Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate RR42_RS02510 RR42_RS02510 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q0KEG0 (807 letters) >FitnessBrowser__Cup4G11:RR42_RS02510 Length = 808 Score = 1485 bits (3844), Expect = 0.0 Identities = 751/808 (92%), Positives = 780/808 (96%), Gaps = 1/808 (0%) Query: 1 MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60 MSNFIVKKVAVLGAGVMGAQIAAHL+NARVPVVLFDLPAKEGPKNGI+LRAIENLKKLSP Sbjct: 1 MSNFIVKKVAVLGAGVMGAQIAAHLVNARVPVVLFDLPAKEGPKNGISLRAIENLKKLSP 60 Query: 61 APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120 APLGI +EAGLIQAANYEDD+ALLKECD+VIEAIAERMDWKHDLYKKVAPHLASH IFAT Sbjct: 61 APLGINDEAGLIQAANYEDDLALLKECDVVIEAIAERMDWKHDLYKKVAPHLASHTIFAT 120 Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQP ILD+LE FLT+T Sbjct: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPAILDRLETFLTST 180 Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEK+GIPFDVVDDLTGSKLGRAKSATFRTA Sbjct: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKYGIPFDVVDDLTGSKLGRAKSATFRTA 240 Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300 DVVGLDTMAHVIKTMQDTL DDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK Sbjct: 241 DVVGLDTMAHVIKTMQDTLMDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300 Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360 VLD KTGQYVD+GKKADEIVVRMLKK+ AERIKLLRESTNPQAQFLWAVFRDVFHYI VY Sbjct: 301 VLDPKTGQYVDSGKKADEIVVRMLKKEPAERIKLLRESTNPQAQFLWAVFRDVFHYIGVY 360 Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKED+EAGK L+ LPAWV Sbjct: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDIEAGKGLANVALPAWV 420 Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480 F GPVAENQGVH A GSWSPA Q+FV R+ LPVY RQ FRAA+KGTAAADPRKAGRTVEE Sbjct: 421 FAGPVAENQGVHGAQGSWSPAAQAFVQRNALPVYARQVFRAALKGTAAADPRKAGRTVEE 480 Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDV DGLTRAIDLA+A YKGLVVWQPTSLQLG Sbjct: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVTDGLTRAIDLAQAEYKGLVVWQPTSLQLG 540 Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVK+FQDGMMRVKY++VPVVSAASGIALGGG Sbjct: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKKFQDGMMRVKYSAVPVVSAASGIALGGG 600 Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660 CELMLHSA RVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTN LQFLT+R Sbjct: 601 CELMLHSAKRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNYLQFLTNR 660 Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLP-TLV 719 FQ+AAMAKVSASAL+A++MGYLQPSD IVFNVHELL+VAQNEVRAL++AGYRAP+P TLV Sbjct: 661 FQAAAMAKVSASALDAQKMGYLQPSDTIVFNVHELLHVAQNEVRALSNAGYRAPVPGTLV 720 Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779 PVAGRSGIATIKASL NMRDGGFIS HDFLIASRIAEAVCGGDVEAGSLVSE+WLLALER Sbjct: 721 PVAGRSGIATIKASLANMRDGGFISAHDFLIASRIAEAVCGGDVEAGSLVSEEWLLALER 780 Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807 KAFVDLLGTGKTQERIMGMLQTGKPVRN Sbjct: 781 KAFVDLLGTGKTQERIMGMLQTGKPVRN 808 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: 1995 Number of extensions: 76 Number of successful extensions: 2 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: 808 Length adjustment: 41 Effective length of query: 766 Effective length of database: 767 Effective search space: 587522 Effective search space used: 587522 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: 56 (26.2 bits)
This GapMind analysis is from Sep 17 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