GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Arcobacter nitrofigilis DSM 7299

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_013134865.1 ARNIT_RS05295 urea ABC transporter ATP-binding protein UrtD

Query= TCDB::P0A9S7
         (255 letters)



>NCBI__GCF_000092245.1:WP_013134865.1
          Length = 262

 Score =  141 bits (355), Expect = 2e-38
 Identities = 81/251 (32%), Positives = 146/251 (58%), Gaps = 10/251 (3%)

Query: 5   LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64
           +L V+G+ + F G  A+NN++  +   E+  +IG NGAGK+T+ + +TG  +P  G ++ 
Sbjct: 21  ILLVDGVSVSFDGFKALNNLSFSINYGELRCIIGANGAGKSTMMDVVTGKTRPDEGEVIF 80

Query: 65  RDQ-HLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSF 123
            +  +L  L    I+ +G+ R FQ   +F+  +V ENL +A     +        KT  F
Sbjct: 81  GEAVNLLELDEPTISEIGIGRKFQKPTVFQNHSVFENLELAMKDDKR------FFKT-LF 133

Query: 124 RRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAG 183
            + +SE  DR    ++ IGL E  N  A  L++G ++ LEI   ++ +P++L++DEP AG
Sbjct: 134 SKLRSEQKDRIEETMKLIGLKELYNLDAGILSHGQKQWLEIGMLIMQEPKLLLVDEPVAG 193

Query: 184 LNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRN 243
           + P+E ++  E++  L   +   ++++EHDM+ +  I+ ++ V+++G+ LA G  + I+N
Sbjct: 194 MTPQEVEKTAEILTSLSKEN--AVVVVEHDMEFIRSIASKVTVLHEGSVLAEGNMDAIQN 251

Query: 244 NPDVIRAYLGE 254
           N  V + YLGE
Sbjct: 252 NEKVRKVYLGE 262


Lambda     K      H
   0.320    0.137    0.395 

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: 168
Number of extensions: 9
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: 255
Length of database: 262
Length adjustment: 24
Effective length of query: 231
Effective length of database: 238
Effective search space:    54978
Effective search space used:    54978
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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