GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluP in Shewanella amazonensis SB2B

Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 6937507 Sama_1663 glucose/galactose transporter (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6937507 Sama_1663 glucose/galactose
           transporter (RefSeq)
          Length = 415

 Score =  419 bits (1078), Expect = e-122
 Identities = 215/380 (56%), Positives = 280/380 (73%), Gaps = 9/380 (2%)

Query: 27  AMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIG 86
           ++T+LFF+WGFIT LNDILIPHLK +F L+Y QAML+QFCFFGAYFLVS  AGVL+ R+G
Sbjct: 26  SLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLVSVPAGVLVKRLG 85

Query: 87  YLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPER 146
           Y +GI+ GL T A GC LFYPA+    Y +FL ALFVLASGIT+LQV+ANP+V  LGP +
Sbjct: 86  YQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVAANPYVTALGPVQ 145

Query: 147 TAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTH-----EAVQLPYLLLAAVIGIIAV 201
           TA+SRL L QA NSLG T+ P FGS+LI   A G       +AV+LPYLLL  ++ ++AV
Sbjct: 146 TASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAEAEADAVKLPYLLLCGMLIVLAV 205

Query: 202 GFIFLGGKVKHADMGVDH--RHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEP 259
            F  L  K+ H     D       S L+H+ L+LGA+ IF+YVG EV+IGSFLVN+  E 
Sbjct: 206 VFALL--KLPHIHDQEDEVAATGQSALAHRHLVLGAIGIFVYVGGEVAIGSFLVNFLGES 263

Query: 260 SIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSG 319
            + G+ E  AA  +++YWGGAM+GRF GAA+ ++ +   VL  NA  A LL+++ + SSG
Sbjct: 264 HVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQKVDAGKVLGFNATMAALLVLVAMNSSG 323

Query: 320 ELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADN 379
            LA+ A+LAVG FNSIMFPTIF+LA++ LG  T++GSG+LC AIVGGAL+P++QG++AD+
Sbjct: 324 ALAMWAILAVGLFNSIMFPTIFSLALKNLGPATAQGSGILCLAIVGGALVPLLQGLLADS 383

Query: 380 VGVQLSFIVPTFCYFYICWY 399
           VG+  SFI+P  CY YI +Y
Sbjct: 384 VGLSASFILPVLCYGYILFY 403


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: 514
Number of extensions: 19
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: 413
Length of database: 415
Length adjustment: 31
Effective length of query: 382
Effective length of database: 384
Effective search space:   146688
Effective search space used:   146688
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: 50 (23.9 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