GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Novosphingobium barchaimii LL02

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_059151353.1 V474_RS10060 aldehyde dehydrogenase family protein

Query= SwissProt::O34660
         (495 letters)



>NCBI__GCF_001046635.1:WP_059151353.1
          Length = 501

 Score =  451 bits (1159), Expect = e-131
 Identities = 231/475 (48%), Positives = 314/475 (66%), Gaps = 9/475 (1%)

Query: 22  LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81
           L I G++  +A+G TF T +PATG  L  + +A AADVD AV AAR A     W    PA
Sbjct: 25  LLIGGEWAQAANGGTFATLDPATGSELGQVAKAGAADVDAAVSAARAAL--AVWGATVPA 82

Query: 82  SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141
            R+R+++K+ADL+E +  +LA+LETLD GKP+      +IP A+   R++AG    I G 
Sbjct: 83  ERARILWKVADLIEANIDDLAELETLDQGKPLFVGRWAEIPGAVSQFRFFAGQAMAIEGS 142

Query: 142 TI-------PVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAE 194
           T+       P       +T  EPVGVV  I+PWN PL++   K+  ALA GCT+VLKPAE
Sbjct: 143 TLESSINYQPAGKQMRTWTVREPVGVVAAIVPWNSPLVLTAMKLAPALAAGCTVVLKPAE 202

Query: 195 QTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMS 254
            T L+AL L EL+ +AG PAGVINI+ G G + G AL  H  V KIAFTGST  G+ ++ 
Sbjct: 203 DTSLTALRLGELMIEAGVPAGVINIVTGLGGETGAALAAHPGVAKIAFTGSTATGRAVLD 262

Query: 255 TAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYD 314
            A  + KRVTLELGGKSP+I++PDA+L +AIPG  N + FN GQVC AGSR+++H+  +D
Sbjct: 263 AAKTNFKRVTLELGGKSPSIIMPDADLSQAIPGVANAIYFNGGQVCIAGSRLYVHRSVHD 322

Query: 315 EVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFE 374
           +VV+ +A YA+ L+ G GL  DTQ+GP+VS    ERV  ++Q+ + EGA  + GG    E
Sbjct: 323 QVVEGVAEYAKGLKLGHGLAADTQMGPVVSLRHAERVEGFLQRARAEGATMLAGGERTGE 382

Query: 375 AGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENV 434
           AG F+ PT+  +V+  M I +EE+FGPVL A  ++ V+EVI  AN SEYGLAA +WTE +
Sbjct: 383 AGTFITPTLVVDVKPGMEIVREEVFGPVLVAQAFDDVEEVIAAANDSEYGLAASVWTEGL 442

Query: 435 KQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSV 489
             AH ++  ++AGTVW+NC+ ++D     GG KQSG GR+ G  AL+NY E K++
Sbjct: 443 SNAHRMSSAIKAGTVWINCHAMYDPTLAIGGVKQSGWGRDSGRQALENYLEWKTI 497


Lambda     K      H
   0.316    0.133    0.391 

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: 646
Number of extensions: 21
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: 495
Length of database: 501
Length adjustment: 34
Effective length of query: 461
Effective length of database: 467
Effective search space:   215287
Effective search space used:   215287
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 (21.6 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