Query 027494
Match_columns 222
No_of_seqs 110 out of 1052
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 10:45:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027494.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027494hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10281 hypothetical protein; 100.0 3.1E-43 6.8E-48 301.8 23.5 207 1-222 71-299 (299)
2 COG0384 Predicted epimerase, P 100.0 2.6E-42 5.6E-47 292.3 22.5 205 1-222 71-291 (291)
3 KOG3033 Predicted PhzC/PhzF-ty 100.0 2.6E-40 5.7E-45 268.1 19.5 205 1-222 75-286 (286)
4 TIGR00654 PhzF_family phenazin 100.0 1.1E-39 2.3E-44 280.2 23.5 207 1-222 71-297 (297)
5 PF02567 PhzC-PhzF: Phenazine 100.0 1.9E-39 4E-44 276.5 12.0 207 1-218 64-281 (281)
6 PRK00450 dapF diaminopimelate 100.0 3E-34 6.5E-39 243.8 16.8 199 1-222 70-272 (274)
7 TIGR00652 DapF diaminopimelate 100.0 3.3E-29 7.1E-34 212.3 18.3 194 1-222 69-268 (268)
8 PRK13577 diaminopimelate epime 100.0 3.4E-29 7.5E-34 213.5 17.1 197 1-222 69-274 (281)
9 PLN02536 diaminopimelate epime 100.0 2.4E-27 5.3E-32 200.4 19.0 199 1-222 55-267 (267)
10 COG0253 DapF Diaminopimelate e 99.9 3.2E-26 6.9E-31 191.8 19.8 195 2-222 71-272 (272)
11 PRK13969 proline racemase; Pro 99.3 9.8E-11 2.1E-15 101.8 15.7 200 1-221 88-321 (334)
12 PRK13971 hydroxyproline-2-epim 99.2 1.7E-09 3.8E-14 93.8 17.8 41 1-41 87-130 (333)
13 PF01678 DAP_epimerase: Diamin 99.1 2.2E-09 4.8E-14 80.3 11.3 112 96-215 3-121 (121)
14 PRK13970 hydroxyproline-2-epim 99.0 8.9E-09 1.9E-13 88.3 13.2 188 1-222 86-299 (311)
15 PF05544 Pro_racemase: Proline 98.8 2.3E-07 4.9E-12 80.4 13.9 193 1-221 80-313 (325)
16 COG3938 Proline racemase [Amin 98.7 3.2E-07 7E-12 77.2 13.2 40 1-40 88-131 (341)
17 PF01678 DAP_epimerase: Diamin 97.0 0.0022 4.7E-08 47.7 6.1 40 2-41 67-106 (121)
18 PRK13577 diaminopimelate epime 95.5 0.21 4.4E-06 42.7 10.8 92 97-199 8-107 (281)
19 COG0253 DapF Diaminopimelate e 95.2 0.14 3E-06 43.6 8.6 93 98-200 9-109 (272)
20 TIGR00654 PhzF_family phenazin 95.1 0.17 3.8E-06 43.3 9.2 89 98-200 17-111 (297)
21 PRK00450 dapF diaminopimelate 94.9 0.27 5.8E-06 41.6 9.6 92 97-200 10-109 (274)
22 TIGR00652 DapF diaminopimelate 94.4 0.54 1.2E-05 39.8 10.2 92 97-199 8-107 (268)
23 PF02567 PhzC-PhzF: Phenazine 91.6 0.68 1.5E-05 39.2 6.8 88 98-198 10-101 (281)
24 PRK10281 hypothetical protein; 91.0 1.8 3.9E-05 37.3 8.8 90 98-200 17-110 (299)
25 COG0384 Predicted epimerase, P 90.3 1.9 4.1E-05 37.2 8.2 94 97-202 17-113 (291)
26 PLN02536 diaminopimelate epime 89.8 3 6.5E-05 35.4 9.1 73 120-199 13-94 (267)
27 PF04303 PrpF: PrpF protein; 74.2 7.3 0.00016 34.7 5.3 77 143-222 281-370 (371)
28 PRK13971 hydroxyproline-2-epim 71.7 29 0.00063 30.5 8.4 33 141-176 71-103 (333)
29 TIGR02334 prpF probable AcnD-a 59.0 31 0.00068 31.0 6.2 77 143-222 294-385 (390)
30 PRK13969 proline racemase; Pro 46.7 1.3E+02 0.0029 26.4 8.2 54 141-200 72-131 (334)
31 PRK13970 hydroxyproline-2-epim 34.0 80 0.0017 27.5 4.7 54 141-200 70-125 (311)
32 PF01170 UPF0020: Putative RNA 29.2 40 0.00088 26.5 2.0 19 2-20 35-53 (179)
33 COG0116 Predicted N6-adenine-s 24.1 56 0.0012 29.3 2.1 18 2-19 198-215 (381)
34 PF13793 Pribosyltran_N: N-ter 24.1 2.7E+02 0.0059 20.3 5.5 39 163-201 5-43 (116)
35 PF01555 N6_N4_Mtase: DNA meth 22.8 25 0.00054 27.9 -0.3 27 148-174 185-211 (231)
36 PF02384 N6_Mtase: N-6 DNA Met 22.8 41 0.00089 28.7 1.0 16 158-173 50-65 (311)
37 PF14354 Lar_restr_allev: Rest 20.6 32 0.0007 21.7 -0.1 8 2-9 7-14 (61)
38 PF10648 Gmad2: Immunoglobulin 20.3 1.4E+02 0.003 20.8 3.1 17 204-221 16-32 (88)
No 1
>PRK10281 hypothetical protein; Provisional
Probab=100.00 E-value=3.1e-43 Score=301.76 Aligned_cols=207 Identities=22% Similarity=0.353 Sum_probs=168.3
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCC-CCcccH
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTAD-FNFSEV 79 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~-~~~~~~ 79 (222)
||||||||||++|+|++.+....+.++|+|++|.+++++.. ++ +.+.++|.+|.+.+.. ....+.
T Consensus 71 v~fcGHaTlaa~~~L~~~~~~~~~~~~~~t~~G~v~v~~~~-----------~~---~~~~~~~~~~~p~~~~~~~~~~~ 136 (299)
T PRK10281 71 VPICGHATVAAHYVRATVLGLGNCTVWQTTLAGILPVDIEK-----------EN---DDYRISMTQGTPEFEPPLEGETR 136 (299)
T ss_pred cccCCcHHHHHHHHHHHhCCCCCCcEEEEcCceEEEEEEEe-----------cC---CeEEEEEecCCCcccCCCCccCH
Confidence 79999999999999998876656679999999999999964 21 2346778887765442 222235
Q ss_pred HHHHHHhCCCceeeee-------ecCCCceEEEEeCChhhhcccCCChhhHhcCCC---CceEEEEeeCCCCCcccEEEe
Q 027494 80 SLILEALGVSSVVDMK-------ITTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG---TRGIIVSGLAPPESGFDFYSR 149 (222)
Q Consensus 80 ~~l~~algl~~~~~~~-------~~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~---~~gv~v~~~~~~~~~~~~~~R 149 (222)
++++++||+++ .++. +++|.+|++|+++|.++|.+++||++++.++++ ..|+++|+..+.+++.++++|
T Consensus 137 ~~l~~~lgl~~-~~i~~~~p~~~~~~G~~~liv~l~~~~~l~~~~pd~~~l~~l~~~~~~~g~~v~~~~~~~~~~~~~~R 215 (299)
T PRK10281 137 AAIINALGLTE-DDILPGLPIQVASTGHSKVMIPLKPEVDLDALSPNLAALTAISKQIGCNGFFPFQIRPGKNEILTDGR 215 (299)
T ss_pred HHHHHHhCCCh-HHcCcCCCcEEEecCCceEEEEeCCHHHHHhCCCCHHHHHHHHHhcCCcEEEEEEecCCCCCceEEEe
Confidence 77889999876 4432 678999999999999999999999999999874 368999887643334569999
Q ss_pred ecCCCCCCCccCccccchhhhHHHHHhh-----hCC-ceEEEeec--cCCCeEEEEEEccCCC---eEEEeeeEEEEEEE
Q 027494 150 FFCPKFGVNEDPVCGSAYCALATYWSQK-----LGK-CDFVAYAA--SPRSGILNIHLDEQNQ---RVQLRGKAITVMQG 218 (222)
Q Consensus 150 ~f~p~~Gv~EDpatGSa~~ala~yl~~~-----~~~-~~~~~~Qg--~~r~g~l~v~~~~~~~---~v~v~G~a~~v~~G 218 (222)
+|+|..|+.||||||||+|+||+||.++ .++ ..+.++|| ++|+|+|+|+++.+++ +|+|+|+|+++++|
T Consensus 216 ~FaP~~Gi~EDPaTGSA~~aLa~yl~~~~~~~~~~~~~~~~~~QG~~~gR~g~l~~~~~~~~~~~~~V~vgG~av~v~~G 295 (299)
T PRK10281 216 MFAPAIGIVEDPVTGNANGPMGAYLVHHNLLPHDGKVLRFKGHQGRALGRDGTIEVTVTIRDNQPEKVTISGQAVILFHA 295 (299)
T ss_pred eCCCCCCCccCcccchhhhHHHHHHHHcCCCCCCCceeEEEEEcCcCcCCCeEEEEEEEecCCCEEEEEEeeEEEEEEEE
Confidence 9999999999999999999999999752 123 46889999 6899999999964334 89999999999999
Q ss_pred EEEC
Q 027494 219 SLLV 222 (222)
Q Consensus 219 ~i~~ 222 (222)
+|.+
T Consensus 296 ~l~~ 299 (299)
T PRK10281 296 EWAI 299 (299)
T ss_pred EEeC
Confidence 9975
No 2
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=100.00 E-value=2.6e-42 Score=292.26 Aligned_cols=205 Identities=30% Similarity=0.475 Sum_probs=170.5
Q ss_pred CCCCChHHHHHHHHHHhcCCCCC-CcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcccH
Q 027494 1 MELCGHAALAAAHTLFSRGLVNS-NTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSEV 79 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~-~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~~ 79 (222)
||||||||||++|+|++.+.... ..++|+|++|.+++++.. .+ +. ..|.+|..........+.
T Consensus 71 vpf~GHaTlga~~~l~~~~~~~~~~~~~~e~~aG~v~i~~~~-----------~~---~~--~~~~~p~~~~~~~~~~~~ 134 (291)
T COG0384 71 VPFAGHATLGAAHVLAELGGLSNDTTLTLETKAGLVPVTVER-----------GG---GQ--AEFDLPQLPPPEEIEAEP 134 (291)
T ss_pred cccCCCHHHHHHHHHHHhcCCCccceEEEEeccCeEEEEEEe-----------CC---Cc--eEEccCCCCCccccccCH
Confidence 69999999999998888876544 479999999999999985 21 22 678888765433333357
Q ss_pred HHHHHHhCCCceeee-------eecCCCceEEEEeCChhhhcccCCChhhHhcCCC-CceEEEEeeCCCCCcccEEEeec
Q 027494 80 SLILEALGVSSVVDM-------KITTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG-TRGIIVSGLAPPESGFDFYSRFF 151 (222)
Q Consensus 80 ~~l~~algl~~~~~~-------~~~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~-~~gv~v~~~~~~~~~~~~~~R~f 151 (222)
++++++||+.+ .++ .+|||.+|++|+|+|.++|.+++||++++.+++. ..++++|+......+.++++|+|
T Consensus 135 ~~la~aLgL~~-~~~~~~~~~~~~stG~~~l~v~l~s~~av~~~~pd~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~R~F 213 (291)
T COG0384 135 AELAEALGLEE-DDLLPEHPPQVVSTGLPDLLVPLESLEALDALRPDFSALTELSAGGGGVYVFAREGAGAEADFHARMF 213 (291)
T ss_pred HHHHHHcCCCh-HHcccccCceEeecCCceEEEEeCCHHHHHhcCCCHHHHHhhcccccceEEEEeccCCCCCcEEEEec
Confidence 89999999987 333 3689999999999999999999999999999862 22378888766556789999999
Q ss_pred CCCCCCCccCccccchhhhHHHHHhhhC---CceEEEeec--cCCCeEEEEEEccCC--CeEEEeeeEEEEEEEEEEC
Q 027494 152 CPKFGVNEDPVCGSAYCALATYWSQKLG---KCDFVAYAA--SPRSGILNIHLDEQN--QRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 152 ~p~~Gv~EDpatGSa~~ala~yl~~~~~---~~~~~~~Qg--~~r~g~l~v~~~~~~--~~v~v~G~a~~v~~G~i~~ 222 (222)
+|.+|+.||||||||+|+|++||.++.. ..++.++|| ++|+|+|+++++.++ ..|+|+|+++.+++|++.|
T Consensus 214 aP~~Gi~EDPaTGSA~~~La~yl~~~~~~~~~~~~~~~QG~~~gR~s~i~~~~~~~~~~~~v~vgG~av~~~~g~l~l 291 (291)
T COG0384 214 APGIGVVEDPATGSAAGALAAYLAKHGGLPDKLRLLIEQGTELGRPSRIEVRVDEDGNKEAVRVGGRAVTVAEGELEL 291 (291)
T ss_pred ccccCCCCCCCcchhhhHHHHHHHHhCCCCCcccEEEEeccccCCCcEEEEEEeccCCceEEEEeeEEEEEEEEEEeC
Confidence 9999999999999999999999988654 467999999 589999999997543 5899999999999999975
No 3
>KOG3033 consensus Predicted PhzC/PhzF-type epimerase [General function prediction only]
Probab=100.00 E-value=2.6e-40 Score=268.14 Aligned_cols=205 Identities=41% Similarity=0.647 Sum_probs=169.1
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCC--Cccc
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADF--NFSE 78 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~--~~~~ 78 (222)
||||||||||+||+|++..++...++.|+|++|.+++++++ .| .+.|++|..+...+ ..+.
T Consensus 75 vplcGHaTLasahvlf~~~~n~n~~l~f~t~sG~l~akrd~-----------~~------~ieln~P~y~~~si~~~~~~ 137 (286)
T KOG3033|consen 75 VPLCGHATLASAHVLFNEIGNVNKELKFDTLSGILTAKRDE-----------LG------SIELNFPEYDTTSINISNEL 137 (286)
T ss_pred CcccCcchhhHHHHHHHhccCCcceEEEEeecceEEEEecc-----------cc------ceEEccCccccccccccchH
Confidence 69999999999999999988777889999999999999963 22 38899999887764 2223
Q ss_pred HHHHHHHhCCCceeeee--ecCCCceEEEEeCChhhhcccCCChhhHhc--CCCCceEEEEeeCCCCCcccEEEeecCCC
Q 027494 79 VSLILEALGVSSVVDMK--ITTTCEDIFVVLPSAKSVTDLQPKFDEMKK--CPGTRGIIVSGLAPPESGFDFYSRFFCPK 154 (222)
Q Consensus 79 ~~~l~~algl~~~~~~~--~~~G~~~lvv~v~~~~~l~~~~pd~~~l~~--~~~~~gv~v~~~~~~~~~~~~~~R~f~p~ 154 (222)
...+.+++|..-+.++. +..+..+++|.|++.++.-.++|+...+.. .+...++.+....+.+...+|++|+|+|+
T Consensus 138 ~~~fska~~~~~i~dv~~~~~~~p~~liVvl~~~~t~~elep~~~d~~di~~~p~~~~~v~~~g~~g~~~dy~~RyFAP~ 217 (286)
T KOG3033|consen 138 EGIFSKAEGPAFIFDVIKCVTPTPRKLIVVLDPWETVFELEPNRIDISDISTCPNNGMIVTFAGSSGSPYDYESRYFAPW 217 (286)
T ss_pred HHHHHHhhCCceeccchhccCCCCceEEEEeCCcceeeecChhhhhhhhhhcCCCCceEEEEecCCCCCCceEeeecccc
Confidence 35666788876655554 233467999999999998888887666542 22335777766655556899999999999
Q ss_pred CCCCccCccccchhhhHHHHHhhhCCceEEEeecc-CCCeEEEEEEccCCCeEEEeeeEEEEEEEEEEC
Q 027494 155 FGVNEDPVCGSAYCALATYWSQKLGKCDFVAYAAS-PRSGILNIHLDEQNQRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 155 ~Gv~EDpatGSa~~ala~yl~~~~~~~~~~~~Qg~-~r~g~l~v~~~~~~~~v~v~G~a~~v~~G~i~~ 222 (222)
+||+||||||||+|+|+.||..++++.++...|.+ .|+|.+.++++++..+|.|.|.+++|++|+|.+
T Consensus 218 ~GVnEDPvtGSa~caL~~yws~~~~k~~~~afqas~~Rgg~~rv~l~~ea~rV~l~G~avtVl~G~i~v 286 (286)
T KOG3033|consen 218 VGVNEDPVTGSAHCALGPYWSLILGKKDFYAFQASPTRGGLFRVSLKKEAQRVILNGGAVTVLRGEILV 286 (286)
T ss_pred ccccCCCCCCceeeehHHHHHHHcCccceeeeeecccCCcEEEEEEcCCceEEEecCCcEEEEeeEEeC
Confidence 99999999999999999999988999999999998 899999999986556999999999999999975
No 4
>TIGR00654 PhzF_family phenazine biosynthesis protein PhzF family. Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear.
Probab=100.00 E-value=1.1e-39 Score=280.18 Aligned_cols=207 Identities=22% Similarity=0.331 Sum_probs=164.3
Q ss_pred CCCCChHHHHHHHHHHhcCCCC-CCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcccH
Q 027494 1 MELCGHAALAAAHTLFSRGLVN-SNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSEV 79 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~-~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~~ 79 (222)
++||||||+|++++|.+.+... ++.++|+|++|.+++++.. .+ +...++|.+|.+.+.+......
T Consensus 71 ~~~CGh~tl~aa~~l~~~~~~~~~~~~~~et~aG~v~v~~~~----------~~----~~~~i~v~~~~p~~~~~~~~~~ 136 (297)
T TIGR00654 71 LPFAGHPTIGSCYALLEFTKLTTATTLVQECKAGAVPVTINE----------KN----GDLRISLEQPMPDFEPISGEMR 136 (297)
T ss_pred cCcCCchHHHHHHHHHHcCCCCCCccEEEEcCceEEEEEEEe----------cC----CcEEEEEECCCCcccCCCchhH
Confidence 6899999999999999886543 4679999999999999963 12 2223566677666655432224
Q ss_pred HHHHHHhCCCceee-------eeecCCCceEEEEeCChhhhcccCCChhhHhcCCC---CceEEEEeeCCC-CCcccEEE
Q 027494 80 SLILEALGVSSVVD-------MKITTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG---TRGIIVSGLAPP-ESGFDFYS 148 (222)
Q Consensus 80 ~~l~~algl~~~~~-------~~~~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~---~~gv~v~~~~~~-~~~~~~~~ 148 (222)
.++.+++|+.. .+ ..+++|+||++|++++.+.|.++.||++++.++++ ..++++|+.... .++.++++
T Consensus 137 ~~~~~~lg~~~-~~~~~~~~~~~v~~G~ph~vv~v~~~~~l~~~~~d~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (297)
T TIGR00654 137 ADLAKALGLTE-DDFIKGLPIQLLSTGPEWIVIPLKDEEACFNASPNFAMLAHQLKQNDHVGVIPFGPKKEAAGKNDYHG 215 (297)
T ss_pred HHHHHHhCCCh-HHhcccCCcEEEecCCCeEEEEeCCHHHHHhCCCCHHHHHHHHhhcCccEEEEEecCCCCCCCceEEE
Confidence 45667888764 21 24789999999999999999999999999988753 368888887642 13457999
Q ss_pred eecCCCCCCCccCccccchhhhHHHHHhhh---CCceEEEeec--cCCCeEEEEEEccCCC---eEEEeeeEEEEEEEEE
Q 027494 149 RFFCPKFGVNEDPVCGSAYCALATYWSQKL---GKCDFVAYAA--SPRSGILNIHLDEQNQ---RVQLRGKAITVMQGSL 220 (222)
Q Consensus 149 R~f~p~~Gv~EDpatGSa~~ala~yl~~~~---~~~~~~~~Qg--~~r~g~l~v~~~~~~~---~v~v~G~a~~v~~G~i 220 (222)
|+|+|..|++||||||||+|+|++||..+. +...+.++|| ++|+|.|+|+++.+++ +|+|+|+|+++++|+|
T Consensus 216 R~f~p~~g~~EDpatGSa~~ala~~l~~~~~~~~~~~~~v~QG~~~~R~g~l~v~~~~~~~~~~~v~i~G~a~~v~~G~i 295 (297)
T TIGR00654 216 RMFAPVIGIYEDPVTGSGSGALGAYLQHVYKNEKTHDITIEQGGALGRDGLMEATVKKEGDNSTKVYIAGTAVTVIDGKI 295 (297)
T ss_pred EeCCCCCCCcCCCcccHHHHHHHHHHHHcCCCCCCceEEEECccCcCCCeEEEEEEEecCCcEEEEEEcCEEEEEEEEEE
Confidence 999999999999999999999999998653 1235889999 7899999999964333 7999999999999999
Q ss_pred EC
Q 027494 221 LV 222 (222)
Q Consensus 221 ~~ 222 (222)
.+
T Consensus 296 ~~ 297 (297)
T TIGR00654 296 KI 297 (297)
T ss_pred EC
Confidence 75
No 5
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=100.00 E-value=1.9e-39 Score=276.47 Aligned_cols=207 Identities=33% Similarity=0.536 Sum_probs=148.7
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcccHH
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSEVS 80 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~~~ 80 (222)
||||||||||++|+|++.+...+..++|+|++|.++++.... .+. .....+++.+|.....+......+
T Consensus 64 v~fcGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~l~v~~~~~---------~~~--~~~~~~~~~~P~~~~~~~~~~~~~ 132 (281)
T PF02567_consen 64 VPFCGHATLAAAHALFERGGLDPGEIVFETKAGILPVEVIVE---------GDG--GDEVFIEQEQPEFEPVPIDREELA 132 (281)
T ss_dssp ESSSHHHHHHHHHHHHHHTTTSSSEEEEEETTEEEEEEEEEE---------ECE--EEEEEEEEEEEEEEEEECHHHHHH
T ss_pred CCCCCcHHHHHHHHHHHhccccCceEEEEcCeEEEEEEEeec---------ccc--ccccceeccCCCCccccchhhhhH
Confidence 699999999999999999887778899999999999973210 010 134567777777644333221122
Q ss_pred HHHHHhCCCc-eeeeeecCCCceEEEEeCChhhhcccCCChhhHhcCCCCceEEEEeeCCCCCcccEEEeecCCCCCCCc
Q 027494 81 LILEALGVSS-VVDMKITTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPGTRGIIVSGLAPPESGFDFYSRFFCPKFGVNE 159 (222)
Q Consensus 81 ~l~~algl~~-~~~~~~~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~~~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~E 159 (222)
.+..+++... ..-..+++|.+|+++++++.++|.++.||++.+...+...+++.+......++.++++|+|+|+.|++|
T Consensus 133 ~~~~~~~~~~~~~~~~~~tg~~~llv~l~~~~~l~~l~pd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~FaP~~Gi~E 212 (281)
T PF02567_consen 133 AALGLLGEDGVLPPQVVSTGNPWLLVPLKSAEALAALKPDFAALLALCDRNGVHVFTFFTDDEDSDFHSRMFAPGIGIPE 212 (281)
T ss_dssp HHHHCHTSGTSS-SEEEESSSEEEEEEBSCHHHHHH---SHHHHHHHHTTCEEEEEEEEEESSTTEEEEEEEEGGGTEEE
T ss_pred HHHhhhcccccCceEEEECCCCcEEEEEecccccccceechhhhcccccccccccccccccCCCceEEEeeeecccCCCC
Confidence 2222232221 112236889999999999999999999999665554333566554443334578899999999999999
Q ss_pred cCccccchhhhHHHHHhhhC---CceEEEeec--cCCCeEEEEEEcc-----CCCeEEEeeeEEEEEEE
Q 027494 160 DPVCGSAYCALATYWSQKLG---KCDFVAYAA--SPRSGILNIHLDE-----QNQRVQLRGKAITVMQG 218 (222)
Q Consensus 160 DpatGSa~~ala~yl~~~~~---~~~~~~~Qg--~~r~g~l~v~~~~-----~~~~v~v~G~a~~v~~G 218 (222)
|||||||+|+|++||.++.. ...+.++|| ++|+|+|+|+++. +..+|+|+|+|++|++|
T Consensus 213 DpaTGSA~~~La~yl~~~~~~~~~~~~~i~QG~~~gR~g~i~v~~~~~~~~~~~~~V~vgG~av~v~~G 281 (281)
T PF02567_consen 213 DPATGSAAGALAAYLAEKGGKPGSHRFTIEQGQEMGRPGRIEVEVDGDRDGGEDERVRVGGRAVTVMEG 281 (281)
T ss_dssp ESS-HHHHHHHHHHHHHHTTSSSCEEEEEEEEGGGTS-EEEEEEEEE-EETTEEEEEEEEEEEEEEEEE
T ss_pred CCCchhhHHHHHHHHHHhCCCCCCceEEEEcccEeCCCEEEEEEEEeeccCCCCceEEEEeEEEEEEeC
Confidence 99999999999999988653 356889999 6899999999853 23589999999999998
No 6
>PRK00450 dapF diaminopimelate epimerase; Provisional
Probab=100.00 E-value=3e-34 Score=243.82 Aligned_cols=199 Identities=24% Similarity=0.349 Sum_probs=144.9
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcccHH
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSEVS 80 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~~~ 80 (222)
+|||||||||++++|++.+...+++++|+|++|.+++++.. + +.+++.|..|.....+.+..+.+
T Consensus 70 v~~CGHat~~~a~~L~~~g~~~~~~~~~~t~~G~l~v~~~~-----------~----~~i~~~~~~P~~~~~~~~~~~~~ 134 (274)
T PRK00450 70 AEMCGNGARCFARFLYEKGLTNKTEIRVETLAGIIEAEVED-----------D----GLVTVDMGEPRFEPAEIPLAEED 134 (274)
T ss_pred HHcCcchHHHHHHHHHHcCCCCCCeEEEEeCCceEEEEEec-----------C----CEEEEECCCCccCcccCcccccc
Confidence 58999999999999999887666689999999999999963 2 24445555555433332211112
Q ss_pred HHHHHhCCCc--eeeeeecCCCceEEEEeCC--hhhhcccCCChhhHhcCCCCceEEEEeeCCCCCcccEEEeecCCCCC
Q 027494 81 LILEALGVSS--VVDMKITTTCEDIFVVLPS--AKSVTDLQPKFDEMKKCPGTRGIIVSGLAPPESGFDFYSRFFCPKFG 156 (222)
Q Consensus 81 ~l~~algl~~--~~~~~~~~G~~~lvv~v~~--~~~l~~~~pd~~~l~~~~~~~gv~v~~~~~~~~~~~~~~R~f~p~~G 156 (222)
.+...+++.. ..-..+++|+||++++++| .+.|.+++||++++..+++ ++++..... .++.++++|+|+| |
T Consensus 135 ~l~~~l~~~~~~~~~~~v~~G~~~lvv~v~~~~~~~l~~l~pd~~~~~~~~~--~~nv~~~~~-~~~~~~~~R~F~~--g 209 (274)
T PRK00450 135 VIEKEYILGGQTVEVTAVSMGNPHAVIFVDDVDAADVEELGPLLENHPRFPE--GVNVNFVQV-VDRDHIRLRVYER--G 209 (274)
T ss_pred ccceeeeeCCcEEEEEEEECCCCcEEEEeCCCCcCchhHhchhcccCCCCCC--CeEEEEEEE-ccCCEEEEEEecC--C
Confidence 2333444321 1112478999999999999 7899999999999877775 555433321 1245799999999 6
Q ss_pred CCccCccccchhhhHHHHHhhhCCceEEEeeccCCCeEEEEEEccCCCeEEEeeeEEEEEEEEEEC
Q 027494 157 VNEDPVCGSAYCALATYWSQKLGKCDFVAYAASPRSGILNIHLDEQNQRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 157 v~EDpatGSa~~ala~yl~~~~~~~~~~~~Qg~~r~g~l~v~~~~~~~~v~v~G~a~~v~~G~i~~ 222 (222)
++|||+||||+||+|.|+.. ++... ...|.+.|+|.|+|+++. +++|+|+|+|+++++|+|.+
T Consensus 210 v~Ed~a~GTg~~a~a~~~~~-~g~~~-~~~~v~~r~G~l~v~~~~-~~~V~i~G~a~~v~~G~i~~ 272 (274)
T PRK00450 210 VGETLACGTGACAAAVAAIR-LGLLD-RKVTVHLPGGDLTIEWKG-DGHVYMTGPATLVFDGEIDL 272 (274)
T ss_pred CCcccccccchHHHHHHHHH-hCCCC-CcEEEEcCCCEEEEEEEC-CCcEEEEeCcEEEEEEEEEe
Confidence 78999999999999998754 44321 225566699999999973 26899999999999999874
No 7
>TIGR00652 DapF diaminopimelate epimerase.
Probab=99.97 E-value=3.3e-29 Score=212.31 Aligned_cols=194 Identities=21% Similarity=0.333 Sum_probs=134.3
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcccHH
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSEVS 80 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~~~ 80 (222)
+|||||||+|++++|.+.+...+++++++|++|.+++++.. + +.+++.|..|......++.
T Consensus 69 ~~~CGh~t~~~a~~l~~~~~~~~~~~~~et~~G~v~v~~~~-----------~----~~i~v~m~~p~~~~~~~~~---- 129 (268)
T TIGR00652 69 AEMCGNGIRCFAKFVYEHGLVNKKDISVETLAGLIVLEVKS-----------E----NKVKVDMGEPNFKPAEIPL---- 129 (268)
T ss_pred HHhCcCcHHHHHHHHHHcCCCCCCeEEEEeCCCcEEEEEec-----------C----CEEEEECCCCccccccCcc----
Confidence 48999999999999998876655679999999999999863 2 2444555444432222221
Q ss_pred HHHHHhCCCc----eeeeeecCCCceEEEEeCChhhhc--ccCCChhhHhcCCCCceEEEEeeCCCCCcccEEEeecCCC
Q 027494 81 LILEALGVSS----VVDMKITTTCEDIFVVLPSAKSVT--DLQPKFDEMKKCPGTRGIIVSGLAPPESGFDFYSRFFCPK 154 (222)
Q Consensus 81 ~l~~algl~~----~~~~~~~~G~~~lvv~v~~~~~l~--~~~pd~~~l~~~~~~~gv~v~~~~~~~~~~~~~~R~f~p~ 154 (222)
....+++.. ..-..+++|+||+++++++.+.+. ++.++.+.+..++. +++|++.... +..++++|+|+|
T Consensus 130 -~~~~~~l~~~~~~~~~~~vstG~ph~vv~v~~~~~l~~~~~~~~~~~~~~fp~--~~nV~~~~~~-~~~~i~~R~fer- 204 (268)
T TIGR00652 130 -TVWKFEEPEVGLFGEILAVDTGNPHLVVFVDDVEGLNLLILGPLLEYHERFPE--GVNVNFVQVK-NDDTIKLRTYER- 204 (268)
T ss_pred -ccccccccccccEeeEEEEecCCCcEEEEeCCcCcccHHHhccccccCCCCCC--CeEEEEEEEC-cCCEEEEEEecC-
Confidence 122344322 111247899999999999987654 55577766555654 7777665422 357899999999
Q ss_pred CCCCccCccccchhhhHHHHHhhhCCceEEEeeccCCCeEEEEEEccCCCeEEEeeeEEEEEEEEEEC
Q 027494 155 FGVNEDPVCGSAYCALATYWSQKLGKCDFVAYAASPRSGILNIHLDEQNQRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 155 ~Gv~EDpatGSa~~ala~yl~~~~~~~~~~~~Qg~~r~g~l~v~~~~~~~~v~v~G~a~~v~~G~i~~ 222 (222)
|++||++|||++||++.+... .+..+-. .+...++|.|+++++. +++|+|+|+|+.+++|+|.+
T Consensus 205 -g~get~acGTGa~A~a~a~~~-~g~~~~~-~~v~~~~G~l~v~~~~-~g~i~l~G~a~~v~~G~i~~ 268 (268)
T TIGR00652 205 -GAGETLACGTGACASAAAALK-LGGTPKK-VTVHLPGGELEIEWKE-DGHVYMTGPAVLVFDGELFL 268 (268)
T ss_pred -CCCcccccHHHHHHHHHHHHH-hCCCCCC-EEEEcCCCEEEEEEEC-CCcEEEEeCCEEEEEEEEeC
Confidence 567999999999998766543 2321100 2233466799999974 35899999999999999974
No 8
>PRK13577 diaminopimelate epimerase; Provisional
Probab=99.96 E-value=3.4e-29 Score=213.51 Aligned_cols=197 Identities=19% Similarity=0.257 Sum_probs=141.2
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcc--c
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFS--E 78 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~--~ 78 (222)
.+||||||+|++++|.+.+...+++++++|.+|.+++++.. ++ ..+.+.|..|......++.. .
T Consensus 69 aemCGNg~Rc~a~~l~~~~~~~~~~~~ieT~aG~~~~~v~~-----------~~---~~v~v~mg~p~~~~~~~~~~~~~ 134 (281)
T PRK13577 69 AEKSGNGLRIFSRYLWDQGLVDDEPFTIETKGGIVECQVLD-----------AG---RTIQVEMGKVSFGSTDIPVAGED 134 (281)
T ss_pred HHhccccHHHHHHHHHHcCCCCCCcEEEEECCceEEEEEEC-----------CC---cEEEEECCCceeccccCCccccc
Confidence 37999999999999998876666689999999999999853 21 24566666555443333321 1
Q ss_pred HHHHHHHhCCCc--eeeeeecCCCceEEEEeCChhh--hcccCCChhhHhcCCCCceEEE-EeeCCCCCcccEEEeecCC
Q 027494 79 VSLILEALGVSS--VVDMKITTTCEDIFVVLPSAKS--VTDLQPKFDEMKKCPGTRGIIV-SGLAPPESGFDFYSRFFCP 153 (222)
Q Consensus 79 ~~~l~~algl~~--~~~~~~~~G~~~lvv~v~~~~~--l~~~~pd~~~l~~~~~~~gv~v-~~~~~~~~~~~~~~R~f~p 153 (222)
...+...+++.. +.-..+++|+||+|+++++.+. +..+.|+++.+..+++ |+++ |... .+...+++|+|+|
T Consensus 135 ~~~i~~~l~i~~~~~~~~~vs~G~PH~Vv~V~~~~~~~~~~~g~~~~~~~~fp~--~~Nv~f~~~--~~~~~i~~R~~Er 210 (281)
T PRK13577 135 REVLNEKLDVDGRRLTYCAATIGNPHCVVLLDEISEELARELGPLIETHPRFPN--RTNVQFLKV--LDRNTIQIEIWER 210 (281)
T ss_pred ccccceEeeeCCcEEeEEEEECCCCcEEEEeCCcchhhHHhhCccccccCCCCC--CceEEEEEE--ccCCeEEEEEECC
Confidence 123344555543 1223478999999999998754 5667799988877765 5554 2221 1245899999999
Q ss_pred CCCCCccCccccchhhhHHHHHhhhCC--ceEEEeeccCCCeEEEEEEccCCCeEEEeeeEEEEEEEEEEC
Q 027494 154 KFGVNEDPVCGSAYCALATYWSQKLGK--CDFVAYAASPRSGILNIHLDEQNQRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 154 ~~Gv~EDpatGSa~~ala~yl~~~~~~--~~~~~~Qg~~r~g~l~v~~~~~~~~v~v~G~a~~v~~G~i~~ 222 (222)
|++||+||||++||++.++.+ ++. ..+.++ .++|.|.++|+. ++.|+++|+|+.|++|+|.+
T Consensus 211 --G~g~T~AcGTga~A~a~~~~~-~g~~~~~~~V~---~pGG~l~v~~~~-~~~v~l~G~a~~v~~G~~~~ 274 (281)
T PRK13577 211 --GAGYTLASGSSSCAAAAVAHR-LGLCDSSITVH---MPGGQIDIEIKD-DFHVSMTGPVTKVAEGSLSP 274 (281)
T ss_pred --CCCCCccCHHHHHHHHHHHHH-hCCCCCeEEEE---cCCCEEEEEEEC-CCcEEEEcCCEEEEEEEEEH
Confidence 556999999999999877654 332 234444 377999999974 34799999999999999863
No 9
>PLN02536 diaminopimelate epimerase
Probab=99.96 E-value=2.4e-27 Score=200.41 Aligned_cols=199 Identities=17% Similarity=0.210 Sum_probs=139.4
Q ss_pred CCCCChHHHHHHHHHHhcCCCC-CCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCccc-
Q 027494 1 MELCGHAALAAAHTLFSRGLVN-SNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSE- 78 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~-~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~- 78 (222)
.+|||||++|++++|++.+... +++++|+|.+|.+++++.. + +.+++.|..|.....+++...
T Consensus 55 a~mCGNg~Rc~a~~l~~~~~~~~~~~~~ieT~aG~i~~~v~~-----------~----~~v~V~mg~p~~~~~~ip~~~~ 119 (267)
T PLN02536 55 PEMCGNGIRCFARFIAELENLQGKNSYKIHTGAGLIIPEMQA-----------D----GQVKVDMGEPILKGPEVPTKLA 119 (267)
T ss_pred hhhCccHHHHHHHHHHHcCCCCCCceEEEEeCCccEEEEEeC-----------C----CEEEEeccCcccccccCccccc
Confidence 3799999999999999987653 3579999999999999853 2 356777777776555554210
Q ss_pred -HHHH---HHHhCC--CceeeeeecCCCceEEEEeCC---hh--hhcccCCChhhHhcCCCCceEEE-EeeCCCCCcccE
Q 027494 79 -VSLI---LEALGV--SSVVDMKITTTCEDIFVVLPS---AK--SVTDLQPKFDEMKKCPGTRGIIV-SGLAPPESGFDF 146 (222)
Q Consensus 79 -~~~l---~~algl--~~~~~~~~~~G~~~lvv~v~~---~~--~l~~~~pd~~~l~~~~~~~gv~v-~~~~~~~~~~~~ 146 (222)
.... ...+.+ ..+.-..+++|+||+|+++++ .+ .|..+.|.++....|++ |+|| |+.. .++..+
T Consensus 120 ~~~~~~~~~~~~~i~~~~~~~~~Vs~GnPH~VifV~~~~~~~~~~~~~~g~~i~~~~~FP~--~~NV~f~~v--~~~~~i 195 (267)
T PLN02536 120 ATKDGAVVQAELDVDGKTWLVTCVSMGNPHCVTFGEKELKVDDLPLEKIGPKFEHHEMFPA--RTNTEFVQV--VSRSHL 195 (267)
T ss_pred ccccccceeeEEeeCCcEEEEEEEECCCCCEEEEECCccccCcCChHHhChhccccCCCCC--CcEEEEEEE--cCCCEE
Confidence 0000 000111 011112478999999999988 43 46677777777666765 7777 3332 236789
Q ss_pred EEeecCCCCCCCccCccccchhhhHHHHHhhhCCceEEEeeccCCCeEEEEEEccCCCeEEEeeeEEEEEEEEEEC
Q 027494 147 YSRFFCPKFGVNEDPVCGSAYCALATYWSQKLGKCDFVAYAASPRSGILNIHLDEQNQRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 147 ~~R~f~p~~Gv~EDpatGSa~~ala~yl~~~~~~~~~~~~Qg~~r~g~l~v~~~~~~~~v~v~G~a~~v~~G~i~~ 222 (222)
++|+|++ |++|+.||||++||.+..... ++..+- ...+..++|.|.++|+++++.|++.|+|+.+++|+|.+
T Consensus 196 ~~rt~ER--Gvg~TlACGTGacA~a~~a~~-~g~~~~-~v~V~~~GG~L~i~~~~~~~~v~m~Gpa~~v~~g~~~~ 267 (267)
T PLN02536 196 KMRVWER--GAGATLACGTGACALVVAAVL-EGRADR-NCTVDLPGGPLEIEWRESDNHIYMTGPAELVFYGEIRL 267 (267)
T ss_pred EEEEecc--CCchhhccCccHHHHHHHHHH-hCCCCC-cEEEEcCCcEEEEEEECCCceEEEEeCeEEEEEEEEEC
Confidence 9999999 668999999999998755443 343221 12345699999999964345799999999999999875
No 10
>COG0253 DapF Diaminopimelate epimerase [Amino acid transport and metabolism]
Probab=99.95 E-value=3.2e-26 Score=191.79 Aligned_cols=195 Identities=24% Similarity=0.380 Sum_probs=147.8
Q ss_pred CCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCcccHHH
Q 027494 2 ELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNFSEVSL 81 (222)
Q Consensus 2 ~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~~~~~~ 81 (222)
.||||+++|.|++|.+++...+.+++++|.+|.+.+++.. + ..+.|.|..|......++.. ...
T Consensus 71 e~CGNG~Rc~a~~l~~~~~~~~~~~~v~T~~G~~~~~~~~-----------~----~~v~VdMg~p~~~~~~ip~~-~~~ 134 (272)
T COG0253 71 EMCGNGARCFARFLAERGLVKKKEISVETLAGILKVKVHD-----------D----NTVSVDMGLPSFKPAEIPLL-EEK 134 (272)
T ss_pred hhcccHHHHHHHHHHHhcCCcCccEEEEeccceEEEEEec-----------C----CEEEEEcCCCccccccCCch-hhh
Confidence 5899999999999999988777789999999999999985 2 37788999988877666542 111
Q ss_pred HHHHhCCCc--eeeeeecCCCceEEEEeCChhh--hcccCCChhhHhcCCCCceEEE-EeeCCCCCcccEEEeecCCCCC
Q 027494 82 ILEALGVSS--VVDMKITTTCEDIFVVLPSAKS--VTDLQPKFDEMKKCPGTRGIIV-SGLAPPESGFDFYSRFFCPKFG 156 (222)
Q Consensus 82 l~~algl~~--~~~~~~~~G~~~lvv~v~~~~~--l~~~~pd~~~l~~~~~~~gv~v-~~~~~~~~~~~~~~R~f~p~~G 156 (222)
+..-..+.+ +.-..+++|+||+++++++.+. +..+.|.++...++++ ++++ |... .++..+++|+|++ |
T Consensus 135 ~~~~~~~~~~~~~~~~vs~GnPH~V~~Vddv~~~~~~~~g~~l~~h~~Fp~--~vNV~F~~v--~~~~~i~vrv~ER--G 208 (272)
T COG0253 135 VEEQYGLGEETVTFYAVSMGNPHLVIFVDDVETANLEELGPLLESHELFPE--GVNVGFVQV--LSRDAIRLRVYER--G 208 (272)
T ss_pred ccccccccccceeEEEEecCCCeEEEEeCCcccchhhhhhhhhhcCccCCC--ceEEEEEEe--CCCCcEEEEEeec--C
Confidence 111111111 1224589999999999998765 8888888888888885 7887 4443 2467899999999 6
Q ss_pred CCccCccccchhhhHHHHHh--hhCCceEEEeeccCCCeEEEEEEccCCCeEEEeeeEEEEEEEEEEC
Q 027494 157 VNEDPVCGSAYCALATYWSQ--KLGKCDFVAYAASPRSGILNIHLDEQNQRVQLRGKAITVMQGSLLV 222 (222)
Q Consensus 157 v~EDpatGSa~~ala~yl~~--~~~~~~~~~~Qg~~r~g~l~v~~~~~~~~v~v~G~a~~v~~G~i~~ 222 (222)
.+|+.||||++||.+....+ +++. ..+++| ++|.|.+.|..++..+.+.|+|+++++|++++
T Consensus 209 ~G~T~ACGTGa~Aa~~~a~~~~~~~~-~v~V~~---pGG~L~i~~~~~g~~v~m~G~a~~v~~G~~~~ 272 (272)
T COG0253 209 AGETLACGTGACAAAVVAARLGLLDR-KVTVHL---PGGTLEIEWKDDGKPVYMTGPATRVAEGKLYI 272 (272)
T ss_pred CcccccchhHHHHHHHHHHHhccCCC-cEEEEc---CCCeEEEEEEcCCceEEEEecEEEEEeeEEcC
Confidence 78999999998886654432 2233 445555 99999999985544699999999999999864
No 11
>PRK13969 proline racemase; Provisional
Probab=99.31 E-value=9.8e-11 Score=101.76 Aligned_cols=200 Identities=17% Similarity=0.193 Sum_probs=106.2
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCC----cEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEEeCCCCCCCCCCc
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSN----TIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIELDFPAAPTADFNF 76 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~----~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~~~p~~~~~~~~~ 76 (222)
.+||||+|+|++.+|.+.+.++.+ .++|+|++|.+.+++.. ++|. ...+.+ ++.|++....--.
T Consensus 88 ~~MCGhgtI~vat~l~e~G~v~~~~~~~~v~ieTPaGlV~a~~~~----------~~g~-v~~Vs~-~nVPsf~~~~d~~ 155 (334)
T PRK13969 88 LNMCGHGSIGAATCAVETGIVKVEEPYTHIKLEAPAGMINARVKV----------EDGK-AKEVSI-VNVPAFLYKKDVE 155 (334)
T ss_pred cccccChHHHHHHHHHHcCCcCCCCCceeEEEECCceEEEEEEEE----------cCCe-EEEEEE-EeeecchhhcCCe
Confidence 479999999999999999976533 58999999999999863 1321 013444 7788875431110
Q ss_pred ccHHHHHHHhCCCceeeeeecCCCceEEEE-------eCCh--hhhcccCCChhh---------HhcCCCCceEEEEeeC
Q 027494 77 SEVSLILEALGVSSVVDMKITTTCEDIFVV-------LPSA--KSVTDLQPKFDE---------MKKCPGTRGIIVSGLA 138 (222)
Q Consensus 77 ~~~~~l~~algl~~~~~~~~~~G~~~lvv~-------v~~~--~~l~~~~pd~~~---------l~~~~~~~gv~v~~~~ 138 (222)
.+.+ .+|--. .|+.. -|+.|.++. +++. ..|.++.+.+.. +..+++..+++..-..
T Consensus 156 v~vp----~~G~v~-~Dia~-GG~~yaiVda~~lG~~v~~~~~~~L~~~g~~I~~a~~~~~~~~HP~~p~~~~v~~v~~~ 229 (334)
T PRK13969 156 IDVP----DYGKVT-LDISF-GGSFFAIVDAEQLGIKISPANSQKLNDLGMKIRHAVNEQIEIKHPVLEHIKTVDLVEIY 229 (334)
T ss_pred EecC----CcCcEE-EEEEE-CCEEEEEEEHHHcCCccChhhHHHHHHHHHHHHHHHHhhccCCCCCCCCcCceEEEEEe
Confidence 0111 233111 34433 255565563 2221 233333333222 1111221233322211
Q ss_pred CCCCcccEEEe---ecCCCCCCCccCccccchhhhHHHHHhh--hCCceEEEeeccCCCeEEEEEEccC---C----CeE
Q 027494 139 PPESGFDFYSR---FFCPKFGVNEDPVCGSAYCALATYWSQK--LGKCDFVAYAASPRSGILNIHLDEQ---N----QRV 206 (222)
Q Consensus 139 ~~~~~~~~~~R---~f~p~~Gv~EDpatGSa~~ala~yl~~~--~~~~~~~~~Qg~~r~g~l~v~~~~~---~----~~v 206 (222)
++.....-..| +|++ |...-..|||++||-.+.+..+ ++... ...+-|-.++....++.+. + -..
T Consensus 230 ~~~~~~~~~~rn~vv~~~--G~~DRSPcGTGtsArlA~l~a~G~l~~g~-~~~~eSiigs~F~~~~~~~~~~g~~~avip 306 (334)
T PRK13969 230 DEAKHPDADYKNVVIFGQ--GQVDRSPCGTGTSAKMATLYAKGKLKVGE-EFVYESIIGTKFKGKILEETKVGEYDAIIP 306 (334)
T ss_pred cCCCcccccceeEEEECC--CceecCCCcHHHHHHHHHHHHcCCCCCCC-ceEEecccCceEEEEEEEEEEECCccEEEE
Confidence 11111101134 5566 5567888999999966666543 33222 2244444566555555310 1 246
Q ss_pred EEeeeEEEEEEEEEE
Q 027494 207 QLRGKAITVMQGSLL 221 (222)
Q Consensus 207 ~v~G~a~~v~~G~i~ 221 (222)
.|.|+|.+...-++.
T Consensus 307 ~i~G~A~itg~~~~~ 321 (334)
T PRK13969 307 EITGSAYITGFNQFV 321 (334)
T ss_pred EEEEEEEEEEEEEEE
Confidence 788888888777764
No 12
>PRK13971 hydroxyproline-2-epimerase; Provisional
Probab=99.20 E-value=1.7e-09 Score=93.76 Aligned_cols=41 Identities=20% Similarity=0.493 Sum_probs=35.6
Q ss_pred CCCCChHHHHHHHHHHhcCCCC---CCcEEEEeceeeEEEEEec
Q 027494 1 MELCGHAALAAAHTLFSRGLVN---SNTIEFTTLSGILIAKKVP 41 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~---~~~~~~~t~~G~v~v~~~~ 41 (222)
+|||||+|||++++|.+.+.+. +..++++|++|.+++++..
T Consensus 87 ~~mcGH~TIg~a~~L~e~G~i~~~~~~~~~letpaG~V~V~v~~ 130 (333)
T PRK13971 87 LPMCGHGTIGTVTAAIEEGLVTPKTPGKLRLDTPAGLVDIEYEQ 130 (333)
T ss_pred cCcCccHHHHHHHHHHHcCCCCCCCCCeEEEECCcEEEEEEEEE
Confidence 6899999999999999987653 3468999999999999964
No 13
>PF01678 DAP_epimerase: Diaminopimelate epimerase; InterPro: IPR001653 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways []. There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different []. The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria. The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified. The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana. The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum. Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways. This entry represents diaminopimelate epimerase (5.1.1.7 from EC), which catalyses the isomerisation of L,L-dimaminopimelate to meso-DAP in the biosynthetic pathway leading from aspartate to lysine. It is a member of the broader family of PLP-independent amino acid racemases. This enzyme is a monomeric protein of about 30 kDa consisting of two domains which are homologus in structure though they share little sequence similarity []. Each domain consists of mixed beta-sheets which fold into a barrel around the central helix. The active site cleft is formed from both domains and contains two conserved cysteines thought to function as the acid and base in the catalytic reaction []. Other PLP-independent racemases such as glutamate racemase have been shown to share a similar structure and mechanism of catalysis.; GO: 0008837 diaminopimelate epimerase activity, 0009089 lysine biosynthetic process via diaminopimelate; PDB: 2OTN_A 3FVE_A 2Q9J_A 2GKJ_A 1GQZ_A 2Q9H_A 1BWZ_A 2GKE_A 3EKM_C 3EJX_D ....
Probab=99.08 E-value=2.2e-09 Score=80.31 Aligned_cols=112 Identities=21% Similarity=0.279 Sum_probs=74.8
Q ss_pred ecCCCceEEEEeCChhhhcccCCChhhHh----cCCCCceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhH
Q 027494 96 ITTTCEDIFVVLPSAKSVTDLQPKFDEMK----KCPGTRGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALA 171 (222)
Q Consensus 96 ~~~G~~~lvv~v~~~~~l~~~~pd~~~l~----~~~~~~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala 171 (222)
+.+|+||.++.+++.+......++..+.. .+....++.+.... ++.++++|+|++ +..|..+|||++++.+
T Consensus 3 k~~G~ph~vi~vd~~~~~~~~~~~~~~~~~~~~~~~~~dnv~fv~~~---~~~~~~~r~~n~--~g~et~aCGnG~~~~a 77 (121)
T PF01678_consen 3 KMHGNPHDVIFVDDREEEDDLDSELARAICDRHFFPGGDNVNFVEIS---DDADIRMRIFNR--DGSETLACGNGCRCAA 77 (121)
T ss_dssp EECSSEEEEEEEETTTCSSTCCHHHHHHHHTTTTSTT-SEEEEEEEE---CTTEEEEEEEET--TSBEESTTHHHHHHHH
T ss_pred EEeCCCcEEEEEcCcccccccchhhhhhhhccccCCcccceEEEEEe---cCCcEEEEEEEC--CCCeeeecCcHHHHHH
Confidence 45799999999988765433321122211 12223345544432 367899999998 5679999999977777
Q ss_pred HHHHhhh--CCceEEEeeccCCCeEEEEEEccCCC-eEEEeeeEEEE
Q 027494 172 TYWSQKL--GKCDFVAYAASPRSGILNIHLDEQNQ-RVQLRGKAITV 215 (222)
Q Consensus 172 ~yl~~~~--~~~~~~~~Qg~~r~g~l~v~~~~~~~-~v~v~G~a~~v 215 (222)
.|+.+.. .+..+.+.. ++|.+.+++..++. .+...|+++.|
T Consensus 78 ~~~~~~~~~~~~~v~v~t---~gG~l~v~~~~~~~~~~v~~G~a~~V 121 (121)
T PF01678_consen 78 AYLLEGGIVGKDEVTVET---PGGILRVEVDEDGNNVVVLMGPARFV 121 (121)
T ss_dssp HHHHHTTSSSSSEEEEEE---TTEEEEEEEETTSSSEEEEEEEEEE-
T ss_pred HHHHHCCCCcceEEEEEe---CCcEEEEEEEcCCCEEEEECCCCEEC
Confidence 7776543 345666555 89999999986555 47888988875
No 14
>PRK13970 hydroxyproline-2-epimerase; Provisional
Probab=99.00 E-value=8.9e-09 Score=88.31 Aligned_cols=188 Identities=17% Similarity=0.189 Sum_probs=101.7
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEE-eCCCCCCCCCCcccH
Q 027494 1 MELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIEL-DFPAAPTADFNFSEV 79 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~-~~p~~~~~~~~~~~~ 79 (222)
++||||+|+|++.+|.+.+.+.+.+.++||++|.+++++.. | .. +++ +.|++....--..+.
T Consensus 86 ~~mCGH~TIa~~t~l~e~G~v~~~~~~ieTpaG~v~v~~~~------------~---~~--V~f~NVPsf~~~~d~~v~v 148 (311)
T PRK13970 86 LGMCGHGTIGVVRTLHHMGRIGPGVHRIETPVGTVEATLHD------------D---LS--VSVRNVLAYRHAKDVVVDV 148 (311)
T ss_pred ccccccchheeeeeeeecceecCCcEEEEcCCceEEEEEEC------------C---Ce--EEEEecchhhhhCCCEEEC
Confidence 58999999999999999988766667999999999999973 1 23 443 566654321100011
Q ss_pred HHHHHHhCCCceeeeeecCCCceEEEEeCChhhhcccCCC-hhhHhcC---------------CCCceEE---EEeeCCC
Q 027494 80 SLILEALGVSSVVDMKITTTCEDIFVVLPSAKSVTDLQPK-FDEMKKC---------------PGTRGII---VSGLAPP 140 (222)
Q Consensus 80 ~~l~~algl~~~~~~~~~~G~~~lvv~v~~~~~l~~~~pd-~~~l~~~---------------~~~~gv~---v~~~~~~ 140 (222)
+ -+|--. .|+.. -|+.|.+|.- ..| .+.|+ ..+|.++ +...+++ ++.. +
T Consensus 149 p----g~G~v~-~Diay-GG~~yaivd~---~~l-~l~~~~~~~l~~~g~~i~~a~~~~~~~~~~~~~i~~v~~~~~-~- 216 (311)
T PRK13970 149 P----GYGPVK-GDIAW-GGNWFFLISD---HGQ-RVAGDNVAALTAYASAVRAGLERAGITGANGGEIDHIELFAD-D- 216 (311)
T ss_pred C----CCCcEE-EEEEe-CCeEEEEEcc---ccC-CCCcccHHHHHHHHHHHHHHHHhhccCCCCCCcceEEEEecC-C-
Confidence 1 122111 34433 3666666652 222 33332 2222221 1112333 3321 1
Q ss_pred CCcccEEEeecC--CCCCCCccCccccchhhhHHHHHhh--hCCceEEEeeccCCCeEEEEEEcc--CCCeEEEeeeEEE
Q 027494 141 ESGFDFYSRFFC--PKFGVNEDPVCGSAYCALATYWSQK--LGKCDFVAYAASPRSGILNIHLDE--QNQRVQLRGKAIT 214 (222)
Q Consensus 141 ~~~~~~~~R~f~--p~~Gv~EDpatGSa~~ala~yl~~~--~~~~~~~~~Qg~~r~g~l~v~~~~--~~~~v~v~G~a~~ 214 (222)
.+. ..|++. +..-++--| |||+.+|=-+.|..+ ++..+ ...|-|-.++..+.++.. .+-...|+|+|.+
T Consensus 217 -~~~--~~rn~vv~~~g~vDRSP-cGTGTsArlA~l~a~G~l~~ge-~~~~eSiiGs~F~g~i~~~~~~viP~I~G~A~i 291 (311)
T PRK13970 217 -PEH--DSRSFVLCPGHAYDRSP-CGTGTSAKLACLAADGKLAPGV-VWRQASVIGSVFSASYAAAEGGIVPTIRGSAHL 291 (311)
T ss_pred -CCc--CceeEEEECCCccccCC-CCccHHHHHHHHHHcCCCCCCC-eEEEEeccCCcEEEEEEeecCCEEEEEEeEEEE
Confidence 111 255542 322356666 999999955555442 33322 223334455544444431 2235678888888
Q ss_pred EEEEEEEC
Q 027494 215 VMQGSLLV 222 (222)
Q Consensus 215 v~~G~i~~ 222 (222)
....++.|
T Consensus 292 tg~~~~~i 299 (311)
T PRK13970 292 SAEATLLI 299 (311)
T ss_pred EEEEEEEe
Confidence 88877653
No 15
>PF05544 Pro_racemase: Proline racemase; InterPro: IPR008794 This family consists of proline racemase (5.1.1.4 from EC) proteins which catalyse the interconversion of L- and D-proline in bacteria []. This family also contains several similar eukaryotic proteins including Q9NCP4 from SWISSPROT a sequence with B-cell mitogenic properties which has been characterised as a co-factor-independent proline racemase [].; GO: 0018112 proline racemase activity; PDB: 1TM0_A 2AZP_A 1W61_B 1W62_A.
Probab=98.76 E-value=2.3e-07 Score=80.42 Aligned_cols=193 Identities=21% Similarity=0.277 Sum_probs=99.1
Q ss_pred CCCCChHHHHHHHHHHhcCCCCC----CcEEEEeceeeEEEEEecCcccccCCCCCCCCCcceeEEEE-eCCCCCCCC-C
Q 027494 1 MELCGHAALAAAHTLFSRGLVNS----NTIEFTTLSGILIAKKVPDVKAMNDSNSQNGEAQECYFIEL-DFPAAPTAD-F 74 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~~----~~~~~~t~~G~v~v~~~~~~~~~~~~~~~~g~~~~~~~v~~-~~p~~~~~~-~ 74 (222)
.+||||+|+|++.+|.+.+.++. .+++++|++|.+++++.- ++| ....+++ +.|++.... .
T Consensus 80 ~~McGh~tI~~~t~lve~G~v~~~~~~t~v~letPaGlV~a~~~~----------~~g---~v~~Vsf~nVPsf~~~~d~ 146 (325)
T PF05544_consen 80 SPMCGHGTIAVATALVETGLVPMKEPETEVRLETPAGLVEATVEV----------EGG---KVESVSFENVPSFVYALDV 146 (325)
T ss_dssp -SSTHHHHHHHHHHHHHTTSS-SECCECEEEEEETTEEEEEEEEE----------TST---SEEEEEEE-S-BEEEEEEE
T ss_pred CCCcccHHHHHHHHHHHCCcccCCCCCEEEEEECCCcEEEEEEEE----------eCC---EEEEEEEeeEEeeeEecCC
Confidence 48999999999999999997642 268999999999999975 243 2234544 355543221 1
Q ss_pred CcccHHHHHHHhCCCceeeeeecCCCceEEEEeCChhhhcccCC-ChhhHhcC----------------C---CCceEE-
Q 027494 75 NFSEVSLILEALGVSSVVDMKITTTCEDIFVVLPSAKSVTDLQP-KFDEMKKC----------------P---GTRGII- 133 (222)
Q Consensus 75 ~~~~~~~l~~algl~~~~~~~~~~G~~~lvv~v~~~~~l~~~~p-d~~~l~~~----------------~---~~~gv~- 133 (222)
.. +.+ -+|--. .|+.. .|+-|.++..++.. | .+.| +.++|.++ + +..+++
T Consensus 147 ~v-~vp----g~G~v~-vDiay-GG~fyaivda~~lG-l-~l~~~~~~~L~~~g~~i~~a~~~~~~v~HP~~~~~~~i~~ 217 (325)
T PF05544_consen 147 PV-EVP----GLGTVT-VDIAY-GGAFYAIVDAAQLG-L-ELEPENARELIRLGRAIKAALNAQIPVVHPENPDIRGIYG 217 (325)
T ss_dssp EE-EET----TTCEEE-EEEEE-SSSEEEEEEGGGCT----SSCCCHHHHHHHHHHHHHHHHHCH---CTC-TTS-SEEE
T ss_pred EE-ECC----CcccEE-EEEEe-CCEEEEEEEHHHcC-C-CcChhhHHHHHHHHHHHHHHHHhhCCCcCCCccccCceeE
Confidence 10 000 122111 34433 47777777665431 1 2222 22323221 1 112333
Q ss_pred --EEeeCCCCCcccEEEeec---CCCCCCCccCccccchhhhHHHHHhh--hCCceEEEeeccCCCeEEEEEEcc----C
Q 027494 134 --VSGLAPPESGFDFYSRFF---CPKFGVNEDPVCGSAYCALATYWSQK--LGKCDFVAYAASPRSGILNIHLDE----Q 202 (222)
Q Consensus 134 --v~~~~~~~~~~~~~~R~f---~p~~Gv~EDpatGSa~~ala~yl~~~--~~~~~~~~~Qg~~r~g~l~v~~~~----~ 202 (222)
++...+. .+. +.|.+ .+ --++--| |||+.+|-.++|..+ ++..+ ...+-|-.++....++.+ .
T Consensus 218 v~~~~~~~~-~~~--~~rn~vv~~~-g~vDRSP-cGTGTsARlA~l~a~G~l~~ge-~~~~eSiiGs~F~g~i~~~~~vg 291 (325)
T PF05544_consen 218 VIFTDPPDD-PDA--HSRNVVVFGD-GQVDRSP-CGTGTSARLALLHARGELKPGE-PFVHESIIGSRFTGRIVEETEVG 291 (325)
T ss_dssp EEEEEEECC-CTS--EEEEEEEETT-TEE-SS---HHHHHHHHHHHHHTTSS-TT--EEEEEETTS-EEEEEEEEEEEET
T ss_pred EEEecCCCC-CCC--cccEEEEECC-CCeeeCC-CchhHHHHHHHHHHCCCCCCCC-cEEEecccCceEEEEEEEEEEEC
Confidence 3433321 112 55544 34 2245556 999999966666543 33322 123335566666666531 1
Q ss_pred CC---eEEEeeeEEEEEEEEEE
Q 027494 203 NQ---RVQLRGKAITVMQGSLL 221 (222)
Q Consensus 203 ~~---~v~v~G~a~~v~~G~i~ 221 (222)
+. ..+|+|+|.+....++.
T Consensus 292 ~~~avip~I~G~A~itG~~~~~ 313 (325)
T PF05544_consen 292 GFPAVIPEITGRAYITGFSQFV 313 (325)
T ss_dssp TCEEEEEEEEE-EEEEEEEEEE
T ss_pred CccEEEEEEEEEEEEEEEEEEE
Confidence 11 57899999988887775
No 16
>COG3938 Proline racemase [Amino acid transport and metabolism]
Probab=98.73 E-value=3.2e-07 Score=77.19 Aligned_cols=40 Identities=20% Similarity=0.419 Sum_probs=36.0
Q ss_pred CCCCChHHHHHHHHHHhcCCCC---C-CcEEEEeceeeEEEEEe
Q 027494 1 MELCGHAALAAAHTLFSRGLVN---S-NTIEFTTLSGILIAKKV 40 (222)
Q Consensus 1 i~~cGH~tlaaa~~l~~~~~~~---~-~~~~~~t~~G~v~v~~~ 40 (222)
.|||||+|||++-+|.+.+.+. + ..+.+||++|.|.++..
T Consensus 88 ~pMsGsntIc~~T~lle~G~v~m~eP~t~l~letP~GlV~~~a~ 131 (341)
T COG3938 88 LPMSGSNTICVVTVLLESGLVPMQEPETVLRLETPAGLVEATAE 131 (341)
T ss_pred CCcCCCCchhhhhHHHHcCCccCCCCceEEEEecCCcEEEEEEE
Confidence 4899999999999999999875 3 56999999999999987
No 17
>PF01678 DAP_epimerase: Diaminopimelate epimerase; InterPro: IPR001653 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways []. There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different []. The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria. The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified. The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana. The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum. Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways. This entry represents diaminopimelate epimerase (5.1.1.7 from EC), which catalyses the isomerisation of L,L-dimaminopimelate to meso-DAP in the biosynthetic pathway leading from aspartate to lysine. It is a member of the broader family of PLP-independent amino acid racemases. This enzyme is a monomeric protein of about 30 kDa consisting of two domains which are homologus in structure though they share little sequence similarity []. Each domain consists of mixed beta-sheets which fold into a barrel around the central helix. The active site cleft is formed from both domains and contains two conserved cysteines thought to function as the acid and base in the catalytic reaction []. Other PLP-independent racemases such as glutamate racemase have been shown to share a similar structure and mechanism of catalysis.; GO: 0008837 diaminopimelate epimerase activity, 0009089 lysine biosynthetic process via diaminopimelate; PDB: 2OTN_A 3FVE_A 2Q9J_A 2GKJ_A 1GQZ_A 2Q9H_A 1BWZ_A 2GKE_A 3EKM_C 3EJX_D ....
Probab=97.01 E-value=0.0022 Score=47.73 Aligned_cols=40 Identities=28% Similarity=0.412 Sum_probs=35.2
Q ss_pred CCCChHHHHHHHHHHhcCCCCCCcEEEEeceeeEEEEEec
Q 027494 2 ELCGHAALAAAHTLFSRGLVNSNTIEFTTLSGILIAKKVP 41 (222)
Q Consensus 2 ~~cGH~tlaaa~~l~~~~~~~~~~~~~~t~~G~v~v~~~~ 41 (222)
..||+++.|+++++.+.+...+.+++++|++|.+.+++..
T Consensus 67 ~aCGnG~~~~a~~~~~~~~~~~~~v~v~t~gG~l~v~~~~ 106 (121)
T PF01678_consen 67 LACGNGCRCAAAYLLEGGIVGKDEVTVETPGGILRVEVDE 106 (121)
T ss_dssp STTHHHHHHHHHHHHHTTSSSSSEEEEEETTEEEEEEEET
T ss_pred eecCcHHHHHHHHHHHCCCCcceEEEEEeCCcEEEEEEEc
Confidence 4799999999999988775556889999999999999985
No 18
>PRK13577 diaminopimelate epimerase; Provisional
Probab=95.50 E-value=0.21 Score=42.69 Aligned_cols=92 Identities=20% Similarity=0.338 Sum_probs=53.5
Q ss_pred cCCCceEEEEeCChhhhcccCCChhhHhcCCC-C-----ceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhh
Q 027494 97 TTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG-T-----RGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCAL 170 (222)
Q Consensus 97 ~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~-~-----~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~al 170 (222)
..||+++||.=.+. ......+.++++++ . .|+.+.... ....++++|+|.|- -.|=+-||.++-++
T Consensus 8 g~GNdfvVvd~~~~----~~~~~~~~~~~i~~R~~gig~Dg~i~~~~~--~~~~d~~mrifn~D--GseaemCGNg~Rc~ 79 (281)
T PRK13577 8 ALGNDYLVIDPRDA----PFDPSADAIRRICHRHFGVGSDGILFGPLP--SEGADFGLRIFNPD--GSEAEKSGNGLRIF 79 (281)
T ss_pred CCCCCEEEEECCCC----CCCCCHHHHHHhhccccCcCCCEEEEEecC--CCCCCEEEEEEcCC--CCHHHhccccHHHH
Confidence 45898888843321 12234555666763 2 234332222 23567999999983 24888899999777
Q ss_pred HHHHHhh--hCCceEEEeeccCCCeEEEEEE
Q 027494 171 ATYWSQK--LGKCDFVAYAASPRSGILNIHL 199 (222)
Q Consensus 171 a~yl~~~--~~~~~~~~~Qg~~r~g~l~v~~ 199 (222)
+.|+.++ .++..+.+.. ..|.+.+++
T Consensus 80 a~~l~~~~~~~~~~~~ieT---~aG~~~~~v 107 (281)
T PRK13577 80 SRYLWDQGLVDDEPFTIET---KGGIVECQV 107 (281)
T ss_pred HHHHHHcCCCCCCcEEEEE---CCceEEEEE
Confidence 8888653 1233454444 335555555
No 19
>COG0253 DapF Diaminopimelate epimerase [Amino acid transport and metabolism]
Probab=95.23 E-value=0.14 Score=43.62 Aligned_cols=93 Identities=19% Similarity=0.266 Sum_probs=56.4
Q ss_pred CCCceEEEEeCChhhhcccCCChhhHhcCCC------CceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhH
Q 027494 98 TTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG------TRGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALA 171 (222)
Q Consensus 98 ~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~------~~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala 171 (222)
+||.+++|.-.+... ....+...++++ +.|+.+..+ +..++.+++.|+|.. --.|=-.||.|+-++|
T Consensus 9 ~GNdfivvd~~~~~~----~~~~~~a~~l~~r~~giGaDgvl~i~~-p~s~~~d~~~rifN~--DGS~ae~CGNG~Rc~a 81 (272)
T COG0253 9 LGNDFIVVDEFDKKD----EETPELARALCDRHFGIGADGVLFVEP-PRSPGADFHLRIFNS--DGSEAEMCGNGARCFA 81 (272)
T ss_pred CCCcEEEEecccccc----ccCHHHHHHHHhcccCcCCceEEEEec-CCCCCCCEEEEEEeC--CCCHHhhcccHHHHHH
Confidence 588888886555322 222333334443 234444332 223467899999975 2246778999999999
Q ss_pred HHHHhhhC--CceEEEeeccCCCeEEEEEEc
Q 027494 172 TYWSQKLG--KCDFVAYAASPRSGILNIHLD 200 (222)
Q Consensus 172 ~yl~~~~~--~~~~~~~Qg~~r~g~l~v~~~ 200 (222)
.|+..+.. +.++.+.. +.|.+.+++.
T Consensus 82 ~~l~~~~~~~~~~~~v~T---~~G~~~~~~~ 109 (272)
T COG0253 82 RFLAERGLVKKKEISVET---LAGILKVKVH 109 (272)
T ss_pred HHHHHhcCCcCccEEEEe---ccceEEEEEe
Confidence 99986532 33355444 5666666664
No 20
>TIGR00654 PhzF_family phenazine biosynthesis protein PhzF family. Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear.
Probab=95.14 E-value=0.17 Score=43.32 Aligned_cols=89 Identities=16% Similarity=0.232 Sum_probs=51.1
Q ss_pred CCCceEEEEeCChhhhcccCCChhhHhcCCC---CceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhHHHH
Q 027494 98 TTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG---TRGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYW 174 (222)
Q Consensus 98 ~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~---~~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl 174 (222)
.||+..||...+ .| +.+.+.++++ ..++.+. ..+..++.++++|+|.| | .|=+-||.+..+.+.++
T Consensus 17 ~GN~~~Vv~~~~--~l-----~~~~mq~iA~~~~~~et~Fv-~~~~~~~~~~~~R~Fnp--g-~E~~~CGh~tl~aa~~l 85 (297)
T TIGR00654 17 MGNPAAVVNFAE--IL-----SEEEMQAIANETNYSETTFL-LKPSSEKYDYRLRIFTP--R-SELPFAGHPTIGSCYAL 85 (297)
T ss_pred CCCceEEEcCCC--CC-----CHHHHHHHHHHhCCCceEEE-cCCCCCCCceEEEEECC--C-CccCcCCchHHHHHHHH
Confidence 599988885432 22 3444544443 1233322 21112345799999999 4 49999999998776666
Q ss_pred Hhhh--C-CceEEEeeccCCCeEEEEEEc
Q 027494 175 SQKL--G-KCDFVAYAASPRSGILNIHLD 200 (222)
Q Consensus 175 ~~~~--~-~~~~~~~Qg~~r~g~l~v~~~ 200 (222)
.+.. . ...+.++. ..|.+.+++.
T Consensus 86 ~~~~~~~~~~~~~~et---~aG~v~v~~~ 111 (297)
T TIGR00654 86 LEFTKLTTATTLVQEC---KAGAVPVTIN 111 (297)
T ss_pred HHcCCCCCCccEEEEc---CceEEEEEEE
Confidence 5421 1 22333222 4577777764
No 21
>PRK00450 dapF diaminopimelate epimerase; Provisional
Probab=94.89 E-value=0.27 Score=41.61 Aligned_cols=92 Identities=17% Similarity=0.281 Sum_probs=53.3
Q ss_pred cCCCceEEEEeCChhhhcccCCChhhHhcCCC-Cc-----eEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhh
Q 027494 97 TTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG-TR-----GIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCAL 170 (222)
Q Consensus 97 ~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~-~~-----gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~al 170 (222)
.+||.++++.-.+. . ...+...++|. .. ++.+..+ +..+..++++|+|.|. ..|=|-||-|.-+.
T Consensus 10 ~~gNdf~~~~~~~~----~--~~~~~~~~~~~r~~gig~det~Fv~~-~~~~~ad~~~R~Ftp~--gsEv~~CGHat~~~ 80 (274)
T PRK00450 10 GLGNDFVVIDARTQ----E--LTPELARKLCDRHFGIGADGLLLVEP-PSSPGADFRMRIFNAD--GSEAEMCGNGARCF 80 (274)
T ss_pred cCCCCEEEEeCCCC----c--CcHHHHHHhhccCCccCCCeEEEEcc-CCCCCCCEEEEEEECC--CCHHHcCcchHHHH
Confidence 46898888864432 1 12333445554 22 3333222 1123567999999993 24889999999988
Q ss_pred HHHHHhhh--CCceEEEeeccCCCeEEEEEEc
Q 027494 171 ATYWSQKL--GKCDFVAYAASPRSGILNIHLD 200 (222)
Q Consensus 171 a~yl~~~~--~~~~~~~~Qg~~r~g~l~v~~~ 200 (222)
+.+|.+.. ....+..+. ..|.+.++++
T Consensus 81 a~~L~~~g~~~~~~~~~~t---~~G~l~v~~~ 109 (274)
T PRK00450 81 ARFLYEKGLTNKTEIRVET---LAGIIEAEVE 109 (274)
T ss_pred HHHHHHcCCCCCCeEEEEe---CCceEEEEEe
Confidence 88876532 222444333 4456666653
No 22
>TIGR00652 DapF diaminopimelate epimerase.
Probab=94.37 E-value=0.54 Score=39.75 Aligned_cols=92 Identities=14% Similarity=0.193 Sum_probs=53.2
Q ss_pred cCCCceEEEEeCChhhhcccCCChhhHhcCCC-C-----ceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhh
Q 027494 97 TTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPG-T-----RGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCAL 170 (222)
Q Consensus 97 ~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~-~-----~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~al 170 (222)
..||.+++|.-.+. .. ..+.+..++++. . .|+.+..+. ..+.++++|+|.|. -.|=|-||-+.-++
T Consensus 8 g~gNdfviid~~~~-~~---~~~~~~~~~l~~r~~~ig~d~~~fv~~~--~~~ad~~~r~Fnpd--g~e~~~CGh~t~~~ 79 (268)
T TIGR00652 8 GLGNDFVLVDDFDA-EL---VFEPEFVRQVCDRHFGIGADGVLFVEPG--SPEADYKMRIFNSD--GSEAEMCGNGIRCF 79 (268)
T ss_pred cCCCcEEEEECCCC-CC---CCCHHHHHHhcccCccccccEEEEEcCC--CCCccEEEEEEeCC--CCHHHhCcCcHHHH
Confidence 46898888864332 11 122344555664 2 244333321 23567999999983 24778899999998
Q ss_pred HHHHHhhh--CCceEEEeeccCCCeEEEEEE
Q 027494 171 ATYWSQKL--GKCDFVAYAASPRSGILNIHL 199 (222)
Q Consensus 171 a~yl~~~~--~~~~~~~~Qg~~r~g~l~v~~ 199 (222)
+.||.++. ....+.++. ..|.+.+++
T Consensus 80 a~~l~~~~~~~~~~~~~et---~~G~v~v~~ 107 (268)
T TIGR00652 80 AKFVYEHGLVNKKDISVET---LAGLIVLEV 107 (268)
T ss_pred HHHHHHcCCCCCCeEEEEe---CCCcEEEEE
Confidence 88887542 123344333 345555555
No 23
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=91.57 E-value=0.68 Score=39.16 Aligned_cols=88 Identities=22% Similarity=0.261 Sum_probs=52.1
Q ss_pred CCCceEEEEeCChhhhcccCCChhhHhcCCCC--ceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhHHHHH
Q 027494 98 TTCEDIFVVLPSAKSVTDLQPKFDEMKKCPGT--RGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWS 175 (222)
Q Consensus 98 ~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~~--~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~ 175 (222)
.|||=.||..++ .++.+.+.++.+. ..-.+|.....++..++++|+|.|. .|=|-||-+.-|.+.+|.
T Consensus 10 ~GNp~aVv~~~~-------~l~~~~mq~iA~e~n~sET~Fv~~~~~~~~~~~vR~FTp~---~Ev~fcGH~tlaaa~~l~ 79 (281)
T PF02567_consen 10 GGNPAAVVLDAD-------GLSDEQMQAIAREFNLSETAFVLPSTDDEADYRVRIFTPT---GEVPFCGHATLAAAHALF 79 (281)
T ss_dssp SSEEEEEEESST-------TS-HHHHHHHHHHHTSSEEEEEEEESSSTTSEEEEEEESS---SEESSSHHHHHHHHHHHH
T ss_pred CCCeEEEEEcCC-------CCCHHHHHHHHHHcCCCeeEEEEeccCCCceeEEEEEecc---CCCCCCCcHHHHHHHHHH
Confidence 488877777655 2234444433210 1112222221124678999999994 599999988888777777
Q ss_pred hhhC--CceEEEeeccCCCeEEEEE
Q 027494 176 QKLG--KCDFVAYAASPRSGILNIH 198 (222)
Q Consensus 176 ~~~~--~~~~~~~Qg~~r~g~l~v~ 198 (222)
+... ...+.... +.|.|.++
T Consensus 80 ~~~~~~~~~~~~~t---~~G~l~v~ 101 (281)
T PF02567_consen 80 ERGGLDPGEIVFET---KAGILPVE 101 (281)
T ss_dssp HHTTTSSSEEEEEE---TTEEEEEE
T ss_pred HhccccCceEEEEc---CeEEEEEE
Confidence 6432 33343333 57888885
No 24
>PRK10281 hypothetical protein; Provisional
Probab=90.96 E-value=1.8 Score=37.35 Aligned_cols=90 Identities=22% Similarity=0.375 Sum_probs=47.1
Q ss_pred CCCceEEEEeCChhhhcccCCChhhHhcCCCC--ceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhHHHHH
Q 027494 98 TTCEDIFVVLPSAKSVTDLQPKFDEMKKCPGT--RGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWS 175 (222)
Q Consensus 98 ~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~~--~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~ 175 (222)
.|||=.||+.++ .| +-+.+.+..+. ..-.+|...+..+..++++|+|.|. .|=|-||-+.-+.+..|.
T Consensus 17 ~GNpaaVv~~a~--~L-----~~~~Mq~IAre~n~SETaFv~~~~~~~~~~~lR~FTP~---~Ev~fcGHaTlaa~~~L~ 86 (299)
T PRK10281 17 RGNSAGVVLNAD--GL-----SEAQMQLIARELNHSETAFLLSSDDSSYDVRVRYFTPT---VEVPICGHATVAAHYVRA 86 (299)
T ss_pred CCCceEEEcCCC--CC-----CHHHHHHHHHHhCCceEEEEccCCCCCCceEEEEECCC---cccccCCcHHHHHHHHHH
Confidence 488877775432 33 33344332211 1112333222122347999999994 499999977666444444
Q ss_pred hhhC--CceEEEeeccCCCeEEEEEEc
Q 027494 176 QKLG--KCDFVAYAASPRSGILNIHLD 200 (222)
Q Consensus 176 ~~~~--~~~~~~~Qg~~r~g~l~v~~~ 200 (222)
+..+ ...+ .|- ...|.|.|+++
T Consensus 87 ~~~~~~~~~~--~~~-t~~G~v~v~~~ 110 (299)
T PRK10281 87 TVLGLGNCTV--WQT-TLAGILPVDIE 110 (299)
T ss_pred HhCCCCCCcE--EEE-cCceEEEEEEE
Confidence 3221 2222 221 24477788775
No 25
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=90.29 E-value=1.9 Score=37.17 Aligned_cols=94 Identities=17% Similarity=0.185 Sum_probs=48.2
Q ss_pred cCCCceEEEEeCChhhhcccCCChhhHhcCCCCceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhHHHHHh
Q 027494 97 TTTCEDIFVVLPSAKSVTDLQPKFDEMKKCPGTRGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWSQ 176 (222)
Q Consensus 97 ~~G~~~lvv~v~~~~~l~~~~pd~~~l~~~~~~~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~~ 176 (222)
..|||=-|+.- .+.|..- +..++++..+ ..=.+|...+.++ .++++|+|.|.. |=|-||-++-+.+..+.+
T Consensus 17 ~~GNp~aVv~~--a~~Lsd~--~MQ~IA~e~n-~SET~Fv~~~~~~-~~~rlR~FTP~~---Evpf~GHaTlga~~~l~~ 87 (291)
T COG0384 17 FGGNPLAVVLD--ADGLSDE--QMQAIAREFN-LSETAFVLPPDDP-ADARLRIFTPTT---EVPFAGHATLGAAHVLAE 87 (291)
T ss_pred CCCCceEEEeC--CCCCCHH--HHHHHHHHhC-CceeEEEcCCCCc-CceEEEEeCCCc---ccccCCCHHHHHHHHHHH
Confidence 35888777763 3334311 2334433222 1222343333222 689999999953 888899776554333344
Q ss_pred hhCCc---eEEEeeccCCCeEEEEEEccC
Q 027494 177 KLGKC---DFVAYAASPRSGILNIHLDEQ 202 (222)
Q Consensus 177 ~~~~~---~~~~~Qg~~r~g~l~v~~~~~ 202 (222)
.++.. .+..+ -.-|.+.++++.+
T Consensus 88 ~~~~~~~~~~~~e---~~aG~v~i~~~~~ 113 (291)
T COG0384 88 LGGLSNDTTLTLE---TKAGLVPVTVERG 113 (291)
T ss_pred hcCCCccceEEEE---eccCeEEEEEEeC
Confidence 33321 22222 2567766666543
No 26
>PLN02536 diaminopimelate epimerase
Probab=89.78 E-value=3 Score=35.38 Aligned_cols=73 Identities=19% Similarity=0.342 Sum_probs=44.2
Q ss_pred hhhHhcCCC------CceEEEEeeCCCCCcccEEEeecCCCCCCCccCccccchhhhHHHHHhhh--C-CceEEEeeccC
Q 027494 120 FDEMKKCPG------TRGIIVSGLAPPESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWSQKL--G-KCDFVAYAASP 190 (222)
Q Consensus 120 ~~~l~~~~~------~~gv~v~~~~~~~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~~~~--~-~~~~~~~Qg~~ 190 (222)
.+...++|+ +.|+.+.... ..+.++++|+|.|- | .|=+-||.|.-+++.|+.++. + ...+.+..
T Consensus 13 ~~~~~~lc~R~~GiGaDgli~i~~~--~~~ad~~mrifN~D-G-Sea~mCGNg~Rc~a~~l~~~~~~~~~~~~~ieT--- 85 (267)
T PLN02536 13 PEQAVKLCDRNFGIGADGVIFAMPG--VNGTDYTMRIFNSD-G-SEPEMCGNGIRCFARFIAELENLQGKNSYKIHT--- 85 (267)
T ss_pred HHHHHHhcccCCCcCCCEEEEEecC--CCCccEEEEEEcCC-C-ChhhhCccHHHHHHHHHHHcCCCCCCceEEEEe---
Confidence 444556665 2355554332 22457999999983 2 477779999999999987642 1 23455444
Q ss_pred CCeEEEEEE
Q 027494 191 RSGILNIHL 199 (222)
Q Consensus 191 r~g~l~v~~ 199 (222)
..|.+.+++
T Consensus 86 ~aG~i~~~v 94 (267)
T PLN02536 86 GAGLIIPEM 94 (267)
T ss_pred CCccEEEEE
Confidence 344444444
No 27
>PF04303 PrpF: PrpF protein; InterPro: IPR007400 PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerise trans-aconitate to cis-aconitate []. ; PDB: 2H9F_A 2PVZ_B 2PW0_A 3G7K_D.
Probab=74.21 E-value=7.3 Score=34.74 Aligned_cols=77 Identities=19% Similarity=0.249 Sum_probs=42.8
Q ss_pred cccEEEeecCCCCCCCccCccccchhhhHHHHH----hhh-CC---ceEEEeeccCCCeEEEEEEcc--CCC---eEEEe
Q 027494 143 GFDFYSRFFCPKFGVNEDPVCGSAYCALATYWS----QKL-GK---CDFVAYAASPRSGILNIHLDE--QNQ---RVQLR 209 (222)
Q Consensus 143 ~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~----~~~-~~---~~~~~~Qg~~r~g~l~v~~~~--~~~---~v~v~ 209 (222)
+.++.+|+|.|..==.-=|.||+.+-+.|+.+- +.+ +. ..+++.+ ..|.+.+.++- +++ .+.+.
T Consensus 281 ~~di~~R~~s~~~~H~A~~~Tgavcla~Aa~i~GTv~~~~~~~~~~~~v~IgH---PSG~l~v~~~~~~~~~~v~~~~v~ 357 (371)
T PF04303_consen 281 DIDIVVRYFSMGKCHKAIAVTGAVCLAAAARIPGTVVHELARGRAPGEVRIGH---PSGVLEVGVEVDGDDGEVESAGVY 357 (371)
T ss_dssp G-SEEEEEEETTEE-SS--HHHHHHHHHHHHSTTSHHHHHTTSST-SEEEEEE---TTEEEEEEEEEEEETTEEEEEEEE
T ss_pred cccEEEEEecCCCcchhhhhHHHHHHHHHHhcCCCcccccccccccccEEEec---CCeEEEEEEEEeccCCceeEEEEE
Confidence 356889999973211234567765555554432 111 21 2233333 77887777642 223 46677
Q ss_pred eeEEEEEEEEEEC
Q 027494 210 GKAITVMQGSLLV 222 (222)
Q Consensus 210 G~a~~v~~G~i~~ 222 (222)
=.|..+|+|++++
T Consensus 358 RTARrLm~G~v~v 370 (371)
T PF04303_consen 358 RTARRLMEGEVFV 370 (371)
T ss_dssp E-EEEEEEEEEEE
T ss_pred EehhhheeEEEEe
Confidence 7899999999975
No 28
>PRK13971 hydroxyproline-2-epimerase; Provisional
Probab=71.75 E-value=29 Score=30.54 Aligned_cols=33 Identities=21% Similarity=0.251 Sum_probs=26.9
Q ss_pred CCcccEEEeecCCCCCCCccCccccchhhhHHHHHh
Q 027494 141 ESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWSQ 176 (222)
Q Consensus 141 ~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~~ 176 (222)
+++.++.+|+|.|. .|-|-||.+.-+++.+|.+
T Consensus 71 ~~~Ad~gvrfFtp~---~e~~mcGH~TIg~a~~L~e 103 (333)
T PRK13971 71 RPDCDFAILFIETS---GCLPMCGHGTIGTVTAAIE 103 (333)
T ss_pred CCCCCEEEEEECCC---cccCcCccHHHHHHHHHHH
Confidence 34678999999983 4899999999888877765
No 29
>TIGR02334 prpF probable AcnD-accessory protein PrpF. The 2-methylcitrate cycle is one of at least five degradation pathways for propionate via propionyl-CoA. Degradation of propionate toward pyruvate consumes oxaloacetate and releases succinate. Oxidation of succinate back into oxaloacetate by the TCA cycle makes the 2-methylcitrate pathway a cycle. This family consists of PrpF, an incompletely characterized protein that appears to be an essential accessory protein for the Fe/S-dependent 2-methylisocitrate dehydratase AcnD (TIGR02333). This protein is related to but distinct from FldA (part of Pfam family pfam04303), a putative fluorene degradation protein of Sphingomonas sp. LB126.
Probab=59.00 E-value=31 Score=30.98 Aligned_cols=77 Identities=16% Similarity=0.047 Sum_probs=42.6
Q ss_pred cccEEEeecCCCCCCCccCccccchhhhHHHHHhh----hCC-c---eEEEeeccCCCeEEEEEEc--cCCC--eE---E
Q 027494 143 GFDFYSRFFCPKFGVNEDPVCGSAYCALATYWSQK----LGK-C---DFVAYAASPRSGILNIHLD--EQNQ--RV---Q 207 (222)
Q Consensus 143 ~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~~~----~~~-~---~~~~~Qg~~r~g~l~v~~~--~~~~--~v---~ 207 (222)
+.++.+|+|.|..-=.-=|.||+-+-|.|+.+-.. ... . .+++ ....|.|.+.++ .+++ .+ -
T Consensus 294 ~~di~~R~~s~~~~H~A~~vTgav~la~Aa~ipGTv~~~~~~~~~~~~v~i---gHPsG~l~v~~~~~~~~~~~~v~~~~ 370 (390)
T TIGR02334 294 EIDLLVRALSMGKLHHAMMGTAAVAIGTAAAVPGTLVNLAAGGGERSAVRF---GHPSGTLRVGAEASQVNGQWTVTKAI 370 (390)
T ss_pred ccCEEEEEecCCCCchhhhHHHHHHHHHHHhcCCchhhhccCCCCcceEEE---eCCCeEEEEEEEEecCCCceEEEEEE
Confidence 34899999998432233455666655555443211 100 0 1222 236777877765 2233 22 2
Q ss_pred EeeeEEEEEEEEEEC
Q 027494 208 LRGKAITVMQGSLLV 222 (222)
Q Consensus 208 v~G~a~~v~~G~i~~ 222 (222)
|-=.|..+|+|++++
T Consensus 371 v~RTARrlm~G~v~v 385 (390)
T TIGR02334 371 MSRSARVLMEGWVRV 385 (390)
T ss_pred EEEehhhhccEEEec
Confidence 446778899999874
No 30
>PRK13969 proline racemase; Provisional
Probab=46.72 E-value=1.3e+02 Score=26.38 Aligned_cols=54 Identities=19% Similarity=0.165 Sum_probs=37.4
Q ss_pred CCcccEEEeecCCCCCCCccCccccchhhhHHHHHhh--hCCc----eEEEeeccCCCeEEEEEEc
Q 027494 141 ESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWSQK--LGKC----DFVAYAASPRSGILNIHLD 200 (222)
Q Consensus 141 ~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~~~--~~~~----~~~~~Qg~~r~g~l~v~~~ 200 (222)
+.+.++-+++|.. .++-+-||++.=+++.|+.+. .... .++++. ..|.+.+++.
T Consensus 72 ~~~Ad~gvif~~~---~gy~~MCGhgtI~vat~l~e~G~v~~~~~~~~v~ieT---PaGlV~a~~~ 131 (334)
T PRK13969 72 DETADFGIIFMDG---GGYLNMCGHGSIGAATCAVETGIVKVEEPYTHIKLEA---PAGMINARVK 131 (334)
T ss_pred CCCCCEEEEEEeC---CcccccccChHHHHHHHHHHcCCcCCCCCceeEEEEC---CceEEEEEEE
Confidence 3457899999953 358899999999999999763 1111 233333 7777777774
No 31
>PRK13970 hydroxyproline-2-epimerase; Provisional
Probab=34.01 E-value=80 Score=27.54 Aligned_cols=54 Identities=13% Similarity=0.123 Sum_probs=35.9
Q ss_pred CCcccEEEeecCCCCCCCccCccccchhhhHHHHHhh--hCCceEEEeeccCCCeEEEEEEc
Q 027494 141 ESGFDFYSRFFCPKFGVNEDPVCGSAYCALATYWSQK--LGKCDFVAYAASPRSGILNIHLD 200 (222)
Q Consensus 141 ~~~~~~~~R~f~p~~Gv~EDpatGSa~~ala~yl~~~--~~~~~~~~~Qg~~r~g~l~v~~~ 200 (222)
+++.++.+|+|.|. .|=+-||.+.=+++..+.+. ......++ -...|.+.+++.
T Consensus 70 ~p~Ad~gvif~~~~---g~~~mCGH~TIa~~t~l~e~G~v~~~~~~i---eTpaG~v~v~~~ 125 (311)
T PRK13970 70 SPDAAAGVIFFNNS---GYLGMCGHGTIGVVRTLHHMGRIGPGVHRI---ETPVGTVEATLH 125 (311)
T ss_pred CcccCEEEEEEcCC---CcccccccchheeeeeeeecceecCCcEEE---EcCCceEEEEEE
Confidence 45789999999973 48899999999988776542 11111122 236677777665
No 32
>PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.
Probab=29.22 E-value=40 Score=26.52 Aligned_cols=19 Identities=16% Similarity=0.522 Sum_probs=14.6
Q ss_pred CCCChHHHHHHHHHHhcCC
Q 027494 2 ELCGHAALAAAHTLFSRGL 20 (222)
Q Consensus 2 ~~cGH~tlaaa~~l~~~~~ 20 (222)
||||-||+..-+++.....
T Consensus 35 P~CGsGtiliEaa~~~~~~ 53 (179)
T PF01170_consen 35 PFCGSGTILIEAALMGANI 53 (179)
T ss_dssp TT-TTSHHHHHHHHHHTTT
T ss_pred cCCCCCHHHHHHHHHhhCc
Confidence 8999999999887766554
No 33
>COG0116 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]
Probab=24.12 E-value=56 Score=29.33 Aligned_cols=18 Identities=17% Similarity=0.516 Sum_probs=15.4
Q ss_pred CCCChHHHHHHHHHHhcC
Q 027494 2 ELCGHAALAAAHTLFSRG 19 (222)
Q Consensus 2 ~~cGH~tlaaa~~l~~~~ 19 (222)
||||-+|++.=++|...+
T Consensus 198 PmCGSGTi~IEAAl~~~n 215 (381)
T COG0116 198 PMCGSGTILIEAALIAAN 215 (381)
T ss_pred CCCCccHHHHHHHHhccc
Confidence 899999999988887654
No 34
>PF13793 Pribosyltran_N: N-terminal domain of ribose phosphate pyrophosphokinase; PDB: 2JI4_A 1DKU_B 1IBS_B 1DKR_B 3MBI_C 3LRT_B 3LPN_B 3NAG_B 2H07_B 2H06_B ....
Probab=24.10 E-value=2.7e+02 Score=20.27 Aligned_cols=39 Identities=21% Similarity=0.077 Sum_probs=26.3
Q ss_pred cccchhhhHHHHHhhhCCceEEEeeccCCCeEEEEEEcc
Q 027494 163 CGSAYCALATYWSQKLGKCDFVAYAASPRSGILNIHLDE 201 (222)
Q Consensus 163 tGSa~~ala~yl~~~~~~~~~~~~Qg~~r~g~l~v~~~~ 201 (222)
+||++-.||.-++++++..-....-.....|+.++++.+
T Consensus 5 ~g~~~~~La~~ia~~L~~~~~~~~~~~F~dGE~~v~i~~ 43 (116)
T PF13793_consen 5 SGSSSQDLAERIAEALGIPLGKVETKRFPDGETYVRIPE 43 (116)
T ss_dssp ESSSGHHHHHHHHHHTTS-EE-EEEEE-TTS-EEEEESS
T ss_pred ECCCCHHHHHHHHHHhCCceeeeEEEEcCCCCEEEEecc
Confidence 678889999888877775433334445788999999963
No 35
>PF01555 N6_N4_Mtase: DNA methylase; InterPro: IPR002941 This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. N-4 cytosine-specific DNA methylases (2.1.1.113 from EC) [] are enzymes that specifically methylate the amino group at the C-4 position of cytosines in DNA. Such enzymes are found as components of type II restriction-modification systems in prokaryotes. Such enzymes recognise a specific sequence in DNA and methylate a cytosine in that sequence. By this action they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2ZIF_A 2ZIE_A 2ZIG_A 1NW6_A 1NW8_A 1NW7_A 1NW5_A 1EG2_A 1BOO_A 1G60_B ....
Probab=22.80 E-value=25 Score=27.89 Aligned_cols=27 Identities=22% Similarity=0.086 Sum_probs=19.0
Q ss_pred EeecCCCCCCCccCccccchhhhHHHH
Q 027494 148 SRFFCPKFGVNEDPVCGSAYCALATYW 174 (222)
Q Consensus 148 ~R~f~p~~Gv~EDpatGSa~~ala~yl 174 (222)
+|+|.+...+--||-+||++.++|+..
T Consensus 185 I~~~t~~gdiVlDpF~GSGTT~~aa~~ 211 (231)
T PF01555_consen 185 IKASTNPGDIVLDPFAGSGTTAVAAEE 211 (231)
T ss_dssp HHHHS-TT-EEEETT-TTTHHHHHHHH
T ss_pred HHhhhccceeeehhhhccChHHHHHHH
Confidence 466666556778999999999988764
No 36
>PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2.1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B.
Probab=22.79 E-value=41 Score=28.68 Aligned_cols=16 Identities=38% Similarity=0.559 Sum_probs=10.9
Q ss_pred CccCccccchhhhHHH
Q 027494 158 NEDPVCGSAYCALATY 173 (222)
Q Consensus 158 ~EDpatGSa~~ala~y 173 (222)
-=||+||||.--++++
T Consensus 50 VlDPacGsG~fL~~~~ 65 (311)
T PF02384_consen 50 VLDPACGSGGFLVAAM 65 (311)
T ss_dssp EEETT-TTSHHHHHHH
T ss_pred eechhhhHHHHHHHHH
Confidence 3599999998765544
No 37
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=20.56 E-value=32 Score=21.74 Aligned_cols=8 Identities=38% Similarity=0.970 Sum_probs=5.3
Q ss_pred CCCChHHH
Q 027494 2 ELCGHAAL 9 (222)
Q Consensus 2 ~~cGH~tl 9 (222)
||||++.+
T Consensus 7 PFCG~~~~ 14 (61)
T PF14354_consen 7 PFCGSADV 14 (61)
T ss_pred CCCCCcce
Confidence 67776653
No 38
>PF10648 Gmad2: Immunoglobulin-like domain of bacterial spore germination; InterPro: IPR018911 This domain is found linked to IPR019606 from INTERPRO in some bacterial proteins. It is predicted to contain an immunoglobulin-like all-beta fold.
Probab=20.28 E-value=1.4e+02 Score=20.76 Aligned_cols=17 Identities=35% Similarity=0.573 Sum_probs=13.2
Q ss_pred CeEEEeeeEEEEEEEEEE
Q 027494 204 QRVQLRGKAITVMQGSLL 221 (222)
Q Consensus 204 ~~v~v~G~a~~v~~G~i~ 221 (222)
..+.|.|.|. ++||++.
T Consensus 16 sp~~V~G~A~-~FEgtv~ 32 (88)
T PF10648_consen 16 SPVKVSGKAR-VFEGTVN 32 (88)
T ss_pred CCEEEEEEEE-EeeeEEE
Confidence 4688888877 8888875
Done!