GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Dechlorosoma suillum PS

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__PS:Dsui_0628
          Length = 358

 Score =  414 bits (1063), Expect = e-120
 Identities = 209/345 (60%), Positives = 261/345 (75%), Gaps = 16/345 (4%)

Query: 13  VALLVLPLILQS-FGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           + L VLP ++ +  GNAW+RI + A+LY++LALGLNIVVG+AGLLDLGY+AFYAVGAYL+
Sbjct: 22  IVLAVLPFLVGAGLGNAWLRILNFAMLYIMLALGLNIVVGFAGLLDLGYIAFYAVGAYLY 81

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           AL+ASPH              GLH  +W ++P+ A++A   GA+LGAPTL+LRGDYLAIV
Sbjct: 82  ALLASPHF-------------GLHWPVWAILPLGAVVAGGAGALLGAPTLRLRGDYLAIV 128

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYY 191
           TLGFGEIIRIF+NNL+ PVN+TNGP+G+  ID   V G+ L K L V G  + S+  YYY
Sbjct: 129 TLGFGEIIRIFMNNLNAPVNITNGPQGISSIDPFHVGGVTLAKPLSVLGVTVPSLHAYYY 188

Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251
           LFL+L +V + +  RL+DSRIGRAW+AIREDEIAAKA GIN RN+KLLAF MGA+FGGV+
Sbjct: 189 LFLLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSMGATFGGVA 248

Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311
           G +F +FQGFVSPESF LMES+M++ MVVLGG+GHIPGVILG +LL+ LPE  R+ A PL
Sbjct: 249 GGLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEAFRHAAVPL 308

Query: 312 QAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEHGKSL 354
           Q    G+  +D   LR LL  LA+I +ML RP GLWPS    + L
Sbjct: 309 QKYAFGKVVVDPESLRMLLFGLALIAVMLYRPAGLWPSATRKREL 353


Lambda     K      H
   0.328    0.144    0.430 

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: 469
Number of extensions: 22
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 358
Length adjustment: 29
Effective length of query: 329
Effective length of database: 329
Effective search space:   108241
Effective search space used:   108241
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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