GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2488 N515DRAFT_2488
           succinate-semialdehyde dehydrogenase /
           glutarate-semialdehyde dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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