Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS17350 BPHYT_RS17350 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__BFirm:BPHYT_RS17350 Length = 263 Score = 152 bits (384), Expect = 7e-42 Identities = 93/264 (35%), Positives = 147/264 (55%), Gaps = 7/264 (2%) Query: 1 MAYENIL--VETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSE 58 M+YE I ++ V +TLNRP LN+ A+ EL AAL + + A A+V+TG+ Sbjct: 1 MSYEAIRLDIDASSHVATITLNRPDKLNSFTRAMHQELSAALDQVETSGA-RALVLTGAG 59 Query: 59 KAFAAGADIGMMSTYTYMDVYKGDYITRNWETV----RSIRKPIIAAVAGFALGGGCELA 114 + F AG D+ + G+ I +++ + +++ P+IAAV G A G G LA Sbjct: 60 RGFCAGQDLADLDFTPGAMTDLGELIEQHFNPLIRRLQALPLPVIAAVNGTAAGAGANLA 119 Query: 115 MMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERA 174 + CD++ AA +A F Q +K+G++P +GGT LP+ V A+A+ L +T + A +AE Sbjct: 120 LACDLVLAARSASFIQAFVKIGLVPDSGGTWFLPQRVGMARALGLAITGDKLSAEKAESW 179 Query: 175 GLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSL 234 GL+ + + A L + A AA +A+ P+ A+ +K ++ TL + + ER L L Sbjct: 180 GLIWQAVDDAELAETAAKLAAQLAQQPTRAIAAIKRAMRAGATQTLDQQLDLERDLQREL 239 Query: 235 FATEDQKEGMAAFVEKRKPVFKHR 258 A+ D EG+ AFVEKR P F+ R Sbjct: 240 GASHDYAEGVQAFVEKRAPRFEGR 263 Lambda K H 0.321 0.134 0.380 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: 157 Number of extensions: 6 Number of successful extensions: 3 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: 258 Length of database: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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 (21.9 bits) S2: 47 (22.7 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