Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_001592305.1:WP_068168204.1 Length = 485 Score = 347 bits (890), Expect = e-100 Identities = 201/482 (41%), Positives = 282/482 (58%), Gaps = 11/482 (2%) Query: 20 PTGLF--INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWST 77 PT LF IN + V + F +V+P+T V+EA +D++ AVEAA A F + WS Sbjct: 3 PTTLFSFINGQTVNGGGQ-VFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGF-ALWSA 60 Query: 78 SDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDK 136 R ++L + AD++ E LA +E D GK + DV A AG Sbjct: 61 MSATERGRILRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAAT 120 Query: 137 IKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTP 196 + G + F YTR+EP+GVC I WN+P+ +A WK P L G + K +E TP Sbjct: 121 LTGQQYPLKNA-FAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTP 179 Query: 197 LSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAA 256 +A+ LA + EAG PPGV NVV G G GA +++HP + KV+ TGS TG+ +M+ AA Sbjct: 180 ATAVKLAEVYLEAGVPPGVFNVVQGRG-AVGAMLAAHPDVAKVSVTGSVPTGKRVMETAA 238 Query: 257 ESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316 LK+VT+ELGGKSP +VFDDAD++ + + G FY GEVC +R++VQ GI + Sbjct: 239 -GTLKRVTMELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAPRF 297 Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKG 376 ++ K L++GDP DT +GA S+ +++ YI G+ EGAT++ GGER +G Sbjct: 298 LARLKERTLLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAVEG 357 Query: 377 Y---FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTN 433 F+ PTIF D ++D +IVR+EIFGPV+++ F T E IA AN S + LAAGV TT+ Sbjct: 358 LGDQFVAPTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTD 417 Query: 434 LSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 L V+ +I +G W+N YN +PFGG +SGIG E ALD+YTQ+K V + L Sbjct: 418 LQRGHRVAAQIRAGICWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVYVEL 477 Query: 494 SQ 495 + Sbjct: 478 GE 479 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: 567 Number of extensions: 32 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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 Apr 09 2024. 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