Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_008511080.1 BIBO1_RS18765 aldehyde dehydrogenase family protein
Query= BRENDA::P49419 (539 letters) >NCBI__GCF_000182725.1:WP_008511080.1 Length = 510 Score = 466 bits (1198), Expect = e-135 Identities = 244/479 (50%), Positives = 325/479 (67%), Gaps = 4/479 (0%) Query: 63 GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122 G + + P + E IA ++ S D E+ + +A EA++ W +PAPKRGE++R +G+ LR Sbjct: 30 GGDLAGFSPVSGEEIASIKTHSKEDAEKIIARADEAFRAWRTVPAPKRGELIRLLGEELR 89 Query: 123 EKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQW 182 + LG LVSLE GKI EG+GEVQE +DICD+AVGLSR + G + +ER+GH ++E W Sbjct: 90 ASKEDLGRLVSLEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERAGHRMMETW 149 Query: 183 NPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLED-N 241 +P+G+VG+I+AFNFPVAV+ WN A+A++CGN +WK + T L ++A I + L+ Sbjct: 150 HPLGVVGVISAFNFPVAVWSWNAALAIVCGNAVVWKPSEKTLLTALACDAIFKRALKRFG 209 Query: 242 KLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNN 301 P I L G +IG + +V ++S TGST++G++VG + +RF R++LELGGNN Sbjct: 210 DAPEGISQLLLGDREIGEVLVDSPKVPVVSATGSTRMGREVGPRLAKRFARAILELGGNN 269 Query: 302 AIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGN 361 A I ADL + + + F A+GTAGQRCTT RRLF+HES++D +V RL+KAYA + VG+ Sbjct: 270 AGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDALVPRLQKAYASVSVGS 329 Query: 362 PWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGN--YVEPTIVTGLGH 419 P + + L GPL KQA A++EA GG V G +V N YV P IV Sbjct: 330 PLETSALVGPLIDKQAFDNMQKALKEAAAHGGKVQGGERVDTGYENAYYVRPAIVEMPRQ 389 Query: 420 DASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCG 479 + + ETFAPILYV K+ + ++V A +N V GLSSSIFT +L R+L +GSDCG Sbjct: 390 EGPVLE-ETFAPILYVMKYSDFDDVLASHNAVGAGLSSSIFTLNLQEAERFLSAEGSDCG 448 Query: 480 IVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSKDLPLAQGIKF 538 I NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK YMRR+T TINYSK LPLAQG+ F Sbjct: 449 IANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTINYSKALPLAQGVSF 507 Lambda K H 0.318 0.136 0.417 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: 839 Number of extensions: 40 Number of successful extensions: 3 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: 539 Length of database: 510 Length adjustment: 35 Effective length of query: 504 Effective length of database: 475 Effective search space: 239400 Effective search space used: 239400 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 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