GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pandoraea thiooxydans ATSB16

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_047214213.1 PATSB16_RS11230 glucose 1-dehydrogenase

Query= reanno::acidovorax_3H11:Ac3H11_614
         (280 letters)



>NCBI__GCF_001931675.1:WP_047214213.1
          Length = 255

 Score = 85.9 bits (211), Expect = 8e-22
 Identities = 76/241 (31%), Positives = 108/241 (44%), Gaps = 6/241 (2%)

Query: 41  VTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPWWRVC--DVRDV 98
           VTG   GIG AI    A++GA++   D  R+ ++A  Q +A          V   +V  V
Sbjct: 10  VTGSAQGIGRAIAVRLAQEGAKIVVED--RQDADAAEQTLAQVRAAGSDGCVIAGNVGSV 67

Query: 99  QALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINERPAFFAIQAVV 158
              +  +  A A+LG    VLVNN   +       V+   YD  + +N + AFF  QAVV
Sbjct: 68  HDARGVVDAAVAKLGR-IDVLVNNAGVERNAPFLEVSEADYDLVLDVNLKGAFFMTQAVV 126

Query: 159 PGMRRLGAGS-VINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQDRIRINTVSP 217
             +R    G  ++N+ S   +     +  Y  +K  +  + R LA  L    I +N V+P
Sbjct: 127 RHLRDSHRGGRIVNISSVHEELPFPHFTSYCASKGGMKMMVRNLAIELAPLGITVNNVAP 186

Query: 218 GWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAMCTAQEFKVDA 277
           G V T    KL  D      L  N  L    +  D+A  VLFLASD+A+  T     VD 
Sbjct: 187 GAVGTAINNKLLHDPAELSALLANIPLKRLGKVEDVANAVLFLASDEASYVTGTTVYVDG 246

Query: 278 G 278
           G
Sbjct: 247 G 247


Lambda     K      H
   0.320    0.133    0.405 

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: 138
Number of extensions: 4
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: 280
Length of database: 255
Length adjustment: 25
Effective length of query: 255
Effective length of database: 230
Effective search space:    58650
Effective search space used:    58650
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: 47 (22.7 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