Query psy10925
Match_columns 214
No_of_seqs 120 out of 1109
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 22:00:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00115 hemE uroporphyrinogen 100.0 7.6E-47 1.7E-51 335.0 19.8 192 13-205 2-196 (346)
2 COG0407 HemE Uroporphyrinogen- 100.0 5.5E-47 1.2E-51 333.6 18.1 191 15-206 6-200 (352)
3 TIGR01464 hemE uroporphyrinoge 100.0 1.2E-44 2.6E-49 319.8 20.4 184 21-205 6-190 (338)
4 PLN02433 uroporphyrinogen deca 100.0 6.2E-44 1.3E-48 316.4 19.8 184 21-205 5-189 (345)
5 cd00717 URO-D Uroporphyrinogen 100.0 1.1E-43 2.3E-48 313.3 20.6 184 21-205 4-187 (335)
6 KOG2872|consensus 100.0 2.9E-42 6.2E-47 290.7 11.8 194 12-206 8-204 (359)
7 PRK06252 methylcobalamin:coenz 100.0 1.1E-41 2.4E-46 300.6 14.2 185 10-205 2-190 (339)
8 TIGR01463 mtaA_cmuA methyltran 100.0 5E-41 1.1E-45 296.8 15.0 175 10-205 2-190 (340)
9 cd03307 Mta_CmuA_like MtaA_Cmu 100.0 3.5E-40 7.6E-45 290.0 16.2 176 21-205 4-181 (326)
10 PF01208 URO-D: Uroporphyrinog 100.0 4.2E-40 9E-45 290.6 15.6 188 12-205 1-192 (343)
11 cd03465 URO-D_like The URO-D _ 100.0 4.3E-34 9.3E-39 250.8 15.7 172 21-205 4-178 (330)
12 cd03308 CmuA_CmuC_like CmuA_Cm 100.0 9.9E-31 2.1E-35 234.6 12.3 178 16-205 6-224 (378)
13 cd00465 URO-D_CIMS_like The UR 99.9 3E-22 6.4E-27 174.0 12.2 153 30-205 1-154 (306)
14 cd03309 CmuC_like CmuC_like. P 98.5 2.1E-07 4.6E-12 82.2 7.1 87 109-205 74-165 (321)
15 PRK04326 methionine synthase; 98.3 6.3E-07 1.4E-11 79.1 3.4 116 61-203 45-173 (330)
16 cd03310 CIMS_like CIMS - Cobal 97.0 0.0019 4E-08 56.5 6.6 63 130-205 99-161 (321)
17 PRK00957 methionine synthase; 94.9 0.057 1.2E-06 47.2 5.6 64 130-202 92-155 (305)
18 PF08885 GSCFA: GSCFA family; 87.5 0.67 1.5E-05 39.7 3.6 71 129-212 151-221 (251)
19 PRK06052 5-methyltetrahydropte 77.5 10 0.00022 34.0 7.1 34 132-165 96-129 (344)
20 PRK05286 dihydroorotate dehydr 66.5 50 0.0011 29.4 9.1 67 129-198 272-341 (344)
21 PRK02506 dihydroorotate dehydr 57.9 94 0.002 27.2 9.1 67 129-198 224-293 (310)
22 cd04741 DHOD_1A_like Dihydroor 50.8 58 0.0012 28.3 6.6 64 129-195 226-292 (294)
23 PLN02826 dihydroorotate dehydr 46.4 1E+02 0.0023 28.3 7.8 66 129-197 324-392 (409)
24 PF11921 DUF3439: Domain of un 46.4 6.6 0.00014 29.2 0.0 12 201-212 88-99 (122)
25 cd04738 DHOD_2_like Dihydrooro 45.8 82 0.0018 27.7 6.9 60 129-191 263-325 (327)
26 cd03311 CIMS_C_terminal_like C 44.9 7.7 0.00017 34.1 0.2 130 51-205 26-165 (332)
27 COG5014 Predicted Fe-S oxidore 44.9 77 0.0017 26.0 5.8 84 57-142 73-184 (228)
28 PF06260 DUF1024: Protein of u 41.7 58 0.0013 22.9 4.1 37 166-202 19-55 (82)
29 COG1659 Uncharacterized protei 39.0 30 0.00066 29.1 2.8 118 80-211 49-172 (267)
30 cd02932 OYE_YqiM_FMN Old yello 38.4 72 0.0016 28.1 5.3 56 132-191 278-335 (336)
31 PF01180 DHO_dh: Dihydroorotat 37.7 55 0.0012 28.2 4.4 65 129-196 227-294 (295)
32 PF00790 VHS: VHS domain; Int 37.2 33 0.00071 26.3 2.6 79 131-211 39-127 (140)
33 cd02810 DHOD_DHPD_FMN Dihydroo 36.6 84 0.0018 26.8 5.4 59 130-191 227-288 (289)
34 cd04733 OYE_like_2_FMN Old yel 35.3 1E+02 0.0023 27.1 5.9 86 51-154 139-224 (338)
35 PRK01221 putative deoxyhypusin 35.1 1E+02 0.0022 27.3 5.7 43 130-182 38-80 (312)
36 COG0167 PyrD Dihydroorotate de 34.7 1.1E+02 0.0024 27.1 5.8 136 53-197 139-292 (310)
37 PF12979 DUF3863: Domain of Un 33.6 33 0.00072 29.7 2.3 80 109-210 20-99 (351)
38 cd02930 DCR_FMN 2,4-dienoyl-Co 31.1 1.3E+02 0.0027 26.8 5.7 59 132-194 264-324 (353)
39 cd04733 OYE_like_2_FMN Old yel 30.2 69 0.0015 28.3 3.9 56 132-191 280-337 (338)
40 smart00288 VHS Domain present 27.4 72 0.0016 24.2 3.1 78 132-211 35-120 (133)
41 TIGR01036 pyrD_sub2 dihydrooro 26.5 3.2E+02 0.0068 24.2 7.4 60 129-191 271-333 (335)
42 PRK13523 NADPH dehydrogenase N 26.3 2E+02 0.0042 25.6 6.0 62 132-197 263-326 (337)
43 cd02932 OYE_YqiM_FMN Old yello 26.2 2.1E+02 0.0046 25.1 6.2 85 51-154 144-229 (336)
44 PF00724 Oxidored_FMN: NADH:fl 26.0 1E+02 0.0023 27.2 4.3 87 51-155 139-225 (341)
45 cd08210 RLP_RrRLP Ribulose bis 25.8 72 0.0016 28.8 3.2 35 126-160 173-207 (364)
46 PLN02495 oxidoreductase, actin 25.0 2.1E+02 0.0045 26.1 6.0 65 129-197 97-181 (385)
47 COG0311 PDX2 Predicted glutami 23.9 90 0.002 25.7 3.1 57 109-165 29-91 (194)
48 cd03572 ENTH_epsin_related ENT 23.8 2.1E+02 0.0045 21.7 4.9 73 109-192 18-90 (122)
49 cd02803 OYE_like_FMN_family Ol 23.5 1.2E+02 0.0026 26.3 4.2 57 130-190 267-325 (327)
50 PRK02301 putative deoxyhypusin 23.0 2.1E+02 0.0045 25.4 5.5 43 130-182 40-83 (316)
51 KOG3818|consensus 22.8 74 0.0016 29.7 2.7 34 130-163 296-329 (525)
52 cd03312 CIMS_N_terminal_like C 22.7 2E+02 0.0043 25.8 5.4 31 51-81 28-58 (360)
53 PRK00805 putative deoxyhypusin 22.5 2.2E+02 0.0048 25.4 5.5 32 130-161 29-61 (329)
54 PRK01207 methionine synthase; 22.2 1.9E+02 0.004 26.0 5.1 96 55-164 30-136 (343)
55 PRK09121 5-methyltetrahydropte 22.0 2.6E+02 0.0057 24.8 6.0 29 51-79 29-57 (339)
56 COG2875 CobM Precorrin-4 methy 21.3 2.4E+02 0.0053 24.1 5.3 104 48-152 73-192 (254)
57 cd02940 DHPD_FMN Dihydropyrimi 21.1 3.6E+02 0.0079 23.2 6.6 65 129-197 83-167 (299)
58 PRK00770 deoxyhypusine synthas 20.5 1.6E+02 0.0035 26.9 4.4 32 130-161 34-66 (384)
59 COG1647 Esterase/lipase [Gener 20.2 1.8E+02 0.004 24.7 4.3 43 113-159 57-100 (243)
No 1
>PRK00115 hemE uroporphyrinogen decarboxylase; Validated
Probab=100.00 E-value=7.6e-47 Score=334.99 Aligned_cols=192 Identities=51% Similarity=0.943 Sum_probs=183.7
Q ss_pred CCccCccc--cCCcccCccchhhhhhhcccchHHHHHHcCC-ChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhh
Q psy10925 13 PLKNDRLL--PRGEEVDKIPIWIMRQAGRYLPEFRELRSKH-DFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIP 89 (214)
Q Consensus 13 ~~~~ER~~--l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~-~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~a 89 (214)
..++||++ ++|+++||+|||+|+|+|+|+|+|.+...|+ ++.|++.|||++|+++++++++||+|++++++|+++++
T Consensus 2 ~~~~er~~~~~~g~~~driPv~~~~~~g~~~pe~~~~~~~~~~f~e~~~~~e~~ae~~~~~~~~~g~D~~~i~~d~~~~~ 81 (346)
T PRK00115 2 ELKNDRFLRALRGEPVDRTPVWMMRQAGRYLPEYRALRAKAGSFLELCKNPELAAEVTLQPVRRYGVDAAILFSDILTPP 81 (346)
T ss_pred CcchhHHHHHHcCCCCCCCCeeehHhhccccHHHHHHHhccCcHHHHhCCHHHHHHHHHHHHHHhCCCeEEecccchhhH
Confidence 34689999 9999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred hhCCCeeeecCCCCCccCCCCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCC
Q psy10925 90 QALGMVVEMKPAVGPVLPEPLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGS 169 (214)
Q Consensus 90 Ea~G~~v~~~~~~~P~v~~~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~ 169 (214)
|||||++.|+++.+|++.++|++.+|+++|+++ ++++|++.+++|++++++++++++|++++++||||+|++|++|+|+
T Consensus 82 ea~G~~i~~~~~~~P~~~~~i~~~~d~~~l~~~-~~~~~~~~~leai~~l~~~~~~~~~vig~v~gP~Tla~~l~~~~~~ 160 (346)
T PRK00115 82 DAMGLDLDFEEGEGPVFDNPIRTEADVEKLPVP-DPEEDLPYVLEAVRLLRRELGGEVPLIGFAGAPWTLATYMVEGGGS 160 (346)
T ss_pred HHcCCeeeeCCCCCCcCCCCcCCHHHHHhcCCC-CchhccHHHHHHHHHHHHHhCCCceEEeeCCcHHHHHHHHHcCCCC
Confidence 999999999998899886699999999999887 7788999999999999999999999999999999999999988888
Q ss_pred CchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 170 KTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 170 ~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
+++.+++++++++||.+|++|+++|+.+++|+++|+
T Consensus 161 ~~~~~~~~~~~~~Pe~v~~ll~~~t~~~~~~~~~~~ 196 (346)
T PRK00115 161 KDYAKTKAMMYAEPELLHALLDKLADATIAYLNAQI 196 (346)
T ss_pred ccHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888888899999999999999999999999999975
No 2
>COG0407 HemE Uroporphyrinogen-III decarboxylase [Coenzyme metabolism]
Probab=100.00 E-value=5.5e-47 Score=333.63 Aligned_cols=191 Identities=52% Similarity=0.918 Sum_probs=183.0
Q ss_pred ccCccc--cCCcccCccchhhhhhhcccchHHHHHHcCC-ChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhh
Q psy10925 15 KNDRLL--PRGEEVDKIPIWIMRQAGRYLPEFRELRSKH-DFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQA 91 (214)
Q Consensus 15 ~~ER~~--l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~-~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa 91 (214)
+++|++ ++|+++||+|||+|+|||||+|+|++.+... |+.|+|.|||+++|++++++++||+|++++++|+++++++
T Consensus 6 ~~~~fl~al~g~~vdr~PVw~mrqAgry~pey~~~r~~~~s~~d~~~~~e~~~evtl~p~~~~~~DAailf~DIlv~~~a 85 (352)
T COG0407 6 KNDRFLRALKGKPVDRTPVWMMRQAGRYLPEYRALREKGGSFLEACKNPELAAEVTLQPVRRYGLDAAILFSDILVPPEA 85 (352)
T ss_pred hHHHHHHHHcCCCCCCCCeEeeecccccccHHHHHHHhcCCHHHHhcCHHHHHHHHhhhHHHhCCCeeeeehhhcccHHH
Confidence 469999 9999999999999999999999999999765 9999999999999999999999999999999999999999
Q ss_pred CCCeeeecCCCCCccCCCCCCHHHHhccCC-CccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCC
Q psy10925 92 LGMVVEMKPAVGPVLPEPLVIPEDIKKLKT-SVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSK 170 (214)
Q Consensus 92 ~G~~v~~~~~~~P~v~~~i~~~edl~~l~~-~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~ 170 (214)
|||+++|.++.+|++..++.+.++++.+.+ + ++.++++.+++|++++|+++++++|+||+++||||+|++|++|+|++
T Consensus 86 lG~~v~f~~~~gP~v~~~~~~~~~~~~~~~~~-~~~~~~~~V~~ai~~lrekl~~~~pLIgf~gsP~TlAsymieg~~s~ 164 (352)
T COG0407 86 LGCEVRFGEGKGPSVLKPIRDKEDVELLVPLL-DPEGRLPYVLDAIKLLREKLGGEVPLIGFAGSPWTLASYLIEGGGSK 164 (352)
T ss_pred cCCeeecCCCCCCccCCCCCchhhhhhccCCc-CcccchHHHHHHHHHHHHHcCCCCCeEEecCCHHHHHHHHHcCCCcc
Confidence 999999999889999889999999887775 5 77889999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhcc
Q psy10925 171 TMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLHY 206 (214)
Q Consensus 171 ~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~~ 206 (214)
++.+++.+|+++|+.+|+||+++||.+++|+++|+-
T Consensus 165 ~~~~~k~~m~~~P~~~~~ll~kltd~~i~Yl~~qi~ 200 (352)
T COG0407 165 DFSKTKAMMYTEPDAVHALLDKLTDAVIEYLKAQIE 200 (352)
T ss_pred cHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999973
No 3
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=100.00 E-value=1.2e-44 Score=319.79 Aligned_cols=184 Identities=58% Similarity=1.026 Sum_probs=175.7
Q ss_pred cCCcccCccchhhhhhhcccchHHHHHHcCC-ChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeec
Q psy10925 21 PRGEEVDKIPIWIMRQAGRYLPEFRELRSKH-DFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMK 99 (214)
Q Consensus 21 l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~-~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~ 99 (214)
++|+++||+|||+|+|+|+++|+|++++.|+ ++.|++.|||++|+++++++++||+|++++++|+++++|||||++.|+
T Consensus 6 ~~g~~~dr~Pv~~~~~~g~~~~~~~~~~~~~~~~~e~~~~~e~~ae~~~~~~~~~~~D~~~i~~d~~~~~ea~G~~i~~~ 85 (338)
T TIGR01464 6 AKGEEVDRPPVWLMRQAGRYLPEYRELRAKAPDFLELCRNPDLAVEVTLQPIRRFGVDAAILFSDILVPLQALGLDVDFV 85 (338)
T ss_pred hCCCCCCCCCeeeehhcccccHHHHHHHhccCcHHHHhCCHHHHHHHHHHHHHHhCCCeEEecccccccHHHcCCeeEec
Confidence 8999999999999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccCCCCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHH
Q psy10925 100 PAVGPVLPEPLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWL 179 (214)
Q Consensus 100 ~~~~P~v~~~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l 179 (214)
++++|++.+++++.+|+++|+++ ++++|++.++||++++++++++++|++++++||||+|++|++|+.++++.++++++
T Consensus 86 ~~~~P~~~~~i~~~~d~~~l~~~-~~~~~~~~~leai~~l~~~~~~~~pi~g~~~gP~Tla~~l~~g~~~~~~~~~~~~~ 164 (338)
T TIGR01464 86 EGKGPVIPEPIRTPEDVERLKEF-DPESELPYVYEAIKLLREELPGEVPLIGFAGAPWTLASYMIEGGGSKDFAKAKRFM 164 (338)
T ss_pred CCCCCccCCCCCCHHHHHhcCCC-ChhhchHHHHHHHHHHHHHcCCCCceEEeCCchHHHHHHHHcCCCCccHHHHHHHH
Confidence 98889886799999999999987 77889999999999999999999999999999999999999865667777788999
Q ss_pred HhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 180 YKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 180 ~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
+++||.+|++|++||+.+++|+++|+
T Consensus 165 ~~~Pe~v~~ll~~~t~~~~~~~~~~~ 190 (338)
T TIGR01464 165 YQEPEVLHALLNKLTDATIEYLVEQV 190 (338)
T ss_pred HhCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999975
No 4
>PLN02433 uroporphyrinogen decarboxylase
Probab=100.00 E-value=6.2e-44 Score=316.37 Aligned_cols=184 Identities=41% Similarity=0.740 Sum_probs=174.7
Q ss_pred cCCcccCccchhhhhhhcccchHHHHHH-cCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeec
Q psy10925 21 PRGEEVDKIPIWIMRQAGRYLPEFRELR-SKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMK 99 (214)
Q Consensus 21 l~Ge~~DriPv~~~~~~g~~~p~~~a~~-~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~ 99 (214)
++|+++||+|||+|+|+|+|.|+|...+ .|+++.|++.|||++|+++++++++||+|++++++|+++++|||||++.|+
T Consensus 5 ~~g~~~dr~Pv~~~~q~g~~~~ey~~~~~~~~~~~e~~~~~e~~ae~~~~~~~~~~~D~~~i~~di~~~~ea~G~~i~~~ 84 (345)
T PLN02433 5 ARGEKVERPPVWLMRQAGRYMKEYRELCKKYPSFRERSETPDLAVEISLQPWRAFKPDGVILFSDILTPLPAMGIPFDIV 84 (345)
T ss_pred HCCCCCCCCCeeeeecchhccHHHHHHHHhcCCHHHHhCCHHHHHHHHHHHHHHhCCCeEEecCCCCcCHHHcCCeEEEC
Confidence 7999999999999999999999998765 478999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccCCCCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHH
Q psy10925 100 PAVGPVLPEPLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWL 179 (214)
Q Consensus 100 ~~~~P~v~~~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l 179 (214)
++.+|++.+||++.+||++|+++ ++++|++.++||++++++++++++|++++++||||+|++|++|++++++.++++++
T Consensus 85 ~~~~P~~~~~i~~~~d~~~l~~~-~~~~~l~~~leai~~l~~~~~~~v~iig~v~gP~Tla~~l~gg~~~~~~~~~~~~l 163 (345)
T PLN02433 85 KGKGPVIPNPIRSEEDVKRLHPL-DPEEKLPFVGEALKILRKEVGNEAAVLGFVGAPWTLATYIVEGGSSKNYKVIKKMA 163 (345)
T ss_pred CCCCCccCCCCCCHHHHHhccCC-CchhhhHHHHHHHHHHHHHhCCCCceeeeCCcHHHHHHHHHcCCCCccHHHHHHHH
Confidence 97789666799999999999987 67899999999999999999999999999999999999999888888888888999
Q ss_pred HhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 180 YKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 180 ~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
+++||.+|++|+++|+.+++|+++|+
T Consensus 164 ~~~Pe~v~~ll~~it~~~~~~~~~~i 189 (345)
T PLN02433 164 FTAPEVLHALLDKLTDAVIEYVDYQI 189 (345)
T ss_pred HhCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999975
No 5
>cd00717 URO-D Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction is located at the branching point of the tetrapyrrole biosynthetic pathway, leading to the biosynthesis of heme, chlorophyll or bacteriochlorophyll. URO-D deficiency is responsible for the human genetic diseases familial porphyria cutanea tarda (fPCT) and hepatoerythropoietic porphyria (HEP).
Probab=100.00 E-value=1.1e-43 Score=313.32 Aligned_cols=184 Identities=57% Similarity=0.985 Sum_probs=174.3
Q ss_pred cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeecC
Q psy10925 21 PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMKP 100 (214)
Q Consensus 21 l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~~ 100 (214)
++|+++||+|||+|+|+|+|+|+|.+.+.|+++.|++.|||++|+++++++++||+|++++++|+++++|||||++.|++
T Consensus 4 ~~g~~~DriPv~~~~~~g~~~~~~~~~~~~~~~~~~~~d~e~~~e~~~~~~~~~g~D~~~i~~d~~~~~ea~G~~i~~~~ 83 (335)
T cd00717 4 LRGEPVDRPPVWFMRQAGRYLPEYRELRAKYSFLELCKNPELAAEVTLQPVRRFGVDAAIIFSDILVPLEAMGMDVEFVE 83 (335)
T ss_pred ccCCCCCCCCeeeehhcccccHHHHHHHccCCHHHHhCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHcCCeEEeCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccCCCCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHH
Q psy10925 101 AVGPVLPEPLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLY 180 (214)
Q Consensus 101 ~~~P~v~~~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~ 180 (214)
+.+|++.+++++.+|+++++.+ ++++|++.+++|++++++++++++|++++++||||+|++|++|++++++.+++++++
T Consensus 84 ~~~p~~~~~i~~~~d~~~~~~~-~~~~~~~~~leai~~l~~~~~~~~~i~g~v~gP~Tla~~l~~~~~~~~~~~~~~~l~ 162 (335)
T cd00717 84 GKGPVIPNPIRTEADVDRLLVP-DPEEELSYVYEAIKLTRKELPGEVPLIGFAGAPWTLASYMIEGGGSKDFAKAKKMMY 162 (335)
T ss_pred CCCCcCCCCCCCHHHHHhccCC-ChhhhhHHHHHHHHHHHHHcCCCceEEeecCCHHHHHHHHHCCCCCccHHHHHHHHH
Confidence 8899886799999999998777 778899999999999999999999999999999999999997555666667779999
Q ss_pred hCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 181 KYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 181 ~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
++||.+|++|+++|+.+++|+++|+
T Consensus 163 ~~Pe~v~~~l~~it~~~~~~~~~~i 187 (335)
T cd00717 163 TDPEAFHALLDKLTDATIEYLKAQI 187 (335)
T ss_pred hCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999975
No 6
>KOG2872|consensus
Probab=100.00 E-value=2.9e-42 Score=290.73 Aligned_cols=194 Identities=67% Similarity=1.159 Sum_probs=184.5
Q ss_pred CCCccCccc--cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhh
Q psy10925 12 PPLKNDRLL--PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIP 89 (214)
Q Consensus 12 t~~~~ER~~--l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~a 89 (214)
..+|+..++ .+||++||+|||+|+|||||+|+|+.+++.++|.+.|.|||...|.++++.++|.+|++++|+|+++++
T Consensus 8 p~~kndlllRAakGE~vdrpPvW~MRQAGRYl~eyqel~~k~~Ff~~c~~~el~~EitlQP~rrF~~DaaIIFSDILvip 87 (359)
T KOG2872|consen 8 PALKNDLLLRAAKGEEVDRPPVWIMRQAGRYLPEYQELRAKQDFFETCRNPELACEITLQPLRRFRLDAAIIFSDILVIP 87 (359)
T ss_pred CCCCchHHHHHhcCcccCCCchHHHHHhhcccHHHHHHHHhccHHHhcCCccceeeEecchhhccCCceeEEeeccccCc
Confidence 334567777 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCeeeecCCCCCccCCCCCCHHHHhccCCCccc-hhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCC
Q psy10925 90 QALGMVVEMKPAVGPVLPEPLVIPEDIKKLKTSVDV-YKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGG 168 (214)
Q Consensus 90 Ea~G~~v~~~~~~~P~v~~~i~~~edl~~l~~~~d~-~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g 168 (214)
.|||..+.+-+..||++.+|+.+.+|++++..+ ++ ..+++.+.+||+++|.++++++|++|++++|||+++++++|||
T Consensus 88 qalgm~v~m~egkGP~~p~Plr~~eDl~rl~~~-~~~~s~L~yVgdAit~~R~kl~g~vpl~GF~GaPwTlm~YmiEGGg 166 (359)
T KOG2872|consen 88 QALGMPVDMVEGKGPVFPEPLRVPEDLKRLRDP-EVVESELGYVGDAITLTRQKLDGRVPLIGFVGAPWTLMTYMIEGGG 166 (359)
T ss_pred hhcCceEEEeeccCCCCCCCCCCHHHHHHhccC-cchhhhcchHHHHHHHHHHHhcCccceeeecCCchhhheeeecCCC
Confidence 999999999999999998899999999999877 55 3379999999999999999999999999999999999999999
Q ss_pred CCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhcc
Q psy10925 169 SKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLHY 206 (214)
Q Consensus 169 ~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~~ 206 (214)
++.+-.+.+|+.++||..|+||..+|+.++.|+..|++
T Consensus 167 Skt~~~aK~w~~~~Pe~sh~lL~~lTda~v~Yl~~Qv~ 204 (359)
T KOG2872|consen 167 SKTFTQAKRWLFQYPEVSHALLQILTDAIVEYLVYQVV 204 (359)
T ss_pred chhHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999988876
No 7
>PRK06252 methylcobalamin:coenzyme M methyltransferase; Validated
Probab=100.00 E-value=1.1e-41 Score=300.62 Aligned_cols=185 Identities=25% Similarity=0.402 Sum_probs=169.2
Q ss_pred CCCCCccCccc--cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcch
Q psy10925 10 TFPPLKNDRLL--PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILV 87 (214)
Q Consensus 10 ~~t~~~~ER~~--l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~ 87 (214)
+||| +||++ ++|+++||+|||+|+|+|++ ++. ...|+++.|+|.|||++|+++++++++||+|++++++|+++
T Consensus 2 ~mt~--~er~~~~~~g~~~dr~Pv~~~~~~g~~--e~~-~~~g~~~~e~~~~~e~~ae~~~~~~~~~g~D~~~~~~di~~ 76 (339)
T PRK06252 2 ELTP--KERLLNALKGKEVDRVPVICVTQTGTV--ELM-DITGAYWPEAHSDPEKMADLAIAGYEVAGFEAVRVPFCMTV 76 (339)
T ss_pred CCCH--HHHHHHHHCCCCCCccCccchhhhHHH--HHH-HHcCCCchhccCCHHHHHHHHHHHHHhcCCCeeccCcchHH
Confidence 7999 59999 99999999999999999987 553 34689999999999999999999999999999999999999
Q ss_pred hhhhCCCeeeecC-CCCCccC-CCCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHc
Q psy10925 88 IPQALGMVVEMKP-AVGPVLP-EPLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIE 165 (214)
Q Consensus 88 ~aEa~G~~v~~~~-~~~P~v~-~~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~ 165 (214)
++||||+++.|++ +.+|.+. ++|++.+|+.++..+...++|++.+++|++++++++++++||+++++||||+|++|+
T Consensus 77 ~aea~G~~v~~~~~~~~P~v~~~~i~~~~d~~~l~~~~~~~~~~~~~leai~~l~~~~~~~~pv~g~v~gP~Tla~~l~- 155 (339)
T PRK06252 77 EAEAMGCEVDMGTKDRQPSVTKYPIKKDVEYRKLPDDLLEEGRIPTVLEAIKILKEKVGEEVPIIAGLTGPISLASSLM- 155 (339)
T ss_pred HHHHhCCeecCCCCCCCCcccccccccChhhhhcccchhhCccHhHHHHHHHHHHHHcCCcCceeCccCChHHHHHHHH-
Confidence 9999999999975 5789865 599999999998764123789999999999999999999999999999999999999
Q ss_pred CCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 166 GGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 166 ~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
|+++++ ++++++||.+|++|+++|+.+++|+++|+
T Consensus 156 --g~~~~~---~~l~~~pe~~~~ll~~i~~~~~~~~~~~~ 190 (339)
T PRK06252 156 --GPKNFL---KWLIKKPELAHEFLDFVTDFCIEYAKAQL 190 (339)
T ss_pred --HHHHHH---HHHHHCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777776 99999999999999999999999999864
No 8
>TIGR01463 mtaA_cmuA methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.
Probab=100.00 E-value=5e-41 Score=296.76 Aligned_cols=175 Identities=25% Similarity=0.438 Sum_probs=165.0
Q ss_pred CCCCCccCccc--cCCcccCccch---------hhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCe
Q psy10925 10 TFPPLKNDRLL--PRGEEVDKIPI---------WIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDA 78 (214)
Q Consensus 10 ~~t~~~~ER~~--l~Ge~~DriPv---------~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~ 78 (214)
+||| +||++ ++|+++||+|+ |+|+|+|+++|+|+ .|||++|+++++++++||+|+
T Consensus 2 ~mt~--~er~~~~~~g~~~dr~Pv~~~~~~~~~~~~~~~G~~~~e~~------------~~~~~~a~~~~~~~~~~~~D~ 67 (340)
T TIGR01463 2 EMTP--KERLFAAVTGQTVDDVPPCVPTQTLTTELMRECGATWPEAH------------RDGEAMAHLAIAAYEKFGGEA 67 (340)
T ss_pred CCCH--HHHHHHHhcCCCCCcCCcccchHHHHHHHHHHhCCcchhhc------------CCHHHHHHHHHHHHHHhCCCe
Confidence 6999 69999 99999999999 99999999999886 999999999999999999999
Q ss_pred eeeCCCcchhhhhCCCeeeecCCCCCccCC-C-CCCHHHHhccCCCccc-hhhHHHHHHHHHHHHHHcCCCccEEEeccc
Q psy10925 79 SIIFSDILVIPQALGMVVEMKPAVGPVLPE-P-LVIPEDIKKLKTSVDV-YKELNYVFEAITLTRHKLEGKVPLIGFSGA 155 (214)
Q Consensus 79 v~i~~d~~~~aEa~G~~v~~~~~~~P~v~~-~-i~~~edl~~l~~~~d~-~~r~~~~leai~~l~~~~g~~vpv~~~v~g 155 (214)
+++++|+++++|||||++.|+++++|.+.+ | +++++|+++++++ +. ++|++.++++++++++++++++|++++++|
T Consensus 68 ~~~~~d~~~~aea~G~~i~~~~~~~P~v~~~~~i~~~~d~~~l~~~-~~~~~~~~~~l~ai~~l~~~~~~~~pv~g~v~G 146 (340)
T TIGR01463 68 VRPPFDLTTEAECVGCELDYGPYAQPSVTKHPTPTNLADYRYPENY-LLKPGRIPVVLEAIKILRERYGDTHPIIGPMGG 146 (340)
T ss_pred eecCCCcchHHHhcCCeecCCCCCCCccccCCCCCCHHHhcccccc-CcCCcchhhHHHHHHHHHHHcCCceeeeCCCCc
Confidence 999999999999999999999988899975 6 6999999999876 44 799999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 156 PWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 156 P~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
|||+|++|+ |+++++ ++++++||.+|++|+++++.+++|+++|+
T Consensus 147 P~Tla~~l~---g~~~~~---~~~~~~pe~v~~ll~~i~~~~~~~~~~~~ 190 (340)
T TIGR01463 147 PFTLAQLMI---GVSEFL---SWISTDPDYAKAVLELALDFVIAYAKAMV 190 (340)
T ss_pred HHHHHHHHH---CHHHHH---HHHHHCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999 777777 99999999999999999999999999975
No 9
>cd03307 Mta_CmuA_like MtaA_CmuA_like family. MtaA/CmuA, also MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M isozymes, are methylcobamide:Coenzyme M methyltransferases, which play a role in metabolic pathways of methane formation from various substrates, such as methylated amines and methanol. Coenzyme M, 2-mercaptoethylsulfonate or CoM, is methylated during methanogenesis in a reaction catalyzed by three proteins. A methyltransferase methylates the corrinoid cofactor, which is bound to a second polypeptide, a corrinoid protein. The methylated corrinoid protein then serves as a substrate for MT2-A and related enzymes, which methylate CoM.
Probab=100.00 E-value=3.5e-40 Score=290.02 Aligned_cols=176 Identities=26% Similarity=0.369 Sum_probs=162.2
Q ss_pred cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeecC
Q psy10925 21 PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMKP 100 (214)
Q Consensus 21 l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~~ 100 (214)
++|+++||+|||+|+|+|+ |++.. ..|.++.||+.|||++||++++++++||+|++++++|+++++||||+++.|++
T Consensus 4 ~~g~~~dr~Pv~~~~~~~~--~e~~~-~~g~~~~e~~~~~e~~ae~~~~~~~~~g~D~~~~~~di~~~~ea~G~~v~~~~ 80 (326)
T cd03307 4 LNGQPVDRVPVICPTQTGT--VELME-ATGAYWPEAHSDAEKMADLAAAGHEVAGFEAVRVPFCMTVEAEALGCEVDWGT 80 (326)
T ss_pred ccCCCCCccCcccchhhHH--HHHHH-HhCCcchhhhcCHHHHHHHHHHHHHHhCCCeeecCCccchHHHhcCCeeccCC
Confidence 7999999999999999998 77754 47889999999999999999999999999999999999999999999999986
Q ss_pred -CCCCccC-CCCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHH
Q psy10925 101 -AVGPVLP-EPLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHW 178 (214)
Q Consensus 101 -~~~P~v~-~~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~ 178 (214)
+++|.+. ++|++.+|++++......++|++.+++|++++++++++++|++++++||||+|++|+ |+++++ ++
T Consensus 81 ~~~~P~v~~~~i~~~~d~~~l~~~~~~~~~~~~v~eai~~l~~~~~~~~pvig~~~gP~Tla~~l~---g~~~~~---~~ 154 (326)
T cd03307 81 KDIQPSVTSHPFKKLEDVEKLPDDFLERGRIPTVLEAIKILKEKYGEEVPVIGGMTGPASLASHLA---GVENFL---KW 154 (326)
T ss_pred CCCCccccCCCCCCHHHHhhccccccccccHHHHHHHHHHHHHHcCCcceeeCCCCCHHHHHHHHH---hHHHHH---HH
Confidence 4589985 699999999998654123789999999999999999999999999999999999999 777777 99
Q ss_pred HHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 179 LYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 179 l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
|+++||.+|++|+++|+.+++|+++|+
T Consensus 155 ~~~~pe~~~~ll~~it~~~~~~~~~~~ 181 (326)
T cd03307 155 LIKKPEKVREFLEFLTEACIEYAKAQL 181 (326)
T ss_pred HHHCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999864
No 10
>PF01208 URO-D: Uroporphyrinogen decarboxylase (URO-D); InterPro: IPR000257 Uroporphyrinogen decarboxylase (URO-D), the fifth enzyme of the haem biosynthetic pathway, catalyses the sequential decarboxylation of the four acetyl side chains of uroporphyrinogen to yield coproporphyrinogen []. URO-D deficiency is responsible for the human genetic diseases familial porphyria cutanea tarda (fPCT) and hepatoerythropoietic porphyria (HEP). The sequence of URO-D has been well conserved throughout evolution. The best conserved region is located in the N-terminal section; it contains a perfectly conserved hexapeptide. There are two arginine residues in this hexapeptide which could be involved in the binding, via salt bridges, to the carboxyl groups of the propionate side chains of the substrate. The crystal structure of human uroporphyrinogen decarboxylase shows it as comprised of a single domain containing a (beta/alpha)8-barrel with a deep active site cleft formed by loops at the C-terminal ends of the barrel strands. URO-D is a dimer in solution. Dimerisation juxtaposes the active site clefts of the monomers, suggesting a functionally important interaction between the catalytic centres [].; GO: 0004853 uroporphyrinogen decarboxylase activity, 0006779 porphyrin-containing compound biosynthetic process; PDB: 4EXQ_A 2INF_C 1J93_A 3GW0_A 1R3Q_A 1JPH_A 1JPI_A 3GVR_A 3GVW_A 3GVV_A ....
Probab=100.00 E-value=4.2e-40 Score=290.62 Aligned_cols=188 Identities=38% Similarity=0.622 Sum_probs=156.5
Q ss_pred CCCccCccc--cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhh
Q psy10925 12 PPLKNDRLL--PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIP 89 (214)
Q Consensus 12 t~~~~ER~~--l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~a 89 (214)
|| |||++ ++|+++||||||+|+|+|++++.+.+...|+++.+++.||+++|+++++++++||+|++.+++|+++++
T Consensus 1 T~--~er~~~~~~~~~~DrvPv~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ae~~~~~~~~~~~D~~~~~~d~~~~a 78 (343)
T PF01208_consen 1 TS--RERVLAALNGEPVDRVPVWPMRQAGRYLPEYAAEKTGISFPEYCRDPEKMAEAQIKAYEKFGPDFIKIPFDLTVEA 78 (343)
T ss_dssp -S----HHHHHHTT---SS--B--TTSSSTTSHHHHHHHHHSSHHHHCTSHHHHHHHHHHHHHHC--SEEE-S--TTHHH
T ss_pred Cc--hhHHHHHHcCCCCCCcCeEccccccccChHHHHHhcCcchHHHhcCHHHHHHHHHHHHHhcCCCEEEecCceeehH
Confidence 56 79999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCeeeecCCCCCccCCCCCCHHHHhccCCCccc--hhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCC
Q psy10925 90 QALGMVVEMKPAVGPVLPEPLVIPEDIKKLKTSVDV--YKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGG 167 (214)
Q Consensus 90 Ea~G~~v~~~~~~~P~v~~~i~~~edl~~l~~~~d~--~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~ 167 (214)
|||||++.|+++.+|.+.+++.+.+|+++|+.+ ++ ++|++.++++++++++++++++||+++++||||+|++|++|+
T Consensus 79 ea~G~~v~~~~~~~P~~~~~~~~~eD~~~l~~~-~~~~~~~~~~~leai~~l~~~~~~~~~v~~~~~gP~t~a~~l~~~~ 157 (343)
T PF01208_consen 79 EALGCEVEFPEDDGPSVEEPIISPEDLDKLKIP-DPENEGRLPEVLEAIKILKEELGDDVPVIGTVFGPFTLASDLMEGR 157 (343)
T ss_dssp HGCTTEEEEETTTEEEESS---SHHHHHTS--G-GHHH-HHTHHHHHHHHHHHHHTTTSSEEEEEEE-HHHHHHHHHHSS
T ss_pred HHcCCeEEecCCCCCccccCcCCHHHHhhhccc-CcchhhhHHHHHHHHHHHHHHhcCcEEEEecCchHHHHHHHHHcCC
Confidence 999999999998889998743399999999998 76 589999999999999999999999999999999999999665
Q ss_pred CCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 168 GSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 168 g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
|.++++ ++++++||.+|++|+++++.+++|+++++
T Consensus 158 g~e~~~---~~~~~~Pe~v~~ll~~~~~~~~~~~~~~~ 192 (343)
T PF01208_consen 158 GFEEFL---MDLYDDPEKVHELLDKITDFIIEYAKAQI 192 (343)
T ss_dssp S-HHHH---HHHHH-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHH---HHHHhCchhHHHHHHHHHHHHHHHHHHHH
Confidence 555555 99999999999999999999999999986
No 11
>cd03465 URO-D_like The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane.
Probab=100.00 E-value=4.3e-34 Score=250.77 Aligned_cols=172 Identities=30% Similarity=0.445 Sum_probs=157.7
Q ss_pred cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeecC
Q psy10925 21 PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMKP 100 (214)
Q Consensus 21 l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~~ 100 (214)
++|+++||+|||+|.+.++ ++ ..|+++.|++.|+|+++|++++.+++||+|++++++|+++++||||+++.|++
T Consensus 4 ~~g~~~drvPv~~~~~~~~--~~----~~g~~~~e~~~d~e~~~e~~~~~~~~~~~D~~~~~~d~~~~~ealG~~i~~~~ 77 (330)
T cd03465 4 LNGEKPDRVPVGPLLHGGA--AE----FIGISLKEYYTDPELGAEAQIALYKKFGPDAIKVFSDLFVEAEAFGAEIRYPE 77 (330)
T ss_pred hcCCCCCccceeeeecccc--hh----hcCccHHHHhcCHHHHHHHHHHHHHHcCCCeEEeccCccchHHhcCCeEeecC
Confidence 7899999999999877665 33 46999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccCC-CCCCHHHHhccCCCccc--hhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHH
Q psy10925 101 AVGPVLPE-PLVIPEDIKKLKTSVDV--YKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKH 177 (214)
Q Consensus 101 ~~~P~v~~-~i~~~edl~~l~~~~d~--~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~ 177 (214)
+++|.+.+ ++++.+|++++.++ ++ ++|++.++++++++++++++++|++++++||||+|++|+ |.++++ +
T Consensus 78 ~~~p~v~~~~~~~~~d~~~~~~~-~~~~~~r~~~~l~a~~~l~~~~~~~~~v~g~~~gP~t~a~~l~---g~~~~~---~ 150 (330)
T cd03465 78 DDTPSVEGPLIEDEEEDDDLLPP-DPGDSPRLPELLEAIRLLKEELGDRVPVIGAVGGPFTLASLLM---GASKFL---M 150 (330)
T ss_pred CCCCccccccCCCHHHHhhccCC-CcCccchHHHHHHHHHHHHHHhCCCeeeeccCCCHHHHHHHHH---hHHHHH---H
Confidence 88999985 89999999976544 34 899999999999999999999999999999999999999 655555 9
Q ss_pred HHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 178 WLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 178 ~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
+++++||.+|++|+.+|+.+++|+++|+
T Consensus 151 ~~~~~pe~~~~~l~~i~~~~~~~~~~~~ 178 (330)
T cd03465 151 LLYTDPELVHKLLEKCTEFIIRYADALI 178 (330)
T ss_pred HHHHCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999875
No 12
>cd03308 CmuA_CmuC_like CmuA_CmuC_like: uncharacterized protein family similar to uroporphyrinogen decarboxylase (URO-D) and the methyltransferases CmuA and CmuC.
Probab=99.97 E-value=9.9e-31 Score=234.56 Aligned_cols=178 Identities=17% Similarity=0.131 Sum_probs=152.1
Q ss_pred cCccc--cCCcccCccchhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcch--hhhh
Q psy10925 16 NDRLL--PRGEEVDKIPIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILV--IPQA 91 (214)
Q Consensus 16 ~ER~~--l~Ge~~DriPv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~--~aEa 91 (214)
.||+. ++|+++||+||.++ ...+.+...|++..|++.|+++||+++.+.++.||+|++.+++|+.. ++||
T Consensus 6 ~eR~~~~~~g~~~DRvP~~~~------~~~~~~~~~G~~~~e~~~d~~~~a~~~~~~~~~~g~D~~~~~~~l~~~~~aea 79 (378)
T cd03308 6 VQRLKDAIEGKKPDRVPILSQ------FTEWFIQYAGMTLKEAQWDTDKLEEAYDKVLKDFDFDITPGSASLRPPSFYQA 79 (378)
T ss_pred HHHHHHHHcCCCCCceeecch------hhHHHHHHcCccHHHHhcCHHHHHHHHHHHHHHcCccccccccccCCchHHHH
Confidence 36666 99999999999776 55556677899999999999999999999999999999999999998 7999
Q ss_pred CCCeeeecC--CCCCccCC-CCCCHHHHhccCC-Cccc--h------------h---hHHHHHHH--------------H
Q psy10925 92 LGMVVEMKP--AVGPVLPE-PLVIPEDIKKLKT-SVDV--Y------------K---ELNYVFEA--------------I 136 (214)
Q Consensus 92 ~G~~v~~~~--~~~P~v~~-~i~~~edl~~l~~-~~d~--~------------~---r~~~~lea--------------i 136 (214)
|||++.|.+ +..|.+.. ++.+.+|++.+.. +.+. + + |++.+++| +
T Consensus 80 lG~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~lpr~~~~~~~~~~~~~~~~l~a~~~~~~~~~~~~~~~ 159 (378)
T cd03308 80 LGSKNFKMSSGGFLQHPEVYEYMEADEYDEFIADPYDFIVEKILPRIYKELAEDPAEKSLALAKAAAAFVDYNNTNGPIG 159 (378)
T ss_pred hcccceecCCCCccCcchhhccCCHHHHHHHHhCHHHHHHHhHhhhhhhhhcccchhhHHHHHHHHHHHHHHHhhHHHHH
Confidence 999998643 44466654 8888899883321 1122 3 5 88899999 9
Q ss_pred HHHH-HHcCCCccEEEecccHHH-HHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 137 TLTR-HKLEGKVPLIGFSGAPWT-LMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 137 ~~l~-~~~g~~vpv~~~v~gP~T-lA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
++|+ +++|+++|+++.+.|||| +|++|+ |.++++ ++|+++||.+|++|+++|+.+++|+++|+
T Consensus 160 ~~l~~~~~g~~vpi~~~~~gPf~~la~~l~---g~~~~~---~~l~~~Pe~v~~ll~~~td~~i~~~~~~i 224 (378)
T cd03308 160 AKLAEKEYGTPLNAGGVSEAPFDIIGDYLR---GFKGIS---IDLRRRPEKVAEACEAVTPLMIKMGTATA 224 (378)
T ss_pred HHHHhhccCCccccceeEeCChHHHHHHHh---CHHHHH---HHHHHCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999 999999999999999997 999999 655555 99999999999999999999999999986
No 13
>cd00465 URO-D_CIMS_like The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane, and methionine synthases transfer a methyl group from a folate cofactor to L-homocysteine in a reaction requiring zinc.
Probab=99.88 E-value=3e-22 Score=174.04 Aligned_cols=153 Identities=23% Similarity=0.211 Sum_probs=135.8
Q ss_pred chhhhhhhcccchHHHHHHcCCChhhhcCCHHHHHHHHHhHHHhcCCCeeeeC-CCcchhhhhCCCeeeecCCCCCccCC
Q psy10925 30 PIWIMRQAGRYLPEFRELRSKHDFFTICQTPELAAEITLQPIRRFNLDASIIF-SDILVIPQALGMVVEMKPAVGPVLPE 108 (214)
Q Consensus 30 Pv~~~~~~g~~~p~~~a~~~g~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~-~d~~~~aEa~G~~v~~~~~~~P~v~~ 108 (214)
|||+|+|+|++.+.+... |.++.+.+.|++.++++....+ ||+|++.++ +|+.+++|+||+++.+.++.+|.+..
T Consensus 1 Pv~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~--~g~D~~~~~~~~~~~~~ealg~~~~~~~~~~p~v~~ 76 (306)
T cd00465 1 PVQCEGQTGIMEASETMA--ISEEPGETSKAEWGITLVEPEE--IPLDVIPVHEDDVLKVAQALGEWAFRYYSQAPSVPE 76 (306)
T ss_pred CeEEEccCccccHHHHhh--cCCchhhhCCchhhceeecccc--CCCCeeeecCcceeehhhhcCceEEecCCCCCCCCC
Confidence 899999999998877532 8999999999999999999988 999999999 99999999999999887777888765
Q ss_pred CCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHH
Q psy10925 109 PLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKK 188 (214)
Q Consensus 109 ~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~ 188 (214)
++.+. ..++++.+++++++++++. ++|+++++.||||+|++++ |.+.++ ++++++|+.+|+
T Consensus 77 ~~~~~-----------~~~~~~~~~~~~~~~~~~~--~~~v~~~~~GP~Tla~~l~---~~~~~~---~~~~~~p~~~~~ 137 (306)
T cd00465 77 IDEEE-----------DPFREAPALEHITAVRSLE--EFPTAGAAGGPFTFTHHSM---SMGDAL---MALYERPEAMHE 137 (306)
T ss_pred cccCC-----------ChhhHHHHHHHHHHHHhcc--ccceEeecCCHHHHHHHHH---cccHHH---HHHHHChHHHHH
Confidence 43321 1358899999999999995 7999999999999999999 556666 999999999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q psy10925 189 LLEILTNVIVDYPTRLH 205 (214)
Q Consensus 189 lL~~~t~~~~~~~~a~~ 205 (214)
+|+.+++.+++|+++|.
T Consensus 138 ll~~i~~~~~~~~~~~~ 154 (306)
T cd00465 138 LIEYLTEFILEYAKTLI 154 (306)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999999875
No 14
>cd03309 CmuC_like CmuC_like. Proteins similar to the putative corrinoid methyltransferase CmuC. Its function has been inferred from sequence similarity to the methyltransferases CmuA and MtaA. Mutants of Methylobacterium sp. disrupted in cmuC and purU appear deficient in some step of chloromethane metabolism.
Probab=98.53 E-value=2.1e-07 Score=82.16 Aligned_cols=87 Identities=18% Similarity=0.190 Sum_probs=65.3
Q ss_pred CCCCHHHHhc-cCCCccc----hhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCH
Q psy10925 109 PLVIPEDIKK-LKTSVDV----YKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYP 183 (214)
Q Consensus 109 ~i~~~edl~~-l~~~~d~----~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~P 183 (214)
.++++.+|+. ++.+ +. +.+-+...++...-|.++ ++.....+||||+|+.|+ |.++++ ++|+++|
T Consensus 74 ~~~~~~~w~~~v~~p-~~~~~~~~~~~~~~~~~~~~r~~~---~~~~~~~~Gpf~~a~~l~---g~e~~~---~~l~~~P 143 (321)
T cd03309 74 VVDDITKWKDYVKPP-DIQHPLDWQAPARADLQSLDRNDL---VIDVPLPGGVFERFRLRM---SMEDAL---MALYEEP 143 (321)
T ss_pred hhHHHHHHHHhccCC-CCCCcccchhhhHHHHHhcccccc---eeccCCCCCHHHHHHHHH---HHHHHH---HHHHHCH
Confidence 5778888844 4444 33 223344444444444443 666778899999999999 656655 9999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q psy10925 184 EESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 184 e~v~~lL~~~t~~~~~~~~a~~ 205 (214)
|.+|++|+++|+.+++|+++|+
T Consensus 144 E~v~~lld~ltd~~i~y~~~qi 165 (321)
T cd03309 144 EAAHELFDYLTDAKLKLYERRI 165 (321)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999876
No 15
>PRK04326 methionine synthase; Provisional
Probab=98.26 E-value=6.3e-07 Score=79.10 Aligned_cols=116 Identities=9% Similarity=0.081 Sum_probs=82.1
Q ss_pred HHHHHHHHhHHHhcCCCee----------eeCCCcchhhhhCCCeeeecCCCC---CccCCCCCCHHHHhccCCCccchh
Q psy10925 61 ELAAEITLQPIRRFNLDAS----------IIFSDILVIPQALGMVVEMKPAVG---PVLPEPLVIPEDIKKLKTSVDVYK 127 (214)
Q Consensus 61 e~~ae~~~~~~~~~g~D~v----------~i~~d~~~~aEa~G~~v~~~~~~~---P~v~~~i~~~edl~~l~~~~d~~~ 127 (214)
+..++.+++.++.+|+|.+ ..+++...+++++|+.++|..++. |.+..++ +.. +
T Consensus 45 ~~a~~~~v~~q~~~Gld~itdGe~~r~~~~~~f~~~~~G~~~~~~~~~~~~~~~~~P~v~g~~---------~~~-~--- 111 (330)
T PRK04326 45 DDAVRLVVKDHERAGVDIPVDGEMRREEMVEYFAERIEGFKFYGPVRVWGNNYFRKPSVVGKI---------EYK-E--- 111 (330)
T ss_pred HHHHHHHHHHHHHhCCCeeeCCeEEcHhHHHHHHHhCCceeccCceeccccccccCCeEEEec---------cCC-C---
Confidence 3348889999999999999 778888888999999988644211 3332221 111 1
Q ss_pred hHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHH
Q psy10925 128 ELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTR 203 (214)
Q Consensus 128 r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a 203 (214)
+.++++++.+++..++ .|+.+.+.||+|+|+.+.+ .+ ..+++|.++.+++.+.+.+.+..++
T Consensus 112 --~~~l~~~~~~~~~~~~-~~vk~~l~GP~Tla~~~~~-----~~------y~~~~e~~~~l~~~~~~~i~~l~~~ 173 (330)
T PRK04326 112 --PMLVDEFEFAKSVTYT-RPVKVPITGPYTIAEWSFN-----EY------YKDKEELVFDLAKVINEEIKNLVEA 173 (330)
T ss_pred --CCcHHHHHHHHhcccC-CCceEeccCHHHHHhhccc-----cc------CCCHHHHHHHHHHHHHHHHHHHHHC
Confidence 3478888888888644 8999999999999987762 12 2245788888887776666666543
No 16
>cd03310 CIMS_like CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers both the N-and C-terminal barrel, and some single-barrel sequences, mostly from Archaea. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding o
Probab=97.00 E-value=0.0019 Score=56.53 Aligned_cols=63 Identities=11% Similarity=0.119 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhc
Q psy10925 130 NYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLH 205 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~ 205 (214)
+..+++++.+++..++.+|+.+.+.||+|+|+.+. +... .|+..+++++.+++.++++++++.
T Consensus 99 ~~~~~~~~~~~~~~~~~~~vk~~l~GP~Tla~~~~---~~~~----------~~~~~~~l~~~l~~~~~~~~~~l~ 161 (321)
T cd03310 99 PLELDYLEEVAEAYKEALKVKVVVTGPLTLALLAF---LPNG----------EPDAYEDLAKSLAEFLREQVKELK 161 (321)
T ss_pred cccHHHHHHHHHhcCCCCceEEEecCHHhHhHhhc---cccC----------CchHHHHHHHHHHHHHHHHHHHHH
Confidence 45678888888887777899999999999999988 3222 167889999999999999999874
No 17
>PRK00957 methionine synthase; Provisional
Probab=94.87 E-value=0.057 Score=47.15 Aligned_cols=64 Identities=16% Similarity=0.011 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Q psy10925 130 NYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPT 202 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~ 202 (214)
.....+.++++++ ++++|+-+.+.||+|+|..+. + +.+. +++ ++++.++++.+.+.+.+.++.+
T Consensus 92 ~~~~~~~~~~~~~-~~~~~vK~~i~GP~Tla~~~~---~-~~~y---~~~-~~~~~~~dla~~~~~~i~~l~~ 155 (305)
T PRK00957 92 KDLKYAKKVAKKK-DPNKGVKGIITGPSTLAYSLR---V-EPFY---SDN-KDEELIYDLARALRKEAEALEK 155 (305)
T ss_pred HHHHHHHHHHhcc-CCCCceeEEecCHHHHHhhcc---c-cccc---CCc-cHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444554 467899999999999999887 3 3333 443 5577777776666666555544
No 18
>PF08885 GSCFA: GSCFA family; InterPro: IPR014982 This group of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment, they are functionally uncharacterised.
Probab=87.52 E-value=0.67 Score=39.69 Aligned_cols=71 Identities=24% Similarity=0.250 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhccCc
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTRLHYFP 208 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a~~~~~ 208 (214)
.......+++|++. .+++-|+-+| +|.-+.+...+ . +-...-..-+..|+.+.+.+.+--....|||
T Consensus 151 ~~~l~~~~~~l~~~-nP~~kiilTV-SPVrl~~T~~~---~--------d~~~an~~SKs~Lr~a~~~l~~~~~~v~YFP 217 (251)
T PF08885_consen 151 LEDLEAIIDLLRSI-NPDIKIILTV-SPVRLIATFRD---R--------DGLVANQYSKSTLRAAAHELVRAFDDVDYFP 217 (251)
T ss_pred HHHHHHHHHHHHhh-CCCceEEEEe-ccchhhccccc---c--------cchhhhhhhHHHHHHHHHHHHhcCCCceEcc
Confidence 34444444455554 6777777666 78888774442 1 1111112235566666666666557889999
Q ss_pred cccc
Q psy10925 209 SYRI 212 (214)
Q Consensus 209 ~~~~ 212 (214)
||.|
T Consensus 218 SYEi 221 (251)
T PF08885_consen 218 SYEI 221 (251)
T ss_pred hHhh
Confidence 9987
No 19
>PRK06052 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=77.53 E-value=10 Score=33.99 Aligned_cols=34 Identities=9% Similarity=-0.035 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHcCCCccEEEecccHHHHHHHHHc
Q psy10925 132 VFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIE 165 (214)
Q Consensus 132 ~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~ 165 (214)
+-+..+.-|++.|...+|=+.++||+|++.+..+
T Consensus 96 ~~~~~~~~~~~~~~~~~VKv~iTGP~tL~~~~f~ 129 (344)
T PRK06052 96 IEEVAKEYKEETGETLEVRVCVTGPTELYLQEFG 129 (344)
T ss_pred HHHHHHHHHHhhCCCCCeEEEecCHHHHHHHHcC
Confidence 3344455666778888899999999999999993
No 20
>PRK05286 dihydroorotate dehydrogenase 2; Reviewed
Probab=66.46 E-value=50 Score=29.39 Aligned_cols=67 Identities=18% Similarity=0.216 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHHHcCCCccEE--EecccHHHHHHHHHcCCCCCchHHHHHHHH-hCHHHHHHHHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLI--GFSGAPWTLMSYMIEGGGSKTMSKSKHWLY-KYPEESKKLLEILTNVIV 198 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~--~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~-~~Pe~v~~lL~~~t~~~~ 198 (214)
.+..++.++.+++.+++++||+ |.|..+=.....|.. |.+ ...+-+.++ ++|..++++.+-+.+...
T Consensus 272 ~~~~l~~v~~l~~~~~~~ipIig~GGI~s~eda~e~l~a--GAd-~V~v~~~~~~~gP~~~~~i~~~L~~~l~ 341 (344)
T PRK05286 272 FERSTEVIRRLYKELGGRLPIIGVGGIDSAEDAYEKIRA--GAS-LVQIYSGLIYEGPGLVKEIVRGLARLLR 341 (344)
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEECCCCCHHHHHHHHHc--CCC-HHHHHHHHHHhCchHHHHHHHHHHHHHH
Confidence 3567889999999987778886 478888888888874 544 455667765 469999888777666543
No 21
>PRK02506 dihydroorotate dehydrogenase 1A; Reviewed
Probab=57.93 E-value=94 Score=27.20 Aligned_cols=67 Identities=12% Similarity=0.137 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHHH-hCHHHHHHHHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWLY-KYPEESKKLLEILTNVIV 198 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l~-~~Pe~v~~lL~~~t~~~~ 198 (214)
.+..++.+..+++++++++||++ .|...=..+-+|+- |... .++...++ +.|+.++++++-+.+.+.
T Consensus 224 ~p~al~~v~~~~~~~~~~ipIig~GGI~s~~da~e~i~a--GA~~-Vqv~ta~~~~gp~~~~~i~~~L~~~l~ 293 (310)
T PRK02506 224 KPTALANVRAFYQRLNPSIQIIGTGGVKTGRDAFEHILC--GASM-VQVGTALHKEGPAVFERLTKELKAIMA 293 (310)
T ss_pred cHHHHHHHHHHHHhcCCCCCEEEECCCCCHHHHHHHHHc--CCCH-HhhhHHHHHhChHHHHHHHHHHHHHHH
Confidence 36778899999999877889865 78888888888886 4433 34445544 579999888887765443
No 22
>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=50.84 E-value=58 Score=28.26 Aligned_cols=64 Identities=13% Similarity=0.116 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHHH-hCHHHHHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWLY-KYPEESKKLLEILTN 195 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l~-~~Pe~v~~lL~~~t~ 195 (214)
.+.-++.++.+++.+++++||++ .|.++=....+|.- |.... ++-..++ ++|..++++++-+.+
T Consensus 226 ~~~al~~v~~~~~~~~~~ipIig~GGI~s~~da~e~l~a--GA~~V-qv~ta~~~~gp~~~~~i~~~L~~ 292 (294)
T cd04741 226 HPLALGNVRTFRRLLPSEIQIIGVGGVLDGRGAFRMRLA--GASAV-QVGTALGKEGPKVFARIEKELED 292 (294)
T ss_pred HHHHHHHHHHHHHhcCCCCCEEEeCCCCCHHHHHHHHHc--CCCce-eEchhhhhcCchHHHHHHHHHHh
Confidence 35668889999999876789876 68999999998885 44443 3445555 699999988776654
No 23
>PLN02826 dihydroorotate dehydrogenase
Probab=46.39 E-value=1e+02 Score=28.26 Aligned_cols=66 Identities=15% Similarity=0.181 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHH-HHhCHHHHHHHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHW-LYKYPEESKKLLEILTNVI 197 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~-l~~~Pe~v~~lL~~~t~~~ 197 (214)
.+.-++.++.+++.+++++||++ .|...-....+|.- |.... ++... +++.|+.++++.+-+.+.+
T Consensus 324 ~~~sl~~v~~l~~~~~~~ipIIgvGGI~sg~Da~e~i~A--GAs~V-Qv~Ta~~~~Gp~~i~~I~~eL~~~l 392 (409)
T PLN02826 324 FDLSTEVLREMYRLTRGKIPLVGCGGVSSGEDAYKKIRA--GASLV-QLYTAFAYEGPALIPRIKAELAACL 392 (409)
T ss_pred cHHHHHHHHHHHHHhCCCCcEEEECCCCCHHHHHHHHHh--CCCee-eecHHHHhcCHHHHHHHHHHHHHHH
Confidence 35678999999999888889865 78888888888886 44332 23344 5556998888877776544
No 24
>PF11921 DUF3439: Domain of unknown function (DUF3439); InterPro: IPR024592 This uncharacterised C-terminal domain is found in variable lymphocyte receptor proteins. VLR are proteins consisting of leucine-rich repeats (LRR) that are assembled into functional receptors through somatic diversification of the incomplete germ-line VLR gene in lamprey and hagfish []. ; PDB: 3RFJ_A 3G3B_A 2R9U_C 2O6S_A 3A79_B 3RFS_A 2O6R_A 3V47_B 3V44_A 3A7C_A ....
Probab=46.37 E-value=6.6 Score=29.20 Aligned_cols=12 Identities=42% Similarity=0.727 Sum_probs=0.0
Q ss_pred HHHhccCccccc
Q psy10925 201 PTRLHYFPSYRI 212 (214)
Q Consensus 201 ~~a~~~~~~~~~ 212 (214)
.+|+.|||||-.
T Consensus 88 ~~~~~~~~~~~~ 99 (122)
T PF11921_consen 88 MNACAYFPSYIF 99 (122)
T ss_dssp ------------
T ss_pred HHHHHhhHHHHH
Confidence 467889999953
No 25
>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=45.82 E-value=82 Score=27.73 Aligned_cols=60 Identities=18% Similarity=0.154 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHH-HhCHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWL-YKYPEESKKLLE 191 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l-~~~Pe~v~~lL~ 191 (214)
.+..++.++.+++.+++++||++ .|..+=.....|.. |.+. ..+-+.+ +++|..++++++
T Consensus 263 ~~~~l~~v~~l~~~~~~~ipIi~~GGI~t~~da~e~l~a--GAd~-V~vg~~~~~~gP~~~~~i~~ 325 (327)
T cd04738 263 KERSTEVLRELYKLTGGKIPIIGVGGISSGEDAYEKIRA--GASL-VQLYTGLVYEGPGLVKRIKR 325 (327)
T ss_pred hHHHHHHHHHHHHHhCCCCcEEEECCCCCHHHHHHHHHc--CCCH-HhccHHHHhhCcHHHHHHHh
Confidence 35678999999999977788864 68888888888874 5444 3455565 456999988765
No 26
>cd03311 CIMS_C_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the C-terminal barrel, and a few single-barrel sequences most similar to the C-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Sidechains from
Probab=44.95 E-value=7.7 Score=34.06 Aligned_cols=130 Identities=15% Similarity=0.049 Sum_probs=68.5
Q ss_pred CChhhhcCCHHHHHHHHHhHHHhcCCCeeeeC----CCc-chhhhhC-CCeee----ecCCCCCccCCCCCCHHHHhccC
Q psy10925 51 HDFFTICQTPELAAEITLQPIRRFNLDASIIF----SDI-LVIPQAL-GMVVE----MKPAVGPVLPEPLVIPEDIKKLK 120 (214)
Q Consensus 51 ~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~----~d~-~~~aEa~-G~~v~----~~~~~~P~v~~~i~~~edl~~l~ 120 (214)
.+-.++..--+..+...++.++..|+|.+.=+ .|. ...++.+ |.+.. +..+.. ...|.. ..++
T Consensus 26 ~~~~~l~~~~~~ai~~~v~~Q~~~GldiitDGe~~r~~~~~~f~~~l~G~~~~~~~~~~~~~~--~~~~~~----~~~~- 98 (332)
T cd03311 26 ISAEELREAEDDAIADAVKDQEEAGLDVVTDGEFRRSDMVEYFLERLDGFEFTGWVQSYGSRY--YKPPGI----VGDV- 98 (332)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCCccccCCcccccHHHHHHHhCCceeeccceeeeccce--eeCCee----eccc-
Confidence 45555555557778888889999999986221 121 1344444 33321 111100 000110 0000
Q ss_pred CCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHH
Q psy10925 121 TSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDY 200 (214)
Q Consensus 121 ~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~ 200 (214)
..+.+.+++..+++++..++ .|+-+.+.||+|+|+.+. +.... .+. ..+++++.+++.+.+.
T Consensus 99 -----~~~~~~~~~~~~~~~~~~~~-~~lk~~l~GP~Tla~~~~---~~~~~------~y~---~~~el~~~la~~~~~e 160 (332)
T cd03311 99 -----SRRPPMTVEEGKIAQSLTHP-KPLKGILTGPVTIPSPSF---VRFRG------YYP---SREELAMDLALALREE 160 (332)
T ss_pred -----ccCCCCeEEEEEEeccCCCC-ccccccCCCCeeECCchh---hcccc------cCC---CHHHHHHHHHHHHHHH
Confidence 00122334444444444322 788999999999999887 21111 222 2345777777777777
Q ss_pred HHHhc
Q psy10925 201 PTRLH 205 (214)
Q Consensus 201 ~~a~~ 205 (214)
++++.
T Consensus 161 ~~~l~ 165 (332)
T cd03311 161 IRDLY 165 (332)
T ss_pred HHHHH
Confidence 77663
No 27
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=44.91 E-value=77 Score=26.00 Aligned_cols=84 Identities=17% Similarity=0.175 Sum_probs=59.4
Q ss_pred cCCHHHHHHHHHhHHHhcCCCeeeeCC------------------CcchhhhhCCCeeeecCC------CCCccC-C-CC
Q psy10925 57 CQTPELAAEITLQPIRRFNLDASIIFS------------------DILVIPQALGMVVEMKPA------VGPVLP-E-PL 110 (214)
Q Consensus 57 ~~d~e~~ae~~~~~~~~~g~D~v~i~~------------------d~~~~aEa~G~~v~~~~~------~~P~v~-~-~i 110 (214)
+..|+..|+-.++..+.-|.|-+.+.. +-+++.|.-|.-+.|..+ +-+.+. + .+
T Consensus 73 f~~P~eVaeRL~ei~K~~g~d~vRiSG~EP~l~~EHvlevIeLl~~~tFvlETNG~~~g~drslv~el~nr~nv~vRVsv 152 (228)
T COG5014 73 FLSPEEVAERLLEISKKRGCDLVRISGAEPILGREHVLEVIELLVNNTFVLETNGLMFGFDRSLVDELVNRLNVLVRVSV 152 (228)
T ss_pred ccCHHHHHHHHHHHHHhcCCcEEEeeCCCccccHHHHHHHHHhccCceEEEEeCCeEEecCHHHHHHHhcCCceEEEEEe
Confidence 368999999999999999999987643 445566666766655431 113332 2 34
Q ss_pred C--CHHHHhccCCCccchhhHHHHHHHHHHHHHH
Q psy10925 111 V--IPEDIKKLKTSVDVYKELNYVFEAITLTRHK 142 (214)
Q Consensus 111 ~--~~edl~~l~~~~d~~~r~~~~leai~~l~~~ 142 (214)
+ +++.+.+|.-. +|+. +..+++|++.|-++
T Consensus 153 KG~dpesF~kIT~a-sp~~-F~~QL~aLr~L~~~ 184 (228)
T COG5014 153 KGWDPESFEKITGA-SPEY-FRYQLKALRHLHGK 184 (228)
T ss_pred cCCCHHHHHHHhcC-ChHH-HHHHHHHHHHHHhc
Confidence 4 56778887755 6665 88999999999988
No 28
>PF06260 DUF1024: Protein of unknown function (DUF1024); InterPro: IPR009368 This entry is represented by Bacteriophage 92, Orf64. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical proteins from Staphylococcus aureus, which are related to Orf64 from Staphylococcus phage 92 (Bacteriophage 92). The function of this family is unknown.
Probab=41.69 E-value=58 Score=22.88 Aligned_cols=37 Identities=24% Similarity=0.379 Sum_probs=32.2
Q ss_pred CCCCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Q psy10925 166 GGGSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPT 202 (214)
Q Consensus 166 ~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~ 202 (214)
|.-++.+++=..+.||.-+.+.++++-+...++.+.+
T Consensus 19 g~dte~llkEiedVYKKAqaFDeI~e~~~~~~~~~~~ 55 (82)
T PF06260_consen 19 GNDTEGLLKEIEDVYKKAQAFDEILEDINNQIQEYRK 55 (82)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4456778878889999999999999999999998876
No 29
>COG1659 Uncharacterized protein, linocin/CFP29 homolog [Function unknown]
Probab=38.98 E-value=30 Score=29.09 Aligned_cols=118 Identities=12% Similarity=0.109 Sum_probs=68.5
Q ss_pred eeCCCcchhhhhCCCeeeecC--CCCCccC-C--CCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecc
Q psy10925 80 IIFSDILVIPQALGMVVEMKP--AVGPVLP-E--PLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSG 154 (214)
Q Consensus 80 ~i~~d~~~~aEa~G~~v~~~~--~~~P~v~-~--~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~ 154 (214)
.+..|..+..++=-|++.-.. ..-|.+. . ..-|..|++.++-- ++.--+.-+-+|.+.|..- .|++-..|+-
T Consensus 49 avs~g~l~~V~~~~nEV~~~qlRKs~Pl~~Lr~~Ftls~~eLd~~erg-~~~VD~~~v~eaa~klA~~-ED~~If~G~~- 125 (267)
T COG1659 49 AVSTGRLIDVKAPTNEVIAHQLRKSKPLVRLRVPFTLSRNELDDVERG-SKDVDWEPVKEAAKKLAFV-EDRTIFEGYS- 125 (267)
T ss_pred eeecceeEEecCCccccccccccccCcceeEeeeeEeeHHHhhHHHhc-CCCCCchHHHHHHHhhhhh-hhhheeecch-
Confidence 333343344444444443322 3346664 2 23356666665544 3321245577888888765 5665444332
Q ss_pred cHHHHHHHHHcCCCCCchHHHHHH-HHhCHHHHHHHHHHHHHHHHHHHHHhccCcccc
Q psy10925 155 APWTLMSYMIEGGGSKTMSKSKHW-LYKYPEESKKLLEILTNVIVDYPTRLHYFPSYR 211 (214)
Q Consensus 155 gP~TlA~~L~~~~g~~~~~~~~~~-l~~~Pe~v~~lL~~~t~~~~~~~~a~~~~~~~~ 211 (214)
-+ |.+.++.+..- -+++++....+++.+.+.+-.+.++=+|=|-|-
T Consensus 126 --------~~---GieG~Lsa~~~~~l~~~e~p~~~~~~iV~alS~l~~~G~~gpY~L 172 (267)
T COG1659 126 --------AA---GIEGILSASSNPALTLPEDPREIPDVIVQALSELRLAGVDGPYSL 172 (267)
T ss_pred --------hh---ccceeeccCCCccccCccccchHHHHHHHHHHHHHHcccCCceEE
Confidence 22 44555433222 467889999999999999999999999887664
No 30
>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=38.42 E-value=72 Score=28.10 Aligned_cols=56 Identities=14% Similarity=0.136 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHcCCCccEE--EecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHH
Q psy10925 132 VFEAITLTRHKLEGKVPLI--GFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLE 191 (214)
Q Consensus 132 ~leai~~l~~~~g~~vpv~--~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~ 191 (214)
.++.++.+++.+ ++||+ +.+..|-.....|.+ |.-++..+-+.++.||+.++++.+
T Consensus 278 ~~~~~~~ir~~~--~iPVi~~G~i~t~~~a~~~l~~--g~aD~V~~gR~~i~dP~~~~k~~~ 335 (336)
T cd02932 278 QVPFAERIRQEA--GIPVIAVGLITDPEQAEAILES--GRADLVALGRELLRNPYWPLHAAA 335 (336)
T ss_pred cHHHHHHHHhhC--CCCEEEeCCCCCHHHHHHHHHc--CCCCeehhhHHHHhCccHHHHHhh
Confidence 357778888887 46765 477888888887775 445667788999999999988754
No 31
>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=37.66 E-value=55 Score=28.17 Aligned_cols=65 Identities=14% Similarity=0.248 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHH-HHHHhCHHHHHHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSK-HWLYKYPEESKKLLEILTNV 196 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~-~~l~~~Pe~v~~lL~~~t~~ 196 (214)
.+.-++.++.+++.+++++||+| .|+.+=....+|+-| .... ++- -.+++.|+.++++++-+.+.
T Consensus 227 ~p~aL~~V~~~~~~~~~~i~Iig~GGI~s~~da~e~l~aG--A~~V-qv~Sal~~~Gp~~~~~i~~~L~~~ 294 (295)
T PF01180_consen 227 RPIALRWVRELRKALGQDIPIIGVGGIHSGEDAIEFLMAG--ASAV-QVCSALIYRGPGVIRRINRELEEW 294 (295)
T ss_dssp HHHHHHHHHHHHHHTTTSSEEEEESS--SHHHHHHHHHHT--ESEE-EESHHHHHHGTTHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHhccccceEEEEeCCcCCHHHHHHHHHhC--CCHh-eechhhhhcCcHHHHHHHHHHHhh
Confidence 47789999999999987899855 788888888888864 3322 122 34488999999988877653
No 32
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=37.17 E-value=33 Score=26.27 Aligned_cols=79 Identities=16% Similarity=0.190 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCC--------CCCchHHHHHHHHhCHHHHHH--HHHHHHHHHHHH
Q psy10925 131 YVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGG--------GSKTMSKSKHWLYKYPEESKK--LLEILTNVIVDY 200 (214)
Q Consensus 131 ~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~--------g~~~~~~~~~~l~~~Pe~v~~--lL~~~t~~~~~~ 200 (214)
.--+|++.|++++...-|=.... -++++-.++... +++.|+..+..+.+++..-.. +=+.+.+.+..|
T Consensus 39 ~~kea~~~l~krl~~~~~~vq~~--aL~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W 116 (140)
T PF00790_consen 39 GAKEAARALRKRLKHGNPNVQLL--ALTLLDALVKNCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEKILELLQEW 116 (140)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHH--HHHHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHhCCCHHHHHH--HHHHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHH
Confidence 34678888888886543311111 155555554332 455566555655555433333 778888999999
Q ss_pred HHHhccCcccc
Q psy10925 201 PTRLHYFPSYR 211 (214)
Q Consensus 201 ~~a~~~~~~~~ 211 (214)
+.++-+=|.|+
T Consensus 117 ~~~f~~~~~~~ 127 (140)
T PF00790_consen 117 AEAFKSDPELS 127 (140)
T ss_dssp HHHTTTSTTGH
T ss_pred HHHHCCCCCch
Confidence 99987777764
No 33
>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=36.62 E-value=84 Score=26.76 Aligned_cols=59 Identities=14% Similarity=0.215 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHHcCCCccEE--EecccHHHHHHHHHcCCCCCchHHHHHHHHhC-HHHHHHHHH
Q psy10925 130 NYVFEAITLTRHKLEGKVPLI--GFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKY-PEESKKLLE 191 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~--~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~-Pe~v~~lL~ 191 (214)
+..++.++.+++.+++++||+ |.|..|-..+..|.. | -+...+-+.++.+ |+.+.++.+
T Consensus 227 ~~~~~~v~~i~~~~~~~ipiia~GGI~~~~da~~~l~~--G-Ad~V~vg~a~~~~GP~~~~~i~~ 288 (289)
T cd02810 227 PLALRWVARLAARLQLDIPIIGVGGIDSGEDVLEMLMA--G-ASAVQVATALMWDGPDVIRKIKK 288 (289)
T ss_pred HHHHHHHHHHHHhcCCCCCEEEECCCCCHHHHHHHHHc--C-ccHheEcHHHHhcCccHHHHHhc
Confidence 345888999999986568887 578888888888875 4 3444566888888 998888654
No 34
>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=35.27 E-value=1e+02 Score=27.10 Aligned_cols=86 Identities=10% Similarity=-0.007 Sum_probs=54.2
Q ss_pred CChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeecCCCCCccCCCCCCHHHHhccCCCccchhhHH
Q psy10925 51 HDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMKPAVGPVLPEPLVIPEDIKKLKTSVDVYKELN 130 (214)
Q Consensus 51 ~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~~~~~P~v~~~i~~~edl~~l~~~~d~~~r~~ 130 (214)
+|..|+...-+.+++++.. .++.|+|+|-+-....+... .+-.|..+... ++.- - ....|+.
T Consensus 139 mt~~eI~~~i~~~~~aA~r-a~~aGfDgVeih~a~gyLl~--------------qFlsp~~N~R~-D~yG-G-slenR~r 200 (338)
T cd04733 139 MTEEEIEDVIDRFAHAARL-AQEAGFDGVQIHAAHGYLLS--------------QFLSPLTNKRT-DEYG-G-SLENRAR 200 (338)
T ss_pred CCHHHHHHHHHHHHHHHHH-HHHcCCCEEEEchhhhhHHH--------------HhcCCcCCCCC-ccCC-C-CHHHHHH
Confidence 6677777888999999887 56789999866432221110 01112211111 1110 0 2245888
Q ss_pred HHHHHHHHHHHHcCCCccEEEecc
Q psy10925 131 YVFEAITLTRHKLEGKVPLIGFSG 154 (214)
Q Consensus 131 ~~leai~~l~~~~g~~vpv~~~v~ 154 (214)
..+|.++.+|+.+|++.+|..-+.
T Consensus 201 f~~EiI~aIR~avG~d~~v~vris 224 (338)
T cd04733 201 LLLEIYDAIRAAVGPGFPVGIKLN 224 (338)
T ss_pred HHHHHHHHHHHHcCCCCeEEEEEc
Confidence 999999999999998888877664
No 35
>PRK01221 putative deoxyhypusine synthase; Provisional
Probab=35.11 E-value=1e+02 Score=27.29 Aligned_cols=43 Identities=9% Similarity=-0.086 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhC
Q psy10925 130 NYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKY 182 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~ 182 (214)
..+.+|++++.+.+.++..++.++.|+++.++ |++ .+ +.|+++
T Consensus 38 ~~l~~A~~i~~~ml~d~~~ifL~~tg~mvs~G-lr~------ii---~~Li~~ 80 (312)
T PRK01221 38 GHIVRASEILKEMISDADLRFLSFTANLVSTG-LRG------LI---ADLIKR 80 (312)
T ss_pred HHHHHHHHHHHHHHcCCCeEEEEecchhHHHH-HHH------HH---HHHHHc
Confidence 46788999999998766688999999998888 552 33 677765
No 36
>COG0167 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]
Probab=34.69 E-value=1.1e+02 Score=27.06 Aligned_cols=136 Identities=13% Similarity=0.114 Sum_probs=78.7
Q ss_pred hhhhcCCHHHHHHHHHhHHHhcC-CCeeeeCCCcc------hhhhhCCCeeeecCCCCCccCCCC-CCHHHHhccCCC-c
Q psy10925 53 FFTICQTPELAAEITLQPIRRFN-LDASIIFSDIL------VIPQALGMVVEMKPAVGPVLPEPL-VIPEDIKKLKTS-V 123 (214)
Q Consensus 53 ~~e~~~d~e~~ae~~~~~~~~~g-~D~v~i~~d~~------~~aEa~G~~v~~~~~~~P~v~~~i-~~~edl~~l~~~-~ 123 (214)
.+++.+|||.+.++..+..+... +=++++.++.. -.++..|++-.- .+.+.+ ...-|++..++. .
T Consensus 139 ~~~l~~~~e~l~~l~~~vk~~~~~Pv~vKl~P~~~di~~iA~~~~~~g~Dgl~------~~NT~~~~~~id~~~~~~~~~ 212 (310)
T COG0167 139 GRALGQDPELLEKLLEAVKAATKVPVFVKLAPNITDIDEIAKAAEEAGADGLI------AINTTKSGMKIDLETKKPVLA 212 (310)
T ss_pred hhhhccCHHHHHHHHHHHHhcccCceEEEeCCCHHHHHHHHHHHHHcCCcEEE------EEeeccccccccccccccccC
Confidence 55666788888888777666665 44467766433 233444544111 000111 111122221211 1
Q ss_pred cc----hh--hHHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHHHhC-HHHHHHHHHHHH
Q psy10925 124 DV----YK--ELNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWLYKY-PEESKKLLEILT 194 (214)
Q Consensus 124 d~----~~--r~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~-Pe~v~~lL~~~t 194 (214)
+. +| -.+.-++.++.+.+++++++||+| .|.+-=...-.|+.| . .+.++...++.+ |..++++.+-+.
T Consensus 213 ~~~GGLSG~~ikp~al~~v~~l~~~~~~~ipIIGvGGI~s~~DA~E~i~aG--A-~~vQv~Tal~~~Gp~i~~~I~~~l~ 289 (310)
T COG0167 213 NETGGLSGPPLKPIALRVVAELYKRLGGDIPIIGVGGIETGEDALEFILAG--A-SAVQVGTALIYKGPGIVKEIIKGLA 289 (310)
T ss_pred cCCCCcCcccchHHHHHHHHHHHHhcCCCCcEEEecCcCcHHHHHHHHHcC--C-chheeeeeeeeeCchHHHHHHHHHH
Confidence 11 33 347788999999999999999976 566766677778753 2 344555666666 887777666555
Q ss_pred HHH
Q psy10925 195 NVI 197 (214)
Q Consensus 195 ~~~ 197 (214)
..+
T Consensus 290 ~~l 292 (310)
T COG0167 290 RWL 292 (310)
T ss_pred HHH
Confidence 444
No 37
>PF12979 DUF3863: Domain of Unknown Function with PDB structure (DUF3863); InterPro: IPR024334 This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences, A6LGL1 from SWISSPROT from Parabacteroides distasonis atcc 8503, has been determined.; PDB: 3LM3_A.
Probab=33.57 E-value=33 Score=29.66 Aligned_cols=80 Identities=20% Similarity=0.383 Sum_probs=37.8
Q ss_pred CCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHH
Q psy10925 109 PLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKK 188 (214)
Q Consensus 109 ~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~ 188 (214)
|++-..|++ |.+- |. .---.++.++.+++.+...+|=.---.| ||+-+ |-+ |. +..++
T Consensus 20 pwEvsRdvk-L~~r-DE--~~wHtl~gVr~~reAfa~~nP~grLTWg-ft~nA-Led--~~--------------~nyr~ 77 (351)
T PF12979_consen 20 PWEVSRDVK-LHPR-DE--TSWHTLEGVRALREAFASNNPDGRLTWG-FTLNA-LED--GR--------------PNYRQ 77 (351)
T ss_dssp TTBSSSS-B-SS-------GGG--HHHHHHHHHHHHTT-TT---EEE-E-HHH-HH----S--------------HHHHH
T ss_pred ceeeecccc-cccc-cc--chhhHHHHHHHHHHHHHhcCCCceEEEe-eecch-hhc--CC--------------hhHHH
Confidence 555444543 3332 22 2223577788888877655553332222 44333 222 33 33456
Q ss_pred HHHHHHHHHHHHHHHhccCccc
Q psy10925 189 LLEILTNVIVDYPTRLHYFPSY 210 (214)
Q Consensus 189 lL~~~t~~~~~~~~a~~~~~~~ 210 (214)
+=+++.++.++|.+..-|||.|
T Consensus 78 IR~y~v~c~~k~GDevsyfPGy 99 (351)
T PF12979_consen 78 IRDYVVECQQKYGDEVSYFPGY 99 (351)
T ss_dssp HHHHHHHHHHHH--EEEE---S
T ss_pred HHHHHHHHHHHhCCceeecccc
Confidence 6778899999999999999987
No 38
>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=31.13 E-value=1.3e+02 Score=26.79 Aligned_cols=59 Identities=14% Similarity=0.102 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHH
Q psy10925 132 VFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILT 194 (214)
Q Consensus 132 ~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t 194 (214)
.++..+.+++.+ .+||++ .+.+|-.....|-+ |.-++..+-+.++.||+.+.++.+--.
T Consensus 264 ~~~~~~~ik~~v--~iPVi~~G~i~~~~~a~~~i~~--g~~D~V~~gR~~l~dP~~~~k~~~g~~ 324 (353)
T cd02930 264 FAWATAKLKRAV--DIPVIASNRINTPEVAERLLAD--GDADMVSMARPFLADPDFVAKAAAGRA 324 (353)
T ss_pred hHHHHHHHHHhC--CCCEEEcCCCCCHHHHHHHHHC--CCCChhHhhHHHHHCccHHHHHHhCCc
Confidence 466778888887 467664 57788777776664 445677788999999999999987543
No 39
>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=30.22 E-value=69 Score=28.26 Aligned_cols=56 Identities=18% Similarity=0.076 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHH
Q psy10925 132 VFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLE 191 (214)
Q Consensus 132 ~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~ 191 (214)
.++.++.+|+.++ +||++ .+..|-.....|-+ |.-++..+-|.++.||+.+.++.+
T Consensus 280 ~~~~~~~ik~~v~--iPVi~~G~i~t~~~a~~~l~~--g~aD~V~lgR~~iadP~~~~k~~~ 337 (338)
T cd04733 280 FLEFAEKIRKVTK--TPLMVTGGFRTRAAMEQALAS--GAVDGIGLARPLALEPDLPNKLLA 337 (338)
T ss_pred hHHHHHHHHHHcC--CCEEEeCCCCCHHHHHHHHHc--CCCCeeeeChHhhhCccHHHHHhc
Confidence 3677788888873 67654 66777777776765 444566678999999999988753
No 40
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=27.41 E-value=72 Score=24.22 Aligned_cols=78 Identities=17% Similarity=0.198 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCC--------CCCchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHH
Q psy10925 132 VFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGG--------GSKTMSKSKHWLYKYPEESKKLLEILTNVIVDYPTR 203 (214)
Q Consensus 132 ~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~--------g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~~~~~~a 203 (214)
..+|++.|++++...-|-.... -+++.-.++... +++.|+.-+..+.+++.....+-+.+.+.+..|+.+
T Consensus 35 ~k~a~r~l~krl~~~n~~v~l~--AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~~ 112 (133)
T smart00288 35 PKDAVRLLKKRLNNKNPHVALL--ALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQEWADA 112 (133)
T ss_pred HHHHHHHHHHHHcCCCHHHHHH--HHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHH
Confidence 4677777777775432211111 133333333221 345566666666666554444888888999999988
Q ss_pred hccCcccc
Q psy10925 204 LHYFPSYR 211 (214)
Q Consensus 204 ~~~~~~~~ 211 (214)
+-.=|+|.
T Consensus 113 f~~~~~~~ 120 (133)
T smart00288 113 FKNDPDLS 120 (133)
T ss_pred HcCCCCch
Confidence 86555553
No 41
>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=26.51 E-value=3.2e+02 Score=24.25 Aligned_cols=60 Identities=17% Similarity=0.208 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHcCCCccEEE--ecccHHHHHHHHHcCCCCCchHHHHHHHHh-CHHHHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIG--FSGAPWTLMSYMIEGGGSKTMSKSKHWLYK-YPEESKKLLE 191 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~--~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~-~Pe~v~~lL~ 191 (214)
.+..++.++.+++.+++++|+++ .|..+=.....|.. | ..+.++-..++. .|+.+.++.+
T Consensus 271 ~p~al~~v~~~~~~~~~~ipiig~GGI~~~~da~e~l~a--G-A~~Vqv~ta~~~~Gp~~~~~i~~ 333 (335)
T TIGR01036 271 QDKSTEIIRRLYAELQGRLPIIGVGGISSAQDALEKIRA--G-ASLLQIYSGFIYWGPPLVKEIVK 333 (335)
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEECCCCCHHHHHHHHHc--C-CcHHHhhHHHHHhCchHHHHHHh
Confidence 46778999999999877889864 78999988888885 4 345566677666 5998888765
No 42
>PRK13523 NADPH dehydrogenase NamA; Provisional
Probab=26.26 E-value=2e+02 Score=25.60 Aligned_cols=62 Identities=10% Similarity=-0.044 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHcCCCccEE--EecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy10925 132 VFEAITLTRHKLEGKVPLI--GFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLLEILTNVI 197 (214)
Q Consensus 132 ~leai~~l~~~~g~~vpv~--~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL~~~t~~~ 197 (214)
..+.++.+|+.++ +||+ |.+..|=.....|-+ |.-++..+-|.++-||+.++++.+.....+
T Consensus 263 ~~~~~~~ik~~~~--ipVi~~G~i~~~~~a~~~l~~--g~~D~V~~gR~~iadP~~~~k~~~~~~~~~ 326 (337)
T PRK13523 263 QVPFAEHIREHAN--IATGAVGLITSGAQAEEILQN--NRADLIFIGRELLRNPYFPRIAAKELGFEI 326 (337)
T ss_pred cHHHHHHHHhhcC--CcEEEeCCCCCHHHHHHHHHc--CCCChHHhhHHHHhCccHHHHHHHHcCCCC
Confidence 3566778888763 6765 677777666666654 445666788999999999999988765443
No 43
>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=26.23 E-value=2.1e+02 Score=25.12 Aligned_cols=85 Identities=12% Similarity=0.148 Sum_probs=49.3
Q ss_pred CChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCc-chhhhhCCCeeeecCCCCCccCCCCCCHHHHhccCCCccchhhH
Q psy10925 51 HDFFTICQTPELAAEITLQPIRRFNLDASIIFSDI-LVIPQALGMVVEMKPAVGPVLPEPLVIPEDIKKLKTSVDVYKEL 129 (214)
Q Consensus 51 ~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~-~~~aEa~G~~v~~~~~~~P~v~~~i~~~edl~~l~~~~d~~~r~ 129 (214)
+|..|+..=-+.+++++..+.+ .|+|+|-+-... ..+.+ +-.|..+... ++.- - ....|.
T Consensus 144 mt~~eI~~ii~~~~~aA~~a~~-aGfDgVei~~~~gyLl~q---------------Flsp~~N~R~-D~yG-g-sl~nr~ 204 (336)
T cd02932 144 LTREEIAEVVDAFVAAARRAVE-AGFDVIEIHAAHGYLLHQ---------------FLSPLSNKRT-DEYG-G-SLENRM 204 (336)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH-cCCCEEEEccccccHHHH---------------hcCCccCCCC-cccC-C-CHHHHh
Confidence 5666666667888888888644 799999775321 11111 1012111100 0000 0 124577
Q ss_pred HHHHHHHHHHHHHcCCCccEEEecc
Q psy10925 130 NYVFEAITLTRHKLEGKVPLIGFSG 154 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~~~v~ 154 (214)
...++.++.+++.+|++.||..-+.
T Consensus 205 rf~~eiv~aIR~~vG~d~~v~vri~ 229 (336)
T cd02932 205 RFLLEVVDAVRAVWPEDKPLFVRIS 229 (336)
T ss_pred HHHHHHHHHHHHHcCCCceEEEEEc
Confidence 7888888888888888877766543
No 44
>PF00724 Oxidored_FMN: NADH:flavin oxidoreductase / NADH oxidase family; InterPro: IPR001155 The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside []. It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions []. The active site is always found at the C-terminal end of this domain. Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include: dimethylamine dehydrogenase trimethylamine dehydrogenase 12-oxophytodienoate reductase NADPH dehydrogenase NADH oxidase ; GO: 0010181 FMN binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GKA_B 3P67_A 3F03_K 2ABA_A 1VYR_A 1GVO_A 3KFT_B 3P8I_A 1GVQ_A 3P74_A ....
Probab=26.03 E-value=1e+02 Score=27.20 Aligned_cols=87 Identities=13% Similarity=0.033 Sum_probs=50.1
Q ss_pred CChhhhcCCHHHHHHHHHhHHHhcCCCeeeeCCCcchhhhhCCCeeeecCCCCCccCCCCCCHHHHhccCCCccchhhHH
Q psy10925 51 HDFFTICQTPELAAEITLQPIRRFNLDASIIFSDILVIPQALGMVVEMKPAVGPVLPEPLVIPEDIKKLKTSVDVYKELN 130 (214)
Q Consensus 51 ~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i~~d~~~~aEa~G~~v~~~~~~~P~v~~~i~~~edl~~l~~~~d~~~r~~ 130 (214)
+|..|+-.=-+..++++..+.+ -|+|+|=+-..-.+... .+-.|..|..+ |+.- .+...|+.
T Consensus 139 mt~~eI~~ii~~f~~AA~~A~~-AGfDGVEIH~ahGyLl~--------------qFLSp~~N~Rt-DeYG--Gs~ENR~R 200 (341)
T PF00724_consen 139 MTEEEIEEIIEDFAQAARRAKE-AGFDGVEIHAAHGYLLS--------------QFLSPLTNRRT-DEYG--GSLENRAR 200 (341)
T ss_dssp --HHHHHHHHHHHHHHHHHHHH-TT-SEEEEEESTTSHHH--------------HHHSTTT---S-STTS--SSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHH-hccCeEeecccchhhhh--------------heeeeccCCCc-hhhh--hhhchhhH
Confidence 4455555556888888888555 89999866432211110 11123332221 1111 13356899
Q ss_pred HHHHHHHHHHHHcCCCccEEEeccc
Q psy10925 131 YVFEAITLTRHKLEGKVPLIGFSGA 155 (214)
Q Consensus 131 ~~leai~~l~~~~g~~vpv~~~v~g 155 (214)
..+|.++.+|+.+|++.||..-+.+
T Consensus 201 f~~Eii~aIr~~vg~d~~v~~Rls~ 225 (341)
T PF00724_consen 201 FLLEIIEAIREAVGPDFPVGVRLSP 225 (341)
T ss_dssp HHHHHHHHHHHHHTGGGEEEEEEET
T ss_pred HHHHHHHHHHHHhcCCceEEEEEee
Confidence 9999999999999998877665543
No 45
>cd08210 RLP_RrRLP Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP. RLP from Rhodospirillum rubrum plays a role in an uncharacterized sulfur salvage pathway and has been shown to catalyze a novel isomerization reaction that converts 5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate.
Probab=25.85 E-value=72 Score=28.80 Aligned_cols=35 Identities=14% Similarity=0.088 Sum_probs=31.4
Q ss_pred hhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHH
Q psy10925 126 YKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLM 160 (214)
Q Consensus 126 ~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA 160 (214)
.+|++.+.++++...++-|+.++.+.+++++.+-+
T Consensus 173 ~eRv~~v~~av~~a~~eTG~~~~y~~Nita~~~em 207 (364)
T cd08210 173 EERVKACQEAVAEANAETGGRTLYAPNVTGPPTQL 207 (364)
T ss_pred HHHHHHHHHHHHHHHhhcCCcceEEEecCCCHHHH
Confidence 68999999999999999999999999999986643
No 46
>PLN02495 oxidoreductase, acting on the CH-CH group of donors
Probab=24.99 E-value=2.1e+02 Score=26.15 Aligned_cols=65 Identities=8% Similarity=0.059 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHcCCCccEEEecccHHH------HHHHHHcCC--------------CCCchHHHHHHHHhCHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIGFSGAPWT------LMSYMIEGG--------------GSKTMSKSKHWLYKYPEESKK 188 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~~v~gP~T------lA~~L~~~~--------------g~~~~~~~~~~l~~~Pe~v~~ 188 (214)
+..+++-++.+++++ +++|+|+++.|+.+ +|..+-+-+ +.+..- ..+-++||.+.+
T Consensus 97 ~~~~l~~i~~~k~~~-~~~pvIaSi~~~~s~~~~~~~a~~~e~~GaD~iELNiSCPn~~~~r~~g---~~~gq~~e~~~~ 172 (385)
T PLN02495 97 FETMLAEFKQLKEEY-PDRILIASIMEEYNKDAWEEIIERVEETGVDALEINFSCPHGMPERKMG---AAVGQDCDLLEE 172 (385)
T ss_pred HHHHHHHHHHHHhhC-CCCcEEEEccCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCCCCcCccc---hhhccCHHHHHH
Q ss_pred HHHHHHHHH
Q psy10925 189 LLEILTNVI 197 (214)
Q Consensus 189 lL~~~t~~~ 197 (214)
+++.+.+.+
T Consensus 173 i~~~Vk~~~ 181 (385)
T PLN02495 173 VCGWINAKA 181 (385)
T ss_pred HHHHHHHhh
No 47
>COG0311 PDX2 Predicted glutamine amidotransferase involved in pyridoxine biosynthesis [Coenzyme metabolism]
Probab=23.91 E-value=90 Score=25.67 Aligned_cols=57 Identities=14% Similarity=0.199 Sum_probs=39.8
Q ss_pred CCCCHHHHhccCCCccc---h---hhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHc
Q psy10925 109 PLVIPEDIKKLKTSVDV---Y---KELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIE 165 (214)
Q Consensus 109 ~i~~~edl~~l~~~~d~---~---~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~ 165 (214)
.++.++|++.+.-..-| + +++-....-.+-|++.+.+..|+.|++.|=.-+|..+.+
T Consensus 29 ~Vk~~~dL~~~d~LIiPGGESTTi~rL~~~~gl~e~l~~~~~~G~Pv~GTCAGlIlLakei~~ 91 (194)
T COG0311 29 EVKRPEDLEGVDGLIIPGGESTTIGRLLKRYGLLEPLREFIADGLPVFGTCAGLILLAKEILD 91 (194)
T ss_pred EEcCHHHhccCcEEEecCccHHHHHHHHHHcCcHHHHHHHHHcCCceEEechhhhhhhhhhcC
Confidence 57778888877654234 2 333333344566777776789999999999999988884
No 48
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=23.78 E-value=2.1e+02 Score=21.73 Aligned_cols=73 Identities=15% Similarity=0.209 Sum_probs=46.1
Q ss_pred CCCCHHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHH
Q psy10925 109 PLVIPEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKK 188 (214)
Q Consensus 109 ~i~~~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~ 188 (214)
|....+|+.++.-- + .....+.+..|-+++.+.-|-+ =.=-+++.-+|++. |++.|. ++++++...+..
T Consensus 18 pgy~~~Eia~~t~~-s----~~~~~ei~d~L~kRL~~~~~hV--K~K~Lrilk~l~~~-G~~~f~---~~~~~~~~~Ik~ 86 (122)
T cd03572 18 PGYLYEEIAKLTRK-S----VGSCQELLEYLLKRLKRSSPHV--KLKVLKIIKHLCEK-GNSDFK---RELQRNSAQIRE 86 (122)
T ss_pred chHHHHHHHHHHHc-C----HHHHHHHHHHHHHHhcCCCCcc--hHHHHHHHHHHHhh-CCHHHH---HHHHHhHHHHHH
Confidence 44445666654332 2 2335577777777776654332 03348889998854 777777 999999887777
Q ss_pred HHHH
Q psy10925 189 LLEI 192 (214)
Q Consensus 189 lL~~ 192 (214)
+.++
T Consensus 87 ~~~f 90 (122)
T cd03572 87 CANY 90 (122)
T ss_pred HHHc
Confidence 6544
No 49
>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=23.54 E-value=1.2e+02 Score=26.25 Aligned_cols=57 Identities=19% Similarity=0.263 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHcCCCccEE--EecccHHHHHHHHHcCCCCCchHHHHHHHHhCHHHHHHHH
Q psy10925 130 NYVFEAITLTRHKLEGKVPLI--GFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKYPEESKKLL 190 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~--~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~Pe~v~~lL 190 (214)
...++.++.+++.++ +||+ |.+..|-.....|..| + -++..+-+.++.||+.+.++.
T Consensus 267 ~~~~~~~~~ir~~~~--iPVi~~Ggi~t~~~a~~~l~~g-~-aD~V~igR~~ladP~l~~k~~ 325 (327)
T cd02803 267 GYFLELAEKIKKAVK--IPVIAVGGIRDPEVAEEILAEG-K-ADLVALGRALLADPDLPNKAR 325 (327)
T ss_pred chhHHHHHHHHHHCC--CCEEEeCCCCCHHHHHHHHHCC-C-CCeeeecHHHHhCccHHHHHh
Confidence 345677888888873 6665 4677788877766642 3 345557799999999998875
No 50
>PRK02301 putative deoxyhypusine synthase; Provisional
Probab=22.97 E-value=2.1e+02 Score=25.44 Aligned_cols=43 Identities=14% Similarity=-0.017 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHc-CCCccEEEecccHHHHHHHHHcCCCCCchHHHHHHHHhC
Q psy10925 130 NYVFEAITLTRHKL-EGKVPLIGFSGAPWTLMSYMIEGGGSKTMSKSKHWLYKY 182 (214)
Q Consensus 130 ~~~leai~~l~~~~-g~~vpv~~~v~gP~TlA~~L~~~~g~~~~~~~~~~l~~~ 182 (214)
..+.+|++++.+.+ .++..++.+..|+++.++ |+ .+++.|+++
T Consensus 40 ~~l~~A~~i~~~ml~~~~~~ifL~~tg~mvsaG-lr---------~ii~~Li~~ 83 (316)
T PRK02301 40 GRLAEAVDIYEEMLADDDVTKFFGLAGAMVPAG-MR---------GIVSDLIRD 83 (316)
T ss_pred HHHHHHHHHHHHHHhCCCCeEEEEcccchhHHH-HH---------HHHHHHHHc
Confidence 46788999999988 557888999999999888 34 223777765
No 51
>KOG3818|consensus
Probab=22.76 E-value=74 Score=29.71 Aligned_cols=34 Identities=15% Similarity=0.048 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHcCCCccEEEecccHHHHHHHH
Q psy10925 130 NYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYM 163 (214)
Q Consensus 130 ~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L 163 (214)
..+++|++++-..+.+..|+.-...|+||-+..-
T Consensus 296 ~~vm~aL~kifqgy~~~pP~~iIlcG~FtS~p~~ 329 (525)
T KOG3818|consen 296 KKVMEALRKIFQGYKDAPPTAIILCGSFTSSPRQ 329 (525)
T ss_pred HHHHHHHHHHHhhccCCCCeEEEEeccccccccc
Confidence 6789999999999999999999999999977643
No 52
>cd03312 CIMS_N_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains fro
Probab=22.72 E-value=2e+02 Score=25.80 Aligned_cols=31 Identities=6% Similarity=-0.124 Sum_probs=24.3
Q ss_pred CChhhhcCCHHHHHHHHHhHHHhcCCCeeee
Q psy10925 51 HDFFTICQTPELAAEITLQPIRRFNLDASII 81 (214)
Q Consensus 51 ~~~~e~~~d~e~~ae~~~~~~~~~g~D~v~i 81 (214)
.+-.++..-.+......++.++..|+|.+..
T Consensus 28 i~~~~L~~~~~~~~~~~~~~Q~~~Gl~~it~ 58 (360)
T cd03312 28 ISEEELLATAKELRLRHWKLQKEAGIDLIPV 58 (360)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHcCCCEecc
Confidence 6666766777888888888899999997644
No 53
>PRK00805 putative deoxyhypusine synthase; Provisional
Probab=22.48 E-value=2.2e+02 Score=25.44 Aligned_cols=32 Identities=6% Similarity=-0.064 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHc-CCCccEEEecccHHHHHH
Q psy10925 130 NYVFEAITLTRHKL-EGKVPLIGFSGAPWTLMS 161 (214)
Q Consensus 130 ~~~leai~~l~~~~-g~~vpv~~~v~gP~TlA~ 161 (214)
..+.+|++++.+.+ ..+..++.++.|+++.++
T Consensus 29 ~~l~~A~~i~~~Ml~d~~~~ifL~~tg~mvsaG 61 (329)
T PRK00805 29 RKLGESVRVWTEMLKDPDNTIFMGLSGAMVPAG 61 (329)
T ss_pred HHHHHHHHHHHHHHhCCCCeEEEEeccchHHHH
Confidence 45788999999987 456888999999999888
No 54
>PRK01207 methionine synthase; Provisional
Probab=22.24 E-value=1.9e+02 Score=26.02 Aligned_cols=96 Identities=16% Similarity=0.211 Sum_probs=49.3
Q ss_pred hhcCCHHHHHHHHHhHHHhcCCCeeee-----CCCcc-hhhhhC-CCe----eeecCCCCCccCCCCCCHHHHhccCCCc
Q psy10925 55 TICQTPELAAEITLQPIRRFNLDASII-----FSDIL-VIPQAL-GMV----VEMKPAVGPVLPEPLVIPEDIKKLKTSV 123 (214)
Q Consensus 55 e~~~d~e~~ae~~~~~~~~~g~D~v~i-----~~d~~-~~aEa~-G~~----v~~~~~~~P~v~~~i~~~edl~~l~~~~ 123 (214)
+++.--....+..++.++..|+|.+.+ -.|+. +.++.+ |.. +.+.++. .+..|+ =+.++...
T Consensus 30 ~~~e~~~~ai~~~v~~Qe~aGlDiv~~dGe~~R~dmv~~f~~~l~G~~~~g~vr~y~~~--~~r~Pi----i~g~i~~~- 102 (343)
T PRK01207 30 KFYELAERATLETLDVFENAGLDNIGIGGEMFRWEMYEHPAERIKGIIFYGMVRSFDNR--YYRKGS----IIDRMERR- 102 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCEEeeCCcEeechHHHHHHHhcCCeEecCeEEEeccc--cccCCe----EEeeccCC-
Confidence 333444567888889999999997631 12322 344444 222 2222211 111111 11112111
Q ss_pred cchhhHHHHHHHHHHHHHHcCCCccEEEecccHHHHHHHHH
Q psy10925 124 DVYKELNYVFEAITLTRHKLEGKVPLIGFSGAPWTLMSYMI 164 (214)
Q Consensus 124 d~~~r~~~~leai~~l~~~~g~~vpv~~~v~gP~TlA~~L~ 164 (214)
. +.+++=++.+++. -+.||=+.+.||+|++....
T Consensus 103 ~-----~~~v~e~~~a~~~--t~kpvK~~ltGP~Ti~~~S~ 136 (343)
T PRK01207 103 S-----SFHLDEVEFVADN--TKKPIKVPITGPYTMMDWSF 136 (343)
T ss_pred C-----CCcHHHHHHHHHc--cCCCcEEEecCHHHHHHHhc
Confidence 1 1233334444443 23799999999999998765
No 55
>PRK09121 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=22.04 E-value=2.6e+02 Score=24.77 Aligned_cols=29 Identities=14% Similarity=0.040 Sum_probs=21.5
Q ss_pred CChhhhcCCHHHHHHHHHhHHHhcCCCee
Q psy10925 51 HDFFTICQTPELAAEITLQPIRRFNLDAS 79 (214)
Q Consensus 51 ~~~~e~~~d~e~~ae~~~~~~~~~g~D~v 79 (214)
.+..++..=-+...+..++.++..|+|.+
T Consensus 29 i~~~~l~~~~~~ai~~~V~~Q~~aGldii 57 (339)
T PRK09121 29 LQGEELIEGKQDALRLSLQEQEDAGIDIV 57 (339)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCCce
Confidence 45555545557777888888999999986
No 56
>COG2875 CobM Precorrin-4 methylase [Coenzyme metabolism]
Probab=21.32 E-value=2.4e+02 Score=24.13 Aligned_cols=104 Identities=12% Similarity=0.231 Sum_probs=63.1
Q ss_pred HcCCChhhhcC-CHHHHHHH--HHhHHHhcCCCeeeeC--CCcchhhhhCCCeeeecCCCCCcc-C-----CCCCCHHHH
Q psy10925 48 RSKHDFFTICQ-TPELAAEI--TLQPIRRFNLDASIIF--SDILVIPQALGMVVEMKPAVGPVL-P-----EPLVIPEDI 116 (214)
Q Consensus 48 ~~g~~~~e~~~-d~e~~ae~--~~~~~~~~g~D~v~i~--~d~~~~aEa~G~~v~~~~~~~P~v-~-----~~i~~~edl 116 (214)
..|...-.+.+ ||...--. |++.-++.|.|+-.++ +....-|-++|+++..|+-..-++ . .|+-..|++
T Consensus 73 ~~Gk~VvRLhSGDpsiYgA~~EQm~~L~~~gI~yevvPGVss~~AAAA~L~~ELT~P~vsQtvilTR~sgrt~vpe~e~l 152 (254)
T COG2875 73 REGKDVVRLHSGDPSIYGALAEQMRELEALGIPYEVVPGVSSFAAAAAALGIELTVPGVSQTVILTRPSGRTPVPEKESL 152 (254)
T ss_pred HcCCeEEEeecCChhHHHHHHHHHHHHHHcCCCeEEeCCchHHHHHHHHhCceeecCCcceeEEEEccccCCCCCchhHH
Confidence 34544433333 66554433 4445588999996665 334457789999999887322222 2 245556677
Q ss_pred hccCCCccc----hhhHHHHHHHHHHHHH-HcCCCccEEEe
Q psy10925 117 KKLKTSVDV----YKELNYVFEAITLTRH-KLEGKVPLIGF 152 (214)
Q Consensus 117 ~~l~~~~d~----~~r~~~~leai~~l~~-~~g~~vpv~~~ 152 (214)
..|-.- .- .=....+-+.++.|.+ .++.++||...
T Consensus 153 ~~la~~-~aTm~I~L~v~~I~~vv~~L~~g~y~~dtPVaVV 192 (254)
T COG2875 153 AALAKH-GATMVIFLGVHAIDKVVEELLEGGYPPDTPVAVV 192 (254)
T ss_pred HHHHhc-CceeEeeehhhHHHHHHHHHhcCCCCCCCCEEEE
Confidence 665432 11 1224667777888888 88889998764
No 57
>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=21.15 E-value=3.6e+02 Score=23.22 Aligned_cols=65 Identities=17% Similarity=0.190 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHcCCCccEEEecccH------HHHHHHHHcCC--------------CCCchHHHHHHHHhCHHHHHH
Q psy10925 129 LNYVFEAITLTRHKLEGKVPLIGFSGAP------WTLMSYMIEGG--------------GSKTMSKSKHWLYKYPEESKK 188 (214)
Q Consensus 129 ~~~~leai~~l~~~~g~~vpv~~~v~gP------~TlA~~L~~~~--------------g~~~~~~~~~~l~~~Pe~v~~ 188 (214)
+...++-++.+++... +.|+++.++|. ...|..+-+.+ +.+..- ..+.++|+.+.+
T Consensus 83 ~~~~~~~~~~~~~~~~-~~p~i~si~G~~~~~~~~~~a~~~~~~gad~ielN~sCP~~~~~~~~G---~~l~~~~~~~~~ 158 (299)
T cd02940 83 LEYWLKEIRELKKDFP-DKILIASIMCEYNKEDWTELAKLVEEAGADALELNFSCPHGMPERGMG---AAVGQDPELVEE 158 (299)
T ss_pred HHHHHHHHHHHHhhCC-CCeEEEEecCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCCCCCCCCc---hhhccCHHHHHH
Q ss_pred HHHHHHHHH
Q psy10925 189 LLEILTNVI 197 (214)
Q Consensus 189 lL~~~t~~~ 197 (214)
+++.+.+.+
T Consensus 159 iv~~v~~~~ 167 (299)
T cd02940 159 ICRWVREAV 167 (299)
T ss_pred HHHHHHHhc
No 58
>PRK00770 deoxyhypusine synthase-like protein; Provisional
Probab=20.46 E-value=1.6e+02 Score=26.88 Aligned_cols=32 Identities=16% Similarity=-0.004 Sum_probs=26.9
Q ss_pred HHHHHHHHHHH-HHcCCCccEEEecccHHHHHH
Q psy10925 130 NYVFEAITLTR-HKLEGKVPLIGFSGAPWTLMS 161 (214)
Q Consensus 130 ~~~leai~~l~-~~~g~~vpv~~~v~gP~TlA~ 161 (214)
..+.+|+++++ +.+.++..|+.+++|.++.++
T Consensus 34 ~~L~~A~~il~~~m~~~~~tvfLtltgamisaG 66 (384)
T PRK00770 34 ARLREACQLLAQRMIDDGVTVGLTLSGAMTPAG 66 (384)
T ss_pred HHHHHHHHHHHHHHHhcCCcEEEEeccchhhhh
Confidence 45778888888 777778999999999998887
No 59
>COG1647 Esterase/lipase [General function prediction only]
Probab=20.22 E-value=1.8e+02 Score=24.73 Aligned_cols=43 Identities=19% Similarity=0.212 Sum_probs=31.8
Q ss_pred HHHHhccCCCccchhhHHHHHHHHHHHHHHcCCCccEEE-ecccHHHH
Q psy10925 113 PEDIKKLKTSVDVYKELNYVFEAITLTRHKLEGKVPLIG-FSGAPWTL 159 (214)
Q Consensus 113 ~edl~~l~~~~d~~~r~~~~leai~~l~~~~g~~vpv~~-~v~gP~Tl 159 (214)
++|+-+ - .|+.|+..+.++-+.|+++--+++.|+| +++|=||+
T Consensus 57 ~e~fl~---t-~~~DW~~~v~d~Y~~L~~~gy~eI~v~GlSmGGv~al 100 (243)
T COG1647 57 PEDFLK---T-TPRDWWEDVEDGYRDLKEAGYDEIAVVGLSMGGVFAL 100 (243)
T ss_pred HHHHhc---C-CHHHHHHHHHHHHHHHHHcCCCeEEEEeecchhHHHH
Confidence 566644 2 6677999999999999966557888777 55666664
Done!