GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudarthrobacter sulfonivorans Ar51

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>NCBI__GCF_001484605.1:WP_058929663.1
          Length = 345

 Score =  177 bits (450), Expect = 2e-49
 Identities = 100/249 (40%), Positives = 148/249 (59%), Gaps = 2/249 (0%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           I+  EN++  FGG+ AV+   L +   ++ ALIGPNGAGKTT+FN LTGF  P  G    
Sbjct: 38  IVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKWQF 97

Query: 65  DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124
           +G  + G+  + +AR G+VRTFQ  ++   +T +EN+ +             LFK   + 
Sbjct: 98  EGNSLAGISPYKVARMGMVRTFQLTKVMGKLTVMENMRLGGSEQPGERLSKALFK-GLWG 156

Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
             E+E    A   L+K  L    +  A +L+ GQ++ LE+AR +M RP+++MLDEP AG+
Sbjct: 157 GREKEITAQANVLLEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRPKLVMLDEPMAGV 216

Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244
           NP  T+ L   I  L+ E  +TVL +EHDM +V  I+D +VV+ +G  +A+G P ++  N
Sbjct: 217 NPALTQSLLDHIKNLKAE-GMTVLFVEHDMNMVRHIADWVVVMAEGKIVAEGPPGEVMKN 275

Query: 245 PEVIKAYLG 253
           P VI AYLG
Sbjct: 276 PAVIDAYLG 284


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: 248
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: 345
Length adjustment: 26
Effective length of query: 229
Effective length of database: 319
Effective search space:    73051
Effective search space used:    73051
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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