GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Williamsia sterculiae CPCC 203464

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit

Query= uniprot:B2TBJ7
         (240 letters)



>NCBI__GCF_900156495.1:WP_083710231.1
          Length = 589

 Score = 96.7 bits (239), Expect = 9e-25
 Identities = 61/195 (31%), Positives = 106/195 (54%), Gaps = 14/195 (7%)

Query: 25  TVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYLFYFGGSTL 84
           T+ L++ +  +G + G ++A A +SR R LR    IYT +FRG+P ++VI +   G   +
Sbjct: 366 TLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVILVVGLGIGPV 425

Query: 85  VTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEAARSIGMPT 144
           V ++          G  P+ +GA+A+ +++ AY  E++RS + +V  G+LEA+R+IG   
Sbjct: 426 VKNL---------TGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSY 476

Query: 145 LTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGL----AELLRTSQVAAGSTHQY 200
               R +++PQ +R  LP + N +   +KDS+L+   GL     EL    +     T   
Sbjct: 477 RQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGN- 535

Query: 201 FTFFVVGGALYLIMT 215
            +  V  G +YL++T
Sbjct: 536 LSPLVAAGLIYLVLT 550


Lambda     K      H
   0.327    0.141    0.403 

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: 209
Number of extensions: 7
Number of successful extensions: 2
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: 240
Length of database: 589
Length adjustment: 30
Effective length of query: 210
Effective length of database: 559
Effective search space:   117390
Effective search space used:   117390
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: 50 (23.9 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