Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate PP_2217 PP_2217 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Putida:PP_2217 Length = 257 Score = 146 bits (369), Expect = 4e-40 Identities = 92/259 (35%), Positives = 142/259 (54%), Gaps = 10/259 (3%) Query: 3 EFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCA 62 E IL + V +TLNRP+ LN+ N ++ ++ + L Q+ERD I C++LTG+ + F A Sbjct: 4 ETILLDIHGKVGLITLNRPQALNALNAQIVGEINQALDQLERDPNIGCVVLTGSAKAFAA 63 Query: 63 GQDLNDRNV--DPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALG 120 G D+ + P DL +R N RR KP+I AV+G A G G LA+ Sbjct: 64 GADIKEMAELQYPQIYVDDLFSDADRIAN---RR-----KPIIAAVSGFALGGGCELAMM 115 Query: 121 GDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGM 180 D ++AA +AKF LG++P GGT L R G+A+AM L L G + AE+A G+ Sbjct: 116 CDFILAADNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMELCLTGRLMGAEEAERAGL 175 Query: 181 IWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGR 240 + ++V L + A ++A +A++ ++K+++N A TL + ER A Sbjct: 176 VARIVPQAELVEEALKVAATIASKSIPVSMMVKESVNRAFEVTLSEGVRFERRVFHAAFS 235 Query: 241 SADYREGVSAFLAKRSPQF 259 + D +EG++AF+AKR QF Sbjct: 236 TEDQKEGMAAFIAKREAQF 254 Lambda K H 0.321 0.136 0.403 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: 130 Number of extensions: 6 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: 262 Length of database: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 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 (21.8 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