Align 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; Beta-oxoacyl-CoA hydrolase; Oah; EC 3.7.1.21 (characterized)
to candidate WP_011384542.1 AMB_RS10830 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
Query= SwissProt::O87872 (377 letters) >NCBI__GCF_000009985.1:WP_011384542.1 Length = 377 Score = 614 bits (1584), Expect = e-180 Identities = 300/376 (79%), Positives = 328/376 (87%), Gaps = 1/376 (0%) Query: 1 MNPTTQKLVEQNAPAQLVDHNLVPETVCPGVLYEKRPARNLKGEVVPGLYNVWISLDNPK 60 M T +V+ APA L DHNLVP TV PGVLYEKRPA+ G V GLYN WI+LDN K Sbjct: 1 MKKETAAIVDSTAPAHLNDHNLVPTTVVPGVLYEKRPAKRADGTVAEGLYNAWITLDNQK 60 Query: 61 QYNSYTTDMVKGLILAFRAASCARDVASVVFTAVGDKAFCTGGNTKEYAEYYAGNPQEYR 120 QYNSYTTDMVKG+I+AFR AS ARDV+SVVFT GDKAFCTGGNTKEYAEYYAGNPQEYR Sbjct: 61 QYNSYTTDMVKGVIMAFRDASNARDVSSVVFTGAGDKAFCTGGNTKEYAEYYAGNPQEYR 120 Query: 121 QYMRLFNDMVSAILGCDKPVICRVNGMRIGGGQEIGMAADFTVAQDLANFGQAGPKHGSA 180 QYMRLFNDMVSAILGCDKPVICRVNGMRIGGGQEIGMAADF+VAQDLA FGQAGPKHGSA Sbjct: 121 QYMRLFNDMVSAILGCDKPVICRVNGMRIGGGQEIGMAADFSVAQDLAKFGQAGPKHGSA 180 Query: 181 AIGGATDFLPLMIGCEQAMVSGTLCEPFSAHKANRLGICMQIVPALKVDGKFIANPLVVT 240 IGGATDFLP+MIGCEQAMVSG+LCEP+SAHKA R GI M +VPALKVDGKF+ANPLV+T Sbjct: 181 PIGGATDFLPVMIGCEQAMVSGSLCEPWSAHKAYRTGIIMDLVPALKVDGKFVANPLVIT 240 Query: 241 DRYLDEFGRIIHGEFKTGDELAAGKELMKRGEIDLSLLDEAVEKLCAKLISTFPECLTKS 300 DRYLDEFG+I+HGE KTG ELAAGKEL+K+G IDLSLLD VE++CAK++ TFP+C TK+ Sbjct: 241 DRYLDEFGKIVHGESKTGAELAAGKELLKKGTIDLSLLDAKVEEICAKILHTFPDCFTKT 300 Query: 301 FEELRKPKLDAWNRNKENSRAWLALNMMNEARTGFRAFNEGNKETGREIEFTDLRQALAK 360 +ELRKPKL+AWN NKENSR WL LNMM EARTGFRAFNEG KE REI+F LRQALAK Sbjct: 301 IQELRKPKLNAWNANKENSRDWLGLNMMTEARTGFRAFNEGPKE-DREIDFVALRQALAK 359 Query: 361 GMPWTPELIESLMPGA 376 G PWTPELIESL+P A Sbjct: 360 GAPWTPELIESLIPKA 375 Lambda K H 0.319 0.136 0.409 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: 587 Number of extensions: 17 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: 377 Length of database: 377 Length adjustment: 30 Effective length of query: 347 Effective length of database: 347 Effective search space: 120409 Effective search space used: 120409 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: 50 (23.9 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