Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 161 bits (407), Expect = 6e-44 Identities = 138/466 (29%), Positives = 208/466 (44%), Gaps = 30/466 (6%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P VI VH + A+ + V AQ A K W +R E + + + + D Sbjct: 38 NPATGEVIGTVHASSAADYETIVKRAQEAFK-TWRTTPAPRRGEAVRLCGEALRKHKDAL 96 Query: 84 LAAEVEDTGKPM-----SLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINY 138 + + GK + +DI A+F + + T E P G Y Sbjct: 97 GSLVALEMGKIKPEGDGEVQEMIDI----ADFAVGQSRMLYGYTMHSERP-----GHRMY 147 Query: 139 AVRRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTA-- 196 P+G+VG+I +N P+ + W A CG+ + KPS +TP +A ++ N A Sbjct: 148 EQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPLSAIATMKICNEALK 207 Query: 197 -GVPPGVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELG 255 G P ++ + + G + + F+ + I+FTG T G + + A LELG Sbjct: 208 AGGFPDIFFLFNDAGTDLSQGFVDDKR-IPLISFTGSTKVGRMVGERVARRMGRSLLELG 266 Query: 256 GKNAAIVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLK---KGAE 312 G NA I+ A DL AI + GQ C T R++V I +L K E Sbjct: 267 GNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIVGEVTDKLVAAYKQVE 326 Query: 313 GMQLGRPEDLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQ 372 G ++G P T MGPL SQ+ + L +KA +G V+TGG + G +V Sbjct: 327 G-KIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAALSD----RKGNFVL 381 Query: 373 PTIWTGLGDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRV 432 PTI TG+ + V + E F P +MPF S +E I ND GL+ I+T +L A + Sbjct: 382 PTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLSSAIFTRDLKAAEQY 441 Query: 433 --AGAIEVGIAWVN-SWFLRDLRTAFGGSKQSGIGREGGVHSLEFY 475 + + GIA VN ++ AFGG K++G GRE G + + Y Sbjct: 442 LSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKVY 487 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: 593 Number of extensions: 27 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: 485 Length of database: 511 Length adjustment: 34 Effective length of query: 451 Effective length of database: 477 Effective search space: 215127 Effective search space used: 215127 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