GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Neptunomonas antarctica S3-22

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_054343024.1 Nant_RS18090 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001305295.1:WP_054343024.1
          Length = 487

 Score =  540 bits (1392), Expect = e-158
 Identities = 263/482 (54%), Positives = 356/482 (73%), Gaps = 6/482 (1%)

Query: 44  ADLLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101
           A LL+  +++ G+W+   A  TF V +PA+G  L  VA  G  E R A+ AA  A  SWK
Sbjct: 8   ARLLKTQAYIDGQWVDGDAGDTFAVTNPATGEHLADVASVGWAETRRAINAAQQAMISWK 67

Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161
            +  K RS LL +W++L+I+N+++LA ++TAE GKPL E++GE+ Y A F++WF+EE +R
Sbjct: 68  ALPAKSRSELLERWFNLVIENQEDLAVLMTAEQGKPLFESRGEVAYGASFIKWFAEEGKR 127

Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221
           VYGDII T   D+RG+V+KQPVGV + ITPWNFP+AMI RKV  ALA GC +V+KPA +T
Sbjct: 128 VYGDIIPTP-NDRRGVVVKQPVGVVAAITPWNFPNAMIARKVAPALAVGCAMVLKPAAET 186

Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281
           P SALAL +LAN+AG+P G+++V+P S   A+E+GE + ++P+V K++FTGST  GK+L+
Sbjct: 187 PLSALALVELANRAGLPAGLFSVLPSSN--AREIGEEMTSNPIVKKVTFTGSTPVGKLLM 244

Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341
              A++VKR SMELGG AP I+FD A++D AVAG + +K+RN+GQTC+C+NR LVQ GI+
Sbjct: 245 KQCADTVKRTSMELGGNAPVIIFDDADLDAAVAGVLVAKYRNSGQTCICANRILVQEGIY 304

Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401
           D+FV KF  A+K   RVGNG +  +T GP+I EKA  +++  V  AVA+GATV+ GGK  
Sbjct: 305 DAFVEKFTAAVK-GFRVGNGMDNNSTHGPVITEKAAAEIDAKVKSAVAEGATVILGGKPG 363

Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461
             G  F+EPT+L+NVT  M    EE FGPVAP+ KF  EE+A+A+AN  + GLA Y Y++
Sbjct: 364 AQGACFYEPTILTNVTDKMRVFREEIFGPVAPIFKFSTEEQAIAMANDTEFGLAAYLYTE 423

Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521
           +  +IWRV+E ++ GMVGVNE  ISS   PFGGVK+SG GREGSKYG+D+YLE KY+C G
Sbjct: 424 NLGRIWRVSEGIDYGMVGVNETAISSEVIPFGGVKESGQGREGSKYGLDDYLETKYICMG 483

Query: 522 GL 523
           GL
Sbjct: 484 GL 485


Lambda     K      H
   0.318    0.135    0.400 

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: 625
Number of extensions: 21
Number of successful extensions: 4
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: 523
Length of database: 487
Length adjustment: 34
Effective length of query: 489
Effective length of database: 453
Effective search space:   221517
Effective search space used:   221517
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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