Align 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) (characterized)
to candidate GFF1134 HP15_1112 2-hydroxymuconic semialdehyde hydrolase
Query= BRENDA::G3KFX4 (282 letters) >FitnessBrowser__Marino:GFF1134 Length = 286 Score = 455 bits (1171), Expect = e-133 Identities = 216/279 (77%), Positives = 249/279 (89%), Gaps = 1/279 (0%) Query: 1 MNAPQQSPEIGREILAAGYRTNLHDQGEG-FPVLLIHGSGPGVTAWANWRLVMPQLAQNR 59 M P++SPEIGREI AAGYRTN+HD GEG PV++IHGSGPGVTAWANWRLV+P+LA+NR Sbjct: 1 MTVPEKSPEIGREITAAGYRTNVHDHGEGGVPVMMIHGSGPGVTAWANWRLVIPELAKNR 60 Query: 60 RVIAPDMLGFGYSDRPADGRYHQQRWVEHAIGVLDALGIQQADIVGNSFGGGLALALAIR 119 RV+APDMLGFGYS+RP D Y+++RWV+HAIGV+D LG++Q D+VGNSFGGGLALALAI Sbjct: 61 RVVAPDMLGFGYSERPEDQIYNRERWVKHAIGVMDELGLEQVDLVGNSFGGGLALALAIE 120 Query: 120 HPERVRRLVLMGSVGVSFPITPGLDAVWGYEPSFASMRRLMDVFAYDRSLVTNELAELRY 179 HP+R+RRLVLMGS GV FPIT GLD VWGYEPS +MRRLMDVFA+++ L+T+ELAE+RY Sbjct: 121 HPKRIRRLVLMGSAGVRFPITEGLDEVWGYEPSLDNMRRLMDVFAFNKGLLTDELAEMRY 180 Query: 180 QASIRPGFQESFAQMFPAPRQRWVDGLASDEADIRALPHETLVIHGREDQVIPLAASLTL 239 +ASIRPGFQESFA MFPAPRQRWVD LAS+E DIRAL HETL+IHGRED+VIPL ASL L Sbjct: 181 EASIRPGFQESFAAMFPAPRQRWVDNLASNEDDIRALTHETLIIHGREDEVIPLEASLRL 240 Query: 240 AEWIARAQLHVFGHCGHWTQIEHAERFARLVENFLAEAD 278 AE I RAQLHVFG CGHWTQIEHA+RFARLV +FL EAD Sbjct: 241 AELIDRAQLHVFGRCGHWTQIEHADRFARLVNDFLTEAD 279 Lambda K H 0.323 0.138 0.432 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: 406 Number of extensions: 18 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: 282 Length of database: 286 Length adjustment: 26 Effective length of query: 256 Effective length of database: 260 Effective search space: 66560 Effective search space used: 66560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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