GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Megamonas funiformis YIT 11815

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_008538445.1 HMPREF9454_RS05535 SDR family oxidoreductase

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



>NCBI__GCF_000245775.1:WP_008538445.1
          Length = 271

 Score = 84.3 bits (207), Expect = 3e-21
 Identities = 77/278 (27%), Positives = 118/278 (42%), Gaps = 47/278 (16%)

Query: 33  SLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPWWRV 92
           +L+G+   VTGG SGIG A+V AF + GA V   D+  +  E      +   L  P    
Sbjct: 5   ALEGKTAVVTGGASGIGKAVVQAFLDNGANVVVCDMNPQTPEYDLHEGSGEFLYVP---- 60

Query: 93  CDVRDVQALQACMADAAAELGSDFAVLVNN---------VASDDRHTLESVTPEYYDERM 143
            DV    +++A +    A+ G    +LVNN         V  DD +    +    +D+  
Sbjct: 61  TDVTKADSVKAMVEAGKAKFGK-LDILVNNAGINIPRLLVDKDDPYGKYELDENVFDKVS 119

Query: 144 AINERPAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAK 203
           A+N +  +   QA+     + G G +IN+ S        G   YA  K++VN  TR  AK
Sbjct: 120 AVNIKGVYLCAQALGHEFVKNGEGVIINMSSESGLEGSEGQSIYAATKNAVNSFTRSWAK 179

Query: 204 TLGQDRIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLP-------DKLRP------ 250
            LG+  +R+  V+PG           L+A G + LA  + L        ++LR       
Sbjct: 180 ELGKHHVRVVGVAPG----------ILEATGLRTLAYEESLAYTRGITVEQLRAGYTNTK 229

Query: 251 ----------HDIARMVLFLASDDAAMCTAQEFKVDAG 278
                      ++A MV+FL+S  A+      F V  G
Sbjct: 230 TTPLGRDGKLTEVADMVMFLSSHRASYVHGVTFNVAGG 267


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: 144
Number of extensions: 6
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: 271
Length adjustment: 25
Effective length of query: 255
Effective length of database: 246
Effective search space:    62730
Effective search space used:    62730
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