GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Burk376:H281DRAFT_03749
          Length = 360

 Score =  351 bits (901), Expect = e-101
 Identities = 189/358 (52%), Positives = 241/358 (67%), Gaps = 8/358 (2%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  + L  I K YG   V+HGIDL I +GEFVV VGPSGCGKSTL+RM+AGLEEI+GGD+
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I G R N++ P +R I+MVFQSYALYPH++VY+N+AFG RI +ES      R+  AA M
Sbjct: 61  MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKM 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L L  YLDRLP+ALSGGQRQRVA+GRA+ R P +FLFDEPLSNLDA LRV  R EI  L 
Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           +R+ + T+IYVTHDQ+EAMT+ADRIVV++AG IEQ+G PLELY+ PANLFVA F+GSP+M
Sbjct: 181 QRLKN-TVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSM 239

Query: 241 NVIPATIT--ATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLR-VTEADDFL 297
           N     +     G   A+ LA G  + L+    ++  G   + GVRPE +  +T+  D  
Sbjct: 240 NFAEGVLVNRTQGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTPDVT 299

Query: 298 FEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDT 355
            +  V +VE  G  T LY  G +  +         ++V  G++V      A +HLFDT
Sbjct: 300 MQ--VEVVEPTGAETHLY--GKIGGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDT 353


Lambda     K      H
   0.320    0.137    0.387 

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: 382
Number of extensions: 15
Number of successful extensions: 4
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: 362
Length of database: 360
Length adjustment: 29
Effective length of query: 333
Effective length of database: 331
Effective search space:   110223
Effective search space used:   110223
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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