GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1896 in Sinorhizobium meliloti 1021

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate SMc04394 SMc04394 ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>FitnessBrowser__Smeli:SMc04394
          Length = 293

 Score =  306 bits (784), Expect = 3e-88
 Identities = 152/278 (54%), Positives = 198/278 (71%), Gaps = 9/278 (3%)

Query: 13  SRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDV--- 69
           +R  IY+ L+L A   L+PL VML+ S K  ++IR G +L+ P       W+ AW     
Sbjct: 16  TRALIYSALILFALYSLLPLYVMLVNSLKPLDEIRQGGMLNLPQTWTVEPWLSAWSTAQI 75

Query: 70  ------VGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQ 123
                 +  +F NS+ + VPAV IST IGA+NGYVL+ WRF G+ +FFG+LL  CF+PFQ
Sbjct: 76  GVQPTGLRPFFINSILMVVPAVAISTIIGALNGYVLTKWRFPGANIFFGMLLLSCFIPFQ 135

Query: 124 TVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGF 183
            VL+P +  LG  G+A +  GL+LVHVVYG+ FTTL+FRNYY + P  LV+AA++DGA F
Sbjct: 136 IVLIPMARILGILGIAGSIWGLILVHVVYGIGFTTLYFRNYYEAFPTELVRAAQIDGASF 195

Query: 184 FTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAK 243
           F IF +ILLP S PI++V +IWQFT IWNDFLFG  F+   + P+TVALNNLV++STG K
Sbjct: 196 FQIFRRILLPSSGPIIVVSVIWQFTNIWNDFLFGASFSGPYSTPMTVALNNLVSSSTGVK 255

Query: 244 EYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           EYNV  A A++A LPTL+VYI +G+YF+RGL SGAVKG
Sbjct: 256 EYNVHFAGAILAALPTLIVYIVSGRYFVRGLMSGAVKG 293


Lambda     K      H
   0.329    0.143    0.447 

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: 264
Number of extensions: 6
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: 281
Length of database: 293
Length adjustment: 26
Effective length of query: 255
Effective length of database: 267
Effective search space:    68085
Effective search space used:    68085
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: 47 (22.7 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