Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__azobra:AZOBR_RS29185 Length = 478 Score = 350 bits (899), Expect = e-101 Identities = 194/454 (42%), Positives = 267/454 (58%), Gaps = 6/454 (1%) Query: 23 NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEF 82 NPA V+ + + +EA+ A A W+ + R +L + G+ + A+E Sbjct: 23 NPARPGEVIGHYAWASVEQAEEALGAAHAALPGWAASNPQTRSDVLRRVGDELNARAEEL 82 Query: 83 ALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVV 142 L+T EEGKTL++ + EV RS + + + G+ LP T +EP+GVV Sbjct: 83 GALLTREEGKTLREGIGEVRRSAQIFHYAAGEPLRQGGEALPGLRDGTTAMVSREPVGVV 142 Query: 143 ALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVV 202 LITPWNFP+++P WK A ALA GNT V+KP+ TP +L ++L +AGLP G NLVV Sbjct: 143 VLITPWNFPMAVPAWKTAYALAFGNTVVLKPSEVTPACAWELADILHRAGLPAGAFNLVV 202 Query: 203 GKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSA 262 G G +G +V D AVSFTGS VG+ I L + RMTR+QLELGGKN L V A Sbjct: 203 GDGRTLGPALV--DGADAVSFTGSPGVGRAI--LERSVARMTRVQLELGGKNPLVVHDDA 258 Query: 263 DLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDVDM 321 DL LA ++A++G F TGQ CTATSR+I+++ V+ F +RL+ R+ RVG P DM Sbjct: 259 DLELAVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRIAALRVGDPMDAATDM 318 Query: 322 GPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTIFEGVTSDMRLFKEEIF 381 GPVV E Q KDL I ++ GA+L +GG + G GYFLEPT+F G + MR+ ++E+F Sbjct: 319 GPVVSEAQLAKDLHCIADARSEGAELAFGGGRMDGDGYFLEPTLFVGTDNAMRINRDEVF 378 Query: 382 GPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVGLE 441 GPV V A LD AI + N D+ ++GIV + + F R AG++ VN PT G++ Sbjct: 379 GPVACVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFRRRSRAGLVMVNAPTAGID 438 Query: 442 LQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 PFGG SG +E G A+EF+ + KT Y Sbjct: 439 YHVPFGGRGPSG-YGGREQGSAAVEFFTEGKTAY 471 Lambda K H 0.316 0.135 0.389 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: 18 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: 478 Length of database: 478 Length adjustment: 34 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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 (21.6 bits) S2: 51 (24.3 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