Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_040581331.1 A3OQ_RS0117130 membrane protein
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000385335.1:WP_040581331.1 Length = 268 Score = 106 bits (264), Expect = 6e-28 Identities = 89/251 (35%), Positives = 117/251 (46%), Gaps = 13/251 (5%) Query: 16 LITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEM----- 70 LI + RP N L+ + LA + D RA VL G + F+ G D+ Sbjct: 22 LIGINRPYIHNRLDPEAFRSLAQAYYDYDHDPSLRAAVLFGHGEHFSRGIDVDAFQALVA 81 Query: 71 AERDLV---GILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARF 127 A++ V G++ DP +R SKPLIAAV+G C EL + AD IA + F Sbjct: 82 ADKPRVDGDGVI-DPLA---KRRPNLSKPLIAAVHGDCWNMAHELFLVADTRIAAANTDF 137 Query: 128 GQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEV-TLPELTI 186 GQ E + G PG G T R +R G AM+ +L+G A+ A R G V EV PEL Sbjct: 138 GQDETSHGRFPGGGSTVRFVREAGWGNAMRYILTGDHWTAQEALRMGTVQEVAATPELAF 197 Query: 187 ERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAF 246 A+A+A IA PL ++ + + A D A L + L T D EG RA Sbjct: 198 AHAIALANKIASCGPLGIKASLVSAHLAIDMAEADALYRLSAQYGALYRTEDFNEGRRAE 257 Query: 247 QEKRRPEFTGR 257 E R P F GR Sbjct: 258 AEHRVPVFHGR 268 Lambda K H 0.320 0.134 0.374 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: 169 Number of extensions: 7 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: 257 Length of database: 268 Length adjustment: 25 Effective length of query: 232 Effective length of database: 243 Effective search space: 56376 Effective search space used: 56376 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 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