Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_061534526.1 CAter10_RS18190 aldehyde dehydrogenase family protein
Query= BRENDA::P49419 (539 letters) >NCBI__GCF_001584165.1:WP_061534526.1 Length = 506 Score = 487 bits (1254), Expect = e-142 Identities = 245/485 (50%), Positives = 333/485 (68%), Gaps = 10/485 (2%) Query: 63 GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122 G + + P + IA +R +VA+ E +K A++A++ W +PAP RGE+VR +G+ LR Sbjct: 20 GNDLHSRSPRDGAAIASLRAHTVAETEAAIKNAQQAYEKWRVVPAPVRGELVRILGEVLR 79 Query: 123 EKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQW 182 E + LG LV+LE GKIL EG+GEVQE +DICD+AVGLSR + G + SER GH ++E W Sbjct: 80 ENREPLGKLVTLESGKILSEGIGEVQEMIDICDFAVGLSRQLYGLTIASERPGHRMMETW 139 Query: 183 NPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVL---- 238 +P+G+ G+ITAFNFPVAV+ WN A+A++CGN +WK + T ++++AV + K + Sbjct: 140 HPLGVCGVITAFNFPVAVWAWNAALALVCGNAVIWKPSEKTPVVALAVHALYEKAVARFS 199 Query: 239 --EDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLE 296 + LP +C + G A+IG ++ V L+S TGS ++G++V V ER GRSLLE Sbjct: 200 QQRPDLLPSNLCQVVLGRAEIGATLSASPLVPLISATGSVRMGRKVATTVAERLGRSLLE 259 Query: 297 LGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQ 356 LGGNN +I ADLSL + + F+AVGTAGQRCT+ RRLF+H SI+D+VVNR+++ YA Sbjct: 260 LGGNNGMIVTPTADLSLALRAITFSAVGTAGQRCTSLRRLFVHSSIYDDVVNRIERIYAS 319 Query: 357 IRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGN---YVEPTI 413 ++VG+P D L GPL +Q+ A+++AK EGG V G +V G YV P + Sbjct: 320 VKVGDPLDAGTLVGPLVDQQSFEAMQTALQQAKAEGGVVTGGERVAVGDGENAYYVRPAL 379 Query: 414 VTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGP 473 V + + I H ETFAPILYV +++N ++ NN V QGLSS+IFT D+ ++ Sbjct: 380 VR-MSQQSDIVHHETFAPILYVLRYENFDDAVRMNNAVPQGLSSAIFTNDVREAEAFMSA 438 Query: 474 KGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSKDLPLA 533 GSDCG+ NVNI TSGAEIGGAFGGEK TGGGRESGSD+WK YMRR+T TINYS+ LPLA Sbjct: 439 SGSDCGLANVNIGTSGAEIGGAFGGEKETGGGRESGSDSWKTYMRRATNTINYSRTLPLA 498 Query: 534 QGIKF 538 QG+KF Sbjct: 499 QGVKF 503 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: 806 Number of extensions: 29 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: 506 Length adjustment: 35 Effective length of query: 504 Effective length of database: 471 Effective search space: 237384 Effective search space used: 237384 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