Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3650 PGA1_262p00540 succinate-semialdehyde dehdyrogenase GabD
Query= BRENDA::A6T8Z5 (462 letters) >FitnessBrowser__Phaeo:GFF3650 Length = 459 Score = 375 bits (963), Expect = e-108 Identities = 200/449 (44%), Positives = 282/449 (62%), Gaps = 2/449 (0%) Query: 11 SVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALRARGEE 70 +VNPTTG+ + + S + ++ A+ + WR T + DRA+ ++ IGAALR R +E Sbjct: 7 TVNPTTGKTLDTYNVLSGKALEDAVQRCHNAFLDWRLTSVEDRANTIKAIGAALRDRKDE 66 Query: 71 VAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQ-AVIEYRPLGA 129 +A+++T EMGK + Q+ E+ A +CD+ A PA A E +E + I Y P+G Sbjct: 67 LAELMTKEMGKLLKQSHQEIDLCAAICDYSAAEAPAAFAPEERDIEGGEKGHIFYSPIGV 126 Query: 130 ILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGVFGWV 189 + + PWNFP +QV+R ++ L+AGN LLKHA NV GS ++L EI+ AAGLP G+F + Sbjct: 127 VYGIQPWNFPAYQVVRYSIASLIAGNGVLLKHASNVTGSGQMLQEIYEAAGLPKGLFQAL 186 Query: 190 NATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLNDADL 249 ++D +I+ D + VT+TGS AG+ +GA+A A+KK VLELG +D +IVL DAD+ Sbjct: 187 VISHDQSDTLISHDLVRGVTLTGSDGAGRKVGAKAAEAVKKTVLELGSNDAYIVLEDADI 246 Query: 250 DEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQNYVGP 309 D AV+ VTGR N+G+ C A+KRFI+ I F +V A+ + +GDP E +GP Sbjct: 247 DAAVQTCVTGRTYNNGETCIAAKRFIVVDAIYNQFRDAYVAAMKRVTLGDPMGEDADIGP 306 Query: 310 MARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQELFGP 369 MAR DLRD+LHQQV +L+ GA LL G E + G +Y TVL NV G + ELFGP Sbjct: 307 MARKDLRDDLHQQVKDSLEGGAKLLCGGEMPDTDGFFYPATVLENVAPGQPAYDDELFGP 366 Query: 370 VATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARE-LECGGVFLNGYCASDAR 428 VA L A+DAD A+ +ANDS FGL + T D +A AR+ + G VF+NG+ + Sbjct: 367 VAALIRAQDADDAMRIANDSRFGLGGGIMTKDTEKALALARDYFDTGMVFINGFGLAIPN 426 Query: 429 VAFGGVKKSGFGRELSHFGLHEFCNAQTV 457 + FGGVK SG+GRE FG+ EF N ++V Sbjct: 427 MPFGGVKDSGYGREHGGFGMKEFVNVKSV 455 Lambda K H 0.319 0.133 0.392 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: 505 Number of extensions: 24 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: 462 Length of database: 459 Length adjustment: 33 Effective length of query: 429 Effective length of database: 426 Effective search space: 182754 Effective search space used: 182754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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