GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Gallaecimonas xiamenensis 3-C-1

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_008483730.1 B3C1_RS06620 sugar MFS transporter

Query= uniprot:A0A1I2JXG1
         (442 letters)



>NCBI__GCF_000299915.1:WP_008483730.1
          Length = 438

 Score =  218 bits (555), Expect = 3e-61
 Identities = 140/443 (31%), Positives = 239/443 (53%), Gaps = 34/443 (7%)

Query: 12  TSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTF 71
           T++  + ++R +  PMA  ++ ++FF++GF+T LN  LIP L+ V  L   +A+ V F+F
Sbjct: 3   TTMSASQQQRSSLMPMA--IIGTLFFIFGFVTWLNGALIPFLQIVCDLTSTQALFVAFSF 60

Query: 72  FGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATG 131
           + AY + +LP   ++ R GYKKG+  GL +  +G  GF PAA    +  FL + FV+ TG
Sbjct: 61  YIAYTVTALPMAWIMERTGYKKGMALGLGLIALGCLGFIPAAMSQTFAIFLVSQFVVGTG 120

Query: 132 ITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAP-KFGGLLILSAAVLSAEQIA 190
           +T+LQ A+N Y+  +GP++SA+ R+++   LN     +AP  F  L++     ++A+ +A
Sbjct: 121 LTILQTASNPYIVHIGPQESAAVRISIMGLLNKGAGVVAPLVFTALVLGDFEGITAKTVA 180

Query: 191 KLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVS 250
            L+PAE+ A   Q A  +  PYLG+A+ + LL + +    LP L   T+ A   +    S
Sbjct: 181 TLAPAERAAQVEQLAHGLILPYLGMALAMVLLTIAMVFSPLPELALDTD-ADDTEDDKRS 239

Query: 251 PLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGR 310
            L+ P ++ G + IF YVG EV     +  + S   + N     A +  +Y     +IG 
Sbjct: 240 VLQFPQLVLGAVGIFCYVGVEVIAADTIGLFGSELGVAN-----ATSLTSYTMAFMVIGY 294

Query: 311 FIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKG----------------------TVA 348
            +G  L+ ++  + L    +A+ + LVL+  +  G                      TVA
Sbjct: 295 LLGLVLIPRVLKQSLALTLSAV-LGLVLSLAVVLGSPEQHWLSDTLWGWLGLPTVPNTVA 353

Query: 349 MYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGV 408
           +  V  +G  N++++P I+ L ++ +G  T + S+LLIM I GGA++P + G  +D    
Sbjct: 354 L--VALLGFANAMVWPAIWPLALDGLGKFTAKGSALLIMGIAGGALLPLLYGYLSDVADH 411

Query: 409 QHAFFLPLLCYAYIVFYGLYGSR 431
           Q A+ + L CY +I+++ L G +
Sbjct: 412 QQAYLMMLPCYLFILYFALAGHK 434


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: 498
Number of extensions: 20
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: 438
Length adjustment: 32
Effective length of query: 410
Effective length of database: 406
Effective search space:   166460
Effective search space used:   166460
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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