GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Vagococcus penaei CD276

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_077274914.1 BW732_RS00300 D-threitol dehydrogenase

Query= reanno::ANA3:7024897
         (256 letters)



>NCBI__GCF_001998885.1:WP_077274914.1
          Length = 254

 Score =  114 bits (284), Expect = 3e-30
 Identities = 73/249 (29%), Positives = 132/249 (53%), Gaps = 12/249 (4%)

Query: 10  LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYH 69
           L+ K   I+GG +GIG+ +   ++++GAK+A  DI   ++ +LV +   T+   ++ F  
Sbjct: 12  LENKVAIITGGLSGIGSAIGELYVKKGAKLAIFDIN-PDTPELVEEQFGTK---AIGF-- 65

Query: 70  CDLVDIAALKRVIAQVEDDLG---PISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHY 126
              VD+ + ++V+  V++ +     I +L+N+A        + ++   WD   N N++  
Sbjct: 66  --AVDVTSKEQVMNAVKETMNHFKKIDILVNSAGVCFLDDAENLSETEWDLTFNINVKGS 123

Query: 127 FFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKI 186
           F   QAV  +M + GGG +IN+ S +          Y ASK   + +T+ LA +  +  I
Sbjct: 124 FLVAQAVGNEMIQSGGGKIINMASQAALVALDNHVAYAASKGAILSMTKVLAYEWAQYSI 183

Query: 187 RINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTA 246
            +N L+P  V+T+     W  +   + ++    I  +  PE++AA ALFLA+D S L T 
Sbjct: 184 NVNCLSPTIVLTELGKKAWAGQ-VGEDMKQQIPIGRFGYPEEVAASALFLASDASNLMTG 242

Query: 247 QNFIVDGGW 255
           +N ++DGG+
Sbjct: 243 ENMVIDGGY 251


Lambda     K      H
   0.320    0.134    0.406 

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: 157
Number of extensions: 11
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: 256
Length of database: 254
Length adjustment: 24
Effective length of query: 232
Effective length of database: 230
Effective search space:    53360
Effective search space used:    53360
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