GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Tistlia consotensis USBA 355

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  193 bits (490), Expect = 6e-54
 Identities = 124/340 (36%), Positives = 187/340 (55%), Gaps = 12/340 (3%)

Query: 7   SATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMI-LFFSFASPNFMEVDNLVS 65
           ++ S + +   +A+A G   RL    A    L    L L+I    S  SP F+   N+ +
Sbjct: 4   TSRSPARSPGRSAAAAG-EGRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFN 62

Query: 66  ILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFF 125
           IL  + V G+L+I  T+VI+T GIDLSVG++     ++ G+ L ++  P+P+ I   +  
Sbjct: 63  ILDQSVVIGILSIGMTFVILTGGIDLSVGSVAGLSGIVLGLALKDY--PIPVAILLGVLT 120

Query: 126 GALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLI 185
           GA  G +SG++I   ++  F+ TLGMM + + L+ + SG   I      GF +     + 
Sbjct: 121 GAGVGLVSGILIGYFRLAAFVVTLGMMAIGRSLAYIFSGQTAI-----SGFPSDLSSIVY 175

Query: 186 GDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAV 245
            D+     IP  VL L    + A   L  T  GR  +A+GSN+EA R +G+ V F+ +  
Sbjct: 176 TDVFG---IPTNVLFLGFAYLLAWGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILP 232

Query: 246 YTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAF 305
           Y  SGA+  +A     +++ S  P  G G ELDAIAAVVIGG SL GG G+I+GT+IG  
Sbjct: 233 YVVSGALAAVAITFSVAQILSVDPLTGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVL 292

Query: 306 IMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345
           IM ++ NGL ++ V+  WQ    G III+A+ ++ L R R
Sbjct: 293 IMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVERLVRAR 332


Lambda     K      H
   0.326    0.139    0.398 

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: 254
Number of extensions: 20
Number of successful extensions: 4
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: 347
Length of database: 335
Length adjustment: 29
Effective length of query: 318
Effective length of database: 306
Effective search space:    97308
Effective search space used:    97308
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 Apr 09 2024. 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