Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_015930052.1 MNOD_RS16435 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000022085.1:WP_015930052.1 Length = 266 Score = 152 bits (385), Expect = 5e-42 Identities = 110/266 (41%), Positives = 142/266 (53%), Gaps = 15/266 (5%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAAG 64 I + G V VT++RP+ALNAL+ A EL AL D+ + IV+TG+ E+AF AG Sbjct: 3 IRISREGAVATVTIDRPEALNALDVAAQAELREALLAARDDEDVRVIVLTGAGERAFCAG 62 Query: 65 ADIGMM--STYTYMDVY---------KGDYIT-RNWETVRSIRKPIIAAVAGFALGGGCE 112 AD+ S +Y + +G Y+ N E +R I KP+IAAV G LGGG E Sbjct: 63 ADLKRTPPSANSYAQAWTASDPIATERGAYVRFMNLERLR-IWKPLIAAVNGHCLGGGME 121 Query: 113 LAMMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAE 172 LA+ CD+ A+DTA F PE+K+G + G G L R + A AM + LT +DAAEA Sbjct: 122 LALQCDLRVASDTASFALPEVKVGSVAGVCGPLLL-RTIPAAHAMKMLLTGARIDAAEAL 180 Query: 173 RAGLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFH 232 R GLVS V PAA L A A TIAE ++M K A + +F Sbjct: 181 RIGLVSDVWPAAELGRRAAELAGTIAENAPLSLMATKRMTRECEVLPRAALMDLTEMVFG 240 Query: 233 SLFATEDQKEGMAAFVEKRKPVFKHR 258 + TED+ EG AF EKRKP F R Sbjct: 241 IMKDTEDRAEGRRAFAEKRKPRFSGR 266 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: 164 Number of extensions: 12 Number of successful extensions: 4 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: 266 Length adjustment: 25 Effective length of query: 233 Effective length of database: 241 Effective search space: 56153 Effective search space used: 56153 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 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