GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Marinobacter adhaerens HP15

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF1118 HP15_1096 branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Marino:GFF1118
          Length = 237

 Score =  175 bits (444), Expect = 6e-49
 Identities = 92/227 (40%), Positives = 146/227 (64%), Gaps = 1/227 (0%)

Query: 2   SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61
           S+L+V+NL+  YG    + D+SF + +G+ +SL+G NG GKTT L+++ G+V P SG + 
Sbjct: 4   SLLEVKNLNTLYGRSHILHDLSFRLGKGQSMSLMGRNGMGKTTTLKSILGIVPPRSGHVH 63

Query: 62  FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFS 121
           F G++I K+P  K +   ++ VPEGR +F  LTV E+L+M A    N + +  + ++V  
Sbjct: 64  FDGEDISKLPTWKRMRRDIAYVPEGRGIFHNLTVKEHLQMAARPDSNGKTSW-DFERVMD 122

Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQD 181
            FPRL+ER +     LSGGEQQMLA+GRAL++ P+L++LDE + GLAP+   +I+ +I  
Sbjct: 123 TFPRLQERLSNLGTELSGGEQQMLAIGRALVTNPRLMILDEATEGLAPLIRADIWKVIAT 182

Query: 182 IQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEE 228
           I++ G + L++++N      + D   V+  GKI   G+ KEL  + E
Sbjct: 183 IRESGISTLVVDKNIKALKKLCDYHVVIVKGKIHFDGSSKELDENLE 229


Lambda     K      H
   0.315    0.134    0.358 

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: 137
Number of extensions: 3
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: 236
Length of database: 237
Length adjustment: 23
Effective length of query: 213
Effective length of database: 214
Effective search space:    45582
Effective search space used:    45582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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