Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 318 bits (816), Expect = 2e-91 Identities = 179/463 (38%), Positives = 254/463 (54%), Gaps = 8/463 (1%) Query: 23 SSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKG-AWGRMSLAQRVEVLYAVADGINRRFD 81 + P V+A+ ++ A++ AVA+AQ A W + A R ++L+ +++ I R D Sbjct: 42 TDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADREKLLFRLSELIERHAD 101 Query: 82 DFLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTP-DGVGAINYAV 140 + A E +GK +AR +D+ GA + A + + + P G + Y Sbjct: 102 ELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEGQTLDNSIPIPGPQWVTYTR 161 Query: 141 RRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPP 200 R PVGVVG I PWN PL + WK+ PALA G TVV+KPSE+TP TA L + AG+P Sbjct: 162 REPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLTALRLAHLALEAGIPE 221 Query: 201 GVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAA 260 GV NVV G G + G L +HP V ++FTG T G+ + AA + +LELGGK+ A Sbjct: 222 GVLNVVCGRGATA-GAALIAHPGVRKLSFTGSTAVGKVVGHAAVENMARFTLELGGKSPA 280 Query: 261 IVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320 +V D D + +G F + GQVC + R+ V R ++ R + L A+GM++G Sbjct: 281 VVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRVLDELAGIAQGMRIGSGF 340 Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380 D AT GPL S+ H +V+ + A GAT+V GG G +VQPTI+ Sbjct: 341 DAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGG-----ERVHDAGCFVQPTIFADTT 395 Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440 V REE+FGP V PFD E+ I AND YGLA +WT +LS AHR+ ++ G+ Sbjct: 396 AQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHAHRIVPRLQAGV 455 Query: 441 AWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483 WVN+ + D GG KQSG GR+ G ++E +TELK+VC+ Sbjct: 456 VWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSVCM 498 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: 553 Number of extensions: 21 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: 500 Length adjustment: 34 Effective length of query: 451 Effective length of database: 466 Effective search space: 210166 Effective search space used: 210166 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