GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Klebsiella michiganensis M5al

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate BWI76_RS18355 BWI76_RS18355 amino acid ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__Koxy:BWI76_RS18355
          Length = 222

 Score =  107 bits (268), Expect = 3e-28
 Identities = 71/219 (32%), Positives = 116/219 (52%), Gaps = 11/219 (5%)

Query: 219 VDSDQF--GGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLI 276
           +DS  F   G +  L + +  +   L LG +LAL R S +  +K L+   I   RG PLI
Sbjct: 9   IDSAPFLLKGAVFTLQLSIGGMFFGLVLGFILALMRMSPVWPIKWLARMYISIFRGTPLI 68

Query: 277 TLLFTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADA 335
             LF    ++ Y LP  G   D I   +I ++L  AAY AE +R  +A++ +GQ+EAA +
Sbjct: 69  AQLF----MIYYGLPQFGIELDPIPAAMIGLSLNTAAYAAETLRAAIASIDKGQWEAAAS 124

Query: 336 LGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMA 395
           +G+  WQA R  I+PQA ++++P + +SFI L KDT+L A + + +  +    +    + 
Sbjct: 125 IGMTRWQAMRRAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLITSRTL- 183

Query: 396 WKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKRDHR 434
                +  Y+  +LI+++    +S    Y E +L R  R
Sbjct: 184 ---EVFTMYLAASLIYWVMATVLSTLQNYFENQLNRQER 219


Lambda     K      H
   0.329    0.143    0.457 

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: 259
Number of extensions: 14
Number of successful extensions: 3
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: 434
Length of database: 222
Length adjustment: 27
Effective length of query: 407
Effective length of database: 195
Effective search space:    79365
Effective search space used:    79365
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 (21.8 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 (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