Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate BPHYT_RS14615 BPHYT_RS14615 fumarate hydratase
Query= curated2:Q9I6Q8 (459 letters) >FitnessBrowser__BFirm:BPHYT_RS14615 Length = 466 Score = 69.3 bits (168), Expect = 3e-16 Identities = 75/235 (31%), Positives = 103/235 (43%), Gaps = 17/235 (7%) Query: 71 LAEAVATAGNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRALAL-L 129 L E +A + + V+ R+V D V+ G +S D + + + A+ L Sbjct: 107 LNEVIANRASELLGGVRGEERKVHPNDD-----VNRGQSSNDVFPTAMHVAAAYAIVKHL 161 Query: 130 EQDLQRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRELRP 189 + L+ L + L +A+ AD GRT LQ ATP+TLG + +G + L + + P Sbjct: 162 QPALKTLRDTLDGKAKAFADIVKIGRTHLQDATPLTLGQEFSGYVAQLDHGIRHVETALP 221 Query: 190 RLLVLQFGG-ASGT-LAALGEQALPVAAALAEELGLALPEQPWHTQ----RDRLVEFASV 243 L L GG A GT L A + A VAAA+ + GL P + D LV Sbjct: 222 HLYELAQGGTAVGTGLNAHPQFADKVAAAIGKLTGLPFVSAPNKFEVMAAADALVFAHGA 281 Query: 244 LGLVAGSLGKFGRDVSLLM---QTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVL 295 L VA SL K DV L + GE+ P GSS MP K NP S L Sbjct: 282 LKTVAASLNKIANDVRWLASGPRCGLGELSIP--ENEPGSSIMPGKVNPTQSEAL 334 Lambda K H 0.320 0.133 0.386 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: 348 Number of extensions: 14 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: 459 Length of database: 466 Length adjustment: 33 Effective length of query: 426 Effective length of database: 433 Effective search space: 184458 Effective search space used: 184458 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: 51 (24.3 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