GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PS:Dsui_0628 Dsui_0628 ABC-type branched-chain
           amino acid transport system, permease component
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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