIR 66 (368)
T ss_pred EHHHHHHHHHHHHHhCCC-----CCeEEEEEeccccCCCHHHHHHHHHHcCCCEEEEccHHHHHH
Confidence 355666666655555432 3689999999 8877776665 68999999999999876
No 17
>cd06820 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like. This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Low specificity D-TAs show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exh
Probab=90.63 E-value=0.29 Score=37.95 Aligned_cols=40 Identities=18% Similarity=-0.013 Sum_probs=33.1
Q ss_pred CcEEEEeccCCCHHHHHHH-HHcCCccccccchHHHHhhcC
Q psy2327 27 RPRLVAVSKTKPKELIIEA-YNGGQRHFGENYVQELLEKGH 66 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a-~~~G~~~fGENrvQEl~~K~~ 66 (97)
.++|.+++|++...+|..+ .++|...|+-.+++|+..-.+
T Consensus 28 ~v~l~~~~K~h~~~~i~~~~~~~G~~~~~vas~~Ea~~~~~ 68 (353)
T cd06820 28 GLSLRPHIKTHKSPEIARLQLAAGAIGITVATVGEAEVMAD 68 (353)
T ss_pred CCccccccccccCHHHHHHHHhCCCCCEEEeeHHHHHHHHH
Confidence 4789999999998877554 578999999999999876543
No 18
>cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=88.12 E-value=1.7 Score=34.20 Aligned_cols=55 Identities=13% Similarity=0.009 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC----CCHHHHH-HHHHcCCccccccchHHHHhh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKT----KPKELII-EAYNGGQRHFGENYVQELLEK 64 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~----~~~e~I~-~a~~~G~~~fGENrvQEl~~K 64 (97)
+..++..++...+..+. ..++++|.|. +....|. .+++.|...||-..+.|+..=
T Consensus 8 l~al~~N~~~i~~~~~~-----~~~i~~vvKAnAYGhG~~~va~~l~~~g~~~f~Vas~~Ea~~l 67 (365)
T cd06826 8 TGAFENNIKLLKKLLGG-----NTKLCAVMKADAYGHGIALVMPSIIAQNIPCVGITSNEEARVV 67 (365)
T ss_pred HHHHHHHHHHHHHhCCC-----CCEEEEEEEeccccccHHHHHHHHHHCCCCEEEEccHHHHHHH
Confidence 55666666655444432 3589999999 8777776 456899999999999998753
No 19
>TIGR03619 F420_Rv2161c probable F420-dependent oxidoreductase, Rv2161c family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a domain found in a distinctive subset of bacterial luciferase homologs, found only in F420-biosynthesizing members of the Actinobacteria.
Probab=85.95 E-value=2 Score=32.13 Aligned_cols=48 Identities=10% Similarity=0.132 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEe------ccCCCHHHHHHHHHcCCccc
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAV------SKTKPKELIIEAYNGGQRHF 53 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAV------SK~~~~e~I~~a~~~G~~~f 53 (97)
.+....+.+.++++++||++. ++++.+. |-..-.+++....++|+++|
T Consensus 189 ~~~~~~~~~~~~~~~~Gr~~~--~~~~~~~~~~~~g~~~~~~~~l~~~~~~G~~~~ 242 (246)
T TIGR03619 189 RLAAAVARLRDLAAAAGRDPD--AVEVVLVRTDPDGDADADAEDLAAYADLGVTRL 242 (246)
T ss_pred HHHHHHHHHHHHHHHcCCCcc--ceeEEeeccccCCCHHHHHHHHHHHHHcCCcEE
Confidence 466778889999999999865 6777665 22333566666667787765
No 20
>COG3457 Predicted amino acid racemase [Amino acid transport and metabolism]
Probab=83.80 E-value=4.1 Score=33.01 Aligned_cols=39 Identities=13% Similarity=0.044 Sum_probs=33.6
Q ss_pred CcEEEEeccCC--CHHHHHHHHHcCCccccccchHHHHhhc
Q psy2327 27 RPRLVAVSKTK--PKELIIEAYNGGQRHFGENYVQELLEKG 65 (97)
Q Consensus 27 ~V~LiAVSK~~--~~e~I~~a~~~G~~~fGENrvQEl~~K~ 65 (97)
+|.|.+|||-. ++...+.+.+.|+...+|+|..++..=.
T Consensus 28 gI~~~~vtK~~~g~~~iae~l~~~Gi~~iaesr~~n~~~lr 68 (353)
T COG3457 28 GIELYGVTKQFGGDPFIAEALLALGIEGIAESRIDNAIRLR 68 (353)
T ss_pred CCEEEEEEeeccCChHHHHHHHhcCcceeeehhHHHHHHHH
Confidence 68999999975 5777788888999999999999988644
No 21
>cd06819 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase. Low specificity D-threonine aldolase (Low specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene from Arthrobacter sp. strain DK-38, is the prototype of this subfamily. Low specificity D-TAs are fold type III PLP-dependent enzymes that catalyze the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Members of this subfamily show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that t
Probab=80.48 E-value=1.7 Score=33.60 Aligned_cols=37 Identities=19% Similarity=0.033 Sum_probs=30.4
Q ss_pred CcEEEEeccCCCHHHHHHH-HHcCCccccccchHHHHh
Q psy2327 27 RPRLVAVSKTKPKELIIEA-YNGGQRHFGENYVQELLE 63 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a-~~~G~~~fGENrvQEl~~ 63 (97)
.+++.+++|+++..+|..+ .++|...|+-.+++|+..
T Consensus 32 ~~~l~~~~K~h~~~~i~~~~~~~G~~~~~vas~~Ea~~ 69 (358)
T cd06819 32 GVRLRPHAKTHKCPAIARRQIAAGAVGVCCQKLSEAEV 69 (358)
T ss_pred CCcccccchhhcCHHHHHHHHhCCCCcEEEccHHHHHH
Confidence 3678899999997777655 577999999999999875
No 22
>PRK03646 dadX alanine racemase; Reviewed
Probab=78.61 E-value=7.2 Score=30.86 Aligned_cols=52 Identities=17% Similarity=0.200 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC----CCHHHHHHHHHcCCccccccchHHHHh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKT----KPKELIIEAYNGGQRHFGENYVQELLE 63 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~----~~~e~I~~a~~~G~~~fGENrvQEl~~ 63 (97)
++.++..++...+..+ .++++||.|. +....|..++. +++.||-.++.|+..
T Consensus 10 l~al~~N~~~i~~~~~------~~~i~aVVKanAYGhG~~~va~~l~-~~~~faVa~l~Ea~~ 65 (355)
T PRK03646 10 LQALKQNLSIVREAAP------GARVWSVVKANAYGHGIERIWSALG-ATDGFAVLNLEEAIT 65 (355)
T ss_pred HHHHHHHHHHHHHhCC------CCeEEEEEeeccccCCHHHHHHHHh-cCCEEEEeeHHHHHH
Confidence 4556666655444432 2689999999 99999988875 499999999999876
No 23
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=76.02 E-value=10 Score=33.04 Aligned_cols=55 Identities=7% Similarity=0.085 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCC-----HHHHHHHHHcCCccccccchHHHHh
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKP-----KELIIEAYNGGQRHFGENYVQELLE 63 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~-----~e~I~~a~~~G~~~fGENrvQEl~~ 63 (97)
++..++..++...+..+. .++++||.|--- .+-.+.+.++|++.||-.++.|+..
T Consensus 465 dl~al~~N~~~i~~~~~~-----~~k~~aVvKa~aYGhG~~~va~~l~~~G~~~f~Va~l~Ea~~ 524 (822)
T PRK11930 465 NLNAIVHNLNYYRSKLKP-----ETKIMCMVKAFAYGSGSYEIAKLLQEHRVDYLAVAYADEGVS 524 (822)
T ss_pred hHHHHHHHHHHHHhhCCC-----CCEEEEEEeeccccCCHHHHHHHHHHCCCCEEEEeeHHHHHH
Confidence 345555656554444321 479999999765 4555556689999999999999875
No 24
>PRK13340 alanine racemase; Reviewed
Probab=69.43 E-value=19 Score=28.89 Aligned_cols=56 Identities=13% Similarity=0.068 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCC----HHH-HHHHHHcCCccccccchHHHHhhc
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKP----KEL-IIEAYNGGQRHFGENYVQELLEKG 65 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~----~e~-I~~a~~~G~~~fGENrvQEl~~K~ 65 (97)
++.++.+++...+..+. ..++.+|.|... ..+ ...+.+.|...|+=..+.|+..=.
T Consensus 47 l~ai~~N~~~i~~~~~~-----~~~i~~vvKAnaYG~G~~~va~~l~~~G~~~~~Vas~~Ea~~lr 107 (406)
T PRK13340 47 PGAFRHNIKTLRSLLAN-----KSKVCAVMKADAYGHGIELLMPSIIKANVPCIGIASNEEARRVR 107 (406)
T ss_pred HHHHHHHHHHHHHhCCC-----CCEEEEEEccccccccHHHHHHHHHHCCCCEEEEccHHHHHHHH
Confidence 45566666555444322 368999999975 333 455668999999999999987533
No 25
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 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 [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=66.14 E-value=9.9 Score=23.30 Aligned_cols=27 Identities=15% Similarity=0.335 Sum_probs=24.3
Q ss_pred CcEEEEeccCCCHHHHHHHHHcCCccc
Q psy2327 27 RPRLVAVSKTKPKELIIEAYNGGQRHF 53 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a~~~G~~~f 53 (97)
.+.+|.+|...+.+.+..++++|...|
T Consensus 71 ~~~ii~~t~~~~~~~~~~~~~~g~~~~ 97 (112)
T PF00072_consen 71 SIPIIVVTDEDDSDEVQEALRAGADDY 97 (112)
T ss_dssp TSEEEEEESSTSHHHHHHHHHTTESEE
T ss_pred cccEEEecCCCCHHHHHHHHHCCCCEE
Confidence 579999999999999999999998754
No 26
>TIGR03856 F420_MSMEG_2906 probable F420-dependent oxidoreductase, MSMEG_2906 family. This model describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN.
Probab=65.31 E-value=22 Score=26.79 Aligned_cols=45 Identities=7% Similarity=-0.013 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCcc
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRH 52 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~ 52 (97)
.+....+.|.+.++++||++. ++.+..-. -+.+.+....++|++.
T Consensus 182 ~~~~~~~~l~~~a~~~Grd~~--~i~~~~~~--~~~~~~~~~~~~G~~~ 226 (249)
T TIGR03856 182 TYRRKSQILDRHCADVGRDPA--TIERSVSW--PGLDSADAYVAAGVTL 226 (249)
T ss_pred HHHHHHHHHHHHHHHcCCChh--HeEEEecC--CCHHHHHHHHHcCCcE
Confidence 466778889999999999864 67766643 3489999988999874
No 27
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=64.90 E-value=23 Score=27.95 Aligned_cols=53 Identities=15% Similarity=0.197 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC----CCHHHHHHHHHcCCccccccchHHHHhh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKT----KPKELIIEAYNGGQRHFGENYVQELLEK 64 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~----~~~e~I~~a~~~G~~~fGENrvQEl~~K 64 (97)
++.++..+....+..+ +++|++|.|. +....|..++.. ...||=..+.|+..=
T Consensus 8 l~~l~~N~~~l~~~~~------~~~l~~vvKanaYGhG~~~ia~~l~~-~~~f~Vas~~Ea~~l 64 (354)
T cd06827 8 LAALRHNLRLVRELAP------NSKILAVVKANAYGHGLVRVAKALAD-ADGFAVACIEEALAL 64 (354)
T ss_pred HHHHHHHHHHHHhhCC------CCeEEEEEeeccccCCHHHHHHHHHc-CCEEEEccHHHHHHH
Confidence 4555555555444432 2589999999 667777776665 889999999998753
No 28
>cd06817 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase. This subfamily is composed of chicken D-serine dehydratase (DSD, EC 4.3.1.18) and similar eukaryotic proteins. Chicken DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. It is a fold type III PLP-dependent enzyme with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Experimental data suggest that chicken DSD also exists as dimers. Sequence comparison and biochemical experiments show that chicken DSD is distinct from the ubiquitous bacterial DSDs coded by dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PL
Probab=62.28 E-value=14 Score=29.78 Aligned_cols=39 Identities=13% Similarity=-0.099 Sum_probs=32.3
Q ss_pred CcEEEEeccCCCHHHHHHH-HHcCC--ccccccchHHHHhhc
Q psy2327 27 RPRLVAVSKTKPKELIIEA-YNGGQ--RHFGENYVQELLEKG 65 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a-~~~G~--~~fGENrvQEl~~K~ 65 (97)
+++|.++.|++-..+|..+ +++|. ..|+=..+.|+..=.
T Consensus 31 ~~~l~phvKaHg~~~ia~~~~~~Ga~~~~~~Vatl~EA~~lr 72 (389)
T cd06817 31 GVKFRPHVKTHKTLEGTRLQLGEGRPSRGIVVSTLAEAEFLL 72 (389)
T ss_pred CCceeeeecCcCCHHHHHHHhhCCCCccCEEEecHHHHHHHH
Confidence 4689999999998888774 56798 999999999988633
No 29
>cd06812 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible mem
Probab=53.26 E-value=30 Score=26.94 Aligned_cols=37 Identities=16% Similarity=0.027 Sum_probs=28.2
Q ss_pred CcEEEEeccCCCHHHHHH-HHHcCCccccccchHHHHh
Q psy2327 27 RPRLVAVSKTKPKELIIE-AYNGGQRHFGENYVQELLE 63 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~-a~~~G~~~fGENrvQEl~~ 63 (97)
.++|.++.|+.+...+.. +.++|..-|+=..+.|+..
T Consensus 31 ~~~l~~~vKa~~~~~i~~~~~~~G~~~~~vas~~Ea~~ 68 (374)
T cd06812 31 GVRLRPHLKTAKSLEVARRLLAAGASPATVSTLKEAEA 68 (374)
T ss_pred CCceeeEecccCCHHHHHHHHhCCCCcEEEccHHHHHH
Confidence 478999999998665554 4578988788888888764
No 30
>cd06818 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase. This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity, it is possible cryptic DSDs may also form dimers. Cryptic DSDs are distinct from the ubiquitous bacterial DSDs coded by the dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. At present, the enzymatic and biochemical properties
Probab=47.42 E-value=49 Score=26.14 Aligned_cols=37 Identities=14% Similarity=0.073 Sum_probs=29.7
Q ss_pred CcEEEEeccCCCHHHHHH-HHHcCCccccccchHHHHh
Q psy2327 27 RPRLVAVSKTKPKELIIE-AYNGGQRHFGENYVQELLE 63 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~-a~~~G~~~fGENrvQEl~~ 63 (97)
.+++.+..|++..-.|.. ..++|..-|+-..+.|+..
T Consensus 28 ~~~l~~h~Kt~~~~~i~~~~~~~G~~g~~vas~~Ea~~ 65 (382)
T cd06818 28 GVKLAPHGKTTMAPQLFRRQLEAGAWGITVATVAQARV 65 (382)
T ss_pred CcEEEeecchhhhHHHHHHHHHcCCCEEEEeEHHHHHH
Confidence 478999999998777643 3567988899999999875
No 31
>cd06814 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible mem
Probab=45.63 E-value=68 Score=25.63 Aligned_cols=54 Identities=11% Similarity=0.018 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHH-H-HcCCccccccchHHHHh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEA-Y-NGGQRHFGENYVQELLE 63 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a-~-~~G~~~fGENrvQEl~~ 63 (97)
+..+...|+...++++ . +++|.+|.|++-..++... + ++|.+-|+=..+.|+..
T Consensus 16 l~al~~Ni~~m~~~~~-~----g~~lrphvKa~ky~~~~~~~l~~~Ga~g~~vat~~Eae~ 71 (379)
T cd06814 16 KDRLDHNIDLLREHLA-G----SLAYRIVAKSLPSPPLLRHIMKRAGTRRLMVFHQPFLNA 71 (379)
T ss_pred HHHHHHHHHHHHHhhC-C----CCcEEEEeccccCHHHHHHHHhhCCCCEEEEecHHHHHH
Confidence 4556666666555554 2 4799999999877655444 4 68999999999888876
No 32
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane]
Probab=42.96 E-value=81 Score=25.55 Aligned_cols=55 Identities=16% Similarity=0.201 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccC----CCHHHHH-HHHHcCCccccccchHHHHhh
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKT----KPKELII-EAYNGGQRHFGENYVQELLEK 64 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~----~~~e~I~-~a~~~G~~~fGENrvQEl~~K 64 (97)
++..++..+....+..+ ..+|+||-|- +....+. .++++|+..||=-+++|+.+=
T Consensus 10 dl~Al~~N~~~i~~~~~------~~~~~AVVKAnAYGhG~~~va~~l~~~g~~~f~VA~l~EAi~L 69 (360)
T COG0787 10 DLGALRHNLRALRELAG------PAKLMAVVKANAYGHGAVRVAKALLDAGADGFGVASLEEAIEL 69 (360)
T ss_pred eHHHHHHHHHHHHHhCC------CcEEEEEEeccccCCCHHHHHHHHHHcCCCEEEECcHHHHHHH
Confidence 35666666666555542 2599999995 5555554 566789999999999999863
No 33
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=40.04 E-value=19 Score=21.56 Aligned_cols=24 Identities=17% Similarity=0.083 Sum_probs=19.6
Q ss_pred HHHcCCccccccchHHHHhhcCCc
Q psy2327 45 AYNGGQRHFGENYVQELLEKGHDP 68 (97)
Q Consensus 45 a~~~G~~~fGENrvQEl~~K~~~~ 68 (97)
.+.+|+.+.|+...+.|.+++..+
T Consensus 3 l~aLGI~~VG~~~ak~L~~~f~sl 26 (64)
T PF12826_consen 3 LFALGIPGVGEKTAKLLAKHFGSL 26 (64)
T ss_dssp HHHCTSTT--HHHHHHHHHCCSCH
T ss_pred eeeCCCCCccHHHHHHHHHHcCCH
Confidence 678999999999999999998764
No 34
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=39.03 E-value=75 Score=22.57 Aligned_cols=53 Identities=17% Similarity=0.182 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHH--cCC-ccccccc--hHHHHhhc
Q psy2327 4 AIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYN--GGQ-RHFGENY--VQELLEKG 65 (97)
Q Consensus 4 nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~--~G~-~~fGENr--vQEl~~K~ 65 (97)
.....++.|.+...+.-|++ .|++..+...++.|++ +|+ ..|| || ++++.++.
T Consensus 64 a~~~ar~~indyvsrYRr~~--------~v~g~~SFttm~TALNsLAGHY~sy~-~rPlPeklk~Rl 121 (135)
T TIGR03044 64 AQAEARQLINDYISRYRRRP--------RVNGLSSFTTMQTALNSLAGHYKSYA-NRPLPEKLKERL 121 (135)
T ss_pred HHHHHHHHHHHHHHHhcCCC--------CcCCcccHHHHHHHHHHHHHHhccCC-CCCCCHHHHHHH
Confidence 34567788888888875553 5788999999999998 586 5578 99 46665554
No 35
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=36.27 E-value=22 Score=29.02 Aligned_cols=38 Identities=32% Similarity=0.275 Sum_probs=25.6
Q ss_pred EEEEeccCCCHHHHHHHHHc--CCccccccc-hHHHHhhcC
Q psy2327 29 RLVAVSKTKPKELIIEAYNG--GQRHFGENY-VQELLEKGH 66 (97)
Q Consensus 29 ~LiAVSK~~~~e~I~~a~~~--G~~~fGENr-vQEl~~K~~ 66 (97)
.+|.|||+.+.++|+.||.- =..|===|. -.|+.+|+.
T Consensus 8 eiLGV~k~As~~EIKkAYRkLA~kyHPD~n~g~~~AeeKFK 48 (371)
T COG0484 8 EILGVSKDASEEEIKKAYRKLAKKYHPDRNPGDKEAEEKFK 48 (371)
T ss_pred hhcCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHH
Confidence 68999999999999999972 222222333 345555554
No 36
>PLN00064 photosystem II protein Psb27; Provisional
Probab=34.41 E-value=96 Score=22.79 Aligned_cols=55 Identities=18% Similarity=0.115 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHH--cCCc-cccccc--hHHHHhhc
Q psy2327 3 AAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYN--GGQR-HFGENY--VQELLEKG 65 (97)
Q Consensus 3 ~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~--~G~~-~fGENr--vQEl~~K~ 65 (97)
+.....++.|.....++-|+. .|+...|...|+.|++ +|+. .||-|| ++.+.+..
T Consensus 92 ~a~aeaR~~iNdyvSrYRr~~--------~v~Gl~SFttMyTALNaLAGHY~SfgpnrPlPeKlK~RL 151 (166)
T PLN00064 92 DAVAELRETSNSWVAKYRREK--------ALLGRPSFRDMYSALNAVSGHYISFGPTAPIPAKRKARI 151 (166)
T ss_pred HHHHHHHHHHHHHHHHhcCCC--------cccCcccHHHHHHHHHHHHHHhhccCCCCCCcHHHHHHH
Confidence 445677888888888875543 5788889999999998 5886 799888 35554443
No 37
>cd06810 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to
Probab=30.35 E-value=1.8e+02 Score=22.26 Aligned_cols=53 Identities=15% Similarity=0.146 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHH-HcCCccccccchHHHHh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAY-NGGQRHFGENYVQELLE 63 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~-~~G~~~fGENrvQEl~~ 63 (97)
+..++++++...+..+ . .+++..+.|+.+...|...+ +.|. .|.=....|+..
T Consensus 8 ~~~l~~n~~~l~~~~~--~---~~~i~~avKan~~~~i~~~l~~~G~-g~~vas~~E~~~ 61 (368)
T cd06810 8 LDIIRAHYAALKEALP--S---GVKLFYAVKANPNPHVLRTLAEAGT-GFDVASKGELAL 61 (368)
T ss_pred HHHHHHHHHHHHHhCC--C---CCeEEEEEccCCCHHHHHHHHHcCC-cEEEeCHHHHHH
Confidence 3455555555444433 1 47999999999887776655 5687 788888888754
No 38
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=29.64 E-value=34 Score=29.30 Aligned_cols=23 Identities=30% Similarity=0.560 Sum_probs=19.3
Q ss_pred EeccCCCHH----HHHHHHHcCCcccc
Q psy2327 32 AVSKTKPKE----LIIEAYNGGQRHFG 54 (97)
Q Consensus 32 AVSK~~~~e----~I~~a~~~G~~~fG 54 (97)
...+++|++ +|.++|++|++||=
T Consensus 210 g~~~~R~~e~Vv~EVkaLY~~GvrhFR 236 (560)
T COG1031 210 GRPEFRPPEDVVEEVKALYRAGVRHFR 236 (560)
T ss_pred CCcccCCHHHHHHHHHHHHHhccceee
Confidence 788899876 56789999999983
No 39
>PF01645 Glu_synthase: Conserved region in glutamate synthase; InterPro: IPR002932 Ferredoxin-dependent glutamate synthases have been implicated in a number of functions including photorespiration in Arabidopsis where they may also play a role in primary nitrogen assimilation in roots []. This region is expressed as a seperate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.; GO: 0015930 glutamate synthase activity, 0016638 oxidoreductase activity, acting on the CH-NH2 group of donors, 0006537 glutamate biosynthetic process, 0055114 oxidation-reduction process; PDB: 1EA0_A 2VDC_E 1OFE_A 1LLW_A 1OFD_A 1LLZ_A 1LM1_A.
Probab=29.58 E-value=1.9e+02 Score=23.55 Aligned_cols=44 Identities=18% Similarity=0.162 Sum_probs=30.0
Q ss_pred HHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccc
Q psy2327 9 LEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGE 55 (97)
Q Consensus 9 ~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGE 55 (97)
..++.+.....+-+ +.|+|++--|..+..++..++.+|...|+=
T Consensus 259 l~~a~~~L~~~glr---~~V~Li~sGgl~t~~dv~kalaLGAD~v~i 302 (368)
T PF01645_consen 259 LARAHQALVKNGLR---DRVSLIASGGLRTGDDVAKALALGADAVYI 302 (368)
T ss_dssp HHHHHHHHHCTT-C---CCSEEEEESS--SHHHHHHHHHCT-SEEE-
T ss_pred HHHHHHHHHHcCCC---CceEEEEeCCccCHHHHHHHHhcCCCeeEe
Confidence 34455555555533 269999999999999999999999877653
No 40
>PF07386 DUF1499: Protein of unknown function (DUF1499); InterPro: IPR010865 This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. The function of this family is unknown.
Probab=29.43 E-value=11 Score=25.23 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=17.8
Q ss_pred HHHHHHcCCccccccc--hHHHHhh
Q psy2327 42 IIEAYNGGQRHFGENY--VQELLEK 64 (97)
Q Consensus 42 I~~a~~~G~~~fGENr--vQEl~~K 64 (97)
|+.+...|..+||-|+ ++.+.++
T Consensus 92 vRS~SR~G~~DlG~Nr~Ri~~~~~~ 116 (118)
T PF07386_consen 92 VRSASRVGYSDLGVNRRRIEALRAA 116 (118)
T ss_pred EEEeccCCCCccchhHHHHHHHHHH
Confidence 6667778999999997 6666654
No 41
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=27.11 E-value=2.2e+02 Score=22.18 Aligned_cols=54 Identities=15% Similarity=0.064 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLE 63 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~ 63 (97)
+..|+++++...+..+ + .+++..+.|..+...|..++..+...|.=.-..|+..
T Consensus 9 ~~~l~~N~~~l~~~~~---~--~~~i~yavKaN~~~~vl~~l~~~g~g~dvaS~~E~~~ 62 (377)
T cd06843 9 LAALRAHARALRASLP---P--GCELFYAIKANSDPPILRALAPHVDGFEVASGGEIAH 62 (377)
T ss_pred HHHHHHHHHHHHHhcC---C--CCeEEEEeccCCCHHHHHHHHHcCCcEEEeCHHHHHH
Confidence 3455555555444332 1 4789999999999998888776666777666666654
No 42
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=27.08 E-value=59 Score=22.47 Aligned_cols=42 Identities=19% Similarity=0.080 Sum_probs=31.0
Q ss_pred ccCCCHHHHHHHHHcCCccccccchHHHHhhcCCcccccccCCceE
Q psy2327 34 SKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGK 79 (97)
Q Consensus 34 SK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~~~~~~~~~~~i~w 79 (97)
|=+.....|++.+++|++.| +-|..+.+||+-. .-+-+++.|
T Consensus 41 T~f~de~vI~~hidaGIs~~--~AVN~LVeKY~Lv--RiD~~gFs~ 82 (114)
T PF06755_consen 41 TPFSDETVIQEHIDAGISPA--DAVNFLVEKYELV--RIDRNGFSW 82 (114)
T ss_pred CccchHHHHHHHHHhCCCHH--HHHHHHHHHHhhh--hcCCcccCc
Confidence 44567788999999999987 5699999999753 223345555
No 43
>PF08799 PRP4: pre-mRNA processing factor 4 (PRP4) like; InterPro: IPR014906 This small protein is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. ; PDB: 1MZW_B 2DK4_A.
Probab=26.16 E-value=28 Score=18.56 Aligned_cols=15 Identities=27% Similarity=0.304 Sum_probs=8.3
Q ss_pred HHcC--CccccccchHH
Q psy2327 46 YNGG--QRHFGENYVQE 60 (97)
Q Consensus 46 ~~~G--~~~fGENrvQE 60 (97)
=+.| ++.|||+..+-
T Consensus 6 R~lgePi~lFGE~~~~R 22 (30)
T PF08799_consen 6 RELGEPITLFGETDADR 22 (30)
T ss_dssp HHCT--SCETT--HHHH
T ss_pred HhcCCChhhhCCChHHH
Confidence 3455 68899987653
No 44
>KOG0713|consensus
Probab=26.05 E-value=34 Score=27.67 Aligned_cols=20 Identities=30% Similarity=0.403 Sum_probs=18.6
Q ss_pred cEEEEeccCCCHHHHHHHHH
Q psy2327 28 PRLVAVSKTKPKELIIEAYN 47 (97)
Q Consensus 28 V~LiAVSK~~~~e~I~~a~~ 47 (97)
=.|+.|+|+.+..+|+.||.
T Consensus 19 YelLgV~k~Asd~eIKkAYR 38 (336)
T KOG0713|consen 19 YELLGVPKNASDQEIKKAYR 38 (336)
T ss_pred HHHhCCCCCCCHHHHHHHHH
Confidence 47999999999999999996
No 45
>cd06813 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 2. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible mem
Probab=25.78 E-value=2.3e+02 Score=22.44 Aligned_cols=53 Identities=11% Similarity=0.026 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHH-HHH-cCCccccccchHHHHh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIE-AYN-GGQRHFGENYVQELLE 63 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~-a~~-~G~~~fGENrvQEl~~ 63 (97)
++.+..+|+...+.++ .++|.+++|++..-.+.. +.+ .|..-|+=..+.|+..
T Consensus 18 ldal~~N~~~l~~~~~------~~~ir~~vKa~~~~~ll~~~l~~~G~~g~~vas~~Ea~~ 72 (388)
T cd06813 18 LDALDANAADLVRRAG------GKPIRVASKSVRCRALLRRVLAAPGFQGVMAFTLAEALW 72 (388)
T ss_pred HHHHHHHHHHHHHHcC------CCcEEEEeccccCHHHHHHHHhhcCCceEEEecHHHHHH
Confidence 4455555655444441 357999999998887653 444 5988888777777654
No 46
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=25.59 E-value=34 Score=22.15 Aligned_cols=19 Identities=26% Similarity=0.385 Sum_probs=15.6
Q ss_pred ccccchHHHHhhcCCcccc
Q psy2327 53 FGENYVQELLEKGHDPEIS 71 (97)
Q Consensus 53 fGENrvQEl~~K~~~~~~~ 71 (97)
-||||+.++.+++-.-|++
T Consensus 11 ~G~~r~~~Av~~Al~spLl 29 (95)
T PF12327_consen 11 SGENRAEEAVEQALNSPLL 29 (95)
T ss_dssp ESTTHHHHHHHHHHTSTTS
T ss_pred CCccHHHHHHHHHHhCccc
Confidence 5899999999999765554
No 47
>KOG0871|consensus
Probab=25.32 E-value=69 Score=23.28 Aligned_cols=29 Identities=38% Similarity=0.501 Sum_probs=22.5
Q ss_pred ccCCCHHHHHHHHH-cCCccccccchHHHHhhcC
Q psy2327 34 SKTKPKELIIEAYN-GGQRHFGENYVQELLEKGH 66 (97)
Q Consensus 34 SK~~~~e~I~~a~~-~G~~~fGENrvQEl~~K~~ 66 (97)
-||..++.+..|++ +| || .|++++.+-+.
T Consensus 64 KKTIa~EHV~KALe~Lg---F~-eYiee~~~vl~ 93 (156)
T KOG0871|consen 64 KKTIAPEHVIKALENLG---FG-EYIEEAEEVLE 93 (156)
T ss_pred cccCCHHHHHHHHHHcc---hH-HHHHHHHHHHH
Confidence 38899999988886 78 77 68888776543
No 48
>PLN00035 histone H4; Provisional
Probab=25.26 E-value=2.2e+02 Score=19.18 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=15.8
Q ss_pred cCCCHHHHHHHHH-cCCcccc
Q psy2327 35 KTKPKELIIEAYN-GGQRHFG 54 (97)
Q Consensus 35 K~~~~e~I~~a~~-~G~~~fG 54 (97)
||++.++|.-|+. .|...+|
T Consensus 80 KTV~~~DV~~Alkr~g~~lyG 100 (103)
T PLN00035 80 KTVTAMDVVYALKRQGRTLYG 100 (103)
T ss_pred CcCcHHHHHHHHHHcCCcCCC
Confidence 7899999988875 6777766
No 49
>PTZ00015 histone H4; Provisional
Probab=24.56 E-value=2.3e+02 Score=19.06 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=16.2
Q ss_pred ccCCCHHHHHHHHH-cCCcccc
Q psy2327 34 SKTKPKELIIEAYN-GGQRHFG 54 (97)
Q Consensus 34 SK~~~~e~I~~a~~-~G~~~fG 54 (97)
-||++.++|.-|+. .|...+|
T Consensus 80 RKTVt~~DV~~AlKr~g~~~yg 101 (102)
T PTZ00015 80 RKTVTAMDVVYALKRQGRTLYG 101 (102)
T ss_pred CCcccHHHHHHHHHhcCCCCCC
Confidence 37899999988875 6777766
No 50
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=23.55 E-value=3e+02 Score=21.14 Aligned_cols=54 Identities=11% Similarity=-0.045 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHH-HcCCccccccchHHHHh
Q psy2327 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAY-NGGQRHFGENYVQELLE 63 (97)
Q Consensus 5 l~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~-~~G~~~fGENrvQEl~~ 63 (97)
+..++++++...+..+. . ++++..+.|..+...|...+ +.| ..|.=.-..|+..
T Consensus 10 ~~~l~~n~~~l~~~~~~-~---~~~~~yavKaN~~~~v~~~l~~~G-~g~~vaS~~E~~~ 64 (373)
T cd06828 10 EATIRENYRRLKEAFSG-P---GFKICYAVKANSNLAILKLLAEEG-LGADVVSGGELYR 64 (373)
T ss_pred HHHHHHHHHHHHHhhCC-C---CcEEEEEehhCCCHHHHHHHHHcC-CcEEEeCHHHHHH
Confidence 44555555554444332 1 58999999999877766554 567 6676666666653
No 51
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=23.10 E-value=95 Score=23.82 Aligned_cols=41 Identities=20% Similarity=0.205 Sum_probs=35.1
Q ss_pred CcEEEEeccCCCHHHHHHHHHcCCcc-----ccccchHHHHhhcCC
Q psy2327 27 RPRLVAVSKTKPKELIIEAYNGGQRH-----FGENYVQELLEKGHD 67 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a~~~G~~~-----fGENrvQEl~~K~~~ 67 (97)
.+.+|.+|=-.+.+.|+.++.+|+.+ |-=-|.|+.+++|..
T Consensus 74 ~~DVI~iTAA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~~ 119 (224)
T COG4565 74 PVDVIVITAASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQ 119 (224)
T ss_pred CCCEEEEeccchHHHHHHHHhcCchhheecceeHHHHHHHHHHHHH
Confidence 57899999999999999999999754 677788888888754
No 52
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=22.12 E-value=88 Score=17.95 Aligned_cols=20 Identities=30% Similarity=0.340 Sum_probs=12.7
Q ss_pred HHHHHHHHcC--CccccccchH
Q psy2327 40 ELIIEAYNGG--QRHFGENYVQ 59 (97)
Q Consensus 40 e~I~~a~~~G--~~~fGENrvQ 59 (97)
+.+..+-.+| ++.|||+-.+
T Consensus 5 eV~~~LR~lgePi~lFGE~~~~ 26 (44)
T smart00500 5 EVIRRLRELGEPITLFGEDDQE 26 (44)
T ss_pred HHHHHHHHcCCCeeecCCChHH
Confidence 3344455566 5889998643
No 53
>COG0074 SucD Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]
Probab=22.04 E-value=1.6e+02 Score=23.44 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHCCCCCCCCCcEEEEeccCCCHHHHHHHHHcCCc---cccccc
Q psy2327 8 TLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQR---HFGENY 57 (97)
Q Consensus 8 I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~~e~I~~a~~~G~~---~fGENr 57 (97)
|.+-+++|.+.-+- ++.||-|.=.+=.+.|.+|+++|++ +|-||=
T Consensus 53 Vf~tV~EA~~~~~a-----~~svI~Vp~~~aadai~EAida~i~liv~ITEgI 100 (293)
T COG0074 53 VFNTVEEAVKETGA-----NASVIFVPPPFAADAILEAIDAGIKLVVIITEGI 100 (293)
T ss_pred HHHHHHHHHHhhCC-----CEEEEecCcHHHHHHHHHHHhCCCcEEEEEeCCC
Confidence 45556666665421 5788988888888999999999865 477775
No 54
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=22.01 E-value=2.3e+02 Score=18.27 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=16.3
Q ss_pred ccCCCHHHHHHHHH-cCCcccc
Q psy2327 34 SKTKPKELIIEAYN-GGQRHFG 54 (97)
Q Consensus 34 SK~~~~e~I~~a~~-~G~~~fG 54 (97)
-||++.++|.-|+. .|...+|
T Consensus 63 RKTVt~~DV~~alkr~g~~~yg 84 (85)
T cd00076 63 RKTVTAMDVVYALKRQGRTLYG 84 (85)
T ss_pred CCcCcHHHHHHHHHHCCCCccC
Confidence 37889999988775 6877766
No 55
>PLN02923 xylose isomerase
Probab=21.56 E-value=1.4e+02 Score=25.37 Aligned_cols=49 Identities=16% Similarity=0.108 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCC---------------------CHHHHHHHHHcCCccccccch
Q psy2327 3 AAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTK---------------------PKELIIEAYNGGQRHFGENYV 58 (97)
Q Consensus 3 ~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~---------------------~~e~I~~a~~~G~~~fGENrv 58 (97)
.||..|.+++.+..+.. .|+|+=+|=+. -...++.+++++...=|||||
T Consensus 159 ~nld~ivd~~ke~~~~T-------GikllwgTaNlFshPrf~~GAaTspd~dV~ayAaaqvk~ald~t~eLGgenYV 228 (478)
T PLN02923 159 ANLDEVVALAKELQEGT-------KIRPLWGTAQLFKHPRYMHGAATSSEVGVYAYAAAQVKKAMEVTHYLGGENYV 228 (478)
T ss_pred hhHHHHHHHHHHHhHhh-------CceeeeeccccccCccccCCcCCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 47889999998887754 46777555321 245677788888888899996
No 56
>PF12684 DUF3799: PDDEXK-like domain of unknown function (DUF3799); InterPro: IPR024432 This entry represents a PDDEXK-like domain of unknown function found in proteins from bacteria and viruses. Many of these proteins are annotated as exodeoxyribonuclease 8, which is involved in the RecE pathway of recombination. The PD-(D/E)XK domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases []. ; PDB: 3L0A_A 3H4R_A.
Probab=21.31 E-value=45 Score=25.19 Aligned_cols=33 Identities=27% Similarity=0.351 Sum_probs=21.3
Q ss_pred CcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcC
Q psy2327 27 RPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGH 66 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~ 66 (97)
..-+|||||..| ++.++..+++...++.++++.
T Consensus 177 ~f~iiaVeKe~P-------~~~~v~~i~~~~l~~g~~~~~ 209 (237)
T PF12684_consen 177 RFVIIAVEKEAP-------YDVRVIEIDDEALEEGLEEVR 209 (237)
T ss_dssp EEEEEEEESSSC---------EEEEEE-HHHHHHHHHHHH
T ss_pred cEEEEEEEecCC-------CceEEEEcCHHHHHHHHHHHH
Confidence 467999999987 556666666666666665554
No 57
>COG2115 XylA Xylose isomerase [Carbohydrate transport and metabolism]
Probab=21.14 E-value=1.8e+02 Score=24.13 Aligned_cols=20 Identities=30% Similarity=0.396 Sum_probs=16.5
Q ss_pred HHHHHHHHHcCCccccccch
Q psy2327 39 KELIIEAYNGGQRHFGENYV 58 (97)
Q Consensus 39 ~e~I~~a~~~G~~~fGENrv 58 (97)
...+..++++..+.=|||||
T Consensus 168 AaqVk~~~~~tk~LggENYV 187 (438)
T COG2115 168 AAQVKTAMEATKKLGGENYV 187 (438)
T ss_pred HHHHHHHHHHHHhcCCcceE
Confidence 34677788889999999997
No 58
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=20.87 E-value=1.3e+02 Score=20.27 Aligned_cols=40 Identities=13% Similarity=0.071 Sum_probs=32.1
Q ss_pred CcEEEEeccCCCHHHHHHHHHcCCccccccchHHHHhhcC
Q psy2327 27 RPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGH 66 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a~~~G~~~fGENrvQEl~~K~~ 66 (97)
.|+++.|++|-+..++.+........+|.+-+.+..+-+.
T Consensus 50 ~v~V~~i~~Y~sF~~ll~~e~~~~~~~~~~s~ee~~~~~~ 89 (109)
T cd06555 50 LVKVVDIRKYDSFRELLEEEGLEKVGPGVDSIEEGVKDTY 89 (109)
T ss_pred EEEEEEEEecCCHHHHHHhcCHhhcCCCCCcHHHHHHHHH
Confidence 4788899999999999999887777777777777666553
No 59
>PRK12465 xylose isomerase; Provisional
Probab=20.71 E-value=1.5e+02 Score=25.02 Aligned_cols=49 Identities=20% Similarity=0.123 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCcEEEEeccCCC---------------------HHHHHHHHHcCCccccccch
Q psy2327 3 AAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKP---------------------KELIIEAYNGGQRHFGENYV 58 (97)
Q Consensus 3 ~nl~~I~~rI~~a~~~~~r~~~~~~V~LiAVSK~~~---------------------~e~I~~a~~~G~~~fGENrv 58 (97)
.||+.|.+.+.+..+.. .|+|+-||=+.= ...++.+++++...=|||+|
T Consensus 125 ~nld~iv~~~k~~~~~t-------Gikllw~TaNlFs~prf~~GA~TnPD~~Vra~A~~qvk~alD~~~eLGgenyV 194 (445)
T PRK12465 125 SNLKHMVGIAKQRQADT-------GIKLLWGTANLFSHPRYMNGASTNPDFNVVARAAVQVKAAIDATVELGGENYV 194 (445)
T ss_pred HHHHHHHHHHHHHhhhh-------CceeeeeccccccCccccCCcCCCCCHHHHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 47888888888887764 577887664422 56677778887777788875
No 60
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=20.71 E-value=21 Score=25.73 Aligned_cols=21 Identities=43% Similarity=0.495 Sum_probs=18.8
Q ss_pred cEEEEeccCC---CHHHHHHHHHc
Q psy2327 28 PRLVAVSKTK---PKELIIEAYNG 48 (97)
Q Consensus 28 V~LiAVSK~~---~~e~I~~a~~~ 48 (97)
.+|.-|||.+ +-++|+.||+.
T Consensus 62 ~rL~eVS~~f~~ysE~dik~AYe~ 85 (159)
T PF05384_consen 62 QRLAEVSRNFDRYSEEDIKEAYEE 85 (159)
T ss_pred HHHHHHHhhhcccCHHHHHHHHHH
Confidence 5899999999 79999999974
No 61
>PF14658 EF-hand_9: EF-hand domain
Probab=20.62 E-value=88 Score=19.46 Aligned_cols=32 Identities=19% Similarity=0.142 Sum_probs=24.4
Q ss_pred ccCCCHHHHHHHHH-cCCccccccchHHHHhhc
Q psy2327 34 SKTKPKELIIEAYN-GGQRHFGENYVQELLEKG 65 (97)
Q Consensus 34 SK~~~~e~I~~a~~-~G~~~fGENrvQEl~~K~ 65 (97)
|..+++..|...++ +|.+..=|+++|++..-+
T Consensus 12 tG~V~v~~l~~~Lra~~~~~p~e~~Lq~l~~el 44 (66)
T PF14658_consen 12 TGRVPVSDLITYLRAVTGRSPEESELQDLINEL 44 (66)
T ss_pred CceEeHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Confidence 34566677777776 588889999999998765
No 62
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=20.51 E-value=1.4e+02 Score=20.79 Aligned_cols=27 Identities=0% Similarity=0.063 Sum_probs=22.8
Q ss_pred CcEEEEeccCCCHHHHHHHHHcCCccc
Q psy2327 27 RPRLVAVSKTKPKELIIEAYNGGQRHF 53 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a~~~G~~~f 53 (97)
.+.+|.+|=+-+.+.+..++++|+..|
T Consensus 80 ~~~iIvls~~~~~~~~~~a~~~Ga~~y 106 (216)
T PRK10840 80 SLSIIVLTMNNNPAILSAVLDLDIEGI 106 (216)
T ss_pred CCcEEEEEecCCHHHHHHHHHCCCeEE
Confidence 468899998888899999999998755
No 63
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=20.39 E-value=1.6e+02 Score=19.68 Aligned_cols=27 Identities=4% Similarity=0.150 Sum_probs=22.9
Q ss_pred CcEEEEeccCCCHHHHHHHHHcCCccc
Q psy2327 27 RPRLVAVSKTKPKELIIEAYNGGQRHF 53 (97)
Q Consensus 27 ~V~LiAVSK~~~~e~I~~a~~~G~~~f 53 (97)
.+.+|.+|-..+.+.+..++++|...|
T Consensus 70 ~~~iivls~~~~~~~~~~~~~~Ga~~~ 96 (218)
T TIGR01387 70 QTPVLFLTARDSVADKVKGLDLGADDY 96 (218)
T ss_pred CCcEEEEEcCCCHHHHHHHHHcCCCeE
Confidence 467888999999999999999998654
No 64
>PF13653 GDPD_2: Glycerophosphoryl diester phosphodiesterase family; PDB: 3RLG_A 2F9R_B 1XX1_A 3RLH_A.
Probab=20.37 E-value=1e+02 Score=16.17 Aligned_cols=20 Identities=15% Similarity=0.041 Sum_probs=14.8
Q ss_pred HHHHHHHHHcCCccccccch
Q psy2327 39 KELIIEAYNGGQRHFGENYV 58 (97)
Q Consensus 39 ~e~I~~a~~~G~~~fGENrv 58 (97)
.+.++.++++|+..+.-|++
T Consensus 10 ~~~~~~~l~~GVDgI~Td~p 29 (30)
T PF13653_consen 10 PASWRELLDLGVDGIMTDYP 29 (30)
T ss_dssp HHHHHHHHHHT-SEEEES-H
T ss_pred HHHHHHHHHcCCCEeeCCCC
Confidence 56789999999988877664
No 65
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=20.23 E-value=69 Score=17.92 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=17.3
Q ss_pred EEEEeccCCCHHHHHHHHHc
Q psy2327 29 RLVAVSKTKPKELIIEAYNG 48 (97)
Q Consensus 29 ~LiAVSK~~~~e~I~~a~~~ 48 (97)
.|+.|+...+.++|+.+|..
T Consensus 5 ~vLgl~~~~~~~~ik~ay~~ 24 (60)
T smart00271 5 EILGVPRDASLDEIKKAYRK 24 (60)
T ss_pred HHcCCCCCCCHHHHHHHHHH
Confidence 57889999999999999863
Done!