Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Cola:Echvi_0535 Length = 514 Score = 172 bits (437), Expect = 2e-47 Identities = 136/465 (29%), Positives = 214/465 (46%), Gaps = 24/465 (5%) Query: 22 SSSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFD 81 S SP++ + KV R + + A+ A K AW ++ QR EV+ + GI R Sbjct: 39 SYSPVDGKELGKVQMTTRESYEKVLDQAEKAFK-AWRKVPAPQRGEVVRQI--GIELRNK 95 Query: 82 DFLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVK---NVPTEFFEMPT-PDGVGAIN 137 L GK +S G + D+ + + + + + Sbjct: 96 KSLL------GKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRM 149 Query: 138 YAVRRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAA----LLGEVM 193 Y P+G+VGVI +N P+ + +W A CG+ V KPSE+TP T+ + +V Sbjct: 150 YEQWHPLGIVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQLIAADVF 209 Query: 194 NTAGVPPGVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLE 253 N G P G+ +++ G G N G FLT P V I+ TG T G+++ + V LE Sbjct: 210 NRNGFPEGITSLLIG-GAN-VGAFLTQDPRVALISATGSTQMGKSVGETVGGRLGKVLLE 267 Query: 254 LGGKNAAIVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEG 313 LGG NA I+ DLD AI G L GQ C T R+ + +F+ R+ Sbjct: 268 LGGNNAIIITEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERMVAAYSK 327 Query: 314 MQLGRPEDLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQP 373 + +G P D +GPLI ++ + L+ ++ G V GG+ E E + G +V+P Sbjct: 328 LTIGNPLDEDNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYV-SGCYVRP 386 Query: 374 TIWTGLGDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVA 433 +++ +V ++E FGP +M + +E I N+ GL+ I TTN+ A R Sbjct: 387 SVFEAENHFQIV-QKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMREAERYL 445 Query: 434 GA--IEVGIAWVN-SWFLRDLRTAFGGSKQSGIGREGGVHSLEFY 475 + + GI+ VN ++ AFGG K++G GRE G + + Y Sbjct: 446 SSEGSDCGISNVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAY 490 Lambda K H 0.318 0.135 0.406 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: 608 Number of extensions: 27 Number of successful extensions: 4 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: 485 Length of database: 514 Length adjustment: 34 Effective length of query: 451 Effective length of database: 480 Effective search space: 216480 Effective search space used: 216480 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