Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 259 bits (662), Expect = 1e-73 Identities = 150/471 (31%), Positives = 255/471 (54%), Gaps = 11/471 (2%) Query: 4 PVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEAL 63 P +H I+G V G +V NPAT+ V++ P+ + +AI AA+ AQP W AL Sbjct: 18 PYRHA--INGALVDSAGS--FEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAAL 73 Query: 64 PAIERASWLRKISAGIRERASEISALIVEEGGKIQQ-LAEVEVAFTADYIDYMAEWARRY 122 ER +++ + + E+ L+ E GK + +A EV + ++ +A+ RR Sbjct: 74 SQDERGAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAIFWVREVAK--RRL 131 Query: 123 EGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTP 182 E E+I+ D P + + LGV I PWNFP L K+AP L+TGNT+V+KPS +TP Sbjct: 132 EDEVIE-DTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTP 190 Query: 183 NNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAA 242 + F +I ++ P GV N+V G G G L +P +A +S TGS + G K+MA+++ Sbjct: 191 LCTLRFGEIAQQV-FPAGVLNVVAG-GNEQGAWLTEHPDIAKISFTGSTATGRKVMASSS 248 Query: 243 KNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFV 302 N+ ++ LELGG PAI++ D + + + D+ NSGQ C +R+YV + +YD F+ Sbjct: 249 CNLKRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFL 308 Query: 303 NRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKG 362 GN + N +GP+ N +++ A +G V GG+ +G G Sbjct: 309 RDFVAHAAEKTVGNGMDPNT-DLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPG 367 Query: 363 YYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNV 422 + P T++ + ++ ++ EE FGP+LP++ + L++ + AND+++GL +S++ + + Sbjct: 368 NFVPITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDT 427 Query: 423 AMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 A+ L+ G ++N + + G ++SG+G +G+ GL E+ T+ Sbjct: 428 AIGVANRLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTK 478 Lambda K H 0.318 0.135 0.392 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: 543 Number of extensions: 26 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: 479 Length of database: 484 Length adjustment: 34 Effective length of query: 445 Effective length of database: 450 Effective search space: 200250 Effective search space used: 200250 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 (21.7 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