GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Paraburkholderia bryophila 376MFSha3.1

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate H281DRAFT_01586 H281DRAFT_01586 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__Burk376:H281DRAFT_01586
          Length = 269

 Score =  154 bits (389), Expect = 2e-42
 Identities = 99/258 (38%), Positives = 142/258 (55%), Gaps = 16/258 (6%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL V  L   FGGL AV+DVSF+   G++ A++GPNGAGK+T FN + G  +P+ G +  
Sbjct: 3   LLHVSGLCKSFGGLKAVDDVSFTLEAGQLLALLGPNGAGKSTCFNMVNGQLSPSSGSIRF 62

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              DG E +  R    R   +  V RTFQ    F  M+VLEN+ +A  ++  +  G    
Sbjct: 63  ---DGHELVGMRP---RDIWRLGVGRTFQIAATFNSMTVLENVQMALVSRERKTFG---- 112

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
             +  P+ +R   EA  L    L++V +   A+   G L YG  +R+E+A A+   P +L
Sbjct: 113 --VWKPAASRYADEAFAL----LEQVGMAADANRACGVLAYGDVKRVELAIALANRPKLL 166

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            +DEP AG+ P+E  EL  L   +  E KIGVL  EH M VV   +D ++VL  G+ I++
Sbjct: 167 LMDEPTAGMAPKERNELMALTKRLVTEQKIGVLFTEHSMDVVFAYADRMIVLARGKLIAE 226

Query: 251 GDPAFVKNDPAVIRAYLG 268
           GD   ++NDP V   Y G
Sbjct: 227 GDGDTIRNDPRVQEVYFG 244


Lambda     K      H
   0.319    0.137    0.397 

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: 177
Number of extensions: 9
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: 294
Length of database: 269
Length adjustment: 26
Effective length of query: 268
Effective length of database: 243
Effective search space:    65124
Effective search space used:    65124
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: 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 (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