Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 316 bits (810), Expect = 1e-90 Identities = 184/477 (38%), Positives = 270/477 (56%), Gaps = 10/477 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 F EF + S K F V+P+T E + + + D+D AV AA AA W+ + R Sbjct: 23 FFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAA-QKEWAKRPVRER 81 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMC-SKGDVALTAAYFRSCAGWTDKIKGSVI 142 K++ + ++D H + +A + AL+ GK+L S+ + + + F G ++KG I Sbjct: 82 GKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGETI 141 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 + T REP+GV G IIPWN PLL+ + K+ P + G V+K+AE PL+ L + Sbjct: 142 PFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPLAVLRV 201 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 LI P GVVN++SG+GP GAP+ +H +KKV FTGS TG+ + K AAE L Sbjct: 202 VQLINTV-IPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIVYKTAAEK-LIP 259 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGI-FYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321 VTLELGGKSP IV DAD+ I + G+ F G+ C A SRI+V + I+D V + K Sbjct: 260 VTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAFVEKLK 319 Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377 ++K+GDP E T +G S QLD++ YI IGK+ GAT + KG Sbjct: 320 EKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSDPKLTKGL 379 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 +++P IF VK +I ++EIFGPV + ++ EEVIA AND+EYGLAA + T +L A Sbjct: 380 YVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWTRDLKVA 439 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEA-LDNYTQVKAVRIGL 493 + +++ +G + VN P + +GG SG+G+E EA L+++T K + I + Sbjct: 440 MDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFTHKKTIIINM 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: 593 Number of extensions: 35 Number of successful extensions: 7 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: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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