GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3610347 Dshi_3728 ABC transporter related (RefSeq)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Dino:3610347
          Length = 236

 Score =  204 bits (520), Expect = 9e-58
 Identities = 104/227 (45%), Positives = 150/227 (66%), Gaps = 1/227 (0%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +L +ENL  HYG+   ++ VS +V  GE++ + G NG GKTT+L+ ++G V+PSSG I  
Sbjct: 5   MLSIENLHSHYGLSHVIQGVSLDVGRGEILGVFGRNGVGKTTLLKNIAGWVKPSSGSIRM 64

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122
            G++I       I   GL+ VPE R +FPGLTV ENLE+G    K  +  ++ L  V  R
Sbjct: 65  DGKQIGGDEPDAINRAGLAIVPEDRRIFPGLTVQENLELGLLGLKGPKP-RSKLDPVLER 123

Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182
           FPRL ER  Q A TLSGGEQQMLAM R +++ P+ +L+DEPS GLAP+ + EIF I++++
Sbjct: 124 FPRLAERAQQPATTLSGGEQQMLAMARIMVAEPRAVLIDEPSEGLAPMIVAEIFAILREM 183

Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEV 229
           +  G  ++L+EQN ++AL+I DR  ++E G IV  G   + A+ EE+
Sbjct: 184 KDAGCAIVLVEQNIHEALSICDRFVLVERGAIVFEGNAGDKAAEEEL 230


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: 149
Number of extensions: 4
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: 236
Length adjustment: 23
Effective length of query: 213
Effective length of database: 213
Effective search space:    45369
Effective search space used:    45369
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