Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate N515DRAFT_2687 N515DRAFT_2687 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q0KEG0 (807 letters) >FitnessBrowser__Dyella79:N515DRAFT_2687 Length = 798 Score = 889 bits (2297), Expect = 0.0 Identities = 468/808 (57%), Positives = 578/808 (71%), Gaps = 23/808 (2%) Query: 2 SNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPA 61 S ++K AVLGAGVMGAQIAAHL NA V VLFDLPAKEGPK+GIAL+AIENLKKLSPA Sbjct: 12 SKLRIRKAAVLGAGVMGAQIAAHLTNANVETVLFDLPAKEGPKSGIALKAIENLKKLSPA 71 Query: 62 PLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATN 121 PL A I ANY+DD+ LK+ DLVIEAIAERMDWK DLYKK+AP++A HA+ A+N Sbjct: 72 PLADGSRAAAIIPANYDDDLEHLKDVDLVIEAIAERMDWKLDLYKKIAPYVAPHAVLASN 131 Query: 122 TSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTL 181 TSGLSI L++ +++ RF GVHFFNPPRYMHLVELIPT T+ ++L+ LEAFLTT + Sbjct: 132 TSGLSINGLAEALPEEMRHRFTGVHFFNPPRYMHLVELIPTRLTEAKVLEGLEAFLTTVV 191 Query: 182 GKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTAD 241 GKGVV AKDTPNFI NR+G+FS+LA E+F + FDVVD LTG +GR KSAT+RTAD Sbjct: 192 GKGVVYAKDTPNFIGNRIGVFSMLATMHHTEQFKLGFDVVDALTGPAVGRPKSATYRTAD 251 Query: 242 VVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKV 301 VVGLDTMAHVIKTM DTL DDP+ +K PA L+GL++ GALGQKTGAGFY+K GK I V Sbjct: 252 VVGLDTMAHVIKTMADTLADDPWHQYFKAPAWLQGLIEQGALGQKTGAGFYRKAGKDIVV 311 Query: 302 LDAKTGQYVDAGKKA-DEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360 LD Y + ++A DE+ + KD AE+ LR S++PQAQFLWA FRD+FHY A + Sbjct: 312 LDVAKRDYRASEQQASDEVAAILAIKDPAEKFAKLRASSDPQAQFLWATFRDLFHYTAYH 371 Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420 L IA +A D+D AIRWG+GW GPFE WQ+AGW+QVA W+ ED+ AGKA+S+APLP WV Sbjct: 372 LADIADTARDVDFAIRWGYGWKLGPFETWQAAGWQQVATWIGEDIAAGKAMSSAPLPKWV 431 Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480 +G GVH +GS+S + + RS+ PVY+RQ F I G + G TV E Sbjct: 432 TDG----RSGVHGKSGSYSASANADKPRSQHPVYRRQLFPDPILG----EKFDQGSTVWE 483 Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540 ND VR+W + G D V ++SFK+KMNT+ V+DG+ +AID+AE K +V+WQ Sbjct: 484 NDGVRLW-TLGDDGVGIISFKTKMNTVNDQVLDGIQQAIDVAEQQLKAVVIWQ------- 535 Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600 G PFSAGA+L+ A+ G E V FQ MR+K++ VPVVSA G+ALGGG Sbjct: 536 -TGEPFSAGADLKGALGLLQAGKLGDFEAMVANFQRTSMRIKHSLVPVVSAVRGLALGGG 594 Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660 CE +HSA VAALE+YIGLVE GVGL+PAGGGL E A+ AA+A A + + L Sbjct: 595 CEFQMHSARTVAALESYIGLVEAGVGLLPAGGGLHELAIRAAQANPA----DPFEALKKV 650 Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT-LV 719 F++ AMAKVS SALEA+Q+G L+ SD +VFN +ELL+VA+ ALA +GYR PLP + Sbjct: 651 FETVAMAKVSGSALEAKQLGLLRDSDVVVFNAYELLHVAKQVAGALAESGYRPPLPARSI 710 Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779 PVAG G AT +ASL NM+ G F+S HD IA+RIA+ +CGG +E GS V E+WLL LER Sbjct: 711 PVAGDVGTATFRASLANMQAGYFVSEHDVAIATRIADTLCGGAIERGSQVDEEWLLQLER 770 Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807 K FV+L T KTQ RI + TGKP+RN Sbjct: 771 KHFVELAQTEKTQARIAHTMTTGKPLRN 798 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: 1652 Number of extensions: 72 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: 798 Length adjustment: 41 Effective length of query: 766 Effective length of database: 757 Effective search space: 579862 Effective search space used: 579862 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 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