GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Shewanella amazonensis SB2B

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 6937507 Sama_1663 glucose/galactose transporter (RefSeq)

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__SB2B:6937507
          Length = 415

 Score =  431 bits (1109), Expect = e-125
 Identities = 228/417 (54%), Positives = 294/417 (70%), Gaps = 24/417 (5%)

Query: 25  YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84
           Y  A+  LT++FFMWGF+TCLNDILIPHLKAVF LNYA+AML+QF FFGAYFL+S+PAG+
Sbjct: 20  YGFALTSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLVSVPAGV 79

Query: 85  LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144
           LV RLGY+KGIV GL  A +G   F+PAA    Y  FLGALFVLA+GITVLQVAAN YV 
Sbjct: 80  LVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVAANPYVT 139

Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAV-LSAEQIAKLSPAEQVAYRVQ 203
            LGP ++ASSRLTL QA NSLGT +AP FG +LILS AV  SAE                
Sbjct: 140 ALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAE---------------A 184

Query: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLA 263
           EA  V+ PYL L  +L +LAV   L +LP + ++ ++ +       S L H H++ G + 
Sbjct: 185 EADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ---SALAHRHLVLGAIG 241

Query: 264 IFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPR 323
           IF YVGGEVAIGSFLVN+L    +  M+E  AA+++A+YW GAM+GRFIG+A++ K+   
Sbjct: 242 IFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQKVDAG 301

Query: 324 KLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASS 383
           K+L   A +   LVL  M + G +AM++++++GLFNSIMFPTIFSL ++ +GP T + S 
Sbjct: 302 KVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNLGPATAQGSG 361

Query: 384 LLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSRIKSDTPVAA 440
           +L +AIVGGA+VP +QGL AD +G+  +F LP+LCY YI+FYGL G +     PVAA
Sbjct: 362 ILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKGCK-----PVAA 413


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: 589
Number of extensions: 24
Number of successful extensions: 2
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: 415
Length adjustment: 32
Effective length of query: 410
Effective length of database: 383
Effective search space:   157030
Effective search space used:   157030
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