GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluP in Dyella japonica UNC79MFTsu3.2

Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease

Query= reanno::SB2B:6936374
         (413 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1918 N515DRAFT_1918 MFS
           transporter, FHS family, L-fucose permease
          Length = 442

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

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

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

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

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

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

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

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

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


Lambda     K      H
   0.329    0.142    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: 529
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: 413
Length of database: 442
Length adjustment: 32
Effective length of query: 381
Effective length of database: 410
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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