GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Streptococcus oralis 7747

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_000590982.1 HK29_RS06510 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_000382825.1:WP_000590982.1
          Length = 247

 Score =  120 bits (300), Expect = 3e-32
 Identities = 74/226 (32%), Positives = 128/226 (56%), Gaps = 5/226 (2%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           ++K+ NLS  +     +  ++ ++ +GEVV+LIG++GAGK+T LR+L+ L  P SG I+ 
Sbjct: 1   MIKISNLSKSFSGQTVLDHLNLDIQKGEVVALIGSSGAGKSTFLRSLNYLETPDSGSIQI 60

Query: 63  --LGQEIQKMPAQKIVA--GGLSQVPEGRHVFPGLTVMENLEMG-AFLKKNREENQANLK 117
                +  K+  ++I+A    LS V +  ++F   T ++N++ G   +KK  ++    + 
Sbjct: 61  DDFSVDFSKITQEEILALRRKLSMVFQQFNLFERRTALDNVKEGLVVVKKLSDQEATKIA 120

Query: 118 KVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFD 177
           K       L +R+N     LSGG++Q +A+ RAL   P +LLLDEP+  L P  + E+  
Sbjct: 121 KEELAKVGLSDRENHYPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK 180

Query: 178 IIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223
            I D  K G T++L+  + +    ++D+   L+ GKI+ SGT  E+
Sbjct: 181 SIADAAKSGQTMILVSHDMSFVAQVADKILFLDKGKIIESGTPDEI 226


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: 123
Number of extensions: 6
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: 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