Query 031564
Match_columns 157
No_of_seqs 128 out of 883
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 15:54:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2368 Hydroxymethylglutaryl- 99.9 1.8E-27 3.9E-32 204.1 6.5 73 82-154 3-75 (316)
2 PLN02746 hydroxymethylglutaryl 99.9 3.1E-25 6.7E-30 192.8 6.8 89 66-154 15-103 (347)
3 PRK05692 hydroxymethylglutaryl 99.8 1.4E-19 3E-24 152.2 6.6 60 94-153 1-60 (287)
4 cd07938 DRE_TIM_HMGL 3-hydroxy 99.7 4.8E-18 1E-22 141.7 5.0 55 100-154 1-55 (274)
5 cd07945 DRE_TIM_CMS Leptospira 99.6 8E-16 1.7E-20 129.1 2.2 53 102-154 2-59 (280)
6 cd07948 DRE_TIM_HCS Saccharomy 99.5 2.8E-14 6.1E-19 118.8 4.9 52 99-153 2-53 (262)
7 cd07942 DRE_TIM_LeuA Mycobacte 99.4 1.5E-13 3.3E-18 116.5 4.1 49 100-155 4-52 (284)
8 cd07941 DRE_TIM_LeuA3 Desulfob 99.4 1.6E-13 3.5E-18 113.7 3.4 52 100-151 1-59 (273)
9 cd07947 DRE_TIM_Re_CS Clostrid 99.4 5.8E-13 1.3E-17 112.4 5.1 45 98-143 1-50 (279)
10 cd03174 DRE_TIM_metallolyase D 99.3 1.2E-12 2.5E-17 103.8 5.4 53 101-153 1-53 (265)
11 PLN02321 2-isopropylmalate syn 99.3 1.1E-12 2.3E-17 122.4 5.9 51 95-145 84-135 (632)
12 PRK03739 2-isopropylmalate syn 99.3 1.1E-12 2.3E-17 119.9 5.3 55 94-155 27-81 (552)
13 COG0119 LeuA Isopropylmalate/h 99.3 9.7E-13 2.1E-17 117.0 4.6 57 97-153 2-58 (409)
14 PLN03228 methylthioalkylmalate 99.3 1.1E-12 2.5E-17 119.3 4.9 56 95-153 82-137 (503)
15 TIGR02090 LEU1_arch isopropylm 99.3 2E-12 4.2E-17 111.7 5.4 56 98-153 1-63 (363)
16 PRK11858 aksA trans-homoaconit 99.3 4.4E-12 9.6E-17 110.0 5.5 54 95-155 2-55 (378)
17 TIGR00970 leuA_yeast 2-isoprop 99.3 4.3E-12 9.2E-17 116.3 4.7 51 94-145 23-73 (564)
18 TIGR00977 LeuA_rel 2-isopropyl 99.3 4.3E-12 9.3E-17 115.4 4.7 55 97-151 1-56 (526)
19 cd07943 DRE_TIM_HOA 4-hydroxy- 99.3 8.5E-12 1.8E-16 102.2 5.9 56 98-153 1-61 (263)
20 cd07940 DRE_TIM_IPMS 2-isoprop 99.2 5.8E-12 1.3E-16 103.4 3.7 45 100-144 1-46 (268)
21 PRK12344 putative alpha-isopro 99.2 1.3E-11 2.8E-16 112.0 5.6 56 94-149 2-64 (524)
22 PRK09389 (R)-citramalate synth 99.2 1.6E-11 3.6E-16 110.5 5.8 56 97-152 2-64 (488)
23 PRK00915 2-isopropylmalate syn 99.2 3E-11 6.5E-16 109.0 5.9 52 94-145 1-53 (513)
24 TIGR02660 nifV_homocitr homoci 99.1 5.3E-11 1.2E-15 102.5 5.1 51 98-155 2-52 (365)
25 TIGR00973 leuA_bact 2-isopropy 99.1 1.4E-10 3.1E-15 104.5 6.1 49 97-145 1-49 (494)
26 TIGR03217 4OH_2_O_val_ald 4-hy 99.1 2.3E-10 5.1E-15 98.6 5.7 56 97-152 2-66 (333)
27 PRK12331 oxaloacetate decarbox 99.0 5.6E-10 1.2E-14 100.3 5.9 50 96-145 2-61 (448)
28 PRK08195 4-hyroxy-2-oxovalerat 99.0 8.1E-10 1.8E-14 95.3 6.7 53 96-148 2-63 (337)
29 PRK14041 oxaloacetate decarbox 98.9 1.2E-09 2.6E-14 98.9 5.8 49 97-145 2-60 (467)
30 cd07939 DRE_TIM_NifV Streptomy 98.9 1.5E-09 3.2E-14 88.9 4.2 42 100-141 1-42 (259)
31 TIGR02146 LysS_fung_arch homoc 98.9 1.4E-09 2.9E-14 90.1 3.4 51 100-153 1-51 (344)
32 PRK14847 hypothetical protein; 98.7 1.6E-08 3.4E-13 88.8 5.8 59 79-140 17-75 (333)
33 TIGR01108 oadA oxaloacetate de 98.7 1.5E-08 3.2E-13 93.7 4.5 46 100-145 1-56 (582)
34 PRK09282 pyruvate carboxylase 98.5 1.3E-07 2.7E-12 87.7 5.7 44 96-139 2-46 (592)
35 cd07937 DRE_TIM_PC_TC_5S Pyruv 98.4 1E-07 2.2E-12 79.5 2.7 41 100-140 1-42 (275)
36 cd07944 DRE_TIM_HOA_like 4-hyd 98.3 5.9E-07 1.3E-11 74.9 4.3 44 100-143 1-44 (266)
37 PRK12330 oxaloacetate decarbox 98.0 7.7E-06 1.7E-10 75.3 5.4 46 94-139 1-47 (499)
38 PRK14040 oxaloacetate decarbox 98.0 7.9E-06 1.7E-10 76.1 5.5 45 95-139 2-47 (593)
39 KOG2367 Alpha-isopropylmalate 97.9 1.4E-05 3.1E-10 74.5 5.0 50 94-143 54-103 (560)
40 PRK12581 oxaloacetate decarbox 97.4 0.0002 4.2E-09 65.8 5.3 46 94-139 9-55 (468)
41 PRK12999 pyruvate carboxylase; 97.4 0.0002 4.4E-09 71.1 5.0 46 95-140 530-578 (1146)
42 PRK14042 pyruvate carboxylase 96.0 0.0092 2E-07 56.3 4.6 45 96-140 2-47 (596)
43 COG5016 Pyruvate/oxaloacetate 90.6 0.13 2.8E-06 48.0 1.5 44 96-139 4-48 (472)
44 PF04481 DUF561: Protein of un 80.9 2.3 5.1E-05 37.0 4.1 60 66-138 92-151 (242)
45 PRK05718 keto-hydroxyglutarate 79.2 2.5 5.4E-05 35.0 3.6 33 116-149 24-56 (212)
46 TIGR01235 pyruv_carbox pyruvat 77.9 2.9 6.2E-05 42.6 4.2 45 96-140 529-576 (1143)
47 PRK06294 coproporphyrinogen II 76.1 7.6 0.00017 33.9 5.9 68 79-146 168-246 (370)
48 PRK05904 coproporphyrinogen II 61.2 27 0.00058 30.6 6.1 69 78-146 167-242 (353)
49 KOG3728 Uridine phosphorylase 58.3 7.9 0.00017 34.6 2.3 25 116-140 226-250 (308)
50 COG0800 Eda 2-keto-3-deoxy-6-p 58.2 13 0.00027 31.7 3.4 30 116-146 22-51 (211)
51 PRK07114 keto-hydroxyglutarate 57.2 14 0.0003 31.1 3.6 34 116-150 24-57 (222)
52 PRK07379 coproporphyrinogen II 56.1 31 0.00068 30.5 5.7 66 81-146 182-258 (400)
53 TIGR00539 hemN_rel putative ox 56.0 24 0.00052 30.4 4.9 70 76-145 162-238 (360)
54 PRK06015 keto-hydroxyglutarate 54.7 17 0.00036 30.2 3.6 34 116-150 13-46 (201)
55 PRK08599 coproporphyrinogen II 54.6 44 0.00095 28.9 6.2 66 81-146 167-243 (377)
56 PRK06552 keto-hydroxyglutarate 53.7 18 0.00039 29.9 3.6 34 117-151 23-56 (213)
57 PRK08898 coproporphyrinogen II 53.5 27 0.0006 30.7 4.9 60 87-146 194-260 (394)
58 PF01081 Aldolase: KDPG and KH 53.4 15 0.00032 30.4 3.0 32 116-148 17-48 (196)
59 TIGR01182 eda Entner-Doudoroff 52.7 19 0.00042 29.9 3.6 32 116-148 17-48 (204)
60 PRK05799 coproporphyrinogen II 51.5 28 0.00061 29.9 4.6 69 78-146 163-242 (374)
61 PRK13347 coproporphyrinogen II 51.4 46 0.00099 29.9 6.0 70 76-145 214-293 (453)
62 PRK09140 2-dehydro-3-deoxy-6-p 49.1 18 0.00038 29.6 2.9 33 117-150 20-52 (206)
63 PF13309 HTH_22: HTH domain 45.7 22 0.00047 24.2 2.5 22 112-133 17-38 (64)
64 PRK08208 coproporphyrinogen II 45.4 55 0.0012 29.2 5.6 67 81-147 208-279 (430)
65 cd02803 OYE_like_FMN_family Ol 44.7 88 0.0019 26.1 6.4 55 84-141 195-250 (327)
66 COG1533 SplB DNA repair photol 43.6 29 0.00062 30.3 3.5 39 110-152 160-198 (297)
67 PRK07028 bifunctional hexulose 42.8 23 0.0005 31.4 2.8 31 109-139 6-36 (430)
68 TIGR00538 hemN oxygen-independ 42.4 78 0.0017 28.3 6.1 70 77-146 214-293 (455)
69 PRK05660 HemN family oxidoredu 39.5 77 0.0017 27.8 5.5 68 79-146 172-246 (378)
70 PHA00675 hypothetical protein 38.7 49 0.0011 24.5 3.5 44 95-139 2-46 (78)
71 cd02933 OYE_like_FMN Old yello 36.7 1.3E+02 0.0029 26.2 6.5 55 86-140 208-262 (338)
72 PRK05628 coproporphyrinogen II 34.2 93 0.002 26.9 5.1 67 80-146 174-251 (375)
73 PRK09058 coproporphyrinogen II 33.0 1.5E+02 0.0032 26.8 6.4 65 82-146 231-307 (449)
74 cd07080 ALDH_Acyl-CoA-Red_LuxC 32.8 30 0.00064 30.9 1.9 30 107-136 365-394 (422)
75 PRK09249 coproporphyrinogen II 32.5 98 0.0021 27.8 5.1 69 77-145 214-292 (453)
76 PF05893 LuxC: Acyl-CoA reduct 30.4 37 0.0008 30.5 2.1 28 109-136 345-372 (399)
77 cd04729 NanE N-acetylmannosami 29.5 94 0.002 24.8 4.1 47 88-141 1-49 (219)
78 cd02932 OYE_YqiM_FMN Old yello 28.3 2.5E+02 0.0053 24.1 6.7 53 84-139 208-261 (336)
79 COG1948 MUS81 ERCC4-type nucle 28.1 1.7E+02 0.0037 25.6 5.7 56 81-138 73-140 (254)
80 TIGR00262 trpA tryptophan synt 28.1 71 0.0015 26.9 3.4 28 117-144 22-50 (256)
81 PF09720 Unstab_antitox: Putat 27.9 60 0.0013 21.0 2.3 15 116-130 2-16 (54)
82 PRK06582 coproporphyrinogen II 27.6 1.4E+02 0.0031 26.5 5.3 58 88-145 184-252 (390)
83 PLN02591 tryptophan synthase 27.5 75 0.0016 27.1 3.4 28 117-144 14-42 (250)
84 PF03446 NAD_binding_2: NAD bi 26.9 1.3E+02 0.0027 22.9 4.2 57 77-143 65-123 (163)
85 cd04733 OYE_like_2_FMN Old yel 26.9 1.8E+02 0.004 24.9 5.7 52 86-140 205-257 (338)
86 CHL00200 trpA tryptophan synth 26.7 78 0.0017 27.1 3.4 24 117-140 27-50 (263)
87 PLN02877 alpha-amylase/limit d 25.9 1.1E+02 0.0024 31.4 4.7 45 95-139 337-393 (970)
88 PRK10605 N-ethylmaleimide redu 25.8 2.6E+02 0.0057 24.7 6.6 56 85-140 214-270 (362)
89 cd02930 DCR_FMN 2,4-dienoyl-Co 25.6 3.3E+02 0.0072 23.6 7.1 54 85-141 192-246 (353)
90 PF14552 Tautomerase_2: Tautom 25.1 1.1E+02 0.0024 21.9 3.5 34 95-135 26-64 (82)
91 PRK08446 coproporphyrinogen II 23.9 1.6E+02 0.0035 25.4 4.8 65 79-143 163-231 (350)
92 TIGR03849 arch_ComA phosphosul 23.9 1.4E+02 0.003 25.8 4.3 38 97-136 114-151 (237)
93 cd00452 KDPG_aldolase KDPG and 22.6 1.3E+02 0.0028 23.6 3.7 33 117-150 14-46 (190)
94 PRK13111 trpA tryptophan synth 22.4 1.1E+02 0.0023 26.1 3.4 24 117-140 24-47 (258)
95 PF00290 Trp_syntA: Tryptophan 22.3 91 0.002 26.8 3.0 24 117-140 22-45 (259)
96 COG0159 TrpA Tryptophan syntha 21.6 1.1E+02 0.0023 26.9 3.3 24 117-140 29-52 (265)
97 TIGR02103 pullul_strch alpha-1 21.1 1.2E+02 0.0026 30.7 4.0 45 94-138 249-305 (898)
98 PF13653 GDPD_2: Glycerophosph 20.7 55 0.0012 19.9 1.0 18 119-136 7-24 (30)
No 1
>KOG2368 consensus Hydroxymethylglutaryl-CoA lyase [Energy production and conversion; Amino acid transport and metabolism]
Probab=99.94 E-value=1.8e-27 Score=204.13 Aligned_cols=73 Identities=64% Similarity=0.925 Sum_probs=69.7
Q ss_pred cchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564 82 STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL 154 (157)
Q Consensus 82 ~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~ 154 (157)
..+.++++.+...|++|+|+|||||||||||+.++||+.|++||++|+++|++.||.||||||||||||||+.
T Consensus 3 ~~~~~s~~a~~t~~~~vkiVEVGpRDGLQnEk~~vpt~vKveLI~~Lse~Gl~~vEtTSFVSpKWVPQl~D~~ 75 (316)
T KOG2368|consen 3 PNRLLSNRAYSTAPKRVKIVEVGPRDGLQNEKNIVPTEVKVELIDRLSECGLQVVETTSFVSPKWVPQLADHN 75 (316)
T ss_pred hhHHHHhhhhhcccceeEEEEecCcccccccCccCCchHHHHHHHHHHHcCCceeeeecccCccccccccchH
Confidence 4577889999999999999999999999999999999999999999999999999999999999999999963
No 2
>PLN02746 hydroxymethylglutaryl-CoA lyase
Probab=99.91 E-value=3.1e-25 Score=192.76 Aligned_cols=89 Identities=67% Similarity=0.966 Sum_probs=86.4
Q ss_pred ccccccccccCCCCcccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564 66 NGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK 145 (157)
.|+++.+||++..+..+++.+++|+..+||++|+|+|||||||+|+++..+|+++|++|+++|.++||++||+|||||||
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~V~I~DtTlRDG~Q~~g~~~s~e~Ki~ia~~L~~~GV~~IEvGs~vspk 94 (347)
T PLN02746 15 SWSFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPK 94 (347)
T ss_pred ccchhhhccccccccccccccccchhhcCCCceEEEECCCCccCcCCCCCCCHHHHHHHHHHHHHcCCCEEEECCCcCcc
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccC
Q 031564 146 WVPQVADAL 154 (157)
Q Consensus 146 ~VPQMADa~ 154 (157)
|||||+|++
T Consensus 95 ~vPqmad~~ 103 (347)
T PLN02746 95 WVPQLADAK 103 (347)
T ss_pred cccccccHH
Confidence 999999863
No 3
>PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional
Probab=99.79 E-value=1.4e-19 Score=152.17 Aligned_cols=60 Identities=63% Similarity=1.016 Sum_probs=58.0
Q ss_pred CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564 94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa 153 (157)
||..|.|+|++||||+|+++..+||++|++|++.|.++||++||+||||+|||+|||+|+
T Consensus 1 m~~~v~I~D~TlRDG~Q~~~~~~s~e~k~~ia~~L~~~Gv~~IEvgsf~~p~~~p~~~d~ 60 (287)
T PRK05692 1 LPKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADA 60 (287)
T ss_pred CCCceEEEECCCCccccCcCCCcCHHHHHHHHHHHHHcCCCEEEeCCCcCcccccccccH
Confidence 477899999999999999999999999999999999999999999999999999999986
No 4
>cd07938 DRE_TIM_HMGL 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain. 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropy
Probab=99.72 E-value=4.8e-18 Score=141.66 Aligned_cols=55 Identities=67% Similarity=1.036 Sum_probs=53.4
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL 154 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~ 154 (157)
|+|++||||+|+++..+|+++|+++++.|.++||++||+|||++||++|||+|.+
T Consensus 1 i~D~TlRDG~Q~~~~~~s~e~K~~i~~~L~~~Gv~~IEvGs~~~~~~~p~~~d~~ 55 (274)
T cd07938 1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADAE 55 (274)
T ss_pred CeeCCCCCCCcCCCCCcCHHHHHHHHHHHHHcCCCEEEeCCCCCcccccccCCHH
Confidence 6899999999999999999999999999999999999999999999999999975
No 5
>cd07945 DRE_TIM_CMS Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain. Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center con
Probab=99.56 E-value=8e-16 Score=129.14 Aligned_cols=53 Identities=25% Similarity=0.241 Sum_probs=49.9
Q ss_pred EeccCccccCCCCCCCHHHHHHHHHHH-HhCCCCeeeeecc-cCC---CccccccccC
Q 031564 102 EVGPRDGLQNEKNIVPAVVKVELIKLL-VSSGLPVVEATSF-VSP---KWVPQVADAL 154 (157)
Q Consensus 102 EVGpRDGLQne~~~vpTe~KIeLI~~L-~~AGv~~IEvgSF-VsP---K~VPQMADa~ 154 (157)
|||||||+|+++..+|+++|++|+++| .++||+.||+||| ||| ++||||+|+.
T Consensus 2 D~TlRDG~Q~~~~~~s~e~K~~i~~~L~~~~Gv~~IEvg~~~~s~~e~~av~~~~~~~ 59 (280)
T cd07945 2 DTTLRDGEQTSGVSFSPSEKLNIAKILLQELKVDRIEVASARVSEGEFEAVQKIIDWA 59 (280)
T ss_pred CCCCCCcCcCCCCccCHHHHHHHHHHHHHHhCCCEEEecCCCCCHHHHHHHHHHHHHh
Confidence 799999999999999999999999997 5669999999999 999 9999999853
No 6
>cd07948 DRE_TIM_HCS Saccharomyces cerevisiae homocitrate synthase and related proteins, catalytic TIM barrel domain. Homocitrate synthase (HCS) catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, the first step in the lysine biosynthesis pathway. This family includes the Yarrowia lipolytica LYS1 protein as well as the Saccharomyces cerevisiae LYS20 and LYS21 proteins. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. Th
Probab=99.48 E-value=2.8e-14 Score=118.84 Aligned_cols=52 Identities=31% Similarity=0.366 Sum_probs=50.1
Q ss_pred EEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564 99 KIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153 (157)
Q Consensus 99 ~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa 153 (157)
.|.|||||||+|+++..+|+++|++|+++|.++||+.||+|+ |+++|||+++
T Consensus 2 ~I~D~TLRDG~Q~~~~~~s~~~k~~i~~~L~~~Gv~~IEvG~---P~~~~~~~~~ 53 (262)
T cd07948 2 KIIDSTLREGEQFANAFFDTEDKIEIAKALDAFGVDYIELTS---PAASPQSRAD 53 (262)
T ss_pred EEEECCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEEC---CCCCHHHHHH
Confidence 699999999999999999999999999999999999999997 9999999875
No 7
>cd07942 DRE_TIM_LeuA Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Alpha-isopropylmalate synthase (LeuA), a key enzyme in leucine biosynthesis, catalyzes the first committed step in the pathway, converting acetyl-CoA and alpha-ketoisovalerate to alpha-isopropyl malate and CoA. Although the reaction catalyzed by LeuA is similar to that of the Arabidopsis thaliana IPMS1 protein, the two fall into phylogenetically distinct families within the same superfamily. LeuA has and N-terminal TIM barrel catalytic domain, a helical linker domain, and a C-terminal regulatory domain. LeuA forms a homodimer in which the linker domain of one monomer sits over the catalytic domain of the other, inserting residues into the active site that may be important for catalysis. Homologs of LeuA are found in bacteria as well as fungi. This family includes alpha-isopropylmalate synthases I (LEU4) and II (LEU9) from Saccharomyces cerevisiae. This family belong
Probab=99.40 E-value=1.5e-13 Score=116.52 Aligned_cols=49 Identities=31% Similarity=0.426 Sum_probs=46.4
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF 155 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~ 155 (157)
-++||||||+|+++..+|+++|++|+++|.++||++||+| | |||+|+++
T Consensus 4 ~~d~tlRDG~Q~~g~~~s~~~Ki~ia~~L~~~Gv~~IE~g-f------P~~~~~e~ 52 (284)
T cd07942 4 WCSVDLRDGNQALAEPMSVEQKLRFFKLLVKIGFKEIEVG-F------PSASQTDF 52 (284)
T ss_pred ccCCCCCCcCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEe-C------CCCCHHHH
Confidence 4689999999999999999999999999999999999999 7 99999874
No 8
>cd07941 DRE_TIM_LeuA3 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Desulfobacterium autotrophicum LeuA3 is sequence-similar to alpha-isopropylmalate synthase (LeuA) but its exact function is unknown. Members of this family have an N-terminal TIM barrel domain that belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of in
Probab=99.39 E-value=1.6e-13 Score=113.69 Aligned_cols=52 Identities=23% Similarity=0.213 Sum_probs=50.0
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCCccc------ccc
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPKWVP------QVA 151 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK~VP------QMA 151 (157)
|.|||||||+|+++..+++++|++++++|.++||++||+|+ |++|+.+| ||+
T Consensus 1 i~D~TLRDG~Q~~~~~~s~e~k~~i~~~L~~~Gv~~IE~G~~~~~~~~~~~~~~~~~~~ 59 (273)
T cd07941 1 IYDTTLRDGTQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFARAKKLK 59 (273)
T ss_pred CCcCCCCCcCCCCCCCCCHHHHHHHHHHHHHcCCCEEEecCCcCCHHHHHHHHHHHHcC
Confidence 57999999999999999999999999999999999999999 99999999 776
No 9
>cd07947 DRE_TIM_Re_CS Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel domain. Re-citrate synthase (Re-CS) is a Clostridium kluyveri enzyme that converts acetyl-CoA and oxaloacetate to citrate. In most organisms, this reaction is catalyzed by Si-citrate synthase which is Si-face stereospecific with respect to C-2 of oxaloacetate, and phylogenetically unrelated to Re-citrate synthase. Re-citrate synthase is also found in a few other strictly anaerobic organisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with
Probab=99.36 E-value=5.8e-13 Score=112.40 Aligned_cols=45 Identities=20% Similarity=0.207 Sum_probs=43.1
Q ss_pred eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCC-----CCeeeeecccC
Q 031564 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSG-----LPVVEATSFVS 143 (157)
Q Consensus 98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AG-----v~~IEvgSFVs 143 (157)
|.|+|||||||+|+++.+ |+++|++|+++|.++| |++||++||++
T Consensus 1 i~i~d~tlRDG~Q~~~~~-~~~~Kv~i~~~L~~~G~~~~~v~~IE~~s~~~ 50 (279)
T cd07947 1 IWITDTTFRDGQQARPPY-TVEQIVKIYDYLHELGGGSGVIRQTEFFLYTE 50 (279)
T ss_pred CEEEeCCCCCcCCCCCCC-CHHHHHHHHHHHHHcCCCCCccceEEecCcCh
Confidence 579999999999999987 9999999999999999 99999999986
No 10
>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Probab=99.34 E-value=1.2e-12 Score=103.80 Aligned_cols=53 Identities=36% Similarity=0.456 Sum_probs=50.9
Q ss_pred EEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564 101 VEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153 (157)
Q Consensus 101 vEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa 153 (157)
.|+++|||+|.....+++++|+++++.|.++||+.||+|++++++++||+.|.
T Consensus 1 ~D~tlRDG~q~~~~~~s~e~~~~i~~~L~~~GV~~IEvg~~~~~~~~p~~~~~ 53 (265)
T cd03174 1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDD 53 (265)
T ss_pred CCCCCCCcccCCCCCCCHHHHHHHHHHHHHcCCCEEEeccCcCccccccCCCH
Confidence 38999999999999999999999999999999999999999999999999874
No 11
>PLN02321 2-isopropylmalate synthase
Probab=99.34 E-value=1.1e-12 Score=122.40 Aligned_cols=51 Identities=27% Similarity=0.502 Sum_probs=49.7
Q ss_pred CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC
Q 031564 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK 145 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK 145 (157)
|+.|.|.||+||||+|+++..+++++|++|+++|.++||+.||+|+ |+||+
T Consensus 84 ~~~V~I~DtTLRDGeQ~~g~~~s~eeKl~Ia~~L~~lGVd~IEvGfP~~Sp~ 135 (632)
T PLN02321 84 PNYVRIFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPIASPD 135 (632)
T ss_pred CCceEEEECCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCcCCCcc
Confidence 7889999999999999999999999999999999999999999999 79998
No 12
>PRK03739 2-isopropylmalate synthase; Validated
Probab=99.33 E-value=1.1e-12 Score=119.89 Aligned_cols=55 Identities=25% Similarity=0.331 Sum_probs=51.7
Q ss_pred CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564 94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF 155 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~ 155 (157)
+.....|+|+|||||+|+++..+++++|++|+++|.++||++||+| | |||++++|
T Consensus 27 ~~~~~~i~dttLRDGeQ~~gv~~s~~~Ki~ia~~L~~~GV~~IE~G-f------P~~s~~e~ 81 (552)
T PRK03739 27 ITKAPIWCSVDLRDGNQALIEPMSPERKLRMFDLLVKIGFKEIEVG-F------PSASQTDF 81 (552)
T ss_pred cCCCCeEeeCCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEE-C------CCcChHHH
Confidence 5667889999999999999999999999999999999999999999 6 99998875
No 13
>COG0119 LeuA Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]
Probab=99.33 E-value=9.7e-13 Score=116.96 Aligned_cols=57 Identities=25% Similarity=0.142 Sum_probs=54.7
Q ss_pred ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564 97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa 153 (157)
.|.|.|+|||||.|+++..+++++|++|+++|.++|++.||+|+++++++.+|+..+
T Consensus 2 ~v~i~DtTLRDG~Q~~g~~~s~e~Ki~Ia~~Ld~lGv~~IE~g~p~~s~~~~~~~~~ 58 (409)
T COG0119 2 KVIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRA 58 (409)
T ss_pred CcEEEeCCCCcCCcCCCCcCCHHHHHHHHHHHHHcCCCEEEEeCCcCChhhHHHHHH
Confidence 589999999999999999999999999999999999999999999999999998754
No 14
>PLN03228 methylthioalkylmalate synthase; Provisional
Probab=99.32 E-value=1.1e-12 Score=119.30 Aligned_cols=56 Identities=20% Similarity=0.303 Sum_probs=52.7
Q ss_pred CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa 153 (157)
+..|.|.|+|||||+|+++..+++++|++|+++|.++||+.||+|+ |++.|+++++
T Consensus 82 ~~~V~I~DtTLRDGeQ~~gv~fs~eeKi~Ia~~L~~~GVd~IEvG~---Pa~s~~e~e~ 137 (503)
T PLN03228 82 KNYVRVLDTTLRDGEQSPGGSLTPPQKLEIARQLAKLRVDIMEVGF---PGSSEEEFEA 137 (503)
T ss_pred CCCeEEEeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeC---CCCCHHHHHH
Confidence 5689999999999999999999999999999999999999999998 8888888764
No 15
>TIGR02090 LEU1_arch isopropylmalate/citramalate/homocitrate synthases. Methanogens, then should and aparrently do contain all three of these enzymes. Unfortunately, phylogenetic trees do not resolve into three unambiguous clades, making assignment of function to particular genes problematic. Other archaea which lack a threonine dehydratase (mainly Euryarchaeota) should contain both a CimA and a LeuA gene. This is true of, for example, archaeoglobus fulgidis, but not for the Pyrococci which have none in this clade, but one in TIGR00973 and one in TIGRT00977 which may fulfill these roles. Other species which have only one hit to this model and lack threonine dehydratase are very likely LeuA enzymes.
Probab=99.31 E-value=2e-12 Score=111.66 Aligned_cols=56 Identities=29% Similarity=0.260 Sum_probs=52.8
Q ss_pred eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCC-------Ccccccccc
Q 031564 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSP-------KWVPQVADA 153 (157)
Q Consensus 98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsP-------K~VPQMADa 153 (157)
|.|.|+|||||.|+.+..+++++|+++++.|.++||+.||+|+|+++ +.+|++++.
T Consensus 1 i~i~DtTLRDG~Q~~~~~~s~~~k~~ia~~L~~~Gv~~IEvG~p~~~~~~~e~i~~i~~~~~~ 63 (363)
T TIGR02090 1 VYIFDTTLRDGEQTPGVSLTVEQKVEIARKLDELGVDVIEAGFPIASEGEFEAIKKISQEGLN 63 (363)
T ss_pred CEEEeCCCCCcCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHHhcCCC
Confidence 57999999999999999999999999999999999999999999999 888888753
No 16
>PRK11858 aksA trans-homoaconitate synthase; Reviewed
Probab=99.27 E-value=4.4e-12 Score=109.99 Aligned_cols=54 Identities=26% Similarity=0.367 Sum_probs=50.2
Q ss_pred CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF 155 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~ 155 (157)
|++|.|.|+|||||.|.++..+++++|++++++|.++||+.||+| +|+|++.+|
T Consensus 2 ~~~v~I~DtTLRDG~Q~~~~~~s~e~k~~ia~~L~~~GV~~IE~G-------~p~~~~~~~ 55 (378)
T PRK11858 2 PKDIEIVDTTLRDGEQTPGVVFTNEEKLAIARMLDEIGVDQIEAG-------FPAVSEDEK 55 (378)
T ss_pred CCeeEEEeCCCCccCcCCCCCCCHHHHHHHHHHHHHhCCCEEEEe-------CCCcChHHH
Confidence 567999999999999999999999999999999999999999998 688887764
No 17
>TIGR00970 leuA_yeast 2-isopropylmalate synthase, yeast type. A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases as found in yeasts and in a minority of studied bacteria.
Probab=99.26 E-value=4.3e-12 Score=116.27 Aligned_cols=51 Identities=24% Similarity=0.282 Sum_probs=48.6
Q ss_pred CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564 94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK 145 (157)
+.....|+|++||||+|+++..+++++|++|+++|.++||++||+| |++|+
T Consensus 23 ~~~~~~~~DtTLRDG~Q~~g~~~s~e~Ki~ia~~L~~~Gvd~IE~G-fp~~s 73 (564)
T TIGR00970 23 ITRAPRWLSTDLRDGNQALPDPMSPARKRRYFDLLVRIGFKEIEVG-FPSAS 73 (564)
T ss_pred cCcCCeEecCCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEe-CCCCC
Confidence 5566889999999999999999999999999999999999999999 99998
No 18
>TIGR00977 LeuA_rel 2-isopropylmalate synthase/homocitrate synthase family protein. This model represents uncharacterized proteins related to 2-isopropylmalate synthases and homocitrate synthases but phylogenetically distint. Each species represented in the seed alignment also has a member of a known family of 2-isopropylmalate synthases.
Probab=99.26 E-value=4.3e-12 Score=115.43 Aligned_cols=55 Identities=22% Similarity=0.164 Sum_probs=52.9
Q ss_pred ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee-cccCCCcccccc
Q 031564 97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT-SFVSPKWVPQVA 151 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg-SFVsPK~VPQMA 151 (157)
.|.|.|+|||||.|.++..+++++|++|+++|.++||+.||+| .++||+.+|+++
T Consensus 1 ~V~I~DtTLRDG~Q~~g~~~s~eeKl~Ia~~L~~~GVd~IE~G~p~~s~~d~~~v~ 56 (526)
T TIGR00977 1 SLWLYDTTLRDGAQREGVSFSLEDKIRIAERLDDLGIHYIEGGWPGANPKDVQFFW 56 (526)
T ss_pred CeEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHH
Confidence 4899999999999999999999999999999999999999999 799999999887
No 19
>cd07943 DRE_TIM_HOA 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate aldolase (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase. In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF ) and is inactive without it. HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate
Probab=99.25 E-value=8.5e-12 Score=102.19 Aligned_cols=56 Identities=20% Similarity=0.232 Sum_probs=50.8
Q ss_pred eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee-----cccCCCcccccccc
Q 031564 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT-----SFVSPKWVPQVADA 153 (157)
Q Consensus 98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg-----SFVsPK~VPQMADa 153 (157)
|.|.|||+|||+|..+..+++++|+++++.|.++||+.||+| ..++++++|+++|.
T Consensus 1 i~i~D~TlRDG~Q~~~~~~~~~~k~~i~~~L~~~Gv~~iEvg~~~~~~~~~~~~~~~~~~~ 61 (263)
T cd07943 1 VYIHDVTLRDGMHAVRHQFTLEQVRAIARALDAAGVPLIEVGHGDGLGGSSLNYGFAAHTD 61 (263)
T ss_pred CEEEeCCCCcCcccCCeecCHHHHHHHHHHHHHcCCCEEEeecCCCCCCcccccCCCCCCh
Confidence 679999999999999999999999999999999999999999 44555888998873
No 20
>cd07940 DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain. 2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis. This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein. This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein. AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin. AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-h
Probab=99.23 E-value=5.8e-12 Score=103.39 Aligned_cols=45 Identities=31% Similarity=0.341 Sum_probs=43.3
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeeccc-CC
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFV-SP 144 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFV-sP 144 (157)
|+|||||||+|+....+++++|++++++|.++||+.||+|+|+ +|
T Consensus 1 i~D~TlRDG~Q~~~~~~~~~~k~~i~~~L~~~Gv~~iEvg~~~~~~ 46 (268)
T cd07940 1 IFDTTLRDGEQTPGVSLTPEEKLEIARQLDELGVDVIEAGFPAASP 46 (268)
T ss_pred CCCCCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCCH
Confidence 5799999999999999999999999999999999999999998 67
No 21
>PRK12344 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional
Probab=99.22 E-value=1.3e-11 Score=112.04 Aligned_cols=56 Identities=20% Similarity=0.203 Sum_probs=52.9
Q ss_pred CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC------cccc
Q 031564 94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK------WVPQ 149 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK------~VPQ 149 (157)
||.+|.|.|++||||.|.++..+++++|+++++.|.++||+.||+|+ +++|+ ++++
T Consensus 2 ~~~~V~I~DtTLRDG~Q~~g~~~s~e~Kl~ia~~L~~~Gvd~IEvG~p~as~~d~~~~~~i~~ 64 (524)
T PRK12344 2 MMERIELYDTTLRDGAQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFKRAKE 64 (524)
T ss_pred CCCceEEEeCCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCcCChhHHHHHHHHHH
Confidence 57789999999999999999999999999999999999999999999 88998 7776
No 22
>PRK09389 (R)-citramalate synthase; Provisional
Probab=99.21 E-value=1.6e-11 Score=110.51 Aligned_cols=56 Identities=27% Similarity=0.317 Sum_probs=51.7
Q ss_pred ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC-------ccccccc
Q 031564 97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK-------WVPQVAD 152 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK-------~VPQMAD 152 (157)
+|.|.|++||||.|.++..+++++|++++++|.++||+.||+|+|++++ .+++++.
T Consensus 2 ~i~I~DtTLRDG~Q~~g~~~s~e~K~~ia~~L~~~Gv~~IE~G~p~~~~~d~e~v~~i~~~~~ 64 (488)
T PRK09389 2 MVRILDTTLRDGEQTPGVSLTPEEKLEIARKLDELGVDVIEAGSAITSEGEREAIKAVTDEGL 64 (488)
T ss_pred ceEEEeCCCCCcCCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCcCCHHHHHHHHHHHhcCC
Confidence 4899999999999999999999999999999999999999999999987 6766543
No 23
>PRK00915 2-isopropylmalate synthase; Validated
Probab=99.18 E-value=3e-11 Score=108.97 Aligned_cols=52 Identities=29% Similarity=0.283 Sum_probs=48.5
Q ss_pred CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC
Q 031564 94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK 145 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK 145 (157)
||..|.|.|++||||.|.++..+++++|++++++|.++||+.||+|+ ++||+
T Consensus 1 m~~~v~I~DtTLRDG~Q~~g~~~s~e~K~~ia~~L~~~Gv~~IE~G~p~~s~~ 53 (513)
T PRK00915 1 MMDRVIIFDTTLRDGEQSPGASLTVEEKLQIAKQLERLGVDVIEAGFPASSPG 53 (513)
T ss_pred CCCCcEEEECCCCcCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCCCChH
Confidence 46789999999999999999999999999999999999999999998 56764
No 24
>TIGR02660 nifV_homocitr homocitrate synthase NifV. This family consists of the NifV clade of homocitrate synthases, most of which are found in operons for nitrogen fixation. Members are closely homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by this enzyme becomes a part of the iron-molybdenum cofactor of nitrogenase.
Probab=99.13 E-value=5.3e-11 Score=102.52 Aligned_cols=51 Identities=24% Similarity=0.293 Sum_probs=47.6
Q ss_pred eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF 155 (157)
Q Consensus 98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~ 155 (157)
|.|.|+|+|||.|.....+++++|+++++.|.++||+.||+| +|+|++.+|
T Consensus 2 v~i~D~TLRDG~Q~~~~~~s~~~k~~ia~~L~~~Gv~~IEvG-------~p~~~~~~~ 52 (365)
T TIGR02660 2 VIINDTTLRDGEQAPGVAFTAAEKLAIARALDEAGVDELEVG-------IPAMGEEER 52 (365)
T ss_pred cEEEeCCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEe-------CCCCCHHHH
Confidence 789999999999999999999999999999999999999998 678877654
No 25
>TIGR00973 leuA_bact 2-isopropylmalate synthase, bacterial type. A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases found primarily in Bacteria. The homologous families in the Archaea may represent isozymes and/or related enzymes.
Probab=99.08 E-value=1.4e-10 Score=104.47 Aligned_cols=49 Identities=24% Similarity=0.242 Sum_probs=46.7
Q ss_pred ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564 97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK 145 (157)
+|.|.|+|+|||.|.++..+++++|++++++|.++||+.||+|+|++++
T Consensus 1 ~v~I~DtTLRDG~Q~~g~~~s~e~K~~ia~~L~~~GV~~IEvG~p~~s~ 49 (494)
T TIGR00973 1 RIIIFDTTLRDGEQSPGASLTVEEKLQIALALERLGVDIIEAGFPVSSP 49 (494)
T ss_pred CeEEEECCCCccCcCCCCCcCHHHHHHHHHHHHHcCCCEEEEECCCCCH
Confidence 4889999999999999999999999999999999999999999998864
No 26
>TIGR03217 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase. Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated.
Probab=99.05 E-value=2.3e-10 Score=98.62 Aligned_cols=56 Identities=20% Similarity=0.181 Sum_probs=51.5
Q ss_pred ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee--------cccC-CCccccccc
Q 031564 97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT--------SFVS-PKWVPQVAD 152 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg--------SFVs-PK~VPQMAD 152 (157)
+|.|.|||+|||.|.....+++++|++++++|.++||+.||+| ||.. +.++|++.+
T Consensus 2 ~i~i~D~TLRDG~q~~~~~f~~~~~~~ia~~Ld~aGV~~IEvg~g~gl~g~s~~~G~~~~~~~e~ 66 (333)
T TIGR03217 2 KLYITDVTLRDGMHAIRHQFTIEQVRAIAAALDEAGVDAIEVTHGDGLGGSSFNYGFSAHTDLEY 66 (333)
T ss_pred CcEEEECCCCCCCcCCCCcCCHHHHHHHHHHHHHcCCCEEEEecCCCCCCccccCCCCCCChHHH
Confidence 5899999999999999999999999999999999999999997 8886 788887653
No 27
>PRK12331 oxaloacetate decarboxylase; Provisional
Probab=98.99 E-value=5.6e-10 Score=100.27 Aligned_cols=50 Identities=22% Similarity=0.256 Sum_probs=47.2
Q ss_pred CceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee---------cccCCC
Q 031564 96 GFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT---------SFVSPK 145 (157)
Q Consensus 96 ~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg---------SFVsPK 145 (157)
++|.|+|+|+|||.|++ ...++|++|+++++.|.++|+..||++ +|++|+
T Consensus 2 ~~V~I~DtTlRDG~Qs~~~~~~~t~dkl~ia~~Ld~~Gv~~IE~~ggatf~~~~~f~~e~ 61 (448)
T PRK12331 2 TKIKITETVLRDGQQSLIATRMTTEEMLPILEKLDNAGYHSLEMWGGATFDACLRFLNED 61 (448)
T ss_pred CccEEEECCCCccccCcCCcccCHHHHHHHHHHHHHcCCCEEEecCCccchhhhccCCCC
Confidence 46999999999999998 779999999999999999999999999 899986
No 28
>PRK08195 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated
Probab=98.99 E-value=8.1e-10 Score=95.30 Aligned_cols=53 Identities=25% Similarity=0.286 Sum_probs=48.9
Q ss_pred CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee--------ccc-CCCccc
Q 031564 96 GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT--------SFV-SPKWVP 148 (157)
Q Consensus 96 ~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg--------SFV-sPK~VP 148 (157)
++|.|.|||+|||.|.....+++++|++++++|.++||+.||+| ||+ .+.++|
T Consensus 2 ~~i~I~D~TLRDG~q~~~~~f~~~~~~~i~~~L~~aGv~~IEvg~~~g~g~~s~~~g~~~~~ 63 (337)
T PRK08195 2 KKIYISDVTLRDGMHAVRHQYTLEQVRAIARALDAAGVPVIEVTHGDGLGGSSFNYGFGAHT 63 (337)
T ss_pred CceEEEECCCCCcCcCCCCccCHHHHHHHHHHHHHcCCCEEEeecCCCCCCccccCCCCCCC
Confidence 46999999999999999999999999999999999999999997 887 776665
No 29
>PRK14041 oxaloacetate decarboxylase; Provisional
Probab=98.93 E-value=1.2e-09 Score=98.86 Aligned_cols=49 Identities=18% Similarity=0.207 Sum_probs=46.1
Q ss_pred ceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeee---------ecccCCC
Q 031564 97 FVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEA---------TSFVSPK 145 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEv---------gSFVsPK 145 (157)
+|.|.||++|||.|++ ...++|++|++++++|.++|+..||+ ++|++|+
T Consensus 2 ~V~I~DtTlRDG~Qs~~~~~~~t~dkl~Ia~~Ld~~Gv~~IE~~ggatfd~~~~Fl~e~ 60 (467)
T PRK14041 2 KVMFVDTTLRDGHQSLIATRMRTEDMLPALEAFDRMGFYSMEVWGGATFDVCVRFLNEN 60 (467)
T ss_pred ceEEEECCCCccccCcCCccCCHHHHHHHHHHHHHcCCCEEEecCCccchhhhcccCCC
Confidence 4899999999999998 58999999999999999999999999 7899876
No 30
>cd07939 DRE_TIM_NifV Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain. FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase. The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic. This protein is also required for assembly of the nitrogenase MoFe complex but its exact role is unknown. This family also includes the NifV proteins of Heliobacterium chlorum and Gluconacetobacter diazotrophicus, which appear to be orthologous to FrbC. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarbox
Probab=98.89 E-value=1.5e-09 Score=88.89 Aligned_cols=42 Identities=21% Similarity=0.200 Sum_probs=39.9
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecc
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSF 141 (157)
|.|||||||+|+....+++++|+++++.|.++||+.||+|..
T Consensus 1 i~D~TlRDG~Q~~~~~~~~~~k~~i~~~L~~~Gv~~iE~g~p 42 (259)
T cd07939 1 INDTTLRDGEQAPGVAFSREEKLAIARALDEAGVDEIEVGIP 42 (259)
T ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 579999999999999999999999999999999999999954
No 31
>TIGR02146 LysS_fung_arch homocitrate synthase. This model includes the yeast LYS21 gene which carries out the first step of the alpha-aminoadipate (AAA) lysine biosynthesis pathway. A related pathway is found in Thermus thermophilus. This enzyme is closely related to 2-isopropylmalate synthase (LeuA) and citramalate synthase (CimA), both of which are present in the euryarchaeota. Some archaea have a separate homocitrate synthase (AksA) which also synthesizes longer homocitrate analogs.
Probab=98.87 E-value=1.4e-09 Score=90.06 Aligned_cols=51 Identities=25% Similarity=0.246 Sum_probs=47.3
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa 153 (157)
|.|+++|||.|++...+++++|+++++.|.++|++.||+|+ |++.||++++
T Consensus 1 i~D~TlRDG~q~~~~~~~~~~ki~i~~~l~~~Gv~~iE~g~---p~~~~~~~~~ 51 (344)
T TIGR02146 1 IIDSTLREGEQFPGANFSTEQKIEIAKALDEFGIDYIEVTH---PAASKQSRID 51 (344)
T ss_pred CCCCCCCccCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEeC---CCCCHHHHHH
Confidence 57899999999999999999999999999999999999998 8889988643
No 32
>PRK14847 hypothetical protein; Provisional
Probab=98.73 E-value=1.6e-08 Score=88.80 Aligned_cols=59 Identities=22% Similarity=0.273 Sum_probs=52.2
Q ss_pred CcccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564 79 TDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 79 ~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
-....|.-+.|.....|. |.|+++|||.|..+..++.++|++|+++|.++||+.||||.
T Consensus 17 ~~~~~~~w~~~~~~~~p~---~~DTTLRDGeQ~pGv~fs~eeKl~IA~~L~~lGVd~IEvG~ 75 (333)
T PRK14847 17 ADHAERAWPARRPAAAPI---WMSTDLRDGNQALIEPMDGARKLRLFEQLVAVGLKEIEVAF 75 (333)
T ss_pred CCCccCCCcccccCCCCc---eecCCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCEEEeeC
Confidence 345556667777777776 99999999999999999999999999999999999999996
No 33
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit. This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.
Probab=98.69 E-value=1.5e-08 Score=93.71 Aligned_cols=46 Identities=20% Similarity=0.156 Sum_probs=43.1
Q ss_pred EEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee---------cccCCC
Q 031564 100 IVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT---------SFVSPK 145 (157)
Q Consensus 100 IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg---------SFVsPK 145 (157)
|.|+++|||+|++ ...++|++|+++++.|.++|+..||++ +|++++
T Consensus 1 I~DtTlRDG~Qs~~~~~~~t~dkl~ia~~L~~~Gv~~IE~~GGatfd~~~~f~~e~ 56 (582)
T TIGR01108 1 ITDVVLRDAHQSLFATRMRTEDMLPIAEKLDDVGYWSLEVWGGATFDACIRFLNED 56 (582)
T ss_pred CccCCCCccccccCCccCCHHHHHHHHHHHHHcCCCEEEecCCcccccccccCCCC
Confidence 6799999999998 679999999999999999999999998 888876
No 34
>PRK09282 pyruvate carboxylase subunit B; Validated
Probab=98.52 E-value=1.3e-07 Score=87.72 Aligned_cols=44 Identities=20% Similarity=0.098 Sum_probs=41.6
Q ss_pred CceEEEEeccCccccCCC-CCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 96 GFVKIVEVGPRDGLQNEK-NIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 96 ~~V~IvEVGpRDGLQne~-~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
++|.|.|+++|||.|+.. ..++|++|++++..|.++|+..||++
T Consensus 2 ~~v~i~DtTlRDG~Qs~~atr~~t~d~l~ia~~l~~~G~~~iE~~ 46 (592)
T PRK09282 2 KKVKITDTTLRDAHQSLLATRMRTEDMLPIAEKLDKVGFWSLEVW 46 (592)
T ss_pred CccEEEECCCCccccccCCccCCHHHHHHHHHHHHHcCCCEEEec
Confidence 459999999999999985 68999999999999999999999998
No 35
>cd07937 DRE_TIM_PC_TC_5S Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain. This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit. Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions catalyzed by TC. The first reaction involves the transfer of carbon dioxide from methylmalonyl-CoA to the 1.3S biotin, and is catalyzed by the 12S subunit. These two steps allow a carboxylate group to be transferred from oxaloacetate to propionyl-CoA to yield pyruvate and methylmalonyl-CoA. The catalytic domain of transcarboxylase 5S has a canonical TIM-barrel fold with a large C-terminal extension that forms a funnel leading to the active site. Transcarboxylase 5S forms a homodimer and there are six dimers per complex
Probab=98.44 E-value=1e-07 Score=79.48 Aligned_cols=41 Identities=17% Similarity=0.139 Sum_probs=39.1
Q ss_pred EEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564 100 IVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 100 IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
|.|+|+|||.|.. +..+++++|++++..|.++||+.||+|.
T Consensus 1 i~DtTlRDG~Qs~~~~~~~~~~~~~ia~~L~~~Gv~~iE~G~ 42 (275)
T cd07937 1 ITDTTLRDAHQSLLATRMRTEDMLPIAEALDEAGFFSLEVWG 42 (275)
T ss_pred CCcCcccchhhchhceeccHHHHHHHHHHHHHcCCCEEEccC
Confidence 5799999999998 8999999999999999999999999996
No 36
>cd07944 DRE_TIM_HOA_like 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain. This family of bacterial enzymes is sequence-similar to 4-hydroxy-2-oxovalerate aldolase (HOA) but its exact function is unknown. This family includes the Bacteroides vulgatus Bvu_2661 protein and belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues t
Probab=98.32 E-value=5.9e-07 Score=74.94 Aligned_cols=44 Identities=20% Similarity=0.144 Sum_probs=41.1
Q ss_pred EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVS 143 (157)
Q Consensus 100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs 143 (157)
|.|+|+|||.|.....+++++|++++..|.++||+.||+|.-.+
T Consensus 1 i~D~TLRDG~q~~~~~f~~~~~~~ia~~L~~~GVd~IEvG~~~~ 44 (266)
T cd07944 1 ILDCTLRDGGYVNNWDFGDEFVKAIYRALAAAGIDYVEIGYRSS 44 (266)
T ss_pred CccCCcccCccccCccCCHHHHHHHHHHHHHCCCCEEEeecCCC
Confidence 57999999999999999999999999999999999999997544
No 37
>PRK12330 oxaloacetate decarboxylase; Provisional
Probab=98.01 E-value=7.7e-06 Score=75.26 Aligned_cols=46 Identities=20% Similarity=0.133 Sum_probs=43.1
Q ss_pred CCCceEEEEeccCccccCCC-CCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 94 VPGFVKIVEVGPRDGLQNEK-NIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~-~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
|++.|.|.|+++|||.|... .-++|++|+.++..|.++|+..||++
T Consensus 1 ~~~~i~i~DTTLRDG~QSl~atr~~t~d~l~ia~~ld~~G~~siE~~ 47 (499)
T PRK12330 1 MPRKIGVTELALRDAHQSLMATRMAMEDMVGACEDIDNAGYWSVECW 47 (499)
T ss_pred CCCCcEEEECCccchhhcccCccCCHHHHHHHHHHHHhcCCCEEEec
Confidence 45679999999999999976 89999999999999999999999997
No 38
>PRK14040 oxaloacetate decarboxylase; Provisional
Probab=98.01 E-value=7.9e-06 Score=76.14 Aligned_cols=45 Identities=18% Similarity=0.039 Sum_probs=42.3
Q ss_pred CCceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 95 PGFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
.++|.|.|+++|||.|.. ...++|++|+.++..|.++|+..||++
T Consensus 2 ~k~v~i~DtTLRDG~Qs~~~tr~~~~d~l~ia~~ld~~G~~siE~~ 47 (593)
T PRK14040 2 SKPLAITDVVLRDAHQSLFATRLRLDDMLPIAAKLDKVGYWSLESW 47 (593)
T ss_pred CCccEEEECCcccccccccccccCHHHHHHHHHHHHHcCCCEEEec
Confidence 457999999999999999 779999999999999999999999994
No 39
>KOG2367 consensus Alpha-isopropylmalate synthase/homocitrate synthase [Amino acid transport and metabolism]
Probab=97.90 E-value=1.4e-05 Score=74.54 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=46.8
Q ss_pred CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564 94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVS 143 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs 143 (157)
.|..|++.+.++|||.|..+.++.+++|+++.++|...||+.||+|+=|.
T Consensus 54 ~~n~vr~~dttLRdGeQs~ga~~~~~qK~eiar~L~~~gvd~IEv~fP~a 103 (560)
T KOG2367|consen 54 DVNYVRVLDTTLRDGEQSPGAFLTTEQKLEIARQLAKLGVDIIEVGFPVA 103 (560)
T ss_pred CcCcceeecccccccccCCCCcCCcHHHHHHHHHHHhcCcCEEEecCccc
Confidence 46789999999999999999999999999999999999999999998554
No 40
>PRK12581 oxaloacetate decarboxylase; Provisional
Probab=97.44 E-value=0.0002 Score=65.77 Aligned_cols=46 Identities=22% Similarity=0.180 Sum_probs=41.9
Q ss_pred CCCceEEEEeccCccccC-CCCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 94 VPGFVKIVEVGPRDGLQN-EKNIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGLQn-e~~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
|.++|.|.|+++|||-|. ..+-+.|++.+.++..|.++|+..||++
T Consensus 9 ~~~~v~i~DtTlRDg~QSl~atr~~t~d~l~ia~~ld~~G~~siE~w 55 (468)
T PRK12581 9 MQQQVAITETVLRDGHQSLMATRLSIEDMLPVLTILDKIGYYSLECW 55 (468)
T ss_pred cCCceEEEECCccchhhhccccCCCHHHHHHHHHHHHhcCCCEEEec
Confidence 345799999999999999 5666999999999999999999999995
No 41
>PRK12999 pyruvate carboxylase; Reviewed
Probab=97.39 E-value=0.0002 Score=71.13 Aligned_cols=46 Identities=15% Similarity=0.005 Sum_probs=43.5
Q ss_pred CCceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhC--CCCeeeeec
Q 031564 95 PGFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSS--GLPVVEATS 140 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~A--Gv~~IEvgS 140 (157)
.++|.|.|+++|||.|.. ..-+.|++|+.++..|.++ |+..||++.
T Consensus 530 ~~~v~i~DtTlRDg~Qs~~atr~~~~d~l~ia~~l~~~~~g~~siE~~g 578 (1146)
T PRK12999 530 QKRVLLTDTTFRDAHQSLLATRVRTKDLLRIAPATARLLPNLFSLEMWG 578 (1146)
T ss_pred cCCcEEEECCcchhhhccccccCCHHHHHHHHHHHHHHhCCCCEEEeeC
Confidence 457999999999999997 7999999999999999999 999999996
No 42
>PRK14042 pyruvate carboxylase subunit B; Provisional
Probab=95.98 E-value=0.0092 Score=56.30 Aligned_cols=45 Identities=16% Similarity=0.042 Sum_probs=41.7
Q ss_pred CceEEEEeccCcccc-CCCCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564 96 GFVKIVEVGPRDGLQ-NEKNIVPAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 96 ~~V~IvEVGpRDGLQ-ne~~~vpTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
++|.|.|+++|||-| ...+-+.|++=+.++..|.++|+..||++.
T Consensus 2 ~~~~i~DttlRDg~QSl~atr~~t~d~~~ia~~~d~~g~~siE~~g 47 (596)
T PRK14042 2 SKTFITDVTLRDAHQCLIATRMRTEDMLPICNKMDDVGFWAMEVWG 47 (596)
T ss_pred CceEEEECCcchhhhhhhhcCCCHHHHHHHHHHHHhcCCCEEEeeC
Confidence 469999999999999 678899999999999999999999999974
No 43
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]
Probab=90.57 E-value=0.13 Score=48.03 Aligned_cols=44 Identities=20% Similarity=0.129 Sum_probs=39.7
Q ss_pred CceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 96 GFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 96 ~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
..|.|.|+.+|||.|+. .+-+.|++=+-+++.|.++|+-.+|+.
T Consensus 4 k~i~itdt~lRDghQSl~ATRmrt~DmlPi~e~lD~~G~~slE~W 48 (472)
T COG5016 4 KKIKITDTVLRDGHQSLLATRMRTEDMLPIAEALDKVGYWSLEVW 48 (472)
T ss_pred ceeeeEeeeechHHHHHHHHHHhHHhhHHHHHHHHhcCeeEEEec
Confidence 56999999999999997 446889999999999999999999985
No 44
>PF04481 DUF561: Protein of unknown function (DUF561); InterPro: IPR007570 Protein in this entry are of unknown function and are found in cyanobacteria and the chloroplasts of algae. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=80.94 E-value=2.3 Score=37.02 Aligned_cols=60 Identities=20% Similarity=0.315 Sum_probs=47.3
Q ss_pred ccccccccccCCCCcccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeee
Q 031564 66 NGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEA 138 (157)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEv 138 (157)
++|-.++.|+. .++-.++.+.+.-+|+- .+.=+ .|+++|.++-++|...|.++|++-|+-
T Consensus 92 sFY~qGr~f~a----~eVL~Lt~~tR~LLP~~-~LsVT--------VPHiL~ld~Qv~LA~~L~~~GaDiIQT 151 (242)
T PF04481_consen 92 SFYAQGRRFSA----EEVLALTRETRSLLPDI-TLSVT--------VPHILPLDQQVQLAEDLVKAGADIIQT 151 (242)
T ss_pred HHHhcCCeecH----HHHHHHHHHHHHhCCCC-ceEEe--------cCccccHHHHHHHHHHHHHhCCcEEEc
Confidence 66666777654 47778888888888883 33322 579999999999999999999999974
No 45
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=79.24 E-value=2.5 Score=35.02 Aligned_cols=33 Identities=36% Similarity=0.441 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeecccCCCcccc
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQ 149 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQ 149 (157)
.+.++=+++++.|.+.|++.||+| |.+|.+...
T Consensus 24 ~~~~~a~~i~~al~~~Gi~~iEit-l~~~~~~~~ 56 (212)
T PRK05718 24 NKLEDAVPLAKALVAGGLPVLEVT-LRTPAALEA 56 (212)
T ss_pred CCHHHHHHHHHHHHHcCCCEEEEe-cCCccHHHH
Confidence 577888999999999999999999 888887643
No 46
>TIGR01235 pyruv_carbox pyruvate carboxylase. This enzyme plays a role in gluconeogensis but not glycolysis.
Probab=77.93 E-value=2.9 Score=42.63 Aligned_cols=45 Identities=16% Similarity=0.022 Sum_probs=39.7
Q ss_pred CceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhC--CCCeeeeec
Q 031564 96 GFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSS--GLPVVEATS 140 (157)
Q Consensus 96 ~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~A--Gv~~IEvgS 140 (157)
++|.|.|+++|||-|+. .+-+.|++=+.++..+..+ |+-.+|+..
T Consensus 529 ~~~~~tdtt~RD~hQSl~atr~rt~d~~~ia~~~~~~~~g~~s~E~wg 576 (1143)
T TIGR01235 529 KRVLLTDTTFRDAHQSLLATRVRTHDLAKIAPTTSHALPNLFSLECWG 576 (1143)
T ss_pred CCeeEEECcccchhhhhhhhCCCHHHHHHHHHHHHHhcCCceEEEeeC
Confidence 56999999999999997 4578899999999999984 999999863
No 47
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=76.13 E-value=7.6 Score=33.88 Aligned_cols=68 Identities=12% Similarity=0.051 Sum_probs=45.6
Q ss_pred CcccchhhHhhhhcCCCCceEEEEeccCccc-----c-CCCCCCCHH-HHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 79 TDNSTKDLTSKLLGRVPGFVKIVEVGPRDGL-----Q-NEKNIVPAV-VKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 79 ~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGL-----Q-ne~~~vpTe-~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
...+++.....+..--|+.|.+...++..|= | .....+|.+ ++.+ ..+.|.++|..+.|+..|+.|..
T Consensus 168 t~~~~~~~l~~~~~l~~~~is~y~l~~~~gT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~Gy~~yeis~fa~~~~ 246 (370)
T PRK06294 168 SLSDFIVDLHQAITLPITHISLYNLTIDPHTSFYKHRKRLLPSIADEEILAEMSLAAEELLTSQGFTRYELASYAKPQA 246 (370)
T ss_pred CHHHHHHHHHHHHccCCCeEEEeeeEecCCChHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHcCCCeeeeeeeeCCCc
Confidence 3344455455555556888999988888882 1 222234543 3343 45679999999999999999864
No 48
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=61.24 E-value=27 Score=30.59 Aligned_cols=69 Identities=7% Similarity=0.081 Sum_probs=46.9
Q ss_pred CCcccchhhHhhhhcCCCCceEEEEeccCcc--ccCCCCCCCHHHHH----HHHHHHHhCCCCeeeeecccC-CCc
Q 031564 78 CTDNSTKDLTSKLLGRVPGFVKIVEVGPRDG--LQNEKNIVPAVVKV----ELIKLLVSSGLPVVEATSFVS-PKW 146 (157)
Q Consensus 78 ~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDG--LQne~~~vpTe~KI----eLI~~L~~AGv~~IEvgSFVs-PK~ 146 (157)
.+..+++.....+..--|+.|.+.-..++.| +-.....++.+.+. ++.+.|.++|..+-|+.+|.. |..
T Consensus 167 qt~e~~~~tl~~~~~l~p~~is~y~L~~~~gT~l~~~~~~~~~~~~~~~~~~~~~~L~~~Gy~~yeisnfa~~~~~ 242 (353)
T PRK05904 167 LKLKDLDEVFNFILKHKINHISFYSLEIKEGSILKKYHYTIDEDKEAEQLNYIKAKFNKLNYKRYEVSNWTNNFKY 242 (353)
T ss_pred CCHHHHHHHHHHHHhcCCCEEEEEeeEecCCChHhhcCCCCChHHHHHHHHHHHHHHHHcCCcEEechhhcCCCCc
Confidence 3344555555555555688999999999988 33222224554444 456779999999999999998 544
No 49
>KOG3728 consensus Uridine phosphorylase [Nucleotide transport and metabolism]
Probab=58.31 E-value=7.9 Score=34.61 Aligned_cols=25 Identities=20% Similarity=0.239 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeec
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
.+..+|.+++++|.++|++-||.-|
T Consensus 226 ysEkdK~afLek~~a~GVrNIEMEs 250 (308)
T KOG3728|consen 226 YSEKDKMAFLEKLHALGVRNIEMES 250 (308)
T ss_pred cchhhHHHHHHHHHHcCceeeehhH
Confidence 4778999999999999999998754
No 50
>COG0800 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]
Probab=58.19 E-value=13 Score=31.72 Aligned_cols=30 Identities=27% Similarity=0.368 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeecccCCCc
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
...|+=+.++++|++.|++.||+|- -+|.+
T Consensus 22 ~~~e~a~~~a~Ali~gGi~~IEITl-~sp~a 51 (211)
T COG0800 22 DDVEEALPLAKALIEGGIPAIEITL-RTPAA 51 (211)
T ss_pred CCHHHHHHHHHHHHHcCCCeEEEec-CCCCH
Confidence 4677889999999999999999985 55544
No 51
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=57.23 E-value=14 Score=31.05 Aligned_cols=34 Identities=21% Similarity=0.059 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeecccCCCccccc
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQM 150 (157)
.+.++=++++++|.+.|++.||+|. -+|.+.+.+
T Consensus 24 ~~~~~a~~~~~al~~gGi~~iEiT~-~tp~a~~~i 57 (222)
T PRK07114 24 ADVEVAKKVIKACYDGGARVFEFTN-RGDFAHEVF 57 (222)
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEeC-CCCcHHHHH
Confidence 4778889999999999999999985 777776654
No 52
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=56.13 E-value=31 Score=30.49 Aligned_cols=66 Identities=14% Similarity=0.222 Sum_probs=42.6
Q ss_pred ccchhhHhhhhcCCCCceEEEEeccCccc----c--CCCCCCCH-HHHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 81 NSTKDLTSKLLGRVPGFVKIVEVGPRDGL----Q--NEKNIVPA-VVKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 81 ~~~~~~~~~~~~~~P~~V~IvEVGpRDGL----Q--ne~~~vpT-e~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
.+++.-...+..--|+.|.+.-..+..|= | .-...+|. +++.+ ..+.|.++|..+.|+..|+.|..
T Consensus 182 e~~~~tl~~~~~l~p~~is~y~L~~~pgT~l~~~~~~g~~~~~~~~~~~~~~~~~~~~L~~~Gy~~yeisnfa~~g~ 258 (400)
T PRK07379 182 EDWQASLEAAIALNPTHLSCYDLVLEPGTAFGKQYQPGKAPLPSDETTAAMYRLAQEILTQAGYEHYEISNYAKPGY 258 (400)
T ss_pred HHHHHHHHHHHcCCCCEEEEecceecCCchhHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHcCCceeeeeheECCCh
Confidence 34444444445455888888877777772 1 11122343 44443 45679999999999999999853
No 53
>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase. Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo.
Probab=56.02 E-value=24 Score=30.44 Aligned_cols=70 Identities=11% Similarity=0.072 Sum_probs=46.6
Q ss_pred CCCCcccchhhHhhhhcCCCCceEEEEeccCcc--ccCCCCCCCH-HHHHH----HHHHHHhCCCCeeeeecccCCC
Q 031564 76 SSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDG--LQNEKNIVPA-VVKVE----LIKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDG--LQne~~~vpT-e~KIe----LI~~L~~AGv~~IEvgSFVsPK 145 (157)
+..+..++.+....+..--|+.|.+.-..|..| +-.....+|. +++.+ ..+.|.++|+.+.|+..|+.|.
T Consensus 162 Pgqt~~~~~~~l~~~~~l~~~~is~y~l~~~~gT~~~~~~~~~~~~~~~~~~~~~~~~~L~~~Gy~~yei~~fa~~~ 238 (360)
T TIGR00539 162 PLQTLNSLKEELKLAKELPINHLSAYALSVEPNTNFEKNAKKLPDDDSCAHFDEVVREILEGFGFKQYEVSNYAKAG 238 (360)
T ss_pred CCCCHHHHHHHHHHHHccCCCEEEeecceEcCCChhhhhhhcCcCHHHHHHHHHHHHHHHHHcCCceeehhhhcCCC
Confidence 334445556655666666688899988888888 2221112344 44444 3466889999999999999985
No 54
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=54.72 E-value=17 Score=30.21 Aligned_cols=34 Identities=26% Similarity=0.365 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeecccCCCccccc
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQM 150 (157)
.+.++=+++++.|.+.|++.||+|. -+|.+...+
T Consensus 13 ~~~~~a~~ia~al~~gGi~~iEit~-~tp~a~~~I 46 (201)
T PRK06015 13 DDVEHAVPLARALAAGGLPAIEITL-RTPAALDAI 46 (201)
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEeC-CCccHHHHH
Confidence 3677889999999999999999986 688876654
No 55
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=54.59 E-value=44 Score=28.89 Aligned_cols=66 Identities=14% Similarity=0.148 Sum_probs=41.2
Q ss_pred ccchhhHhhhhcCCCCceEEEEeccCcc--cc---CCCC--CCCHHHHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 81 NSTKDLTSKLLGRVPGFVKIVEVGPRDG--LQ---NEKN--IVPAVVKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 81 ~~~~~~~~~~~~~~P~~V~IvEVGpRDG--LQ---ne~~--~vpTe~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
.++.+....+..--|..|.+.-..++.| +- ..+. ..+.+.+.+ ..+.|.++|..++|+..|+.|..
T Consensus 167 ~~~~~~l~~~~~l~~~~i~~y~l~~~pgT~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~Gy~~~~~~~fa~~~~ 243 (377)
T PRK08599 167 EDFKESLAKALALDIPHYSAYSLILEPKTVFYNLMRKGKLRLPGEDLEAEMYEYLMDEMEAHGFHQYEISNFAKPGF 243 (377)
T ss_pred HHHHHHHHHHHccCCCEEeeeceeecCCChhHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHcCCcEeeeeeeeCCCh
Confidence 4444444444444567777776666665 21 1111 223445554 56789999999999999999864
No 56
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=53.66 E-value=18 Score=29.88 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeecccCCCcccccc
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVA 151 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMA 151 (157)
+.++=+.+++.|.+.|++.||+|. -+|.+...++
T Consensus 23 ~~~~a~~~~~al~~~Gi~~iEit~-~~~~a~~~i~ 56 (213)
T PRK06552 23 SKEEALKISLAVIKGGIKAIEVTY-TNPFASEVIK 56 (213)
T ss_pred CHHHHHHHHHHHHHCCCCEEEEEC-CCccHHHHHH
Confidence 788889999999999999999986 6888766543
No 57
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=53.45 E-value=27 Score=30.73 Aligned_cols=60 Identities=12% Similarity=0.092 Sum_probs=41.0
Q ss_pred HhhhhcCCCCceEEEEeccCccccC--CCCCCCHHHH-H----HHHHHHHhCCCCeeeeecccCCCc
Q 031564 87 TSKLLGRVPGFVKIVEVGPRDGLQN--EKNIVPAVVK-V----ELIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 87 ~~~~~~~~P~~V~IvEVGpRDGLQn--e~~~vpTe~K-I----eLI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
...+..--|+.|.+....+..|--. ....+|.+++ . ...+.|.++|..+.|+..|+.|..
T Consensus 194 l~~~~~l~p~~is~y~l~~~~gT~l~~~~~~~~~~~~~~~~~~~~~~~L~~~Gy~~ye~~~fa~~~~ 260 (394)
T PRK08898 194 VETALAFGPPHLSLYHLTLEPNTLFAKFPPALPDDDASADMQDWIEARLAAAGYAHYEVSAYAKPGR 260 (394)
T ss_pred HHHHHhcCCCEEEEeeeEECCCChhhhccCCCCChHHHHHHHHHHHHHHHHcCCchhccccccCCCc
Confidence 3444444578899888888877422 2223454433 2 346789999999999999999854
No 58
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=53.42 E-value=15 Score=30.41 Aligned_cols=32 Identities=19% Similarity=0.258 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeecccCCCccc
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATSFVSPKWVP 148 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VP 148 (157)
.+.++=++++++|.+.|++.||+|. -+|.+.-
T Consensus 17 ~~~~~a~~~~~al~~gGi~~iEiT~-~t~~a~~ 48 (196)
T PF01081_consen 17 DDPEDAVPIAEALIEGGIRAIEITL-RTPNALE 48 (196)
T ss_dssp SSGGGHHHHHHHHHHTT--EEEEET-TSTTHHH
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEec-CCccHHH
Confidence 4566778999999999999999986 5565543
No 59
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=52.71 E-value=19 Score=29.89 Aligned_cols=32 Identities=28% Similarity=0.277 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHHhCCCCeeeeecccCCCccc
Q 031564 116 VPAVVKVELIKLLVSSGLPVVEATSFVSPKWVP 148 (157)
Q Consensus 116 vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VP 148 (157)
.+.++=+++++.|.+.|++.||+|. -+|.+..
T Consensus 17 ~~~e~a~~~~~al~~~Gi~~iEit~-~t~~a~~ 48 (204)
T TIGR01182 17 DDVDDALPLAKALIEGGLRVLEVTL-RTPVALD 48 (204)
T ss_pred CCHHHHHHHHHHHHHcCCCEEEEeC-CCccHHH
Confidence 3677889999999999999999987 6777754
No 60
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=51.47 E-value=28 Score=29.95 Aligned_cols=69 Identities=20% Similarity=0.181 Sum_probs=44.1
Q ss_pred CCcccchhhHhhhhcCCCCceEEEEeccCccccCC------CCCCCHH-HHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 78 CTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNE------KNIVPAV-VKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 78 ~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne------~~~vpTe-~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
.+..++++....+..--|+.|.+.-..+..|=+.. ...+|++ ++.+ ..+.|.++|..+.|+..|+.|..
T Consensus 163 qt~e~~~~~l~~~~~l~~~~is~y~l~~~pgT~l~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~Gy~~ye~~~fa~~~~ 242 (374)
T PRK05799 163 QTLEDWKETLEKVVELNPEHISCYSLIIEEGTPFYNLYENGKLKLPDEEEEREMYHYTIEFLKEKGYHQYEISNFAKPGK 242 (374)
T ss_pred CCHHHHHHHHHHHHhcCCCEEEEeccEecCCCHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHcCCcEEeeeeeECCCc
Confidence 33344555455555455788888888887774321 1223443 3333 34679999999999999999864
No 61
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=51.36 E-value=46 Score=29.93 Aligned_cols=70 Identities=16% Similarity=0.217 Sum_probs=43.7
Q ss_pred CCCCcccchhhHhhhhcCCCCceEEEEeccCcc---cc---CCCCCCCHHHHHH----HHHHHHhCCCCeeeeecccCCC
Q 031564 76 SSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDG---LQ---NEKNIVPAVVKVE----LIKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDG---LQ---ne~~~vpTe~KIe----LI~~L~~AGv~~IEvgSFVsPK 145 (157)
+..+..++.+....+..--|+.|.+.......+ .| .+....+.++|++ .++.|.++|...+|+..|+.|.
T Consensus 214 Pgqt~e~~~~tl~~~~~l~p~~i~~y~l~~~p~~~~~~~~~~~~~lp~~~~~~~~~~~~~~~L~~~Gy~~~~~~~far~~ 293 (453)
T PRK13347 214 PHQTVESFRETLDKVIALSPDRIAVFGYAHVPSRRKNQRLIDEAALPDAEERLRQARAVADRLLAAGYVPIGLDHFALPD 293 (453)
T ss_pred CCCCHHHHHHHHHHHHhcCCCEEEEeccccccchhhHHhcCCccCCcCHHHHHHHHHHHHHHHHHCCCEEEeccceeCCC
Confidence 333444555555555556678887765432222 12 1222334566665 4678999999999999999875
No 62
>PRK09140 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed
Probab=49.12 E-value=18 Score=29.61 Aligned_cols=33 Identities=15% Similarity=0.263 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeecccCCCccccc
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQM 150 (157)
+.++=++++++|.+.|++.||++ +-+|.+...+
T Consensus 20 ~~~~~~~~~~a~~~gGi~~iEvt-~~~~~~~~~i 52 (206)
T PRK09140 20 TPDEALAHVGALIEAGFRAIEIP-LNSPDPFDSI 52 (206)
T ss_pred CHHHHHHHHHHHHHCCCCEEEEe-CCCccHHHHH
Confidence 77888999999999999999999 6777765443
No 63
>PF13309 HTH_22: HTH domain
Probab=45.73 E-value=22 Score=24.22 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=19.3
Q ss_pred CCCCCCHHHHHHHHHHHHhCCC
Q 031564 112 EKNIVPAVVKVELIKLLVSSGL 133 (157)
Q Consensus 112 e~~~vpTe~KIeLI~~L~~AGv 133 (157)
....++.++|+++|+.|.+.|+
T Consensus 17 ~~~~l~~~~k~~iV~~L~~~G~ 38 (64)
T PF13309_consen 17 PPSRLSKEEKKEIVRQLYEKGI 38 (64)
T ss_pred ChhhCCHHHHHHHHHHHHHCCC
Confidence 3457899999999999999997
No 64
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=45.41 E-value=55 Score=29.22 Aligned_cols=67 Identities=12% Similarity=-0.014 Sum_probs=43.4
Q ss_pred ccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCC-HHHHHH----HHHHHHhCCCCeeeeecccCCCcc
Q 031564 81 NSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVP-AVVKVE----LIKLLVSSGLPVVEATSFVSPKWV 147 (157)
Q Consensus 81 ~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vp-Te~KIe----LI~~L~~AGv~~IEvgSFVsPK~V 147 (157)
..+++....+...-|+.|.+....+..|=..-....+ .+++.+ ..+.|.++|..++|++.|+.|..-
T Consensus 208 e~~~~~l~~~~~l~~~~is~y~L~~~~~T~l~~~~~~~~~~~~~m~~~~~~~L~~~Gy~~yei~~far~~~~ 279 (430)
T PRK08208 208 ASWMESLDQALVYRPEELFLYPLYVRPLTGLGRRARAWDDQRLSLYRLARDLLLEAGYTQTSMRMFRRNDAP 279 (430)
T ss_pred HHHHHHHHHHHhCCCCEEEEccccccCCCccchhcCCCHHHHHHHHHHHHHHHHHcCCeEEeecceecCCcc
Confidence 4455555555555678888887776666332233333 344443 456789999999999999987543
No 65
>cd02803 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=44.73 E-value=88 Score=26.14 Aligned_cols=55 Identities=15% Similarity=0.145 Sum_probs=38.7
Q ss_pred hhhHhhhhcCCC-CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecc
Q 031564 84 KDLTSKLLGRVP-GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141 (157)
Q Consensus 84 ~~~~~~~~~~~P-~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSF 141 (157)
.++...++...+ +....+.+.+-+.... -++.++-++++++|.++|+..|+++..
T Consensus 195 ~eii~avr~~~g~d~~i~vris~~~~~~~---g~~~~e~~~la~~l~~~G~d~i~vs~g 250 (327)
T cd02803 195 LEIVAAVREAVGPDFPVGVRLSADDFVPG---GLTLEEAIEIAKALEEAGVDALHVSGG 250 (327)
T ss_pred HHHHHHHHHHcCCCceEEEEechhccCCC---CCCHHHHHHHHHHHHHcCCCEEEeCCC
Confidence 344555565553 4456667777655422 267788899999999999999998764
No 66
>COG1533 SplB DNA repair photolyase [DNA replication, recombination, and repair]
Probab=43.61 E-value=29 Score=30.29 Aligned_cols=39 Identities=31% Similarity=0.492 Sum_probs=32.7
Q ss_pred cCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccc
Q 031564 110 QNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152 (157)
Q Consensus 110 Qne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMAD 152 (157)
=.|+..-|++++++.+.+|.++|++. +-||.| -+|..-|
T Consensus 160 ~~EP~apsp~~Ri~al~~l~eaGi~~---~v~v~P-IiP~~~d 198 (297)
T COG1533 160 ILEPRAPSPEERLEALKELSEAGIPV---GLFVAP-IIPGLND 198 (297)
T ss_pred hcCCCCcCHHHHHHHHHHHHHCCCeE---EEEEec-ccCCCCh
Confidence 46888889999999999999999865 588988 5676655
No 67
>PRK07028 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator; Validated
Probab=42.81 E-value=23 Score=31.41 Aligned_cols=31 Identities=29% Similarity=0.275 Sum_probs=27.5
Q ss_pred ccCCCCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 109 LQNEKNIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 109 LQne~~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
||---...+.++++++++.|.+.|++.||+|
T Consensus 6 l~~alD~~~~~~~~~~~~~~~~~Gv~~ie~g 36 (430)
T PRK07028 6 LQVALDLLELDRAVEIAKEAVAGGADWIEAG 36 (430)
T ss_pred EEEEeccCCHHHHHHHHHHHHhcCCcEEEeC
Confidence 5556677899999999999999999999996
No 68
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=42.36 E-value=78 Score=28.34 Aligned_cols=70 Identities=17% Similarity=0.178 Sum_probs=43.1
Q ss_pred CCCcccchhhHhhhhcCCCCceEEEEeccCccc---c--CCCCCC-CHHHHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 77 SCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGL---Q--NEKNIV-PAVVKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGL---Q--ne~~~v-pTe~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
..+..++......+..--|+.|.+.-..+..+. | .....+ +.+++.+ +++.|.++|..++|+..|+.|..
T Consensus 214 gqt~e~~~~tl~~~~~l~~~~is~y~L~~~p~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~L~~~Gy~~~~~~~fa~~~~ 293 (455)
T TIGR00538 214 KQTKESFAKTLEKVAELNPDRLAVFNYAHVPWVKPAQRKIPEAALPSAEEKLDILQETIAFLTEAGYQFIGMDHFAKPDD 293 (455)
T ss_pred CCCHHHHHHHHHHHHhcCCCEEEEecCccccchhHHHhcccccCCCCHHHHHHHHHHHHHHHHHCCCEEEeccceeCCCh
Confidence 334445555555555556777877766443331 1 111223 4566664 45667889999999999999853
No 69
>PRK05660 HemN family oxidoreductase; Provisional
Probab=39.50 E-value=77 Score=27.79 Aligned_cols=68 Identities=12% Similarity=0.198 Sum_probs=44.2
Q ss_pred CcccchhhHhhhhcCCCCceEEEEeccCcc--ccCCCCCCCH-HHHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 79 TDNSTKDLTSKLLGRVPGFVKIVEVGPRDG--LQNEKNIVPA-VVKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 79 ~~~~~~~~~~~~~~~~P~~V~IvEVGpRDG--LQne~~~vpT-e~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
+...++.....+..--|+.|.+.-..+..| |-.....+|. +++.+ ..+.|.++|+.+.|+..|..|..
T Consensus 172 t~~~~~~~l~~~~~l~p~~is~y~l~~~~gT~l~~~~~~~~~~~~~~~~~~~~~~~L~~~Gy~~yei~~fa~~~~ 246 (378)
T PRK05660 172 SLEEALDDLRQAIALNPPHLSWYQLTIEPNTLFGSRPPVLPDDDALWDIFEQGHQLLTAAGYQQYETSAYAKPGY 246 (378)
T ss_pred CHHHHHHHHHHHHhcCCCeEEeeccEeccCCcccccCCCCcCHHHHHHHHHHHHHHHHHcCCcEeecccccCCCh
Confidence 334455545555555688888887777776 2111222454 34444 35679999999999999999864
No 70
>PHA00675 hypothetical protein
Probab=38.75 E-value=49 Score=24.55 Aligned_cols=44 Identities=20% Similarity=0.210 Sum_probs=32.9
Q ss_pred CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHH-hCCCCeeeee
Q 031564 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLV-SSGLPVVEAT 139 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~-~AGv~~IEvg 139 (157)
.+.|.+.|-|.|-|.-+..+-|. +..++.|++|. .+|...-++.
T Consensus 2 ~~~~~~~~~~~~~Ge~h~~AKLt-~~qV~~IR~l~~r~G~s~~~IA 46 (78)
T PHA00675 2 LKTVAVNDAGLRVGEDHPNAKLT-DAEVERIRELHEVEGMSYAVLA 46 (78)
T ss_pred CceeccccccccCCCCCCCcccC-HHHHHHHHHHHHhcCccHHHHH
Confidence 45788999999999776666655 55588888888 7887655444
No 71
>cd02933 OYE_like_FMN Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include 12-oxophytodienoate reductase, pentaerythritol tetranitrate reductase, morphinone reductase, and related enzymes.
Probab=36.74 E-value=1.3e+02 Score=26.23 Aligned_cols=55 Identities=13% Similarity=0.098 Sum_probs=35.7
Q ss_pred hHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564 86 LTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 86 ~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
+...++...+.....+-+.+-|+.+....-.+.++=+++++.|.++|+..|+++.
T Consensus 208 ii~air~~vg~d~v~vRis~~~~~~~~~~~~~~ee~~~~~~~l~~~g~d~i~vs~ 262 (338)
T cd02933 208 VVDAVAEAIGADRVGIRLSPFGTFNDMGDSDPEATFSYLAKELNKRGLAYLHLVE 262 (338)
T ss_pred HHHHHHHHhCCCceEEEECccccCCCCCCCCCHHHHHHHHHHHHHcCCcEEEEec
Confidence 3333444444433445566666654332235678888999999999999999943
No 72
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=34.16 E-value=93 Score=26.94 Aligned_cols=67 Identities=15% Similarity=0.086 Sum_probs=40.7
Q ss_pred cccchhhHhhhhcCCCCceEEEEeccCccccCCC-------CCCCHHHHHH----HHHHHHhCCCCeeeeecccCCCc
Q 031564 80 DNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEK-------NIVPAVVKVE----LIKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 80 ~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~-------~~vpTe~KIe----LI~~L~~AGv~~IEvgSFVsPK~ 146 (157)
..++++....+..--|+.|.+.-..++.|-.... ...+.+.+.+ +.+.|.++|+..+|+..|+.|.-
T Consensus 174 ~~~~~~tl~~~~~l~~~~i~~y~l~~~~gT~l~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~G~~~ye~s~fa~~~~ 251 (375)
T PRK05628 174 DDDWRASLDAALEAGVDHVSAYALIVEDGTALARRVRRGELPAPDDDVLADRYELADARLSAAGFDWYEVSNWARPGG 251 (375)
T ss_pred HHHHHHHHHHHHhcCCCEEEeeeeecCCCChHHHHhhcCCCCCCChHHHHHHHHHHHHHHHHcCCCeeeeccccCCCc
Confidence 3444444444444557878777666666632111 1233444444 34668889999999999999853
No 73
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=33.01 E-value=1.5e+02 Score=26.80 Aligned_cols=65 Identities=9% Similarity=0.112 Sum_probs=42.7
Q ss_pred cchhhHhhhhcCCCCceEEEEeccCccc--cC--CCC-C-C--CHHHHHHH----HHHHHhCCCCeeeeecccCCCc
Q 031564 82 STKDLTSKLLGRVPGFVKIVEVGPRDGL--QN--EKN-I-V--PAVVKVEL----IKLLVSSGLPVVEATSFVSPKW 146 (157)
Q Consensus 82 ~~~~~~~~~~~~~P~~V~IvEVGpRDGL--Qn--e~~-~-v--pTe~KIeL----I~~L~~AGv~~IEvgSFVsPK~ 146 (157)
.+++-...+..--|+.|.+.-..+..|- +. +.. + . ..+++.++ .+.|.++|..++|+..|+.|..
T Consensus 231 ~~~~~l~~~~~l~~~~is~y~L~~~pgT~l~~~~~~g~l~~~~~~~~~~~my~~~~~~L~~~Gy~~yeis~far~~~ 307 (449)
T PRK09058 231 IWQQDLAIVRDLGLDGVDLYALNLLPGTPLAKAVEKGKLPPPATPAERADMYAYGVEFLAKAGWRQLSNSHWARTTR 307 (449)
T ss_pred HHHHHHHHHHhcCCCEEEEeccccCCCCHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHHCCCeEEeeeeeecCCc
Confidence 3444344444455788888888777763 11 111 1 2 35666655 6789999999999999999863
No 74
>cd07080 ALDH_Acyl-CoA-Red_LuxC Acyl-CoA reductase LuxC. Acyl-CoA reductase, LuxC, (EC=1.2.1.50) is the fatty acid reductase enzyme responsible for synthesis of the aldehyde substrate for the luminescent reaction catalyzed by luciferase. The fatty acid reductase, a luminescence-specific, multienzyme complex (LuxCDE), reduces myristic acid to generate the long chain fatty aldehyde required for the luciferase-catalyzed reaction resulting in the emission of blue-green light. Mutational studies of conserved cysteines of LuxC revealed that the cysteine which aligns with the catalytic cysteine conserved throughout the ALDH superfamily is the LuxC acylation site. This CD is composed of mainly bacterial sequences but also includes a few archaeal sequences similar to the Methanospirillum hungateiacyl acyl-CoA reductase RfbN.
Probab=32.82 E-value=30 Score=30.86 Aligned_cols=30 Identities=20% Similarity=0.135 Sum_probs=26.8
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHhCCCCee
Q 031564 107 DGLQNEKNIVPAVVKVELIKLLVSSGLPVV 136 (157)
Q Consensus 107 DGLQne~~~vpTe~KIeLI~~L~~AGv~~I 136 (157)
.-+|...-+.+.+++.++++.|..+|+.+|
T Consensus 365 ~~lQTvg~~~~~~~~~~~~~~l~~~Gv~Ri 394 (422)
T cd07080 365 PYLQTVGLAPSPAELAELADALAAAGVDRI 394 (422)
T ss_pred hhcceeEeecChhhHHHHHHHHHHcCcccc
Confidence 378988888888888999999999999998
No 75
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=32.49 E-value=98 Score=27.77 Aligned_cols=69 Identities=17% Similarity=0.195 Sum_probs=41.5
Q ss_pred CCCcccchhhHhhhhcCCCCceEEEEeccCcc---ccC--CCCCC-CHHHHHHH----HHHHHhCCCCeeeeecccCCC
Q 031564 77 SCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDG---LQN--EKNIV-PAVVKVEL----IKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDG---LQn--e~~~v-pTe~KIeL----I~~L~~AGv~~IEvgSFVsPK 145 (157)
..+..++......+..--|+.|.+.-..+..+ .|. .+..+ +.+++.++ .+.|.++|..++|+..|..|.
T Consensus 214 gqt~e~~~~~l~~~~~l~~~~i~~y~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~Gy~~ye~s~far~~ 292 (453)
T PRK09249 214 KQTPESFARTLEKVLELRPDRLAVFNYAHVPWLFKAQRKIDEADLPSPEEKLAILQQTIETLTEAGYQYIGMDHFALPD 292 (453)
T ss_pred CCCHHHHHHHHHHHHhcCCCEEEEccCccchhhhhHhcCCCcccCCCHHHHHHHHHHHHHHHHHCCCEEEeccceeCCC
Confidence 33444455555555555577787776542222 121 12223 44555444 567899999999999999885
No 76
>PF05893 LuxC: Acyl-CoA reductase (LuxC); InterPro: IPR008670 This family consists of several bacterial Acyl-CoA reductase (LuxC) proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalysed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0008218 bioluminescence, 0055114 oxidation-reduction process
Probab=30.39 E-value=37 Score=30.48 Aligned_cols=28 Identities=21% Similarity=0.127 Sum_probs=22.8
Q ss_pred ccCCCCCCCHHHHHHHHHHHHhCCCCee
Q 031564 109 LQNEKNIVPAVVKVELIKLLVSSGLPVV 136 (157)
Q Consensus 109 LQne~~~vpTe~KIeLI~~L~~AGv~~I 136 (157)
+|...-..+.+...++++.|..+|+.+|
T Consensus 345 lQTvgi~~~~~~~~~~~~~l~~~Gv~Ri 372 (399)
T PF05893_consen 345 LQTVGIYPWSERLEELARALAAAGVDRI 372 (399)
T ss_pred CeeEEEecChhhHHHHHHHHHhcCCeee
Confidence 8998876666666677777999999998
No 77
>cd04729 NanE N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.
Probab=29.46 E-value=94 Score=24.76 Aligned_cols=47 Identities=17% Similarity=0.141 Sum_probs=33.3
Q ss_pred hhhhcCCCCceEEEEeccCccccCCC-CCCCH-HHHHHHHHHHHhCCCCeeeeecc
Q 031564 88 SKLLGRVPGFVKIVEVGPRDGLQNEK-NIVPA-VVKVELIKLLVSSGLPVVEATSF 141 (157)
Q Consensus 88 ~~~~~~~P~~V~IvEVGpRDGLQne~-~~vpT-e~KIeLI~~L~~AGv~~IEvgSF 141 (157)
+|||..+|..+.+.= |.++ ..+.. ++=.++++++.++|+..+++++|
T Consensus 1 ~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~i~~~a~~~~~~G~~~~~~~~~ 49 (219)
T cd04729 1 MKLLEQLKGGLIVSC-------QALPGEPLHSPEIMAAMALAAVQGGAVGIRANGV 49 (219)
T ss_pred CcHHHHhcCCeEEEc-------cCCCCCCcCcHHHHHHHHHHHHHCCCeEEEcCCH
Confidence 578888888876543 3332 23433 33478999999999999998776
No 78
>cd02932 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.
Probab=28.34 E-value=2.5e+02 Score=24.09 Aligned_cols=53 Identities=17% Similarity=0.174 Sum_probs=36.4
Q ss_pred hhhHhhhhcCCC-CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564 84 KDLTSKLLGRVP-GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 84 ~~~~~~~~~~~P-~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg 139 (157)
.++...++...+ +....+.+.+-|+.. .-...++=++++++|.++|+..||++
T Consensus 208 ~eiv~aIR~~vG~d~~v~vri~~~~~~~---~g~~~~e~~~ia~~Le~~gvd~iev~ 261 (336)
T cd02932 208 LEVVDAVRAVWPEDKPLFVRISATDWVE---GGWDLEDSVELAKALKELGVDLIDVS 261 (336)
T ss_pred HHHHHHHHHHcCCCceEEEEEcccccCC---CCCCHHHHHHHHHHHHHcCCCEEEEC
Confidence 455566666664 445667777755432 12345666899999999999999985
No 79
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=28.15 E-value=1.7e+02 Score=25.63 Aligned_cols=56 Identities=32% Similarity=0.408 Sum_probs=44.6
Q ss_pred ccchhhHhhhhc------------CCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeee
Q 031564 81 NSTKDLTSKLLG------------RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEA 138 (157)
Q Consensus 81 ~~~~~~~~~~~~------------~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEv 138 (157)
+...||.++++. .++..|.|+|=. |.+=....+-|-+.|=+|+...++.||+.|.-
T Consensus 73 Ks~~Dfv~Si~dgRlfeQ~~rL~~~y~rpvliVegd--~~~~~~~~i~~~av~~al~s~~vdfg~~vi~t 140 (254)
T COG1948 73 KSISDFVSSIIDGRLFEQAKRLKKSYERPVLIVEGD--DSFSRRPKIHPNAVRGALASLAVDFGLPVIWT 140 (254)
T ss_pred ccHHHHHHHHhcchHHHHHHHHHhcCCccEEEEEcc--cccccccccCHHHHHHHHHHHHhhcCceEEEe
Confidence 666777776654 478899999986 56655655788999999999999999999864
No 80
>TIGR00262 trpA tryptophan synthase, alpha subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences.
Probab=28.14 E-value=71 Score=26.90 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeec-ccCC
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATS-FVSP 144 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgS-FVsP 144 (157)
..+.=++++++|.++|++.||+|- |-.|
T Consensus 22 ~~~~~~~~~~~l~~~Gad~iElGiPfsDP 50 (256)
T TIGR00262 22 TLETSLEIIKTLIEAGADALELGVPFSDP 50 (256)
T ss_pred CHHHHHHHHHHHHHcCCCEEEECCCCCCC
Confidence 456678999999999999999996 4444
No 81
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=27.87 E-value=60 Score=20.96 Aligned_cols=15 Identities=27% Similarity=0.352 Sum_probs=13.7
Q ss_pred CCHHHHHHHHHHHHh
Q 031564 116 VPAVVKVELIKLLVS 130 (157)
Q Consensus 116 vpTe~KIeLI~~L~~ 130 (157)
+|+++|+.|++.|.+
T Consensus 2 L~~~er~~L~e~L~~ 16 (54)
T PF09720_consen 2 LPPEERAELAEELWD 16 (54)
T ss_pred cCHHHHHHHHHHHHH
Confidence 789999999999986
No 82
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=27.63 E-value=1.4e+02 Score=26.47 Aligned_cols=58 Identities=12% Similarity=0.120 Sum_probs=37.6
Q ss_pred hhhhcCCCCceEEEEeccCccc----c--CCCCCCCH-HHHHH----HHHHHHhCCCCeeeeecccCCC
Q 031564 88 SKLLGRVPGFVKIVEVGPRDGL----Q--NEKNIVPA-VVKVE----LIKLLVSSGLPVVEATSFVSPK 145 (157)
Q Consensus 88 ~~~~~~~P~~V~IvEVGpRDGL----Q--ne~~~vpT-e~KIe----LI~~L~~AGv~~IEvgSFVsPK 145 (157)
.++..--|+.|.+....+..|= + .....+|. +++.+ ..+.|.++|..+.|+..|+.|.
T Consensus 184 ~~~~~l~p~his~y~L~i~~gT~l~~~~~~g~~~~p~~~~~~~~~~~~~~~L~~~Gy~~yeis~fa~~g 252 (390)
T PRK06582 184 KQAMQLATSHISLYQLTIEKGTPFYKLFKEGNLILPHSDAAAEMYEWTNHYLESKKYFRYEISNYAKIG 252 (390)
T ss_pred HHHHhcCCCEEEEecCEEccCChHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHcCCceeeceeeeCCC
Confidence 3333345888888887776651 1 11122343 34443 4567899999999999999985
No 83
>PLN02591 tryptophan synthase
Probab=27.51 E-value=75 Score=27.07 Aligned_cols=28 Identities=25% Similarity=0.398 Sum_probs=22.6
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeec-ccCC
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATS-FVSP 144 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgS-FVsP 144 (157)
..+.=+++++.|.++|++.||+|- |-.|
T Consensus 14 ~~e~~~~~~~~l~~~Gad~iElGiPfSDP 42 (250)
T PLN02591 14 DLDTTAEALRLLDACGADVIELGVPYSDP 42 (250)
T ss_pred CHHHHHHHHHHHHHCCCCEEEECCCCCCC
Confidence 456668999999999999999985 4444
No 84
>PF03446 NAD_binding_2: NAD binding domain of 6-phosphogluconate dehydrogenase; InterPro: IPR006115 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [, ]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved []. The protein is a homodimer in which the monomers act independently []: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet []. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket []. This family represents the NADP binding domain of 6-phosphogluconate dehydrogenase which adopts a Rossman fold. The C-terminal domain is described in IPR006114 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0006098 pentose-phosphate shunt, 0055114 oxidation-reduction process; PDB: 3AX6_D 3PDU_G 3Q3C_A 3OBB_A 4DLL_B 1PGP_A 1PGN_A 2PGD_A 1PGQ_A 1PGO_A ....
Probab=26.94 E-value=1.3e+02 Score=22.91 Aligned_cols=57 Identities=16% Similarity=0.172 Sum_probs=39.9
Q ss_pred CCCcccchhhHhh--hhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564 77 SCTDNSTKDLTSK--LLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVS 143 (157)
Q Consensus 77 ~~~~~~~~~~~~~--~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs 143 (157)
-.++..++++... +...++..-.|+|. ..++.+.+.++.++|.+.|+..|++.-+-.
T Consensus 65 v~~~~~v~~v~~~~~i~~~l~~g~iiid~----------sT~~p~~~~~~~~~~~~~g~~~vdapV~Gg 123 (163)
T PF03446_consen 65 VPDDDAVEAVLFGENILAGLRPGKIIIDM----------STISPETSRELAERLAAKGVRYVDAPVSGG 123 (163)
T ss_dssp SSSHHHHHHHHHCTTHGGGS-TTEEEEE-----------SS--HHHHHHHHHHHHHTTEEEEEEEEESH
T ss_pred cccchhhhhhhhhhHHhhccccceEEEec----------CCcchhhhhhhhhhhhhccceeeeeeeecc
Confidence 3444555665555 66777777777777 457899999999999999999999876544
No 85
>cd04733 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=26.93 E-value=1.8e+02 Score=24.94 Aligned_cols=52 Identities=17% Similarity=0.235 Sum_probs=35.4
Q ss_pred hHhhhhcCCC-CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564 86 LTSKLLGRVP-GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 86 ~~~~~~~~~P-~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
+...++...+ +....+.+.+-|+.+. -++.++=+++++.|.++|+..||++.
T Consensus 205 iI~aIR~avG~d~~v~vris~~~~~~~---g~~~eea~~ia~~Le~~Gvd~iev~~ 257 (338)
T cd04733 205 IYDAIRAAVGPGFPVGIKLNSADFQRG---GFTEEDALEVVEALEEAGVDLVELSG 257 (338)
T ss_pred HHHHHHHHcCCCCeEEEEEcHHHcCCC---CCCHHHHHHHHHHHHHcCCCEEEecC
Confidence 3444454554 3456667776665432 24566778999999999999999764
No 86
>CHL00200 trpA tryptophan synthase alpha subunit; Provisional
Probab=26.73 E-value=78 Score=27.06 Aligned_cols=24 Identities=21% Similarity=0.333 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeec
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
..+.=+++++.|.++|++.||+|-
T Consensus 27 ~~~~~~~~~~~l~~~Gad~iElGi 50 (263)
T CHL00200 27 DIVITKKALKILDKKGADIIELGI 50 (263)
T ss_pred CHHHHHHHHHHHHHCCCCEEEECC
Confidence 466778999999999999999995
No 87
>PLN02877 alpha-amylase/limit dextrinase
Probab=25.92 E-value=1.1e+02 Score=31.43 Aligned_cols=45 Identities=24% Similarity=0.177 Sum_probs=32.8
Q ss_pred CCceEEEEeccCccccC--------CCCCCCHHHH----HHHHHHHHhCCCCeeeee
Q 031564 95 PGFVKIVEVGPRDGLQN--------EKNIVPAVVK----VELIKLLVSSGLPVVEAT 139 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQn--------e~~~vpTe~K----IeLI~~L~~AGv~~IEvg 139 (157)
+....|-|+-.||==.. -+.++-..+| +..|..|.++||.+||+=
T Consensus 337 ~~D~VIYElHVRDFS~~d~sv~~~~RGtylgftE~~s~gi~hLk~LkelGVThVeLL 393 (970)
T PLN02877 337 FSDISIYELHVRDFSANDETVHPDFRGGYLAFTSQDSAGVLHLKKLADAGLTHVHLL 393 (970)
T ss_pred CcccEEEEEeccccccCCCCCCcCCCCcchhhhhhhhhHHHHHHHHHHcCCCEEEeC
Confidence 45789999999974332 2444444444 888999999999999963
No 88
>PRK10605 N-ethylmaleimide reductase; Provisional
Probab=25.83 E-value=2.6e+02 Score=24.71 Aligned_cols=56 Identities=13% Similarity=0.104 Sum_probs=33.9
Q ss_pred hhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHH-HHHHHHHHHhCCCCeeeeec
Q 031564 85 DLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVV-KVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 85 ~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~-KIeLI~~L~~AGv~~IEvgS 140 (157)
++...++...+..+..+-+.+=|-+.....-...++ =++++..|.++|+..|+++.
T Consensus 214 Eiv~aVr~~vg~~~igvRis~~~~~~~~~~G~~~~e~~~~~~~~L~~~giD~i~vs~ 270 (362)
T PRK10605 214 EVVDAGIAEWGADRIGIRISPLGTFNNVDNGPNEEADALYLIEQLGKRGIAYLHMSE 270 (362)
T ss_pred HHHHHHHHHcCCCeEEEEECCccccccCCCCCCHHHHHHHHHHHHHHcCCCEEEecc
Confidence 445555555655444444544221111112245555 59999999999999999986
No 89
>cd02930 DCR_FMN 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provi
Probab=25.61 E-value=3.3e+02 Score=23.58 Aligned_cols=54 Identities=15% Similarity=0.054 Sum_probs=35.8
Q ss_pred hhHhhhhcCCCCc-eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecc
Q 031564 85 DLTSKLLGRVPGF-VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141 (157)
Q Consensus 85 ~~~~~~~~~~P~~-V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSF 141 (157)
++...++...+.. ...+-+++-|..+. ..+.++=++++++|.++|++.|+++..
T Consensus 192 eiv~aIR~~vG~d~~v~iRi~~~D~~~~---g~~~~e~~~i~~~Le~~G~d~i~vs~g 246 (353)
T cd02930 192 EIVRAVRAAVGEDFIIIYRLSMLDLVEG---GSTWEEVVALAKALEAAGADILNTGIG 246 (353)
T ss_pred HHHHHHHHHcCCCceEEEEecccccCCC---CCCHHHHHHHHHHHHHcCCCEEEeCCC
Confidence 4445555556543 33445556565432 256677789999999999999999643
No 90
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=25.11 E-value=1.1e+02 Score=21.86 Aligned_cols=34 Identities=18% Similarity=0.215 Sum_probs=20.5
Q ss_pred CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHh-----CCCCe
Q 031564 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVS-----SGLPV 135 (157)
Q Consensus 95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~-----AGv~~ 135 (157)
++.+.+++++.+.| =++++|.+|.++|++ +|++-
T Consensus 26 s~~~v~I~It~~~g-------Rs~e~K~~ly~~l~~~L~~~~gi~p 64 (82)
T PF14552_consen 26 SDDFVIIQITSGAG-------RSTEQKKALYRALAERLAEKLGIRP 64 (82)
T ss_dssp -TT-EEEEEEECS----------HHHHHHHHHHHHHHHHHHH---G
T ss_pred CCCEEEEEEEECCC-------CCHHHHHHHHHHHHHHHHHHcCCCH
Confidence 46789999988776 489999998877653 66653
No 91
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=23.87 E-value=1.6e+02 Score=25.45 Aligned_cols=65 Identities=11% Similarity=-0.010 Sum_probs=40.4
Q ss_pred CcccchhhHhhhhcCCCCceEEEEeccCccccC----CCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564 79 TDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQN----EKNIVPAVVKVELIKLLVSSGLPVVEATSFVS 143 (157)
Q Consensus 79 ~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQn----e~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs 143 (157)
+..++++....+..--|+.|.+...++..|-.. ....-..+.-....+.|.++|..+.|+..|+.
T Consensus 163 t~~~~~~~l~~~~~l~~~~is~y~L~~~~gT~l~~~~~~~~~~~~~~~~~~~~l~~~Gy~~yeis~fa~ 231 (350)
T PRK08446 163 NKKLLKEELKLAKELPINHLSAYSLTIEENTPFFEKNHKKKDDENLAKFFIEQLEELGFKQYEISNFGK 231 (350)
T ss_pred CHHHHHHHHHHHHhcCCCEEEeccceecCCChhHHhhhcCCCHHHHHHHHHHHHHHCCCcEEEeehhhC
Confidence 334455444555555688888877777666221 11111122334456779999999999999986
No 92
>TIGR03849 arch_ComA phosphosulfolactate synthase. This model finds the ComA (Coenzyme M biosynthesis A) protein, phosphosulfolactate synthase, in methanogenic archaea. The ComABC pathway is one of at least two pathways to the intermediate sulfopyruvate. Coenzyme M occurs rarely and sporadically outside of the archaea, as for expoxide metabolism in Xanthobacter autotrophicus Py2, but candidate phosphosulfolactate synthases from that and other species occur fall below the cutoff and outside the scope of this model. This model deliberately is narrower in scope than pfam02679.
Probab=23.87 E-value=1.4e+02 Score=25.84 Aligned_cols=38 Identities=21% Similarity=0.355 Sum_probs=30.7
Q ss_pred ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCee
Q 031564 97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVV 136 (157)
Q Consensus 97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~I 136 (157)
...+.|||..+. .....+++++.|+.+++-.+||...|
T Consensus 114 ~~v~~EvG~K~~--~~~~~~~~~~~i~~~~~~LeAGA~~V 151 (237)
T TIGR03849 114 FMVLSEVGKKSP--EKDSELTPDDRIKLINKDLEAGADYV 151 (237)
T ss_pred CeEeccccccCC--cccccCCHHHHHHHHHHHHHCCCcEE
Confidence 356889999885 23347899999999999999999986
No 93
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=22.63 E-value=1.3e+02 Score=23.59 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeecccCCCccccc
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQM 150 (157)
+.++=+++++.|.++|++.||++. -+|.+.+.+
T Consensus 14 ~~~~~~~~~~~l~~~G~~~vev~~-~~~~~~~~i 46 (190)
T cd00452 14 DAEDALALAEALIEGGIRAIEITL-RTPGALEAI 46 (190)
T ss_pred CHHHHHHHHHHHHHCCCCEEEEeC-CChhHHHHH
Confidence 456667899999999999999985 566665543
No 94
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=22.44 E-value=1.1e+02 Score=26.13 Aligned_cols=24 Identities=29% Similarity=0.412 Sum_probs=21.3
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeec
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
+.+.=++++..|.+.|++.||+|-
T Consensus 24 ~~~~~~~~~~~l~~~Gad~iElGi 47 (258)
T PRK13111 24 DLETSLEIIKALVEAGADIIELGI 47 (258)
T ss_pred CHHHHHHHHHHHHHCCCCEEEECC
Confidence 466778999999999999999995
No 95
>PF00290 Trp_syntA: Tryptophan synthase alpha chain; InterPro: IPR002028 Tryptophan synthase (4.2.1.20 from EC) catalyzes the last step in the biosynthesis of tryptophan [, ]: L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the 2 subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 from INTERPRO is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) [, ]. The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process; PDB: 1TJR_B 1RD5_B 1K8X_A 1QOQ_A 1KFE_A 1KFB_A 2CLO_A 1TTP_A 2RH9_A 1K7F_A ....
Probab=22.31 E-value=91 Score=26.85 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeec
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
+.+.=+++++.|.++|++.||+|-
T Consensus 22 ~~~~~~~~~~~l~~~GaD~iEiGi 45 (259)
T PF00290_consen 22 DLETTLEILKALEEAGADIIEIGI 45 (259)
T ss_dssp SHHHHHHHHHHHHHTTBSSEEEE-
T ss_pred CHHHHHHHHHHHHHcCCCEEEECC
Confidence 456668999999999999999995
No 96
>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=21.65 E-value=1.1e+02 Score=26.90 Aligned_cols=24 Identities=29% Similarity=0.404 Sum_probs=21.5
Q ss_pred CHHHHHHHHHHHHhCCCCeeeeec
Q 031564 117 PAVVKVELIKLLVSSGLPVVEATS 140 (157)
Q Consensus 117 pTe~KIeLI~~L~~AGv~~IEvgS 140 (157)
..+.=++++..|.++|.+.||+|-
T Consensus 29 ~~e~s~e~i~~L~~~GaD~iELGv 52 (265)
T COG0159 29 DLETSLEIIKTLVEAGADILELGV 52 (265)
T ss_pred CHHHHHHHHHHHHhCCCCEEEecC
Confidence 467778999999999999999995
No 97
>TIGR02103 pullul_strch alpha-1,6-glucosidases, pullulanase-type. Members of this protein family include secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyze alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family is closely homologous to, but architecturally different from, the Gram-positive pullulanases of Gram-positive bacteria (TIGR02102).
Probab=21.14 E-value=1.2e+02 Score=30.73 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=33.4
Q ss_pred CCCceEEEEeccCccc--------cCCCCCCCHHHH----HHHHHHHHhCCCCeeee
Q 031564 94 VPGFVKIVEVGPRDGL--------QNEKNIVPAVVK----VELIKLLVSSGLPVVEA 138 (157)
Q Consensus 94 ~P~~V~IvEVGpRDGL--------Qne~~~vpTe~K----IeLI~~L~~AGv~~IEv 138 (157)
-+....|-|+-.||== ++.+.++-..+| +..|..|.++||.+||+
T Consensus 249 ~~~d~iIYElHVRDFS~~d~s~~~~~rGtYla~tE~~t~gi~hLk~L~eLGVThVeL 305 (898)
T TIGR02103 249 SFADMVLYELHIRDFSANDESVPAELRGKYLAFTAADSAGVQHLKKLADAGVTHLHL 305 (898)
T ss_pred CCcccEEEEEeccccccCCCCCCcCcCceeeehhccchhhhHHHHHHHhCCCcEEEE
Confidence 3567899999999732 233455555555 78899999999999996
No 98
>PF13653 GDPD_2: Glycerophosphoryl diester phosphodiesterase family; PDB: 3RLG_A 2F9R_B 1XX1_A 3RLH_A.
Probab=20.65 E-value=55 Score=19.90 Aligned_cols=18 Identities=17% Similarity=0.084 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHhCCCCee
Q 031564 119 VVKVELIKLLVSSGLPVV 136 (157)
Q Consensus 119 e~KIeLI~~L~~AGv~~I 136 (157)
-+|.+.++.|.++|++.|
T Consensus 7 ~d~~~~~~~~l~~GVDgI 24 (30)
T PF13653_consen 7 PDKPASWRELLDLGVDGI 24 (30)
T ss_dssp --SHHHHHHHHHHT-SEE
T ss_pred CCCHHHHHHHHHcCCCEe
Confidence 356788899999999988
Done!