GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Shewanella amazonensis SB2B

Align Glucose/galactose transporter (characterized, see rationale)
to candidate 6936374 Sama_0562 glucose/galactose transporter (RefSeq)

Query= uniprot:A0KXM0
         (423 letters)



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

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

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

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

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

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

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

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

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


Lambda     K      H
   0.326    0.138    0.402 

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: 520
Number of extensions: 23
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: 423
Length of database: 413
Length adjustment: 32
Effective length of query: 391
Effective length of database: 381
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 (21.7 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