Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_041303771.1 BTUS_RS05345 aldehyde dehydrogenase family protein
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000092905.1:WP_041303771.1 Length = 497 Score = 252 bits (644), Expect = 2e-71 Identities = 162/464 (34%), Positives = 234/464 (50%), Gaps = 36/464 (7%) Query: 55 WNPARKDQLVGSVSKANQDL-----------AEKAIQSADEAFQ-TWRNVNPEERANILV 102 W P+ Q SV A+ ++ E A+Q+A A W+N++P ERA +L Sbjct: 31 WVPSASGQTFQSVDPASGEVLCTLYAADDPDVEAAVQAARRALDGPWKNISPMERARLLW 90 Query: 103 KAAAIIRRRKHEFSAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIELNRGKEILSRP 161 + + ++ E S + GKP E A D AID Y+A +L+ +S P Sbjct: 91 RLSDLLEAHAEELSQLESLDTGKPIAETSAVDIPYAIDHFRYFAGWTTKLSGENLPVSMP 150 Query: 162 GEQNRYFYT-PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEV 220 G+ Y P+GV I PWNF L I + GNTVVLKP+ TP+ A + E+ Sbjct: 151 GQYLVYTRREPVGVVGAIVPWNFPLMITSWKVAPALACGNTVVLKPSELTPLTALRLGEL 210 Query: 221 LEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHL 280 +AG+P GV+N VPG G G L H I+FTGS VG + +A Sbjct: 211 ALEAGIPPGVLNVVPGYGHTAGAALTHHRGVDKISFTGSTRVGREIVHASAA------DF 264 Query: 281 KRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKT 340 KR+ +E+GGK +V DADLD+ A I++S F G+ C AGSR +HK VYD VLE Sbjct: 265 KRLSLELGGKSPNIVFPDADLDMVAGGIMMSIFFNQGEVCCAGSRLYLHKQVYDRVLEAI 324 Query: 341 VALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGDSSTGFFIQ 399 V AK + G + MGP++ E+ +++ YIE G +EG + +TGG S+G+F++ Sbjct: 325 VRRAKTIRQGAGVDPATQMGPLVSEQHMNRVLGYIEKGLEEGAKRLTGGVRKGSSGYFVE 384 Query: 400 PTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQA 459 PT++ D + I +EE+FGPV+A D + AN+TEYGL + T + + Sbjct: 385 PTVLEARD-DMTIAREEVFGPVLAVMPFEDVRDVVRRANDTEYGLAAGIWTSDVRRAIRV 443 Query: 460 KREFHVGNLYFNRNCTGAIVGYH------PFGGFKMSGTDSKAG 497 E G ++ N GY+ P+GGFK SG + G Sbjct: 444 AHELRAGTVWIN--------GYNLLDPTSPWGGFKQSGLGREMG 479 Lambda K H 0.316 0.134 0.388 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: 515 Length of database: 497 Length adjustment: 34 Effective length of query: 481 Effective length of database: 463 Effective search space: 222703 Effective search space used: 222703 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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