Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Putida:PP_2694 Length = 480 Score = 230 bits (586), Expect = 1e-64 Identities = 150/462 (32%), Positives = 230/462 (49%), Gaps = 11/462 (2%) Query: 56 NGSWGGRGEVITTYCPANN-EPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIV 114 +G W + Y P++ + I + QAS + ++ AR A +WA R +++ Sbjct: 11 DGQWCEGHATLGNYSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGLESRQQVL 70 Query: 115 RQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERS 174 IGD L + + LG L+S E GK L EG+GEV Y G S R Sbjct: 71 MAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGETAASVRP 130 Query: 175 GHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKII 234 G + PVG+VGIIT +NFP+A W A A+ GN ++K A + A+T+II Sbjct: 131 GVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASAWALTEII 190 Query: 235 AKVLEDNKLPGAICSLTCG-GADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRS 293 ++ LP +L G GAD+G A+ + ++ L+FTGS Q G++V + R Sbjct: 191 SR----QGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATAGNLVRC 246 Query: 294 LLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKA 353 LE+G NA++ +DADL L V AL A GQ+CT + RL + + IHD V L+ Sbjct: 247 QLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHDRFVEALRLR 306 Query: 354 YAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDR--PGNYVEP 411 Q++VG+ + V GP+ + + L ++ A+ EG T++ GG+ + G Y+ P Sbjct: 307 MRQLKVGHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQLACDGYYMRP 366 Query: 412 TIVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWL 471 + +D I E F PI V + ++ EE A N+ + GL++ I T+ L + Sbjct: 367 ALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIITQSLRHASHF- 425 Query: 472 GPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTG-GGRESGSDA 512 + + G V VN+PT+G + FGG K + G RE G A Sbjct: 426 -KRRAQTGCVMVNLPTAGTDYHVPFGGRKASSFGPREQGQYA 466 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: 671 Number of extensions: 43 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: 539 Length of database: 480 Length adjustment: 34 Effective length of query: 505 Effective length of database: 446 Effective search space: 225230 Effective search space used: 225230 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