Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AO353_29295 AO353_29295 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29295 Length = 496 Score = 353 bits (907), Expect = e-102 Identities = 197/475 (41%), Positives = 276/475 (58%), Gaps = 5/475 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQV 82 FI+ + + S+ TF VSP + V D + AV+ A AF S W+ P Sbjct: 22 FIDGHYCSALSRDTFECVSPVDGRFLANVASTDEADANAAVQVARRAFDSGVWAKLAPAE 81 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSV 141 R ++L + ADLI + + LA +E LD GK + S D+ TA R A DKI V Sbjct: 82 RKRILIRFADLILANQEELALLETLDMGKPISDSMAIDIPATANAIRWSAEAIDKIYDEV 141 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 T REP GV I+PWNFPL+MASWK P L G + +LK +E +PL+A+ Sbjct: 142 AATPHDQLGLVTREPSGVVAAIVPWNFPLIMASWKFAPALAAGNSFILKPSEKSPLTAIR 201 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 +A L +AG P GV NV+ GFG T G ++ H + +AFTGSTA + ++ A +SN+K Sbjct: 202 IAQLALDAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFTGSTAIAKQLLIYAGQSNMK 261 Query: 262 KVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 +V LE GGKSPN+VF DA D+++ + I +N GEVC AGSR+ V+ I ++ + Sbjct: 262 RVWLEAGGKSPNVVFADAPDLRAAATAAASAIAFNQGEVCTAGSRLLVERSIREQFIPLL 321 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERF--GNKGYF 378 A ++ K G +T +GA Q QLD +L+YI IGK++GA +I GG R G + Sbjct: 322 VEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYISIGKEQGAQLIAGGNRALEDTGGLY 381 Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438 ++P IF V I R+EIFGPV+++ F T EE +A+ANDS +GLAAGV T+NLS A Sbjct: 382 VEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALAIANDSIFGLAAGVWTSNLSKAH 441 Query: 439 SVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 + + + +G++WVN Y+ PFGG+ QSG GR+ A D YT++KA I L Sbjct: 442 TFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIKL 496 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: 538 Number of extensions: 27 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: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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 17 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