Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf1N1B4_679 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_679 Length = 249 Score = 101 bits (252), Expect = 1e-26 Identities = 71/241 (29%), Positives = 118/241 (48%), Gaps = 9/241 (3%) Query: 15 GLVTL--NRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGADIG--MM 70 GL+TL NRP+ NAL A+ +L LR D+D I A+++TGS + F AG DI + Sbjct: 12 GLLTLRINRPEKKNALTRAMYSQLAEGLRLADSDPEINAVLITGSAECFTAGNDIFDFLQ 71 Query: 71 STYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADTAKFGQ 130 + +D ++ E RKP+IAAVAG A+G G L + CD+++ + A+ Sbjct: 72 QPPSILDSPVYHFMLNLLEC----RKPVIAAVAGAAVGIGTTLLLHCDLVYVSTDARLRM 127 Query: 131 PEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAA-SLVDE 189 P + LG+ P G + LPR + AKA +L L +A G+ + + + + + + Sbjct: 128 PFVNLGLCPEFGSSLILPRMLGHAKAAELLLLGEGFSGEQAAAWGIATEALGSGEAALAK 187 Query: 190 AIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMAAFVE 249 A A P AV + K+ + L + + E LF + + ++AF++ Sbjct: 188 AREMALRFEALPPEAVRISKQLMKAPGREQLRKVIEEEGALFTQRLRSPEAMAALSAFIK 247 Query: 250 K 250 + Sbjct: 248 R 248 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: 132 Number of extensions: 3 Number of successful extensions: 2 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: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 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