GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Dyella japonica UNC79MFTsu3.2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase

Query= BRENDA::A6T8Z5
         (462 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2488
          Length = 463

 Score =  332 bits (851), Expect = 2e-95
 Identities = 182/450 (40%), Positives = 265/450 (58%), Gaps = 3/450 (0%)

Query: 11  SVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALRARGEE 70
           ++NP TGE V + P A++ EV  A+  A A +  W+   +A R   L++    LR    +
Sbjct: 5   TINPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQ 64

Query: 71  VAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVEN---NQAVIEYRPL 127
            A+++TLEMGK I +A GEV   A + ++YA+H   +LA E     +    Q+ +E+ P 
Sbjct: 65  YAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHVPQ 124

Query: 128 GAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGVFG 187
           G +LAV PWNFP +Q++R A P L AGN  +LKHA NV   A     +F  AGLP G F 
Sbjct: 125 GILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGGFT 184

Query: 188 WVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLNDA 247
            + AT D +  II D R+  V +TGS  AG  + AQAG ALKK  +ELGG+D F+VL DA
Sbjct: 185 NLYATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVVLADA 244

Query: 248 DLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQNYV 307
           DLD+AV+ AVTGR+ N+GQVC +SKR I+   I +AF  K+   VA L+ GDP +    +
Sbjct: 245 DLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEPSTTL 304

Query: 308 GPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQELF 367
            PM+     D+L +Q+   +  GA + +   ++   G ++ P +L +V+        E F
Sbjct: 305 APMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARYWEFF 364

Query: 368 GPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCASDA 427
           GPV+ +  ARD   A+ +ANDS FGL  +V+TTD       A+++  G V++N      A
Sbjct: 365 GPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPTGVAA 424

Query: 428 RVAFGGVKKSGFGRELSHFGLHEFCNAQTV 457
            + FGGV++SG+GREL+  G+ EF N + +
Sbjct: 425 DLPFGGVRRSGYGRELTGLGIKEFVNHKLI 454


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: 518
Number of extensions: 20
Number of successful extensions: 2
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: 463
Length adjustment: 33
Effective length of query: 429
Effective length of database: 430
Effective search space:   184470
Effective search space used:   184470
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