GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Phaeobacter inhibens BS107

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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