GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_01057
          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:

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