GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Phyllobacterium brassicacearum STM 196

Align TreV, component of Trehalose porter (characterized)
to candidate WP_106710281.1 CU102_RS06970 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_003010955.1:WP_106710281.1
          Length = 333

 Score =  260 bits (665), Expect = 3e-74
 Identities = 145/337 (43%), Positives = 208/337 (61%), Gaps = 22/337 (6%)

Query: 2   TVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61
           ++++ +I K +G   V+ GI  +++ GEF + +GPSG GKSTLL+++AG+E    G I+ 
Sbjct: 3   SLKIENIRKSFGHVDVLKGIDLEVKDGEFVIFVGPSGCGKSTLLRVIAGLEDATSGDILI 62

Query: 62  DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121
           DG  + + PP KR +AMVFQ YALYP++SVRDN+   LK  G   +EI ER   A+ +L 
Sbjct: 63  DGKKVNNTPPAKRGIAMVFQTYALYPHLSVRDNMGLGLKQAGKPADEIKERTGIASSMLS 122

Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181
           + E L+++  ++SGGQ+QRVA+ RAIVR P  FL DEPLSNLDA +R   R E+ R+ ++
Sbjct: 123 LDEYLERRPAELSGGQRQRVAIGRAIVREPQLFLFDEPLSNLDAALRVNTRLEIARLHRQ 182

Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241
           LK T IYVTHDQ EA++LAD+I +L+KGK EQV  P  LY  P+T +VA F+G   MN +
Sbjct: 183 LKATMIYVTHDQVEAMTLADKIVVLNKGKIEQVGSPMELYNAPQTIFVAGFIGSPQMNLI 242

Query: 242 -PGELMKEKAQEIGFRPEWVEVGK--GNLSCMVESVEASGESR--YLICNFKNNNITILS 296
              +L +  A+ IG RPE ++V K  G     V  VE  G     YL  +F    + +  
Sbjct: 243 DAAKLGQSGAKTIGIRPEHIQVSKTSGEWKGSVIHVEHLGADTIIYLQTDFGPLTVRLFG 302

Query: 297 QEFYDV----------GQEVRFEIIKYRKYNDGRLVQ 323
           +  YDV          G+  RF+       NDG++++
Sbjct: 303 EHNYDVDGVLYATPDAGRTYRFD-------NDGQVIK 332


Lambda     K      H
   0.318    0.137    0.385 

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: 263
Number of extensions: 13
Number of successful extensions: 1
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: 324
Length of database: 333
Length adjustment: 28
Effective length of query: 296
Effective length of database: 305
Effective search space:    90280
Effective search space used:    90280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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