GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Mesorhizobium ciceri biovar biserrulae WSM1271

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_013529094.1 MESCI_RS06155 ATP-binding cassette domain-containing protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>NCBI__GCF_000185905.1:WP_013529094.1
          Length = 518

 Score =  261 bits (666), Expect = 3e-74
 Identities = 136/262 (51%), Positives = 182/262 (69%), Gaps = 9/262 (3%)

Query: 1   MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60
           M+  IL+V++LSM+FGGL+A+  ++   K  ++ ALIGPNGAGKTTVFNC+TGFY+P+ G
Sbjct: 13  MNDAILQVDHLSMKFGGLVAIGDLSFAAKRGEITALIGPNGAGKTTVFNCITGFYKPSEG 72

Query: 61  TILL---DGEP--IQGLPGHHI-ARKGVVRTFQNVRLFKDMTAVENLLIAQHRHL---NT 111
            I L   DG    ++ LP H I AR  V RTFQN+RLF  MT +ENLL+AQH  L   + 
Sbjct: 73  MITLNRNDGSTFLLERLPNHEIPARAKVARTFQNIRLFSGMTLLENLLVAQHNKLMKASG 132

Query: 112 NFFAGLFKTPAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTR 171
               GLF    +RK+  E++E A++WL+K +L + A+ PAG L YG QRRLEIAR M T 
Sbjct: 133 YTVLGLFGFSGYRKASAESVELAKHWLEKADLVDRADDPAGDLPYGAQRRLEIARAMCTG 192

Query: 172 PRILMLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGT 231
           P +L LDEPAAGLNPKE+  L  L+  ++     ++LLIEHDM +VM ISDH+VV+  G 
Sbjct: 193 PELLCLDEPAAGLNPKESAALNELLIDIKNTSGASILLIEHDMSVVMQISDHVVVLEYGR 252

Query: 232 PLADGTPEQIRDNPEVIKAYLG 253
            ++DG+P+ +R +P VI AYLG
Sbjct: 253 KISDGSPQSVRTDPRVIAAYLG 274


Lambda     K      H
   0.321    0.138    0.398 

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: 303
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: 518
Length adjustment: 29
Effective length of query: 226
Effective length of database: 489
Effective search space:   110514
Effective search space used:   110514
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: 49 (23.5 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