GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Collimonas arenae Ter10

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_061534737.1 CAter10_RS19525 branched-chain amino acid ABC transporter ATP-binding protein/permease

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_001584165.1:WP_061534737.1
          Length = 601

 Score =  205 bits (522), Expect = 2e-57
 Identities = 111/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 7   EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66
           +VVL++    K FGGL A++D+   ++ GQ+ GLIGPNGAGK+T FN++TG+    +GT 
Sbjct: 342 DVVLEIENARKEFGGLVAVNDISFNVRAGQIVGLIGPNGAGKSTMFNLVTGVLPLTSGTI 401

Query: 67  ---------ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTG--- 114
                    +++G P       ++   GIARTFQ++RL   MT LENV +G H+R     
Sbjct: 402 RFRAQRELQQISGLPSR-----QIVARGIARTFQHVRLMPAMTVLENVAIGAHLRGSHND 456

Query: 115 -SGLFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALA 173
            +G+  ++ R    + EE A+   A++ L+ VG+G     +A +L+ G QR LEIARAL 
Sbjct: 457 VNGIAVSLLRLN--RNEERALLFEAKQQLERVGLGHLLYEEAGSLALGQQRILEIARALC 514

Query: 174 TDPQLIALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYG 233
            DP L+ LDEPAAG+   EK  L EL+ +++ +  +ILL+EHD+  VM L D++ V+++G
Sbjct: 515 CDPTLLLLDEPAAGLRYQEKQALAELLRKLKAEGMSILLVEHDMDFVMNLTDQLVVMEFG 574

Query: 234 KQIAEGNPAEVQKNEKVIEAYLG 256
            +IA+G PAE+Q++  V+EAYLG
Sbjct: 575 TKIAQGLPAEIQQDPAVLEAYLG 597


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: 377
Number of extensions: 19
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: 260
Length of database: 601
Length adjustment: 31
Effective length of query: 229
Effective length of database: 570
Effective search space:   130530
Effective search space used:   130530
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 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