GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00885 in Dechlorosoma suillum PS

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component

Query= uniprot:D8IUY4
         (309 letters)



>lcl|FitnessBrowser__PS:Dsui_2060 Dsui_2060 branched-chain amino
           acid ABC-type transport system, permease component
          Length = 293

 Score =  195 bits (495), Expect = 1e-54
 Identities = 113/307 (36%), Positives = 182/307 (59%), Gaps = 20/307 (6%)

Query: 6   QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65
           QQ++N L LGS+YAL ALG+T+V+GVL +IN +HG + MVG+   L+++  +   AP   
Sbjct: 4   QQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAALAMVSHLN--AP--- 58

Query: 66  GIVQLVIAIVGAIPVCIVVSLLIERIAYRPLR--NAPRLAPLITAIGVSILLQTLAMMIW 123
               L +A++GA+ V   + LL++ +  +PLR  NAP L P+I  IGV I+L + A  ++
Sbjct: 59  ----LWVAMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLF 114

Query: 124 GRSPLPFPQ-VMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAE 182
           G   L FP+ VMP+    +    +   +I ++A+A L M  L  I+++T++GRA+RA AE
Sbjct: 115 GAEVLRFPEDVMPAGEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAE 174

Query: 183 NPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLG 242
           +P+ A L+G++   +  +T  + A L  IAGV+   N++     MG     K  +  +LG
Sbjct: 175 SPKAAYLLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILG 234

Query: 243 GIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIMG 302
           G+G+I GA++GG+ LG  E +   Y        L S   D  AF +L ++L +RPSG+ G
Sbjct: 235 GMGDIRGALIGGLFLGFAEVISKAY--------LSSQMGDAVAFGLLFLILLVRPSGLFG 286

Query: 303 ERVADRA 309
            ++  +A
Sbjct: 287 RKLERKA 293


Lambda     K      H
   0.328    0.144    0.416 

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: 232
Number of extensions: 12
Number of successful extensions: 5
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: 309
Length of database: 293
Length adjustment: 27
Effective length of query: 282
Effective length of database: 266
Effective search space:    75012
Effective search space used:    75012
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: 48 (23.1 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