GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Klebsiella michiganensis M5al

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  322 bits (825), Expect = 9e-93
 Identities = 178/354 (50%), Positives = 225/354 (63%), Gaps = 21/354 (5%)

Query: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60
           M+ I++  + K +G+T  L  +NLDIEDGEF VFVGPSGCGKSTLLR +AGLE VS G +
Sbjct: 1   MSNIRLRNVTKRFGSTVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEV 60

Query: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120
            IG   +  V PA R +AMVFQSYALYPHMTV ENM +G+KVN    D  + ++   A+ 
Sbjct: 61  LIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKT 120

Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180
           LQL   LDRKP QLSGGQRQRVAIGRAIV+NP VF+FDEPLSNLDA+LRV+MR+ +  LH
Sbjct: 121 LQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLH 180

Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240
            +L  TM+YVTHDQVEAMT+ADKIVV+N G++EQ+GSPM LY+ P ++FVA FIGSP MN
Sbjct: 181 HELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMN 240

Query: 241 VFSSDVG-----------LQDISL----------DASAAFVGCRPEHIEIVPDGDGHIAA 279
              + V             QD +L            +A  +G RPEH+    +    +  
Sbjct: 241 FLPATVTAWQPGQLSVKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHLSTDVNIGTVVEF 300

Query: 280 TVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDE 333
              V ERLG  + L+    G   +   + GD   +    +S+ F       FDE
Sbjct: 301 QCEVVERLGNNTYLFGQCYGHDNVKILLPGDVHFRPWQKISVAFDDRYCMVFDE 354


Lambda     K      H
   0.320    0.139    0.396 

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: 364
Number of extensions: 14
Number of successful extensions: 1
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: 338
Length of database: 369
Length adjustment: 29
Effective length of query: 309
Effective length of database: 340
Effective search space:   105060
Effective search space used:   105060
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.

Links

Downloads

Related tools

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