Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_058932587.1 AU252_RS22410 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_001484605.1:WP_058932587.1 Length = 504 Score = 351 bits (900), Expect = e-101 Identities = 197/491 (40%), Positives = 277/491 (56%), Gaps = 11/491 (2%) Query: 6 FVPIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVE 65 +VP LP + +IN +FV S TF + P + + EDID AV Sbjct: 12 YVPQDLPTHIQH------YINGQFVDSVGGATFDVLDPVSNQNYATAAAGQKEDIDLAVA 65 Query: 66 AATAAF-HSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTA 124 AA AF + W P+ R +VL ++AD ++ LA +E D G + +KG A Sbjct: 66 AARDAFVNGPWPRMKPRERARVLNRIADAVEAQEARLAELETFDTGLPITQAKGQALRAA 125 Query: 125 AYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTG 184 FR A ++ NY R+PIGV G I PWN P ++ SWKL P L TG Sbjct: 126 ENFRFFADLIVAQFDDAMKVPGAQINYVNRKPIGVAGLITPWNTPFMLESWKLAPALATG 185 Query: 185 CTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGS 244 T VLK AE TPLSA A + K+AG P GV N+V+G G AG + HP + ++FTG Sbjct: 186 NTVVLKPAEFTPLSASLWAQIFKDAGLPDGVFNLVNGLGEEAGDALVKHPDVPLISFTGE 245 Query: 245 TATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGS 304 T TG+ I + AA +NLK +++ELGGKSP +VF DAD+ + I + G+F GE C AGS Sbjct: 246 TTTGQTIFRNAA-ANLKGLSMELGGKSPCVVFADADLDAAIDSALFGVFSLNGERCTAGS 304 Query: 305 RIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGAT 364 RI V+ IYD+ ++ A+++ +GDP T +GA K+ Y++IGK EG Sbjct: 305 RILVERAIYDEFCEKYAARAKNIVVGDPHDPTTEVGALVHPEHYAKVASYVEIGKSEG-R 363 Query: 365 VITGGERFGN--KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSE 422 ++ GG R + +G +I PT+F DV D +I ++EIFGPVV IT F+ +E +ALAN++ Sbjct: 364 LLAGGGRPDHLPEGNYIAPTVFADVAPDARIFQEEIFGPVVAITPFENDDEALALANNTR 423 Query: 423 YGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDN 482 YGLAA + T NL+ A + S + +G +W+N++N PFGG SG+G E G ++D Sbjct: 424 YGLAAYIWTQNLTRAHNFSQNVEAGMVWLNSHNVRDLRTPFGGVKASGLGHEGGYRSIDF 483 Query: 483 YTQVKAVRIGL 493 YT +AV I L Sbjct: 484 YTDQQAVHISL 494 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: 628 Number of extensions: 30 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: 495 Length of database: 504 Length adjustment: 34 Effective length of query: 461 Effective length of database: 470 Effective search space: 216670 Effective search space used: 216670 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