Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298 Length = 481 Score = 222 bits (566), Expect = 2e-62 Identities = 147/445 (33%), Positives = 224/445 (50%), Gaps = 10/445 (2%) Query: 44 IASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEA 103 I AA+ IE A AF AW R + + +G E+ A + +LG+L++ E Sbjct: 34 IGEYAKADAAQVNAAIEAARAAFPAWSTSGIQARHDALDKVGSEILARREELGQLLAREE 93 Query: 104 GKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNF 163 GK E +GEV +I F G +L G + + RPG + T LGVVG+I+ +NF Sbjct: 94 GKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPSVRPGVNVEVTREALGVVGLITPWNF 153 Query: 164 PVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIGD- 222 P+A+ +W A AL G+ VV KP+E P A A I+ RA P G +++G Sbjct: 154 PIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALAEIISRA-----GFPAGAFNLVMGSG 208 Query: 223 RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMA 282 R +G++LV+ PKV +S TGS +GR++ R A+ LE+GG N I+ ADL A Sbjct: 209 RVVGDILVNSPKVDGISFTGSVGVGRQIAVNCVSRQAKVQLEMGGKNPQIILDDADLKQA 268 Query: 283 LRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVD 342 + A + GQRCT RL V ++D+ V + + QS+ VG+ L++ +GP+V Sbjct: 269 VELAVQSAFYSTGQRCTASSRLIVTAGIHDKFVAAMAERMQSIKVGHALKAGTDIGPVVS 328 Query: 343 KAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALVEMPKQEGPV-LEETFAPI 401 +A K I ++ G + G + GY++ P L + + EE F P+ Sbjct: 329 EAQLSQDLKYIDIGQSEGARLVSGGGLVTCDTEGYFLAPTLFADSEASMRISREEIFGPV 388 Query: 402 LYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEI 461 V++ +D++A LA N GLS+ I T ++ + F S G+ VN+ T+G + Sbjct: 389 ANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHF--KRHSQAGMVMVNLPTAGVDY 446 Query: 462 GGAFGGEKETG-GGRESGSDAWKAY 485 FGG K + G RE G A + Y Sbjct: 447 HVPFGGRKGSSYGSREQGRYAQEFY 471 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: 510 Number of extensions: 25 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: 481 Length adjustment: 34 Effective length of query: 476 Effective length of database: 447 Effective search space: 212772 Effective search space used: 212772 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