GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Desulfovibrio vulgaris Hildenborough

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate 207079 DVU1627 ABC transporter, ATP-binding protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>MicrobesOnline__882:207079
          Length = 241

 Score =  161 bits (407), Expect = 1e-44
 Identities = 96/250 (38%), Positives = 145/250 (58%), Gaps = 18/250 (7%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           +L+ E+L  RFG    V GV+++V++ ++V L+GPNGAGKTT F  LTG  +PT G + L
Sbjct: 4   VLQGEDLRKRFGQREVVRGVSVSVQQGEIVGLLGPNGAGKTTTFYMLTGIIKPTAGIVRL 63

Query: 65  DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENL-LIAQHRHLNTNFFAGLFKTPAF 123
           DG+ I   P H  AR G+    Q   +FK +T  ENL +I +H  L           PA 
Sbjct: 64  DGQDIADWPLHERARVGLSYLPQESSVFKRLTVRENLEIILEHTGL-----------PAA 112

Query: 124 RKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
           R+ ER     AE  +    +   A+  A  L+ G++RRLEIARCM+  P+ ++LDEP AG
Sbjct: 113 RQKER-----AEALMADFGIAHLASSRAMHLSGGERRRLEIARCMIREPKFVLLDEPFAG 167

Query: 184 LNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243
           ++P    D++ LI  LR +  + VL+ +H+++  ++I D   +++QG  + DGTPE I  
Sbjct: 168 IDPLAVGDIQGLIRKLR-DRGIGVLISDHNVRETLTICDRAYLVHQGQVILDGTPEHIVG 226

Query: 244 NPEVIKAYLG 253
           + +    YLG
Sbjct: 227 DEQARLVYLG 236


Lambda     K      H
   0.321    0.138    0.398 

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: 198
Number of extensions: 10
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: 255
Length of database: 241
Length adjustment: 24
Effective length of query: 231
Effective length of database: 217
Effective search space:    50127
Effective search space used:    50127
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 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