Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_027179882.1 G496_RS0114360 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000429985.1:WP_027179882.1 Length = 491 Score = 387 bits (995), Expect = e-112 Identities = 210/483 (43%), Positives = 294/483 (60%), Gaps = 8/483 (1%) Query: 18 EQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWST 77 +Q L+I+ +++++K KTF P+ ++++ A E++D AVEAA AF W Sbjct: 6 DQSYKLYIDGKWIENKEGKTFKVFCPANGQQLSTCVNAGKEEVDMAVEAAKKAFEL-WKD 64 Query: 78 SDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDK 136 PQ R L K+AD ID AD LA +E LDNGK + +K D+ L + +FR A Sbjct: 65 ISPQDRASYLLKIADAIDAEADKLAMVETLDNGKPIRETKNIDIPLASDHFRYFASAVRT 124 Query: 137 IKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTP 196 +GS + EPIGV GQIIPWNFP LMA+WK+ P + G T V+K + T Sbjct: 125 DEGSATMIDKDTMSIILHEPIGVVGQIIPWNFPFLMAAWKIAPAIAAGNTVVIKPSSETS 184 Query: 197 LSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAA 256 LS L A +I + PPGVVN+V+G G + G I H K+AFTGST G I AAA Sbjct: 185 LSMLEFAKIIDKI-LPPGVVNIVTGGGSSTGNYILEHEGFSKLAFTGSTDIGYMIADAAA 243 Query: 257 ESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316 + L TLELGGKS NI F D + ++ + GI +N G+VCCAGSRI+V E IYD+ Sbjct: 244 KK-LIPATLELGGKSANIYFPDCPWEKAVEGALLGILFNQGQVCCAGSRIFVHEEIYDRF 302 Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN-- 374 ++ ES+K+G P++EDT MG+ ++ QL++++ I+ GKKEGA ++TGG + Sbjct: 303 LAAITEKFESVKVGLPWEEDTMMGSIINEKQLNQVMGCIEAGKKEGAKLVTGGTKITEGE 362 Query: 375 --KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 KG F+KPTIF DV I + EIFGPVV + KFK +EVIA+ANDSE+GL V + Sbjct: 363 LGKGSFLKPTIFADVDNSMDIAQQEIFGPVVCVIKFKDEDEVIAMANDSEFGLGGAVWSK 422 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 +++ A+ V+ K+ +G +W+NTYN PFGGY +SGIGRE + L +Y+Q K + I Sbjct: 423 DINCAMRVARKVETGRMWINTYNQLPAHSPFGGYKKSGIGRETHKMMLAHYSQTKNIFIS 482 Query: 493 LSQ 495 + + Sbjct: 483 MDE 485 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: 612 Number of extensions: 34 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: 491 Length adjustment: 34 Effective length of query: 461 Effective length of database: 457 Effective search space: 210677 Effective search space used: 210677 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