Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 198 bits (503), Expect = 4e-55 Identities = 150/455 (32%), Positives = 226/455 (49%), Gaps = 23/455 (5%) Query: 37 SPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLG 96 +P TGE I + + + + A A + W A RG+LV G L A +LG Sbjct: 39 NPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQSARARGKLVAECGRVLSAHVEELG 98 Query: 97 RLVSIEAGK-IPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVV 155 RLV++E GK + +E E + D+ F GL +L G TI P + P+GVV Sbjct: 99 RLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETIPFN-PDMLTVTVREPVGVV 157 Query: 156 GIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGL 215 G I +N P+ + + AA ALV G++VV K +E+ PLT L I+ + P GL Sbjct: 158 GCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRVAEIMNTVL------PPGL 211 Query: 216 SQVLIG-DRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVC 274 +L G G LV+HP V V+ TGS GR V A++ LELGG + IVC Sbjct: 212 FNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIPVTLELGGKSPMIVC 271 Query: 275 PSADLDMALRAIAFGAMGT-AGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLES 333 AD+D A+ G T GQ CT RLFVHES++D+ V ++K ++ +G+PL+ Sbjct: 272 ADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKAKVDAMVMGDPLDE 331 Query: 334 AALVGPLVDKAAFDGMQKAIAEAKNHGGA---VTGGERVELGHENGYYVKPAL-VEMPKQ 389 +G +V + ++ I + GA V + G +V+P + M Sbjct: 332 KTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPKLAKGRFVQPVIFTGMKNS 391 Query: 390 EGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGS---D 446 + EE F P+ V+K+SD++ VLA+ N GL++SI+TRD + LA D + + Sbjct: 392 DRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFK-----LAMDATKRLE 446 Query: 447 CGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDA 481 G VN + G ++GG K +G G+E+ ++ Sbjct: 447 AGFVQVNQNLV-VQPGLSYGGVKTSGIGKEASLES 480 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: 549 Number of extensions: 28 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: 496 Length adjustment: 34 Effective length of query: 476 Effective length of database: 462 Effective search space: 219912 Effective search space used: 219912 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