GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01057 H281DRAFT_01057
           monosaccharide ABC transporter ATP-binding protein, CUT2
           family (TC 3.A.1.2.-)
          Length = 517

 Score =  391 bits (1005), Expect = e-113
 Identities = 213/499 (42%), Positives = 322/499 (64%), Gaps = 7/499 (1%)

Query: 8   SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67
           S+G+ LLE+  I K FPGVK+LD V+L VR   IHAL+GENGAGKSTL K + G+Y  DS
Sbjct: 8   SAGD-LLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDS 66

Query: 68  GTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYP-TKGMFVDQDKM 126
           G I F G+ + + SA +A  +GI ++HQEL L  Q +V +N++ G  P T+   +D  +M
Sbjct: 67  GEIRFAGQPLQWKSAADAKRHGIHVIHQELVLFPQSTVAENIFAGAEPRTRIGVLDHGRM 126

Query: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
            R+ +A+  EL + +D R RVG LSV+  QM+EIAKA +   +++I+DEPT+ +  KEV 
Sbjct: 127 NRDAQALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQ 186

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246
            LF  +R L+ +G  IVYISH+++EIF+LCD VTV++DG+ +AT+ +A  T D+++ +MV
Sbjct: 187 LLFARVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRDQLVRLMV 246

Query: 247 GRSLNQRFPDKE-NKPG-EVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304
           GR +   +PDK    PG   +LEV  L    +  + D S  +  GEI+GIAG+VG+ RT+
Sbjct: 247 GREMKDIYPDKPILAPGVPNVLEVNGLCVGNR--VVDASLTVRAGEIVGIAGMVGSGRTE 304

Query: 305 IVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364
           +   +FG      GT+ + G +        AI  G   VTE+R+S G+   LD+  N   
Sbjct: 305 LAAGIFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLMLLDVAQNVTA 364

Query: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQ 424
           + +    ++ GL+  +  ++  Q  I+  R+        + +LSGGNQQKV+I RW+   
Sbjct: 365 TTLAQV-SRFGLMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVLISRWVRVC 423

Query: 425 PEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLV 484
             +L+LDEPTRG+DVGAK EIY+++ EL  +G GI++ISSE+ E++G++DR+LVM  G +
Sbjct: 424 KRVLILDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRVLVMREGRI 483

Query: 485 SGIVDTKTTTQNEILRLAS 503
           +G V  +  T+++I+RLA+
Sbjct: 484 NGEVSGEQMTEHDIMRLAT 502


Lambda     K      H
   0.318    0.136    0.384 

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: 590
Number of extensions: 29
Number of successful extensions: 9
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: 506
Length of database: 517
Length adjustment: 35
Effective length of query: 471
Effective length of database: 482
Effective search space:   227022
Effective search space used:   227022
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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