GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglG in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate PfGW456L13_1896 Glucose ABC transport system, inner membrane component 2

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1896 Glucose ABC
           transport system, inner membrane component 2
          Length = 281

 Score =  116 bits (291), Expect = 7e-31
 Identities = 72/219 (32%), Positives = 111/219 (50%), Gaps = 9/219 (4%)

Query: 163 IGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPL 222
           +G  F NS+ + VP+ +I   I A   Y L+   F G  +   +++    +P Q  L+P 
Sbjct: 70  VGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPA 129

Query: 223 LQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDF 282
                  G      A T  G+ L H  +GL       RNY   +P  ++++AR+DGA  F
Sbjct: 130 SFTLGKFGL-----ANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFF 184

Query: 283 DIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGG- 341
            IF+KI+LP+S P +    I+QF   WND L  +VF  A  D   +T  L NL+ +  G 
Sbjct: 185 TIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVF--ASGDAQPITVALNNLVNTSTGA 242

Query: 342 -NWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
             + +  A+A I  +  L+V+    +Y +RGL +G+VKG
Sbjct: 243 KEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281


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: 12
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: 281
Length adjustment: 28
Effective length of query: 352
Effective length of database: 253
Effective search space:    89056
Effective search space used:    89056
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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