GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Marinobacter adhaerens HP15

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1118 HP15_1096 branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Marino:GFF1118
          Length = 237

 Score =  172 bits (435), Expect = 7e-48
 Identities = 98/226 (43%), Positives = 140/226 (61%), Gaps = 1/226 (0%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           LL+V  + T YG    L  +   + KG+ +SL+G NG GK+T + +I G    R+G V F
Sbjct: 5   LLEVKNLNTLYGRSHILHDLSFRLGKGQSMSLMGRNGMGKTTTLKSILGIVPPRSGHVHF 64

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLF 130
           +G DI+++PT +  R  IA  PEGR IF  +TV E+LQM A  D+    + D E++   F
Sbjct: 65  DGEDISKLPTWKRMRRDIAYVPEGRGIFHNLTVKEHLQMAARPDSNGKTSWDFERVMDTF 124

Query: 131 PRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLN 190
           PRL+ER +  G  LSGGEQQML+IGRAL+  P+L++LDE + GLAPLI   I++ I  + 
Sbjct: 125 PRLQERLSNLGTELSGGEQQMLAIGRALVTNPRLMILDEATEGLAPLIRADIWKVIATIR 184

Query: 191 EAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236
           E+ G++  +V++N  A  +L     V+V GK+   GS KEL  N E
Sbjct: 185 ES-GISTLVVDKNIKALKKLCDYHVVIVKGKIHFDGSSKELDENLE 229


Lambda     K      H
   0.320    0.137    0.387 

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: 154
Number of extensions: 7
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: 247
Length of database: 237
Length adjustment: 23
Effective length of query: 224
Effective length of database: 214
Effective search space:    47936
Effective search space used:    47936
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