GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Escherichia coli BW25113

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 17272 b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Keio:17272
          Length = 241

 Score =  140 bits (352), Expect = 3e-38
 Identities = 80/239 (33%), Positives = 132/239 (55%), Gaps = 7/239 (2%)

Query: 1   MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60
           M+ L  +NL+  Y   + V DVS  VN GE+V L+G NGAGKTT    + G+V   +G I
Sbjct: 1   MATLTAKNLAKAYKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNI 60

Query: 61  EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENL----EMGAFLKKNREENQANL 116
                +I  +P       G+  +P+   +F  L+V +NL    ++   L   + E++AN 
Sbjct: 61  IIDDDDISLLPLHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLSAEQREDRAN- 119

Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176
            ++   F  +E  ++    +LSGGE++ + + RAL + PK +LLDEP  G+ PI + +I 
Sbjct: 120 -ELMEEF-HIEHLRDSMGQSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIK 177

Query: 177 DIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
            II+ ++  G  VL+ + N  + LA+ +R Y++  G ++  GT  E+   E V++ YLG
Sbjct: 178 RIIEHLRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPTEILQDEHVKRVYLG 236


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: 241
Length adjustment: 23
Effective length of query: 213
Effective length of database: 218
Effective search space:    46434
Effective search space used:    46434
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