Aligments for a candidate for fruP in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruP in Shewanella amazonensis SB2B

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 6936374 Sama_0562 glucose/galactose transporter (RefSeq)

Query= uniprot:A0A1I2JXG1
         (442 letters)



>lcl|FitnessBrowser__SB2B:6936374 Sama_0562 glucose/galactose
           transporter (RefSeq)
          Length = 413

 Score =  380 bits (976), Expect = e-110
 Identities = 209/438 (47%), Positives = 283/438 (64%), Gaps = 29/438 (6%)

Query: 1   MAFAAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLN 60
           MAF +   P      G+A    +   +  G +TS+FF+WGF+T LNDILIPHLK +F L+
Sbjct: 1   MAFVSSTTPQN----GSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLS 56

Query: 61  YAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPA 120
           Y +AMLVQF FFGAYFL+S  AG+L+AR+GY +GI+ GL+    G   F+PA+++  Y  
Sbjct: 57  YTQAMLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYAL 116

Query: 121 FLGALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILS 180
           FL ALFVLA+GIT+LQV+AN +VA LGPE++A+SRL LAQALNSLG  L P FG LLI  
Sbjct: 117 FLLALFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFG 176

Query: 181 AAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAV-FVYLFRLPALTEKTE 239
           AA  + E                    VQ PYL LA V+ ++AV F++L        K  
Sbjct: 177 AAAGTHE-------------------AVQLPYLLLAAVIGIIAVGFIFL----GGKVKHA 213

Query: 240 QASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWV 299
              V      S L H  +L G LAIF YVG EV+IGSFLVNY + P IG + E++AA  V
Sbjct: 214 DMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELV 273

Query: 300 AYYWLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFN 359
           ++YW GAMIGRF G+AL  + +P  +LA  A     L++ T+++ G +A+ +V+++G FN
Sbjct: 274 SWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFN 333

Query: 360 SIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCY 419
           SIMFPTIF+L IE +G +T   S LL  AIVGGA++P +QG+ AD++GVQ +F +P  CY
Sbjct: 334 SIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCY 393

Query: 420 AYIVFYGLYG-SRIKSDT 436
            YI +Y  +  +R+  +T
Sbjct: 394 FYICWYAFFARNRMNGET 411


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: 543
Number of extensions: 24
Number of successful extensions: 4
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: 413
Length adjustment: 32
Effective length of query: 410
Effective length of database: 381
Effective search space:   156210
Effective search space used:   156210
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources