Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Dino:3607155 Length = 483 Score = 219 bits (559), Expect = 1e-61 Identities = 148/438 (33%), Positives = 226/438 (51%), Gaps = 16/438 (3%) Query: 56 AGKIEKADEAFR----AWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGL 111 AG+++ A A R AW KR +++ +G EL A ++GRL+S E GK +EG Sbjct: 40 AGQLDTALAAARRAQPAWWAAGIQKRHDVLMAIGTELMARSDEIGRLLSREEGKPLAEGK 99 Query: 112 GEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWN 171 GEV + + + +G + RPG + +GVV IIS +NFPVA +W Sbjct: 100 GEVYRAGQFFTYFAAEALRQHGDLAESVRPGIEIDVRREAVGVVAIISPWNFPVATPAWK 159 Query: 172 AALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIG-DRAIGEVLV 230 A AL G+AVVWKP+ TP +A+A I+ R D P+GL ++ G R +G+ LV Sbjct: 160 IAPALAFGNAVVWKPANVTPASAIALTEIIARQ-----DIPKGLFNLVAGPGRDVGQRLV 214 Query: 231 DHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGA 290 + +V +S TGS +GR + + + +E+G N IV DLD+A+ A A Sbjct: 215 ESAEVDAISFTGSVPVGRGIAAAAVQNMTKVQMEMGSKNPLIVMDDCDLDLAVAHAASSA 274 Query: 291 MGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQ 350 G GQ+CT RL VH +V+D V +L A +++ VG+ LE +GP+V ++ + Sbjct: 275 FGGTGQKCTAASRLIVHSAVHDAFVEKLVAAARAMKVGHALEDGTQLGPVVSESQLNQNM 334 Query: 351 KAIAEAKNHGG-AVTGGERVELGHENGYYVKPALVEMPKQEGPV-LEETFAPILYVMKYS 408 + I K+ G + GG+R+E+ +GY++ PA+ + + EE FAPI V + Sbjct: 335 EYIGVGKDEGAELLCGGDRLEMA-TDGYFMAPAVFAGTANDMRINREEMFAPITAVQRVD 393 Query: 409 DFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGE 468 +D LA N GL++ I T + + F A + C VN+ T+G + FGG Sbjct: 394 SYDEALARANDTQFGLTAGIMTTSLARASHFRAHMRAGC--VMVNLPTAGTDYHVPFGGR 451 Query: 469 KETG-GGRESGSDAWKAY 485 + G RE GS A + Y Sbjct: 452 GASSFGPREQGSYAAEFY 469 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: 533 Number of extensions: 33 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: 483 Length adjustment: 34 Effective length of query: 476 Effective length of database: 449 Effective search space: 213724 Effective search space used: 213724 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