Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_051956125.1 DL88_RS17100 2-hydroxymuconic semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000745425.1:WP_051956125.1 Length = 503 Score = 304 bits (778), Expect = 5e-87 Identities = 186/481 (38%), Positives = 255/481 (53%), Gaps = 12/481 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FIN F + + + P I V E +ID AV AA AA W R Sbjct: 24 FINGTFTAGSTNRGWDNHCPVDNSVIGFVPEGGKVEIDQAVSAARAALEGPWGRMSVVER 83 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKGSVI 142 +L +AD I D E+LD GK + + S D+ AA F+ I Sbjct: 84 TDLLGAVADEITRRFDEFLEAESLDTGKPMSLASHIDIPRGAANFKMFTDIAKTISTECF 143 Query: 143 ET----GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198 +T G NY R P GV I PWN PLL+ +WK+GP L G T V+K +E TPL+ Sbjct: 144 QTPTVDGTGAINYGVRRPKGVIAVISPWNLPLLLMTWKVGPALALGNTVVVKPSEETPLT 203 Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGP-TAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 A L ++ + G P GV NVV GFGP +AG ++ HP + + FTG T TG IM+ AA Sbjct: 204 ATLLGEVMNKVGIPKGVYNVVHGFGPNSAGEFLTQHPDVNGITFTGETRTGEAIMRQAA- 262 Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 L++V+ ELGGK+P IVF DAD+ I+ +F NTG+VC RIYVQ I+D+ V Sbjct: 263 LGLRQVSFELGGKNPAIVFADADLDKAIEGTTRSVFSNTGQVCLGTERIYVQRPIFDEFV 322 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGE-----RF 372 K AAE+L++G P +T +G S +K+L + +EGATVITGG Sbjct: 323 CRLKQAAETLRLGRPEDPNTNLGPLVSLEHREKVLSFYRKAVEEGATVITGGSIPEMPED 382 Query: 373 GNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 G +++PTI+ + + V +EIFGP I F T EE +++AN + YGLAA + T Sbjct: 383 LAAGAWVQPTIWTGLPDHAAAVNEEIFGPCCHIRPFDTEEEAVSVANSTRYGLAAAIWTE 442 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 +LS A V++++ G WVN++ FGG SGIGRE G +L+ YT++ V I Sbjct: 443 SLSRAHRVASRMEVGICWVNSWFLRDLRTAFGGSKTSGIGREGGVHSLEFYTELSNVCIK 502 Query: 493 L 493 L Sbjct: 503 L 503 Lambda K H 0.316 0.133 0.389 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: 630 Number of extensions: 31 Number of successful extensions: 6 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: 495 Length of database: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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 (21.6 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