GapMind for catabolism of small carbon sources

 

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

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate AO353_25100 AO353_25100 glucose transporter

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25100
          Length = 425

 Score =  323 bits (827), Expect = 8e-93
 Identities = 176/395 (44%), Positives = 244/395 (61%), Gaps = 3/395 (0%)

Query: 34  SIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKK 93
           S+FF+ G +T LND+L+P LK +F L+Y EAMLVQ +FF AYF+ ++PAGLL++R+GY +
Sbjct: 28  SLFFILGSITSLNDVLVPKLKHLFSLSYTEAMLVQSSFFFAYFIFAIPAGLLISRIGYMR 87

Query: 94  GIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGPEKSAS 153
             V GL +   G   F PA     +PAFLGALFVLA G+T +QV AN  ++LLG   +A 
Sbjct: 88  AAVLGLLLMAGGCLLFIPATQSALFPAFLGALFVLAIGVTTVQVVANPLLSLLGTAATAP 147

Query: 154 SRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYL 213
           SRLTL  A NSLGT +AP  G +LIL +  L+A   + LSPAE  ++  QEA  +   Y 
Sbjct: 148 SRLTLGHAFNSLGTTVAPYLGAILILGS--LNAVDTSALSPAELTSFLSQEASVISNTYA 205

Query: 214 GLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVA 273
            + + + ++A+ V+L R   L   T    +   + ++ L+ P    G  +IF YVG EV 
Sbjct: 206 SITLFICMVALIVWLKR-NELQPSTRPERLNPLAALNLLKQPRFALGTASIFLYVGAEVT 264

Query: 274 IGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRKLLAIFAAIN 333
           IGS + +YL +P    +  +AA   VA+YW GA++GRFIGSAL+   +P KLLA  A   
Sbjct: 265 IGSLITDYLMLPTTLALPAEAAGKHVAFYWGGALVGRFIGSALMRTFAPGKLLAFAATAV 324

Query: 334 MALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGA 393
           + L+  +  T+G VA +S++++GLFNSIMFPTIF+L    +G    E S L   AIVGGA
Sbjct: 325 IVLLTISATTQGVVAGWSLLAVGLFNSIMFPTIFTLATAGLGHRAAEGSGLFCCAIVGGA 384

Query: 394 IVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLY 428
            +P + G  AD   +  A  +P  CYA I  YG Y
Sbjct: 385 FIPPLTGYAADLSTLAMALSVPATCYACIAIYGWY 419


Lambda     K      H
   0.327    0.140    0.414 

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: 510
Number of extensions: 26
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: 442
Length of database: 425
Length adjustment: 32
Effective length of query: 410
Effective length of database: 393
Effective search space:   161130
Effective search space used:   161130
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