GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Lactobacillus silagei IWT126

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_089137090.1 CES79_RS10020 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_002217945.1:WP_089137090.1
          Length = 236

 Score =  140 bits (353), Expect = 2e-38
 Identities = 85/253 (33%), Positives = 145/253 (57%), Gaps = 18/253 (7%)

Query: 1   MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60
           M +LEVK L  ++G + AV  V+  +N+GE+V LIG NGAGKTT+   ++G+ +P  GT+
Sbjct: 1   MTMLEVKDLAVNYGVINAVKGVSFHINKGEIVSLIGANGAGKTTILKTISGLLKPVSGTI 60

Query: 61  TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLI-AFGNHHKQHVFTSFLRLP 119
           T +G  +      KI + G+ +  +   +F  ++V +N+ + AF  ++   + +SF  + 
Sbjct: 61  TYEGKTIQKHKAPKIVAAGISQVPEGRHIFAGMSVRENLQMGAFLQNNHAEITSSFETVY 120

Query: 120 AFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPA 179
           + +   KE             ++ DA T    LS G+Q+ L + RAL ++PK+L LDEP+
Sbjct: 121 SRFPVLKE------------RINQDAAT----LSGGEQQMLAMGRALMSKPKLLLLDEPS 164

Query: 180 AGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239
            G+ P    E+ E+++ IK++   T++LIE +    + + +R YVL  G++   GT  E+
Sbjct: 165 MGLAPIFINEIFEIVKAIKEQ-GTTVLLIEQNAKKALSIADRGYVLASGKVKMTGTGQEL 223

Query: 240 KTNKRVIEAYLGG 252
             N+ V +AYLGG
Sbjct: 224 LANQDVQKAYLGG 236


Lambda     K      H
   0.319    0.139    0.385 

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: 135
Number of extensions: 6
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: 254
Length of database: 236
Length adjustment: 24
Effective length of query: 230
Effective length of database: 212
Effective search space:    48760
Effective search space used:    48760
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 (21.7 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