GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapM in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate Pf6N2E2_5568 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= reanno::Smeli:SMc02120
         (384 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5568 Glutamate Aspartate
           transport system permease protein GltK (TC 3.A.1.3.4)
          Length = 223

 Score =  110 bits (274), Expect = 5e-29
 Identities = 64/203 (31%), Positives = 107/203 (52%), Gaps = 9/203 (4%)

Query: 172 LWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMA 231
           LW G+++TL L  +G+   + LG +LAL R S+  ++  +   ++   R +PL+ V+   
Sbjct: 15  LWNGMVMTLKLMALGVVGGIILGTILALMRLSHNKLVSNIAGAYVNYFRSIPLLLVITWF 74

Query: 232 SVMLPLFLP----QGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGL 287
            + +P  L     +      F   ++   +F +AY  E+VR G+Q+IPKGQ   A +LG+
Sbjct: 75  YLAVPFVLRWITGEDTPIGAFGSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134

Query: 288 SFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATA 347
           ++ Q M  I+LPQA + + P ++   I LF+DTSLV  +G+ D L   R +      +  
Sbjct: 135 NYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNASRASGDIIGRSNE 194

Query: 348 VTPLTGLIFAGFVFWLFCFGMSR 370
                 LI AG V++   F  S+
Sbjct: 195 F-----LIIAGLVYFTVSFAASQ 212


Lambda     K      H
   0.329    0.144    0.454 

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: 249
Number of extensions: 12
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: 384
Length of database: 223
Length adjustment: 26
Effective length of query: 358
Effective length of database: 197
Effective search space:    70526
Effective search space used:    70526
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 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