Align Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 5207485 Shew_0019 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= reanno::ANA3:7022769 (716 letters) >FitnessBrowser__PV4:5207485 Length = 716 Score = 1216 bits (3145), Expect = 0.0 Identities = 614/716 (85%), Positives = 651/716 (90%) Query: 1 MIYQSPTIQVELLEDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSG 60 MIYQSPTIQVELLEDNIA+LCFNA GSVNKFDRETL SL+ ALD++ Q ++ L+LTSG Sbjct: 1 MIYQSPTIQVELLEDNIARLCFNAEGSVNKFDRETLNSLNDALDALAQTQGVKGLMLTSG 60 Query: 61 KDTFIVGADITEFLGLFAQDDAVLLSWIEQANAVFNKLEDLPFPTASAIKGFALGGGCET 120 KD FIVGADITEFLGLFAQDD VL W+E AN VFNKLEDLPFPT SAIKGFALGGGCET Sbjct: 61 KDAFIVGADITEFLGLFAQDDNVLQGWLEDANKVFNKLEDLPFPTISAIKGFALGGGCET 120 Query: 121 ILATDFRIADTTAKIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEDALK 180 ILATD RIADT+A+IGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPE ALK Sbjct: 121 ILATDLRIADTSARIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEAALK 180 Query: 181 VGAVDAVVAPEALEAAAIQMLKDAVAEKLDWQARRQRKMSPLTLPKLEAMMSFTTAKGMV 240 VGA+DAVVAPE LE AA QML+DA++EK+DWQARRQRK+SPLTLPKLEAMMSF TAKGMV Sbjct: 181 VGAIDAVVAPELLETAACQMLQDAISEKIDWQARRQRKLSPLTLPKLEAMMSFATAKGMV 240 Query: 241 FAVAGKHYPAPMAAVSVVEQAATKGRSDALQIEHQAFIKLAKTDVAKALIGIFLNDQLVK 300 F VAGKHYPAPMA V V+E+AA R++ALQ+EHQAFIKLAKTDVAKALIGIFLNDQLVK Sbjct: 241 FKVAGKHYPAPMAVVEVIEKAALSERAEALQVEHQAFIKLAKTDVAKALIGIFLNDQLVK 300 Query: 301 GKAKKAGKLAKDVKSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLGEAAKLL 360 GKAKKA K A+ V SAAVLGAGIMGGGIAYQSASKGTPIVMKDI Q ALDLGL EAAKLL Sbjct: 301 GKAKKAAKQAQAVNSAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGLNEAAKLL 360 Query: 361 SAQVARGRSTPEKMAKVLNNITPALDYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSE 420 +AQ+ RGRSTP KMA VLNNIT LDY +K ADVVVEAVVEHPKVKA VLAEVEQ V E Sbjct: 361 TAQINRGRSTPAKMAGVLNNITATLDYNALKQADVVVEAVVEHPKVKATVLAEVEQVVGE 420 Query: 421 DAIIASNTSTISINLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAY 480 DAII SNTSTISINLLAKS++KPERFCGMHFFNPVHKMPLVEVIRGEHSSEET+ASVVAY Sbjct: 421 DAIITSNTSTISINLLAKSLQKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETVASVVAY 480 Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYL 540 A+KMGKTPIVVNDCPGFFVNRVLFPYFAGF+GLL +G DFAAIDKVMEKQFGWPMGPAYL Sbjct: 481 AAKMGKTPIVVNDCPGFFVNRVLFPYFAGFSGLLEDGADFAAIDKVMEKQFGWPMGPAYL 540 Query: 541 LDVVGLDTGHHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRGKP 600 LDVVGLDTGHHAQAVMAEGFPDRM K G DAIDVMFE R GQKNGKGFY YSVD RGKP Sbjct: 541 LDVVGLDTGHHAQAVMAEGFPDRMAKEGKDAIDVMFEADRFGQKNGKGFYQYSVDRRGKP 600 Query: 601 KKDVDPTSYELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVY 660 KK+VDP SYELL AFGEQK F +DEIIARTMIPMIIETVRCLEEGI+A+PAEADMGLVY Sbjct: 601 KKEVDPLSYELLGNAFGEQKEFSSDEIIARTMIPMIIETVRCLEEGIIATPAEADMGLVY 660 Query: 661 GLGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRALAANNGSYYQA 716 GLGFPPFRGGVFRYLDT+GVANFVALAD+YAHLGGLYQVTD MR LAA NGSYY A Sbjct: 661 GLGFPPFRGGVFRYLDTLGVANFVALADQYAHLGGLYQVTDKMRELAATNGSYYPA 716 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: 1508 Number of extensions: 50 Number of successful extensions: 1 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: 716 Length adjustment: 40 Effective length of query: 676 Effective length of database: 676 Effective search space: 456976 Effective search space used: 456976 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: 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