GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Paraburkholderia phymatum STM815

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_000020045.1:WP_012402388.1
          Length = 594

 Score =  212 bits (539), Expect = 2e-59
 Identities = 112/252 (44%), Positives = 161/252 (63%), Gaps = 2/252 (0%)

Query: 5   SNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAG 64
           + E +L V    K+FGGL A++DV   +K GQ+ GLIGPNGAGK+T FN++TG+    +G
Sbjct: 342 TGEPLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSG 401

Query: 65  TFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRT 124
                G+  +     E+ K GI RTFQ+++L   MT LENV +G H+R  +G++ +V R 
Sbjct: 402 AITFRGERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGHLRGRAGVWRSVARL 461

Query: 125 KGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEP 184
            G  AEE  +   A   +  VG+ +    +A +L+ G QR LEIARAL  DP L+ LDEP
Sbjct: 462 NG--AEEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALCCDPTLLLLDEP 519

Query: 185 AAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244
           AAG+   EK QL  L+ ++R +  ++LL+EHD+  VM L DR+ V+++G +IAEG P +V
Sbjct: 520 AAGLRYQEKQQLATLLRKLREEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQDV 579

Query: 245 QKNEKVIEAYLG 256
           Q +  V+EAYLG
Sbjct: 580 QNDPAVLEAYLG 591


Lambda     K      H
   0.319    0.137    0.384 

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: 369
Number of extensions: 10
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: 260
Length of database: 594
Length adjustment: 31
Effective length of query: 229
Effective length of database: 563
Effective search space:   128927
Effective search space used:   128927
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: 50 (23.9 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