Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067645581.1 I596_RS06330 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_001632775.1:WP_067645581.1 Length = 790 Score = 879 bits (2272), Expect = 0.0 Identities = 462/808 (57%), Positives = 569/808 (70%), Gaps = 23/808 (2%) Query: 2 SNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPA 61 + +++K AVLGAGVMGAQIAAHL+NA + +LFDLPAKEG KNGI +AI NL KLSPA Sbjct: 4 NTLLIRKAAVLGAGVMGAQIAAHLVNAGIETILFDLPAKEGDKNGIVTQAIANLAKLSPA 63 Query: 62 PLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATN 121 PL K A I ANY++D+ L ECDLVIEAIAERMDWK DLY+++APHL+ A A+N Sbjct: 64 PLAEKSLAAAIVPANYDEDLGRLGECDLVIEAIAERMDWKLDLYRRIAPHLSDSAFVASN 123 Query: 122 TSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTL 181 TSGLSI L+D A L+ RF G+HFFNPPRYMHLVE+IP T P +L LEAFLTT L Sbjct: 124 TSGLSINTLADALPAALRRRFSGIHFFNPPRYMHLVEVIPARETDPALLAGLEAFLTTQL 183 Query: 182 GKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTAD 241 GKGVV A+DTPNFI NR+G+FSILA E+FG+ FD VD +TG +GR KSAT+RT+D Sbjct: 184 GKGVVYARDTPNFIGNRIGVFSILATMHHTEQFGLGFDEVDAITGPAIGRPKSATYRTSD 243 Query: 242 VVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKV 301 VVGLDTMAHVIKTM DTL +DP+ +K PA L+ L+D GALGQKTGAGF++K GK I V Sbjct: 244 VVGLDTMAHVIKTMADTLPEDPWHAYFKAPAWLQALIDQGALGQKTGAGFFRKVGKDIHV 303 Query: 302 LDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360 LD Y AG+ A E V +L +D AE+ LR ST+ QAQFLWA+FRD+FHY A + Sbjct: 304 LDLAQRDYRPAGRAASEEVAAILAIRDPAEKFAKLRASTDRQAQFLWAMFRDLFHYSAYH 363 Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420 L +A +A ++DLAIRWG+GW GPFE WQ+AGW+QVA+W+ ED+ AGKA+S+APLPAWV Sbjct: 364 LADLAETAREVDLAIRWGYGWKLGPFETWQAAGWRQVAQWINEDIAAGKAMSSAPLPAWV 423 Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480 +G +GVH A G++S + + RS PVY+RQ F + G + G T E Sbjct: 424 TDG----REGVHVAEGAYSASAGRPLPRSAHPVYRRQRFPDPLLG----ERFDTGTTAWE 475 Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540 N+ VR+W D+V +VSFK+KMNT+ V+DG+ RAID AE +KG+V+WQ Sbjct: 476 NEGVRLW--HLGDEVGIVSFKTKMNTVNDAVLDGIQRAIDEAEKTFKGVVLWQ------- 526 Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600 G PFSAGA+L+ A+ G + V FQ R+KYA VPVV+A G+A GGG Sbjct: 527 -TGEPFSAGADLKGALGLLQAGKVDAFDAMVANFQATSQRIKYALVPVVAAVRGMAFGGG 585 Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660 CE +HSA VAALE+YIGLVE GVGL+PAGGGLKE AL RAA AG + + Sbjct: 586 CEFQMHSARTVAALESYIGLVEAGVGLLPAGGGLKEIAL---RAATQAGGGDPFDGVKRM 642 Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT-LV 719 F++ AMAKVS SALEA+Q+G L+P D +VFN +ELL+VA ALA GYR PLP + Sbjct: 643 FETIAMAKVSGSALEAKQLGLLRPDDVVVFNAYELLHVASTVAGALAEQGYRPPLPARAI 702 Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779 PVAG G AT+K LVNM +G FIS HDF +ASRIA+ +CGG +E GS V E WLL LER Sbjct: 703 PVAGDVGTATLKMLLVNMLEGRFISPHDFDVASRIADTLCGGSIERGSQVDERWLLDLER 762 Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807 + FV+L T KTQERI L TGKP+RN Sbjct: 763 RHFVELAQTAKTQERIAHTLATGKPLRN 790 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: 1633 Number of extensions: 69 Number of successful extensions: 8 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: 790 Length adjustment: 41 Effective length of query: 766 Effective length of database: 749 Effective search space: 573734 Effective search space used: 573734 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