GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Desulfovibrio vulgaris Hildenborough

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 206140 DVU0715 branched-chain amino acid ABC transporter, ATP binding protein

Query= uniprot:D8J1T6
         (255 letters)



>lcl|MicrobesOnline__882:206140 DVU0715 branched-chain amino acid
           ABC transporter, ATP binding protein
          Length = 255

 Score =  248 bits (632), Expect = 1e-70
 Identities = 125/250 (50%), Positives = 168/250 (67%)

Query: 4   TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63
           +LL +R+++K FGGL A+N V   ++ G I GLIGPNGAGKTT FN+ITG Y+PD+G   
Sbjct: 2   SLLSLRNLTKTFGGLVAVNSVSFDVDEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDIF 61

Query: 64  LDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAA 123
            DG+       H + + GIARTFQ IRLF  M+V+ENV+ GCH R    VF A+      
Sbjct: 62  FDGRAIKGLLTHRIVQMGIARTFQTIRLFQNMSVMENVLAGCHCRMTAGVFSAMLGTAGH 121

Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183
           R EE    E++ + L+FVG+       A++LSYG+QR LEIARALATDP+ + LDEPA G
Sbjct: 122 RREEKRAIERAVRELEFVGLADQHDNLAKNLSYGNQRLLEIARALATDPRFIILDEPAGG 181

Query: 184 MNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243
           MN  E   L   +  I+  G ++LLIEHD+ L+M +C ++ VL+YG  IAEG P+ ++++
Sbjct: 182 MNDQETAALIGTIRAIRDRGISVLLIEHDMSLVMKVCEKLVVLEYGALIAEGTPSVIKRD 241

Query: 244 PAVIEAYLGA 253
           P VIEAYLGA
Sbjct: 242 PRVIEAYLGA 251


Lambda     K      H
   0.320    0.138    0.394 

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: 196
Number of extensions: 4
Number of successful extensions: 1
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: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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