GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Shewanella amazonensis SB2B

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 6937839 Sama_1980 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= metacyc::MONOMER-16230
         (256 letters)



>FitnessBrowser__SB2B:6937839
          Length = 248

 Score =  138 bits (348), Expect = 9e-38
 Identities = 88/251 (35%), Positives = 138/251 (54%), Gaps = 10/251 (3%)

Query: 3   LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62
           L  K  +VTGASRGIG+A A   A  GA VV    G+     GA ++++ +   G     
Sbjct: 7   LTGKVALVTGASRGIGKAIALTLAEAGATVV----GTATSEKGAAAISDYL---GDKGFG 59

Query: 63  VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122
           +  +    +S  ++  A  E  G VD+LVNNAGI   +  + M  E + + + TNL   Y
Sbjct: 60  LVLNVTSSESVAEMYTAIKEKAGDVDILVNNAGITRDNLLMRMKDEEWEEIIDTNLTSLY 119

Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182
              +   R M ++ R G II++ S+   +G A Q +Y+  KAGL+   +S A  +    I
Sbjct: 120 RLSKPVMRSMMKK-RHGRIISIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVASRQI 178

Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242
             NA+ PG I TD+  E     E+++ + S+VP+ RLG+  ++A  ++FLASD A Y+TG
Sbjct: 179 TVNAIAPGFIQTDMTDELTP--EQQQGIMSQVPMERLGQAQEIANAVLFLASDAAAYITG 236

Query: 243 ASLLVDGGLFV 253
            +L V+GG+++
Sbjct: 237 ETLHVNGGMYM 247


Lambda     K      H
   0.319    0.136    0.383 

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: 166
Number of extensions: 10
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: 248
Length adjustment: 24
Effective length of query: 232
Effective length of database: 224
Effective search space:    51968
Effective search space used:    51968
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: 46 (22.3 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