Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 189 bits (481), Expect = 1e-52 Identities = 142/480 (29%), Positives = 222/480 (46%), Gaps = 28/480 (5%) Query: 10 GAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAERAEI 69 G + ++ + +NP+ G+VIG VH + A+ + VK A+ A K W R E Sbjct: 23 GEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIVKRAQEAFK-TWRTTPAPRRGEA 81 Query: 70 LHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEAFEM- 128 + + + D L+ GK K P G + D+ ++ + Sbjct: 82 VRLCGEALRKHKDALGSLVALEMGKIK--------PEGDGEVQEMIDIADFAVGQSRMLY 133 Query: 129 ---ATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPL 185 + G Y P G++G+IS +N P+ + W A CG+ + KPS +TPL Sbjct: 134 GYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPL 193 Query: 186 TAT----LLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIM 241 +A + E ++A G P ++ + + G D + F+ + + +FTG T G ++ Sbjct: 194 SAIATMKICNEALKAGGFP-DIFFLFNDAGTDLSQGFVDDKR-IPLISFTGSTKVGRMVG 251 Query: 242 RAAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIF 301 A+ + + LELGG NA I+ A D+ AI + A GQ C T R++V I Sbjct: 252 ERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIV 311 Query: 302 DEFVARLKAGAESL--MIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGV 359 E +L A + + IG P A++ GPL S + L ++A GG V+TGG Sbjct: 312 GEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAA 371 Query: 360 PDMPAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLA 419 G +V PTI TG+ + VV E F P +I PF + +EAIEL N +P GL+ Sbjct: 372 LSDRK----GNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLS 427 Query: 420 SAIWTENGSRAHRVAGQI--EAGIVWVN-SWFLRDLRTAFGGSKQSGIGREGGVHSLEFY 476 SAI+T + A + + GI VN ++ AFGG K++G GRE G + + Y Sbjct: 428 SAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKVY 487 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: 649 Number of extensions: 38 Number of successful extensions: 6 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: 511 Length adjustment: 34 Effective length of query: 452 Effective length of database: 477 Effective search space: 215604 Effective search space used: 215604 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