Alignments for a candidate for exuT in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for exuT in Pseudomonas fluorescens FW300-N2E3

Align MFS transporter (characterized, see rationale)
to candidate AO353_06195 AO353_06195 hypothetical protein

Query= uniprot:A0A166QG26
         (467 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_06195
          Length = 450

 Score =  299 bits (765), Expect = 1e-85
 Identities = 162/452 (35%), Positives = 246/452 (54%), Gaps = 40/452 (8%)

Query: 11  RIGQAVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVY 70
           R   AVG  RW + AL+FFATT+NY+DR  L ++ P L+ +  W+  DYANI   FQ  Y
Sbjct: 30  RGAMAVGKTRWGMLALVFFATTLNYIDRAALGVMQPILAKEMSWTAMDYANINFWFQVGY 89

Query: 71  AISMLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSI 130
           A+  +  GR++D+IG K  +  A+ +WS     H          G  +SALG        
Sbjct: 90  AVGFVLQGRLIDRIGVKRVFFCAVLLWSLATGAH----------GLATSALG-------- 131

Query: 131 AGFMVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIA 190
             FMV R +L + EA N+P  +K T  +FP  ER+ ATGIFN+G NVGA+  P+ +PLI 
Sbjct: 132 --FMVCRFILGLTEAANYPACVKTTRLWFPAGERAVATGIFNAGTNVGAMFTPMLLPLIL 189

Query: 191 SLWGWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGV 250
            +WGW+AAF+ +  LG +W+  W   Y  PE    +   EL YI+++        P    
Sbjct: 190 HVWGWQAAFLCMSALGGIWLVFWGLKYFNPEDHPSVKQSELDYIQNE------AEP---- 239

Query: 251 ADKKVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQY--GMKGQAIVMPLAV 308
              +V + ++L  R TWAFA    MT  V+WF+L+WLP +L+ QY  G+    + +PL +
Sbjct: 240 EQARVPFSRILRMRGTWAFALAYSMTAPVFWFYLYWLPPFLNQQYNLGINVTQMGIPLII 299

Query: 309 LYSMTMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISFWVPVL 368
           +Y     GS+GGG   S+ + RG  P   R+ +ML+ A   + V++A   G  + WV V 
Sbjct: 300 IYMTADFGSVGGGILSSFLIGRGVNPIKARLMSMLLFACCIIGVIMA--AGSSNLWVAVF 357

Query: 369 LIGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKL 428
            I +   AHQAW+ NI++ V D  P+  +++V G GG+   +GG+ MT++ G ++     
Sbjct: 358 AISLAIGAHQAWTANIWSLVMDYTPKHMMSTVFGFGGMCAAIGGMFMTQLVGHILT---- 413

Query: 429 IGDIHTGYMIMFAICALAYLVAWSVMKALVPR 460
               +  Y ++F +    Y +A   +  + PR
Sbjct: 414 --ITNNNYTVLFTMIPAMYFIALIWLYFMAPR 443


Lambda     K      H
   0.327    0.140    0.449 

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: 724
Number of extensions: 33
Number of successful extensions: 6
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: 467
Length of database: 450
Length adjustment: 33
Effective length of query: 434
Effective length of database: 417
Effective search space:   180978
Effective search space used:   180978
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources