Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__azobra:AZOBR_RS29185 Length = 478 Score = 239 bits (609), Expect = 2e-67 Identities = 159/456 (34%), Positives = 225/456 (49%), Gaps = 14/456 (3%) Query: 75 EPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGSLVSL 134 E I ASV EE + A A WA R +++R++GD L + + LG+L++ Sbjct: 29 EVIGHYAWASVEQAEEALGAAHAALPGWAASNPQTRSDVLRRVGDELNARAEELGALLTR 88 Query: 135 EMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVGIITAF 194 E GK L EG+GEV+ I YA G GG LP R G + PVG+V +IT + Sbjct: 89 EEGKTLREGIGEVRRSAQIFHYAAGEPLRQGGEALPGLRDGTTAMVSREPVGVVVLITPW 148 Query: 195 NFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICSLTCG- 253 NFP+AV W A A+ GN + K + T A +A +L LP +L G Sbjct: 149 NFPMAVPAWKTAYALAFGNTVVLKPSEVTP----ACAWELADILHRAGLPAGAFNLVVGD 204 Query: 254 GADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNNAIIAFEDADLSL 313 G +G A+ + + +SFTGS VG+ + R R LELGG N ++ +DADL L Sbjct: 205 GRTLGPALV--DGADAVSFTGSPGVGRAILERSVARMTRVQLELGGKNPLVVHDDADLEL 262 Query: 314 VVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNVLYGPLH 373 V AL A + GQRCT R+ + +HD V RL A +RVG+P D GP+ Sbjct: 263 AVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRIAALRVGDPMDAATDMGPVV 322 Query: 374 TKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLGHDASIAHTETFAPIL 433 ++ ++ L + +A+ EG + +GG MD G ++EPT+ G + I E F P+ Sbjct: 323 SEAQLAKDLHCIADARSEGAELAFGGGRMDGDGYFLEPTLFVGTDNAMRINRDEVFGPVA 382 Query: 434 YVFKFKNEEEVFAWNNEVKQGLSSSIFTKDL--GRIFRWLGPKGSDCGIVNVNIPTSGAE 491 V + A N+ LSS I T+ L FR + S G+V VN PT+G + Sbjct: 383 CVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFR----RRSRAGLVMVNAPTAGID 438 Query: 492 IGGAFGGEKHTG-GGRESGSDAWKQYMRRSTCTINY 526 FGG +G GGRE GS A + + T IN+ Sbjct: 439 YHVPFGGRGPSGYGGREQGSAAVEFFTEGKTAYINH 474 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: 716 Number of extensions: 36 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: 539 Length of database: 478 Length adjustment: 34 Effective length of query: 505 Effective length of database: 444 Effective search space: 224220 Effective search space used: 224220 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