GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudarthrobacter sulfonivorans Ar51

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_058929111.1 AU252_RS00890 ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWL6
         (233 letters)



>NCBI__GCF_001484605.1:WP_058929111.1
          Length = 247

 Score =  152 bits (385), Expect = 4e-42
 Identities = 84/220 (38%), Positives = 131/220 (59%), Gaps = 2/220 (0%)

Query: 2   LQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYM 61
           L  + +S +YG+  A+  V+  V  G  V ++G NGAGK+TLL+ L G     +GS  + 
Sbjct: 11  LAVDRMSAYYGQAVAVRDVSFSVPVGASVGILGPNGAGKTTLLLALAGHLPI-TGSYSFN 69

Query: 62  GEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENL-AMGGFFTDKGDYQEQMDKVLHLF 120
           G +      S + R+ +A+VP+   V A +T+E NL A     T    +   M +VL LF
Sbjct: 70  GVKRRQHRPSTLRRRGVALVPQTHAVIAEMTIERNLRAAWSTGTKDTSFANAMGEVLELF 129

Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180
           P L+ R  +  G +SGG++QMLA+GR L+S+P++L+LDEP+ GL+P ++ ++ + +  LR
Sbjct: 130 PALRGRAAELAGNLSGGQRQMLAVGRGLISRPRVLMLDEPTAGLSPKLVNELVEALITLR 189

Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEAL 220
             G+TV LVEQN + A +  DR +VL +G +   G  E L
Sbjct: 190 GSGLTVLLVEQNFSAAQRACDRLHVLRDGTIRWSGAAEDL 229


Lambda     K      H
   0.320    0.137    0.381 

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: 149
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: 233
Length of database: 247
Length adjustment: 23
Effective length of query: 210
Effective length of database: 224
Effective search space:    47040
Effective search space used:    47040
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: 46 (22.3 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