Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BPHYT_RS09900 BPHYT_RS09900 aldehyde dehydrogenase
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__BFirm:BPHYT_RS09900 Length = 492 Score = 347 bits (891), Expect = e-100 Identities = 195/482 (40%), Positives = 276/482 (57%), Gaps = 10/482 (2%) Query: 7 FINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGP-WGKLSVAE 65 FING GSA+G+TF NP+ + I + +A A++D AV+ ++AA + W ++ A Sbjct: 15 FINGEKTGSAAGKTFPVFNPATAEEIAQIPDASEADIDHAVRTSKAAFESDAWRRMPPAV 74 Query: 66 RAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEA 125 R +L ++AD + DE E L+ GK + +++ + A + Sbjct: 75 REGLLLKLADLVERHSDELATLETLNQGKLIGFSKMLEVAGSVQWLRYMAGWATKIEGST 134 Query: 126 FEMATPDGAGA-INYAVRR-PKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEET 183 F+++ P G N + +R P GV+ I PWN PLL+ WK+ PALACG TVV+KP+EET Sbjct: 135 FDLSIPFPPGTRYNASTKRVPAGVVAAIVPWNFPLLMAVWKIAPALACGCTVVLKPAEET 194 Query: 184 PLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRA 243 PLTA L E+ AG PAGV+NVV G G++AGA L HP V TFTG T G +I R Sbjct: 195 PLTAIRLAELAHEAGFPAGVFNVVTG-RGETAGAALVRHPLVKKVTFTGSTEVGRIIGRQ 253 Query: 244 AAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDE 303 A +++ SLELGGK+ IV DCD KAIEG + F N GQVC R+YV R I+DE Sbjct: 254 CADDLKRASLELGGKSPVIVLDDCDPRKAIEGAAGAIFFNHGQVCTAGSRLYVARSIYDE 313 Query: 304 FVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMP 363 V + A A+ + +G DA++ GP+VS +HR+KV Q D+GG +++ + Sbjct: 314 VVQGIAAVADGITLGSGFDAATQMGPMVSARHRDKVAGMIAQGKDEGGEIVSRDARVERE 373 Query: 364 AHLAGGAWVQPTIWTGLS-DDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAI 422 G +V+PT+ + AVV EE+FGP P+D +E + AN+ YGL +++ Sbjct: 374 -----GYFVRPTVIANRACKPLAVVKEEVFGPVLVAMPYDDLDEVLAQANASEYGLGASV 428 Query: 423 WTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNI 482 WT +A R+ IEAG VWVN+ + D FGG K SGIGRE G +E YTE K++ Sbjct: 429 WTNQLDKALRLVDGIEAGTVWVNTHNMVDPAMPFGGFKASGIGREHGKSIIESYTESKSV 488 Query: 483 CV 484 C+ Sbjct: 489 CI 490 Lambda K H 0.318 0.136 0.411 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: 628 Number of extensions: 29 Number of successful extensions: 5 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: 486 Length of database: 492 Length adjustment: 34 Effective length of query: 452 Effective length of database: 458 Effective search space: 207016 Effective search space used: 207016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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