GapMind for catabolism of small carbon sources

 

Alignments 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 208247 DVU2741 high-affinity branched chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>MicrobesOnline__882:208247
          Length = 255

 Score =  256 bits (655), Expect = 2e-73
 Identities = 134/255 (52%), Positives = 178/255 (69%), Gaps = 4/255 (1%)

Query: 1   MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60
           MALLE+K LT+ FGGL AV D  +EL  GEL GLIGPNGAGKTT+FNL +G Y P+EG++
Sbjct: 1   MALLEIKGLTQRFGGLQAVSDFNIELEAGELAGLIGPNGAGKTTVFNLTSGFYTPTEGSI 60

Query: 61  TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHK--QHVFTSFLRL 118
           T DG    G  P+++ +LG+ RTFQNIRL+ DL+VLDN+ IA   HH+    ++ +FLR 
Sbjct: 61  TFDGTPTRGLRPHQVTALGIARTFQNIRLWHDLSVLDNIRIA--QHHRLGYTLWDAFLRT 118

Query: 119 PAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEP 178
             +   EK + A A E+L+  DL   A  + +NL YG QRR+EI RA++ +PK+L LDEP
Sbjct: 119 RRYTAGEKAIDAIAWEMLEAMDLKEYANEVPRNLPYGMQRRVEIARAMSMKPKLLLLDEP 178

Query: 179 AAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238
           AAG+N  +   L  LIR I DEF ITI +IEH M +VM + +RI V+++G  IA GTP+ 
Sbjct: 179 AAGLNSVDVDGLIRLIRWIHDEFDITIWMIEHQMKVVMSLCQRIKVIDFGSTIADGTPET 238

Query: 239 IKTNKRVIEAYLGGE 253
           I+TN  VI+AYLG +
Sbjct: 239 IQTNPVVIKAYLGDD 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: 3
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: 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.

Links

Downloads

Related tools

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