GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluP in Shewanella sp. ANA-3

Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 7025545 Shewana3_2696 major facilitator transporter (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7025545 Shewana3_2696 major facilitator
           transporter (RefSeq)
          Length = 452

 Score =  182 bits (461), Expect = 2e-50
 Identities = 145/462 (31%), Positives = 235/462 (50%), Gaps = 66/462 (14%)

Query: 1   MAFVSSTTPQNGSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQA 60
           M F S +T    +A+P  S   +L   +  LFF++GF+T LN  LIP LK    L+  +A
Sbjct: 1   MKFTSDST--QATASPQGSFIPMLLIGI--LFFVFGFVTWLNGALIPFLKIACQLNEFEA 56

Query: 61  MLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLA 120
            LV F F+ AYF+++     ++ R+GY  G+  GL  MA G  LF  A+ +  +A FLLA
Sbjct: 57  YLVTFVFYIAYFVMALPTSSILTRLGYKMGMTLGLGIMAAGAGLFIVAALVGHFATFLLA 116

Query: 121 LFVLASGITILQVSANPFVARLGPERTAASRLNLAQALN-SLGHTLGPLFGSLLIFG--- 176
           LFVL +G+T+LQ +ANP++  +GP  +AA R++L   +N   G  +  +F + ++ G   
Sbjct: 117 LFVLGTGLTLLQTAANPYIVCIGPRESAAMRISLMGIVNKGAGFIVPIIFTAWILTGMEP 176

Query: 177 ----AAAGTHEAVQL------------PYLLLAAV-IGIIAVGFIF--------LGGKVK 211
               A A   EA +             PYL++  V +G++A  F++        LG +V+
Sbjct: 177 YSETALASLSEAQRQLALTELANRLVHPYLMMMLVLLGLMA--FVWFSPLPEPELGERVE 234

Query: 212 HADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAE 271
                 D +   ++L + +++LGAL +F YVGAEV  G   +  F++    GL       
Sbjct: 235 RTQ--TDWK---AILQYPQVILGALTLFCYVGAEVIAGD-SIGLFSQ----GLGVAHFGM 284

Query: 272 LVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGE---------LA 322
           + S+  G  ++G   G  L  R+         +  A LL  L ++ S           L 
Sbjct: 285 MTSYTMGFMVLGYVLGILLIPRWISQQTALVGSAIAGLLFTLGVLLSDSQSQALSELLLG 344

Query: 323 LVAVLAV----------GFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVI 372
            + VL V          G  N++++P ++ LA+EGLG LT+  S LL   I GGA+LP++
Sbjct: 345 WLGVLPVPDPVLYLALLGLANALVWPAVWPLALEGLGRLTATASALLIMGIAGGAILPLL 404

Query: 373 QGVVADNVG-VQLSFIVPTFCYFYICWYAFFARNRMNGETAS 413
            G +A + G  Q+++ +   CY  I +YA +  +++  + AS
Sbjct: 405 YGYIAHSQGDSQMAYFLLLPCYGLIFYYAIWG-HKLTAKVAS 445


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: 490
Number of extensions: 23
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: 452
Length adjustment: 32
Effective length of query: 381
Effective length of database: 420
Effective search space:   160020
Effective search space used:   160020
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.

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 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