Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1480 Length = 486 Score = 329 bits (844), Expect = 1e-94 Identities = 195/465 (41%), Positives = 267/465 (57%), Gaps = 4/465 (0%) Query: 9 RNYIDGAFVES--AAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE 66 R YIDG +V++ A L V NPANGAL+ +P A A + + A+AAA A W + A + Sbjct: 15 RCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDRTAED 74 Query: 67 RAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEII 126 RA LRR + +A +T EQGK + A E+ + A Y+++ AE ARR+ GE+I Sbjct: 75 RARILRRWFELMLQHQEDLALIMTSEQGKPLAEARGEIAYAASYIEWFAEEARRIYGEVI 134 Query: 127 ASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFE 186 S + I + R+P+GV A I PWNFP +I RK+APAL G TI+VKP+ +TP + Sbjct: 135 PSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQTPLSALA 194 Query: 187 FARLVAETDLPRGVFNVVCG-AGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTK 245 A L A +P GVF+V+ G A +G L++ P V ++FTGS E G + A AP L K Sbjct: 195 MAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQCAPTLKK 254 Query: 246 LNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAA 305 ++LELGG AP IV DADL+ AV S+ N+GQ C CA R+ VQ V + F E++A Sbjct: 255 MSLELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDAFAEKLAR 314 Query: 306 AMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQP 365 +AA + G L E VE GPLI+ L K++A V A A+GA +VTGG G Y+P Sbjct: 315 TVAALKVGHGL-EEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRRHALGGTFYEP 373 Query: 366 TVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHAL 425 T+L D R+ REEIFGPV P+ EAI +AND E+GL + ++RD+ + Sbjct: 374 TILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDVGRVWRVS 433 Query: 426 RELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHT 470 L +G IN GV++SG+G HG+ EY T Sbjct: 434 GALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDT 478 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: 558 Number of extensions: 21 Number of successful extensions: 4 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: 486 Length adjustment: 34 Effective length of query: 443 Effective length of database: 452 Effective search space: 200236 Effective search space used: 200236 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: 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