GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Herbaspirillum seropedicae SmR1

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS08285 HSERO_RS08285 amino acid ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__HerbieS:HSERO_RS08285
          Length = 258

 Score =  263 bits (671), Expect = 4e-75
 Identities = 137/260 (52%), Positives = 188/260 (72%), Gaps = 9/260 (3%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           +L V +L+MRFGGL+AV+ VS +    E+ AIIGPNGAGKTT+FNCI+GFY PT G + L
Sbjct: 8   MLEVSNLSMRFGGLLAVDGVSLAVQEREVFAIIGPNGAGKTTVFNCISGFYRPTSGEIML 67

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
             A      + R P ++++Q+  V RTFQNIRLF  M+V+ENL+VAQH ++   +   ++
Sbjct: 68  DGAS-----IARQPSHQVAQQGLV-RTFQNIRLFKSMTVVENLLVAQHQQV---NTNLLS 118

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
           GLL  P+Y ++E+EA+  A YWLD++ L   A+ EAG L YG QRR+EIAR M T+P +L
Sbjct: 119 GLLKTPAYRKSEQEALQRAAYWLDQLGLTALANREAGTLSYGLQRRVEIARCMITKPRLL 178

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            LDEPAAGLNP+E  EL+ L+  +R EH + VLLIEHDMS++M ISD ++V+++G+ I  
Sbjct: 179 LLDEPAAGLNPQEKQELSQLIDRLRREHGVAVLLIEHDMSLIMGISDRILVMEHGKPIVT 238

Query: 251 GDPAFVKNDPAVIRAYLGEE 270
           G P  V++D  VI+AYLGEE
Sbjct: 239 GTPEQVRSDERVIKAYLGEE 258


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: 205
Number of extensions: 5
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: 258
Length adjustment: 25
Effective length of query: 269
Effective length of database: 233
Effective search space:    62677
Effective search space used:    62677
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