Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_012648616.1 GEOB_RS17645 aldehyde dehydrogenase
Query= CharProtDB::CH_007936 (497 letters) >NCBI__GCF_000022265.1:WP_012648616.1 Length = 475 Score = 302 bits (774), Expect = 1e-86 Identities = 175/473 (36%), Positives = 272/473 (57%), Gaps = 14/473 (2%) Query: 21 LFINNEFVKGVEGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFEGPWRQVTPSE 80 + I+ E++ G + +VINP ++ +I V EAT +DV+ A+ AA FE + + Sbjct: 7 MLIDGEWL-GDDRSGIEVINPFDDSLIGLVPEATAEDVEAAIIAAAKGFERI-SAMPAHK 64 Query: 81 RGILINKLADLMERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQTI 140 R ++ K A+L+ RD D +A I + + GK++ A + S ++ A A HG+ + Sbjct: 65 RSDILEKTAELILRDKDEIAGIIAREAGKSWKYAVAEAERSAETFKFAAIEAKASHGEIV 124 Query: 141 DTNPETLTYTR-----HEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPL 195 + ++ R P+G+ G I P+NFPL + + K+ PA+A GN VVLK A +TPL Sbjct: 125 PMDASAVSAGRFGFYIRTPIGIIGAITPFNFPLNLVAHKLAPAIATGNAVVLKPATKTPL 184 Query: 196 SALYAAKLIKEAGFPAGVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAK 255 ++L A+L+ EAG PAG +NV+ G G T G + + + FTGS VGR I ++ Sbjct: 185 TSLKLAELLMEAGLPAGALNVLIGSGSTVGNRLVEDNRLAMITFTGSPPVGRGI---KSR 241 Query: 256 SNLKKVTLELGGKSPNIVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFV 315 S LK+VTLELG SP I+ +D D+D A+S G F N GQ C + RI V + YD+F+ Sbjct: 242 SGLKRVTLELGSNSPTIIEEDGDVDKAVSRCVVGSFANSGQVCISVQRIFVHKDRYDEFI 301 Query: 316 ARFKERAQKNKVGNPFEQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGNEGY 375 A+F E KVG+PF++ + GP ++ + +R +E++ K GA VA GG+ GN Sbjct: 302 AKFVEATCALKVGDPFDKSSDIGPMITTKELNRALEWLEEAKNLGAVVAAGGNAIGN--- 358 Query: 376 FIQPTVFTDVTSDMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTA 435 ++PT+ T VT +MK+ E+F P+V++ + EA+++ + + YGL A ++T+++N A Sbjct: 359 CLEPTILTGVTREMKVMCSEVFAPIVSVLPYDTFDEALEMADDSVYGLQAGIYTRDINKA 418 Query: 436 IRVSNALKAGTVWINNYNMISY-QAPFGGFKQSGLGRELGSYALENYTQIKTV 487 + L G V IN+ P+GG K+SGLGRE YA+E T IK V Sbjct: 419 FKAIKKLDVGGVIINDVPTFRVDHMPYGGNKESGLGREGLKYAMEEMTNIKMV 471 Lambda K H 0.318 0.134 0.397 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: 556 Number of extensions: 16 Number of successful extensions: 6 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: 497 Length of database: 475 Length adjustment: 34 Effective length of query: 463 Effective length of database: 441 Effective search space: 204183 Effective search space used: 204183 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 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