GapMind for catabolism of small carbon sources

 

Alignments for a candidate for exuT in Pseudomonas fluorescens FW300-N1B4

Align MFS transporter (characterized, see rationale)
to candidate Pf1N1B4_2746 Hexuronate transporter

Query= uniprot:A0A166QG26
         (467 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2746
          Length = 445

 Score =  296 bits (758), Expect = 9e-85
 Identities = 161/452 (35%), Positives = 242/452 (53%), Gaps = 40/452 (8%)

Query: 11  RIGQAVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVY 70
           R   AVG  RW + AL+FFATT+NY+DR  L ++ P L+ +  W+  DYANI   FQ  Y
Sbjct: 25  RGAMAVGKTRWGMLALVFFATTLNYIDRAALGVMQPILAKEMSWTAMDYANINFWFQVGY 84

Query: 71  AISMLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSI 130
           AI  +  GR++D++G K  +  A+ +WS     H  A                     S 
Sbjct: 85  AIGFVLQGRLIDRVGVKRVFFCAVLLWSLATGAHGLAT--------------------SA 124

Query: 131 AGFMVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIA 190
            GFMV R +L + EA N+P  +K T  +FP  ER+ ATGIFN+G NVGA+  P+ +PLI 
Sbjct: 125 VGFMVCRFILGLTEAANYPACVKTTRLWFPAGERAVATGIFNAGTNVGAMFTPMLLPLIL 184

Query: 191 SLWGWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGV 250
             WGW+AAF+ +  LG +W+  W   Y  PE    +   EL YI+  +V P  +R     
Sbjct: 185 HAWGWQAAFLCMAALGGIWLLFWGLKYFNPEDHPSVKQSELDYIQK-EVEPEQSR----- 238

Query: 251 ADKKVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQY--GMKGQAIVMPLAV 308
               V + ++L  R TWAFA    +T  V+WF+L+WLP +L+ QY  G+    + +PL +
Sbjct: 239 ----VPFSRILRMRGTWAFALAYSITAPVFWFYLYWLPPFLNQQYNLGINVTQMGIPLII 294

Query: 309 LYSMTMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISFWVPVL 368
           +Y     GS+GGG   S+ + RG  P   R+ +M + A   + V++A   G  + W+ V 
Sbjct: 295 IYLTADFGSVGGGILSSFLIGRGINPIKARLMSMFLFACCIIGVVMA--AGSSNLWLAVF 352

Query: 369 LIGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKL 428
            I +   AHQAW+ NI++ V D  P+  +++V G GG+   +GG+ MT++ G ++     
Sbjct: 353 AISLAIGAHQAWTANIWSLVMDYTPKHMMSTVFGFGGMCAAIGGMFMTQLVGHILT---- 408

Query: 429 IGDIHTGYMIMFAICALAYLVAWSVMKALVPR 460
               +  Y ++F I    Y +A   M  + PR
Sbjct: 409 --VTNNNYTVLFTIIPAMYFIALIWMYFMAPR 438


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: 720
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: 445
Length adjustment: 33
Effective length of query: 434
Effective length of database: 412
Effective search space:   178808
Effective search space used:   178808
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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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