Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011829868.1 MPE_RS11480 2-hydroxymuconic semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000015725.1:WP_011829868.1 Length = 484 Score = 316 bits (810), Expect = 1e-90 Identities = 188/481 (39%), Positives = 264/481 (54%), Gaps = 14/481 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI+ EFV + KTF +P + V+EA ++D AV AA A W R Sbjct: 7 FIDGEFVATD--KTFANRAPVDNRVLGLVHEAGRAEVDAAVAAARGALKGEWGRMPVAKR 64 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKGSVI 142 +++LY +AD I+ D E D GK L + S D+ AA F+ A + Sbjct: 65 VELLYAVADEINRRFDDFLAAEIADTGKPLSLASHIDIPRGAANFKVFADIIKNVPAETF 124 Query: 143 ET----GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198 E G NY R P+GV G + PWN PLL+ +WK+GP L G T V+K +E TP + Sbjct: 125 EMATPDGGQALNYAVRTPVGVVGVVCPWNLPLLLMTWKVGPALACGNTVVVKPSEETPAT 184 Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGP-TAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 A L ++++ G P GV NVV GFGP +AGA ++ HP + + FTG T TG IM AAA+ Sbjct: 185 ATLLGEVMQKVGMPKGVYNVVHGFGPDSAGAFLTQHPDVDAITFTGETRTGEAIMAAAAK 244 Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 ++ V+ ELGGK+ IVF DAD + + F N G+VC R+YVQ I++K V Sbjct: 245 G-VRPVSFELGGKNAGIVFADADFDKAVAGITRSAFENCGQVCLGTERVYVQRPIFEKFV 303 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG---ERFG- 373 K AE+LKIG + +G S DK+L Y ++GATV+TGG + G Sbjct: 304 QALKAKAEALKIGPSEEPGVGLGPLISAEHRDKVLSYYRKAVEQGATVVTGGGVPKMSGA 363 Query: 374 -NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 +G++++PTI+ + E ++R+EIFGP I F T EE IALAN ++YGLA V T Sbjct: 364 LAEGHWVQPTIWTGLPESAAVIREEIFGPCCHIAPFDTEEEAIALANATDYGLATTVWTQ 423 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 NL TA V+ ++ G W+N++ FGG SGIGRE G +L+ YT+++ V + Sbjct: 424 NLGTAHRVARQVEVGICWINSWFLRDLRTAFGGAKASGIGREGGVHSLEFYTELRNVCVK 483 Query: 493 L 493 L Sbjct: 484 L 484 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: 581 Number of extensions: 28 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: 484 Length adjustment: 34 Effective length of query: 461 Effective length of database: 450 Effective search space: 207450 Effective search space used: 207450 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