GapMind for catabolism of small carbon sources

 

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

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate AO353_25100 AO353_25100 glucose transporter

Query= SwissProt::P11551
         (438 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25100
          Length = 425

 Score =  197 bits (500), Expect = 7e-55
 Identities = 132/401 (32%), Positives = 200/401 (49%), Gaps = 17/401 (4%)

Query: 33  SLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKA 92
           SLFF+     +LND+L+P+ +  F+L+  +A L+QS+F+F YFI  IPAG+L+ ++ Y  
Sbjct: 28  SLFFILGSITSLNDVLVPKLKHLFSLSYTEAMLVQSSFFFAYFIFAIPAGLLISRIGYMR 87

Query: 93  GIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPESSGH 152
             + GL L A G  LF PA +   +  FL  LF++A G+  ++  ANP +++LG  ++  
Sbjct: 88  AAVLGLLLMAGGCLLFIPATQSALFPAFLGALFVLAIGVTTVQVVANPLLSLLGTAATAP 147

Query: 153 FRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPY 212
            RL L   FNS G  +A   G  LIL ++       L   SP +L+++       +   Y
Sbjct: 148 SRLTLGHAFNSLGTTVAPYLGAILILGSLNAVDTSAL---SPAELTSFLSQEASVISNTY 204

Query: 213 MIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIRHWRWAVLAQFCYVG 272
             I   + +VAL++ L K   LQ     +      + +L +  R   +     + F YVG
Sbjct: 205 ASITLFICMVALIVWL-KRNELQPSTRPERLNPLAALNLLKQPR---FALGTASIFLYVG 260

Query: 273 AQTACWS----YLIRYAVEEIPGMTAG-FAANYLTGTMVCFFIGRFTGTWLISRFAPHKV 327
           A+    S    YL+      +P   AG   A Y  G +V    GRF G+ L+  FAP K+
Sbjct: 261 AEVTIGSLITDYLMLPTTLALPAEAAGKHVAFYWGGALV----GRFIGSALMRTFAPGKL 316

Query: 328 LAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSSFI 387
           LA  A   + L  ISA   G V   +L     F SI +PTIF+L    LG     GS   
Sbjct: 317 LAFAATAVIVLLTISATTQGVVAGWSLLAVGLFNSIMFPTIFTLATAGLGHRAAEGSGLF 376

Query: 388 VMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428
              I+GG  + P+ G+ +D +  +  A  +PA C+A I I+
Sbjct: 377 CCAIVGGAFIPPLTGYAADLS-TLAMALSVPATCYACIAIY 416


Lambda     K      H
   0.329    0.140    0.425 

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: 423
Number of extensions: 22
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: 438
Length of database: 425
Length adjustment: 32
Effective length of query: 406
Effective length of database: 393
Effective search space:   159558
Effective search space used:   159558
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: 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