Query psy5901
Match_columns 122
No_of_seqs 111 out of 1022
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 21:12:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02826 dihydroorotate dehydr 99.9 8E-27 1.7E-31 195.8 4.3 83 37-119 34-116 (409)
2 KOG1436|consensus 99.9 2.2E-27 4.7E-32 194.1 -0.5 106 13-118 19-125 (398)
3 PRK05286 dihydroorotate dehydr 99.8 3E-21 6.6E-26 158.1 5.2 83 36-118 1-90 (344)
4 TIGR01036 pyrD_sub2 dihydrooro 99.8 2.6E-20 5.5E-25 152.6 3.5 79 39-118 2-87 (335)
5 cd04738 DHOD_2_like Dihydrooro 99.7 5.1E-18 1.1E-22 138.1 3.5 77 42-118 1-80 (327)
6 COG0167 PyrD Dihydroorotate de 99.2 4.1E-12 8.8E-17 104.0 0.9 42 77-118 2-44 (310)
7 PF01180 DHO_dh: Dihydroorotat 98.9 1.1E-10 2.5E-15 93.2 -1.0 43 76-118 1-43 (295)
8 PRK02506 dihydroorotate dehydr 98.9 2.8E-10 6.1E-15 92.4 1.1 42 77-118 2-44 (310)
9 PRK07259 dihydroorotate dehydr 98.9 7.2E-10 1.6E-14 88.7 1.7 42 77-118 2-44 (301)
10 cd04741 DHOD_1A_like Dihydroor 98.8 7.8E-10 1.7E-14 89.1 0.2 40 79-118 1-41 (294)
11 cd02940 DHPD_FMN Dihydropyrimi 98.8 1.2E-09 2.5E-14 88.0 0.8 42 77-118 2-44 (299)
12 cd04740 DHOD_1B_like Dihydroor 98.7 2.9E-09 6.2E-14 84.9 1.0 42 78-119 1-43 (296)
13 cd04739 DHOD_like Dihydroorota 98.7 2.8E-09 6.2E-14 87.0 0.6 42 77-118 2-44 (325)
14 cd02810 DHOD_DHPD_FMN Dihydroo 98.7 6E-09 1.3E-13 82.5 0.7 40 79-118 1-41 (289)
15 PRK08318 dihydropyrimidine deh 98.4 5.7E-08 1.2E-12 81.3 0.1 42 76-118 3-46 (420)
16 TIGR01037 pyrD_sub1_fam dihydr 98.3 1.3E-07 2.7E-12 75.7 0.7 42 77-118 1-43 (300)
17 PRK07565 dihydroorotate dehydr 98.0 1.1E-06 2.4E-11 71.8 0.2 43 76-118 2-45 (334)
18 PLN02495 oxidoreductase, actin 83.4 0.44 9.5E-06 40.4 0.6 42 74-115 8-50 (385)
19 PLN02535 glycolate oxidase 64.8 9.8 0.00021 32.1 3.9 46 49-94 32-79 (364)
20 PLN02493 probable peroxisomal 60.3 14 0.0003 31.3 4.1 54 49-102 30-90 (367)
21 TIGR02708 L_lactate_ox L-lacta 58.0 15 0.00033 31.0 3.9 46 49-94 40-87 (367)
22 PRK11197 lldD L-lactate dehydr 58.0 14 0.00031 31.3 3.8 53 49-101 30-89 (381)
23 cd03332 LMO_FMN L-Lactate 2-mo 56.8 18 0.00038 30.8 4.1 46 49-94 45-92 (383)
24 cd04736 MDH_FMN Mandelate dehy 56.8 18 0.00039 30.5 4.2 46 49-94 24-71 (361)
25 cd04737 LOX_like_FMN L-Lactate 56.5 14 0.0003 31.0 3.4 47 48-94 31-79 (351)
26 cd02809 alpha_hydroxyacid_oxid 55.4 33 0.00071 27.5 5.3 51 44-94 19-71 (299)
27 PF01070 FMN_dh: FMN-dependent 54.4 13 0.00027 31.1 2.9 47 48-94 17-65 (356)
28 cd02922 FCB2_FMN Flavocytochro 53.7 24 0.00051 29.4 4.4 53 49-101 24-83 (344)
29 PF01881 Cas_Cas6: CRISPR asso 44.1 9.4 0.0002 27.5 0.5 12 105-116 143-154 (155)
30 PLN02979 glycolate oxidase 35.1 29 0.00062 29.5 2.1 30 65-94 46-76 (366)
31 KOG4056|consensus 32.6 51 0.0011 24.6 2.8 23 10-32 8-30 (143)
32 PRK09853 putative selenate red 29.5 29 0.00063 33.2 1.4 26 70-95 35-60 (1019)
33 TIGR03315 Se_ygfK putative sel 29.4 29 0.00063 33.2 1.4 26 70-95 34-59 (1012)
34 PF13765 PRY: SPRY-associated 29.0 11 0.00024 22.4 -1.0 10 47-56 2-11 (49)
35 PF15141 DUF4574: Domain of un 27.6 54 0.0012 22.3 2.1 37 7-43 4-40 (84)
36 PF06881 Elongin_A: RNA polyme 27.5 62 0.0013 22.2 2.5 21 39-59 10-30 (109)
37 COG0812 MurB UDP-N-acetylmuram 27.1 42 0.00091 27.6 1.8 49 43-95 175-223 (291)
38 PF12704 MacB_PCD: MacB-like p 26.4 22 0.00048 25.3 0.0 22 2-23 1-23 (232)
39 PF01436 NHL: NHL repeat; Int 25.2 30 0.00066 18.0 0.4 14 86-101 1-14 (28)
40 COG2838 Icd Monomeric isocitra 23.7 19 0.00041 32.5 -0.9 17 42-58 484-500 (744)
41 PF11171 DUF2958: Protein of u 23.4 21 0.00045 25.6 -0.6 35 84-118 29-68 (112)
42 PRK15463 cold shock-like prote 22.6 38 0.00082 21.8 0.6 10 108-117 15-24 (70)
43 KOG3342|consensus 22.5 1.2E+02 0.0027 23.2 3.4 34 1-34 14-47 (180)
44 PRK10354 RNA chaperone/anti-te 20.8 47 0.001 21.2 0.7 9 108-116 15-23 (70)
45 PRK10943 cold shock-like prote 20.7 47 0.001 21.2 0.7 9 108-116 14-22 (69)
46 PF02937 COX6C: Cytochrome c o 20.3 1.5E+02 0.0032 19.4 3.1 23 31-57 41-63 (73)
47 PRK09890 cold shock protein Cs 20.1 49 0.0011 21.1 0.7 10 108-117 15-24 (70)
No 1
>PLN02826 dihydroorotate dehydrogenase
Probab=99.93 E-value=8e-27 Score=195.76 Aligned_cols=83 Identities=27% Similarity=0.393 Sum_probs=75.4
Q ss_pred HHHhHHHHhcCCChhHHHHHHHHHHhhccCCCCCCCCCCCCceeecCcccCCceeeccCCCCCCccCCCCCCCCCceEee
Q psy5901 37 YNNVLLPILFKFDAETAHNIAIWTAKYKLLPKSVYEDPPQLASQVWNLKFPNPLAELRTQKPTEVSIQGPPTVSISGVEP 116 (122)
Q Consensus 37 Y~~l~~plLf~ldPE~AH~lai~~lk~~l~~~~~~~~~~~L~~~v~Gl~F~NPvGLAAGfDKna~~i~~l~~lGFGfvEv 116 (122)
++.+++|+||++|||+||++++.+|++.+.|.....++++|+++++|++|+|||||||||||||++++.|.++||||||+
T Consensus 34 ~~~~~~~~l~~~dpE~aH~~~~~~l~~~~~~~~~~~~~~~L~~~~~Gl~f~NPvglAAG~dkn~~~~~~l~~lGfG~vev 113 (409)
T PLN02826 34 ATKLVNPLFRLLDPETAHSLAISAAARGLVPREKRPDPSVLGVEVWGRTFSNPIGLAAGFDKNAEAVEGLLGLGFGFVEI 113 (409)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHhhcccccccCCCCCcceEECCEECCCCCEECcccCCCHHHHHHHHhcCCCeEEe
Confidence 56789999999999999999999999876664334567899999999999999999999999999999999999999999
Q ss_pred CCC
Q psy5901 117 QVP 119 (122)
Q Consensus 117 G~~ 119 (122)
||=
T Consensus 114 gTV 116 (409)
T PLN02826 114 GSV 116 (409)
T ss_pred CCc
Confidence 983
No 2
>KOG1436|consensus
Probab=99.93 E-value=2.2e-27 Score=194.07 Aligned_cols=106 Identities=25% Similarity=0.373 Sum_probs=98.7
Q ss_pred HHHHHHhHHhhhhhheeeeCChhHHHHhHHHHhc-CCChhHHHHHHHHHHhhccCCCCCCCCCCCCceeecCcccCCcee
Q psy5901 13 LAAVSSGSFALFSGINIYQNNENYYNNVLLPILF-KFDAETAHNIAIWTAKYKLLPKSVYEDPPQLASQVWNLKFPNPLA 91 (122)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~Y~~l~~plLf-~ldPE~AH~lai~~lk~~l~~~~~~~~~~~L~~~v~Gl~F~NPvG 91 (122)
..++++++++++++++.+.+.+.+|...++|.++ .+|||.+|++++.+.+|+++|+....+++.|.+++||.+|+||||
T Consensus 19 ~~i~~~gg~~~~~a~~~~~~~~~f~~~~~mp~~~~lld~E~sHrlAv~aas~gl~Pr~~~~d~~~L~~k~~g~~f~NPig 98 (398)
T KOG1436|consen 19 KGIVLAGGAALGTAIEAMSGVELFYARIVMPPFHALLDPEFSHRLAVLAASWGLLPRDRVADDASLETKVLGRKFSNPIG 98 (398)
T ss_pred eEEEEeccHHHHHHHHHhcCceeeeeeeecchhhhhCCHHHHHHHHHHHHHhCCCchhccCCccchhhHHhhhhccCchh
Confidence 4456778889999999999998899988999886 569999999999999999999988899999999999999999999
Q ss_pred eccCCCCCCccCCCCCCCCCceEeeCC
Q psy5901 92 ELRTQKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 92 LAAGfDKna~~i~~l~~lGFGfvEvG~ 118 (122)
+|||||||++++++|..+||||+|||+
T Consensus 99 lAAGfdk~~eaidgL~~~gfG~ieigS 125 (398)
T KOG1436|consen 99 LAAGFDKNAEAIDGLANSGFGFIEIGS 125 (398)
T ss_pred hhhccCcchHHHHHHHhCCCceEEecc
Confidence 999999999999999999999999995
No 3
>PRK05286 dihydroorotate dehydrogenase 2; Reviewed
Probab=99.83 E-value=3e-21 Score=158.12 Aligned_cols=83 Identities=30% Similarity=0.426 Sum_probs=74.5
Q ss_pred HHHHhHHHHhcCCChhHHHHHHHHHHhhc----cCC---CCCCCCCCCCceeecCcccCCceeeccCCCCCCccCCCCCC
Q psy5901 36 YYNNVLLPILFKFDAETAHNIAIWTAKYK----LLP---KSVYEDPPQLASQVWNLKFPNPLAELRTQKPTEVSIQGPPT 108 (122)
Q Consensus 36 ~Y~~l~~plLf~ldPE~AH~lai~~lk~~----l~~---~~~~~~~~~L~~~v~Gl~F~NPvGLAAGfDKna~~i~~l~~ 108 (122)
||+.+++|+||++|||+||++++.++|+. +.+ +....++|.|+++++|++|+||||+|||+|||++.++.+..
T Consensus 1 ~~~~~~~~~l~~~~~e~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~Gl~l~nPi~~AsG~~~~~~~~~~~~~ 80 (344)
T PRK05286 1 MYYPLARPLLFKLDPETAHELTIRALKRASRTPLLSLLRQRLTYTDPRLPVTVMGLTFPNPVGLAAGFDKNGEAIDALGA 80 (344)
T ss_pred ChHHHHHHHHHcCCHHHHHHHHHHHHHHhccCCchhhhhhccCCCCCCCceEECCEECCCCCEECCCCCCChHHHHHHHH
Confidence 57889999999999999999999999973 222 22356788999999999999999999999999999999999
Q ss_pred CCCceEeeCC
Q psy5901 109 VSISGVEPQV 118 (122)
Q Consensus 109 lGFGfvEvG~ 118 (122)
+|||+||+||
T Consensus 81 ~G~Gavv~kt 90 (344)
T PRK05286 81 LGFGFVEVGT 90 (344)
T ss_pred cCCCEEEeCC
Confidence 9999999998
No 4
>TIGR01036 pyrD_sub2 dihydroorotate dehydrogenase, subfamily 2. The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region.
Probab=99.79 E-value=2.6e-20 Score=152.62 Aligned_cols=79 Identities=24% Similarity=0.325 Sum_probs=68.5
Q ss_pred HhHHHHhcCCChhHHHHHHHHHHhhc----cCC---CCCCCCCCCCceeecCcccCCceeeccCCCCCCccCCCCCCCCC
Q psy5901 39 NVLLPILFKFDAETAHNIAIWTAKYK----LLP---KSVYEDPPQLASQVWNLKFPNPLAELRTQKPTEVSIQGPPTVSI 111 (122)
Q Consensus 39 ~l~~plLf~ldPE~AH~lai~~lk~~----l~~---~~~~~~~~~L~~~v~Gl~F~NPvGLAAGfDKna~~i~~l~~lGF 111 (122)
++++|+||++|||+||++++.+||.. +.+ .....+++ |.++++|++|+||||+|||+|||++.++.+..+||
T Consensus 2 ~~~~~~l~~~~~e~ah~~~~~~l~~~~~~~~~~~~~~~~~~~~~-L~~~~~Gl~l~NPi~lAsG~~~~~~~~~~~~~~G~ 80 (335)
T TIGR01036 2 PLVRKLLFLLDPESAHELTFQFLRLGTGTPFLALLRSLFGASDP-LEVTVLGLKFPNPLGLAAGFDKDGEAIDALGAMGF 80 (335)
T ss_pred chhhhhhhcCCHHHHHHHHHHHHHhcccCCchhhhhhhccCCCC-CcEEECCEECCCCcEeCCccCCCHHHHHHHHhcCC
Confidence 57899999999999999999999962 221 11223455 99999999999999999999999999999999999
Q ss_pred ceEeeCC
Q psy5901 112 SGVEPQV 118 (122)
Q Consensus 112 GfvEvG~ 118 (122)
||||+||
T Consensus 81 Gavv~kT 87 (335)
T TIGR01036 81 GFLEIGT 87 (335)
T ss_pred CEEEeCC
Confidence 9999998
No 5
>cd04738 DHOD_2_like Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.
Probab=99.70 E-value=5.1e-18 Score=138.05 Aligned_cols=77 Identities=31% Similarity=0.415 Sum_probs=68.3
Q ss_pred HHHhcCCChhHHHHHHHHHHhhc-cCCC--CCCCCCCCCceeecCcccCCceeeccCCCCCCccCCCCCCCCCceEeeCC
Q psy5901 42 LPILFKFDAETAHNIAIWTAKYK-LLPK--SVYEDPPQLASQVWNLKFPNPLAELRTQKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 42 ~plLf~ldPE~AH~lai~~lk~~-l~~~--~~~~~~~~L~~~v~Gl~F~NPvGLAAGfDKna~~i~~l~~lGFGfvEvG~ 118 (122)
+|+||++|||+||+++++++|.. ..|. .+..+++.|+++++|++|+||||+|||+|||++.+..+...||||||+||
T Consensus 1 ~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~Gl~l~nPi~~AsG~~~~~~~~~~~~~~G~Gavv~kt 80 (327)
T cd04738 1 RPLLFLLDPETAHRLAIRALKLGLGPPLLLLLVYDDPRLEVEVFGLTFPNPVGLAAGFDKNAEAIDALLALGFGFVEVGT 80 (327)
T ss_pred CCceecCCHHHHHHHHHHHHHhcCCCCCccccCCCCCCcceEECCEECCCCCEeCcCCCCCHHHHHHHHHCCCcEEEEec
Confidence 47899999999999999999974 2231 23467889999999999999999999999999999999999999999997
No 6
>COG0167 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]
Probab=99.19 E-value=4.1e-12 Score=103.97 Aligned_cols=42 Identities=19% Similarity=0.383 Sum_probs=40.5
Q ss_pred CceeecCcccCCceeeccCCC-CCCccCCCCCCCCCceEeeCC
Q psy5901 77 LASQVWNLKFPNPLAELRTQK-PTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 77 L~~~v~Gl~F~NPvGLAAGfD-Kna~~i~~l~~lGFGfvEvG~ 118 (122)
|.++++|++|+||+|||||+| ||++.++.|.++||||||+||
T Consensus 2 l~~~~~Gl~f~NPl~lAaG~~~~~~~~~~~~~~~g~G~i~~kt 44 (310)
T COG0167 2 LSTEILGLKFPNPLGLAAGFDGKNGEELDALAALGFGAIVTKT 44 (310)
T ss_pred CceeecceecCCCCeEcccCCccCHHHHHHHHhcCCceEEecC
Confidence 577899999999999999999 999999999999999999997
No 7
>PF01180 DHO_dh: Dihydroorotate dehydrogenase; InterPro: IPR012135 Dihydroorotate dehydrogenase (DHOD), also known as dihydroorotate oxidase, catalyses the fourth step in de novo pyrimidine biosynthesis, the stereospecific oxidation of (S)-dihydroorotate to orotate, which is the only redox reaction in this pathway. DHODs can be divided into two mains classes: class 1 cytosolic enzymes found primarily in Gram-positive bacteria, and class 2 membrane-associated enzymes found primarily in eukaryotic mitochondria and Gram-negative bacteria []. The class 1 DHODs can be further divided into subclasses 1A and 1B, which differ in their structural organisation and use of electron acceptors. The 1A enzyme is a homodimer of two PyrD subunits where each subunit forms a TIM barrel fold with a bound FMN cofactor located near the top of the barrel []. Fumarate is the natural electron acceptor for this enzyme. The 1B enzyme, in contrast is a heterotetramer composed of a central, FMN-containing, PyrD homodimer resembling the 1A homodimer, and two additional PyrK subunits which contain FAD and a 2Fe-2S cluster []. These additional groups allow the enzyme to use NAD(+) as its natural electron acceptor. The class 2 membrane-associated enzymes are monomers which have the FMN-containing TIM barrel domain found in the class 1 PyrD subunit, and an additional N-terminal alpha helical domain [, ]. These enzymes use respiratory quinones as the physiological electron acceptor. This entry represents the FMN-binding subunit common to all classes of dihydroorotate dehydrogenase.; GO: 0004152 dihydroorotate dehydrogenase activity, 0006222 UMP biosynthetic process, 0055114 oxidation-reduction process; PDB: 3GYE_A 3GZ3_A 3MHU_B 3MJY_A 3TQ0_A 2B4G_C 1EP3_A 1EP2_A 1EP1_A 3I6R_A ....
Probab=98.92 E-value=1.1e-10 Score=93.20 Aligned_cols=43 Identities=14% Similarity=0.156 Sum_probs=39.4
Q ss_pred CCceeecCcccCCceeeccCCCCCCccCCCCCCCCCceEeeCC
Q psy5901 76 QLASQVWNLKFPNPLAELRTQKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 76 ~L~~~v~Gl~F~NPvGLAAGfDKna~~i~~l~~lGFGfvEvG~ 118 (122)
.|.++++|++|+||||+|||+|||++.+..+.++|||+||++|
T Consensus 1 ~L~~~~~Gl~l~nPi~~asG~~~~~~~~~~~~~~G~Gavv~ks 43 (295)
T PF01180_consen 1 MLSTNFCGLTLKNPIGLASGLDKNGEEIKRLFDAGFGAVVTKS 43 (295)
T ss_dssp GG-EEETTEEESSSEEE-TTSSTSSHHHHHHHHHSSSEEEEEE
T ss_pred CccEEECCEEcCCCcEECCcCCCCchhhhhhhcCCccEEEecc
Confidence 4789999999999999999999999999999999999999986
No 8
>PRK02506 dihydroorotate dehydrogenase 1A; Reviewed
Probab=98.92 E-value=2.8e-10 Score=92.40 Aligned_cols=42 Identities=14% Similarity=0.116 Sum_probs=40.6
Q ss_pred CceeecCcccCCceeeccCCC-CCCccCCCCCCCCCceEeeCC
Q psy5901 77 LASQVWNLKFPNPLAELRTQK-PTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 77 L~~~v~Gl~F~NPvGLAAGfD-Kna~~i~~l~~lGFGfvEvG~ 118 (122)
|+++++|++|+|||++|||+| ||++.++.+...|||+||++|
T Consensus 2 L~~~~~Gl~l~NPv~~AsG~~~~~~e~~~~~~~~g~Gavv~kt 44 (310)
T PRK02506 2 TSTQIAGFKFDNCLMNAAGVYCMTKEELEEVEASAAGAFVTKS 44 (310)
T ss_pred CceEECCEECCCCCEeCCCCCCCCHHHHHHHHHcCCcEEEeCc
Confidence 688999999999999999999 899999999999999999997
No 9
>PRK07259 dihydroorotate dehydrogenase 1B; Reviewed
Probab=98.87 E-value=7.2e-10 Score=88.72 Aligned_cols=42 Identities=12% Similarity=0.018 Sum_probs=40.6
Q ss_pred CceeecCcccCCceeeccC-CCCCCccCCCCCCCCCceEeeCC
Q psy5901 77 LASQVWNLKFPNPLAELRT-QKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 77 L~~~v~Gl~F~NPvGLAAG-fDKna~~i~~l~~lGFGfvEvG~ 118 (122)
|.++++|++|+|||++||| +|||++.++.+...|||+||+||
T Consensus 2 l~~~~~G~~~~nPv~~aag~~~~~~~~~~~~~~~g~g~v~~kt 44 (301)
T PRK07259 2 LSVELPGLKLKNPVMPASGTFGFGGEYARFYDLNGLGAIVTKS 44 (301)
T ss_pred CceEECCEECCCCcEECCcCCCCCHHHHHHhhhcCCcEEEeCC
Confidence 6889999999999999999 99999999999999999999998
No 10
>cd04741 DHOD_1A_like Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Probab=98.81 E-value=7.8e-10 Score=89.06 Aligned_cols=40 Identities=15% Similarity=0.052 Sum_probs=38.2
Q ss_pred eeecCcccCCceeeccCC-CCCCccCCCCCCCCCceEeeCC
Q psy5901 79 SQVWNLKFPNPLAELRTQ-KPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 79 ~~v~Gl~F~NPvGLAAGf-DKna~~i~~l~~lGFGfvEvG~ 118 (122)
++++|++|+|||++|||+ |||++.++.+...||||||++|
T Consensus 1 ~~~~Gl~l~nPi~~Asg~~~~~~e~~~~~~~~G~Gavv~kt 41 (294)
T cd04741 1 VTPPGLTISPPLMNAAGPWCTTLEDLLELAASSTGAVTTRS 41 (294)
T ss_pred CccCCeeCCCCCEECCCCCCCCHHHHHHHHHcCCcEEEeCc
Confidence 468999999999999999 9999999999999999999997
No 11
>cd02940 DHPD_FMN Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.
Probab=98.80 E-value=1.2e-09 Score=87.97 Aligned_cols=42 Identities=19% Similarity=0.291 Sum_probs=40.0
Q ss_pred CceeecCcccCCceeeccC-CCCCCccCCCCCCCCCceEeeCC
Q psy5901 77 LASQVWNLKFPNPLAELRT-QKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 77 L~~~v~Gl~F~NPvGLAAG-fDKna~~i~~l~~lGFGfvEvG~ 118 (122)
|.++++|++|+|||++||| +|||++.+..+..+|||+||++|
T Consensus 2 l~~~~~Gl~l~nPi~~aag~~~~~~~~~~~~~~~G~Gavv~kt 44 (299)
T cd02940 2 LSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKT 44 (299)
T ss_pred CceEECCEEcCCCCEeCCcCCCCCHHHHHHHHHhCCCEEEecc
Confidence 6789999999999999999 59999999999999999999996
No 12
>cd04740 DHOD_1B_like Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Probab=98.73 E-value=2.9e-09 Score=84.86 Aligned_cols=42 Identities=7% Similarity=0.094 Sum_probs=39.1
Q ss_pred ceeecCcccCCceeeccCCCCCCccCCCCCCCC-CceEeeCCC
Q psy5901 78 ASQVWNLKFPNPLAELRTQKPTEVSIQGPPTVS-ISGVEPQVP 119 (122)
Q Consensus 78 ~~~v~Gl~F~NPvGLAAGfDKna~~i~~l~~lG-FGfvEvG~~ 119 (122)
.++++|++|+||||+|||+|||++.+..+..+| ||+||+||=
T Consensus 1 ~~~~~G~~~~nP~~~aag~~~~~~~~~~~~~~g~~g~v~~~ti 43 (296)
T cd04740 1 SVELAGLRLKNPVILASGTFGFGEELSRVADLGKLGAIVTKSI 43 (296)
T ss_pred CeEECCEEcCCCCEECCCCCCCHHHHHHHHhcCCceEEEECCc
Confidence 368999999999999999999999999999998 999999973
No 13
>cd04739 DHOD_like Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.
Probab=98.72 E-value=2.8e-09 Score=86.96 Aligned_cols=42 Identities=14% Similarity=0.139 Sum_probs=40.5
Q ss_pred CceeecCcccCCceeec-cCCCCCCccCCCCCCCCCceEeeCC
Q psy5901 77 LASQVWNLKFPNPLAEL-RTQKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 77 L~~~v~Gl~F~NPvGLA-AGfDKna~~i~~l~~lGFGfvEvG~ 118 (122)
|+++++|++|+|||++| |+||||++.+..+...|||+||++|
T Consensus 2 L~v~~~Gl~l~nPv~~ASg~~~~~~e~~~~~~~~G~Gavv~kt 44 (325)
T cd04739 2 LSTTYLGLSLKNPLVASASPLSRNLDNIRRLEDAGAGAIVLPS 44 (325)
T ss_pred ceEEECCEecCCCCEeCCcCCCCCHHHHHHHHHCCCcEEEecc
Confidence 68899999999999996 9999999999999999999999998
No 14
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=98.65 E-value=6e-09 Score=82.51 Aligned_cols=40 Identities=18% Similarity=0.155 Sum_probs=38.3
Q ss_pred eeecCcccCCceeeccCCC-CCCccCCCCCCCCCceEeeCC
Q psy5901 79 SQVWNLKFPNPLAELRTQK-PTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 79 ~~v~Gl~F~NPvGLAAGfD-Kna~~i~~l~~lGFGfvEvG~ 118 (122)
++++|++|+||||+|||+| ||++.++.+...|||+|+++|
T Consensus 1 ~~~~G~~~~nPv~~aag~~~~~~~~~~~~~~~g~g~vv~kt 41 (289)
T cd02810 1 VNFLGLKLKNPFGVAAGPLLKTGELIARAAAAGFGAVVYKT 41 (289)
T ss_pred CeECCEECCCCCEeCCCCCCCCHHHHHHHHHcCCCeEEeCc
Confidence 4689999999999999999 999999999999999999997
No 15
>PRK08318 dihydropyrimidine dehydrogenase subunit B; Validated
Probab=98.40 E-value=5.7e-08 Score=81.30 Aligned_cols=42 Identities=17% Similarity=0.111 Sum_probs=38.1
Q ss_pred CCceeecCcccCCceeeccC--CCCCCccCCCCCCCCCceEeeCC
Q psy5901 76 QLASQVWNLKFPNPLAELRT--QKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 76 ~L~~~v~Gl~F~NPvGLAAG--fDKna~~i~~l~~lGFGfvEvG~ 118 (122)
.|+++++|++|+||||+||| +||+.++.+.+. +|||+||++|
T Consensus 3 ~L~~~~~Gl~l~nPv~~aag~~~~~~~~~~~~~~-~g~Gavv~kt 46 (420)
T PRK08318 3 DLSITFCGIKSPNPFWLASAPPTNKYYNVARAFE-AGWGGVVWKT 46 (420)
T ss_pred CceEEECCEecCCCcEeCCcCCCCCHHHHHHHHH-hCCCEEEEee
Confidence 47899999999999999999 999988888774 7999999986
No 16
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.
Probab=98.33 E-value=1.3e-07 Score=75.68 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=39.1
Q ss_pred CceeecCcccCCceeeccC-CCCCCccCCCCCCCCCceEeeCC
Q psy5901 77 LASQVWNLKFPNPLAELRT-QKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 77 L~~~v~Gl~F~NPvGLAAG-fDKna~~i~~l~~lGFGfvEvG~ 118 (122)
|++++.|++|+|||++||| +|++.+.++.+...|||+++++|
T Consensus 1 l~~~~~g~~l~npi~~aag~~~~~~~~~~~~~~~G~g~iv~kt 43 (300)
T TIGR01037 1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKS 43 (300)
T ss_pred CcEEECCEECCCCCEeCCcCCCCCHHHHHHHHHcCCcEEEeCc
Confidence 5688999999999999999 89999999999999999999964
No 17
>PRK07565 dihydroorotate dehydrogenase 2; Reviewed
Probab=98.03 E-value=1.1e-06 Score=71.75 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=40.6
Q ss_pred CCceeecCcccCCce-eeccCCCCCCccCCCCCCCCCceEeeCC
Q psy5901 76 QLASQVWNLKFPNPL-AELRTQKPTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 76 ~L~~~v~Gl~F~NPv-GLAAGfDKna~~i~~l~~lGFGfvEvG~ 118 (122)
.|+++++|++|+||| +.|+++||+++.++.+...|+|+|+++|
T Consensus 2 ~l~~~~~Gl~l~nPv~~asg~~~~~~~~~~~~~~~g~Gavv~kt 45 (334)
T PRK07565 2 DLSTTYLGLTLRNPLVASASPLSESVDNVKRLEDAGAGAVVLKS 45 (334)
T ss_pred CceEEECCEecCCCCEecCcCCCCCHHHHHHHHHCCCeEEEEee
Confidence 478999999999999 8889999999999999999999999987
No 18
>PLN02495 oxidoreductase, acting on the CH-CH group of donors
Probab=83.41 E-value=0.44 Score=40.40 Aligned_cols=42 Identities=24% Similarity=0.270 Sum_probs=32.2
Q ss_pred CCCCceeecCcccCCceeeccCCC-CCCccCCCCCCCCCceEe
Q psy5901 74 PPQLASQVWNLKFPNPLAELRTQK-PTEVSIQGPPTVSISGVE 115 (122)
Q Consensus 74 ~~~L~~~v~Gl~F~NPvGLAAGfD-Kna~~i~~l~~lGFGfvE 115 (122)
-+.|.++++|++|+||+-+|+|-= .+.+.++.+...|.|.|-
T Consensus 8 ~~dLst~~~Gl~l~NP~i~ASgp~t~~~e~~~~~~~~g~GAVV 50 (385)
T PLN02495 8 EPDLSVTVNGLKMPNPFVIGSGPPGTNYTVMKRAFDEGWGGVI 50 (385)
T ss_pred CCcceEEECCEEcCCCcEeCCccCCCCHHHHHHHHhcCCeEEE
Confidence 356899999999999999999854 444554665566888774
No 19
>PLN02535 glycolate oxidase
Probab=64.79 E-value=9.8 Score=32.11 Aligned_cols=46 Identities=7% Similarity=0.141 Sum_probs=33.4
Q ss_pred ChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 49 DAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 49 dPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
+-|..++.-..+++. .+.|+ ......+.+.++++|.++.-|+++|.
T Consensus 32 ~~e~t~~~N~~af~~~~l~Pr~L~dv~~~d~~t~~lG~~~~~P~~iaP 79 (364)
T PLN02535 32 EDQHTLKENVQAFRRITFRPRVLVDVSKIDMSTTILGYTISAPIMIAP 79 (364)
T ss_pred cccHHHHHHHHHHHhCCeecccccCCCCCCCceEECCccccccceech
Confidence 556666666666654 46776 33456678999999999999999874
No 20
>PLN02493 probable peroxisomal (S)-2-hydroxy-acid oxidase
Probab=60.28 E-value=14 Score=31.26 Aligned_cols=54 Identities=9% Similarity=0.067 Sum_probs=36.7
Q ss_pred ChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc-----CCCCCCcc
Q psy5901 49 DAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR-----TQKPTEVS 102 (122)
Q Consensus 49 dPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA-----GfDKna~~ 102 (122)
+-|..++.-..+.+. .+.|+ ........+.++++|.+++-||++|. =+..+||.
T Consensus 30 ~de~t~~~N~~af~r~~l~PRvLrdv~~~d~~t~~lG~~~~~Pi~iAP~g~~~l~hp~gE~ 90 (367)
T PLN02493 30 EDQWTLQENRNAFARILFRPRILIDVSKIDMTTTVLGFKISMPIMVAPTAMQKMAHPDGEY 90 (367)
T ss_pred chhHHHHHHHHHHHhCCeecccccCCCCCCCceEECCccccccceechHHHHhhcCCchHH
Confidence 556666665666654 46776 33455677899999999999998874 23555543
No 21
>TIGR02708 L_lactate_ox L-lactate oxidase. Members of this protein oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence.
Probab=58.02 E-value=15 Score=31.03 Aligned_cols=46 Identities=11% Similarity=0.086 Sum_probs=30.7
Q ss_pred ChhHHHHHHHHHHh-hccCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 49 DAETAHNIAIWTAK-YKLLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 49 dPE~AH~lai~~lk-~~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
+-|..++.-..+.+ +.+.|+ ......+.+.++++|.++.-||++|.
T Consensus 40 ~de~t~~~N~~af~~~~l~PR~L~dv~~~d~~t~llG~~~~~Pv~iaP 87 (367)
T TIGR02708 40 GDTFTLRENIRAFNHKLIVPHLLQDVENPSTEIEFLGHKLKSPFIMAP 87 (367)
T ss_pred chHHHHHHHHHHHHhcCeecccccCCCCCCCceeeCCcccccccccCc
Confidence 34444444444444 356776 33355678999999999999998863
No 22
>PRK11197 lldD L-lactate dehydrogenase; Provisional
Probab=57.99 E-value=14 Score=31.31 Aligned_cols=53 Identities=13% Similarity=-0.014 Sum_probs=36.1
Q ss_pred ChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc-----CCCCCCc
Q psy5901 49 DAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR-----TQKPTEV 101 (122)
Q Consensus 49 dPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA-----GfDKna~ 101 (122)
+-|..++.-..+... .+.|+ ........+.++++|.++.-|+++|. =++++||
T Consensus 30 ~de~t~~~N~~af~~~~l~PR~L~dv~~~d~~t~llG~~~~~Pi~iAP~g~~~l~hp~gE 89 (381)
T PRK11197 30 YAEYTLRRNVEDLADIALRQRVLKDMSDLSLETTLFGEKLSMPVALAPVGLTGMYARRGE 89 (381)
T ss_pred chHHHHHHHHHHHHhcceecccccCCCCCCCceEECCcccccchhhChHHHhhccCCchH
Confidence 456666655555554 46675 33355667999999999999998873 2366665
No 23
>cd03332 LMO_FMN L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases. It is thought to be a homooctamer with two- and four- fold axes in the center of the octamer.
Probab=56.82 E-value=18 Score=30.81 Aligned_cols=46 Identities=11% Similarity=0.135 Sum_probs=33.2
Q ss_pred ChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 49 DAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 49 dPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
+-|..++.-..+.+. .+.|+ ........+.++++|.++.-|+++|.
T Consensus 45 ~de~t~~~N~~af~~~~l~PRvL~dv~~~dt~t~llG~~~~~P~~iAP 92 (383)
T cd03332 45 GSESTARANRDAFSRWRIVPRMLRGVTERDLSVELFGRTLAAPLLLAP 92 (383)
T ss_pred chHHHHHHHHHHHHhcCccccccccCCCCCCceeeCCccccccceech
Confidence 456666666666654 46675 33456677899999999999999984
No 24
>cd04736 MDH_FMN Mandelate dehydrogenase (MDH)-like FMN-binding domain. MDH is part of a widespread family of homologous FMN-dependent a-hydroxy acid oxidizing enzymes that oxidizes (S)-mandelate to phenylglyoxalate. MDH is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).
Probab=56.78 E-value=18 Score=30.51 Aligned_cols=46 Identities=11% Similarity=0.176 Sum_probs=32.3
Q ss_pred ChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 49 DAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 49 dPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
+-|..++-=..+.+. .+.|+ ........+.++++|.++.-|+++|.
T Consensus 24 ~de~t~~~N~~af~~~~l~PRvLr~v~~~d~~ttllG~~~~~P~~iaP 71 (361)
T cd04736 24 EDEKGLRHNRDAFDRWRFIPRRLVDVSKRDISASLFGKVWSAPLVIAP 71 (361)
T ss_pred chHHHHHHHHHHHHHcCccccccCCCCCCCCceeECCccccccccccH
Confidence 456666555555554 47776 33355667999999999999999874
No 25
>cd04737 LOX_like_FMN L-Lactate oxidase (LOX) FMN-binding domain. LOX is a member of the family of FMN-containing alpha-hydroxyacid oxidases and catalyzes the oxidation of l-lactate using molecular oxygen to generate pyruvate and H2O2. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).
Probab=56.47 E-value=14 Score=30.99 Aligned_cols=47 Identities=11% Similarity=0.192 Sum_probs=33.8
Q ss_pred CChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 48 FDAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 48 ldPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
-+-|..++.-..+++. .+.|+ ......+.+.++++|.++.-|+++|.
T Consensus 31 a~~e~t~~~N~~a~~~~~l~prvL~dv~~~d~~t~~lG~~~~~P~~iaP 79 (351)
T cd04737 31 SEDEWTLRENTRAFNHKQIVPRVLQGVESPDTSTELLGIKLKTPIIMAP 79 (351)
T ss_pred cchHHHHHHHHHHHHhcCeechhccCCCCCCCceEeCCccccchhhhHH
Confidence 3567776666666664 46665 33355677999999999999998874
No 26
>cd02809 alpha_hydroxyacid_oxid_FMN Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate.
Probab=55.43 E-value=33 Score=27.53 Aligned_cols=51 Identities=12% Similarity=0.020 Sum_probs=35.9
Q ss_pred HhcCCChhHHHHHHHHHHhh-ccCCCCC-CCCCCCCceeecCcccCCceeecc
Q psy5901 44 ILFKFDAETAHNIAIWTAKY-KLLPKSV-YEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 44 lLf~ldPE~AH~lai~~lk~-~l~~~~~-~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
.....+.|.+++.....+.. .+.|+.. ..++..+.++++|.+|..|+.+|+
T Consensus 19 ~~~~~~~~~~~~~n~~~~~~i~~~~~~l~~~~~id~~~~~lg~~~~~Pi~iap 71 (299)
T cd02809 19 IDGGAGDEVTLRRNRAAFDRIRLRPRVLRDVSKRDTSTTLLGQKLAMPFGIAP 71 (299)
T ss_pred hccccchHHHHHHHHHHHHhceeecccCCCCCCCCCceEECCeecCCCeeeCc
Confidence 34456778888777777664 3555422 245667899999999999998873
No 27
>PF01070 FMN_dh: FMN-dependent dehydrogenase; InterPro: IPR000262 A number of oxidoreductases that act on alpha-hydroxy acids and which are FMN-containing flavoproteins have been shown [, , ] to be structurally related. These enzymes are: Lactate dehydrogenase (1.1.2.3 from EC), which consists of a dehydrogenase domain and a haem-binding domain called cytochrome b2 and which catalyses the conversion of lactate into pyruvate. Glycolate oxidase (1.1.3.15 from EC) ((S)-2-hydroxy-acid oxidase), a peroxisomal enzyme that catalyses the conversion of glycolate and oxygen to glyoxylate and hydrogen peroxide. Long chain alpha-hydroxy acid oxidase from rat (1.1.3.15 from EC), a peroxisomal enzyme. Lactate 2-monooxygenase (1.13.12.4 from EC) (lactate oxidase) from Mycobacterium smegmatis, which catalyses the conversion of lactate and oxygen to acetate, carbon dioxide and water. (S)-mandelate dehydrogenase from Pseudomonas putida (gene mdlB), which catalyses the reduction of (S)-mandelate to benzoylformate. The first step in the reaction mechanism of these enzymes is the abstraction of the proton from the alpha-carbon of the substrate producing a carbanion which can subsequently attach to the N5 atom of FMN. A conserved histidine has been shown [] to be involved in the removal of the proton. The region around this active site residue is highly conserved and contains an arginine residue which is involved in substrate binding.; GO: 0016491 oxidoreductase activity; PDB: 1VCG_C 1VCF_A 1P0N_B 1P0K_A 2A85_A 2A7P_A 3GIY_A 2A7N_A 3DH7_A 2RDU_A ....
Probab=54.43 E-value=13 Score=31.12 Aligned_cols=47 Identities=13% Similarity=0.068 Sum_probs=30.2
Q ss_pred CChhHHHHHHHHHHhh-ccCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 48 FDAETAHNIAIWTAKY-KLLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 48 ldPE~AH~lai~~lk~-~l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
.+-|.+.+--..+++. .+.|+ ....+++.+.+++||.+++-|+++|+
T Consensus 17 a~~e~t~~~N~~af~~i~l~prvL~dv~~~D~st~~lG~~~s~P~~iaP 65 (356)
T PF01070_consen 17 AGDEVTFRRNREAFDRIRLRPRVLRDVSDPDTSTTFLGQKLSMPFFIAP 65 (356)
T ss_dssp STTTHHHHHHHHGGGGEEE---SSSBGSS-BSSEEETTEEESSSEEEEE
T ss_pred CCCcHHHHHHHHHHHHhcccccccCCcccCCCCeeeCCccCCCCeEEcc
Confidence 3555555555555554 46665 33456788999999999999999874
No 28
>cd02922 FCB2_FMN Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.
Probab=53.73 E-value=24 Score=29.43 Aligned_cols=53 Identities=11% Similarity=0.095 Sum_probs=35.6
Q ss_pred ChhHHHHHHHHHHhh-ccCCCC-CCCCCCCCceeecCcccCCceeecc-----CCCCCCc
Q psy5901 49 DAETAHNIAIWTAKY-KLLPKS-VYEDPPQLASQVWNLKFPNPLAELR-----TQKPTEV 101 (122)
Q Consensus 49 dPE~AH~lai~~lk~-~l~~~~-~~~~~~~L~~~v~Gl~F~NPvGLAA-----GfDKna~ 101 (122)
+-|...+.-..++.. .+.|+- ...++..+.++++|.++.-|+++|. ++..+|+
T Consensus 24 ~~e~t~~~N~~af~~~~l~pr~L~dv~~~d~~~~~lG~~~~~Pi~iaP~~~~~~~~~~ge 83 (344)
T cd02922 24 DDEITLRENLEAFQRIRFRPRVLRDVEKVDTSTTILGHKVSLPFFISPAALAKLAHPDGE 83 (344)
T ss_pred chHHHHHHHHHHHHhCceeccccCCCCCCCCceEECCcccCCceeeChHHHhhhCCchHH
Confidence 446655555555554 466652 2346678999999999999998875 4466554
No 29
>PF01881 Cas_Cas6: CRISPR associated protein Cas6; InterPro: IPR002743 This entry is represented by Bacteriophage c-st, ORF: CST018. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3PKM_A 3I4H_X 3QJJ_B 3QJP_A 3QJL_B 3UFC_X.
Probab=44.11 E-value=9.4 Score=27.52 Aligned_cols=12 Identities=17% Similarity=0.036 Sum_probs=7.1
Q ss_pred CCCCCCCceEee
Q psy5901 105 GPPTVSISGVEP 116 (122)
Q Consensus 105 ~l~~lGFGfvEv 116 (122)
..-+.|||++||
T Consensus 143 ~kns~GFG~vev 154 (155)
T PF01881_consen 143 EKNSQGFGMVEV 154 (155)
T ss_dssp S-GGGT-S-EEE
T ss_pred CCCCcccceEEE
Confidence 455789999997
No 30
>PLN02979 glycolate oxidase
Probab=35.13 E-value=29 Score=29.52 Aligned_cols=30 Identities=13% Similarity=0.254 Sum_probs=23.3
Q ss_pred cCCC-CCCCCCCCCceeecCcccCCceeecc
Q psy5901 65 LLPK-SVYEDPPQLASQVWNLKFPNPLAELR 94 (122)
Q Consensus 65 l~~~-~~~~~~~~L~~~v~Gl~F~NPvGLAA 94 (122)
+.|+ ......+.+.++++|.+++-|+++|.
T Consensus 46 lrPRvLrdv~~~dtst~llG~~~~~P~~iAP 76 (366)
T PLN02979 46 FRPRILIDVSKIDMTTTVLGFKISMPIMVAP 76 (366)
T ss_pred EECccccCCCCCCCceEECCcccCccceecH
Confidence 4565 33455677899999999999999874
No 31
>KOG4056|consensus
Probab=32.56 E-value=51 Score=24.60 Aligned_cols=23 Identities=22% Similarity=0.176 Sum_probs=16.5
Q ss_pred HHHHHHHHHhHHhhhhhheeeeC
Q psy5901 10 LVSLAAVSSGSFALFSGINIYQN 32 (122)
Q Consensus 10 ~r~~~~~~~~~~~~~~~~~~~~~ 32 (122)
+|..+++.|..++++.+|++|-+
T Consensus 8 ~~~~vI~agiag~af~gYciYFd 30 (143)
T KOG4056|consen 8 LRTSVIAAGIAGLAFIGYCIYFD 30 (143)
T ss_pred hhhHHHHHHHHHHHHHHHHhhcc
Confidence 45667777777777888887654
No 32
>PRK09853 putative selenate reductase subunit YgfK; Provisional
Probab=29.52 E-value=29 Score=33.25 Aligned_cols=26 Identities=12% Similarity=0.232 Sum_probs=21.4
Q ss_pred CCCCCCCCceeecCcccCCceeeccC
Q psy5901 70 VYEDPPQLASQVWNLKFPNPLAELRT 95 (122)
Q Consensus 70 ~~~~~~~L~~~v~Gl~F~NPvGLAAG 95 (122)
.+..++.-..++||.+..+|+|=|||
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~gpaag 60 (1019)
T PRK09853 35 FYKPDKGKTISVFGETLATPIGPAAG 60 (1019)
T ss_pred ceeCCCCCeeehhcccCCCCCCCCCC
Confidence 34455666778999999999999999
No 33
>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.
Probab=29.40 E-value=29 Score=33.17 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=21.5
Q ss_pred CCCCCCCCceeecCcccCCceeeccC
Q psy5901 70 VYEDPPQLASQVWNLKFPNPLAELRT 95 (122)
Q Consensus 70 ~~~~~~~L~~~v~Gl~F~NPvGLAAG 95 (122)
.+..++.-..++||.+..+|||=|||
T Consensus 34 ~~~~~~~~~~~~~~~~~~~~~gpaag 59 (1012)
T TIGR03315 34 FYRADPGKYISLFGEKLETPVGPAAG 59 (1012)
T ss_pred ceeCCCCCeeehhcccCCCCCCCCCC
Confidence 34555666778999999999999999
No 34
>PF13765 PRY: SPRY-associated domain; PDB: 3KB5_A 2VOK_A 2VOL_B 2FBE_B 2WL1_A 2IWG_E.
Probab=28.99 E-value=11 Score=22.37 Aligned_cols=10 Identities=40% Similarity=0.541 Sum_probs=5.7
Q ss_pred CCChhHHHHH
Q psy5901 47 KFDAETAHNI 56 (122)
Q Consensus 47 ~ldPE~AH~l 56 (122)
.|||++||.-
T Consensus 2 tlDp~TAh~~ 11 (49)
T PF13765_consen 2 TLDPNTAHPS 11 (49)
T ss_dssp EB-TTTS-TT
T ss_pred EECcccCCCC
Confidence 3789999864
No 35
>PF15141 DUF4574: Domain of unknown function (DUF4574)
Probab=27.65 E-value=54 Score=22.35 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhHHhhhhhheeeeCChhHHHHhHHH
Q psy5901 7 LKKLVSLAAVSSGSFALFSGINIYQNNENYYNNVLLP 43 (122)
Q Consensus 7 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Y~~l~~p 43 (122)
.+++++.++.+|.++..|..|.+.+..+--=...++-
T Consensus 4 ~r~~~~~~~llG~GGvG~~L~~LvtPgeerK~e~lK~ 40 (84)
T PF15141_consen 4 LRKALSVVALLGFGGVGYALFVLVTPGEERKQEMLKE 40 (84)
T ss_pred HHHHHHHHHHHHccchhheeeeEeCCcHHHHHHHHHH
Confidence 3567788888888888899999888876633334443
No 36
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=27.53 E-value=62 Score=22.19 Aligned_cols=21 Identities=33% Similarity=0.313 Sum_probs=17.7
Q ss_pred HhHHHHhcCCChhHHHHHHHH
Q psy5901 39 NVLLPILFKFDAETAHNIAIW 59 (122)
Q Consensus 39 ~l~~plLf~ldPE~AH~lai~ 59 (122)
.+++|+|.++.||.-+++-..
T Consensus 10 ~ll~piL~~~~~~QL~~iE~~ 30 (109)
T PF06881_consen 10 HLLRPILEKCSPEQLRRIEDN 30 (109)
T ss_pred HHHHHHHccCCHHHHHHHHHh
Confidence 699999999999998887553
No 37
>COG0812 MurB UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=27.14 E-value=42 Score=27.65 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=27.7
Q ss_pred HHhcCCChhHHHHHHHHHHhhccCCCCCCCCCCCCceeecCcccCCceeeccC
Q psy5901 43 PILFKFDAETAHNIAIWTAKYKLLPKSVYEDPPQLASQVWNLKFPNPLAELRT 95 (122)
Q Consensus 43 plLf~ldPE~AH~lai~~lk~~l~~~~~~~~~~~L~~~v~Gl~F~NPvGLAAG 95 (122)
.+-|+++|++++.+.-.+.+..-... ..++. ...-.|-.|+||+|-.||
T Consensus 175 ~v~f~L~~~~~~~I~~~~~~ir~~R~--~~qP~--~~ps~GS~FKNP~~~~Ag 223 (291)
T COG0812 175 SVEFKLTKGDPEDILAAMCAIRRRRE--LKQPI--DLPSAGSFFKNPVGDFAG 223 (291)
T ss_pred EEEEEeCCCCHHHHHHHHHHHHHhhc--cCCCC--cCCCCCccccCCCcchHH
Confidence 34567888876666555554321000 01111 112369999999998876
No 38
>PF12704 MacB_PCD: MacB-like periplasmic core domain; PDB: 3FTJ_A 3IS6_B.
Probab=26.36 E-value=22 Score=25.29 Aligned_cols=22 Identities=14% Similarity=0.058 Sum_probs=0.0
Q ss_pred ChhHHHH-HHHHHHHHHHhHHhh
Q psy5901 2 KKPTLLK-KLVSLAAVSSGSFAL 23 (122)
Q Consensus 2 ~~~~~~~-~~r~~~~~~~~~~~~ 23 (122)
|||++++ |.|+++.++++++++
T Consensus 1 A~r~l~~~k~r~~l~~l~i~l~~ 23 (232)
T PF12704_consen 1 AWRNLRRNKGRSILTILGIALGV 23 (232)
T ss_dssp -----------------------
T ss_pred ChhHHHHCHHHHHHHHHHHHHHH
Confidence 6888665 678777777766554
No 39
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=25.15 E-value=30 Score=18.01 Aligned_cols=14 Identities=14% Similarity=0.078 Sum_probs=10.5
Q ss_pred cCCceeeccCCCCCCc
Q psy5901 86 FPNPLAELRTQKPTEV 101 (122)
Q Consensus 86 F~NPvGLAAGfDKna~ 101 (122)
|.+|-|+|.. ++|.
T Consensus 1 f~~P~gvav~--~~g~ 14 (28)
T PF01436_consen 1 FNYPHGVAVD--SDGN 14 (28)
T ss_dssp BSSEEEEEEE--TTSE
T ss_pred CcCCcEEEEe--CCCC
Confidence 6789999986 5554
No 40
>COG2838 Icd Monomeric isocitrate dehydrogenase [Energy production and conversion]
Probab=23.72 E-value=19 Score=32.46 Aligned_cols=17 Identities=29% Similarity=0.595 Sum_probs=14.5
Q ss_pred HHHhcCCChhHHHHHHH
Q psy5901 42 LPILFKFDAETAHNIAI 58 (122)
Q Consensus 42 ~plLf~ldPE~AH~lai 58 (122)
.|.+|+|||++||+.-+
T Consensus 484 ~pavFWLDp~Rahd~~l 500 (744)
T COG2838 484 MPAVFWLDPYRAHDKEL 500 (744)
T ss_pred CceEEEeCcCccchHHH
Confidence 67899999999998744
No 41
>PF11171 DUF2958: Protein of unknown function (DUF2958); InterPro: IPR021341 Some members are annotated as lipoproteins however this cannot be confirmed. This family of proteins has no known function.
Probab=23.42 E-value=21 Score=25.60 Aligned_cols=35 Identities=14% Similarity=0.047 Sum_probs=25.6
Q ss_pred cccCCcee----eccCCC-CCCccCCCCCCCCCceEeeCC
Q psy5901 84 LKFPNPLA----ELRTQK-PTEVSIQGPPTVSISGVEPQV 118 (122)
Q Consensus 84 l~F~NPvG----LAAGfD-Kna~~i~~l~~lGFGfvEvG~ 118 (122)
.+|-||.| +.+-+| .+++..=++..+|+|+=|.|.
T Consensus 29 VklF~P~g~atWlltE~Dp~d~D~~FGl~dlG~g~pElGy 68 (112)
T PF11171_consen 29 VKLFTPDGAATWLLTELDPEDGDTAFGLCDLGLGEPELGY 68 (112)
T ss_pred EEEECCCCCceEEEEeeccCCCceEEEEEecCCCCceeeE
Confidence 45777777 567788 677666677788888888774
No 42
>PRK15463 cold shock-like protein CspF; Provisional
Probab=22.61 E-value=38 Score=21.77 Aligned_cols=10 Identities=10% Similarity=0.142 Sum_probs=7.9
Q ss_pred CCCCceEeeC
Q psy5901 108 TVSISGVEPQ 117 (122)
Q Consensus 108 ~lGFGfvEvG 117 (122)
.=|||||+.-
T Consensus 15 ~kGfGFI~~~ 24 (70)
T PRK15463 15 KSGKGLITPS 24 (70)
T ss_pred CCceEEEecC
Confidence 4799999873
No 43
>KOG3342|consensus
Probab=22.48 E-value=1.2e+02 Score=23.18 Aligned_cols=34 Identities=21% Similarity=0.476 Sum_probs=26.9
Q ss_pred CChhHHHHHHHHHHHHHHhHHhhhhhheeeeCCh
Q psy5901 1 MKKPTLLKKLVSLAAVSSGSFALFSGINIYQNNE 34 (122)
Q Consensus 1 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 34 (122)
|..||...++-+++.+.+.+.-.|-++...++.+
T Consensus 14 mn~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~se 47 (180)
T KOG3342|consen 14 MNIRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSE 47 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhheeeeCCC
Confidence 5567777788888888888888888888877755
No 44
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=20.77 E-value=47 Score=21.15 Aligned_cols=9 Identities=11% Similarity=0.206 Sum_probs=7.6
Q ss_pred CCCCceEee
Q psy5901 108 TVSISGVEP 116 (122)
Q Consensus 108 ~lGFGfvEv 116 (122)
.-|||||+.
T Consensus 15 ~kGfGFI~~ 23 (70)
T PRK10354 15 DKGFGFITP 23 (70)
T ss_pred CCCcEEEec
Confidence 579999985
No 45
>PRK10943 cold shock-like protein CspC; Provisional
Probab=20.68 E-value=47 Score=21.16 Aligned_cols=9 Identities=11% Similarity=0.261 Sum_probs=7.4
Q ss_pred CCCCceEee
Q psy5901 108 TVSISGVEP 116 (122)
Q Consensus 108 ~lGFGfvEv 116 (122)
.-|||||+.
T Consensus 14 ~kGfGFI~~ 22 (69)
T PRK10943 14 SKGFGFITP 22 (69)
T ss_pred CCCcEEEec
Confidence 479999986
No 46
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=20.27 E-value=1.5e+02 Score=19.42 Aligned_cols=23 Identities=9% Similarity=0.198 Sum_probs=10.7
Q ss_pred eCChhHHHHhHHHHhcCCChhHHHHHH
Q psy5901 31 QNNENYYNNVLLPILFKFDAETAHNIA 57 (122)
Q Consensus 31 ~~~~~~Y~~l~~plLf~ldPE~AH~la 57 (122)
..+..-|... ...-||+..-+..
T Consensus 41 ~pRKk~YadF----YknYD~~k~fe~M 63 (73)
T PF02937_consen 41 EPRKKAYADF----YKNYDPMKDFEEM 63 (73)
T ss_dssp HHHHHHHHHH----HHT--HHHHHHHH
T ss_pred hHHHHHHHHH----HHccChHHHHHHH
Confidence 3334445543 4457887765543
No 47
>PRK09890 cold shock protein CspG; Provisional
Probab=20.13 E-value=49 Score=21.12 Aligned_cols=10 Identities=10% Similarity=0.215 Sum_probs=7.9
Q ss_pred CCCCceEeeC
Q psy5901 108 TVSISGVEPQ 117 (122)
Q Consensus 108 ~lGFGfvEvG 117 (122)
.=|||||+.-
T Consensus 15 ~kGfGFI~~~ 24 (70)
T PRK09890 15 DKGFGFITPD 24 (70)
T ss_pred CCCcEEEecC
Confidence 4799999863
Done!