GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Geobacter daltonii FRC-32

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_012647880.1 GEOB_RS13900 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_000022265.1:WP_012647880.1
          Length = 247

 Score =  256 bits (653), Expect = 4e-73
 Identities = 123/238 (51%), Positives = 185/238 (77%), Gaps = 5/238 (2%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +L+++N++ +YG + A+++VS  + +GE+V+LIGANGAGKTTIL T+SG+   + G+I F
Sbjct: 1   MLRLKNINTYYGKVHALKNVSIHLGQGEIVTLIGANGAGKTTILNTISGVTPAAGGEILF 60

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLK----K 118
             + +Q +   +IV  G++QVPEGR VF  L+V +NL++GA+L+  + E ++ ++    +
Sbjct: 61  EKEPVQALSPDRIVRLGIAQVPEGRQVFKPLSVEDNLDLGAYLRHRQREAKSRIRQDKQE 120

Query: 119 VFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDI 178
           +F+ FPRLEER+ Q A TLSGGEQQMLA+GRA+M+ PKL+LLDEPSMGLAP+ +QEIF +
Sbjct: 121 IFTLFPRLEERRKQPAGTLSGGEQQMLAIGRAMMTRPKLMLLDEPSMGLAPLVVQEIFRV 180

Query: 179 IQDIQKQ-GTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
           I ++++Q GTT+LL+EQNA  AL ++DRGYVLETGK++L G    L  +++V++AYLG
Sbjct: 181 IDNLRRQHGTTILLVEQNAKAALNLADRGYVLETGKVILEGLSSNLLENKDVQRAYLG 238


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: 201
Number of extensions: 10
Number of successful extensions: 3
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: 247
Length adjustment: 23
Effective length of query: 213
Effective length of database: 224
Effective search space:    47712
Effective search space used:    47712
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 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