Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 313 bits (801), Expect = 1e-89 Identities = 173/455 (38%), Positives = 262/455 (57%), Gaps = 13/455 (2%) Query: 31 IAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFLAAEVED 90 IA VH A A V+ A++ A+AA K AW RM+ +R +L AD + R D E D Sbjct: 37 IATVHAATPAIVEQALSTAKAAQK-AWARMTGTERGRILRRAADIMRERNHDLSVLETYD 95 Query: 91 TGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPVGVVGVI 150 TGKP+ D GA + F + ++ E + D V Y R +G+ I Sbjct: 96 TGKPLQETLVADATSGADALEYFGGLAASLTGEHIPLGE-DWV----YTKREALGLCVGI 150 Query: 151 CPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYNVVHGFG 210 WN P + WK PALACGN++V KPSE TP A + E++ AG P GV+NVV G G Sbjct: 151 GAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALKVAEILIEAGAPAGVFNVVQGMG 210 Query: 211 PNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFADCDLDK 270 G L + P V+ ++ TG TG+ + AAA+G + V++ELGGK+ I+F D D+D Sbjct: 211 --EVGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEGMKHVTMELGGKSPLIIFDDADIDN 268 Query: 271 AIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLATGMGPLI 330 A+ G + F + GQVC RV+V++ I ++F++RL + LG P D AT GP++ Sbjct: 269 AVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARLAERTGNAILGDPMDEATSFGPMV 328 Query: 331 SQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSVVAREEI 390 ++ VL Y +K E GA ++ GG +M G +++PT++ + DD +AREEI Sbjct: 329 TENQMNIVLGYIEKGKEEGARLICGGRRADM-----DGYFIEPTVFADVTDDMTIAREEI 383 Query: 391 FGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVNSWFLRD 450 FGP V+ FD+EEEV+ RAND ++GL+ ++T + +RAHRV G +E G ++NS+ Sbjct: 384 FGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHRVIGNLEAGSCFINSYNDAP 443 Query: 451 LRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 + FGG K SG+GRE +++ ++++K+V +++ Sbjct: 444 VEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVRM 478 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: 578 Number of extensions: 29 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: 485 Length adjustment: 34 Effective length of query: 451 Effective length of database: 451 Effective search space: 203401 Effective search space used: 203401 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