Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_054256649.1 BN2503_RS10700 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_001298675.1:WP_054256649.1 Length = 800 Score = 981 bits (2537), Expect = 0.0 Identities = 506/810 (62%), Positives = 615/810 (75%), Gaps = 13/810 (1%) Query: 1 MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60 MS F VKKVAVLGAGVMGAQIAAHL+N +VPVVLFDLPAKEGPK+ IA RAI NLKKL P Sbjct: 1 MSRFNVKKVAVLGAGVMGAQIAAHLVNVKVPVVLFDLPAKEGPKSSIAERAIANLKKLKP 60 Query: 61 APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120 +P+G+ E+A LIQAANYE+ + LLKECDLVIEAIAERMDWK DLY K+AP +A HAI A+ Sbjct: 61 SPIGVAEDADLIQAANYEEHLKLLKECDLVIEAIAERMDWKLDLYTKIAPFVAKHAIVAS 120 Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180 NTSGLSIT LS+ +K RFCG+HFFNPPRYM LVELIPT TT+P +LDQLEAF+T+ Sbjct: 121 NTSGLSITKLSEALPEAIKPRFCGIHFFNPPRYMPLVELIPTPTTEPVVLDQLEAFVTSG 180 Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240 LGKGVVRAKDTPNFIANR+GI +L+ E E FG+ +DVVDDLTG KLGRA S TFRTA Sbjct: 181 LGKGVVRAKDTPNFIANRIGIAGMLSTMKEVENFGLTYDVVDDLTGKKLGRASSGTFRTA 240 Query: 241 DVVGLDTMAHVIKTMQD--TLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKA 298 DVVGLDTMAHVIKT+QD +L DPF + TPAVL+ L++ G LGQKT AGF+KK G+ Sbjct: 241 DVVGLDTMAHVIKTLQDNLSLESDPFYGSFGTPAVLQKLIELGNLGQKTKAGFFKKVGRD 300 Query: 299 IKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358 I + ++ YV AG+KAD++ RMLK+ AAER++LLR + QFLWA+ R+ FHY A Sbjct: 301 ILRFELESESYVPAGQKADDVYARMLKRPAAERLQLLRNAEGAPGQFLWAILRNSFHYAA 360 Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418 ++LE IA SA D+D A+RWGFG GPFE WQ AGW +VA V+ED++AGKAL APLP Sbjct: 361 LHLETIADSARDVDQAMRWGFGMKQGPFELWQEAGWLEVARMVQEDIDAGKALCKAPLPK 420 Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAA-ADPRKAGRT 477 WVFEGPVA+ GVH A GSWSPA FV R LPVY+RQ F + G A+ D + AG T Sbjct: 421 WVFEGPVAQAGGVHTAEGSWSPALGKFVPRRVLPVYERQLFPEKLLGEASLPDWQTAGTT 480 Query: 478 VEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSL 537 + E+ A+R W +GQ VL+ S K+KM+ I P+V++GL A++LAEA Y+G+V+W Sbjct: 481 LFESKALRTWTLDGQ--VLIASIKNKMHAISPEVMEGLVEAVELAEAEYQGMVIW----- 533 Query: 538 QLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIAL 597 + PFS GA+LEA MPAF++GGA IE + Q+ MMR++YA VPVV+A G+AL Sbjct: 534 ---SGDAPFSVGADLEATMPAFVVGGADAIESVEQELQNLMMRIRYAQVPVVAAIHGMAL 590 Query: 598 GGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFL 657 GGGCEL ++SA RVA +E+YIGLVEVGVGLVP GGL A AA + S ++L FL Sbjct: 591 GGGCELAVYSARRVAHMESYIGLVEVGVGLVPGAGGLTYIARRAAENMAKSTSRDLLPFL 650 Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT 717 T F +AAMAKV SA+E+R++GYL SD IV + E+L+VA NE +A+A+ G+RAPL Sbjct: 651 TEGFTAAAMAKVGTSAIESRKLGYLLDSDLIVPHKDEVLFVAINEAKAMAAGGWRAPLKR 710 Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777 L PVAGRSG+ATIKA LVNMRDGGFIS +DF IAS I + VCGGDV+AGSLVSE++LL L Sbjct: 711 LFPVAGRSGLATIKAQLVNMRDGGFISAYDFKIASMIGDVVCGGDVDAGSLVSEEYLLTL 770 Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807 ERK F L+ KT ERI+GML TGKPVRN Sbjct: 771 ERKVFCHLIAQPKTHERILGMLNTGKPVRN 800 Lambda K H 0.319 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1642 Number of extensions: 70 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 807 Length of database: 800 Length adjustment: 41 Effective length of query: 766 Effective length of database: 759 Effective search space: 581394 Effective search space used: 581394 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory