GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Novosphingobium barchaimii LL02

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_059152522.1 V474_RS16500 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::A6T8Z5
         (462 letters)



>NCBI__GCF_001046635.1:WP_059152522.1
          Length = 472

 Score =  519 bits (1337), Expect = e-152
 Identities = 256/454 (56%), Positives = 326/454 (71%), Gaps = 1/454 (0%)

Query: 6   ATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALR 65
           A+  VS NP TGE +++ P+ +  EV+A +  +A  +R WR TP+  R  A RR+   LR
Sbjct: 14  ASGGVSRNPATGETIATYPYQTVDEVEATMQASAEAFRVWRDTPMEQRVAAYRRLAETLR 73

Query: 66  ARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAV-IEY 124
            R + +A +IT EMGK I  AR E+ KSA   DW AEHGPA+LA E   V+ +  V + Y
Sbjct: 74  ERSDTLAALITAEMGKTIGAARSEIEKSAGTLDWLAEHGPAILADEPVSVDGDDEVHVSY 133

Query: 125 RPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDG 184
            P+G IL VMPWN P+WQV+R + PI+L+GN +LLKHAPNVMGSA  L + + A+G P G
Sbjct: 134 LPIGTILGVMPWNLPIWQVIRASGPIMLSGNGFLLKHAPNVMGSAYALQQAYEASGFPKG 193

Query: 185 VFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVL 244
           +FG +N  N+ V+++I D RIAAVT+TGS+RAG A+ A A  ALKK +LELGGSD FIVL
Sbjct: 194 LFGNLNTDNETVARVIEDPRIAAVTLTGSMRAGAAVAATAARALKKSLLELGGSDAFIVL 253

Query: 245 NDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQ 304
            DA+LD AV A +  R+ NSGQVC A+KRF+LE  IA+ FTRKFV+A + LK+GDP D  
Sbjct: 254 ADANLDLAVAAGIQARFGNSGQVCLAAKRFLLERPIAQEFTRKFVEAASKLKVGDPLDAS 313

Query: 305 NYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQ 364
             +GPMAR DLRDELH+QV  TL +GA LLLG +K+EG GN+YAPTVL +V  GM  F +
Sbjct: 314 TALGPMARHDLRDELHEQVERTLAQGAKLLLGGQKVEGPGNFYAPTVLADVAPGMAAFEE 373

Query: 365 ELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCA 424
           E FGPVA +T   D +HA+AL N SE+GL  +++T D A+AQR AR LE GGVF+NG+ A
Sbjct: 374 ETFGPVAAITMVEDVEHAIALTNASEYGLGGSLWTADTARAQRIARRLETGGVFINGFSA 433

Query: 425 SDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVW 458
           S+ R+  GGVKKSG+GRELSHFGL EF N Q VW
Sbjct: 434 SNPRIPVGGVKKSGYGRELSHFGLREFTNPQAVW 467


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: 575
Number of extensions: 22
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: 472
Length adjustment: 33
Effective length of query: 429
Effective length of database: 439
Effective search space:   188331
Effective search space used:   188331
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 24 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