Query 045992
Match_columns 213
No_of_seqs 238 out of 1045
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:36:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045992hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0622 Ornithine decarboxylas 100.0 1.4E-39 3E-44 302.8 13.4 72 120-195 363-434 (448)
2 cd06831 PLPDE_III_ODC_like_AZI 99.9 1.8E-27 4E-32 219.7 13.5 68 122-193 323-390 (394)
3 cd06840 PLPDE_III_Bif_AspK_Dap 99.9 5.2E-24 1.1E-28 194.2 12.7 59 122-181 310-368 (368)
4 cd06829 PLPDE_III_CANSDC Type 99.9 5.2E-24 1.1E-28 192.3 11.1 61 121-182 286-346 (346)
5 cd06836 PLPDE_III_ODC_DapDC_li 99.9 3.7E-22 8.1E-27 182.4 11.9 60 122-182 319-378 (379)
6 TIGR01047 nspC carboxynorsperm 99.9 3.5E-21 7.7E-26 176.7 13.7 73 121-204 300-372 (380)
7 PRK08961 bifunctional aspartat 99.9 2.2E-21 4.8E-26 194.3 12.4 61 121-182 800-860 (861)
8 TIGR03099 dCO2ase_PEP1 pyridox 99.9 4.5E-21 9.8E-26 174.9 12.8 60 122-181 339-398 (398)
9 cd06843 PLPDE_III_PvsE_like Ty 99.9 3.9E-21 8.3E-26 174.5 11.6 60 122-181 318-377 (377)
10 TIGR01048 lysA diaminopimelate 99.8 6.3E-21 1.4E-25 174.7 12.7 61 121-182 336-396 (417)
11 cd06828 PLPDE_III_DapDC Type I 99.8 3.7E-21 8.1E-26 172.7 9.9 60 121-181 314-373 (373)
12 COG0019 LysA Diaminopimelate d 99.8 7.3E-21 1.6E-25 177.0 11.7 60 121-181 334-394 (394)
13 PLN02537 diaminopimelate decar 99.8 1.3E-20 2.9E-25 173.2 12.7 61 121-182 326-386 (410)
14 cd06839 PLPDE_III_Btrk_like Ty 99.8 2.1E-20 4.5E-25 168.6 12.8 61 121-181 322-382 (382)
15 cd00622 PLPDE_III_ODC Type III 99.8 1.3E-19 2.9E-24 162.9 14.1 59 121-180 302-361 (362)
16 cd06810 PLPDE_III_ODC_DapDC_li 99.8 1.1E-19 2.3E-24 163.0 12.6 60 121-181 309-368 (368)
17 PRK11165 diaminopimelate decar 99.8 7.9E-19 1.7E-23 163.1 13.9 60 122-182 332-398 (420)
18 cd06830 PLPDE_III_ADC Type III 99.8 3E-19 6.5E-24 165.2 9.9 60 121-181 339-409 (409)
19 PF00278 Orn_DAP_Arg_deC: Pyri 99.8 1.9E-19 4.1E-24 137.8 5.5 63 118-181 53-116 (116)
20 cd06841 PLPDE_III_MccE_like Ty 99.8 1.9E-18 4.1E-23 157.0 11.8 60 121-182 317-376 (379)
21 cd06842 PLPDE_III_Y4yA_like Ty 99.5 1.6E-14 3.4E-19 134.4 2.8 61 121-181 361-423 (423)
22 PF02784 Orn_Arg_deC_N: Pyrido 97.6 5.9E-05 1.3E-09 65.2 3.9 47 56-102 1-117 (251)
23 cd06842 PLPDE_III_Y4yA_like Ty 97.3 0.00027 5.8E-09 66.3 4.6 34 48-81 8-46 (423)
24 PRK05354 arginine decarboxylas 96.7 0.0045 9.8E-08 61.8 7.1 51 29-81 45-106 (634)
25 TIGR01273 speA arginine decarb 95.6 0.027 5.9E-07 56.2 6.6 50 30-81 39-99 (624)
26 PRK05354 arginine decarboxylas 83.4 2.1 4.6E-05 43.1 5.4 67 117-184 488-565 (634)
27 cd06812 PLPDE_III_DSD_D-TA_lik 81.0 1.9 4.1E-05 39.3 3.8 34 48-81 4-40 (374)
28 cd06813 PLPDE_III_DSD_D-TA_lik 80.7 3.4 7.4E-05 38.5 5.5 35 47-81 8-43 (388)
29 cd06808 PLPDE_III Type III Pyr 77.1 1.9 4E-05 35.4 2.3 21 61-81 2-24 (211)
30 cd00430 PLPDE_III_AR Type III 76.8 5.1 0.00011 36.4 5.3 31 51-81 2-34 (367)
31 cd00430 PLPDE_III_AR Type III 75.2 2.3 5E-05 38.7 2.6 35 122-158 297-332 (367)
32 PLN02439 arginine decarboxylas 67.4 10 0.00022 37.8 5.2 67 117-184 415-491 (559)
33 cd06819 PLPDE_III_LS_D-TA Type 66.1 5.6 0.00012 36.0 3.0 34 48-81 5-41 (358)
34 cd06811 PLPDE_III_yhfX_like Ty 65.2 9.5 0.00021 35.6 4.4 36 46-81 24-62 (382)
35 TIGR00492 alr alanine racemase 63.0 16 0.00034 33.5 5.3 32 50-81 2-35 (367)
36 cd06826 PLPDE_III_AR2 Type III 57.7 21 0.00046 32.9 5.2 31 51-81 2-34 (365)
37 cd06820 PLPDE_III_LS_D-TA_like 56.6 11 0.00024 34.1 3.1 33 49-81 2-37 (353)
38 PRK13340 alanine racemase; Rev 56.5 20 0.00044 33.5 4.9 32 50-81 40-73 (406)
39 TIGR01273 speA arginine decarb 54.1 28 0.0006 35.2 5.7 67 117-184 481-558 (624)
40 PRK00053 alr alanine racemase; 53.9 25 0.00055 32.1 5.0 32 50-81 3-36 (363)
41 COG4078 Predicted membrane pro 53.5 3.9 8.5E-05 35.8 -0.3 13 71-83 178-190 (221)
42 cd06821 PLPDE_III_D-TA Type II 53.4 15 0.00032 33.4 3.4 35 47-81 6-42 (361)
43 cd06827 PLPDE_III_AR_proteobac 43.9 47 0.001 30.7 5.1 31 51-81 2-33 (354)
44 cd06818 PLPDE_III_cryptic_DSD 42.5 30 0.00064 32.1 3.7 33 49-81 2-37 (382)
45 PRK00364 groES co-chaperonin G 35.8 1.3E+02 0.0029 22.9 5.7 65 93-161 8-73 (95)
46 cd00320 cpn10 Chaperonin 10 Kd 35.5 2E+02 0.0043 21.9 6.8 62 94-159 8-70 (93)
47 PRK14533 groES co-chaperonin G 34.8 1.4E+02 0.003 22.9 5.7 60 93-161 8-68 (91)
48 KOG3638 Sonic hedgehog and rel 33.6 46 0.00099 31.9 3.5 55 129-185 206-265 (414)
49 PF01455 HupF_HypC: HupF/HypC 32.9 29 0.00062 25.2 1.6 16 142-157 33-48 (68)
50 TIGR00074 hypC_hupF hydrogenas 29.5 37 0.0008 25.4 1.7 15 143-157 32-46 (76)
51 PF10125 NADHdeh_related: NADH 28.3 18 0.00039 32.1 -0.2 25 72-100 178-202 (219)
52 PF11213 DUF3006: Protein of u 28.0 45 0.00099 24.0 1.9 20 143-162 29-49 (71)
53 PF01729 QRPTase_C: Quinolinat 27.2 34 0.00074 28.8 1.3 36 66-101 22-89 (169)
54 PF06183 DinI: DinI-like famil 26.4 77 0.0017 22.9 2.9 24 78-101 8-32 (65)
55 PRK10597 DNA damage-inducible 24.1 62 0.0013 24.6 2.1 25 78-102 20-47 (81)
56 TIGR02683 upstrm_HI1419 probab 22.5 70 0.0015 23.9 2.1 10 196-205 69-78 (95)
57 PF02559 CarD_CdnL_TRCF: CarD- 22.3 50 0.0011 24.6 1.3 18 146-163 1-18 (98)
58 PRK10413 hydrogenase 2 accesso 22.0 58 0.0013 24.7 1.6 13 145-157 41-53 (82)
59 COG4067 Uncharacterized protei 21.9 1.2E+02 0.0025 26.1 3.5 69 130-199 16-92 (162)
60 PF12024 DUF3512: Domain of un 21.2 1.8E+02 0.0038 26.5 4.7 86 84-173 44-134 (245)
61 PF01870 Hjc: Archaeal hollida 20.6 90 0.002 23.8 2.4 32 48-81 45-76 (88)
62 PF11948 DUF3465: Protein of u 20.5 2.9E+02 0.0063 22.9 5.5 52 93-156 42-95 (131)
No 1
>KOG0622 consensus Ornithine decarboxylase [Amino acid transport and metabolism]
Probab=100.00 E-value=1.4e-39 Score=302.80 Aligned_cols=72 Identities=25% Similarity=0.402 Sum_probs=63.5
Q ss_pred CceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEEEEecccccccccC
Q 045992 120 QTTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFSVRIQAHTACEYEN 195 (213)
Q Consensus 120 ~~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~~~~~~~~~~~~ 195 (213)
++.+.++|||||||+.|++++++.||+|++||||+|+||||||++++| .||+.+.|.+.++.- .|.|.+++-
T Consensus 363 e~~~~ssIwGPtcD~lD~i~~~~~lp~l~vGdwLvf~~mGAYT~~~aS-~fNgf~~p~~~y~~s---~~~~e~~r~ 434 (448)
T KOG0622|consen 363 EPLYKSSIWGPTCDGLDVIAEDCLLPQLNVGDWLVFENMGAYTMSAAS-TFNGFQRPKIYYVMS---DGDWEKIRD 434 (448)
T ss_pred cceeeeeeecCCcchHHHHHhhccCCCCCccCeEEEccCCcccccccc-ccCCCCCCceEEEec---cccHHHhhc
Confidence 358999999999999999999999999999999999999999999997 999999999776653 456665543
No 2
>cd06831 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor. Antizyme inhibitor (AZI) is homologous to the fold type III PLP-dependent enzyme ODC but does not retain any decarboxylase activity. Like ODC, AZI is presumed to exist as a homodimer. Antizyme is a regulatory protein that binds directly to the ODC monomer to block its active site, leading to its degradation by the 26S proteasome. AZI binds to Antizyme with a higher affinity than ODC, preventing the formation of the Antizyme-ODC complex. Thus, AZI blocks the ability of Antizyme to promote ODC degradation, which leads to increased ODC enzymatic activity and polyamine levels. AZI also prevents the degradation of other proteins regulated by Antizyme, such as cyclin D1.
Probab=99.95 E-value=1.8e-27 Score=219.67 Aligned_cols=68 Identities=24% Similarity=0.445 Sum_probs=59.6
Q ss_pred eeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEEEEecccccccc
Q 045992 122 TYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFSVRIQAHTACEY 193 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~~~~~~~~~~ 193 (213)
..+++||||+|||.|++.+++.||++++||||+|.+|||||.+|++ +||+|++|+|+++.= .-+|.+.
T Consensus 323 ~~~~~v~Gp~C~s~D~l~~~~~Lp~l~~GD~l~i~~~GAY~~s~ss-~Fn~~~~p~~v~~~~---~~~~~~~ 390 (394)
T cd06831 323 LFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGAGSLHEPS-TFNDFQRPAIYYMMS---FSDWYEM 390 (394)
T ss_pred ceeEEEEeCCCCHHHeecccCcCCCCCCCCEEEECCCCCccccccc-CCCCCCCCcEEEEEC---cchhhhh
Confidence 4568999999999999999999999999999999999999999996 999999999776543 5555443
No 3
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=99.91 E-value=5.2e-24 Score=194.22 Aligned_cols=59 Identities=19% Similarity=0.242 Sum_probs=56.0
Q ss_pred eeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 122 TYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
..+++|+||+|++.|++.+++.||++++||||+|.|||||++++++ +||+||+|+|+++
T Consensus 310 ~~~~~v~Gp~C~~~D~l~~~~~lp~l~~GD~l~~~~~GAY~~~~~s-~fn~~~~~~~v~~ 368 (368)
T cd06840 310 AGNADVVGPICESGDVLGRDRLLPETEEGDVILIANAGAYGFCMAS-TYNLREPAEEVVL 368 (368)
T ss_pred cceEEEEeCCcCCCCEEeecccCCCCCCCCEEEEecCCcchHhhhh-hccCCCCCCEEeC
Confidence 4678999999999999999999999999999999999999999996 9999999999873
No 4
>cd06829 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which 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. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity.
Probab=99.90 E-value=5.2e-24 Score=192.32 Aligned_cols=61 Identities=20% Similarity=0.073 Sum_probs=54.0
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
+..+++|+||+|++.|++.+...+|++++||||+|.|+||||++|++ +||+|++|.|++++
T Consensus 286 ~~~~~~v~Gp~C~s~D~l~~~~~~~~l~~GD~l~~~~~GAY~~s~ss-~fn~~~~p~~v~~~ 346 (346)
T cd06829 286 GAHTYRLGGNSCLAGDVIGDYSFDEPLQVGDRLVFEDMAHYTMVKTN-TFNGVRLPSIAIRD 346 (346)
T ss_pred CceEEEEEcCCCCcccEEeecccCCCCCCCCEEEEeCchhhhhhhhc-cccCCCCCeEEecC
Confidence 35678999999999999987554447999999999999999999995 99999999998864
No 5
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to 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. 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. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=99.87 E-value=3.7e-22 Score=182.45 Aligned_cols=60 Identities=22% Similarity=0.220 Sum_probs=56.5
Q ss_pred eeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 122 TYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
..+++|+||+|++.|++.+++.||++++||||+|.+|||||.++|+ +||+|++|++++.+
T Consensus 319 ~~~~~v~G~~C~~~D~l~~~~~lp~l~~GD~l~~~~~GAY~~~~ss-~fn~~~~p~~~~~~ 378 (379)
T cd06836 319 EVVTDVAGPCCFAGDVLAKERALPPLEPGDYVAVHDTGAYYFSSHS-SYNSLPRPAVYGVR 378 (379)
T ss_pred ceEEEEEeCCCCCCCEEeecccCCCCCCCCEEEEeCCCcchHHHHH-hhhCCCCCeEEEec
Confidence 4589999999999999999999999999999999999999999996 99999999988764
No 6
>TIGR01047 nspC carboxynorspermidine decarboxylase. This protein is related to diaminopimelate decarboxylase. It is the last enzyme in norspermidine biosynthesis by an unusual pathway shown in Vibrio alginolyticus.
Probab=99.86 E-value=3.5e-21 Score=176.70 Aligned_cols=73 Identities=21% Similarity=0.104 Sum_probs=62.9
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEEEEecccccccccCcEEEe
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFSVRIQAHTACEYENEVILL 200 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~~~~~~~~~~~~~~~~~ 200 (213)
+..+++|+||+|++.|++.++..+|++++||||+|.|+||||++|++ +||+|++|+|++++ -.|++-++
T Consensus 300 ~~~~~~v~G~~C~s~D~l~~~~~lp~l~~GD~l~~~~~GAY~~smss-~fn~~~~p~~v~~~----------~~g~~~li 368 (380)
T TIGR01047 300 GQFSYVLGGCTCLAGDVMGEYAFDEPLKVGDKLVFLDMIHYTMVKNT-TFNGVKLPSLGCLR----------ANGEFQKI 368 (380)
T ss_pred CceeEEEEcCCCCcccEEeecccCCCCCCCCEEEEcCcCChhhhccC-CCCCCCCCcEEEEe----------cCCcEEEE
Confidence 34578999999999999999888999999999999999999999996 99999999999983 24555555
Q ss_pred ehhh
Q 045992 201 HGFA 204 (213)
Q Consensus 201 ~~~~ 204 (213)
-.|.
T Consensus 369 r~~~ 372 (380)
T TIGR01047 369 RTFG 372 (380)
T ss_pred EecC
Confidence 5554
No 7
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=99.86 E-value=2.2e-21 Score=194.32 Aligned_cols=61 Identities=15% Similarity=0.196 Sum_probs=57.4
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
+..+++|+||+|++.|++.+++.||++++||||+|.++||||.++++ +||+||+|+|++++
T Consensus 800 ~~~~~~v~Gp~C~~~D~l~~~~~lp~l~~GD~l~~~~~GAY~~~~ss-~fn~~p~p~ev~~~ 860 (861)
T PRK08961 800 AAGTADVVGPICESSDVLGKRRRLPATAEGDVILIANAGAYGYSMSS-TYNLREPAREVVLD 860 (861)
T ss_pred CceEEEEEcCCCCCCCEEEecccCCCCCCCCEEEEeCCCcchHHHhh-hhhCCCCCcEEEEc
Confidence 45678999999999999999999999999999999999999999996 99999999999874
No 8
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048
Probab=99.85 E-value=4.5e-21 Score=174.90 Aligned_cols=60 Identities=20% Similarity=0.198 Sum_probs=57.0
Q ss_pred eeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 122 TYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
..+++|+||+|++.|++.+++.||++++||||+|.++|||++++|+.+||+||+|.|+++
T Consensus 339 ~~~~~i~G~~C~~~D~~~~~~~lp~~~~GD~l~~~~~GAY~~~~s~~~fn~~~~~~~v~~ 398 (398)
T TIGR03099 339 REIASIVGPLCTPLDLLAEKGTLPVAEPGDLVVIFQSGAYGASASPLAFLGHPEAVELLV 398 (398)
T ss_pred ceEEEEEeCCCCCCCEEeecCcCCCCCCCCEEEEcCCCCcchhhChHhhhCCCCCCEEeC
Confidence 567899999999999999999999999999999999999999999789999999999873
No 9
>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=99.85 E-value=3.9e-21 Score=174.49 Aligned_cols=60 Identities=18% Similarity=0.210 Sum_probs=56.9
Q ss_pred eeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 122 TYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
..+++|+||+|++.|++.+++.||++++||||+|.++||||.+||+.+||+||+|+|+++
T Consensus 318 ~~~~~v~G~~C~~~D~l~~~~~lp~~~~GD~l~i~~~GAY~~~~s~~~fn~~~~p~~v~~ 377 (377)
T cd06843 318 DTPVTLVGQLCTPKDVLARDVPVDRLRAGDLVVFPLAGAYGWNISHHDFLMHPHPERIYL 377 (377)
T ss_pred ceEEEEEeCCCCCCCEEeeccccCCCCCCCEEEEcCCCccchhhchhhhhCCCCCCEEeC
Confidence 467899999999999999999999999999999999999999999889999999999873
No 10
>TIGR01048 lysA diaminopimelate decarboxylase. This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis.
Probab=99.85 E-value=6.3e-21 Score=174.67 Aligned_cols=61 Identities=23% Similarity=0.245 Sum_probs=57.6
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
+..+++|+||||++.|++.+++.||++++||||+|.++||||.++++ +||+||+|.|++++
T Consensus 336 ~~~~~~v~G~~C~~~D~l~~~~~lp~l~~GD~l~~~~~GAY~~~~~~-~fn~~~~p~~v~~~ 396 (417)
T TIGR01048 336 PTEVADVVGPLCESGDVLARDRELPEVEPGDLLAVFDAGAYGASMSS-NYNSRPRPAEVLVD 396 (417)
T ss_pred CceEEEEEeCCcCCCCEEeeccCCCCCCCCCEEEEeCCCcchHHHHH-HhhCCCCCeEEEEE
Confidence 45788999999999999999999999999999999999999999996 99999999999985
No 11
>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=99.85 E-value=3.7e-21 Score=172.67 Aligned_cols=60 Identities=25% Similarity=0.283 Sum_probs=56.4
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
..++++|+||||++.|++.++..||++++||||+|.++||||+++++ +||+||+|.|+++
T Consensus 314 ~~~~~~v~G~~C~~~D~l~~~~~lp~l~~GD~l~~~~~GAY~~~~~~-~f~~~~~p~~v~~ 373 (373)
T cd06828 314 ETEKVDVVGPICESGDVFAKDRELPEVEEGDLLAIHDAGAYGYSMSS-NYNSRPRPAEVLV 373 (373)
T ss_pred CceEEEEEeCCCCCCCEEeecccCCCCCCCCEEEEeCCCcchHHHHH-HhhCCCCCcEEeC
Confidence 45789999999999999999999999999999999999999999885 9999999999873
No 12
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]
Probab=99.84 E-value=7.3e-21 Score=177.03 Aligned_cols=60 Identities=27% Similarity=0.302 Sum_probs=55.6
Q ss_pred ceeeeeEEccCCCCCCccccccCCCC-CCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPE-LEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPe-l~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
+...++|+||+|+|.|++++++.||+ +++||||+|.++||||++|++ +||++++|+|+++
T Consensus 334 ~~~~~~v~G~~CesgD~~~~d~~lp~~~~~GD~l~i~~aGAY~~sm~s-~yN~~~~~~ev~v 394 (394)
T COG0019 334 EREEYDVVGPTCESGDVLARDRALPEPLKVGDLLVILDAGAYGASMSS-NYNGRPRPAEVLV 394 (394)
T ss_pred CeEEEEEECCCcCCCCeeeeeeeCCCCCCCCCEEEEcccchhhhhhhc-cccCCCCCceeeC
Confidence 45788999999999999999999997 559999999999999999997 9999999999874
No 13
>PLN02537 diaminopimelate decarboxylase
Probab=99.84 E-value=1.3e-20 Score=173.16 Aligned_cols=61 Identities=21% Similarity=0.220 Sum_probs=57.8
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
+..+++|+||+|++.|++.+++.||++++||||+|.|+||||.++++ +||+|++|+|++++
T Consensus 326 ~~~~~~v~G~~C~~~D~l~~~~~lp~~~~GD~l~~~~~GAY~~s~~s-~fn~~~~p~~v~~~ 386 (410)
T PLN02537 326 EVSTFDVVGPVCESADFLGKDRELPTPPKGAGLVVHDAGAYCMSMAS-TYNLKMRPPEYWVE 386 (410)
T ss_pred CceEEEEecCccCCCCEEEEcccCCCCCCCCEEEEeCCCcccHhhhH-HhcCCCCCeEEEEE
Confidence 45678999999999999999999999999999999999999999997 99999999999986
No 14
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins 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, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=99.84 E-value=2.1e-20 Score=168.62 Aligned_cols=61 Identities=25% Similarity=0.270 Sum_probs=57.5
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
+..+++|+||+|++.|++.++..||++++||||+|.+||||+++|++.+||+||+|+|+++
T Consensus 322 ~~~~~~v~G~~C~~~D~~~~~~~lp~l~~GD~l~~~~~GAY~~~~~~~~fn~~~~p~~~~~ 382 (382)
T cd06839 322 ERETVTVVGPLCTPLDLLGRNVELPPLEPGDLVAVLQSGAYGLSASPLAFLSHPAPAEVLV 382 (382)
T ss_pred CceEEEEEeCCCCCCCEEeecccCCCCCCCCEEEEecCCCcccccChhhHhCCCCCCEEeC
Confidence 4568899999999999999999999999999999999999999999889999999999874
No 15
>cd00622 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase. This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. 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. Also members of this su
Probab=99.82 E-value=1.3e-19 Score=162.85 Aligned_cols=59 Identities=29% Similarity=0.505 Sum_probs=55.5
Q ss_pred ceeeeeEEccCCCCCCccccccCCCC-CCCCCEEEEcCCCcccCCcCcccccCCCCcceEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPE-LEVNDWLVFPDKRANTLFVEPISMDLAMLPFELK 180 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPe-l~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~ 180 (213)
...+++|+||+|++.|++.+++.||+ +++||||+|.++|||+.++++ +||+|++|.|++
T Consensus 302 ~~~~~~v~G~~C~~~D~l~~~~~lp~~l~~GD~l~~~~~GAY~~~~~~-~fn~~~~p~~v~ 361 (362)
T cd00622 302 ELYPSSLWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGAYTTAYAS-TFNGFPPPKIVY 361 (362)
T ss_pred CeeeEEEEcCCCCcccEecccCcCcccCCCCCEEEEcCCCCccccccC-CCCCCCCCeeEe
Confidence 45678999999999999999999998 999999999999999999995 999999999986
No 16
>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=99.82 E-value=1.1e-19 Score=163.00 Aligned_cols=60 Identities=28% Similarity=0.321 Sum_probs=56.8
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
+..+++|+||||++.|++.++..||++++||||+|.++|||+.++++ +||+|++|.|+++
T Consensus 309 ~~~~~~i~G~~C~~~D~~~~~~~lp~l~~GD~l~~~~~GAY~~~~~~-~fn~~~~p~~v~~ 368 (368)
T cd06810 309 PLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSESS-NFNSHPRPAEYLV 368 (368)
T ss_pred CceeEEEECCCCCCCcEEeecccCCCCCCCCEEEEcCCCCCchhhcc-cccCCCCCcEEeC
Confidence 46789999999999999999999999999999999999999999997 9999999998864
No 17
>PRK11165 diaminopimelate decarboxylase; Provisional
Probab=99.79 E-value=7.9e-19 Score=163.08 Aligned_cols=60 Identities=27% Similarity=0.368 Sum_probs=55.9
Q ss_pred eeeeeEEccCCCCCCccccc-------cCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 122 TYKSTVFRPTCTAVGKVFAG-------HPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~-------~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
..+++|+||+|++.|++..+ +.||++++||||+|.++||||+++++ +||+||+|+|++++
T Consensus 332 ~~~~~v~Gp~C~~~D~l~~~~~~~~~~~~lP~l~~GD~l~i~~~GAY~~~~ss-~fn~~~~p~~v~~~ 398 (420)
T PRK11165 332 TVDTVVAGPLCESGDVFTQQEGGVVETRALPQVQVGDYLVFHDTGAYGASMSS-NYNSRPLLPEVLFD 398 (420)
T ss_pred ceEEEEEeCCCCCCCEEeeccCcccceeECCCCCCCCEEEEecCCCCcHHHHH-hhcCCCCCcEEEEE
Confidence 46899999999999999865 89999999999999999999999996 99999999999973
No 18
>cd06830 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase. This subfamily includes plants and biosynthetic prokaryotic arginine decarboxylases (ADC, EC 4.1.1.19). ADC is involved in the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. It catalyzes the decarboxylation of L-arginine to agmatine, which is then hydrolyzed to putrescine by agmatinase. ADC is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which 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. Homodimer formation and the presence of both PLP and Mg2+ cofactors may be required for catalytic activity. Prokaryotic ADCs (biodegradative), which are fold type I PLP-dependent enzymes, are not included in this family.
Probab=99.79 E-value=3e-19 Score=165.24 Aligned_cols=60 Identities=17% Similarity=0.030 Sum_probs=53.8
Q ss_pred ceeeeeEEccCCCCCCccccccCCC---------C--CCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLP---------E--LEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LP---------e--l~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
+..+++||||+|||.|++++++.+| + +++||||+|.++||||.+||+ +||+|++|+|+++
T Consensus 339 ~~~~~~v~Gp~C~s~D~~~~~~~l~~~~~~~~lp~~~~~~GD~l~~~~~GAY~~s~ss-~fn~~~~p~~v~v 409 (409)
T cd06830 339 PTRRAVLGDITCDSDGKIDSFIDPPDILPTLPLHPLRKDEPYYLGFFLVGAYQEILGD-LHNLFGDTNAVHV 409 (409)
T ss_pred CceeEEEeccCcCCCCEEeeecccccccccccCCCCCCCCCCEEEEEeccHhhHHHHh-cccCCCCCCEEeC
Confidence 3467899999999999999998854 3 479999999999999999996 9999999999874
No 19
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=99.78 E-value=1.9e-19 Score=137.80 Aligned_cols=63 Identities=33% Similarity=0.545 Sum_probs=56.1
Q ss_pred CCCceeeeeEEccCCCCCCccccccCCC-CCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 118 NNQTTYKSTVFRPTCTAVGKVFAGHPLP-ELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 118 ~~~~~~~ssI~GPtCds~D~i~~~~~LP-el~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
++.+..+++||||||++.|++.+++.|| ++++||||+|+|||||+.++++ +||+++.|.++++
T Consensus 53 ~~~~~~~~~i~GptC~~~D~i~~~~~lP~~l~~GD~l~f~~~GAYt~~~~~-~Fn~~~~p~~v~v 116 (116)
T PF00278_consen 53 DEEPCYPSTIWGPTCDSGDVIARDVMLPKELEVGDWLVFENMGAYTISLSS-NFNGFPRPAEVYV 116 (116)
T ss_dssp TTSTEEEEEEEESSSSTTSEEEEEEEEESTTTTT-EEEESS-SSSSGGGSB-CGGGT-SCEEEEE
T ss_pred cccCcEEEEEEECCcCCCceEeeeccCCCCCCCCCEEEEecCcccchhhCc-cccCCCCCCEEEC
Confidence 3457899999999999999999999999 9999999999999999999998 9999999998874
No 20
>cd06841 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that 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. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus.
Probab=99.77 E-value=1.9e-18 Score=157.02 Aligned_cols=60 Identities=22% Similarity=0.318 Sum_probs=55.8
Q ss_pred ceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFS 182 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~ 182 (213)
...+++|+||+|++.|++.+++.||++++||||+|.++||||+++|+ +| +|++|+|++++
T Consensus 317 ~~~~~~v~G~~C~~~D~~~~~~~lp~l~~GD~l~~~~~GAY~~~~s~-~f-~~~~p~~v~~~ 376 (379)
T cd06841 317 TSKNYDVYGFNCMESDVLFPNVPLPPLNVGDILAIRNVGAYNMTQSN-QF-IRPRPAVYLID 376 (379)
T ss_pred CcceEEEECCCcCCCCEEeeCCcCCCCCCCCEEEEeCCCCCChhhCc-cc-cCCCCcEEEEe
Confidence 35678999999999999999999999999999999999999999996 99 89999999873
No 21
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA. This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are 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. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases.
Probab=99.47 E-value=1.6e-14 Score=134.45 Aligned_cols=61 Identities=16% Similarity=0.233 Sum_probs=54.7
Q ss_pred ceeeeeEEccCCCCCCcccc-ccCCC-CCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEE
Q 045992 121 TTYKSTVFRPTCTAVGKVFA-GHPLP-ELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKF 181 (213)
Q Consensus 121 ~~~~ssI~GPtCds~D~i~~-~~~LP-el~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~ 181 (213)
...+++|+||+|++.|++++ +..|| ++++||+|+|.++||||+++++.+||+||+|+|+++
T Consensus 361 ~~~~~~v~Gp~C~~~D~l~~~~~~lp~~~~~GD~l~~~~~GAY~~~~~~~~fn~~~~p~ev~~ 423 (423)
T cd06842 361 APIEAYLAGASCLESDLITRRKIPFPRLPKPGDLLVFPNTAGYQMDFLESRFHRHPLPRRVVV 423 (423)
T ss_pred CCceEEEeCccccchhhhhhhhccCCCCCCCCCEEEEecchHHHHHhhhhhhcCCCCCccccC
Confidence 34678999999999999994 67899 699999999999999999877679999999999863
No 22
>PF02784 Orn_Arg_deC_N: Pyridoxal-dependent decarboxylase, pyridoxal binding domain; InterPro: IPR022644 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region [].; GO: 0003824 catalytic activity; PDB: 2OO0_A 2ON3_A 1D7K_B 3VAB_A 2J66_A 3C5Q_A 2QGH_A 1TWI_B 1TUF_A 3N2O_A ....
Probab=97.60 E-value=5.9e-05 Score=65.17 Aligned_cols=47 Identities=26% Similarity=0.457 Sum_probs=42.5
Q ss_pred ehHHHHHHhh--hhhcCCC-ccceeeccc---------------------------------------------------
Q 045992 56 DLGHHFSLLS--LISNLPM-VHPYYAVKG--------------------------------------------------- 81 (213)
Q Consensus 56 DL~~V~~~~~--W~~~LPr-V~PfYAVKC--------------------------------------------------- 81 (213)
|++.++++.+ |++.+|. +++||||||
T Consensus 1 d~~~~~~~~~~~~~~~~~~~~~i~yA~KaN~~~~vl~~l~~~g~g~dv~S~~El~~a~~~g~~~~~Ii~~gp~k~~~~l~ 80 (251)
T PF02784_consen 1 DLDRIIERIRAAWKAFLPYNVKIFYAVKANPNPAVLKILAEEGCGFDVASPGELELALKAGFPPDRIIFTGPGKSDEELE 80 (251)
T ss_dssp EHHHHHHHHHHHHHHHTTT-EEEEEEGGGS--HHHHHHHHHTTCEEEESSHHHHHHHHHTTTTGGGEEEECSS--HHHHH
T ss_pred ChHHHHHHHHHHHHhcCCCCcEEEEEECcCCCHHHHHHHHHcCCceEEecccchHHHHhhhccccceeEecCcccHHHHH
Confidence 7887777776 9999998 999999999
Q ss_pred ----------------hhhHHHhhCCCCeEEEEEecC
Q 045992 82 ----------------KLDKIRMWHSKCELSIRIKSP 102 (213)
Q Consensus 82 ----------------EL~KI~~~~P~a~LlLRI~~d 102 (213)
||.+|.+..++.+++|||..+
T Consensus 81 ~a~~~~~~~i~vDs~~el~~l~~~~~~~~v~lRin~~ 117 (251)
T PF02784_consen 81 EAIENGVATINVDSLEELERLAELAPEARVGLRINPG 117 (251)
T ss_dssp HHHHHTESEEEESSHHHHHHHHHHHCTHEEEEEBE-S
T ss_pred HHHhCCceEEEeCCHHHHHHHhccCCCceeeEEEeec
Confidence 999999999999999999987
No 23
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA. This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are 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. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases.
Probab=97.30 E-value=0.00027 Score=66.26 Aligned_cols=34 Identities=21% Similarity=0.114 Sum_probs=31.1
Q ss_pred CCCcEEEeehHHHHHHhh-hhhcCC----Cccceeeccc
Q 045992 48 LDETFYVLDLGHHFSLLS-LISNLP----MVHPYYAVKG 81 (213)
Q Consensus 48 ~~~pF~V~DL~~V~~~~~-W~~~LP----rV~PfYAVKC 81 (213)
-..||||.|++.|.+.++ .++.+| +++|||||||
T Consensus 8 ~~TP~~v~d~~~l~~N~~~l~~~~~~~~~~~~~~yavKa 46 (423)
T cd06842 8 YGSPLNVLFPQTFRENIAALRAVLDRHGVDGRVYFARKA 46 (423)
T ss_pred hCCCEEEEcHHHHHHHHHHHHHHHHHhCCCeEEEEEecc
Confidence 358999999999999999 999886 6899999999
No 24
>PRK05354 arginine decarboxylase; Provisional
Probab=96.67 E-value=0.0045 Score=61.80 Aligned_cols=51 Identities=12% Similarity=0.015 Sum_probs=43.5
Q ss_pred cCcccHHHHHHHHhhhcCCCCCcEEEeehHHHHHHhh-hhhcCC----------Cccceeeccc
Q 045992 29 TTEDGFVEFMKSTVLKRQELDETFYVLDLGHHFSLLS-LISNLP----------MVHPYYAVKG 81 (213)
Q Consensus 29 ~~~~~~~~~I~~ii~~~~~~~~pF~V~DL~~V~~~~~-W~~~LP----------rV~PfYAVKC 81 (213)
..+.++.++++++... +-..||||.|.+.|.++++ |+++|| +.+++|||||
T Consensus 45 ~~~i~L~~l~~~~~~~--~~gtPlyV~~~~~L~~ri~~L~~aF~~a~~~~~y~g~~~~~YAiKa 106 (634)
T PRK05354 45 GASIDLAELVKELRER--GLRLPLLLRFPDILQDRVRSLNAAFKKAIEEYGYQGDYRGVYPIKV 106 (634)
T ss_pred CCCcCHHHHHHHhhcc--CCCCCEEEEcHHHHHHHHHHHHHHHHHHHHhhccCCCceEEEEecc
Confidence 3457788888887653 6789999999999999999 999998 4589999999
No 25
>TIGR01273 speA arginine decarboxylase, biosynthetic. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not similar in sequence.
Probab=95.64 E-value=0.027 Score=56.24 Aligned_cols=50 Identities=12% Similarity=0.069 Sum_probs=43.5
Q ss_pred CcccHHHHHHHHhhhcCCCCCcEEEeehHHHHHHhh-hhhcCC----------Cccceeeccc
Q 045992 30 TEDGFVEFMKSTVLKRQELDETFYVLDLGHHFSLLS-LISNLP----------MVHPYYAVKG 81 (213)
Q Consensus 30 ~~~~~~~~I~~ii~~~~~~~~pF~V~DL~~V~~~~~-W~~~LP----------rV~PfYAVKC 81 (213)
.+-++.++|+++... +-..||||.|.+.|.++++ ++++|| +.+++|||||
T Consensus 39 ~~i~l~~~v~~~~~~--g~~tPl~V~d~~iL~~~i~~l~~aF~~a~~~~~Y~g~~~~~YavKa 99 (624)
T TIGR01273 39 QSIDLLELVDQVRAR--GLQLPLLVRFPDILQHRIRSLNDAFANAIEEYQYAGHYQGVYPIKV 99 (624)
T ss_pred CCcCHHHHHHHHHhc--CCCCCEEEEcHHHHHHHHHHHHHHHHHHHHhhccCCCeeEEEEecc
Confidence 457889999888664 6779999999999999999 999997 4689999999
No 26
>PRK05354 arginine decarboxylase; Provisional
Probab=83.42 E-value=2.1 Score=43.15 Aligned_cols=67 Identities=21% Similarity=0.202 Sum_probs=53.1
Q ss_pred CCCCceeeeeEEccCCCCCCcccc---------ccCCCCCCCCC--EEEEcCCCcccCCcCcccccCCCCcceEEEEEE
Q 045992 117 SNNQTTYKSTVFRPTCTAVGKVFA---------GHPLPELEVND--WLVFPDKRANTLFVEPISMDLAMLPFELKFSVR 184 (213)
Q Consensus 117 ~~~~~~~~ssI~GPtCds~D~i~~---------~~~LPel~vGD--wLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~ 184 (213)
.++.+....+|+.-||||.+.|.+ ..+||+++.|+ +|-|-.+|||==.++. .=|..+.|-++-+++.
T Consensus 488 l~e~p~~~~~l~DiTCDSDg~i~~fi~~~~~~~~l~lh~~~~~e~y~lg~FlvGAYQe~lg~-~HNLfg~~~~v~v~~~ 565 (634)
T PRK05354 488 LDEEPTRRAVLADITCDSDGKIDQFIDGQGIKTTLPLHELDPGEPYYLGFFLVGAYQEILGD-MHNLFGDTNAVHVRVD 565 (634)
T ss_pred cCCCcceeeEEecccccCCCchhcccCCcCCcCceeCCccCCCCccEEEEEecchhhHhhcc-ccccCCCCCEEEEEEC
Confidence 444678889999999999997765 35677888887 8889999999988886 5677777877766553
No 27
>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=81.00 E-value=1.9 Score=39.33 Aligned_cols=34 Identities=26% Similarity=0.220 Sum_probs=30.9
Q ss_pred CCCcEEEeehHHHHHHhh-hhhcCC--Cccceeeccc
Q 045992 48 LDETFYVLDLGHHFSLLS-LISNLP--MVHPYYAVKG 81 (213)
Q Consensus 48 ~~~pF~V~DL~~V~~~~~-W~~~LP--rV~PfYAVKC 81 (213)
...|++++|++.+.+.++ .++.++ +++-+|+||+
T Consensus 4 ~~tP~~vid~~~l~~Ni~~~~~~~~~~~~~l~~~vKa 40 (374)
T cd06812 4 LDTPFLLLDEARMDRNIARLRQRLSRLGVRLRPHLKT 40 (374)
T ss_pred CCCceEEEeHHHHHHHHHHHHHHHHHcCCceeeEecc
Confidence 468999999999999999 888887 6889999999
No 28
>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=80.73 E-value=3.4 Score=38.46 Aligned_cols=35 Identities=23% Similarity=0.115 Sum_probs=31.9
Q ss_pred CCCCcEEEeehHHHHHHhh-hhhcCCCccceeeccc
Q 045992 47 ELDETFYVLDLGHHFSLLS-LISNLPMVHPYYAVKG 81 (213)
Q Consensus 47 ~~~~pF~V~DL~~V~~~~~-W~~~LPrV~PfYAVKC 81 (213)
+-+.|++++||+.+.+..+ -++.++.++.+|+||+
T Consensus 8 ~~~tP~~viDldal~~N~~~l~~~~~~~~ir~~vKa 43 (388)
T cd06813 8 GLDAPFAFVDLDALDANAADLVRRAGGKPIRVASKS 43 (388)
T ss_pred cCCCCEEEEEHHHHHHHHHHHHHHcCCCcEEEEecc
Confidence 4579999999999999999 8888898999999998
No 29
>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=77.10 E-value=1.9 Score=35.37 Aligned_cols=21 Identities=19% Similarity=0.135 Sum_probs=18.5
Q ss_pred HHHhh-hhhcCC-Cccceeeccc
Q 045992 61 FSLLS-LISNLP-MVHPYYAVKG 81 (213)
Q Consensus 61 ~~~~~-W~~~LP-rV~PfYAVKC 81 (213)
.+.++ |++.+| .++++|+||+
T Consensus 2 ~~N~~~i~~~~~~~~~i~~~vKa 24 (211)
T cd06808 2 RHNYRRLREAAPAGITLFAVVKA 24 (211)
T ss_pred hHHHHHHHHhCCCCCEEEEEEec
Confidence 45677 999999 8999999999
No 30
>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=76.83 E-value=5.1 Score=36.44 Aligned_cols=31 Identities=23% Similarity=0.080 Sum_probs=28.3
Q ss_pred cEEEeehHHHHHHhh-hhhcCC-Cccceeeccc
Q 045992 51 TFYVLDLGHHFSLLS-LISNLP-MVHPYYAVKG 81 (213)
Q Consensus 51 pF~V~DL~~V~~~~~-W~~~LP-rV~PfYAVKC 81 (213)
+..++|++.|.+.++ -++.+| .++.+|+||+
T Consensus 2 ~~l~Id~~~i~~N~~~l~~~~~~~~~l~~vvKa 34 (367)
T cd00430 2 TWAEIDLDALRHNLRVIRRLLGPGTKIMAVVKA 34 (367)
T ss_pred EEEEEEHHHHHHHHHHHHHhCCCCCEEEEEEee
Confidence 468899999999999 899998 7999999999
No 31
>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=75.24 E-value=2.3 Score=38.66 Aligned_cols=35 Identities=14% Similarity=0.404 Sum_probs=29.5
Q ss_pred eeeeeEEccCCCCCCcccccc-CCCCCCCCCEEEEcCC
Q 045992 122 TYKSTVFRPTCTAVGKVFAGH-PLPELEVNDWLVFPDK 158 (213)
Q Consensus 122 ~~~ssI~GPtCds~D~i~~~~-~LPel~vGDwLvf~n~ 158 (213)
...+.|.|+.| +|.+.-++ .+|++++||.+.|-..
T Consensus 297 ~~~~~ivG~v~--mD~~~vdv~~~~~~~~GD~v~l~g~ 332 (367)
T cd00430 297 GKRAPIVGRVC--MDQTMVDVTDIPDVKVGDEVVLFGR 332 (367)
T ss_pred CEEcceeceee--ccEEEEECCCCCCCCCCCEEEEEcC
Confidence 46788999999 89999887 6889999999977654
No 32
>PLN02439 arginine decarboxylase
Probab=67.40 E-value=10 Score=37.84 Aligned_cols=67 Identities=22% Similarity=0.156 Sum_probs=48.9
Q ss_pred CCCCceeeeeEEccCCCCCCccccc------cCCCCCCC--CC--EEEEcCCCcccCCcCcccccCCCCcceEEEEEE
Q 045992 117 SNNQTTYKSTVFRPTCTAVGKVFAG------HPLPELEV--ND--WLVFPDKRANTLFVEPISMDLAMLPFELKFSVR 184 (213)
Q Consensus 117 ~~~~~~~~ssI~GPtCds~D~i~~~------~~LPel~v--GD--wLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~ 184 (213)
.++.+....+|++=||||.+.+.+- .+|++++. |+ +|-|-.+|||==.++. .=|..+.|-++-++..
T Consensus 415 l~e~p~~~~~l~diTCDsDg~i~~~~~~~~~lplh~~~~~~~e~y~lg~Fl~GAYQe~lg~-~HnLfg~~~~v~v~~~ 491 (559)
T PLN02439 415 LDERPTVRGILSDLTCDSDGKIDKFIGGEGSLPLHELEKNGGGPYYLGMFLGGAYQEALGS-LHNLFGGPSVVRVSQS 491 (559)
T ss_pred cCCCcceeEEEeccccCCCCchhcccCCCCCCCCCCCCCCCCCCCEEEEEeccHhHHHhcc-ccccCCCCCEEEEEEc
Confidence 3446788999999999999997643 23335555 43 5668899999988886 4577777887776554
No 33
>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=66.15 E-value=5.6 Score=35.98 Aligned_cols=34 Identities=21% Similarity=0.075 Sum_probs=29.9
Q ss_pred CCCcEEEeehHHHHHHhh-hhhcCC--Cccceeeccc
Q 045992 48 LDETFYVLDLGHHFSLLS-LISNLP--MVHPYYAVKG 81 (213)
Q Consensus 48 ~~~pF~V~DL~~V~~~~~-W~~~LP--rV~PfYAVKC 81 (213)
-..|++++|++.+.+.++ .++.++ .++.+|++|+
T Consensus 5 ~~tP~~~id~~~l~~N~~~l~~~~~~~~~~l~~~~K~ 41 (358)
T cd06819 5 IDTPALVLDLDALERNIKRMAAFAKAHGVRLRPHAKT 41 (358)
T ss_pred cCCceEEEEHHHHHHHHHHHHHHHHHcCCcccccchh
Confidence 358999999999999999 888886 5778888998
No 34
>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=65.23 E-value=9.5 Score=35.62 Aligned_cols=36 Identities=19% Similarity=0.246 Sum_probs=32.0
Q ss_pred CCCCCcEEEeehHHHHHHhh-hhhcCC--Cccceeeccc
Q 045992 46 QELDETFYVLDLGHHFSLLS-LISNLP--MVHPYYAVKG 81 (213)
Q Consensus 46 ~~~~~pF~V~DL~~V~~~~~-W~~~LP--rV~PfYAVKC 81 (213)
+.-.-.+|++|++.|.+.++ -++.++ .++.+|+||+
T Consensus 24 g~~~~~~yvIDl~~I~~N~~~l~~~~~~~~~~l~~vvKA 62 (382)
T cd06811 24 GAIPPDTYVIDLDQIEENARLLAETAEKYGIELYFMTKQ 62 (382)
T ss_pred CCCCCCEEEecHHHHHHHHHHHHHHHhhCCCEEEEEEcc
Confidence 45578899999999999999 998887 6888999999
No 35
>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=63.02 E-value=16 Score=33.46 Aligned_cols=32 Identities=19% Similarity=0.085 Sum_probs=27.9
Q ss_pred CcEEEeehHHHHHHhh-hhhcCC-Cccceeeccc
Q 045992 50 ETFYVLDLGHHFSLLS-LISNLP-MVHPYYAVKG 81 (213)
Q Consensus 50 ~pF~V~DL~~V~~~~~-W~~~LP-rV~PfYAVKC 81 (213)
.++..+|++.|.+.++ -++.+| .++.+|+||+
T Consensus 2 ~~~~~Idl~~l~~N~~~i~~~~~~~~~i~~vvKA 35 (367)
T TIGR00492 2 PATVEIDLAALKHNLSAIRNHIGPKSKIMAVVKA 35 (367)
T ss_pred CEEEEEEHHHHHHHHHHHHHhcCCCCEEEEEEEc
Confidence 4578999999999999 888887 5788999998
No 36
>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=57.70 E-value=21 Score=32.89 Aligned_cols=31 Identities=13% Similarity=0.079 Sum_probs=27.8
Q ss_pred cEEEeehHHHHHHhh-hhhcCC-Cccceeeccc
Q 045992 51 TFYVLDLGHHFSLLS-LISNLP-MVHPYYAVKG 81 (213)
Q Consensus 51 pF~V~DL~~V~~~~~-W~~~LP-rV~PfYAVKC 81 (213)
++..+||+.|...++ -++.+| ..+.+|+||+
T Consensus 2 ~~l~Idl~al~~N~~~i~~~~~~~~~i~~vvKA 34 (365)
T cd06826 2 AWLEISTGAFENNIKLLKKLLGGNTKLCAVMKA 34 (365)
T ss_pred EEEEEEHHHHHHHHHHHHHhCCCCCEEEEEEEe
Confidence 567899999999999 888888 6789999999
No 37
>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=56.56 E-value=11 Score=34.10 Aligned_cols=33 Identities=12% Similarity=0.056 Sum_probs=28.8
Q ss_pred CCcEEEeehHHHHHHhh-hhhcCC--Cccceeeccc
Q 045992 49 DETFYVLDLGHHFSLLS-LISNLP--MVHPYYAVKG 81 (213)
Q Consensus 49 ~~pF~V~DL~~V~~~~~-W~~~LP--rV~PfYAVKC 81 (213)
..|++++|++.+.+..+ -++.++ .++.+|++|+
T Consensus 2 ~tP~l~id~~~l~~Ni~~~~~~~~~~~v~l~~~~K~ 37 (353)
T cd06820 2 DTPALLIDLDRLERNIARMQAYADAHGLSLRPHIKT 37 (353)
T ss_pred CCceEEEeHHHHHHHHHHHHHHHHHcCCcccccccc
Confidence 47999999999999999 777775 4788899999
No 38
>PRK13340 alanine racemase; Reviewed
Probab=56.49 E-value=20 Score=33.55 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=28.9
Q ss_pred CcEEEeehHHHHHHhh-hhhcCCC-ccceeeccc
Q 045992 50 ETFYVLDLGHHFSLLS-LISNLPM-VHPYYAVKG 81 (213)
Q Consensus 50 ~pF~V~DL~~V~~~~~-W~~~LPr-V~PfYAVKC 81 (213)
.+...+|++.|...++ -++.+|. .+.+|+||+
T Consensus 40 ~~~l~Idl~ai~~N~~~i~~~~~~~~~i~~vvKA 73 (406)
T PRK13340 40 NAWLEISPGAFRHNIKTLRSLLANKSKVCAVMKA 73 (406)
T ss_pred ceEEEEcHHHHHHHHHHHHHhCCCCCEEEEEEcc
Confidence 4788899999999999 8888886 789999999
No 39
>TIGR01273 speA arginine decarboxylase, biosynthetic. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not similar in sequence.
Probab=54.14 E-value=28 Score=35.22 Aligned_cols=67 Identities=21% Similarity=0.236 Sum_probs=48.8
Q ss_pred CCCCceeeeeEEccCCCCCCcccc-----c----cCCCCCCCCC--EEEEcCCCcccCCcCcccccCCCCcceEEEEEE
Q 045992 117 SNNQTTYKSTVFRPTCTAVGKVFA-----G----HPLPELEVND--WLVFPDKRANTLFVEPISMDLAMLPFELKFSVR 184 (213)
Q Consensus 117 ~~~~~~~~ssI~GPtCds~D~i~~-----~----~~LPel~vGD--wLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~ 184 (213)
.++.+....+|+.-||||.+.|.. + .+||.++.|+ +|-|-.+|||==.++. .=|..+.|-++-+.+.
T Consensus 481 l~e~p~~~~~l~DiTCDSDg~i~~fi~~~~~~~~l~lh~~~~~e~y~lg~FlvGAYQe~lg~-~HNLfg~~~~v~v~~~ 558 (624)
T TIGR01273 481 LDEKPTRRAVLQDITCDSDGKIDQFIGEQGITSTLPLHELDPDEGYFLGFFLVGAYQEILGD-MHNLFGDTSAVRVVFD 558 (624)
T ss_pred CCCCccceEEEeccCCCCCCchhccCCCcCccCCccCCCcCCCCCcEEEEEeccHhHHHhcc-ccccCCCCCEEEEEEC
Confidence 344678889999999999996653 1 3566766654 6778899999988886 4577777776665553
No 40
>PRK00053 alr alanine racemase; Reviewed
Probab=53.90 E-value=25 Score=32.12 Aligned_cols=32 Identities=19% Similarity=0.084 Sum_probs=28.1
Q ss_pred CcEEEeehHHHHHHhh-hhhcCCC-ccceeeccc
Q 045992 50 ETFYVLDLGHHFSLLS-LISNLPM-VHPYYAVKG 81 (213)
Q Consensus 50 ~pF~V~DL~~V~~~~~-W~~~LPr-V~PfYAVKC 81 (213)
.++.++|++.+.+.++ -++.+|. ++.+|+||+
T Consensus 3 ~~~l~Idl~~l~~N~~~i~~~~~~~~~i~~vvKa 36 (363)
T PRK00053 3 PATAEIDLDALRHNLRQIRKHAPPKSKLMAVVKA 36 (363)
T ss_pred CeEEEEeHHHHHHHHHHHHHhCCCCCEEEEEEee
Confidence 3788999999999999 8888884 888999996
No 41
>COG4078 Predicted membrane protein [Function unknown]
Probab=53.53 E-value=3.9 Score=35.81 Aligned_cols=13 Identities=46% Similarity=0.851 Sum_probs=10.9
Q ss_pred CCccceeeccchh
Q 045992 71 PMVHPYYAVKGKL 83 (213)
Q Consensus 71 PrV~PfYAVKCEL 83 (213)
-.|.||||+|.|.
T Consensus 178 tGvaPFYA~Kaem 190 (221)
T COG4078 178 TGVAPFYAVKAEM 190 (221)
T ss_pred cccchhHHHHHHH
Confidence 4699999999965
No 42
>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=53.39 E-value=15 Score=33.39 Aligned_cols=35 Identities=11% Similarity=-0.115 Sum_probs=29.4
Q ss_pred CCCCcEEEeehHHHHHHhh-hhhcCC-Cccceeeccc
Q 045992 47 ELDETFYVLDLGHHFSLLS-LISNLP-MVHPYYAVKG 81 (213)
Q Consensus 47 ~~~~pF~V~DL~~V~~~~~-W~~~LP-rV~PfYAVKC 81 (213)
+...|++++|++.+.+.++ .++.++ .++..|+||+
T Consensus 6 ~~~tP~~~id~~~l~~Ni~~~~~~~~~~~~l~~~vKa 42 (361)
T cd06821 6 EIISPALAVYPDRIEENIRRMIRMAGDPQRLRPHVKT 42 (361)
T ss_pred cCCCceEEEeHHHHHHHHHHHHHHHhcCCCccccchh
Confidence 3469999999999999999 887776 4566778999
No 43
>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=43.89 E-value=47 Score=30.72 Aligned_cols=31 Identities=19% Similarity=0.053 Sum_probs=27.7
Q ss_pred cEEEeehHHHHHHhh-hhhcCCCccceeeccc
Q 045992 51 TFYVLDLGHHFSLLS-LISNLPMVHPYYAVKG 81 (213)
Q Consensus 51 pF~V~DL~~V~~~~~-W~~~LPrV~PfYAVKC 81 (213)
+...+||+.+...++ -++.+|.++..|+||+
T Consensus 2 ~~~~Idl~~l~~N~~~l~~~~~~~~l~~vvKa 33 (354)
T cd06827 2 ARATIDLAALRHNLRLVRELAPNSKILAVVKA 33 (354)
T ss_pred eEEEEEHHHHHHHHHHHHhhCCCCeEEEEEee
Confidence 356799999999999 8989998888999998
No 44
>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=42.50 E-value=30 Score=32.08 Aligned_cols=33 Identities=18% Similarity=-0.007 Sum_probs=28.7
Q ss_pred CCcEEEeehHHHHHHhh-hhhcC-CC-ccceeeccc
Q 045992 49 DETFYVLDLGHHFSLLS-LISNL-PM-VHPYYAVKG 81 (213)
Q Consensus 49 ~~pF~V~DL~~V~~~~~-W~~~L-Pr-V~PfYAVKC 81 (213)
+.|++++|++.+.+.++ .++.+ +. ++..|.+|+
T Consensus 2 ~tP~l~idl~~l~~N~~~m~~~~~~~~~~l~~h~Kt 37 (382)
T cd06818 2 SLPLLVLDASALAHNLAWMQAFAAAHGVKLAPHGKT 37 (382)
T ss_pred CCcEEEEEHHHHHHHHHHHHHHHhhcCcEEEeecch
Confidence 47999999999999999 88887 43 788889998
No 45
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=35.82 E-value=1.3e+02 Score=22.94 Aligned_cols=65 Identities=11% Similarity=0.157 Sum_probs=33.7
Q ss_pred CeEEEEEecCCCCCceeeeccCCCCCCCceeeeeEEccCCCCCCccccccCCC-CCCCCCEEEEcCCCcc
Q 045992 93 CELSIRIKSPVDGGARTHICTSASSNNQTTYKSTVFRPTCTAVGKVFAGHPLP-ELEVNDWLVFPDKRAN 161 (213)
Q Consensus 93 a~LlLRI~~dd~~~A~c~~~~~~~~~~~~~~~ssI~GPtCds~D~i~~~~~LP-el~vGDwLvf~n~GAY 161 (213)
-++|+|.....++++--+--+..+......-...=.||-+...+ ....| .+++||.++|...++.
T Consensus 8 drVLV~~~~~e~~T~gGI~Lp~~a~~k~~~G~VvaVG~G~~~~~----G~~~~~~vk~GD~Vlf~~~~g~ 73 (95)
T PRK00364 8 DRVLVKRLEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRLDN----GERVPLDVKVGDKVLFGKYAGT 73 (95)
T ss_pred CEEEEEEcccCccccceEEcCccccCCcceEEEEEECCCeECCC----CCEeecccCCCCEEEEcCCCCe
Confidence 46777765433223333222222222223344445788653321 22334 7999999999986643
No 46
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=35.51 E-value=2e+02 Score=21.85 Aligned_cols=62 Identities=15% Similarity=0.228 Sum_probs=33.3
Q ss_pred eEEEEEecCCCCCceeeeccCCCCCCCceeeeeEEccCCCCCCccccccCCC-CCCCCCEEEEcCCC
Q 045992 94 ELSIRIKSPVDGGARTHICTSASSNNQTTYKSTVFRPTCTAVGKVFAGHPLP-ELEVNDWLVFPDKR 159 (213)
Q Consensus 94 ~LlLRI~~dd~~~A~c~~~~~~~~~~~~~~~ssI~GPtCds~D~i~~~~~LP-el~vGDwLvf~n~G 159 (213)
++|++......+++--+--+..+..........=.||-....+ ....| .+++||.++|...+
T Consensus 8 rVLV~~~~~e~~T~~GI~Lp~~~~~k~~~g~VvAVG~g~~~~~----g~~~~~~vk~GD~Vl~~~~~ 70 (93)
T cd00320 8 RVLVKRIEAEEKTKGGIILPDSAKEKPQEGKVVAVGPGRRNEN----GERVPLSVKVGDKVLFPKYA 70 (93)
T ss_pred EEEEEEccccceecceEEeCCCcCCCceEEEEEEECCCeECCC----CCCccccccCCCEEEECCCC
Confidence 5666665433323333222222222223444555688754332 23344 79999999999866
No 47
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=34.76 E-value=1.4e+02 Score=22.90 Aligned_cols=60 Identities=8% Similarity=0.055 Sum_probs=32.5
Q ss_pred CeEEEEEecCCCCCceeeeccCCCCCCCceeeeeEEccCCCCCCccccccCCC-CCCCCCEEEEcCCCcc
Q 045992 93 CELSIRIKSPVDGGARTHICTSASSNNQTTYKSTVFRPTCTAVGKVFAGHPLP-ELEVNDWLVFPDKRAN 161 (213)
Q Consensus 93 a~LlLRI~~dd~~~A~c~~~~~~~~~~~~~~~ssI~GPtCds~D~i~~~~~LP-el~vGDwLvf~n~GAY 161 (213)
-++|+|....+.+++-...-+..+..........=.||-- + ..| .+++||.++|...++.
T Consensus 8 DRVLVk~~~~e~~T~gGI~Lp~~a~ek~~~G~VvavG~g~---~------~~~~~Vk~GD~Vl~~~y~g~ 68 (91)
T PRK14533 8 ERLLIKPIKEEKKTEGGIVLPDSAKEKPMKAEVVAVGKLD---D------EEDFDIKVGDKVIFSKYAGT 68 (91)
T ss_pred CEEEEEEccccceecccEEecccccCCcceEEEEEECCCC---c------cccccccCCCEEEEccCCCe
Confidence 4677776654432333322222222222334455578732 1 224 7999999999887643
No 48
>KOG3638 consensus Sonic hedgehog and related proteins [Signal transduction mechanisms]
Probab=33.64 E-value=46 Score=31.89 Aligned_cols=55 Identities=20% Similarity=0.204 Sum_probs=39.8
Q ss_pred ccCCCCCCcccc----ccCCCCCCCCCEEEEcC-CCcccCCcCcccccCCCCcceEEEEEEe
Q 045992 129 RPTCTAVGKVFA----GHPLPELEVNDWLVFPD-KRANTLFVEPISMDLAMLPFELKFSVRI 185 (213)
Q Consensus 129 GPtCds~D~i~~----~~~LPel~vGDwLvf~n-~GAYt~s~s~~~f~s~~~p~E~~~~~~~ 185 (213)
+.+|.+.|.+.- ...|+++.+||||.-.+ -|-++. ++..+-.|..|..+-=-+.|
T Consensus 206 ~~cf~~~~~~~~~~~~~k~m~el~iGD~Vla~~~~~~~~~--spv~~~lhR~pe~~~~F~~i 265 (414)
T KOG3638|consen 206 PVCFPTDATVVLEQGGRKRMDELSIGDYVLAADQGGQTTY--SPVALFLHREPEARAEFVVI 265 (414)
T ss_pred CCCCCCCCEeEEecCceeecCCCCCCCeeeccccCCcccc--CchhhhhccCccccccceEE
Confidence 577888777652 36799999999999888 465544 67788888888755444444
No 49
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=32.92 E-value=29 Score=25.23 Aligned_cols=16 Identities=19% Similarity=0.561 Sum_probs=11.4
Q ss_pred cCCCCCCCCCEEEEcC
Q 045992 142 HPLPELEVNDWLVFPD 157 (213)
Q Consensus 142 ~~LPel~vGDwLvf~n 157 (213)
..+|++++|||+++..
T Consensus 33 ~lv~~v~~Gd~VLVHa 48 (68)
T PF01455_consen 33 ALVPDVKVGDYVLVHA 48 (68)
T ss_dssp TTCTSB-TT-EEEEET
T ss_pred EEeCCCCCCCEEEEec
Confidence 3588899999999875
No 50
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=29.46 E-value=37 Score=25.37 Aligned_cols=15 Identities=20% Similarity=0.375 Sum_probs=12.9
Q ss_pred CCCCCCCCCEEEEcC
Q 045992 143 PLPELEVNDWLVFPD 157 (213)
Q Consensus 143 ~LPel~vGDwLvf~n 157 (213)
.+|+..+|||+++..
T Consensus 32 lv~~~~vGD~VLVH~ 46 (76)
T TIGR00074 32 LVGEVKVGDYVLVHV 46 (76)
T ss_pred eeCCCCCCCEEEEec
Confidence 468999999999876
No 51
>PF10125 NADHdeh_related: NADH dehydrogenase I, subunit N related protein; InterPro: IPR017059 This group contains membrane proteins that are predicted to be transmembrane subunits (EhaH) of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes. The energy-converting hydrogenase A (eha) operon encodes a putative multisubunit membrane-bound [NiFe]-hydrogenase Eha in Methanobacterium thermoautotrophicum (strain Marburg / DSM 2133). Sequence analysis of the eha operon indicates that it encodes at least 20 proteins, including the [NiFe]-hydrogenase large subunit (IPR014363 from INTERPRO), the [NiFe]-hydrogenase small subunit (PIRSF002913 from PIRSF), and two broadly conserved integral membrane proteins (this entry and PIRSF000215 from PIRSF). These four proteins show high sequence similarity to subunits of the Ech hydrogenase from Methanosarcina barkeri, Escherichia coli hydrogenases 3 and 4 (Hyc and Hyf), and CO-induced hydrogenase from Rhodospirillum rubrum (Coo), all of which form a distinct group of multisubunit membrane-bound [NiFe]-hydrogenases (together called hydrogenase-3-type hydrogenases). In addition to these four subunits, the eha operon encodes a 6[4Fe-4S] polyferredoxin, a 10[4Fe-4S] polyferredoxin, ten other predicted integral membrane proteins (PIRSF005019 from PIRSF, PIRSF019706 from PIRSF, PIRSF036534 from PIRSF, PIRSF006581 from PIRSF, PIRSF036535 from PIRSF, PIRSF019373 from PIRSF, PIRSF019136 from PIRSF, PIRSF036537 from PIRSF, PIRSF036538 from PIRSF, PIRSF004953 from PIRSF), and four hydrophilic subunits (PIRSF005292 from PIRSF, PIRSF019370 from PIRSF, PIRSF006414 from PIRSF, PIRSF000536 from PIRSF) (the latter two hydrophilic subunits are members of well-characterised enzyme families but lack the essential amino acids assumed to form the active site []). All of these proteins are expressed and therefore thought to be functional subunits of the Eha hydrogenase complex []. Note, however, that the ten additional predicted integral membrane proteins are absent from Ech, Coo, Hyc, and Hyf complexes (and therefore from corresponding organisms), indicating that those complexes have a simpler membrane component than Eha []. Members of this group are homologous to the N-terminal domain of PIRSF006542 from PIRSF members (e.g., EhbF, HyfF of E. coli hydrogenase 4, amongst others). Therefore, this type of membrane subunit of Eha complex is conserved across the various hydrogenase-3-type hydrogenases (that is, they are not limited to the Eha subgroup). A protein with sequence similarity to the C-terminal part of EhbF (PIRSF006542 from PIRSF) is not present in the Eha complex (not encoded by the eha operon). Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri,Methanocaldococcus jannaschii, and M. thermoautotrophicum also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure.
Probab=28.27 E-value=18 Score=32.11 Aligned_cols=25 Identities=24% Similarity=0.406 Sum_probs=18.1
Q ss_pred CccceeeccchhhHHHhhCCCCeEEEEEe
Q 045992 72 MVHPYYAVKGKLDKIRMWHSKCELSIRIK 100 (213)
Q Consensus 72 rV~PfYAVKCEL~KI~~~~P~a~LlLRI~ 100 (213)
.|.||||.|+|.-. .|.+.-+|=|.
T Consensus 178 GvAPFYaaKAEmfR----apGaPyilmIH 202 (219)
T PF10125_consen 178 GVAPFYAAKAEMFR----APGAPYILMIH 202 (219)
T ss_pred CcchhhhhHHHHhc----CCCCCEEEeeh
Confidence 69999999998642 46666655543
No 52
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=27.97 E-value=45 Score=24.03 Aligned_cols=20 Identities=20% Similarity=0.209 Sum_probs=14.9
Q ss_pred CCC-CCCCCCEEEEcCCCccc
Q 045992 143 PLP-ELEVNDWLVFPDKRANT 162 (213)
Q Consensus 143 ~LP-el~vGDwLvf~n~GAYt 162 (213)
.|| ..++||||.+.+-|.|.
T Consensus 29 ~LP~~~keGDvl~i~~~~~~~ 49 (71)
T PF11213_consen 29 RLPEGAKEGDVLEIGEDGSIE 49 (71)
T ss_pred HCCCCCCcccEEEECCCceEE
Confidence 588 79999999884445543
No 53
>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....
Probab=27.24 E-value=34 Score=28.78 Aligned_cols=36 Identities=17% Similarity=0.349 Sum_probs=27.3
Q ss_pred hhhcCCCccce--eeccc-----------------------------hhhHHHhhCCCCe-EEEEEec
Q 045992 66 LISNLPMVHPY--YAVKG-----------------------------KLDKIRMWHSKCE-LSIRIKS 101 (213)
Q Consensus 66 W~~~LPrV~Pf--YAVKC-----------------------------EL~KI~~~~P~a~-LlLRI~~ 101 (213)
+|+.+|..|++ |||.| =+.++++..|... +.+....
T Consensus 22 TRKt~Pg~r~l~~~Av~~GGg~~hR~gl~d~ili~~nHi~~~g~i~~av~~~~~~~~~~~~I~VEv~~ 89 (169)
T PF01729_consen 22 TRKTIPGLRPLEKYAVLAGGGDNHRLGLSDMILIKDNHIAFFGGIEEAVKAARQAAPEKKKIEVEVEN 89 (169)
T ss_dssp GSGS-TTTHHHHHHHHHHTTSBHHHSSTTSSEEE-HHHHHHHSSHHHHHHHHHHHSTTTSEEEEEESS
T ss_pred cCCCCcccCHHHHHHHHhcCceeEECCCCCcEEehHHHHHHhCCHHHHHHHHHHhCCCCceEEEEcCC
Confidence 88999999999 99999 4566888888875 5555544
No 54
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=26.37 E-value=77 Score=22.89 Aligned_cols=24 Identities=25% Similarity=0.333 Sum_probs=16.1
Q ss_pred eccchhhH-HHhhCCCCeEEEEEec
Q 045992 78 AVKGKLDK-IRMWHSKCELSIRIKS 101 (213)
Q Consensus 78 AVKCEL~K-I~~~~P~a~LlLRI~~ 101 (213)
|...||.| |.+.||++.+-+|-..
T Consensus 8 AL~~EL~kRl~~~yPd~~v~Vr~~s 32 (65)
T PF06183_consen 8 ALESELTKRLHRQYPDAEVRVRPGS 32 (65)
T ss_dssp HHHHHHHHHHHHH-SS-EEEEEEES
T ss_pred HHHHHHHHHHHHHCCCceEeeeecc
Confidence 34448877 9999999888777553
No 55
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=24.15 E-value=62 Score=24.62 Aligned_cols=25 Identities=28% Similarity=0.470 Sum_probs=19.2
Q ss_pred eccchhhH-HHhhCCCCe--EEEEEecC
Q 045992 78 AVKGKLDK-IRMWHSKCE--LSIRIKSP 102 (213)
Q Consensus 78 AVKCEL~K-I~~~~P~a~--LlLRI~~d 102 (213)
|...||.| |.+.||++. +-+|-...
T Consensus 20 AL~~EL~kRl~~~fPd~~~~v~Vr~~s~ 47 (81)
T PRK10597 20 ALAGELSRRIQYAFPDNEGHVSVRYAAA 47 (81)
T ss_pred HHHHHHHHHHHhhCCCCCccEEEeecCC
Confidence 56669988 999999998 66665543
No 56
>TIGR02683 upstrm_HI1419 probable addiction module killer protein. Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family pfam01381. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both integrated plasmid regions and near housekeeping genes. Analysis suggests that the gene pair may serve as an addiction module.
Probab=22.47 E-value=70 Score=23.94 Aligned_cols=10 Identities=30% Similarity=0.371 Sum_probs=7.8
Q ss_pred cEEEeehhhh
Q 045992 196 EVILLHGFAS 205 (213)
Q Consensus 196 ~~~~~~~~~~ 205 (213)
.|||||||.-
T Consensus 69 ~vvll~gf~K 78 (95)
T TIGR02683 69 IILLLCGGDK 78 (95)
T ss_pred EEEEEeCEec
Confidence 4779999863
No 57
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=22.30 E-value=50 Score=24.62 Aligned_cols=18 Identities=17% Similarity=0.577 Sum_probs=13.8
Q ss_pred CCCCCCEEEEcCCCcccC
Q 045992 146 ELEVNDWLVFPDKRANTL 163 (213)
Q Consensus 146 el~vGDwLvf~n~GAYt~ 163 (213)
++++||+|+.++-|..-.
T Consensus 1 mf~~GD~VVh~~~Gv~~i 18 (98)
T PF02559_consen 1 MFKIGDYVVHPNHGVGRI 18 (98)
T ss_dssp T--TTSEEEETTTEEEEE
T ss_pred CCCCCCEEEECCCceEEE
Confidence 368999999999998755
No 58
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=21.98 E-value=58 Score=24.67 Aligned_cols=13 Identities=15% Similarity=0.457 Sum_probs=11.2
Q ss_pred CCCCCCCEEEEcC
Q 045992 145 PELEVNDWLVFPD 157 (213)
Q Consensus 145 Pel~vGDwLvf~n 157 (213)
|++.+|||+++..
T Consensus 41 ~~~~vGDyVLVHa 53 (82)
T PRK10413 41 PADLLGQWVLVHV 53 (82)
T ss_pred cccccCCEEEEec
Confidence 5688999999887
No 59
>COG4067 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]
Probab=21.89 E-value=1.2e+02 Score=26.14 Aligned_cols=69 Identities=22% Similarity=0.155 Sum_probs=47.3
Q ss_pred cCCCCCCccc---cccCCCCCCCCCEEEEcCCCcccCCcCcccccCCCCcceEEEEEEec-----ccccccccCcEEE
Q 045992 130 PTCTAVGKVF---AGHPLPELEVNDWLVFPDKRANTLFVEPISMDLAMLPFELKFSVRIQ-----AHTACEYENEVIL 199 (213)
Q Consensus 130 PtCds~D~i~---~~~~LPel~vGDwLvf~n~GAYt~s~s~~~f~s~~~p~E~~~~~~~~-----~~~~~~~~~~~~~ 199 (213)
|.|...+.+. +...||.+.++ .=.=.+.||+|++++..+--+..+--|=-+..++- .-..+|.+..||-
T Consensus 16 ~s~~~~~~v~G~~E~~~l~~l~~~-~kAkiDTGA~TSsL~A~dI~~fkRdGe~WVRF~~~~~~~~~~~~~~~e~pvi~ 92 (162)
T COG4067 16 TSCAAEKMVLGWIEWVSLPGLKIQ-LKAKIDTGAVTSSLSASDIERFKRDGERWVRFRLADTDNLDQRSEECEAPVIR 92 (162)
T ss_pred ccccccceEeeeEEEEEcCcccce-eeeeecccceeeeEEeecceeeeeCCceEEEEEeecccCccccceeeccceEE
Confidence 3666666665 34679998888 55566789999999887766666666666666654 2244566666664
No 60
>PF12024 DUF3512: Domain of unknown function (DUF3512); InterPro: IPR021900 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 231 to 249 amino acids in length. This domain is found associated with PF00439 from PFAM.
Probab=21.20 E-value=1.8e+02 Score=26.54 Aligned_cols=86 Identities=6% Similarity=-0.010 Sum_probs=49.8
Q ss_pred hHHHhhCCCCeE-EEEEecCCCCCcee-eeccCCCCCCCceeee---eEEccCCCCCCccccccCCCCCCCCCEEEEcCC
Q 045992 84 DKIRMWHSKCEL-SIRIKSPVDGGART-HICTSASSNNQTTYKS---TVFRPTCTAVGKVFAGHPLPELEVNDWLVFPDK 158 (213)
Q Consensus 84 ~KI~~~~P~a~L-lLRI~~dd~~~A~c-~~~~~~~~~~~~~~~s---sI~GPtCds~D~i~~~~~LPel~vGDwLvf~n~ 158 (213)
.||.+..|++++ .||-..|.+ +... ++...+...+....++ .+.|++=.+...+.. +.=-..+.--.|-+.|-
T Consensus 44 ~rl~~~~~~~k~gFlr~~~DGt-t~l~vln~~~~~~~~~~~~pV~Lg~l~gkL~~G~~tL~g-fkEdrrnkvtpv~yl~Y 121 (245)
T PF12024_consen 44 DRLNRRLPNSKMGFLRRKKDGT-TTLNVLNPVDPEAGEEEYRPVDLGSLSGKLQSGTNTLQG-FKEDRRNKVTPVSYLNY 121 (245)
T ss_pred HHHhhcccccccchhcccCCCC-EEEEEeecCCCCCCCCCCceeeHHHhhccccCCcccccc-cchhhccceeeeccccc
Confidence 567888888887 677776654 2222 5544443333334444 467777777766632 11011233345678888
Q ss_pred CcccCCcCcccccCC
Q 045992 159 RANTLFVEPISMDLA 173 (213)
Q Consensus 159 GAYt~s~s~~~f~s~ 173 (213)
|+|++ .+| .|+|.
T Consensus 122 GpfsS-~AP-~yDSt 134 (245)
T PF12024_consen 122 GPFSS-FAP-TYDST 134 (245)
T ss_pred Ccccc-ccc-ccccc
Confidence 99987 576 67664
No 61
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=20.58 E-value=90 Score=23.77 Aligned_cols=32 Identities=19% Similarity=0.204 Sum_probs=24.8
Q ss_pred CCCcEEEeehHHHHHHhhhhhcCCCccceeeccc
Q 045992 48 LDETFYVLDLGHHFSLLSLISNLPMVHPYYAVKG 81 (213)
Q Consensus 48 ~~~pF~V~DL~~V~~~~~W~~~LPrV~PfYAVKC 81 (213)
.++++|+ +=.++.+...|.+.. +.+||+|||=
T Consensus 45 ~~~~~~l-~~eqve~L~~f~~~f-g~~p~iAvK~ 76 (88)
T PF01870_consen 45 SKDKIYL-EKEQVEKLKEFSKRF-GAEPLIAVKF 76 (88)
T ss_dssp SSSEEEE-EHHHHHHHHHHHHHH-TCEEEEEEEE
T ss_pred cCCceeE-CHHHHHHHHHHHHHh-CCeEEEEEEE
Confidence 4557887 777777777788887 6899999983
No 62
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=20.50 E-value=2.9e+02 Score=22.92 Aligned_cols=52 Identities=15% Similarity=0.213 Sum_probs=31.4
Q ss_pred CeEEEEEecCCCCCceeeec--cCCCCCCCceeeeeEEccCCCCCCccccccCCCCCCCCCEEEEc
Q 045992 93 CELSIRIKSPVDGGARTHIC--TSASSNNQTTYKSTVFRPTCTAVGKVFAGHPLPELEVNDWLVFP 156 (213)
Q Consensus 93 a~LlLRI~~dd~~~A~c~~~--~~~~~~~~~~~~ssI~GPtCds~D~i~~~~~LPel~vGDwLvf~ 156 (213)
+-.|+||+.||.++++.-.| .=++ +. ..-|. ...|..- .+|.+++||.|.|.
T Consensus 42 ~G~V~~vLpdd~~GsrHQ~Fiv~l~~---g~--tllIa----hNIDlap---rip~l~~GD~V~f~ 95 (131)
T PF11948_consen 42 CGTVVKVLPDDNKGSRHQRFIVRLSS---GQ--TLLIA----HNIDLAP---RIPWLQKGDQVEFY 95 (131)
T ss_pred cEEEEEECcccCCCCcceEEEEEeCC---CC--EEEEE----eccCccc---cCcCcCCCCEEEEE
Confidence 78899999998766555111 1111 11 11121 4455552 57899999999885
Done!