GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6936374
          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:

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