Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 238 bits (607), Expect = 3e-67 Identities = 141/456 (30%), Positives = 231/456 (50%), Gaps = 4/456 (0%) Query: 24 IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83 + ++NPAT +I+ + + + DA ++AQP+W ER + + S + Sbjct: 1 MQIINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEI 60 Query: 84 SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRAL 143 ++++++ E GK Q + E+ I +M A +Y + + +D PG ++ L Sbjct: 61 EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL 120 Query: 144 GVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFN 203 GV I WN+P+ + PALL+GNT++ KPSE+ I K++ + G+P VF+ Sbjct: 121 GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH 180 Query: 204 LVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDD 263 + +G ET L N TGS G+ I A + LELGGK P + DD Sbjct: 181 IAIGAKETGSALL--NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDD 238 Query: 264 -ADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERND 322 D+ A D N+GQ C ER+YVQ+ YD + N +++ + G P Sbjct: 239 VTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEG- 297 Query: 323 IAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHE 382 + +G L + +E +V A+ +GA++ GGKAVEGKGYY+ PT+L DV +M +M E Sbjct: 298 VYIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQE 357 Query: 383 ETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENF 442 E+FGP++ ++ +A+ M D+DYGLT+S+YT + A K + L G Y N + Sbjct: 358 ESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDR 417 Query: 443 EAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478 + +G + SGIG G+ + + + +L+ Sbjct: 418 VSAALPWSGRKYSGIGATLSHQGIRAFTKPKGYHLR 453 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: 489 Number of extensions: 17 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: 454 Length adjustment: 33 Effective length of query: 446 Effective length of database: 421 Effective search space: 187766 Effective search space used: 187766 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: 51 (24.3 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