GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Desulfovibrio vulgaris Hildenborough

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 206140 DVU0715 branched-chain amino acid ABC transporter, ATP binding protein

Query= TCDB::Q8DQH8
         (254 letters)



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

 Score =  251 bits (641), Expect = 1e-71
 Identities = 130/254 (51%), Positives = 175/254 (68%), Gaps = 1/254 (0%)

Query: 1   MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60
           M+LL ++ LTK FGGL AV  V+ +++EG +VGLIGPNGAGKTT+FNL+TG Y+P  G +
Sbjct: 1   MSLLSLRNLTKTFGGLVAVNSVSFDVDEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDI 60

Query: 61  TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120
             DG  + G   ++I  +G+ RTFQ IRLF++++V++NVL          VF++ L    
Sbjct: 61  FFDGRAIKGLLTHRIVQMGIARTFQTIRLFQNMSVMENVLAGCHCRMTAGVFSAMLGTAG 120

Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180
             + EK    +A+  L+   L    + LAKNLSYG QR LEI RALAT+P+ + LDEPA 
Sbjct: 121 HRREEKRAIERAVRELEFVGLADQHDNLAKNLSYGNQRLLEIARALATDPRFIILDEPAG 180

Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240
           GMN QETA L   IR I+D   I+++LIEHDM+LVM+V E++ VLEYG LIA+GTP  IK
Sbjct: 181 GMNDQETAALIGTIRAIRDR-GISVLLIEHDMSLVMKVCEKLVVLEYGALIAEGTPSVIK 239

Query: 241 TNKRVIEAYLGGEA 254
            + RVIEAYLG ++
Sbjct: 240 RDPRVIEAYLGADS 253


Lambda     K      H
   0.319    0.139    0.385 

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: 184
Number of extensions: 7
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: 254
Length of database: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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: 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