GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Planococcus halocryophilus Or1

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_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= TCDB::P0A9S7
         (255 letters)



>NCBI__GCF_000342445.1:WP_008497300.1
          Length = 310

 Score =  121 bits (303), Expect = 2e-32
 Identities = 73/238 (30%), Positives = 123/238 (51%), Gaps = 17/238 (7%)

Query: 5   LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64
           +L    L  +F   LAV+ V +EL   E V L+GPNGAGK+T  + ++   +PT G + L
Sbjct: 1   MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60

Query: 65  RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFR 124
             + +   PG+    +GVV   Q + L+ E++  ENL            F G +   S +
Sbjct: 61  NGKSVLKKPGEMRKVLGVVP--QKIALYEELSAYENLK-----------FFGRIYGLSGK 107

Query: 125 RAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGL 184
           + +    +R    LE +GL +         + G QRR+ +A  M+ +PE+L++DEP  G+
Sbjct: 108 KLE----ERIQIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGI 163

Query: 185 NPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIR 242
           +P+    L E I +L      T+L   H M+ V  + DR+Y+++ G  +A GT ++++
Sbjct: 164 DPQSRNHLLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDELK 221


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: 190
Number of extensions: 9
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: 255
Length of database: 310
Length adjustment: 26
Effective length of query: 229
Effective length of database: 284
Effective search space:    65036
Effective search space used:    65036
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 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