GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Haloterrigena daqingensis JX313

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_076582356.1 BB347_RS07330 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_001971705.1:WP_076582356.1
          Length = 383

 Score =  112 bits (280), Expect = 1e-29
 Identities = 77/249 (30%), Positives = 136/249 (54%), Gaps = 28/249 (11%)

Query: 1   MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60
           M+ + ++ L   YG   AV DVS E+++GE++ L+G +G+GK+T LR L+GL  P+ G I
Sbjct: 1   MTDITLQGLEKRYGETTAVEDVSVEIDDGELLCLLGPSGSGKSTTLRMLAGLETPTEGAI 60

Query: 61  EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLK-----KNREENQAN 115
              G+++   PA        S V +   +FP  TV+EN+  G  ++     + RE  QA 
Sbjct: 61  RLDGEDVTDQPAYD---RNTSTVFQDWALFPHKTVLENVAFGLKMRDVSKDERRERAQAM 117

Query: 116 LKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGL-------A 168
           L++V     ++    ++D  TLSGG++Q +A+ R+L   P +LLLDEP   L        
Sbjct: 118 LERV-----QMGGYDDEDPTTLSGGQKQRVALARSLAVNPDVLLLDEPLSNLDKRLREDM 172

Query: 169 PIFIQEIFDIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEE 228
            I ++EI D +++      T + +  + ++A  ++DR  ++  G+++  G   E+  + +
Sbjct: 173 QIELREIHDDLEE------TFVHVTHDQDEAFTLADRIGIMNEGELIQVGDPDEVYENPK 226

Query: 229 VR--KAYLG 235
            R  +A+LG
Sbjct: 227 NRFIEAFLG 235


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: 178
Number of extensions: 8
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: 383
Length adjustment: 27
Effective length of query: 209
Effective length of database: 356
Effective search space:    74404
Effective search space used:    74404
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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