Query 040560
Match_columns 454
No_of_seqs 295 out of 644
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 09:36:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040560.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040560hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4698 Uncharacterized conser 100.0 2E-80 4.4E-85 638.5 17.8 440 2-452 7-469 (475)
2 PF04577 DUF563: Protein of un 100.0 5E-28 1.1E-32 227.2 19.4 198 165-391 1-204 (206)
3 COG4421 Capsular polysaccharid 99.8 4.1E-18 8.9E-23 169.2 15.8 272 71-395 52-331 (368)
4 cd05212 NAD_bind_m-THF_DH_Cycl 79.0 6.4 0.00014 35.7 6.6 69 287-362 28-98 (140)
5 cd00316 Oxidoreductase_nitroge 72.6 7.4 0.00016 40.3 6.0 97 285-385 150-251 (399)
6 cd01971 Nitrogenase_VnfN_like 71.9 6.8 0.00015 41.7 5.6 99 286-386 154-261 (427)
7 PF02882 THF_DHG_CYH_C: Tetrah 69.2 14 0.00031 34.2 6.4 70 287-363 36-107 (160)
8 COG3959 Transketolase, N-termi 67.8 8.3 0.00018 37.9 4.6 48 289-337 173-226 (243)
9 PRK14178 bifunctional 5,10-met 66.8 22 0.00048 36.0 7.7 72 287-364 152-224 (279)
10 cd01080 NAD_bind_m-THF_DH_Cycl 63.0 17 0.00036 33.9 5.6 73 286-364 43-116 (168)
11 cd01967 Nitrogenase_MoFe_alpha 62.6 34 0.00075 35.7 8.6 96 286-385 159-258 (406)
12 PF00148 Oxidored_nitro: Nitro 60.1 16 0.00034 38.1 5.5 97 285-384 142-243 (398)
13 PF01520 Amidase_3: N-acetylmu 60.0 17 0.00038 33.0 5.2 44 307-350 33-81 (175)
14 cd01972 Nitrogenase_VnfE_like 59.1 21 0.00045 38.0 6.2 98 286-385 160-265 (426)
15 cd02696 MurNAc-LAA N-acetylmur 58.1 26 0.00056 31.9 6.0 45 306-350 33-82 (172)
16 PF05222 AlaDh_PNT_N: Alanine 57.7 57 0.0012 29.2 7.9 91 298-392 10-116 (136)
17 PRK02910 light-independent pro 56.4 30 0.00066 37.9 7.1 100 285-386 156-261 (519)
18 cd01981 Pchlide_reductase_B Pc 55.8 45 0.00098 35.3 8.1 99 286-386 161-265 (430)
19 PF00389 2-Hacid_dh: D-isomer 55.2 44 0.00095 29.1 6.7 79 304-388 8-87 (133)
20 PRK14188 bifunctional 5,10-met 52.4 71 0.0015 32.7 8.5 70 287-363 158-229 (296)
21 cd01980 Chlide_reductase_Y Chl 50.1 20 0.00044 37.9 4.4 95 287-386 159-254 (416)
22 COG1920 Predicted nucleotidylt 47.4 57 0.0012 31.5 6.4 58 327-391 104-163 (210)
23 TIGR02883 spore_cwlD N-acetylm 45.4 55 0.0012 30.7 6.1 45 306-350 34-97 (189)
24 PRK10319 N-acetylmuramoyl-l-al 44.1 45 0.00098 33.8 5.6 54 308-366 92-150 (287)
25 PRK08306 dipicolinate synthase 43.7 96 0.0021 31.4 7.9 80 305-391 15-121 (296)
26 PRK14194 bifunctional 5,10-met 41.7 74 0.0016 32.6 6.7 71 287-364 159-231 (301)
27 CHL00076 chlB photochlorophyll 41.1 98 0.0021 34.0 8.0 100 285-386 161-266 (513)
28 PF13271 DUF4062: Domain of un 40.9 66 0.0014 26.0 5.1 42 306-347 17-63 (83)
29 PRK02261 methylaspartate mutas 39.9 95 0.0021 27.8 6.5 54 286-339 2-55 (137)
30 COG2185 Sbm Methylmalonyl-CoA 39.4 1.3E+02 0.0029 27.6 7.3 57 285-345 10-71 (143)
31 KOG4698 Uncharacterized conser 38.4 7.1 0.00015 42.2 -1.3 100 299-401 192-295 (475)
32 PRK14175 bifunctional 5,10-met 37.9 74 0.0016 32.4 6.0 72 287-364 158-230 (286)
33 cd01968 Nitrogenase_NifE_I Nit 37.7 68 0.0015 33.8 6.0 96 287-386 158-257 (410)
34 PRK14179 bifunctional 5,10-met 37.7 93 0.002 31.6 6.7 70 287-363 158-229 (284)
35 TIGR02853 spore_dpaA dipicolin 37.3 1.6E+02 0.0034 29.8 8.3 58 327-389 200-260 (287)
36 TIGR01501 MthylAspMutase methy 36.2 91 0.002 28.1 5.7 40 305-344 19-59 (134)
37 TIGR00640 acid_CoA_mut_C methy 35.4 1.1E+02 0.0023 27.4 6.0 65 287-351 2-67 (132)
38 TIGR02667 moaB_proteo molybden 32.7 1.3E+02 0.0027 27.8 6.2 55 302-356 22-83 (163)
39 PRK14190 bifunctional 5,10-met 32.3 1E+02 0.0022 31.3 6.0 71 287-364 158-230 (284)
40 PF02310 B12-binding: B12 bind 31.6 1.9E+02 0.0042 24.2 6.8 54 289-343 2-57 (121)
41 PRK08306 dipicolinate synthase 30.8 1.5E+02 0.0033 29.9 7.0 58 328-390 202-262 (296)
42 COG1703 ArgK Putative periplas 30.6 61 0.0013 33.5 4.0 42 305-347 133-177 (323)
43 TIGR01284 alt_nitrog_alph nitr 30.4 65 0.0014 34.7 4.5 96 287-386 199-298 (457)
44 PRK14189 bifunctional 5,10-met 29.5 1.2E+02 0.0026 30.8 5.9 70 287-363 158-229 (285)
45 PF01976 DUF116: Protein of un 29.4 1.2E+02 0.0026 28.1 5.4 39 304-343 75-113 (158)
46 cd03129 GAT1_Peptidase_E_like 29.4 1.7E+02 0.0037 27.7 6.7 62 286-347 28-91 (210)
47 PF03575 Peptidase_S51: Peptid 28.0 98 0.0021 27.8 4.6 37 306-342 4-41 (154)
48 PRK14191 bifunctional 5,10-met 27.9 1.6E+02 0.0034 30.0 6.5 72 287-364 157-229 (285)
49 PF02737 3HCDH_N: 3-hydroxyacy 27.8 68 0.0015 29.9 3.6 74 306-386 95-173 (180)
50 cd03146 GAT1_Peptidase_E Type 27.4 1.3E+02 0.0028 28.8 5.5 61 285-346 29-90 (212)
51 cd01977 Nitrogenase_VFe_alpha 27.1 1.9E+02 0.0041 30.6 7.2 96 287-386 162-261 (415)
52 COG0190 FolD 5,10-methylene-te 27.0 1.2E+02 0.0026 30.9 5.3 70 286-363 155-227 (283)
53 TIGR00177 molyb_syn molybdenum 26.3 1E+02 0.0022 27.6 4.3 52 300-351 25-81 (144)
54 PRK15469 ghrA bifunctional gly 25.8 1.7E+02 0.0038 29.8 6.4 57 305-361 149-223 (312)
55 PLN02897 tetrahydrofolate dehy 25.6 1.5E+02 0.0033 31.0 5.9 70 287-363 214-285 (345)
56 PF03358 FMN_red: NADPH-depend 25.2 1.7E+02 0.0037 25.7 5.6 52 289-341 2-75 (152)
57 PF08370 PDR_assoc: Plant PDR 24.5 80 0.0017 25.1 2.9 30 18-47 30-59 (65)
58 cd01976 Nitrogenase_MoFe_alpha 24.5 1.6E+02 0.0035 31.3 6.1 96 287-386 172-271 (421)
59 PRK14182 bifunctional 5,10-met 24.2 1.9E+02 0.004 29.5 6.1 70 287-363 157-228 (282)
60 cd01078 NAD_bind_H4MPT_DH NADP 24.2 3.2E+02 0.0069 25.2 7.4 70 289-363 54-128 (194)
61 TIGR01283 nifE nitrogenase mol 24.1 1.4E+02 0.003 32.1 5.5 95 287-385 197-295 (456)
62 PRK12548 shikimate 5-dehydroge 23.9 3.6E+02 0.0078 27.0 8.2 93 289-387 152-255 (289)
63 TIGR01282 nifD nitrogenase mol 23.9 1.7E+02 0.0036 31.7 6.1 95 287-385 207-305 (466)
64 TIGR01862 N2-ase-Ialpha nitrog 23.9 1.6E+02 0.0034 31.6 5.9 95 287-385 191-289 (443)
65 cd03789 GT1_LPS_heptosyltransf 23.8 1.1E+02 0.0024 29.9 4.5 41 324-366 186-226 (279)
66 PRK14183 bifunctional 5,10-met 23.5 1.9E+02 0.0042 29.4 6.1 70 287-363 157-228 (281)
67 cd01965 Nitrogenase_MoFe_beta_ 23.2 1.2E+02 0.0025 32.3 4.7 98 286-386 154-274 (428)
68 PF02423 OCD_Mu_crystall: Orni 22.9 1.2E+02 0.0026 30.8 4.7 69 289-367 155-227 (313)
69 PLN02928 oxidoreductase family 22.6 1.5E+02 0.0032 30.8 5.2 60 306-365 173-263 (347)
70 cd01079 NAD_bind_m-THF_DH NAD 22.5 1.5E+02 0.0034 28.5 4.9 74 286-363 61-155 (197)
71 PRK02842 light-independent pro 22.4 1.8E+02 0.0038 31.0 5.9 94 287-386 166-262 (427)
72 PF15183 MRAP: Melanocortin-2 22.2 81 0.0017 26.4 2.5 21 19-39 44-64 (90)
73 TIGR00507 aroE shikimate 5-deh 22.1 3.3E+02 0.0071 26.8 7.4 51 334-388 176-234 (270)
74 TIGR02370 pyl_corrinoid methyl 21.9 2.9E+02 0.0063 26.1 6.7 61 285-345 82-143 (197)
75 PRK14180 bifunctional 5,10-met 21.9 1.6E+02 0.0035 29.9 5.2 70 287-363 158-229 (282)
76 PRK14186 bifunctional 5,10-met 21.8 2.1E+02 0.0046 29.3 6.1 70 287-363 158-229 (297)
77 PRK06932 glycerate dehydrogena 21.7 1.2E+02 0.0027 30.9 4.4 60 306-365 161-234 (314)
78 PRK03094 hypothetical protein; 21.6 1.3E+02 0.0029 24.8 3.7 20 303-322 9-28 (80)
79 PRK15438 erythronate-4-phospha 21.6 1.6E+02 0.0035 31.1 5.3 60 306-365 130-208 (378)
80 PRK00258 aroE shikimate 5-dehy 21.4 2.6E+02 0.0055 27.8 6.5 53 332-388 181-241 (278)
81 TIGR02015 BchY chlorophyllide 21.4 1.4E+02 0.0031 31.8 5.0 81 303-386 178-260 (422)
82 TIGR01860 VNFD nitrogenase van 21.4 1.4E+02 0.0029 32.3 4.9 96 287-386 201-300 (461)
83 PLN02616 tetrahydrofolate dehy 21.3 2E+02 0.0043 30.4 5.8 70 287-363 231-302 (364)
84 PRK14166 bifunctional 5,10-met 20.8 2.2E+02 0.0048 28.9 6.0 70 287-363 157-228 (282)
85 PRK06487 glycerate dehydrogena 20.7 1.4E+02 0.0031 30.4 4.6 59 306-364 162-233 (317)
86 cd00758 MoCF_BD MoCF_BD: molyb 20.5 1.4E+02 0.003 26.2 4.0 54 302-355 19-77 (133)
87 TIGR02690 resist_ArsH arsenica 20.3 4.4E+02 0.0096 25.7 7.7 57 284-341 23-95 (219)
88 PRK14170 bifunctional 5,10-met 20.2 2.7E+02 0.0057 28.4 6.3 70 287-363 157-228 (284)
89 cd08190 HOT Hydroxyacid-oxoaci 20.2 3.3E+02 0.0071 28.9 7.4 58 289-346 25-90 (414)
90 cd08192 Fe-ADH7 Iron-containin 20.2 3.6E+02 0.0078 27.9 7.6 57 289-345 26-90 (370)
91 PRK09860 putative alcohol dehy 20.1 3.5E+02 0.0075 28.3 7.5 57 289-345 33-97 (383)
No 1
>KOG4698 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2e-80 Score=638.52 Aligned_cols=440 Identities=37% Similarity=0.617 Sum_probs=388.6
Q ss_pred chHHHhhhhcchhhhhhhhhhHHHHHHHHHHHHHHhhhccccCcccccccccccccccccc---cc-------cCCCCCC
Q 040560 2 LYDSILARSFSKHEQKKFKYGALIGLFVIALSFCTVLKPYLAPLPAALNLRVPMDIGLKKL---MV-------KDTKIEP 71 (454)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-------~~~~~~~ 71 (454)
++++++.|++.+..+..+.+|++.+++|.++..|++.||++++.|. . +..-+.+..+. .. .++..++
T Consensus 7 ~i~~i~~~~~~~~~~~~~~~~~f~~~~~~vl~~~~v~kp~~l~~~~-~--~~~~~tg~~~~~~~~~~~~~~q~~~~~~e~ 83 (475)
T KOG4698|consen 7 LILHIFLREDKKNLLGLLIYGVFHSSLLSVLPKCVVVKPYLLLLPR-F--QPDLPTGSFEDELLPLSQLLRQPPGSALED 83 (475)
T ss_pred hhHHHHHHhhhhcCccceecCcchhhhhhhcccceecCCeecccCc-c--ccCcccceeeccCCChhhcccCCCCcccCC
Confidence 6789999999999999999999999999999999999999777653 1 11111111110 00 1222233
Q ss_pred --CccC-CCCCccceeeeCcEEeeCCceEEEEecCCC-CCCCCCceeeCCCccCCcccccCceeeEEEEEecCCCCCCCC
Q 040560 72 --SYCS-TTQRSEFCDIKDDIRIEASSGTVFISSSEA-AGINNRSWIIRPYARKADSTAMNWVRKWAVKSVTNRQELPKC 147 (454)
Q Consensus 72 --~~C~-~~~r~d~C~~~gdvr~~~~~~tv~~~~~~~-~~~~~~~~~i~Py~Rk~~~~~m~~v~e~~~~~~~~~~~~p~C 147 (454)
..|| ++.++|+|+++||+|+|+.++|++..-..- .+..+.+|+||||+||||..+|++|+|+++...+ .+...+|
T Consensus 84 ~~~~C~~~g~~s~~c~~kg~~r~h~~~~~~~~~~~~~~~~s~~~~e~ikpy~rk~~~~vmp~vre~~l~~~~-~~~~r~c 162 (475)
T KOG4698|consen 84 SSFFCDRSGTRSDFCEMKGDVRTHPDSSTVLLTLGRLLTFSGRLVEKIKPYTRKGETWVMPEVRELNLLVRP-GSEIRRC 162 (475)
T ss_pred ceEEeeccccccchhhhcCccccCcchhhhhhhccchhhhccccchhcccccccccccccccccccceEEcC-Cccccee
Confidence 6788 567899999999999999999998865531 1345789999999999999999999999999875 3567899
Q ss_pred ceeecccEEEEEcCCcccccchhhhhhHHHHHHhhh--ccCCceEEEEeCCCCCchhHHHHHHHhhcCCCccccCCcCCC
Q 040560 148 TQNHGVPAILFSNGGYAGNHFHDFTDIIVPLYLTSR--QFNGEVQFLVTNKKYDWIDKFRELLQKLSNHDIIDVDQENDI 225 (454)
Q Consensus 148 ~~~h~~Pavvfs~~gy~~N~~H~~~D~liPLf~t~~--~f~~~vqlli~d~~p~w~~ky~~ll~~lS~~~vidl~~~~~~ 225 (454)
+++|++||++|++|||+||.||+|+|+++|||+|.+ .|++++|+++++.++||..||.+++++||+||+++++++..
T Consensus 163 ~v~~~~pa~vfs~Gg~tgn~yhdf~d~~ipL~it~~~~~~n~ev~~li~~~~~ww~~kf~Dvv~~lSn~~~v~~~~~~~- 241 (475)
T KOG4698|consen 163 DVNHEVPAIVFSTGGYTGNEYHDFNDGIIPLFITEAELRFNKEVQFLITETHSWWDMKFGDVVRQLSNYPVVDFDAELR- 241 (475)
T ss_pred eeecccchheeecCCcchhhHHHHHhhhhhhhcccchhcccccEEEEEEEcchhhhhhHHHHHHhcCCCceEEecCCce-
Confidence 999999999999999999999999999999999999 79999999999999999999999999999999999999887
Q ss_pred CceeecCceEEecccccCccccccCCCCC----ccHHHHHHHHHhhhcCCcccchhcccccccCCCcEEEEEEeCCCccc
Q 040560 226 GKVHCFRGGIIGLKAHDQKELIIDPSKSS----YTMTDFKQFLRSCYSLQKSTAITINNKESKKKMPRLLIISRKRTRTF 301 (454)
Q Consensus 226 g~~~CF~~aiVGl~~h~~~~l~idp~~~p----~si~~F~~flr~~y~L~r~~~~~i~~~~~~~~~prl~~i~R~~~R~i 301 (454)
+|||.+++|||..|. ++.++|+..+ ++|.+|++|+..+|+...+.+ .+. .....++||+++++|.++|.|
T Consensus 242 --ThcF~~~~vgL~~h~--~y~v~~t~~~~~~~~s~~~fr~~l~~a~~~~i~~~-~~t-~~~~~kkpri~~lsR~~~r~I 315 (475)
T KOG4698|consen 242 --THCFKEAIVGLVSHF--PYAVNPTQPPPNGTLSMLDFRNLLDKALSPRIPEA-NVT-APEPWKKPRITILSRAGSRAI 315 (475)
T ss_pred --EEEeeeeeeeeeecc--cccccCCcCCCccccccccHHHHHHHHhccccccc-ccC-CcChhhCCceEEEecccchhh
Confidence 999999999999996 8988888754 689999999999998643211 111 112356799999999999999
Q ss_pred cCHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHccCCEEEEechhhhhhhcccCCCcEEEEEeeCc-cccccccchHhH
Q 040560 302 TNASKIARMARRLGFKVVVAEAD-MRLSRFARIVNSCDVLLGVHGAGLANIVFLPENAVFIQVVPIA-VEWLARDYFEEP 379 (454)
Q Consensus 302 ~Ne~ev~~~l~~~gf~V~~~~~~-~s~~eq~~l~~~advlVGvHGAgLtn~lFl~pga~vIEi~P~g-~~~~~~~~y~~~ 379 (454)
+||+||.+++++.||+|.+++++ +++.+|+++.+++|||+|+|||||||++|+||++++|||.|.| .+|.+..+|..+
T Consensus 316 lne~el~~~~~~~gf~v~~~~~~~t~v~~~~~i~~s~~vmiGvHGa~lth~lfl~~~~~~iqi~pcg~~~w~a~~a~~~p 395 (475)
T KOG4698|consen 316 LNEDELPRMLEDIGFEVSVLRPDRTEVAKQLRITNSSDVMIGVHGAGLTHLLFLPPWAGVIQIYPCGDPGWAAKLARLRP 395 (475)
T ss_pred hcchhhhHHHHhCCCceEEecccccchhhhhheeeccceeeeccCccceeEEecCCcceEEEEEECCCccchhhhhhccc
Confidence 99999999999999999999996 9999999999999999999999999999999999999999999 999999999999
Q ss_pred HhhCCCeEEEEEeccccccccccCCCCCccccCchhhhhcChhhhh-hhhcCCCcEEEehhhHHHHHHHHHHHh
Q 040560 380 SKAMKLRYLEYKIKAEESTLIQQYPIDHQVVRDPSSILKMGWSAFK-SLYLDKQNVQLDLNRFGGTLLKALELL 452 (454)
Q Consensus 380 A~~~gl~Y~~y~~~~~EssL~~~y~~dh~~~~dP~~~~~~gW~~~~-~~yl~~QdV~ld~~rF~~~L~~Al~~L 452 (454)
|+.|+++|.+|++.++|++|.++|++||+++.||.+..+.||+..+ .+||..|+|++|+.||++.+.+|++..
T Consensus 396 ~k~~~l~y~~ykI~~~es~l~~~y~~d~~~v~dp~s~~~~~f~~~k~~~yl~~q~v~ld~nRf~~~~~~a~~~~ 469 (475)
T KOG4698|consen 396 AKYMTLEYAEYKIRAEESELYHKYGGDNTIVFDPISFQKKGFEETKKKVYLELQAVRLDINRFRKTLVKAYLKE 469 (475)
T ss_pred cceeccccceeEEeecccceeeeccCCCceecccceeccccceeeeeeeeEeEeeeehhhhhcccchhHHHHHH
Confidence 9999999999999999999999999999999999999999999988 899999999999999999999998764
No 2
>PF04577 DUF563: Protein of unknown function (DUF563); InterPro: IPR007657 This is a family of uncharacterised glycosyltransferases belonging to glycosyltransferase family 61. Sequences are further processed into a mature form.; GO: 0016757 transferase activity, transferring glycosyl groups
Probab=99.96 E-value=5e-28 Score=227.22 Aligned_cols=198 Identities=24% Similarity=0.431 Sum_probs=145.1
Q ss_pred cccchhhhhhHHHHHHhhhcc--CCceEEEEeCCCCCchhHH-HHHHHhhcC-CCccccCCcCCCCceeecCceEEeccc
Q 040560 165 GNHFHDFTDIIVPLYLTSRQF--NGEVQFLVTNKKYDWIDKF-RELLQKLSN-HDIIDVDQENDIGKVHCFRGGIIGLKA 240 (454)
Q Consensus 165 ~N~~H~~~D~liPLf~t~~~f--~~~vqlli~d~~p~w~~ky-~~ll~~lS~-~~vidl~~~~~~g~~~CF~~aiVGl~~ 240 (454)
.|++|++.|++ |.+.+++++ ..+..+++.+.. ...+| .++|+.|+- .+.+.+... + ..||++++++...
T Consensus 1 ~~~gH~l~d~l-~~l~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~l~~lg~~~~~i~~~~~-~---~~~~~~l~~~~~~ 73 (206)
T PF04577_consen 1 NNFGHFLIDFL-PRLWYLPQYIPDSDIIILVPDDF--DNPPFIREILELLGIPENRIKIDSD-E---PVCFERLIVPSPP 73 (206)
T ss_pred CCCcEEHHHHH-HHHHHHHHHCCCCCeEEEEcCCc--cccHHHHHHHHHcCCCccEEEEcCC-C---eEEECEEEEeCCC
Confidence 47889999999 555777765 344456666521 12233 477776663 333322222 3 8999999997754
Q ss_pred ccCccccccCCCCCccHHHHHHHHHhhhcCCcccchhcccccccCCCcEEEEEEe--CCCccccCHHHHHHHHHHcCCEE
Q 040560 241 HDQKELIIDPSKSSYTMTDFKQFLRSCYSLQKSTAITINNKESKKKMPRLLIISR--KRTRTFTNASKIARMARRLGFKV 318 (454)
Q Consensus 241 h~~~~l~idp~~~p~si~~F~~flr~~y~L~r~~~~~i~~~~~~~~~prl~~i~R--~~~R~i~Ne~ev~~~l~~~gf~V 318 (454)
.. .+...+.....|++++++.++++. ..+||++|++| ++.|+|.||+|+++.+++.||++
T Consensus 74 ~~------~~~~~~~~~~~~~~~~~~~~~~~~------------~~~p~i~~i~R~~~~~R~i~Ne~el~~~l~~~~~~~ 135 (206)
T PF04577_consen 74 YS------PSDFNPSFFPALRDRIRRKLNLPP------------PKRPRILYISRRKSGSRRILNEDELLEILKKYGFEV 135 (206)
T ss_pred cc------ccCcCchHHHHHHHHHHHHhCCcc------------cCCCeEEEEecCCCCCCcCcCHHHHHHHHhhCCeEE
Confidence 31 111112233378888888776532 24679999999 57999999999999999999887
Q ss_pred EEEeCCCCHHHHHHHHccCCEEEEechhhhhhhcccCCCcEEEEEeeCccccccccchHhHHhhCCCeEEEEE
Q 040560 319 VVAEADMRLSRFARIVNSCDVLLGVHGAGLANIVFLPENAVFIQVVPIAVEWLARDYFEEPSKAMKLRYLEYK 391 (454)
Q Consensus 319 ~~~~~~~s~~eq~~l~~~advlVGvHGAgLtn~lFl~pga~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y~~y~ 391 (454)
+-.+ ++|+.||++++++||++||+|||||+|++|||||+.||||.|.... ...|..+|+.+|++|..+.
T Consensus 136 v~~~-~~s~~eqv~~~~~a~viig~hGs~l~n~~F~~~~s~viei~~~~~~---~~~~~~~a~~~~~~y~~v~ 204 (206)
T PF04577_consen 136 VDPE-DLSFEEQVKLFASAKVIIGPHGSALTNLLFMPPGSTVIEIFPPNYY---NRHYRNLAQALGIHYYAVY 204 (206)
T ss_pred EeCC-CCCHHHHHHHhcCCCEEEecCchHhheeeecCCCCEEEEEeCCCCC---CHHHHHHHHHcCCeEEEEe
Confidence 5433 8999999999999999999999999999999999999999876522 2349999999999998754
No 3
>COG4421 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism]
Probab=99.78 E-value=4.1e-18 Score=169.25 Aligned_cols=272 Identities=19% Similarity=0.268 Sum_probs=163.7
Q ss_pred CCccC---CCCCccceeeeCcEEeeCCceEEEEecCCCCCCCCCceeeCCCccCCcccccCceeeEEEEEecCCCCCCCC
Q 040560 71 PSYCS---TTQRSEFCDIKDDIRIEASSGTVFISSSEAAGINNRSWIIRPYARKADSTAMNWVRKWAVKSVTNRQELPKC 147 (454)
Q Consensus 71 ~~~C~---~~~r~d~C~~~gdvr~~~~~~tv~~~~~~~~~~~~~~~~i~Py~Rk~~~~~m~~v~e~~~~~~~~~~~~p~C 147 (454)
.++|- .+.++-+|-+.=-+-+.+...+. ..+.+- ..+.+--+|.--++ |+.=.-|...+ .++|
T Consensus 52 p~v~~~g~~~a~~v~~~~~~~vvvg~~gq~~-~l~d~~----~~~~~ad~~~~~h~------~~~~~~Rl~~~-edAp-- 117 (368)
T COG4421 52 PSVCEPGPFYAASVWQPPCFGVVVGLYGQTL-LLPDSF----AHETSADLHAAPHD------VKTGGYRLKRP-EDAP-- 117 (368)
T ss_pred CccCCCcccccccccccccceEEEecCccee-cCcHHh----hhccCCChhhCccc------cccCceeecCC-cCCC--
Confidence 45776 35678888887666665544333 332221 12222222222211 11111111112 3445
Q ss_pred ceeecccEEEEEcCCcccccchhhhhhHHHHHHhhhccC--CceEEEEeCCCCCchhHHHHHHHhhc-CCCccccCCcCC
Q 040560 148 TQNHGVPAILFSNGGYAGNHFHDFTDIIVPLYLTSRQFN--GEVQFLVTNKKYDWIDKFRELLQKLS-NHDIIDVDQEND 224 (454)
Q Consensus 148 ~~~h~~Pavvfs~~gy~~N~~H~~~D~liPLf~t~~~f~--~~vqlli~d~~p~w~~ky~~ll~~lS-~~~vidl~~~~~ 224 (454)
+-+.- .||.-.|+..||-|++.|.| |..+.++..+ .+-.++.....+ |. .+++..+. +.++|.. ..
T Consensus 118 --~L~r~-~v~~~~~~~~~Yghflle~L-p~l~~i~~l~i~~~~pLl~P~~~~-wq---adll~m~~~~~~ii~~---~p 186 (368)
T COG4421 118 --RLPRG-AVFKEWGFSFEYGHFLLENL-PYLWQIKSLGILSDPPLLYPRLTE-WQ---ADLLFMAGPDCPIIAT---AP 186 (368)
T ss_pred --cCCCc-ceecccccccccchhHHhhh-HHHHHHhhhcccccCcccCCcchH-HH---HhHHhhcCCCCceeec---cc
Confidence 33333 44555667899999999999 6655555442 222233333333 32 36676555 4555554 22
Q ss_pred CCceeecCceEEecccccCccccccCCCCCccHHHHHHHHHhhhcCCcccchhcccccccCCCcEEEEEEeC--CCcccc
Q 040560 225 IGKVHCFRGGIIGLKAHDQKELIIDPSKSSYTMTDFKQFLRSCYSLQKSTAITINNKESKKKMPRLLIISRK--RTRTFT 302 (454)
Q Consensus 225 ~g~~~CF~~aiVGl~~h~~~~l~idp~~~p~si~~F~~flr~~y~L~r~~~~~i~~~~~~~~~prl~~i~R~--~~R~i~ 302 (454)
.+|-..+++.... +| .-+++++... ..|..... .+...++.+||||+ ..|+++
T Consensus 187 ---~V~~~~avl~~~~--------s~-------~~~ha~l~~~--~eR~~~~~-----~~~~~adkiYVSR~~qS~R~lv 241 (368)
T COG4421 187 ---AVPLGPAVLPVSG--------SP-------RYTHALLAWK--DERVIAIK-----GKGKVADKIYVSRKAQSMRVLV 241 (368)
T ss_pred ---ceeecccccCCCC--------Cc-------hhhhHHHHHH--hhhhhccc-----CCCCCcceEEEechhhHHHHhh
Confidence 5565554432211 11 1234444322 23332211 23567889999997 379999
Q ss_pred CHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEechhhhhhhcccCCCcEEEEEeeCccccccccchHhHHhh
Q 040560 303 NASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHGAGLANIVFLPENAVFIQVVPIAVEWLARDYFEEPSKA 382 (454)
Q Consensus 303 Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHGAgLtn~lFl~pga~vIEi~P~g~~~~~~~~y~~~A~~ 382 (454)
||+|+.+.+++.||.++..| +++..||+++|+.|.|+||.||+||.|++|+++|+.||||.|--.+. +..+-..+.-
T Consensus 242 nE~evE~~~q~~G~~IVrPE-tl~~~eQ~~LFr~AkvIvG~~GS~laNavF~~~~~kvvEI~~~~~~~--~s~~vr~~~~ 318 (368)
T COG4421 242 NEEEVERLLQRSGLTIVRPE-TLGPREQARLFRKAKVIVGPHGSGLANAVFAAPGCKVVEIQPGTTNF--RSFWVRMANY 318 (368)
T ss_pred CHHHHHHHHHhcCcEEEech-hcCHHHHHHHhhcceEEeccccchhhhheecCCCceEEEeccCCCcc--hHHHHHHhhh
Confidence 99999999999999997655 89999999999999999999999999999999999999999933222 3455555666
Q ss_pred CCCeEEEEEeccc
Q 040560 383 MKLRYLEYKIKAE 395 (454)
Q Consensus 383 ~gl~Y~~y~~~~~ 395 (454)
|+..|..+.+.+.
T Consensus 319 ~~g~~~~~~ve~q 331 (368)
T COG4421 319 MSGDYYPGYVEHQ 331 (368)
T ss_pred cccceeecccccC
Confidence 6655555555443
No 4
>cd05212 NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding domain of methylene-tetrahydrofolate dehydrogenase and methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NAD(P) binding domains of methylene-tetrahydrofolate dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional
Probab=79.05 E-value=6.4 Score=35.68 Aligned_cols=69 Identities=16% Similarity=0.209 Sum_probs=50.8
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEechhh-hhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHGAG-LANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHGAg-Ltn~lFl~pga~vIE 362 (454)
.-+++++.|+. ..-..+..+|.+.|..|.+.+. +-++.| .+++|||+|..=|.. +-..=|++||++||-
T Consensus 28 gk~v~VvGrs~----~vG~pla~lL~~~gatV~~~~~~t~~l~~---~v~~ADIVvsAtg~~~~i~~~~ikpGa~Vid 98 (140)
T cd05212 28 GKKVLVVGRSG----IVGAPLQCLLQRDGATVYSCDWKTIQLQS---KVHDADVVVVGSPKPEKVPTEWIKPGATVIN 98 (140)
T ss_pred CCEEEEECCCc----hHHHHHHHHHHHCCCEEEEeCCCCcCHHH---HHhhCCEEEEecCCCCccCHHHcCCCCEEEE
Confidence 45788888764 4455777788888999988875 335554 578899999988765 334457999999984
No 5
>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molec
Probab=72.59 E-value=7.4 Score=40.30 Aligned_cols=97 Identities=13% Similarity=0.203 Sum_probs=70.2
Q ss_pred CCCcEEEEEEeCC-CccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEe---chhhhhhhcccCCCcE
Q 040560 285 KKMPRLLIISRKR-TRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGV---HGAGLANIVFLPENAV 359 (454)
Q Consensus 285 ~~~prl~~i~R~~-~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGv---HGAgLtn~lFl~pga~ 359 (454)
..++.+-+|.-.. .. -|.+|+.+.+++.|++|..+-+ +.+++|. +-+.+|++-|.+ +|..++..|=-+-|.-
T Consensus 150 ~~~~~vNlig~~~~~~--~d~~el~~ll~~~G~~v~~~~~~~~s~~~i-~~~~~A~~nlv~~~~~g~~~a~~l~~~~g~p 226 (399)
T cd00316 150 TEPGSVNLIGGYNLGG--GDLRELKRLLEEMGIRVNALFDGGTTVEEL-RELGNAKLNLVLCRESGLYLARYLEEKYGIP 226 (399)
T ss_pred CCCCcEEEECCCCCch--hhHHHHHHHHHHcCCcEEEEcCCCCCHHHH-HhhccCcEEEEecHhHHHHHHHHHHHHhCCC
Confidence 3456677776542 11 5889999999999999987765 5777554 456777877777 5677777775566777
Q ss_pred EEEEeeCccccccccchHhHHhhCCC
Q 040560 360 FIQVVPIAVEWLARDYFEEPSKAMKL 385 (454)
Q Consensus 360 vIEi~P~g~~~~~~~~y~~~A~~~gl 385 (454)
.+...|+|++- ...+++.+++.+|+
T Consensus 227 ~~~~~p~G~~~-t~~~l~~i~~~~g~ 251 (399)
T cd00316 227 YILINPIGLEA-TDAFLRKLAELFGI 251 (399)
T ss_pred eEEeCCcCHHH-HHHHHHHHHHHhCC
Confidence 77777999654 35789999999995
No 6
>cd01971 Nitrogenase_VnfN_like Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like. This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protien for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.
Probab=71.89 E-value=6.8 Score=41.67 Aligned_cols=99 Identities=13% Similarity=0.124 Sum_probs=69.1
Q ss_pred CCcEEEEEEeCC---CccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEec---hhhhhhhcccCCCc
Q 040560 286 KMPRLLIISRKR---TRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVH---GAGLANIVFLPENA 358 (454)
Q Consensus 286 ~~prl~~i~R~~---~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvH---GAgLtn~lFl~pga 358 (454)
.++++-+|.... .-.--|.+|+.+.|++.|+++..+-+ +.++ ++++-+.+|.+-|.++ |-..+..|.-+=|.
T Consensus 154 ~~~~VNiiG~~~~~~~~~~~d~~elk~lL~~~Gl~v~~~~~~~~~~-~ei~~~~~A~~niv~~~~~g~~~a~~L~~~~gi 232 (427)
T cd01971 154 EPGLVNLWGPVPYQDPFWRGDLEEIKRVLEGIGLKVNILFGPESNG-EELRSIPKAQFNLVLSPWVGLEFAQHLEEKYGQ 232 (427)
T ss_pred CCCeEEEEeccCCccccccccHHHHHHHHHHCCCeEEEEECCCCCH-HHHHhcccCcEEEEEcHhhHHHHHHHHHHHhCC
Confidence 355676775431 11225789999999999999977755 6676 7777788888655555 44566666656677
Q ss_pred EEEEE--eeCccccccccchHhHHhhCCCe
Q 040560 359 VFIQV--VPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 359 ~vIEi--~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
-.+.. .|+|++- ...++..+++.+|+.
T Consensus 233 P~i~~~~~P~G~~~-t~~~l~~i~~~~g~~ 261 (427)
T cd01971 233 PYIHSPTLPIGAKA-TAEFLRQVAKFAGIE 261 (427)
T ss_pred ceEecCCCccCHHH-HHHHHHHHHHHhCCC
Confidence 67766 7999643 346788999998864
No 7
>PF02882 THF_DHG_CYH_C: Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain; InterPro: IPR020631 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the NAD(P)-binding domain found in these enzymes.; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 1B0A_A 2C2X_B 2C2Y_A 3NGL_C 3NGX_A 4A26_B 1EDZ_A 1EE9_A 3P2O_B 1DIA_A ....
Probab=69.24 E-value=14 Score=34.24 Aligned_cols=70 Identities=19% Similarity=0.338 Sum_probs=45.4
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+. .=..-+..+|.+.|..|.+... +..+.+ ...+|||+|..-| +++-..=|.+||++||-+
T Consensus 36 Gk~v~VvGrs~----~VG~Pla~lL~~~~atVt~~h~~T~~l~~---~~~~ADIVVsa~G~~~~i~~~~ik~gavVIDv 107 (160)
T PF02882_consen 36 GKKVVVVGRSN----IVGKPLAMLLLNKGATVTICHSKTKNLQE---ITRRADIVVSAVGKPNLIKADWIKPGAVVIDV 107 (160)
T ss_dssp T-EEEEE-TTT----TTHHHHHHHHHHTT-EEEEE-TTSSSHHH---HHTTSSEEEE-SSSTT-B-GGGS-TTEEEEE-
T ss_pred CCEEEEECCcC----CCChHHHHHHHhCCCeEEeccCCCCcccc---eeeeccEEeeeeccccccccccccCCcEEEec
Confidence 34788998874 2223567778888999988775 444555 4578999998887 677777899999999975
No 8
>COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]
Probab=67.78 E-value=8.3 Score=37.93 Aligned_cols=48 Identities=13% Similarity=0.301 Sum_probs=42.5
Q ss_pred EEEEEEeCC------CccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccC
Q 040560 289 RLLIISRKR------TRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSC 337 (454)
Q Consensus 289 rl~~i~R~~------~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~a 337 (454)
-+.||+|++ +..|.|.+.+.+..+++|++|+.++ +.++++.++.+.++
T Consensus 173 LiaivD~N~~QldG~t~~i~~~~pL~~k~eAFGw~V~evd-G~d~~~i~~a~~~~ 226 (243)
T COG3959 173 LIAIVDRNKLQLDGETEEIMPKEPLADKWEAFGWEVIEVD-GHDIEEIVEALEKA 226 (243)
T ss_pred EEEEEecCCcccCCchhhccCcchhHHHHHhcCceEEEEc-CcCHHHHHHHHHhh
Confidence 578899995 7999999999999999999999888 78899988887765
No 9
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=66.80 E-value=22 Score=35.98 Aligned_cols=72 Identities=17% Similarity=0.250 Sum_probs=52.5
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEEe
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQVV 364 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi~ 364 (454)
.-+++++.|+.. --.-+..++...|..|.+..... ....+.+.+||++|+.=| +++-..=+.+||++||.+-
T Consensus 152 Gk~V~ViGrs~~----vGrpla~lL~~~~atVtv~hs~t--~~L~~~~~~ADIvI~Avgk~~lv~~~~vk~GavVIDVg 224 (279)
T PRK14178 152 GKRAVVVGRSID----VGRPMAALLLNADATVTICHSKT--ENLKAELRQADILVSAAGKAGFITPDMVKPGATVIDVG 224 (279)
T ss_pred CCEEEEECCCcc----ccHHHHHHHHhCCCeeEEEecCh--hHHHHHHhhCCEEEECCCcccccCHHHcCCCcEEEEee
Confidence 458889988742 22356667777899988776421 233446688999999998 7777777789999999974
No 10
>cd01080 NAD_bind_m-THF_DH_Cyclohyd NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well a
Probab=63.02 E-value=17 Score=33.90 Aligned_cols=73 Identities=14% Similarity=0.161 Sum_probs=50.3
Q ss_pred CCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEechhhh-hhhcccCCCcEEEEEe
Q 040560 286 KMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHGAGL-ANIVFLPENAVFIQVV 364 (454)
Q Consensus 286 ~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHGAgL-tn~lFl~pga~vIEi~ 364 (454)
...++++|..... =...+++.|.+.|.+|.+.+ -+..+..+.++.|||+|+.-|+.- -..=.+++|.++|.+-
T Consensus 43 ~gk~vlViG~G~~----~G~~~a~~L~~~g~~V~v~~--r~~~~l~~~l~~aDiVIsat~~~~ii~~~~~~~~~viIDla 116 (168)
T cd01080 43 AGKKVVVVGRSNI----VGKPLAALLLNRNATVTVCH--SKTKNLKEHTKQADIVIVAVGKPGLVKGDMVKPGAVVIDVG 116 (168)
T ss_pred CCCEEEEECCcHH----HHHHHHHHHhhCCCEEEEEE--CCchhHHHHHhhCCEEEEcCCCCceecHHHccCCeEEEEcc
Confidence 4568888887621 01135677777899887776 345677789999999999999952 1111257788888875
No 11
>cd01967 Nitrogenase_MoFe_alpha_like Nitrogenase_MoFe_alpha_like: Nitrogenase MoFe protein, alpha subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. Three genetically distinct types of nitrogenase systems are known to exist: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). This group contains the alpha subunit of component 1 of all three different forms. The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having alpha and beta subunits similar to the alpha and beta subunits of MoFe. The role of the delta subunit is unknown. For MoFe, each alphabeta pair of subunits contains one
Probab=62.57 E-value=34 Score=35.72 Aligned_cols=96 Identities=16% Similarity=0.037 Sum_probs=66.5
Q ss_pred CCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEec---hhhhhhhcccCCCcEEE
Q 040560 286 KMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVH---GAGLANIVFLPENAVFI 361 (454)
Q Consensus 286 ~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvH---GAgLtn~lFl~pga~vI 361 (454)
.+..+-||.-.. ..-|..|+.+.|++.|+++..+-+ +.+++|.-+ +.+|.+-|.+. |-.++..|-=+-|.-.+
T Consensus 159 ~~~~VNiig~~~--~~~d~~el~~lL~~~Gi~~~~~~~~~~~~~~i~~-~~~A~~niv~~~~~~~~~a~~L~~r~GiP~~ 235 (406)
T cd01967 159 TPYDVNIIGEYN--IGGDAWVIKPLLEELGIRVNATFTGDGTVDELRR-AHRAKLNLVHCSRSMNYLAREMEERYGIPYM 235 (406)
T ss_pred CCCeEEEEeccc--cchhHHHHHHHHHHcCCEEEEEeCCCCCHHHHhh-CccCCEEEEEChHHHHHHHHHHHHhhCCCEE
Confidence 455677776432 234889999999999999987666 678866554 78888766654 44455545444566566
Q ss_pred EEeeCccccccccchHhHHhhCCC
Q 040560 362 QVVPIAVEWLARDYFEEPSKAMKL 385 (454)
Q Consensus 362 Ei~P~g~~~~~~~~y~~~A~~~gl 385 (454)
...|+|++- ...+++.+++.+|.
T Consensus 236 ~~~p~G~~~-t~~~l~~l~~~lg~ 258 (406)
T cd01967 236 EVNFYGFED-TSESLRKIAKFFGD 258 (406)
T ss_pred EecCCcHHH-HHHHHHHHHHHhCC
Confidence 778888653 34678899999886
No 12
>PF00148 Oxidored_nitro: Nitrogenase component 1 type Oxidoreductase; InterPro: IPR000510 Enzymes belonging to this family include cofactor-requiring nitrogenases and protochlorophyllide reductase. The key enzymatic reactions in nitrogen fixation are catalysed by the nitrogenase complex, which has two components, the iron protein (component 2), and a component (component 1) which is either a molybdenum-iron, vanadium-iron or iron-iron protein. The enzyme (1.18.6.1 from EC) forms a hexamer of two alpha, two beta and two delta chains. Protochlorophyllide reductase (1.3.1.33 from EC) is involved in the light-dependent accumulation of chlorophyll, probably at the step of reduction of protochlorophyllide to chlorophyllide.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QH1_C 1QH8_A 1H1L_C 1QGU_A 3AEK_C 3AET_C 3AER_C 3AEU_A 3AES_C 3AEQ_C ....
Probab=60.13 E-value=16 Score=38.08 Aligned_cols=97 Identities=16% Similarity=0.194 Sum_probs=70.4
Q ss_pred CCCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEechhhhh-hhcccCC--CcEE
Q 040560 285 KKMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHGAGLA-NIVFLPE--NAVF 360 (454)
Q Consensus 285 ~~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHGAgLt-n~lFl~p--ga~v 360 (454)
..++.+-+|.....- .-|.+|+.+.|+++|++|...-+ ..+++| ++-+.+|++-|.++..+.. =.=+|.. |.-.
T Consensus 142 ~~~~~VNiiG~~~~~-~~d~~el~~lL~~~Gi~v~~~~~~~~t~~e-~~~~~~A~lniv~~~~~~~~~a~~L~e~~giP~ 219 (398)
T PF00148_consen 142 KKPRSVNIIGGSPLG-PGDLEELKRLLEELGIEVNAVFPGGTTLEE-IRKAPEAALNIVLCPEGGPYAAEWLEERFGIPY 219 (398)
T ss_dssp TSSSEEEEEEESTBT-HHHHHHHHHHHHHTTEEEEEEEETTBCHHH-HHHGGGSSEEEESSCCHHHHHHHHHHHHHT-EE
T ss_pred CCCCceEEecCcCCC-cccHHHHHHHHHHCCCceEEEeCCCCCHHH-HHhCCcCcEEEEeccchhhHHHHHHHHHhCCCe
Confidence 345577778765311 27888999999999999887765 677754 5567888999999888665 4445544 7777
Q ss_pred EE-EeeCccccccccchHhHHhhCC
Q 040560 361 IQ-VVPIAVEWLARDYFEEPSKAMK 384 (454)
Q Consensus 361 IE-i~P~g~~~~~~~~y~~~A~~~g 384 (454)
+. -.|+|++.. ..+|+.+++.+|
T Consensus 220 ~~~~~p~G~~~t-~~~l~~i~~~lg 243 (398)
T PF00148_consen 220 LYFPSPYGIEGT-DAWLRAIAEALG 243 (398)
T ss_dssp EEEC-SBSHHHH-HHHHHHHHHHHT
T ss_pred eeccccccHHHH-HHHHHHHHHHhC
Confidence 77 779997653 578999999999
No 13
>PF01520 Amidase_3: N-acetylmuramoyl-L-alanine amidase; InterPro: IPR002508 The cell wall envelope of Gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows Gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialised binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections []. Autolysin 3.5.1.28 from EC hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell wall glycopeptides.; GO: 0008745 N-acetylmuramoyl-L-alanine amidase activity, 0009253 peptidoglycan catabolic process; PDB: 3QAY_A 3CZX_A 1JWQ_A 1XOV_A 3NE8_A.
Probab=60.00 E-value=17 Score=32.99 Aligned_cols=44 Identities=18% Similarity=0.320 Sum_probs=32.9
Q ss_pred HHHHHHHcCCEEEEEeC---CCCHHHHHHHH--ccCCEEEEechhhhhh
Q 040560 307 IARMARRLGFKVVVAEA---DMRLSRFARIV--NSCDVLLGVHGAGLAN 350 (454)
Q Consensus 307 v~~~l~~~gf~V~~~~~---~~s~~eq~~l~--~~advlVGvHGAgLtn 350 (454)
|.+.|++.|++|..... ..++.+.++.. ..+|++|+.|--+-.+
T Consensus 33 l~~~L~~~g~~V~~tr~~d~~~~l~~R~~~an~~~ad~~isiH~na~~~ 81 (175)
T PF01520_consen 33 LKKELEKHGIKVYLTRDNDSDVSLQERAALANSWGADLFISIHFNASNG 81 (175)
T ss_dssp HHHHHHHTTEEEEESSSSSHCCCHHHHHHHHHHTTSSEEEEEEEE-SSS
T ss_pred HHHHHhcCCcEEEEeCCCCCCCCHHHHHHHHHhcccCEEEEEeecCccC
Confidence 34556667999887665 46899988888 7899999999665533
No 14
>cd01972 Nitrogenase_VnfE_like Nitrogenase_VnfE_like: VnfE subunit of the VnfEN complex_like. This group in addition to VnfE contains a subset of the alpha subunit of the nitrogenase MoFe protein and NifE-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protein for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.
Probab=59.14 E-value=21 Score=37.96 Aligned_cols=98 Identities=16% Similarity=0.183 Sum_probs=66.6
Q ss_pred CCcEEEEEEeCCC--cc-ccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hh--hhhhcccCCCc
Q 040560 286 KMPRLLIISRKRT--RT-FTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AG--LANIVFLPENA 358 (454)
Q Consensus 286 ~~prl~~i~R~~~--R~-i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-Ag--Ltn~lFl~pga 358 (454)
.++.+=+|.-... +. --|..|+.+.|++.|++|+.+-+ +.+++|. +-+.+|.+-|.++. +| ++..|-=+=|.
T Consensus 160 ~~~~VNliG~~~~~~~~~~~d~~ei~~lL~~~Gi~v~~~~~~~~~~~ei-~~~~~A~lniv~~~~~g~~~a~~Lee~~Gi 238 (426)
T cd01972 160 QEDSVNIIGLWGGPERTEQEDVDEFKRLLNELGLRVNAIIAGGCSVEEL-ERASEAAANVTLCLDLGYYLGAALEQRFGV 238 (426)
T ss_pred CCCCEEEEccCCCccccccccHHHHHHHHHHcCCeEEEEeCCCCCHHHH-HhcccCCEEEEEChhHHHHHHHHHHHHhCC
Confidence 3456666654431 11 36779999999999999987766 5777655 45788888888774 44 44444334566
Q ss_pred EEEEE-eeCccccccccchHhHHhhCCC
Q 040560 359 VFIQV-VPIAVEWLARDYFEEPSKAMKL 385 (454)
Q Consensus 359 ~vIEi-~P~g~~~~~~~~y~~~A~~~gl 385 (454)
-.+++ +|+|++- ...++..+|+.+|+
T Consensus 239 P~~~~~~P~G~~~-T~~~l~~ia~~~g~ 265 (426)
T cd01972 239 PEIKAPQPYGIEA-TDKWLREIAKVLGM 265 (426)
T ss_pred CeEecCCccCHHH-HHHHHHHHHHHhCC
Confidence 67776 6899642 34678888888886
No 15
>cd02696 MurNAc-LAA N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs
Probab=58.11 E-value=26 Score=31.86 Aligned_cols=45 Identities=29% Similarity=0.449 Sum_probs=35.1
Q ss_pred HHHHHHHHcCCEEEEEeC---CCCHHHHHHHHcc--CCEEEEechhhhhh
Q 040560 306 KIARMARRLGFKVVVAEA---DMRLSRFARIVNS--CDVLLGVHGAGLAN 350 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~---~~s~~eq~~l~~~--advlVGvHGAgLtn 350 (454)
.+.+.|++.|++|..... ..++.+.++..+. +|++|..|-.+-.+
T Consensus 33 ~l~~~L~~~G~~v~~~r~~~~~~~l~~r~~~an~~~~d~~islH~na~~~ 82 (172)
T cd02696 33 KLAKLLEAAGAKVVLTRDDDTFVSLSERVAIANRAGADLFISIHANAAPN 82 (172)
T ss_pred HHHHHHHHCCCEEEEEecCCCCCCHHHHHHHHHhcCCCEEEEEeecCCCC
Confidence 344555666999987776 2689999998886 99999999877766
No 16
>PF05222 AlaDh_PNT_N: Alanine dehydrogenase/PNT, N-terminal domain; InterPro: IPR007886 Alanine dehydrogenases (1.4.1.1 from EC) and pyridine nucleotide transhydrogenase (1.6.1.1 from EC) have been shown to share regions of similarity []. Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. Pyridine nucleotide transhydrogenase catalyzes the reduction of NADP+ to NADPH with the concomitant oxidation of NADH to NAD+. This enzyme is located in the plasma membrane of prokaryotes and in the inner membrane of the mitochondria of eukaryotes. The transhydrogenation between NADH and NADP is coupled with the translocation of a proton across the membrane. In prokaryotes the enzyme is composed of two different subunits, an alpha chain (gene pntA) and a beta chain (gene pntB), while in eukaryotes it is a single chain protein. The sequence of alanine dehydrogenase from several bacterial species are related with those of the alpha subunit of bacterial pyridine nucleotide transhydrogenase and of the N-terminal half of the eukaryotic enzyme. The two most conserved regions correspond respectively to the N-terminal extremity of these proteins, represented in this entry, and to a central glycine-rich region which is part of the NAD(H)-binding site.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1X15_A 2BRU_A 1X14_B 1X13_A 2EEZ_F 2VOE_F 2VHV_B 2VHY_A 2VHX_A 2VHW_A ....
Probab=57.72 E-value=57 Score=29.21 Aligned_cols=91 Identities=14% Similarity=0.211 Sum_probs=53.1
Q ss_pred CccccCHHHHHHHHHHcCCEEEEEeC-C--CCHHH-------------HHHHHccCCEEEEechhhhhhhcccCCCcEEE
Q 040560 298 TRTFTNASKIARMARRLGFKVVVAEA-D--MRLSR-------------FARIVNSCDVLLGVHGAGLANIVFLPENAVFI 361 (454)
Q Consensus 298 ~R~i~Ne~ev~~~l~~~gf~V~~~~~-~--~s~~e-------------q~~l~~~advlVGvHGAgLtn~lFl~pga~vI 361 (454)
-||+-=..+.++.|.+.|++|.+-.. + ..|.+ .-+++..||||+++..-...-.-.|++|.++|
T Consensus 10 E~RVal~P~~v~~L~~~G~~V~VE~gaG~~a~fsD~~Y~~aGA~I~~~~~ev~~~adiIl~v~~p~~~e~~~l~~g~~li 89 (136)
T PF05222_consen 10 ERRVALTPEDVKKLVKLGHEVLVESGAGEGAGFSDEEYEEAGAEIVSRAEEVYSDADIILKVKPPSEEELALLKPGQTLI 89 (136)
T ss_dssp ---BSS-HHHHHHHHHTTSEEEEETTTTGGGTB-HHHHHHTTEEEESSHHHHHTTSSEEEESS---GGGGGGS-TTCEEE
T ss_pred CcEecccHHHHHHHHhCCCEEEEECCCCCcCcccHHHHhhCCcEEecCchhhcccCCEEEEECCCCHHHHhhcCCCcEEE
Confidence 34544456667777777999875443 1 22322 12678899999999999999999999999999
Q ss_pred EEeeCccccccccchHhHHhhCCCeEEEEEe
Q 040560 362 QVVPIAVEWLARDYFEEPSKAMKLRYLEYKI 392 (454)
Q Consensus 362 Ei~P~g~~~~~~~~y~~~A~~~gl~Y~~y~~ 392 (454)
=+.-.. .+...-.-....|+..+.|..
T Consensus 90 ~~~~~~----~~~~~~~~l~~~~it~~a~E~ 116 (136)
T PF05222_consen 90 GFLHPA----QNKELLEALAKKGITAFALEL 116 (136)
T ss_dssp EE--GG----GHHHHHHHHHHCTEEEEEGGG
T ss_pred Eeeccc----cCHHHHHHHHHCCCEEEEhhh
Confidence 766432 112222334446888777653
No 17
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=56.37 E-value=30 Score=37.86 Aligned_cols=100 Identities=14% Similarity=0.212 Sum_probs=71.9
Q ss_pred CCCcEEEEEEeC--CCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCC--Cc
Q 040560 285 KKMPRLLIISRK--RTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPE--NA 358 (454)
Q Consensus 285 ~~~prl~~i~R~--~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~p--ga 358 (454)
..++.+-||.=. +.+.--|..|+.+.|++.|.+|..+-+ +.++ ++++-+.+|++-|.+++ .|..=.-+|.. |.
T Consensus 156 ~~~~~VNIiG~~~l~f~~~~D~~EikrlL~~~Gi~vn~v~p~g~s~-~di~~l~~A~~nivl~~~~g~~~A~~Lee~fGi 234 (519)
T PRK02910 156 TARPSVNLLGPTALGFHHRDDLTELRRLLATLGIDVNVVAPLGASP-ADLKRLPAAWFNVVLYREIGESAARYLEREFGQ 234 (519)
T ss_pred CCCCeEEEEecCccCCCChhHHHHHHHHHHHcCCeEEEEeCCCCCH-HHHHhcccCcEEEEeCHHHHHHHHHHHHHHhCC
Confidence 346777777643 345557888999999999999988776 6676 55666788999888887 56555555543 45
Q ss_pred EEEEEeeCccccccccchHhHHhhCCCe
Q 040560 359 VFIQVVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 359 ~vIEi~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
-.+...|+|++- ...+-..+++.+|+.
T Consensus 235 P~i~~~PiG~~~-T~~fL~~la~~~g~~ 261 (519)
T PRK02910 235 PYVKTVPIGVGA-TARFIREVAELLNLD 261 (519)
T ss_pred cccccccccHHH-HHHHHHHHHHHhCCC
Confidence 556779999643 346778888888864
No 18
>cd01981 Pchlide_reductase_B Pchlide_reductase_B: B protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=55.79 E-value=45 Score=35.33 Aligned_cols=99 Identities=13% Similarity=0.156 Sum_probs=70.3
Q ss_pred CCcEEEEEEeC--CCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEec---hhhhhhhcccCCCcE
Q 040560 286 KMPRLLIISRK--RTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVH---GAGLANIVFLPENAV 359 (454)
Q Consensus 286 ~~prl~~i~R~--~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvH---GAgLtn~lFl~pga~ 359 (454)
.++++-+|.-. +...--|..|+.+.|++.|.+|..+-+ +.+++|. +-+.+|++-|.++ |..++..|--.=|.-
T Consensus 161 ~~~~VNiiG~~~~~~~~~~d~~ei~~lL~~~Gl~v~~~~~~~~~~~~i-~~~~~A~lniv~~~~~~~~~a~~L~~~~GiP 239 (430)
T cd01981 161 EKPSVNLIGPSSLGFHNRHDCRELKRLLHTLGIEVNVVIPEGASVDDL-NELPKAWFNIVPYREYGLSAALYLEEEFGMP 239 (430)
T ss_pred CCCcEEEEcCCCCCCCCcchHHHHHHHHHHcCCeEEEEEcCCCCHHHH-HhhhhCeEEEEecHHHHHHHHHHHHHHhCCC
Confidence 34566666544 234567888999999999999987665 6777554 4467777766654 455666666556766
Q ss_pred EEEEeeCccccccccchHhHHhhCCCe
Q 040560 360 FIQVVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 360 vIEi~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
.+...|+|++- ...+.+.+++.+|+.
T Consensus 240 ~~~~~p~G~~~-t~~~l~~i~~~~g~~ 265 (430)
T cd01981 240 SVKITPIGVVA-TARFLREIQELLGIQ 265 (430)
T ss_pred eEeccCCChHH-HHHHHHHHHHHhCCc
Confidence 77779999653 346788999998876
No 19
>PF00389 2-Hacid_dh: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; InterPro: IPR006139 A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related. The catalytic domain contains a number of conserved charged residues which may play a role in the catalytic mechanism. The NAD-binding domain is described in IPR006140 from INTERPRO ; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 2DLD_A 2G76_B 3DC2_B 1YGY_B 3DDN_A 3KB6_B 3K5P_A 3EVT_A 1WWK_B 1GDH_A ....
Probab=55.22 E-value=44 Score=29.11 Aligned_cols=79 Identities=16% Similarity=0.186 Sum_probs=58.5
Q ss_pred HHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEechhhhhhhcccC-CCcEEEEEeeCccccccccchHhHHhh
Q 040560 304 ASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHGAGLANIVFLP-ENAVFIQVVPIAVEWLARDYFEEPSKA 382 (454)
Q Consensus 304 e~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHGAgLtn~lFl~-pga~vIEi~P~g~~~~~~~~y~~~A~~ 382 (454)
.++.++.|++ |++|...+ ..+-++..+.+..+|++|+-++..++--++-. |+-.+|...--|++... -..|+.
T Consensus 8 ~~~~~~~l~~-~~~v~~~~-~~~~~~~~~~l~~~d~ii~~~~~~~~~~~l~~~~~Lk~I~~~~~G~d~id----~~~a~~ 81 (133)
T PF00389_consen 8 PDEEIERLEE-GFEVEFCD-SPSEEELAERLKDADAIIVGSGTPLTAEVLEAAPNLKLISTAGAGVDNID----LEAAKE 81 (133)
T ss_dssp SHHHHHHHHH-TSEEEEES-SSSHHHHHHHHTTESEEEESTTSTBSHHHHHHHTT-SEEEESSSSCTTB-----HHHHHH
T ss_pred CHHHHHHHHC-CceEEEeC-CCCHHHHHHHhCCCeEEEEcCCCCcCHHHHhccceeEEEEEcccccCccc----HHHHhh
Confidence 3567788888 88888777 67888889999999999998777677666632 88899988877765431 244778
Q ss_pred CCCeEE
Q 040560 383 MKLRYL 388 (454)
Q Consensus 383 ~gl~Y~ 388 (454)
.|+...
T Consensus 82 ~gI~V~ 87 (133)
T PF00389_consen 82 RGIPVT 87 (133)
T ss_dssp TTSEEE
T ss_pred CeEEEE
Confidence 887763
No 20
>PRK14188 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=52.44 E-value=71 Score=32.65 Aligned_cols=70 Identities=17% Similarity=0.256 Sum_probs=50.9
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|.+ .--.-++..|.+.|++|.+.+. +.+++| ..+.|||+|..=| +.+-...|++||++||.+
T Consensus 158 Gk~V~viGrs~----~mG~PmA~~L~~~g~tVtv~~~rT~~l~e---~~~~ADIVIsavg~~~~v~~~~lk~GavVIDv 229 (296)
T PRK14188 158 GLNAVVIGRSN----LVGKPMAQLLLAANATVTIAHSRTRDLPA---VCRRADILVAAVGRPEMVKGDWIKPGATVIDV 229 (296)
T ss_pred CCEEEEEcCCc----chHHHHHHHHHhCCCEEEEECCCCCCHHH---HHhcCCEEEEecCChhhcchheecCCCEEEEc
Confidence 44788898875 2223566677778999998863 445543 5568999887665 567778889999999985
No 21
>cd01980 Chlide_reductase_Y Chlide_reductase_Y : Y subunit of chlorophyllide (chlide) reductase (BchY). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=50.14 E-value=20 Score=37.94 Aligned_cols=95 Identities=12% Similarity=0.132 Sum_probs=65.2
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHH-ccCCEEEEechhhhhhhcccCCCcEEEEEee
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIV-NSCDVLLGVHGAGLANIVFLPENAVFIQVVP 365 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~-~~advlVGvHGAgLtn~lFl~pga~vIEi~P 365 (454)
++++.+|..- + -.+.+|+.+.+++.|.+++.+-++.+++|..++= +.+.+.++.++...+..|= .-|.-.+...|
T Consensus 159 ~~~vniiG~~-~--~~d~~ei~~lL~~~Gl~~~~~l~~~~~~el~~~~~A~~~i~~~~~~~~~a~~Le-~~GvP~~~~~p 234 (416)
T cd01980 159 EPSLALLGEM-F--PADPVAIGSVLERMGLAAVPVVPTREWRELYAAGDAAAVAALHPFYTATIRELE-EAGRPIVSGAP 234 (416)
T ss_pred CCeEEEEccC-C--CCCHHHHHHHHHHcCCceeeEeCCCCHHHHhhcccCcEEEEeChhHHHHHHHHH-HcCCceecCCC
Confidence 4578787532 1 3366799999999999997644467886665554 2334455566555555554 34777777789
Q ss_pred CccccccccchHhHHhhCCCe
Q 040560 366 IAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 366 ~g~~~~~~~~y~~~A~~~gl~ 386 (454)
.|++ ....+++.+|+..|..
T Consensus 235 iG~~-~td~~l~~la~~~g~~ 254 (416)
T cd01980 235 VGAD-GTAAWLEAVGEALGLD 254 (416)
T ss_pred cCch-HHHHHHHHHHHHhCcC
Confidence 9976 3467899999999964
No 22
>COG1920 Predicted nucleotidyltransferase, CobY/MobA/RfbA family [General function prediction only]
Probab=47.44 E-value=57 Score=31.52 Aligned_cols=58 Identities=16% Similarity=0.222 Sum_probs=43.7
Q ss_pred HHHHHHHHccCCEEEEechhhhhhhcccCCCcEEEEEeeCccccccccchHhH--HhhCCCeEEEEE
Q 040560 327 LSRFARIVNSCDVLLGVHGAGLANIVFLPENAVFIQVVPIAVEWLARDYFEEP--SKAMKLRYLEYK 391 (454)
Q Consensus 327 ~~eq~~l~~~advlVGvHGAgLtn~lFl~pga~vIEi~P~g~~~~~~~~y~~~--A~~~gl~Y~~y~ 391 (454)
+++.++.-.++||+|++-=-|=||++|.++ .-+++.=. .-.++.++ |+.+|+.+.-|.
T Consensus 104 i~~~~~~~~d~dvviaP~~gGGTn~L~~r~--~~~~~~y~-----g~SF~~Hl~~Ark~G~~~~~~d 163 (210)
T COG1920 104 IERALSAAKDADVVIAPGRGGGTNVLFARK--SAFRPRYG-----GVSFLRHLEEARKRGLVVLTYD 163 (210)
T ss_pred HHHHHHhcCCCcEEEecCCCCceEEEEEec--cccccccc-----CccHHHHHHHHHHcCCEEEEec
Confidence 677888889999999999999999999998 33333211 12345554 999999998775
No 23
>TIGR02883 spore_cwlD N-acetylmuramoyl-L-alanine amidase CwlD. Members of this protein family are the CwlD family of N-acetylmuramoyl-L-alanine amidase. This family has been called the germination-specific N-acetylmuramoyl-L-alanine amidase. CwlD is required, along with the putative deactylase PdaA, to make muramic delta-lactam, a novel peptidoglycan constituent found only in spores. CwlD mutants show a germination defect.
Probab=45.45 E-value=55 Score=30.67 Aligned_cols=45 Identities=20% Similarity=0.409 Sum_probs=32.0
Q ss_pred HHHHHHHHcCCEEEEEeC-CC----------------CHHHHHHHHc--cCCEEEEechhhhhh
Q 040560 306 KIARMARRLGFKVVVAEA-DM----------------RLSRFARIVN--SCDVLLGVHGAGLAN 350 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~-~~----------------s~~eq~~l~~--~advlVGvHGAgLtn 350 (454)
.|.+.|++.|++|+.... +. ++.+.+++.+ .||++|++|--+..+
T Consensus 34 ~l~~~L~~~G~~V~ltr~~d~~~~~~~~~~~~~~~~~~L~~R~~~An~~~adlfiSiH~Na~~~ 97 (189)
T TIGR02883 34 KLKDYLQEQGALVVMTREDDSDLASEGTKGYSRRKIEDLRKRVKLINESEADLFISIHLNAFPS 97 (189)
T ss_pred HHHHHHHhCCCEEEEEecCCcCccccccccccccccCCHHHHHHHHHhcCCCEEEEEecCCCCC
Confidence 344556667999876665 21 5777777777 589999999876543
No 24
>PRK10319 N-acetylmuramoyl-l-alanine amidase I; Provisional
Probab=44.12 E-value=45 Score=33.84 Aligned_cols=54 Identities=19% Similarity=0.333 Sum_probs=37.3
Q ss_pred HHHHHHcCCEEEEEeC---CCCHHHHHHHHc--cCCEEEEechhhhhhhcccCCCcEEEEEeeC
Q 040560 308 ARMARRLGFKVVVAEA---DMRLSRFARIVN--SCDVLLGVHGAGLANIVFLPENAVFIQVVPI 366 (454)
Q Consensus 308 ~~~l~~~gf~V~~~~~---~~s~~eq~~l~~--~advlVGvHGAgLtn~lFl~pga~vIEi~P~ 366 (454)
.+.|++.|++|+.... ..++.+-+++.+ .||++|++|--+.++ |.+.=+|++-+
T Consensus 92 ~~~L~~~G~~V~lTR~~D~~vsL~~R~~~An~~~ADlFISIH~Ns~~~-----~~a~G~evy~~ 150 (287)
T PRK10319 92 RSILRNHGIDARLTRSGDTFIPLYDRVEIAHKHGADLFMSIHADGFTN-----PKAAGASVFAL 150 (287)
T ss_pred HHHHHHCCCEEEEeCCCCCCCCHHHHHHHHHhcCCCEEEEecCCCCCC-----CCCcEEEEEEe
Confidence 3445556999987776 368888888877 799999999655332 34445566543
No 25
>PRK08306 dipicolinate synthase subunit A; Reviewed
Probab=43.69 E-value=96 Score=31.36 Aligned_cols=80 Identities=19% Similarity=0.292 Sum_probs=50.8
Q ss_pred HHHHHHHHHcCCEEEEEeC-CCC-------HH-HHHHHHccCCEEEEe----------chh------hhhh--hcccCCC
Q 040560 305 SKIARMARRLGFKVVVAEA-DMR-------LS-RFARIVNSCDVLLGV----------HGA------GLAN--IVFLPEN 357 (454)
Q Consensus 305 ~ev~~~l~~~gf~V~~~~~-~~s-------~~-eq~~l~~~advlVGv----------HGA------gLtn--~lFl~pg 357 (454)
-++++.|.+.|++|.+..+ +.. +. ..-+.+.+||++|.+ ++. +++. +=-||+|
T Consensus 15 ~~~~~~l~~~G~~v~~~g~~~~~~~~~g~~~~~~~~~~~~~ad~ii~~~p~~~~~~~i~~~~~~~~~~~~~~~l~~l~~~ 94 (296)
T PRK08306 15 LELIRKLVELGAKVSLVGFDQLDHGFTGATKSSSLEEALSDVDVIILPVPGTNDEGNVDTVFSNEKLVLTEELLELTPEH 94 (296)
T ss_pred HHHHHHHHHCCCEEEEEeccccccccCCceeeccHHHHhccCCEEEECCccccCCceeeccccccCCcchHHHHHhcCCC
Confidence 3788889899999998655 211 21 223568999999988 443 2333 4458999
Q ss_pred cEEEEEeeCccccccccchHhHHhhCCCeEEEEE
Q 040560 358 AVFIQVVPIAVEWLARDYFEEPSKAMKLRYLEYK 391 (454)
Q Consensus 358 a~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y~~y~ 391 (454)
..++ . |+- .....+.+...|+..++|.
T Consensus 95 ~~v~--~--G~~---~~~~~~~~~~~gi~~~~~~ 121 (296)
T PRK08306 95 CTIF--S--GIA---NPYLKELAKETNRKLVELF 121 (296)
T ss_pred CEEE--E--ecC---CHHHHHHHHHCCCeEEEEe
Confidence 7444 2 311 1123466788899887765
No 26
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=41.72 E-value=74 Score=32.63 Aligned_cols=71 Identities=18% Similarity=0.257 Sum_probs=51.1
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEEe
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQVV 364 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi~ 364 (454)
.-++++|.|++. =-.-+...|.+.|+.|.+..- +.+++ +..++|||+|.+=| +++....|++||++||.+-
T Consensus 159 Gk~V~vIG~s~i----vG~PmA~~L~~~gatVtv~~~~t~~l~---e~~~~ADIVIsavg~~~~v~~~~ik~GaiVIDvg 231 (301)
T PRK14194 159 GKHAVVIGRSNI----VGKPMAALLLQAHCSVTVVHSRSTDAK---ALCRQADIVVAAVGRPRLIDADWLKPGAVVIDVG 231 (301)
T ss_pred CCEEEEECCCCc----cHHHHHHHHHHCCCEEEEECCCCCCHH---HHHhcCCEEEEecCChhcccHhhccCCcEEEEec
Confidence 458899998741 112456677778999998865 34444 45577999887765 5677778899999999863
No 27
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=41.13 E-value=98 Score=33.97 Aligned_cols=100 Identities=12% Similarity=0.167 Sum_probs=70.8
Q ss_pred CCCcEEEEEEeC--CCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEe-chhhhhhhcccCC--Cc
Q 040560 285 KKMPRLLIISRK--RTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGV-HGAGLANIVFLPE--NA 358 (454)
Q Consensus 285 ~~~prl~~i~R~--~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGv-HGAgLtn~lFl~p--ga 358 (454)
..++++=||.-. +.+.--|..|+.+.|++.|.+|..+-+ +.++++ ++-+.+|++=|.+ +-.|+.-+=+|.. |.
T Consensus 161 ~~~~~VNIIG~~~l~f~~~~Dl~eikrLL~~~Gi~vn~v~~~g~sl~d-i~~~~~A~~NIvl~~~~g~~~A~~Le~~fgi 239 (513)
T CHL00076 161 TDKPSVNIIGIFTLGFHNQHDCRELKRLLQDLGIEINQIIPEGGSVED-LKNLPKAWFNIVPYREVGLMTAKYLEKEFGM 239 (513)
T ss_pred CCCCcEEEEecCCCCCCCcchHHHHHHHHHHCCCeEEEEECCCCCHHH-HHhcccCcEEEEechhhhHHHHHHHHHHhCC
Confidence 345677777655 456667889999999999999987666 677755 5556778887766 3356555556654 66
Q ss_pred EEEEEeeCccccccccchHhHHhhCCCe
Q 040560 359 VFIQVVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 359 ~vIEi~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
-.+...|+|+.- ...+-..+++.+|..
T Consensus 240 P~i~~~PiGi~~-T~~fLr~la~~lg~~ 266 (513)
T CHL00076 240 PYISTTPMGIVD-TAECIRQIQKILNKL 266 (513)
T ss_pred CeEeeccCCHHH-HHHHHHHHHHHhCCC
Confidence 667778999642 346778889988863
No 28
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=40.87 E-value=66 Score=26.04 Aligned_cols=42 Identities=26% Similarity=0.400 Sum_probs=29.9
Q ss_pred HHHHHHHHcCCEEEEEeC-----CCCHHHHHHHHccCCEEEEechhh
Q 040560 306 KIARMARRLGFKVVVAEA-----DMRLSRFARIVNSCDVLLGVHGAG 347 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~-----~~s~~eq~~l~~~advlVGvHGAg 347 (454)
.+.+.+.+.|++.+..+. ..+..--.+.+.+||++||.=|.-
T Consensus 17 ~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~r 63 (83)
T PF13271_consen 17 ALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNR 63 (83)
T ss_pred HHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccc
Confidence 445666777887766654 234555678899999999987754
No 29
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=39.89 E-value=95 Score=27.84 Aligned_cols=54 Identities=13% Similarity=0.093 Sum_probs=38.7
Q ss_pred CCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCE
Q 040560 286 KMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDV 339 (454)
Q Consensus 286 ~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~adv 339 (454)
++|++++..=.+-..-+...-+..+++..||+|+.+-.+.|.++.++.+.+.++
T Consensus 2 ~~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~~~ 55 (137)
T PRK02261 2 KKKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAAIETDA 55 (137)
T ss_pred CCCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCC
Confidence 356776666555555555555667788889999876668899999888777444
No 30
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=39.45 E-value=1.3e+02 Score=27.55 Aligned_cols=57 Identities=26% Similarity=0.318 Sum_probs=33.9
Q ss_pred CCCcEEEEEEeC---CCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHH--ccCCEEEEech
Q 040560 285 KKMPRLLIISRK---RTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIV--NSCDVLLGVHG 345 (454)
Q Consensus 285 ~~~prl~~i~R~---~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~--~~advlVGvHG 345 (454)
.+|||+++..=. ..|.. .-+..+++..||+|+..-...|-.|.++.. +++|| ||+-+
T Consensus 10 g~rprvlvak~GlDgHd~ga---kvia~~l~d~GfeVi~~g~~~tp~e~v~aA~~~dv~v-IgvSs 71 (143)
T COG2185 10 GARPRVLVAKLGLDGHDRGA---KVIARALADAGFEVINLGLFQTPEEAVRAAVEEDVDV-IGVSS 71 (143)
T ss_pred CCCceEEEeccCccccccch---HHHHHHHHhCCceEEecCCcCCHHHHHHHHHhcCCCE-EEEEe
Confidence 478998876433 13432 234467788999997554345666766665 44444 34433
No 31
>KOG4698 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.37 E-value=7.1 Score=42.15 Aligned_cols=100 Identities=14% Similarity=0.125 Sum_probs=67.8
Q ss_pred ccccCHHHHHHHHHHcCCEEEEEeC--CCCHHHHHHHHccCCEEEEechhhhhhhcccCCCcEEEEEeeCccccccccch
Q 040560 299 RTFTNASKIARMARRLGFKVVVAEA--DMRLSRFARIVNSCDVLLGVHGAGLANIVFLPENAVFIQVVPIAVEWLARDYF 376 (454)
Q Consensus 299 R~i~Ne~ev~~~l~~~gf~V~~~~~--~~s~~eq~~l~~~advlVGvHGAgLtn~lFl~pga~vIEi~P~g~~~~~~~~y 376 (454)
+.++|+.+ +...++.-|-+....+ ++.+.+-++.+++.. +.+|+++..--.|.+.+..|++-.|++.+.....+|
T Consensus 192 pL~it~~~-~~~n~ev~~li~~~~~ww~~kf~Dvv~~lSn~~--~v~~~~~~~ThcF~~~~vgL~~h~~y~v~~t~~~~~ 268 (475)
T KOG4698|consen 192 PLFITEAE-LRFNKEVQFLITETHSWWDMKFGDVVRQLSNYP--VVDFDAELRTHCFKEAIVGLVSHFPYAVNPTQPPPN 268 (475)
T ss_pred hhhcccch-hcccccEEEEEEEcchhhhhhHHHHHHhcCCCc--eEEecCCceEEEeeeeeeeeeecccccccCCcCCCc
Confidence 56666666 3333332222221122 678999999999999 889999999999999999999999999877666667
Q ss_pred Hh--HHhhCCCeEEEEEeccccccccc
Q 040560 377 EE--PSKAMKLRYLEYKIKAEESTLIQ 401 (454)
Q Consensus 377 ~~--~A~~~gl~Y~~y~~~~~EssL~~ 401 (454)
+. +...+.+-|..|+....|..+..
T Consensus 269 ~~~s~~~fr~~l~~a~~~~i~~~~~t~ 295 (475)
T KOG4698|consen 269 GTLSMLDFRNLLDKALSPRIPEANVTA 295 (475)
T ss_pred cccccccHHHHHHHHhcccccccccCC
Confidence 43 33344455666665544444443
No 32
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=37.87 E-value=74 Score=32.37 Aligned_cols=72 Identities=18% Similarity=0.255 Sum_probs=50.5
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEechhh-hhhhcccCCCcEEEEEe
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHGAG-LANIVFLPENAVFIQVV 364 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHGAg-Ltn~lFl~pga~vIEi~ 364 (454)
.-++++|.|++. =-.-+..+|.+.|..|.+..- .+ .+..+.+.+|||+|+.=|.. +-.-=+.+||++||.+=
T Consensus 158 Gk~vvVIGrs~~----VG~pla~lL~~~gatVtv~~s-~t-~~l~~~~~~ADIVIsAvg~p~~i~~~~vk~gavVIDvG 230 (286)
T PRK14175 158 GKNAVVIGRSHI----VGQPVSKLLLQKNASVTILHS-RS-KDMASYLKDADVIVSAVGKPGLVTKDVVKEGAVIIDVG 230 (286)
T ss_pred CCEEEEECCCch----hHHHHHHHHHHCCCeEEEEeC-Cc-hhHHHHHhhCCEEEECCCCCcccCHHHcCCCcEEEEcC
Confidence 448889998741 112456667777999988874 22 23445789999999888876 55555689999999864
No 33
>cd01968 Nitrogenase_NifE_I Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
Probab=37.69 E-value=68 Score=33.79 Aligned_cols=96 Identities=11% Similarity=0.080 Sum_probs=62.1
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEe-c--hhhhhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGV-H--GAGLANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGv-H--GAgLtn~lFl~pga~vIE 362 (454)
+..+-||.- ....-|.+|+.+.|++.|++|...-+ +.+++|.-+ +.+|.+-|.+ + |..++..|=-+=|.-.+.
T Consensus 158 ~~~VNiig~--~~~~~d~~el~~lL~~~Gl~v~~~~~~~~s~eei~~-~~~A~lniv~~~~~~~~~a~~L~~~fGip~~~ 234 (410)
T cd01968 158 PYDINLIGE--FNVAGELWGVKPLLEKLGIRVLASITGDSRVDEIRR-AHRAKLNVVQCSKSMIYLARKMEEKYGIPYIE 234 (410)
T ss_pred CCcEEEECC--CCCcccHHHHHHHHHHcCCeEEEEeCCCCCHHHHHh-hhhCcEEEEEchhHHHHHHHHHHHHhCCCeEe
Confidence 345556652 23345778999999999999986555 678866555 5666665544 2 223333332233666677
Q ss_pred EeeCccccccccchHhHHhhCCCe
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
..|+|++. ...+++.+|+.+|..
T Consensus 235 ~~p~G~~~-t~~~l~~ia~~~g~~ 257 (410)
T cd01968 235 VSFYGIRD-TSKSLRNIAELLGDE 257 (410)
T ss_pred cCcCcHHH-HHHHHHHHHHHhCCc
Confidence 77899754 357899999998864
No 34
>PRK14179 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=37.68 E-value=93 Score=31.64 Aligned_cols=70 Identities=20% Similarity=0.311 Sum_probs=50.0
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|++. +. .-+...|.+.|..|.+... +-+++ +..++|||+|.+=| +++....|++||++||.+
T Consensus 158 Gk~v~vIG~S~i---vG-~Pla~lL~~~gatVtv~~s~t~~l~---~~~~~ADIVI~avg~~~~v~~~~ik~GavVIDv 229 (284)
T PRK14179 158 GKHAVVIGRSNI---VG-KPMAQLLLDKNATVTLTHSRTRNLA---EVARKADILVVAIGRGHFVTKEFVKEGAVVIDV 229 (284)
T ss_pred CCEEEEECCCCc---Cc-HHHHHHHHHCCCEEEEECCCCCCHH---HHHhhCCEEEEecCccccCCHHHccCCcEEEEe
Confidence 458899998641 11 1456667777999988754 33333 45678999888766 567777889999999986
No 35
>TIGR02853 spore_dpaA dipicolinic acid synthetase, A subunit. This predicted Rossman fold-containing protein is the A subunit of dipicolinic acid synthetase as found in most, though not all, endospore-forming low-GC Gram-positive bacteria; it is absent in Clostridium. The B subunit is represented by TIGR02852. This protein is also known as SpoVFA.
Probab=37.28 E-value=1.6e+02 Score=29.76 Aligned_cols=58 Identities=24% Similarity=0.280 Sum_probs=39.8
Q ss_pred HHHHHHHHccCCEEEEechhhhhh-hc--ccCCCcEEEEEeeCccccccccchHhHHhhCCCeEEE
Q 040560 327 LSRFARIVNSCDVLLGVHGAGLAN-IV--FLPENAVFIQVVPIAVEWLARDYFEEPSKAMKLRYLE 389 (454)
Q Consensus 327 ~~eq~~l~~~advlVGvHGAgLtn-~l--Fl~pga~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y~~ 389 (454)
+.+.-+.+.++|++|-.=..++.+ -+ .|++++.+|.+.- .+ ..+.| ..|+..|++.+-
T Consensus 200 ~~~l~~~l~~aDiVint~P~~ii~~~~l~~~k~~aliIDlas---~P-g~tdf-~~Ak~~G~~a~~ 260 (287)
T TIGR02853 200 LNKLEEKVAEIDIVINTIPALVLTADVLSKLPKHAVIIDLAS---KP-GGTDF-EYAKKRGIKALL 260 (287)
T ss_pred HHHHHHHhccCCEEEECCChHHhCHHHHhcCCCCeEEEEeCc---CC-CCCCH-HHHHHCCCEEEE
Confidence 445556778999999765555533 22 3799999999863 11 23457 789999998764
No 36
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=36.22 E-value=91 Score=28.12 Aligned_cols=40 Identities=15% Similarity=0.110 Sum_probs=29.5
Q ss_pred HHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCE-EEEec
Q 040560 305 SKIARMARRLGFKVVVAEADMRLSRFARIVNSCDV-LLGVH 344 (454)
Q Consensus 305 ~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~adv-lVGvH 344 (454)
.-+..+++..||+|+-.-.+.|.++.++...+.|+ +||+-
T Consensus 19 ~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~~adiVglS 59 (134)
T TIGR01501 19 KILDHAFTNAGFNVVNLGVLSPQEEFIKAAIETKADAILVS 59 (134)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEe
Confidence 34556788899999655447899999998887666 55553
No 37
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=35.40 E-value=1.1e+02 Score=27.36 Aligned_cols=65 Identities=26% Similarity=0.287 Sum_probs=35.9
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCE-EEEechhhhhhh
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDV-LLGVHGAGLANI 351 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~adv-lVGvHGAgLtn~ 351 (454)
+||+++-.=.+--.=.--+=+..+++..||+|+-.....|.++.++...+.++ +||+-+.-=+++
T Consensus 2 ~~~v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~~adii~iSsl~~~~~ 67 (132)
T TIGR00640 2 RPRILVAKMGQDGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQAVEADVHVVGVSSLAGGHL 67 (132)
T ss_pred CCEEEEEeeCCCccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCCEEEEcCchhhhH
Confidence 45655544333111111123446677889999655446788888777766665 555544333333
No 38
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=32.72 E-value=1.3e+02 Score=27.78 Aligned_cols=55 Identities=16% Similarity=0.222 Sum_probs=38.7
Q ss_pred cCHHHHHHHHHHcCCEEEEEeC---C-CCHHHHHHHH---ccCCEEEEechhhhhhhcccCC
Q 040560 302 TNASKIARMARRLGFKVVVAEA---D-MRLSRFARIV---NSCDVLLGVHGAGLANIVFLPE 356 (454)
Q Consensus 302 ~Ne~ev~~~l~~~gf~V~~~~~---~-~s~~eq~~l~---~~advlVGvHGAgLtn~lFl~p 356 (454)
.|-.-+.+.+++.|+++....- + -.+.+.++-. +.+|++|.-=|+|.+--=+.|+
T Consensus 22 ~n~~~l~~~L~~~G~~v~~~~iv~Dd~~~i~~~l~~~~~~~~~DlVIttGGtg~g~~D~t~e 83 (163)
T TIGR02667 22 TSGQYLVERLTEAGHRLADRAIVKDDIYQIRAQVSAWIADPDVQVILITGGTGFTGRDVTPE 83 (163)
T ss_pred CcHHHHHHHHHHCCCeEEEEEEcCCCHHHHHHHHHHHHhcCCCCEEEECCCcCCCCCCCcHH
Confidence 3566777889999999875543 2 2355665543 5799999999988876655554
No 39
>PRK14190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=32.29 E-value=1e+02 Score=31.32 Aligned_cols=71 Identities=17% Similarity=0.260 Sum_probs=49.4
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEEe
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQVV 364 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi~ 364 (454)
.-++++|.|+.. =-.-+..+|.+.|..|.+... +.++. +.+++|||+|+.=| +++-..=|.+||++||-+=
T Consensus 158 Gk~vvViGrS~i----VG~Pla~lL~~~~atVt~chs~t~~l~---~~~~~ADIvI~AvG~p~~i~~~~ik~gavVIDvG 230 (284)
T PRK14190 158 GKHVVVVGRSNI----VGKPVGQLLLNENATVTYCHSKTKNLA---ELTKQADILIVAVGKPKLITADMVKEGAVVIDVG 230 (284)
T ss_pred CCEEEEECCCCc----cHHHHHHHHHHCCCEEEEEeCCchhHH---HHHHhCCEEEEecCCCCcCCHHHcCCCCEEEEee
Confidence 458899998741 112455666677899988764 32333 46789999987665 4566666789999999863
No 40
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=31.59 E-value=1.9e+02 Score=24.18 Aligned_cols=54 Identities=17% Similarity=0.250 Sum_probs=34.2
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHc--cCCEEEEe
Q 040560 289 RLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVN--SCDVLLGV 343 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~--~advlVGv 343 (454)
|+++..+.....=+...-+...+++.|++|..++.+.+..+..+.+. +.|+ ||+
T Consensus 2 ~v~~~~~~~~~~~lGl~~la~~l~~~G~~v~~~d~~~~~~~l~~~~~~~~pd~-V~i 57 (121)
T PF02310_consen 2 RVVLACVPGEVHPLGLLYLAAYLRKAGHEVDILDANVPPEELVEALRAERPDV-VGI 57 (121)
T ss_dssp EEEEEEBTTSSTSHHHHHHHHHHHHTTBEEEEEESSB-HHHHHHHHHHTTCSE-EEE
T ss_pred EEEEEeeCCcchhHHHHHHHHHHHHCCCeEEEECCCCCHHHHHHHHhcCCCcE-EEE
Confidence 45666666555556667788889999999998887544444433332 5566 444
No 41
>PRK08306 dipicolinate synthase subunit A; Reviewed
Probab=30.80 E-value=1.5e+02 Score=29.92 Aligned_cols=58 Identities=21% Similarity=0.245 Sum_probs=37.4
Q ss_pred HHHHHHHccCCEEEEechhhh-hhhcc--cCCCcEEEEEeeCccccccccchHhHHhhCCCeEEEE
Q 040560 328 SRFARIVNSCDVLLGVHGAGL-ANIVF--LPENAVFIQVVPIAVEWLARDYFEEPSKAMKLRYLEY 390 (454)
Q Consensus 328 ~eq~~l~~~advlVGvHGAgL-tn~lF--l~pga~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y~~y 390 (454)
.+-.+.++++|++|..=++++ +.-++ |+||+++|.+--. + ....| ..|+..|++...+
T Consensus 202 ~~l~~~l~~aDiVI~t~p~~~i~~~~l~~~~~g~vIIDla~~---p-ggtd~-~~a~~~Gv~~~~~ 262 (296)
T PRK08306 202 SELAEEVGKIDIIFNTIPALVLTKEVLSKMPPEALIIDLASK---P-GGTDF-EYAEKRGIKALLA 262 (296)
T ss_pred HHHHHHhCCCCEEEECCChhhhhHHHHHcCCCCcEEEEEccC---C-CCcCe-eehhhCCeEEEEE
Confidence 344566789999997555553 33333 8999999998631 1 11334 4578888888654
No 42
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=30.57 E-value=61 Score=33.46 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=27.6
Q ss_pred HHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHccCCEEEEechhh
Q 040560 305 SKIARMARRLGFKVVVAEA---DMRLSRFARIVNSCDVLLGVHGAG 347 (454)
Q Consensus 305 ~ev~~~l~~~gf~V~~~~~---~~s~~eq~~l~~~advlVGvHGAg 347 (454)
.|++++|+.+||+++++|. +.|=. .+.-+..+-+++.++|+|
T Consensus 133 ~~~i~~ldAaG~DvIIVETVGvGQsev-~I~~~aDt~~~v~~pg~G 177 (323)
T COG1703 133 REAIKLLDAAGYDVIIVETVGVGQSEV-DIANMADTFLVVMIPGAG 177 (323)
T ss_pred HHHHHHHHhcCCCEEEEEecCCCcchh-HHhhhcceEEEEecCCCC
Confidence 4888999999999999996 22222 233334445566666665
No 43
>TIGR01284 alt_nitrog_alph nitrogenase alpha chain. This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model TIGR01282. It appears by phylogenetic and UPGMA trees that this model represents a distinct clade of NifD homologs, in which arose several molybdenum-independent forms.
Probab=30.39 E-value=65 Score=34.71 Aligned_cols=96 Identities=8% Similarity=0.048 Sum_probs=63.9
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEec---hhhhhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVH---GAGLANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvH---GAgLtn~lFl~pga~vIE 362 (454)
+..+-+|. ..-.--|.+|+.+.+++.|++|+..-+ +.+++|. +-+.+|+.-|.+. |..++..|=-+=|.-.+.
T Consensus 199 ~~~VNiiG--~~~~~gd~~el~~lL~~~Gl~v~~~~~g~~s~~ei-~~~~~A~lniv~~~~~~~~~A~~Le~~~GiP~~~ 275 (457)
T TIGR01284 199 EYDVNLIG--EYNIQGDLWVLKKYFERMGIQVLSTFTGNGCYDEL-RWMHRAKLNVVRCARSANYIANELEERYGIPRLD 275 (457)
T ss_pred CCeEEEEc--cCCchhhHHHHHHHHHHcCCeEEEEECCCCCHHHH-HhccccCEEEEEChHHHHHHHHHHHHHhCCCeEe
Confidence 34566664 222234567888999999999975444 6677554 4567777755433 334566554455777888
Q ss_pred EeeCccccccccchHhHHhhCCCe
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
+-|+|++. ...+...+|+.+|+.
T Consensus 276 ~~~~G~~~-T~~~l~~ia~~~g~~ 298 (457)
T TIGR01284 276 IDFFGFEY-CAKNLRKIGEFFGIE 298 (457)
T ss_pred cccCCHHH-HHHHHHHHHHHhCCc
Confidence 88899754 346789999999965
No 44
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=29.45 E-value=1.2e+02 Score=30.84 Aligned_cols=70 Identities=16% Similarity=0.250 Sum_probs=49.8
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|++. =-.-+..+|.+.|..|.+... +-++. ..+.+||++|..=| +++-+.=|++||++||-+
T Consensus 158 Gk~vvViGrs~i----VGkPla~lL~~~~atVt~~hs~t~~l~---~~~~~ADIVV~avG~~~~i~~~~ik~gavVIDV 229 (285)
T PRK14189 158 GAHAVVIGRSNI----VGKPMAMLLLQAGATVTICHSKTRDLA---AHTRQADIVVAAVGKRNVLTADMVKPGATVIDV 229 (285)
T ss_pred CCEEEEECCCCc----cHHHHHHHHHHCCCEEEEecCCCCCHH---HHhhhCCEEEEcCCCcCccCHHHcCCCCEEEEc
Confidence 458889988752 123566777788999987664 33343 56778999988776 455666678999999885
No 45
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=29.40 E-value=1.2e+02 Score=28.10 Aligned_cols=39 Identities=23% Similarity=0.371 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEe
Q 040560 304 ASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGV 343 (454)
Q Consensus 304 e~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGv 343 (454)
..++.+.+++.||+|.++. +.|+..++-.=..-+.+|||
T Consensus 75 Ig~l~~lae~~g~~v~i~~-Ggt~ar~~ik~~~p~~iigV 113 (158)
T PF01976_consen 75 IGDLKKLAEKYGYKVYIAT-GGTLARKIIKEYRPKAIIGV 113 (158)
T ss_pred hhHHHHHHHHcCCEEEEEc-ChHHHHHHHHHhCCCEEEEE
Confidence 4689999999999998887 56666655555556777765
No 46
>cd03129 GAT1_Peptidase_E_like Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins. Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins. This group contains proteins similar to the aspartyl dipeptidases Salmonella typhimurium peptidase E and Xenopus laevis peptidase E and, extracellular cyanophycinases from Pseudomonas anguilliseptica BI (CphE) and Synechocystis sp. PCC 6803 CphB. In bacteria peptidase E is believed to play a role in degrading peptides generated by intracellular protein breakdown or imported into the cell as nutrient sources. Peptidase E uniquely hydrolyses only Asp-X dipeptides (where X is any amino acid), and one tripeptide Asp-Gly-Gly. Cyanophycinases are intracellular exopeptidases which hydrolyze the polymer cyanophycin (multi L-arginyl-poly-L-aspartic acid) to the dipeptide beta-Asp-Arg. Peptidase E and cyanophycinases are thought to have a Ser-His-Glu catalytic triad which differs from
Probab=29.39 E-value=1.7e+02 Score=27.67 Aligned_cols=62 Identities=16% Similarity=0.074 Sum_probs=43.0
Q ss_pred CCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC--CCCHHHHHHHHccCCEEEEechhh
Q 040560 286 KMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA--DMRLSRFARIVNSCDVLLGVHGAG 347 (454)
Q Consensus 286 ~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~--~~s~~eq~~l~~~advlVGvHGAg 347 (454)
..+++++|.-...-.=...++..++++++|+++..+.. ..+-++..+.+.+||+++=.=|.-
T Consensus 28 ~~~~i~~iptA~~~~~~~~~~~~~~~~~lG~~~~~~~~~~~~~~~~~~~~l~~ad~I~~~GG~~ 91 (210)
T cd03129 28 AGARVLFIPTASGDRDEYGEEYRAAFERLGVEVVHLLLIDTANDPDVVARLLEADGIFVGGGNQ 91 (210)
T ss_pred CCCeEEEEeCCCCChHHHHHHHHHHHHHcCCceEEEeccCCCCCHHHHHHHhhCCEEEEcCCcH
Confidence 57899999766422223345677888889998876553 235578889999999987554544
No 47
>PF03575 Peptidase_S51: Peptidase family S51; InterPro: IPR005320 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S51 (clan PC(S)). The type example being dipeptidase E (alpha-aspartyl dipeptidase) from Escherichia coli. The family contains alpha-aspartyl dipeptidases (dipeptidase E) and cyanophycinases. The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E has been determine at 1.2-A resolution. The structure of this 25kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organisation of the catalytic triad differ from those of the known serine proteases. This enzyme appears to represent a new example of convergent evolution of peptidase activity []. Alpha-aspartyl dipeptidase hydrolyses dipeptides containing N-terminal aspartate residues, asp-|-xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides. In the cyanobacteria, cyanophycinase is an exopeptidase that catalyses the hydrolytic cleavage of multi-l-arginyl-poly-l-aspartic acid (cyanophycin; a water- insoluble reserve polymer) into aspartate-arginine dipeptides.; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis; PDB: 3EN0_B 1FYE_A 1FY2_A 3L4E_A.
Probab=28.02 E-value=98 Score=27.83 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=19.8
Q ss_pred HHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEE
Q 040560 306 KIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLG 342 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVG 342 (454)
++.++++++|++|..++. +.+-.+..+.+.+||++.=
T Consensus 4 ~~~~~f~~~g~~v~~l~~~~~~~~~~~~~i~~ad~I~~ 41 (154)
T PF03575_consen 4 KFRKAFRKLGFEVDQLDLSDRNDADILEAIREADAIFL 41 (154)
T ss_dssp HHHHHHHHCT-EEEECCCTSCGHHHHHHHHHHSSEEEE
T ss_pred HHHHHHHHCCCEEEEEeccCCChHHHHHHHHhCCEEEE
Confidence 445555666666655554 3344455555666666543
No 48
>PRK14191 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.92 E-value=1.6e+02 Score=30.02 Aligned_cols=72 Identities=15% Similarity=0.215 Sum_probs=48.5
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEEe
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQVV 364 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi~ 364 (454)
.-++++|.|+.. + -.-+..+|.+.|..|.+... .+ .+..+.+++|||+|+.=| +++-..=|.+||++||.+=
T Consensus 157 Gk~vvVvGrs~~---V-G~Pla~lL~~~gAtVtv~hs-~t-~~l~~~~~~ADIvV~AvG~p~~i~~~~vk~GavVIDvG 229 (285)
T PRK14191 157 GKDVVIIGASNI---V-GKPLAMLMLNAGASVSVCHI-LT-KDLSFYTQNADIVCVGVGKPDLIKASMVKKGAVVVDIG 229 (285)
T ss_pred CCEEEEECCCch---h-HHHHHHHHHHCCCEEEEEeC-Cc-HHHHHHHHhCCEEEEecCCCCcCCHHHcCCCcEEEEee
Confidence 458899998741 1 11345566677999987763 12 223457889999887766 4555555679999999864
No 49
>PF02737 3HCDH_N: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; InterPro: IPR006176 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major regions of similarity in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3K6J_A 1ZCJ_A 2X58_A 1ZEJ_A 3HDH_B 2WTB_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B ....
Probab=27.82 E-value=68 Score=29.92 Aligned_cols=74 Identities=15% Similarity=0.244 Sum_probs=44.3
Q ss_pred HHHHHHHHc-CCEEEEEeC--CCCHHHHHHHHccCCEEEEechhhhhhhcccCCC-cEEEEEeeCc-cccccccchHhHH
Q 040560 306 KIARMARRL-GFKVVVAEA--DMRLSRFARIVNSCDVLLGVHGAGLANIVFLPEN-AVFIQVVPIA-VEWLARDYFEEPS 380 (454)
Q Consensus 306 ev~~~l~~~-gf~V~~~~~--~~s~~eq~~l~~~advlVGvHGAgLtn~lFl~pg-a~vIEi~P~g-~~~~~~~~y~~~A 380 (454)
++.+.+++. .-+.++... .+++.+....+..-+=+||+| .|.||. ..++||+|.. +.......-..++
T Consensus 95 ~~~~~l~~~~~~~~ilasnTSsl~i~~la~~~~~p~R~ig~H-------f~~P~~~~~lVEvv~~~~T~~~~~~~~~~~~ 167 (180)
T PF02737_consen 95 ELFAELDEICPPDTILASNTSSLSISELAAALSRPERFIGMH-------FFNPPHLMPLVEVVPGPKTSPETVDRVRALL 167 (180)
T ss_dssp HHHHHHHCCS-TTSEEEE--SSS-HHHHHTTSSTGGGEEEEE-------E-SSTTT--EEEEEE-TTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCceEEecCCCCCHHHHHhccCcCceEEEEe-------cccccccCceEEEeCCCCCCHHHHHHHHHHH
Confidence 666667665 334443443 688999999988888999999 355775 8999999965 3332223344556
Q ss_pred hhCCCe
Q 040560 381 KAMKLR 386 (454)
Q Consensus 381 ~~~gl~ 386 (454)
+.+|..
T Consensus 168 ~~~gk~ 173 (180)
T PF02737_consen 168 RSLGKT 173 (180)
T ss_dssp HHTT-E
T ss_pred HHCCCE
Confidence 666654
No 50
>cd03146 GAT1_Peptidase_E Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E. Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E. This group contains proteins similar to the aspartyl dipeptidases Salmonella typhimurium peptidase E and Xenopus laevis peptidase E. In bacteria peptidase E is believed to play a role in degrading peptides generated by intracellular protein breakdown or imported into the cell as nutrient sources. Peptidase E uniquely hydrolyses only Asp-X dipeptides (where X is any amino acid), and one tripeptide Asp-Gly-Gly. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad typical of GATase1 domains by having a Ser in place of the reactive Cys at the nucleophile elbow. Xenopus PepE is developmentally regulated in response to thyroid hormone and, it is thought to play a role in apoptosis during tail reabsorption.
Probab=27.39 E-value=1.3e+02 Score=28.76 Aligned_cols=61 Identities=15% Similarity=0.144 Sum_probs=41.2
Q ss_pred CCCcEEEEEEeCCCccccCHHHHHHHHHHc-CCEEEEEeCCCCHHHHHHHHccCCEEEEechh
Q 040560 285 KKMPRLLIISRKRTRTFTNASKIARMARRL-GFKVVVAEADMRLSRFARIVNSCDVLLGVHGA 346 (454)
Q Consensus 285 ~~~prl~~i~R~~~R~i~Ne~ev~~~l~~~-gf~V~~~~~~~s~~eq~~l~~~advlVGvHGA 346 (454)
+.+++++||.-...-.=.-.+.+.++++++ |+++..+.. .+-++..+.+.+||+++=.=|.
T Consensus 29 ~~~~~i~~IptAs~~~~~~~~~~~~a~~~l~G~~~~~~~~-~~~~~~~~~l~~ad~I~l~GG~ 90 (212)
T cd03146 29 KARPKVLFVPTASGDRDEYTARFYAAFESLRGVEVSHLHL-FDTEDPLDALLEADVIYVGGGN 90 (212)
T ss_pred cCCCeEEEECCCCCCHHHHHHHHHHHHhhccCcEEEEEec-cCcccHHHHHhcCCEEEECCch
Confidence 467899999877641112234566778889 999987763 3334447788899998765453
No 51
>cd01977 Nitrogenase_VFe_alpha Nitrogenase_VFe_alpha -like: Nitrogenase VFe protein, alpha subunit like. This group contains proteins similar to the alpha subunits of, the VFe protein of the vanadium-dependent (V-) nitrogenase and the FeFe protein of the iron only (Fe-) nitrogenase Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V- and Fe- nitrogenases there is a molybdenum (Mo)-dependent nitrogenase which is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha sub
Probab=27.08 E-value=1.9e+02 Score=30.58 Aligned_cols=96 Identities=8% Similarity=0.028 Sum_probs=62.8
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccC--CCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLP--ENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~--pga~vIE 362 (454)
+..+-+|. ....--|.+|+.+.+++.|++++..-+ +.+++| ++-+.+|.+-|.+.+ .|.--+-+|. =|.-.+.
T Consensus 162 ~~~VNliG--~~~~~~d~~ei~~lL~~~Gl~v~~~~~~~~t~~e-i~~~~~A~lnlv~~~~~~~~~A~~L~er~GiP~~~ 238 (415)
T cd01977 162 DYTINYIG--DYNIQGDTEVLQKYFERMGIQVLSTFTGNGTYDD-LRWMHRAKLNVVNCARSAGYIANELKKRYGIPRLD 238 (415)
T ss_pred CCcEEEEc--cCCCcccHHHHHHHHHHcCCeEEEEECCCCCHHH-HHhcccCCEEEEEchhHHHHHHHHHHHHhCCCeEE
Confidence 34566664 233345667899999999999974444 677766 556777777555443 3433333343 3666777
Q ss_pred EeeCccccccccchHhHHhhCCCe
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
+.|+|++- ...+++.+|+.+|+.
T Consensus 239 ~~~~G~~~-t~~~l~~la~~~g~~ 261 (415)
T cd01977 239 VDGFGFEY-CAESLRKIGAFFGIE 261 (415)
T ss_pred eccCCHHH-HHHHHHHHHHHhCcc
Confidence 77888654 347889999998865
No 52
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]
Probab=26.97 E-value=1.2e+02 Score=30.92 Aligned_cols=70 Identities=17% Similarity=0.282 Sum_probs=52.9
Q ss_pred CCcEEEEEEeCC--CccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEE
Q 040560 286 KMPRLLIISRKR--TRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQ 362 (454)
Q Consensus 286 ~~prl~~i~R~~--~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIE 362 (454)
..-++++|.|+. .| =+..+|...+..|.+... .+ ++-.+..++|||+|..=| +++-..=|..||++||-
T Consensus 155 ~Gk~~vVVGrS~iVGk------Pla~lL~~~naTVtvcHs-~T-~~l~~~~k~ADIvv~AvG~p~~i~~d~vk~gavVID 226 (283)
T COG0190 155 RGKNVVVVGRSNIVGK------PLALLLLNANATVTVCHS-RT-KDLASITKNADIVVVAVGKPHFIKADMVKPGAVVID 226 (283)
T ss_pred CCCEEEEECCCCcCcH------HHHHHHHhCCCEEEEEcC-CC-CCHHHHhhhCCEEEEecCCccccccccccCCCEEEe
Confidence 355889999985 34 356667778999987764 22 455667788999988777 67888889999999998
Q ss_pred E
Q 040560 363 V 363 (454)
Q Consensus 363 i 363 (454)
+
T Consensus 227 V 227 (283)
T COG0190 227 V 227 (283)
T ss_pred c
Confidence 5
No 53
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=26.32 E-value=1e+02 Score=27.64 Aligned_cols=52 Identities=25% Similarity=0.359 Sum_probs=37.0
Q ss_pred cccCHHHHHHHHHHcCCEEEEEeC---C-CCHHHHHH-HHccCCEEEEechhhhhhh
Q 040560 300 TFTNASKIARMARRLGFKVVVAEA---D-MRLSRFAR-IVNSCDVLLGVHGAGLANI 351 (454)
Q Consensus 300 ~i~Ne~ev~~~l~~~gf~V~~~~~---~-~s~~eq~~-l~~~advlVGvHGAgLtn~ 351 (454)
.=.|..-+.+.+++.|+++..... + -.+.++++ ...++|++|..=|+|.+.-
T Consensus 25 ~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~l~~~~~~~DliIttGG~g~g~~ 81 (144)
T TIGR00177 25 YDSNGPLLAALLEEAGFNVSRLGIVPDDPEEIREILRKAVDEADVVLTTGGTGVGPR 81 (144)
T ss_pred EeCcHHHHHHHHHHCCCeEEEEeecCCCHHHHHHHHHHHHhCCCEEEECCCCCCCCC
Confidence 345667788899999999875553 2 24566555 3468999999988887654
No 54
>PRK15469 ghrA bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional
Probab=25.77 E-value=1.7e+02 Score=29.84 Aligned_cols=57 Identities=21% Similarity=0.384 Sum_probs=0.0
Q ss_pred HHHHHHHHHcCCEEEEEeC-CCC---------HHHHHHHHccCCEEEEech-----hhhhhh-cc--cCCCcEEE
Q 040560 305 SKIARMARRLGFKVVVAEA-DMR---------LSRFARIVNSCDVLLGVHG-----AGLANI-VF--LPENAVFI 361 (454)
Q Consensus 305 ~ev~~~l~~~gf~V~~~~~-~~s---------~~eq~~l~~~advlVGvHG-----AgLtn~-lF--l~pga~vI 361 (454)
.++++.++.+|++|...+. ... ..+.-+++..||+++-.-- -++-|. .| |+||+++|
T Consensus 149 ~~vA~~l~afG~~V~~~~~~~~~~~~~~~~~~~~~l~e~l~~aDvvv~~lPlt~~T~~li~~~~l~~mk~ga~lI 223 (312)
T PRK15469 149 SKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGREELSAFLSQTRVLINLLPNTPETVGIINQQLLEQLPDGAYLL 223 (312)
T ss_pred HHHHHHHHHCCCEEEEEeCCCCCCCCceeecccccHHHHHhcCCEEEECCCCCHHHHHHhHHHHHhcCCCCcEEE
No 55
>PLN02897 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=25.59 E-value=1.5e+02 Score=31.03 Aligned_cols=70 Identities=20% Similarity=0.290 Sum_probs=50.1
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|.+ ++. .-+..+|.+.|..|.+... +-++ -+..++|||+|..=| +++-..=|.+||++||-+
T Consensus 214 GK~vvVIGRS~---iVG-kPla~LL~~~~ATVTicHs~T~nl---~~~~~~ADIvIsAvGkp~~v~~d~vk~GavVIDV 285 (345)
T PLN02897 214 GKNAVVIGRSN---IVG-LPMSLLLQRHDATVSTVHAFTKDP---EQITRKADIVIAAAGIPNLVRGSWLKPGAVVIDV 285 (345)
T ss_pred CCEEEEECCCc---ccc-HHHHHHHHHCCCEEEEEcCCCCCH---HHHHhhCCEEEEccCCcCccCHHHcCCCCEEEEc
Confidence 44888999884 111 1345566677888887765 3344 446788999887665 677777889999999985
No 56
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=25.24 E-value=1.7e+02 Score=25.69 Aligned_cols=52 Identities=23% Similarity=0.374 Sum_probs=33.7
Q ss_pred EEEEEEeCCCccccCHHHHHHHH----HHcCCEEEEEeC-CC-----------------CHHHHHHHHccCCEEE
Q 040560 289 RLLIISRKRTRTFTNASKIARMA----RRLGFKVVVAEA-DM-----------------RLSRFARIVNSCDVLL 341 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l----~~~gf~V~~~~~-~~-----------------s~~eq~~l~~~advlV 341 (454)
++++|.=. .|.=-|-..+++.+ ++.|.++.+++. +. .+.+.++.+.+||.+|
T Consensus 2 kilii~gS-~r~~~~t~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD~iI 75 (152)
T PF03358_consen 2 KILIINGS-PRKNSNTRKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEADGII 75 (152)
T ss_dssp EEEEEESS-SSTTSHHHHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSSEEE
T ss_pred EEEEEECc-CCCCCHHHHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCCeEE
Confidence 45666422 35555665555544 445999999988 53 2345588899999876
No 57
>PF08370 PDR_assoc: Plant PDR ABC transporter associated; InterPro: IPR013581 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This domain is found on the C terminus of ABC-2 type transporter domains (IPR013525 from INTERPRO). It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters. Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [] (see also IPR010929 from INTERPRO). The PDR family is characterised by a configuration in which the ABC domain is nearer the N terminus of the protein than the transmembrane domain [].
Probab=24.50 E-value=80 Score=25.07 Aligned_cols=30 Identities=33% Similarity=0.481 Sum_probs=23.1
Q ss_pred hhhhhHHHHHHHHHHHHHHhhhccccCccc
Q 040560 18 KFKYGALIGLFVIALSFCTVLKPYLAPLPA 47 (454)
Q Consensus 18 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 47 (454)
=+|.|+++|+.++.-.++++.=.|+.|...
T Consensus 30 WIgvgaL~G~~vlFNil~~laL~yL~p~~k 59 (65)
T PF08370_consen 30 WIGVGALLGFIVLFNILFTLALTYLNPLGK 59 (65)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHhcCCcCC
Confidence 389999999999887777676666666544
No 58
>cd01976 Nitrogenase_MoFe_alpha Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Mo-nitrogenase is the most widespread and best characterized of these systems. Mo-nitrogenase consists of the MoFe protein (component 1) and the Fe protein (component 2). MoFe is an alpha2beta2 tetramer. Each alphabeta pair of MoFe contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction.
Probab=24.46 E-value=1.6e+02 Score=31.28 Aligned_cols=96 Identities=10% Similarity=-0.009 Sum_probs=63.7
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEechhh---hhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHGAG---LANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHGAg---Ltn~lFl~pga~vIE 362 (454)
+..+-+|. ....--|..|+.+.|++.|.+|...-+ +.+++| ++-+.+|.+-|.+...+ ++..|==+=|.-.++
T Consensus 172 ~~~VNiiG--~~~~~~d~~el~~lL~~~Gi~v~~~~~~~~t~ee-i~~~~~A~lniv~~~~~~~~~a~~Le~~fGiP~~~ 248 (421)
T cd01976 172 PYDVNIIG--DYNIGGDAWASRILLEEMGLRVVAQWSGDGTLNE-MENAHKAKLNLIHCYRSMNYIARMMEEKYGIPWME 248 (421)
T ss_pred CCeEEEEe--cCCCCccHHHHHHHHHHcCCeEEEEeCCCCCHHH-HHhcccCCEEEEECcHHHHHHHHHHHHHhCCcEEe
Confidence 45566664 222345778999999999999985444 667755 45567777766664322 344443344777777
Q ss_pred EeeCccccccccchHhHHhhCCCe
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
..|+|++- ...+++.+|+..|..
T Consensus 249 ~~p~Gi~~-t~~~l~~ia~~~g~~ 271 (421)
T cd01976 249 YNFFGPTK-IAESLRKIAAYFDDE 271 (421)
T ss_pred cccCCHHH-HHHHHHHHHHHhCch
Confidence 77999653 357889999988864
No 59
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.20 E-value=1.9e+02 Score=29.51 Aligned_cols=70 Identities=27% Similarity=0.333 Sum_probs=49.3
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+.. =-.-+..+|.+.|..|.+... +-++. ...++|||+|+.=| +++-..=|.+||++||-+
T Consensus 157 Gk~vvViGrS~i----VGkPla~lL~~~~AtVtichs~T~nl~---~~~~~ADIvI~AvGk~~~i~~~~ik~gaiVIDv 228 (282)
T PRK14182 157 GKRALVVGRSNI----VGKPMAMMLLERHATVTIAHSRTADLA---GEVGRADILVAAIGKAELVKGAWVKEGAVVIDV 228 (282)
T ss_pred CCEEEEECCCCc----chHHHHHHHHHCCCEEEEeCCCCCCHH---HHHhhCCEEEEecCCcCccCHHHcCCCCEEEEe
Confidence 447889998741 112456667677888887775 33454 45688999988766 566666678999999985
No 60
>cd01078 NAD_bind_H4MPT_DH NADP binding domain of methylene tetrahydromethanopterin dehydrogenase. Methylene Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP binding domain. NADP-dependent H4MPT DH catalyzes the dehydrogenation of methylene- H4MPT and methylene-tetrahydrofolate (H4F) with NADP+ as cofactor. H4F and H4MPT are both cofactors that carry the one-carbon units between the formyl and methyl oxidation level. H4F and H4MPT are structurally analogous to each other with respect to the pterin moiety, but each has distinct side chain. H4MPT is present only in anaerobic methanogenic archaea and aerobic methylotrophic proteobacteria. H4MPT seems to have evolved independently from H4F and functions as a distinct carrier in C1 metabolism. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclo
Probab=24.16 E-value=3.2e+02 Score=25.25 Aligned_cols=70 Identities=24% Similarity=0.236 Sum_probs=42.5
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHH-cCCEEEEEeCCCCHHHHHHHHccCCEEEEechhhhhhh----cccCCCcEEEEE
Q 040560 289 RLLIISRKRTRTFTNASKIARMARR-LGFKVVVAEADMRLSRFARIVNSCDVLLGVHGAGLANI----VFLPENAVFIQV 363 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~-~gf~V~~~~~~~s~~eq~~l~~~advlVGvHGAgLtn~----lFl~pga~vIEi 363 (454)
++++++|+. ...+++.+.+++ .+.++...+ ..+..+..+.++.+|++|..=.+|..+. .+..++.+++.+
T Consensus 54 ~V~l~~R~~----~~~~~l~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~diVi~at~~g~~~~~~~~~~~~~~~vv~D~ 128 (194)
T cd01078 54 RVVLVGRDL----ERAQKAADSLRARFGEGVGAVE-TSDDAARAAAIKGADVVFAAGAAGVELLEKLAWAPKPLAVAADV 128 (194)
T ss_pred EEEEEcCCH----HHHHHHHHHHHhhcCCcEEEee-CCCHHHHHHHHhcCCEEEECCCCCceechhhhcccCceeEEEEc
Confidence 677777752 223444444432 366665554 3466666778899999999888887421 123346667764
No 61
>TIGR01283 nifE nitrogenase molybdenum-iron cofactor biosynthesis protein NifE. This protein is part of the NifEN complex involved in biosynthesis of the molybdenum-iron cofactor used by the homologous NifDK complex of nitrogenase. In a few species, the protein is found as a NifEN fusion protein.
Probab=24.09 E-value=1.4e+02 Score=32.09 Aligned_cols=95 Identities=9% Similarity=0.068 Sum_probs=63.2
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-h--hhhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-A--GLANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-A--gLtn~lFl~pga~vIE 362 (454)
+..+-+|.-. ...-+..|+.+.|++.|++|...-+ +.++ ++++-+.+|.+-|.+.+ + .++..|==+=|.-.++
T Consensus 197 ~~~VNiiG~~--~~~~d~~el~~lL~~~Gl~v~~~~~~~~s~-eei~~~~~A~lniv~~~~~~~~~a~~L~e~~GiP~~~ 273 (456)
T TIGR01283 197 VHDINLIGEF--NVAGEFWHVKPLLEKLGIRVLATITGDSRY-AEVQTAHRAKLNMVQCSKSMINLARKMEEKYGIPYFE 273 (456)
T ss_pred CCcEEEEcCC--CCcccHHHHHHHHHHcCCeEEEEeCCCCcH-HHHHhcccCcEEEEECHhHHHHHHHHHHHHcCCCEEe
Confidence 4556666532 2234667999999999999986555 5677 55556777788776543 3 3444443344777777
Q ss_pred EeeCccccccccchHhHHhhCCC
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKL 385 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl 385 (454)
..|+|++. ...+++.+|+.+|.
T Consensus 274 ~~~~G~~~-T~~~L~~Ia~~lg~ 295 (456)
T TIGR01283 274 GSFYGIED-TSKALRDIADLFGD 295 (456)
T ss_pred cCCCcHHH-HHHHHHHHHHHhCC
Confidence 77888654 34678889988884
No 62
>PRK12548 shikimate 5-dehydrogenase; Provisional
Probab=23.91 E-value=3.6e+02 Score=27.03 Aligned_cols=93 Identities=15% Similarity=0.149 Sum_probs=53.9
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHHcCCE--EEEEeCCCCHHHHHHHHccCCEEEEechhhhhh---------hcccCCC
Q 040560 289 RLLIISRKRTRTFTNASKIARMARRLGFK--VVVAEADMRLSRFARIVNSCDVLLGVHGAGLAN---------IVFLPEN 357 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~~gf~--V~~~~~~~s~~eq~~l~~~advlVGvHGAgLtn---------~lFl~pg 357 (454)
++++++|+.. .....+++.+.+.+.+.. +...+. .+..+.-+.+..+|++|.---.|+.. .-+++++
T Consensus 152 ~V~I~~R~~~-~~~~a~~l~~~l~~~~~~~~~~~~d~-~~~~~~~~~~~~~DilINaTp~Gm~~~~~~~~~~~~~~l~~~ 229 (289)
T PRK12548 152 EITIFNIKDD-FYERAEQTAEKIKQEVPECIVNVYDL-NDTEKLKAEIASSDILVNATLVGMKPNDGETNIKDTSVFRKD 229 (289)
T ss_pred EEEEEeCCch-HHHHHHHHHHHHhhcCCCceeEEech-hhhhHHHhhhccCCEEEEeCCCCCCCCCCCCCCCcHHhcCCC
Confidence 5888888631 012234555555444322 222222 11222234667889999777666643 2247888
Q ss_pred cEEEEEeeCccccccccchHhHHhhCCCeE
Q 040560 358 AVFIQVVPIAVEWLARDYFEEPSKAMKLRY 387 (454)
Q Consensus 358 a~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y 387 (454)
.+|++++- .+ ..+.+-..|+..|.+.
T Consensus 230 ~~v~D~vY---~P-~~T~ll~~A~~~G~~~ 255 (289)
T PRK12548 230 LVVADTVY---NP-KKTKLLEDAEAAGCKT 255 (289)
T ss_pred CEEEEecC---CC-CCCHHHHHHHHCCCee
Confidence 99999873 11 2366888899998765
No 63
>TIGR01282 nifD nitrogenase molybdenum-iron protein alpha chain. Nitrogenase consists of alpha (NifD) and beta (NifK) subunits of the molybdenum-iron protein and an ATP-binding iron-sulfur protein (NifH). This model describes a large clade of NifD proteins, but excludes a lineage that contains putative NifD and NifD homologs from species with vanadium-dependent nitrogenases.
Probab=23.89 E-value=1.7e+02 Score=31.74 Aligned_cols=95 Identities=9% Similarity=-0.052 Sum_probs=62.7
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEechh-h--hhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHGA-G--LANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHGA-g--Ltn~lFl~pga~vIE 362 (454)
+.++-+|. +.-.--|..|+.+.|++.|.++...-+ +.++ ++++.+.+|.+-|.+... + ++..|==+=|.-.++
T Consensus 207 ~~~VNiiG--~~~~~gd~~eik~lL~~~Gi~v~~~~sg~~t~-~~i~~~~~A~lniv~~~~~~~~~A~~Le~~fGiP~~~ 283 (466)
T TIGR01282 207 PYDVAIIG--DYNIGGDAWESRILLEEIGLRVVAQWSGDGTL-NEMENAPKAKLNLIHCYRSMNYISRHMEEKYGIPWME 283 (466)
T ss_pred CCeEEEEe--cCCCcccHHHHHHHHHHcCCeEEEEECCCCCH-HHHHhcccCCEEEEEChHHHHHHHHHHHHHhCCceEe
Confidence 45666665 222335778999999999999975444 5666 455567788877766432 2 233332234777888
Q ss_pred EeeCccccccccchHhHHhhCCC
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKL 385 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl 385 (454)
+.|+|++- ...+++.+|+.+|.
T Consensus 284 ~~~~Gi~~-T~~~Lr~ia~~~g~ 305 (466)
T TIGR01282 284 YNFFGPTK-IAESLRKIAEFFDD 305 (466)
T ss_pred CCCCCHHH-HHHHHHHHHHHHCc
Confidence 88899654 34678889988884
No 64
>TIGR01862 N2-ase-Ialpha nitrogenase component I, alpha chain. This model represents the alpha chain of all three varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of nitrogenase.
Probab=23.87 E-value=1.6e+02 Score=31.63 Aligned_cols=95 Identities=12% Similarity=0.090 Sum_probs=63.1
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEechh-h--hhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHGA-G--LANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHGA-g--Ltn~lFl~pga~vIE 362 (454)
+..+-||.= ....-|.+|+.+.|+++|++++..-+ +.+++| ++-+.+|..-|.+.+. + ++..|==+=|.-.+.
T Consensus 191 ~~~VNiig~--~~~~~d~~el~~lL~~~Gl~v~~~~~~~~t~ee-i~~~~~A~lniv~~~~~~~~~A~~L~er~GiP~~~ 267 (443)
T TIGR01862 191 EYDVNIIGE--YNIGGDAWVMRIYLEEMGIQVVATFTGDGTYDE-IRLMHKAKLNLVHCARSANYIANELEERYGIPWMK 267 (443)
T ss_pred CCeEEEEcc--CcCcccHHHHHHHHHHcCCeEEEEECCCCCHHH-HHhcccCCEEEEEChHHHHHHHHHHHHHhCCCeEe
Confidence 445666652 22345788999999999999976444 566754 5557777777665542 2 344443234777777
Q ss_pred EeeCccccccccchHhHHhhCCC
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKL 385 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl 385 (454)
..|+|++- ...++..+++..|+
T Consensus 268 ~~p~G~~~-t~~~l~~la~~~gi 289 (443)
T TIGR01862 268 IDFFGFTY-TAESLRAIAAFFGI 289 (443)
T ss_pred cccCCHHH-HHHHHHHHHHHhCC
Confidence 77888653 34788899988884
No 65
>cd03789 GT1_LPS_heptosyltransferase Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=23.84 E-value=1.1e+02 Score=29.86 Aligned_cols=41 Identities=10% Similarity=0.168 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHccCCEEEEechhhhhhhcccCCCcEEEEEeeC
Q 040560 324 DMRLSRFARIVNSCDVLLGVHGAGLANIVFLPENAVFIQVVPI 366 (454)
Q Consensus 324 ~~s~~eq~~l~~~advlVGvHGAgLtn~lFl~pga~vIEi~P~ 366 (454)
..++.|.+++++.||++||+-. |..|+-- --|.-+|-|++.
T Consensus 186 ~~~l~e~~~li~~~~l~I~~Ds-g~~HlA~-a~~~p~i~l~g~ 226 (279)
T cd03789 186 KTSLRELAALLARADLVVTNDS-GPMHLAA-ALGTPTVALFGP 226 (279)
T ss_pred CCCHHHHHHHHHhCCEEEeeCC-HHHHHHH-HcCCCEEEEECC
Confidence 5789999999999999999964 4444442 225666667754
No 66
>PRK14183 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=23.48 E-value=1.9e+02 Score=29.39 Aligned_cols=70 Identities=13% Similarity=0.183 Sum_probs=49.2
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+. ++ -.-+..+|.+.|..|.+... +-++ .+.+++|||+|..=| +++-..=|.+||++||.+
T Consensus 157 Gk~vvViGrS~---~V-G~Pla~lL~~~~AtVti~hs~T~~l---~~~~~~ADIvV~AvGkp~~i~~~~vk~gavvIDv 228 (281)
T PRK14183 157 GKDVCVVGASN---IV-GKPMAALLLNANATVDICHIFTKDL---KAHTKKADIVIVGVGKPNLITEDMVKEGAIVIDI 228 (281)
T ss_pred CCEEEEECCCC---cc-hHHHHHHHHHCCCEEEEeCCCCcCH---HHHHhhCCEEEEecCcccccCHHHcCCCcEEEEe
Confidence 34889999874 11 11345666667888876653 3233 357889999888766 677777788999999986
No 67
>cd01965 Nitrogenase_MoFe_beta_like Nitrogenase_MoFe_beta_like: Nitrogenase MoFe protein, beta subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. This group contains the beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having alpha and beta subunits similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (Fe
Probab=23.21 E-value=1.2e+02 Score=32.26 Aligned_cols=98 Identities=14% Similarity=0.174 Sum_probs=67.1
Q ss_pred CCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-------------------CCCHHHHHHHHccCCEEEEech-
Q 040560 286 KMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-------------------DMRLSRFARIVNSCDVLLGVHG- 345 (454)
Q Consensus 286 ~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-------------------~~s~~eq~~l~~~advlVGvHG- 345 (454)
.+.++-+|.-.. -.--|.+|+.+.+++.|.++..+-+ +.++ |+++-+.+|.+-|.++-
T Consensus 154 ~~~~VNlig~~~-~~~~d~~el~~lL~~~Gl~v~~~~~~s~~~d~~~~~~~~~~~~gg~~~-e~i~~~~~A~lniv~~~~ 231 (428)
T cd01965 154 KNGKVNLLPGFP-LTPGDVREIKRILEAFGLEPIILPDLSDSLDGHLTDGYSPLTKGGTTL-EEIRDAGNAKATIALGEY 231 (428)
T ss_pred CCCeEEEECCCC-CCccCHHHHHHHHHHcCCCEEEecCcccccCCCCCCCccccCCCCCcH-HHHHHhccCcEEEEEChh
Confidence 345566664321 1112889999999999999987532 2344 56667888888888877
Q ss_pred hhhhhhcccC--CCcEEEEEe-eCccccccccchHhHHhhCCCe
Q 040560 346 AGLANIVFLP--ENAVFIQVV-PIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 346 AgLtn~lFl~--pga~vIEi~-P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
+|..-.-+|. -|.-.+..- |+|++- ...+++.+++.+|..
T Consensus 232 ~~~~~a~~L~e~~GiP~~~~~~p~G~~~-t~~~l~~l~~~~g~~ 274 (428)
T cd01965 232 SGRKAAKALEEKFGVPYILFPTPIGLKA-TDEFLRALSKLSGKP 274 (428)
T ss_pred hhHHHHHHHHHHHCCCeeecCCCcChHH-HHHHHHHHHHHHCCC
Confidence 7766666665 366667765 888643 346788888888864
No 68
>PF02423 OCD_Mu_crystall: Ornithine cyclodeaminase/mu-crystallin family; InterPro: IPR003462 This entry represents the bacterial ornithine cyclodeaminase enzyme family, which catalyse the deamination of ornithine to proline []. The family also includes mu-crystallin, a mammalian homologue of bacterial ornithine cyclodeaminase [], which is the major component of the eye lens in several Australian marsupials. mRNA for mu-crystallin has also been found in human retina [].; PDB: 1U7H_B 1X7D_B 2I99_B 3HDJ_A 1VLL_B 1OMO_A.
Probab=22.94 E-value=1.2e+02 Score=30.84 Aligned_cols=69 Identities=17% Similarity=0.214 Sum_probs=42.3
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEechhhh----hhhcccCCCcEEEEEe
Q 040560 289 RLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHGAGL----ANIVFLPENAVFIQVV 364 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHGAgL----tn~lFl~pga~vIEi~ 364 (454)
++.+.+|+ -.+.+++++.+++.|++++..+ +. -+.+.+|||++..-.+.- -..=|++||+.|+-|=
T Consensus 155 ~v~v~~r~----~~~~~~~~~~~~~~~~~v~~~~---~~---~~av~~aDii~taT~s~~~~P~~~~~~l~~g~hi~~iG 224 (313)
T PF02423_consen 155 EVRVYSRS----PERAEAFAARLRDLGVPVVAVD---SA---EEAVRGADIIVTATPSTTPAPVFDAEWLKPGTHINAIG 224 (313)
T ss_dssp EEEEE-SS----HHHHHHHHHHHHCCCTCEEEES---SH---HHHHTTSSEEEE----SSEEESB-GGGS-TT-EEEE-S
T ss_pred EEEEEccC----hhHHHHHHHhhccccccceecc---ch---hhhcccCCEEEEccCCCCCCccccHHHcCCCcEEEEec
Confidence 55666654 3555788888877788887766 23 345889999999888766 4555789999988776
Q ss_pred eCc
Q 040560 365 PIA 367 (454)
Q Consensus 365 P~g 367 (454)
.+.
T Consensus 225 s~~ 227 (313)
T PF02423_consen 225 SYT 227 (313)
T ss_dssp -SS
T ss_pred CCC
Confidence 543
No 69
>PLN02928 oxidoreductase family protein
Probab=22.64 E-value=1.5e+02 Score=30.82 Aligned_cols=60 Identities=15% Similarity=0.294 Sum_probs=39.6
Q ss_pred HHHHHHHHcCCEEEEEeCCC-----------------------CHHHHHHHHccCCEEEEech-----hhhhhh---ccc
Q 040560 306 KIARMARRLGFKVVVAEADM-----------------------RLSRFARIVNSCDVLLGVHG-----AGLANI---VFL 354 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~~~-----------------------s~~eq~~l~~~advlVGvHG-----AgLtn~---lFl 354 (454)
++++.++.+|++|...+... +..+.-+++.+||+++-.=- -+|-|. --|
T Consensus 173 ~vA~~l~afG~~V~~~dr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ell~~aDiVvl~lPlt~~T~~li~~~~l~~M 252 (347)
T PLN02928 173 ELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSM 252 (347)
T ss_pred HHHHHHhhCCCEEEEECCCCChhhhhhhccccccccccccccCcccCHHHHHhhCCEEEECCCCChHhhcccCHHHHhcC
Confidence 67788888899998876521 11233478899999886421 233332 238
Q ss_pred CCCcEEEEEee
Q 040560 355 PENAVFIQVVP 365 (454)
Q Consensus 355 ~pga~vIEi~P 365 (454)
+||+.+|-+--
T Consensus 253 k~ga~lINvaR 263 (347)
T PLN02928 253 KKGALLVNIAR 263 (347)
T ss_pred CCCeEEEECCC
Confidence 99999998754
No 70
>cd01079 NAD_bind_m-THF_DH NAD binding domain of methylene-tetrahydrofolate dehydrogenase. The NAD-binding domain of methylene-tetrahydrofolate dehydrogenase (m-THF DH). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. M-THF DH is a component of an unusual monofunctional enzyme; in eukaryotes, m-THF DH is typically found as part of a multifunctional protein. NADP-dependent m-THF DHs in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofunctional DH, as well as bifunctional DH/cyclodrolase are found. In addition, yeast (S. cerevisiae) also express an monofunctional DH. This family contains only the monofunctional
Probab=22.53 E-value=1.5e+02 Score=28.53 Aligned_cols=74 Identities=15% Similarity=0.160 Sum_probs=49.5
Q ss_pred CCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEe--------------C-CC---CHHH-HHHHHccCCEEEEech-
Q 040560 286 KMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAE--------------A-DM---RLSR-FARIVNSCDVLLGVHG- 345 (454)
Q Consensus 286 ~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~--------------~-~~---s~~e-q~~l~~~advlVGvHG- 345 (454)
..-++++|.|+. ++ -.-+..+|.+.|..|.+.+ . .+ +... -.+.+++|||+|..=|
T Consensus 61 ~GK~vvVIGrS~---iV-GkPla~lL~~~~AtVti~~~~~~~~~~~~~~~~hs~t~~~~~~~~l~~~~~~ADIVIsAvG~ 136 (197)
T cd01079 61 YGKTITIINRSE---VV-GRPLAALLANDGARVYSVDINGIQVFTRGESIRHEKHHVTDEEAMTLDCLSQSDVVITGVPS 136 (197)
T ss_pred CCCEEEEECCCc---cc-hHHHHHHHHHCCCEEEEEecCcccccccccccccccccccchhhHHHHHhhhCCEEEEccCC
Confidence 345889999874 11 1245566777799998883 1 11 2222 3357899999988666
Q ss_pred hhh-hhhcccCCCcEEEEE
Q 040560 346 AGL-ANIVFLPENAVFIQV 363 (454)
Q Consensus 346 AgL-tn~lFl~pga~vIEi 363 (454)
+++ -..=|..||++||-+
T Consensus 137 ~~~~i~~d~ik~GavVIDV 155 (197)
T cd01079 137 PNYKVPTELLKDGAICINF 155 (197)
T ss_pred CCCccCHHHcCCCcEEEEc
Confidence 444 566788999999985
No 71
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=22.41 E-value=1.8e+02 Score=31.03 Aligned_cols=94 Identities=16% Similarity=0.223 Sum_probs=59.0
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCEEEEech--hhhhhhcccCCCcEEEEE-
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDVLLGVHG--AGLANIVFLPENAVFIQV- 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~advlVGvHG--AgLtn~lFl~pga~vIEi- 363 (454)
+..+.++.--. .-+..|+.+.|++.|+++..+=++.++.| +..+..+..++..+. ...+..| =+-|.-.+..
T Consensus 166 ~~~VniiG~~~---~~d~~el~~lL~~~Gi~v~~~lp~~~~~d-~~~~~~~~~~~~~~~~~~~~A~~L-~~~GiP~~~~~ 240 (427)
T PRK02842 166 HPSLVLVGSLA---DVVEDQLTLEFKKLGIGVVGFLPARRFTE-LPAIGPGTVVALAQPFLSDTARAL-RERGAKVLTAP 240 (427)
T ss_pred CCcEEEEEeCC---cchHHHHHHHHHHcCCeeEEEeCCccHHH-HhhcCcCcEEEEeCHHHHHHHHHH-HHcCCccccCC
Confidence 44556665432 35568899999999999863334555544 444444445544443 3455555 4556666555
Q ss_pred eeCccccccccchHhHHhhCCCe
Q 040560 364 VPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 364 ~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
+|+|++- ...+++.+|+..|+.
T Consensus 241 ~P~G~~~-T~~~L~~la~~~g~~ 262 (427)
T PRK02842 241 FPLGPEG-TRAWLEAAAAAFGID 262 (427)
T ss_pred CCcChHH-HHHHHHHHHHHhCcC
Confidence 7888653 356788999888864
No 72
>PF15183 MRAP: Melanocortin-2 receptor accessory protein family
Probab=22.18 E-value=81 Score=26.40 Aligned_cols=21 Identities=10% Similarity=0.205 Sum_probs=16.5
Q ss_pred hhhhHHHHHHHHHHHHHHhhh
Q 040560 19 FKYGALIGLFVIALSFCTVLK 39 (454)
Q Consensus 19 ~~~~~~~~~~l~~~~~~~~~~ 39 (454)
+|+++|++++.+.|++++-+.
T Consensus 44 v~LA~FV~~lF~iL~~ms~sg 64 (90)
T PF15183_consen 44 VSLAAFVVFLFLILLYMSWSG 64 (90)
T ss_pred HHHHHHHHHHHHHHHHHhccC
Confidence 688899999888888875443
No 73
>TIGR00507 aroE shikimate 5-dehydrogenase. This model finds proteins from prokaryotes and functionally equivalent domains from larger, multifunctional proteins of fungi and plants. Below the trusted cutoff of 180, but above the noise cutoff of 20, are the putative shikimate dehydrogenases of Thermotoga maritima and Mycobacterium tuberculosis, and uncharacterized paralogs of shikimate dehydrogenase from E. coli and H. influenzae. The related enzyme quinate 5-dehydrogenase scores below the noise cutoff. A neighbor-joining tree, constructed with quinate 5-dehydrogenases as the outgroup, shows the Clamydial homolog as clustering among the shikimate dehydrogenases, although the sequence is unusual in the degree of sequence divergence and the presence of an additional N-terminal domain.
Probab=22.11 E-value=3.3e+02 Score=26.83 Aligned_cols=51 Identities=18% Similarity=0.239 Sum_probs=36.8
Q ss_pred HccCCEEEEechhhhhhh----c----ccCCCcEEEEEeeCccccccccchHhHHhhCCCeEE
Q 040560 334 VNSCDVLLGVHGAGLANI----V----FLPENAVFIQVVPIAVEWLARDYFEEPSKAMKLRYL 388 (454)
Q Consensus 334 ~~~advlVGvHGAgLtn~----l----Fl~pga~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y~ 388 (454)
..++|++|..=++|+..- . +++++..|+++.-. + ..+.+...|+..|.+++
T Consensus 176 ~~~~DivInatp~gm~~~~~~~~~~~~~l~~~~~v~D~~y~---p-~~T~ll~~A~~~G~~~v 234 (270)
T TIGR00507 176 LHRVDLIINATSAGMSGNIDEPPVPAEKLKEGMVVYDMVYN---P-GETPFLAEAKSLGTKTI 234 (270)
T ss_pred ccCccEEEECCCCCCCCCCCCCCCCHHHcCCCCEEEEeccC---C-CCCHHHHHHHHCCCeee
Confidence 357999999988886432 1 36889999998632 1 13457788999998874
No 74
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=21.91 E-value=2.9e+02 Score=26.13 Aligned_cols=61 Identities=13% Similarity=0.130 Sum_probs=44.0
Q ss_pred CCCcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCCE-EEEech
Q 040560 285 KKMPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEADMRLSRFARIVNSCDV-LLGVHG 345 (454)
Q Consensus 285 ~~~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~adv-lVGvHG 345 (454)
+.++++++-.=.|-..=+...-+..+++..||+|+.+..+.|.++.++.+...+. +||+-.
T Consensus 82 ~~~~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~~pd~v~lS~ 143 (197)
T TIGR02370 82 EVLGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKPLMLTGSA 143 (197)
T ss_pred CCCCeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCCEEEEcc
Confidence 3467888877666555566666667788889999876668999999888877655 454433
No 75
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.85 E-value=1.6e+02 Score=29.88 Aligned_cols=70 Identities=14% Similarity=0.212 Sum_probs=49.2
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+.. + -.-+..+|.+.|..|.+... +-++. +..++|||+|..=| +++-..=|.+||++||-+
T Consensus 158 Gk~vvViGrS~~---V-GkPla~lL~~~~ATVt~chs~T~dl~---~~~k~ADIvIsAvGkp~~i~~~~vk~gavVIDv 229 (282)
T PRK14180 158 GAYAVVVGASNV---V-GKPVSQLLLNAKATVTTCHRFTTDLK---SHTTKADILIVAVGKPNFITADMVKEGAVVIDV 229 (282)
T ss_pred CCEEEEECCCCc---c-hHHHHHHHHHCCCEEEEEcCCCCCHH---HHhhhcCEEEEccCCcCcCCHHHcCCCcEEEEe
Confidence 347889998741 1 12455666667889987764 33344 45788999988766 567677778999999986
No 76
>PRK14186 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.76 E-value=2.1e+02 Score=29.30 Aligned_cols=70 Identities=20% Similarity=0.321 Sum_probs=48.4
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+. ++ -.-+..+|.+.|..|.+... +-++. +..++|||+|..=| +++-..=|.+||++||-+
T Consensus 158 Gk~vvVIGrS~---iV-GkPla~lL~~~~atVtv~hs~T~~l~---~~~~~ADIvIsAvGkp~~i~~~~ik~gavVIDv 229 (297)
T PRK14186 158 GKKAVVVGRSI---LV-GKPLALMLLAANATVTIAHSRTQDLA---SITREADILVAAAGRPNLIGAEMVKPGAVVVDV 229 (297)
T ss_pred CCEEEEECCCc---cc-hHHHHHHHHHCCCEEEEeCCCCCCHH---HHHhhCCEEEEccCCcCccCHHHcCCCCEEEEe
Confidence 34788999874 11 12455667677999988765 43444 45678999988766 455555588999999985
No 77
>PRK06932 glycerate dehydrogenase; Provisional
Probab=21.74 E-value=1.2e+02 Score=30.89 Aligned_cols=60 Identities=23% Similarity=0.368 Sum_probs=38.8
Q ss_pred HHHHHHHHcCCEEEEEeC-C-----CCHHHHHHHHccCCEEEE-----echhhhhhhc---ccCCCcEEEEEee
Q 040560 306 KIARMARRLGFKVVVAEA-D-----MRLSRFARIVNSCDVLLG-----VHGAGLANIV---FLPENAVFIQVVP 365 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~-~-----~s~~eq~~l~~~advlVG-----vHGAgLtn~l---Fl~pga~vIEi~P 365 (454)
++++.++.+|.+|...+. . ....+.-.++..||+++- ..--||-|.= -|+||+++|-+--
T Consensus 161 ~va~~l~~fg~~V~~~~~~~~~~~~~~~~~l~ell~~sDiv~l~~Plt~~T~~li~~~~l~~mk~ga~lIN~aR 234 (314)
T PRK06932 161 EVGRLAQALGMKVLYAEHKGASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGR 234 (314)
T ss_pred HHHHHHhcCCCEEEEECCCcccccccccCCHHHHHHhCCEEEEcCCCChHHhcccCHHHHHhCCCCeEEEECCC
Confidence 677888888999987765 1 112234577889999873 2222333322 2899999997653
No 78
>PRK03094 hypothetical protein; Provisional
Probab=21.56 E-value=1.3e+02 Score=24.83 Aligned_cols=20 Identities=15% Similarity=0.396 Sum_probs=16.5
Q ss_pred CHHHHHHHHHHcCCEEEEEe
Q 040560 303 NASKIARMARRLGFKVVVAE 322 (454)
Q Consensus 303 Ne~ev~~~l~~~gf~V~~~~ 322 (454)
++..|.+.|++.||+|+-++
T Consensus 9 ~Ls~i~~~L~~~GYeVv~l~ 28 (80)
T PRK03094 9 SLTDVQQALKQKGYEVVQLR 28 (80)
T ss_pred CcHHHHHHHHHCCCEEEecC
Confidence 56678899999999997655
No 79
>PRK15438 erythronate-4-phosphate dehydrogenase PdxB; Provisional
Probab=21.55 E-value=1.6e+02 Score=31.11 Aligned_cols=60 Identities=18% Similarity=0.248 Sum_probs=38.9
Q ss_pred HHHHHHHHcCCEEEEEeC-C------CCHHHHHHHHccCCEEE--Eech-------hhhhhh---cccCCCcEEEEEee
Q 040560 306 KIARMARRLGFKVVVAEA-D------MRLSRFARIVNSCDVLL--GVHG-------AGLANI---VFLPENAVFIQVVP 365 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~-~------~s~~eq~~l~~~advlV--GvHG-------AgLtn~---lFl~pga~vIEi~P 365 (454)
.+++.++.+|++|...++ . ..+.+.-.++..|||++ .+.- -||-|. ==|+||+.+|-+--
T Consensus 130 ~vA~~l~a~G~~V~~~dp~~~~~~~~~~~~~L~ell~~sDiI~lh~PLt~~g~~~T~~li~~~~l~~mk~gailIN~aR 208 (378)
T PRK15438 130 RLQARLEALGIKTLLCDPPRADRGDEGDFRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACR 208 (378)
T ss_pred HHHHHHHHCCCEEEEECCcccccccccccCCHHHHHhhCCEEEEeCCCCCCcccccccccCHHHHhcCCCCcEEEECCC
Confidence 677888889999998876 1 12333456778899998 3321 133332 22799999886543
No 80
>PRK00258 aroE shikimate 5-dehydrogenase; Reviewed
Probab=21.42 E-value=2.6e+02 Score=27.81 Aligned_cols=53 Identities=15% Similarity=0.196 Sum_probs=38.8
Q ss_pred HHHccCCEEEEechhhhhh--------hcccCCCcEEEEEeeCccccccccchHhHHhhCCCeEE
Q 040560 332 RIVNSCDVLLGVHGAGLAN--------IVFLPENAVFIQVVPIAVEWLARDYFEEPSKAMKLRYL 388 (454)
Q Consensus 332 ~l~~~advlVGvHGAgLtn--------~lFl~pga~vIEi~P~g~~~~~~~~y~~~A~~~gl~Y~ 388 (454)
..+..+|++|..-.+|+-. .-++++++.|++++-. + ..+.|-..|+..|++.+
T Consensus 181 ~~~~~~DivInaTp~g~~~~~~~~~~~~~~l~~~~~v~DivY~---P-~~T~ll~~A~~~G~~~~ 241 (278)
T PRK00258 181 EELADFDLIINATSAGMSGELPLPPLPLSLLRPGTIVYDMIYG---P-LPTPFLAWAKAQGARTI 241 (278)
T ss_pred hccccCCEEEECCcCCCCCCCCCCCCCHHHcCCCCEEEEeecC---C-CCCHHHHHHHHCcCeec
Confidence 4567899999999998843 1346888999999742 1 23567788999998653
No 81
>TIGR02015 BchY chlorophyllide reductase subunit Y. This model represents the Y subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Probab=21.41 E-value=1.4e+02 Score=31.77 Aligned_cols=81 Identities=11% Similarity=0.148 Sum_probs=57.6
Q ss_pred CHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHccCC--EEEEechhhhhhhcccCCCcEEEEEeeCccccccccchHhHH
Q 040560 303 NASKIARMARRLGFKVVVAEADMRLSRFARIVNSCD--VLLGVHGAGLANIVFLPENAVFIQVVPIAVEWLARDYFEEPS 380 (454)
Q Consensus 303 Ne~ev~~~l~~~gf~V~~~~~~~s~~eq~~l~~~ad--vlVGvHGAgLtn~lFl~pga~vIEi~P~g~~~~~~~~y~~~A 380 (454)
|..|+.+.+++.|.++.++-+..+++|.-+ +.+|. ++++.+. +.+-.++..-|.-.++..|+|++- ...+.+.+|
T Consensus 178 d~~eik~lL~~~Gi~~~~~~~G~~~~ei~~-a~~A~~~i~l~~~~-~~a~~l~~~~GvP~~~~~PiG~~~-Td~fL~~la 254 (422)
T TIGR02015 178 DAMVIGGVLQPIGVESGPTVPGRDWRELYA-ALDSSAVAVLHPFY-EATARLFEAAGVKIVGSAPVGANG-TGEWLERIG 254 (422)
T ss_pred cHHHHHHHHHHcCCCeEEecCCCCHHHHHh-hhcCeEEEEeCccc-hHHHHHHHHcCCceeccCCCChHH-HHHHHHHHH
Confidence 677889999999999977666557755544 44444 4444333 456677777777778888999754 356788899
Q ss_pred hhCCCe
Q 040560 381 KAMKLR 386 (454)
Q Consensus 381 ~~~gl~ 386 (454)
+..|..
T Consensus 255 ~~~G~~ 260 (422)
T TIGR02015 255 EALDLD 260 (422)
T ss_pred HHhCcC
Confidence 998864
No 82
>TIGR01860 VNFD nitrogenase vanadium-iron protein, alpha chain. This model represents the alpha chain of the vanadium-containing component of the vanadium-iron nitrogenase compound I. The complex also includes a second alpha chain, two beta chains and two delta chains. Compount I interacts with compound II also known as the iron-protein which transfers electrons to compound I where the catalysis occurs.
Probab=21.41 E-value=1.4e+02 Score=32.34 Aligned_cols=96 Identities=9% Similarity=0.108 Sum_probs=64.0
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech--hh-hhhhcccCCCcEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG--AG-LANIVFLPENAVFIQ 362 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG--Ag-Ltn~lFl~pga~vIE 362 (454)
+..+-+|. +....-|..|+.+.|++.|+++...-+ +.+++|. +-+.+|.+-|.+.+ ++ ++..|-=+=|.-.++
T Consensus 201 ~~~VNiiG--~~~~~gd~~el~~lL~~~Gi~v~~~~~g~~t~~ei-~~~~~A~lnlv~~~~~~~~~A~~Leer~GiP~~~ 277 (461)
T TIGR01860 201 EYTINVIG--DYNIQGDTQVLQKYWDKMGIQVIAHFTGNGTYDDL-RCMHRAQLNVVNCARSAGYIANELKKRYGIPRLD 277 (461)
T ss_pred CCcEEEEC--CCCCcccHHHHHHHHHHcCCcEEEEeCCCCCHHHH-HhcccCcEEEEECchHHHHHHHHHHHHhCCCeec
Confidence 34566664 333445778999999999999975444 6778664 45677777554433 22 444444455777788
Q ss_pred EeeCccccccccchHhHHhhCCCe
Q 040560 363 VVPIAVEWLARDYFEEPSKAMKLR 386 (454)
Q Consensus 363 i~P~g~~~~~~~~y~~~A~~~gl~ 386 (454)
+.|+|++- ...+.+.+|+..|+.
T Consensus 278 ~~p~Gi~~-T~~~L~~la~~~g~~ 300 (461)
T TIGR01860 278 VDTWGFNY-MAEALRKIGAFFGIE 300 (461)
T ss_pred CCcCCHHH-HHHHHHHHHHHhCCc
Confidence 88999654 346788899988854
No 83
>PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=21.31 E-value=2e+02 Score=30.39 Aligned_cols=70 Identities=19% Similarity=0.277 Sum_probs=49.7
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|.. +=-.-+..+|.+.|..|.+... +-++.+ ..++|||+|..=| +++-..=|.+||++||-+
T Consensus 231 GK~vvVIGRS~----iVGkPLa~LL~~~~ATVTicHs~T~nl~~---~~r~ADIVIsAvGkp~~i~~d~vK~GAvVIDV 302 (364)
T PLN02616 231 GKRAVVIGRSN----IVGMPAALLLQREDATVSIVHSRTKNPEE---ITREADIIISAVGQPNMVRGSWIKPGAVVIDV 302 (364)
T ss_pred CCEEEEECCCc----cccHHHHHHHHHCCCeEEEeCCCCCCHHH---HHhhCCEEEEcCCCcCcCCHHHcCCCCEEEec
Confidence 34788999874 1112455666677888888775 444444 5688999887666 667777789999999985
No 84
>PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.84 E-value=2.2e+02 Score=28.92 Aligned_cols=70 Identities=19% Similarity=0.235 Sum_probs=49.1
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+.. =-.-+..+|.+.|..|.+... +-++ .+..++|||+|..=| +++-..=|.+||++||-+
T Consensus 157 Gk~vvVvGrS~i----VGkPla~lL~~~~atVt~chs~T~nl---~~~~~~ADIvIsAvGkp~~i~~~~vk~GavVIDv 228 (282)
T PRK14166 157 GKDAVIIGASNI----VGRPMATMLLNAGATVSVCHIKTKDL---SLYTRQADLIIVAAGCVNLLRSDMVKEGVIVVDV 228 (282)
T ss_pred CCEEEEECCCCc----chHHHHHHHHHCCCEEEEeCCCCCCH---HHHHhhCCEEEEcCCCcCccCHHHcCCCCEEEEe
Confidence 447888998741 112455666667999987764 3333 336788999887766 567777788999999985
No 85
>PRK06487 glycerate dehydrogenase; Provisional
Probab=20.70 E-value=1.4e+02 Score=30.44 Aligned_cols=59 Identities=19% Similarity=0.321 Sum_probs=37.7
Q ss_pred HHHHHHHHcCCEEEEEeCC-----CCHHHHHHHHccCCEEEE-----echhhhhhh---cccCCCcEEEEEe
Q 040560 306 KIARMARRLGFKVVVAEAD-----MRLSRFARIVNSCDVLLG-----VHGAGLANI---VFLPENAVFIQVV 364 (454)
Q Consensus 306 ev~~~l~~~gf~V~~~~~~-----~s~~eq~~l~~~advlVG-----vHGAgLtn~---lFl~pga~vIEi~ 364 (454)
++++.++.+|++|...+.. ....+.-.++..||+++- ..--||-|. =-|+||+.+|-+-
T Consensus 162 ~vA~~l~~fgm~V~~~~~~~~~~~~~~~~l~ell~~sDiv~l~lPlt~~T~~li~~~~~~~mk~ga~lIN~a 233 (317)
T PRK06487 162 AVARLAEAFGMRVLIGQLPGRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTA 233 (317)
T ss_pred HHHHHHhhCCCEEEEECCCCCcccccccCHHHHHHhCCEEEECCCCChHHhcCcCHHHHhcCCCCeEEEECC
Confidence 6778888889999877741 111233457888999873 222233332 2289999998764
No 86
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=20.49 E-value=1.4e+02 Score=26.19 Aligned_cols=54 Identities=22% Similarity=0.328 Sum_probs=37.1
Q ss_pred cCHHHHHHHHHHcCCEEEEEeC---C-CCHHHHHH-HHccCCEEEEechhhhhhhcccC
Q 040560 302 TNASKIARMARRLGFKVVVAEA---D-MRLSRFAR-IVNSCDVLLGVHGAGLANIVFLP 355 (454)
Q Consensus 302 ~Ne~ev~~~l~~~gf~V~~~~~---~-~s~~eq~~-l~~~advlVGvHGAgLtn~lFl~ 355 (454)
.|-.-+.+.+++.|+++..... + -.+.++++ ...++|++|.-=|.|.+--=++|
T Consensus 19 ~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~i~~~~~~~DlvittGG~g~g~~D~t~ 77 (133)
T cd00758 19 TNGPALEALLEDLGCEVIYAGVVPDDADSIRAALIEASREADLVLTTGGTGVGRRDVTP 77 (133)
T ss_pred chHHHHHHHHHHCCCEEEEeeecCCCHHHHHHHHHHHHhcCCEEEECCCCCCCCCcchH
Confidence 4556677889999999865543 1 34666665 44669999999888876543333
No 87
>TIGR02690 resist_ArsH arsenical resistance protein ArsH. Members of this protein family occur in arsenate resistance operons that include at least two different types of arsenate reductase. ArsH is not required for arsenate resistance in some systems. This family belongs to the larger family of NADPH-dependent FMN reductases (Pfam model pfam03358). The function of ArsH is not known.
Probab=20.30 E-value=4.4e+02 Score=25.69 Aligned_cols=57 Identities=12% Similarity=0.232 Sum_probs=34.6
Q ss_pred cCCCcEEEEEEeCCCccccCHHHHHH----HHHHcCCEEEEEeC-CCC-----------HHHHHHHHccCCEEE
Q 040560 284 KKKMPRLLIISRKRTRTFTNASKIAR----MARRLGFKVVVAEA-DMR-----------LSRFARIVNSCDVLL 341 (454)
Q Consensus 284 ~~~~prl~~i~R~~~R~i~Ne~ev~~----~l~~~gf~V~~~~~-~~s-----------~~eq~~l~~~advlV 341 (454)
+++.++|++|.... |.=.+-..+++ .+.+.|+++.+++. +++ +.+..+.+..||.+|
T Consensus 23 ~~~~~kI~~I~GSl-R~~S~n~~la~~~~~~~~~~g~~v~~idl~~lPl~~~d~~~~p~v~~l~~~v~~ADgvi 95 (219)
T TIGR02690 23 KPHIPRILLLYGSL-RERSYSRLLAEEAARLLGCEGRETRIFDPPGLPLPDAAHADHPKVRELRQLSEWSEGQV 95 (219)
T ss_pred CCCCCEEEEEECCC-CCcchHHHHHHHHHHHHhhcCCEEEEeCcccCCCCCcCcccCHHHHHHHHHHHhCCEEE
Confidence 36778999998663 33333333333 33434899888875 332 234556778888765
No 88
>PRK14170 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.24 E-value=2.7e+02 Score=28.43 Aligned_cols=70 Identities=20% Similarity=0.342 Sum_probs=49.5
Q ss_pred CcEEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHccCCEEEEech-hhhhhhcccCCCcEEEEE
Q 040560 287 MPRLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA-DMRLSRFARIVNSCDVLLGVHG-AGLANIVFLPENAVFIQV 363 (454)
Q Consensus 287 ~prl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~-~~s~~eq~~l~~~advlVGvHG-AgLtn~lFl~pga~vIEi 363 (454)
.-++++|.|+.. + -.-+..+|.+.|..|.+... +-++ -+..++|||+|..=| +++-..=|..||++||-+
T Consensus 157 Gk~vvVvGrS~i---V-GkPla~lL~~~~atVtichs~T~~l---~~~~~~ADIvI~AvG~~~~i~~~~vk~GavVIDv 228 (284)
T PRK14170 157 GKRAVVIGRSNI---V-GKPVAQLLLNENATVTIAHSRTKDL---PQVAKEADILVVATGLAKFVKKDYIKPGAIVIDV 228 (284)
T ss_pred CCEEEEECCCCc---c-hHHHHHHHHHCCCEEEEeCCCCCCH---HHHHhhCCEEEEecCCcCccCHHHcCCCCEEEEc
Confidence 448899998841 1 12355666667889987775 3334 345788999988776 567777788999999985
No 89
>cd08190 HOT Hydroxyacid-oxoacid transhydrogenase (HOT) involved in gamma-hydroxybutyrate metabolism. Hydroxyacid-oxoacid transhydrogenase (HOT), also known as D-2-hydroxyglutarate transhydrogenase. It catalyzes the conversion of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA), coupled to the stoichiometric conversion of alpha-ketoglutarate to D-2-hydroxyglutarate in gamma-Hydroxybutyrate catabolism. Unlike many other alcohols, which are oxidized by NAD-linked dehydrogenases, gamma-hydroxybutyrate is metabolized to succinate semialdehyde by hydroxyacid-oxoacid transhydrogenase which does not require free NAD or NADP, but instead using alpha -ketoglutarate as an acceptor, converting it to d-2-hydroxyglutarate. Alpha-ketoglutarate serves as an intermediate acceptor to regenerate NAD(P) required for the oxidation of GHB. HOT also catalyzes the reversible oxidation of a hydroxyacid obligatorily coupled to the reduction of an oxoacid, and requires no cofactor. In mammals, the HOT
Probab=20.21 E-value=3.3e+02 Score=28.88 Aligned_cols=58 Identities=10% Similarity=0.201 Sum_probs=38.3
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC---CCC---HHHHHHHH--ccCCEEEEechh
Q 040560 289 RLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA---DMR---LSRFARIV--NSCDVLLGVHGA 346 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~---~~s---~~eq~~l~--~~advlVGvHGA 346 (454)
|+++|.-++.++.--.+++.+.|++.|.++.+.+. +-+ +.+-++.+ .++|+|||+=|-
T Consensus 25 ~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (414)
T cd08190 25 RVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGG 90 (414)
T ss_pred eEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 66777655555544468899999988988876642 222 34444444 368999999664
No 90
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=20.19 E-value=3.6e+02 Score=27.89 Aligned_cols=57 Identities=12% Similarity=0.248 Sum_probs=37.7
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC---CCC---HHHHHHHH--ccCCEEEEech
Q 040560 289 RLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA---DMR---LSRFARIV--NSCDVLLGVHG 345 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~---~~s---~~eq~~l~--~~advlVGvHG 345 (454)
|++++.-++.++.--.+++.+.|++.|.++.+++. +-+ +.+-++.+ .++|++||+=|
T Consensus 26 ~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGG 90 (370)
T cd08192 26 RPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGG 90 (370)
T ss_pred eEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 66666655544433456889999998988876542 222 44444444 57899999988
No 91
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=20.13 E-value=3.5e+02 Score=28.35 Aligned_cols=57 Identities=16% Similarity=0.335 Sum_probs=37.7
Q ss_pred EEEEEEeCCCccccCHHHHHHHHHHcCCEEEEEeC---CCC---HHHHHHHH--ccCCEEEEech
Q 040560 289 RLLIISRKRTRTFTNASKIARMARRLGFKVVVAEA---DMR---LSRFARIV--NSCDVLLGVHG 345 (454)
Q Consensus 289 rl~~i~R~~~R~i~Ne~ev~~~l~~~gf~V~~~~~---~~s---~~eq~~l~--~~advlVGvHG 345 (454)
|++++.-++-++.--.+++.+.|++.|.++.+.+. +-+ +.+-++++ .++|++||+=|
T Consensus 33 ~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGG 97 (383)
T PRK09860 33 RTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGG 97 (383)
T ss_pred EEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 66667654444444456899999998988766542 222 44444444 56899999988
Done!