GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Dinoroseobacter shibae DFL-12

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate 3607835 Dshi_1243 short-chain dehydrogenase/reductase SDR (RefSeq)

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



>FitnessBrowser__Dino:3607835
          Length = 258

 Score =  218 bits (556), Expect = 8e-62
 Identities = 115/249 (46%), Positives = 156/249 (62%), Gaps = 5/249 (2%)

Query: 7   YPSLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVT 66
           +  L G ++F++GG +GIGA L + FL QGA+VAF+     +++  VA ++     A + 
Sbjct: 9   FHDLDGASVFVTGGGSGIGAALTDGFLAQGAQVAFIGR--SDASAFVAKMRAAHGRAPL- 65

Query: 67  FYHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHY 126
           F   D+ D  AL+  IAQ     GPI+ L+NNAA D+RHS  EVTPE+WDQ    NL+ Y
Sbjct: 66  FVQGDITDTDALRAAIAQATAAHGPITALVNNAANDKRHSTAEVTPEFWDQMQAINLKAY 125

Query: 127 FFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKI 186
           FFA QAV P M   GGG+++N  S+S+    AG   YTA+ AG  GLTR LA + G D I
Sbjct: 126 FFAAQAVTPGMAEAGGGAIVNFSSISYMMGNAGYPAYTAANAGITGLTRSLAREFGPDGI 185

Query: 187 RINTLTPGWVMTKRQLTHW-VDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCT 245
           R+N L PGWV+T +QL  W   +D A H++  QC+K ++ PEDI    LFLA+  SK+ T
Sbjct: 186 RVNALAPGWVLTPKQLEMWATPEDLAAHLD-RQCLKTHLAPEDIVEATLFLASGASKMMT 244

Query: 246 AQNFIVDGG 254
            Q  +VDGG
Sbjct: 245 GQCMVVDGG 253


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: 206
Number of extensions: 11
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: 256
Length of database: 258
Length adjustment: 24
Effective length of query: 232
Effective length of database: 234
Effective search space:    54288
Effective search space used:    54288
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 17 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