Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate NP_662456.1 CT1573 aldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000006985.1:NP_662456.1 Length = 457 Score = 254 bits (649), Expect = 4e-72 Identities = 160/454 (35%), Positives = 236/454 (51%), Gaps = 8/454 (1%) Query: 27 NPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKIRADAGRIA 86 NPA G L+ P A +++ L A A + W ER ++R+A +R A + Sbjct: 6 NPATGEQLAEYPVMIAGQIDSVLRQADADFRRWRSTSFGERRTCMKRLAELLREQAEKHG 65 Query: 87 RTITLEQGKIASLAEVEVNFTADYLDYMAEWARR-LEGEIIASDRPGENIFLFRKPLGVV 145 R ITLE GK S A EVN A DY A+ A L+ E S+ G + +PLGV+ Sbjct: 66 RIITLEMGKPFSQAVAEVNKCAWVCDYFADHAEEFLQPE--QSEIDGAKGIVAFEPLGVI 123 Query: 146 AGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVFNVVC 205 G++PWNFP++ + R AP L+ GN IVVK + +L + P ++ V Sbjct: 124 LGVMPWNFPYWQVLRFAAPILMAGNGIVVKHAPNVTGCAIAIEKLFRDAGFPEHLYRAVH 183 Query: 206 ----GAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLAD 261 ++ G + HP + +S TGS G + A A L + LELGG P IVL D Sbjct: 184 IDLDEVDRLTGFMIDHPVIKAVSVTGSTGAGQAVAAKAGKALKRSVLELGGSDPYIVLED 243 Query: 262 ADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAEPEV 321 ADL AV A R++N+GQ C A+R V++++ F ++I M GDP A+ Sbjct: 244 ADLAQAVDACVAGRLLNAGQSCIAAKRFIVRKEIIGEFTKKIVQRMQTAVMGDPFAK-ST 302 Query: 322 EMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREE 381 E+GP+ + + ++V+ ++ GA L+ GG + PG +Y PTVL+G + EE Sbjct: 303 EVGPIAREDLRDLVHSQVQRSVEAGAELLWGGHVPNAPGWYYPPTVLSGVKPGMPAYSEE 362 Query: 382 IFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFE 441 IFGPV I V D DEA+A+AND E+GL S+VF++D+ +A+ R L+ G +IN Sbjct: 363 IFGPVATIIEVADDDEAVAIANDSEFGLGSAVFSQDVERALGIARRLEAGSCFINTMVKS 422 Query: 442 AMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYL 475 + GV++SG G HG+ E+ + YL Sbjct: 423 DPRLPFGGVKQSGYGRELSHHGIREFVNIKTFYL 456 Lambda K H 0.320 0.136 0.395 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: 507 Number of extensions: 23 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: 477 Length of database: 457 Length adjustment: 33 Effective length of query: 444 Effective length of database: 424 Effective search space: 188256 Effective search space used: 188256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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