Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 159 bits (401), Expect = 3e-43 Identities = 132/446 (29%), Positives = 214/446 (47%), Gaps = 20/446 (4%) Query: 37 SPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLG 96 +P GE + T +A +A + A A + +R + + +L K D+ Sbjct: 22 NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIA 81 Query: 97 RLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATER--PGHRMMETWH--PL 152 + ++ E GK + EV+ I+ A R ++G T+ T+ G + + + P Sbjct: 82 KTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVPC 141 Query: 153 GVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAP 212 GVV I+ FNFP+ + + A ALV G+AV+ KP+ + PLTA + + DA Sbjct: 142 GVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA- 200 Query: 213 EGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGI 272 V+ GD +G LV ++S TGS +G + + + LELGGN A Sbjct: 201 ---LSVVYGDADVGGTLVTSEIPRVISFTGSVGVGEIITKSAGIK--KVSLELGGNAATF 255 Query: 273 VCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLE 332 + SA+LD+A + A GA +GQ C +L+R++VH+ +Y + ++ +A + + VG+P E Sbjct: 256 IDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYE 315 Query: 333 SAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALVEMPKQE-G 391 +GPLV+ A + + A G RVE G P ++ K++ Sbjct: 316 EDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPRVE-----GRVFYPCVMADVKEDMA 370 Query: 392 PVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIAN 451 V +E FAPI+ +++ DFD L N GL SIFT D+ ++R A + D G Sbjct: 371 IVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKR--AINELDAGGIV 428 Query: 452 VN-IGTSGAEIGGAFGGEKETGGGRE 476 +N + T +I +GG K +G GRE Sbjct: 429 INDMPTLRFDI-QPYGGVKLSGVGRE 453 Lambda K H 0.317 0.134 0.390 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: 483 Number of extensions: 21 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: 510 Length of database: 471 Length adjustment: 34 Effective length of query: 476 Effective length of database: 437 Effective search space: 208012 Effective search space used: 208012 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 Apr 09 2024. 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