GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Croceitalea dokdonensis DOKDO 023

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_054558079.1 I595_RS03740 gliding motility-associated ABC transporter ATP-binding subunit GldA

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_001306415.1:WP_054558079.1
          Length = 297

 Score =  105 bits (262), Expect = 1e-27
 Identities = 69/225 (30%), Positives = 120/225 (53%), Gaps = 7/225 (3%)

Query: 4   LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63
           + V N++  +G  +A+ ++SF V++GE+V  +G NGAGK+T++R L+      SGK    
Sbjct: 3   ITVTNITKTFGAQKAINNISFSVDKGEIVGFLGPNGAGKSTMMRLLTTYYTADSGKAIVN 62

Query: 64  GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSRF 123
           G ++QK    K V   +  +PE   ++  + V E L   A L    ++   N+ ++    
Sbjct: 63  GFDVQK--DNKAVKKSIGYLPEHNPLYLEMYVREYLNFHANLHHAPKDRVRNVVELTGLV 120

Query: 124 PRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDIQ 183
           P   ++  Q    LS G +Q + +  AL+  P++L+LDEP+ GL P  + EI  +I++I 
Sbjct: 121 PEAHKKIGQ----LSKGYRQRVGLAAALLHDPEVLILDEPTTGLDPNQLIEIRKLIREIG 176

Query: 184 KQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEE 228
           K+  T+LL      +  A+ DR  ++  G++V      EL  +EE
Sbjct: 177 KE-KTILLSTHIMKEVEAVCDRVIIINKGEVVADKKLVELRKAEE 220


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: 155
Number of extensions: 8
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: 297
Length adjustment: 25
Effective length of query: 211
Effective length of database: 272
Effective search space:    57392
Effective search space used:    57392
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: 47 (22.7 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