Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_011778897.1 MVAN_RS08280 aldehyde dehydrogenase family protein
Query= BRENDA::P49419 (539 letters) >NCBI__GCF_000015305.1:WP_011778897.1 Length = 514 Score = 462 bits (1189), Expect = e-134 Identities = 247/485 (50%), Positives = 320/485 (65%), Gaps = 7/485 (1%) Query: 57 GSWGGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQ 116 G+ G G +T P + + V QAS AD + V A EA+ W PAP RG +V + Sbjct: 33 GAPGSEGLPAST--PITGDVLFSVPQASAADADAAVAAAAEAFSTWRTTPAPVRGALVAR 90 Query: 117 IGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGH 176 +G L E L +LV++E GKI E +GEVQE +DIC++AVGLSR + G + SER GH Sbjct: 91 LGQLLVEHKTALATLVTIEAGKINSEALGEVQEMIDICEFAVGLSRQLYGRTIASERPGH 150 Query: 177 ALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAK 236 L+E W+P+G+VG+ITAFNFPVAV+ WN AIA++CG+ +WK + T L +VA ++ + Sbjct: 151 RLMENWHPLGVVGVITAFNFPVAVWAWNTAIALVCGDTVVWKPSELTPLTAVACQALLER 210 Query: 237 VLEDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLE 296 D P A+ L G ++G + D RV L+S TGS ++G++VG V RFGR+LLE Sbjct: 211 ACADVGAPAAVGRLVLGEREVGEKLVDDPRVALVSATGSVRMGREVGPRVAARFGRALLE 270 Query: 297 LGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQ 356 LGGNNA I ADL L V +F+A GTAGQRCTT RRL +H S+ DE+V+R+ AY Q Sbjct: 271 LGGNNAAIVTPAADLDLAVRGIVFSAAGTAGQRCTTLRRLIVHSSVADELVSRIVAAYKQ 330 Query: 357 IRVGNPWDPNVLYGPL-HTKQAVSMFLGAVEEAKKEGGTVVYGGK--VMDRPGNYVEPTI 413 + VG+P+ L GPL HT M L A+++A EGGTV+ G + V D YV P + Sbjct: 331 LPVGDPFADRTLVGPLIHTASYRDMVL-ALQQATAEGGTVLGGERVDVGDEGAFYVTPAV 389 Query: 414 VTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGP 473 V + +++ H ETFAPILYV ++ +E A NN V QGLSSSIFT D+ R+L Sbjct: 390 VR-MPAQSAVVHKETFAPILYVMTYETLDEAIALNNAVPQGLSSSIFTLDMREAERFLAA 448 Query: 474 KGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSKDLPLA 533 GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSD+WK YMRR+T T+NYS +LPLA Sbjct: 449 DGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDSWKAYMRRATNTVNYSTELPLA 508 Query: 534 QGIKF 538 QG+ F Sbjct: 509 QGVHF 513 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: 817 Number of extensions: 34 Number of successful extensions: 2 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: 514 Length adjustment: 35 Effective length of query: 504 Effective length of database: 479 Effective search space: 241416 Effective search space used: 241416 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