Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_090439664.1 BLS63_RS03170 aldehyde dehydrogenase family protein
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_900100495.1:WP_090439664.1 Length = 478 Score = 224 bits (570), Expect = 7e-63 Identities = 150/446 (33%), Positives = 228/446 (51%), Gaps = 12/446 (2%) Query: 52 AAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGL 111 AA+ I A AF AW R + + +G E+ A + +LG L++ E GK +E + Sbjct: 40 AAQVEQAIAAARAAFPAWSTSAIQARSDALDKVGSEILARREELGSLLAREEGKTLAEAI 99 Query: 112 GEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWN 171 GEV +I F G + G +A+ RPG + T PLGV+G+I+ +NFP+A+ +W Sbjct: 100 GEVSRAGNIFKFFAGECLRQAGELLASVRPGVSVEVTREPLGVIGLITPWNFPIAIPAWK 159 Query: 172 AALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIGD-RAIGEVLV 230 A AL G+ VV+KP++ P A A I+ RA P G+ +++G R +GE LV Sbjct: 160 IAPALAYGNCVVFKPADLVPGCAWAIAEIIARA-----GFPAGVFNLVMGSGRVVGETLV 214 Query: 231 DHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGA 290 HP+V VS TGS +GR + R A+ LE+GG N ++ ADL+ A+ A Sbjct: 215 QHPQVDGVSFTGSVGVGRSIAAVCVARGAKVQLEMGGKNPQVILDDADLNTAVELSVQSA 274 Query: 291 MGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQ 350 + GQRCT RL V ++D+ V + + +S+ VG+ LE +GP+V +A + Sbjct: 275 FYSTGQRCTASSRLIVTAGIHDRFVEAMAERMRSLRVGHALERGVDIGPVVSQAQLEQDL 334 Query: 351 KAIAEAKNHGG-AVTGGERVELGHENGYYVKPALVEMPKQEGPV-LEETFAPILYVMKYS 408 + I ++ G V GGERV E GY++ P L + EE F P+ ++K + Sbjct: 335 RYIGIGRDEGARLVCGGERVSCATE-GYFLAPTLFADSTAAMRINREEIFGPVANILKVA 393 Query: 409 DFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGE 468 D++ LA N GLS+ I T ++ + F + G+ VN+ T+G + FGG Sbjct: 394 DYEEALAMANDTEFGLSAGICTTSLKYANHF--KRHAQAGMVMVNLPTAGVDYHVPFGGR 451 Query: 469 KETG-GGRESGSDAWKAYMRRATNTV 493 K + G RE G A + Y T V Sbjct: 452 KGSSYGSREQGRYAQEFYTTVKTTYV 477 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: 524 Number of extensions: 23 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: 510 Length of database: 478 Length adjustment: 34 Effective length of query: 476 Effective length of database: 444 Effective search space: 211344 Effective search space used: 211344 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