Align Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_017598291.1 D471_RS0108855 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::ANA3:7022769 (716 letters) >NCBI__GCF_000341125.1:WP_017598291.1 Length = 697 Score = 305 bits (780), Expect = 7e-87 Identities = 227/687 (33%), Positives = 341/687 (49%), Gaps = 60/687 (8%) Query: 29 NKFDRETLASLDAALDSIKQQSNIQALVLTSGKDTFIVGADITEFLGLFAQDDAVLLSWI 88 N F L SLDAA+++ + +++I A+ +T F VGAD+T L ++ A + + Sbjct: 49 NTFGPGGLMSLDAAIEAARARTDIVAVAVTGKPFIFAVGADLTGVPALQNREQAHAIGKL 108 Query: 89 EQANAVFNKLEDLPFPTASAIKGFALGGGCETILATDFR-IADTTAKIGLPETKLGIIPG 147 + VF KL +L PT + + G A+GGG E L +R ++ LPE LG++PG Sbjct: 109 --GHDVFRKLGELDVPTFALVNGAAMGGGVEVALHCTYRTVSSGVPAFALPEAFLGLVPG 166 Query: 148 FGGTVRLPRVIGADNALEWITTG-----KDQRPEDALKVGAVDAVVAPEALEAAAIQMLK 202 +GGT LP +IGA+ AL+ I K + + ++G DA+ P Sbjct: 167 WGGTYLLPNLIGAEKALKLIVDNPLAQNKMIKGKQVFEMGIADAIFEPA----------- 215 Query: 203 DAVAEKLDWQARRQRKMSPLTLPKLEAMMSFTTAKGMV-FAVAGKHY---PAPMAAVSVV 258 D V E L W A+ + + P+++ ++ A M F V GK + PAP A+ +V Sbjct: 216 DFVEESLRWAAKVVKGDVEVERPEVDKGEAWDNAVNMARFVVEGKLHGAAPAPARAIELV 275 Query: 259 EQAATKGRSDALQIEHQAFIKLAKTDVAKALIGIFLNDQLVKGKAKKAG----KLAKDVK 314 +A + R + E A L ++ K+ G++ D + K + AG +LA+ V Sbjct: 276 AEAKNRTRDEGFAAEDDALADLIMSEELKS--GLYAFDLVQKRAKRPAGAPDKQLARKVT 333 Query: 315 SAAVLGAGIMGGGIAYQSASK-GTPIVMKDIAQPALDLGL----GEAAKLLSAQVARGRS 369 V+GAG+M G +A A + P+VM D+ Q LD G+ GE KLL +GR Sbjct: 334 KVGVVGAGLMAGQLALLFARRLDVPVVMTDLDQERLDKGVAYVHGEVDKLLK----KGRV 389 Query: 370 TPEKMAKVLNNITPALDYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSEDAIIASNTS 429 + +K ++ ++ +L AD V+EAV E +VK QV AEVE VS +AI+A+NTS Sbjct: 390 SQDKANRLKGLVSGSLTKDAFSDADFVIEAVFEKMEVKQQVFAEVEAVVSPEAILATNTS 449 Query: 430 TISINLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAYASKMGKTPI 489 ++SIN +A ++ PER G HFFNPV +PL+E+IRGE + + +A+ A A K+ KT + Sbjct: 450 SLSINEMAAKLQHPERVVGFHFFNPVAVLPLLEIIRGEKTDDAALATAFATAKKLKKTAV 509 Query: 490 VVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYLLDVVGLDTG 549 + D P F VNR+L + + EG + D+ + G PM P LL +VG Sbjct: 510 LCKDAPAFVVNRLLTLFMGEVLAAVEEGTEPEVADRAV-APLGLPMSPLMLLQLVGPAVA 568 Query: 550 HHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRGKPKKDVDPTSY 609 H + E FP+R S A V K GK P +DP Sbjct: 569 LHVSETLHEAFPERFAVSQQLAEVV---------KAGK-------TQIFAPDLTIDPEVK 612 Query: 610 ELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYGLGFPPFRG 669 ELL G + I+ R + + E L+EG+VA PA+ D+ L+ G G+P G Sbjct: 613 ELLS---GGTNPSEESAILDRALRALAREVRIMLDEGVVAEPADIDLCLITGAGWPFHTG 669 Query: 670 GVFRYLDTMGVANFVALADKYAHLGGL 696 G+ YLD GV+ A+ K H G L Sbjct: 670 GITPYLDRSGVSE--AVNGKPFHEGAL 694 Lambda K H 0.318 0.135 0.384 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: 1048 Number of extensions: 58 Number of successful extensions: 7 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: 716 Length of database: 697 Length adjustment: 39 Effective length of query: 677 Effective length of database: 658 Effective search space: 445466 Effective search space used: 445466 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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