GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 8500845 DvMF_1583 ABC transporter related (RefSeq)

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__Miya:8500845
          Length = 240

 Score =  209 bits (531), Expect = 5e-59
 Identities = 111/253 (43%), Positives = 165/253 (65%), Gaps = 16/253 (6%)

Query: 1   MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60
           M++LE+++L+  FGGL A+ DV  ++ +GE++ LIGPNGAGKTTLFN + G Y PSEG V
Sbjct: 1   MSMLEIRKLSMFFGGLAALHDVNFDVRQGEILALIGPNGAGKTTLFNCVNGFYTPSEGQV 60

Query: 61  TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120
              G  ++G  P+K+  +G+ RTFQ ++    ++V DNVL            ++FLR P 
Sbjct: 61  LFKGQPISGLKPHKVCQMGIARTFQVVKPLSRMSVFDNVLA-----------SAFLRNP- 108

Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180
              + K  +  A E+L    L  D + L+K L  G+++RLEI RALAT+P+ L LDE  A
Sbjct: 109 ---TRKGAQDVADEVLHFTGLWDDRDQLSKGLPLGKRKRLEIARALATQPEFLLLDESFA 165

Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240
           G+NP E     ++IR IK +  IT+M+IEH M ++M +++RI VL +G+ IA+GTP +I 
Sbjct: 166 GLNPAELDVSIDIIRGIKQQ-GITVMIIEHHMKVIMAISDRIVVLNFGQKIAEGTPAQIS 224

Query: 241 TNKRVIEAYLGGE 253
            +++V+EAYLG E
Sbjct: 225 ADRQVVEAYLGEE 237


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: 145
Number of extensions: 4
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: 254
Length of database: 240
Length adjustment: 24
Effective length of query: 230
Effective length of database: 216
Effective search space:    49680
Effective search space used:    49680
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: 46 (22.3 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 (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