GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Klebsiella michiganensis M5al

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate BWI76_RS17835 BWI76_RS17835 sugar ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__Koxy:BWI76_RS17835
          Length = 279

 Score =  120 bits (302), Expect = 3e-32
 Identities = 71/235 (30%), Positives = 129/235 (54%), Gaps = 4/235 (1%)

Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205
           P +F+ +N+       G+ +  LNS+ V    TV+ + ++A AAYALA   F G A++  
Sbjct: 48  PNQFSFENFIFAWMDIGVWQYLLNSILVVFFGTVLQVSVSALAAYALARKKFRGVALVSL 107

Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSA-KTYMGIWLAHTGFGLPLAIYLLRNYMA 264
           V++  +++P ++  IPL  + N    F   S   +Y+G+ L   G+    +I++L  +M+
Sbjct: 108 VILSTMMLPEEVIAIPLYMIINWRLPFIDASLYNSYLGMILPVVGWAF--SIFVLTEFMS 165

Query: 265 GLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDD 324
            +P+E+ E+AR+DGA+++ IF  +ILPL  PAL +   F F+  W+  L+ ++ +   D 
Sbjct: 166 AIPKELEEAARIDGANEWQIFFHVILPLVKPALGTVVTFGFIMIWDQYLLPLIVVNQ-DS 224

Query: 325 KLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
              +   L  L         I  A   + ++  +IV+  LQ++  RG+++G+VKG
Sbjct: 225 LNTIPVILGTLRTDESITPNIFIAITLLAMLPSIIVYLGLQKHFNRGIMSGAVKG 279


Lambda     K      H
   0.324    0.139    0.418 

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: 255
Number of extensions: 13
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: 380
Length of database: 279
Length adjustment: 28
Effective length of query: 352
Effective length of database: 251
Effective search space:    88352
Effective search space used:    88352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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