Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate H281DRAFT_02680 H281DRAFT_02680 succinate semialdehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Burk376:H281DRAFT_02680 Length = 492 Score = 219 bits (558), Expect = 2e-61 Identities = 147/452 (32%), Positives = 232/452 (51%), Gaps = 14/452 (3%) Query: 38 PVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGR 97 P TGEKIA + ++ AE IE + A R WR + A +R +++ + A DL Sbjct: 42 PATGEKIADVPLMTGAETRRAIEAGEHAQRGWRKLTAAQRSTILKRWHALMIANTDDLAI 101 Query: 98 LVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGI 157 ++S E GK +E GE+ ++ ++++ G +A+ RM+ T P+GV Sbjct: 102 IMSAEQGKPLAEAKGEIGYAASFIEWFAEQAKRVDGDVLASPAADKRMLVTKEPIGVCAA 161 Query: 158 ISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQ 217 I+ +NFP A+ + A AL G A++ KP+E TPL+ALA + RA P G+ Sbjct: 162 ITPWNFPAAMITRKVAPALAAGCAMILKPAEATPLSALALAELAHRA-----GVPAGVFS 216 Query: 218 VLIGD-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPS 276 V++GD R+IG + +P V +S TGST +GR + + A + LELGGN IV Sbjct: 217 VVVGDPRSIGAEMTSNPIVRKLSFTGSTPVGRMLMSQCAPTVKKLSLELGGNAPFIVFDD 276 Query: 277 ADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAAL 336 ADLD A+ AGQ C R++V + VYD + A + VGN ES Sbjct: 277 ADLDAAVEGALASKYRNAGQTCVCTNRVYVQDGVYDAFAEKFAAAVGRIKVGNGFESGVT 336 Query: 337 VGPLVDKAAFDGMQKAIAEAKNHGGAV-TGGERVELGHENGYYVKPALV-EMPKQEGPVL 394 GPL+++AA + ++ IA+A HG V TGG+R G + +P +V ++ + Sbjct: 337 QGPLINEAAVEKVEAHIADAVAHGARVLTGGKRHAAGK---LFFEPTVVGDVTARMRFAT 393 Query: 395 EETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNI 454 EETF P+ + ++++ +A NA GL++ ++RD+ R A+ + G+ +N Sbjct: 394 EETFGPVAPLFRFTNEREAIAAANATEFGLAAYFYSRDIGRIWR--VAEALEYGMVGINT 451 Query: 455 GTSGAEIGGAFGGEKETGGGRESGSDAWKAYM 486 G E+ FGG K++G GRE + Y+ Sbjct: 452 GLISNEV-APFGGVKQSGLGREGSKYGIEDYL 482 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: 569 Number of extensions: 29 Number of successful extensions: 3 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: 492 Length adjustment: 34 Effective length of query: 476 Effective length of database: 458 Effective search space: 218008 Effective search space used: 218008 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