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 7025147 Shewana3_2310 glucose/galactose transporter (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7025147 Shewana3_2310 glucose/galactose
           transporter (RefSeq)
          Length = 423

 Score =  420 bits (1080), Expect = e-122
 Identities = 223/416 (53%), Positives = 291/416 (69%), Gaps = 17/416 (4%)

Query: 1   MAFVSSTTPQNGSAAPA-QSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQ 59
           MA   +T+    S + A   + +    ++TSLFF+WGFIT LNDILIPHLK +F L+YTQ
Sbjct: 1   MASSINTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQ 60

Query: 60  AMLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLL 119
           AML+QFCFFGAYFLVS  AG L+ R+GY +GI+ GL   + GC LFYPA+S   Y LFL 
Sbjct: 61  AMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLG 120

Query: 120 ALFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAA 179
           ALFVLASGITILQV+ANP+V  LG   TA+SRLNL QA N+LG T+ P FGS+LI   AA
Sbjct: 121 ALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAA 180

Query: 180 GTH----------EAVQLPYLLLAAVIGIIAVGFIFLGGKV--KHADMGVD----HRHKG 223
                        E V+LPYLLLAA + ++A+ F  L   V  +H+    +    H  K 
Sbjct: 181 SVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKT 240

Query: 224 SLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIG 283
           S L    L+LGA+ IF+YVGAEVSIGSFLVN+  E  I G+ E+ AA  +++YWGGAM+G
Sbjct: 241 SALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVG 300

Query: 284 RFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTL 343
           RF G+A+ ++     VLA NA  A LL+++ + +SG +A+ A+L VG FNSIMFPTIF+L
Sbjct: 301 RFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSL 360

Query: 344 AIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWY 399
           A+  LG  TS+GSG+LC AIVGGA++P++QGV+ADN+G+QL+FI+P  CY +I +Y
Sbjct: 361 ALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFY 416


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: 496
Number of extensions: 20
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: 423
Length adjustment: 32
Effective length of query: 381
Effective length of database: 391
Effective search space:   148971
Effective search space used:   148971
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 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