Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Dsui_0521 Dsui_0521 enoyl-CoA hydratase/carnithine racemase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__PS:Dsui_0521 Length = 258 Score = 132 bits (332), Expect = 7e-36 Identities = 90/257 (35%), Positives = 127/257 (49%), Gaps = 11/257 (4%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 ILV G + VTL+ P+ LNA+N A+ +L AA+ E AD ++ +V+ G+ +AFAAG Sbjct: 5 ILVSRDGDIATVTLSNPEKLNAVNYAMWCDLAAAMAELSADSSLRCVVLAGAGEAFAAGG 64 Query: 66 DIG---MMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122 DI + T ++ D + + VR P +A + G +GGG E+A CD+ A Sbjct: 65 DIEEFLVKRTNLEQALHYHDKVGAALDAVRDCPHPTVALIRGACIGGGLEIAGNCDLRIA 124 Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182 + AKFG P +LG G L A ++ L R + AAEA GL++RV+ Sbjct: 125 GEGAKFGAPINRLGFSMYPGEMSGLLALAGPAVMSEILLEGRILSAAEAYAKGLLTRVVA 184 Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHF---ERRLFHSLFATED 239 A L DE A A IA K+ + R LA G E+ + T D Sbjct: 185 DAQLEDEVTATARRIAAGAPLVARWHKQWMRR-----LASGAPLTQEEKAASFAFLDTAD 239 Query: 240 QKEGMAAFVEKRKPVFK 256 KEG+ AF+ KRKP FK Sbjct: 240 YKEGLDAFLAKRKPAFK 256 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: 152 Number of extensions: 11 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: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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