GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>FitnessBrowser__BFirm:BPHYT_RS35680
          Length = 360

 Score =  340 bits (871), Expect = 5e-98
 Identities = 180/355 (50%), Positives = 232/355 (65%), Gaps = 3/355 (0%)

Query: 1   MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60
           MA+V L  I K Y + +V+  I+LDI DGEFVV VGPSGCGKSTLMRM+AGLE+ISGGDL
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120
            I G R N +AP +R I+MVFQSYALYPH+++Y+N+AFG ++           +  AAK+
Sbjct: 61  MIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKM 120

Query: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180
           L++   LDR P+ LSGGQRQRVA+GRA+ R+P +FLFDEPLSNLDA LRV+MR E   LH
Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180

Query: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240
             LK T+IYVTHDQ+EAMT+AD+IVV++AG +EQ+G P  LY  PAN FVA F+GSP MN
Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240

Query: 241 FMEGVVQS-VTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISA 299
           F EGV+ S     G+ +    G    +   PA+   G KVT+G+RPEH+         + 
Sbjct: 241 FAEGVIASRAQGQGLALNLTGGGEIVLEGAPASAVVGAKVTLGVRPEHIETMTPTPDATM 300

Query: 300 RTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLFDS 354
               VE  G   +LY +   +   +  R     +   G+   L    EH HLFD+
Sbjct: 301 EVEVVEPTGAETHLYGKIGGSTWCVTTR--QRSKIEPGQRVTLRLPAEHIHLFDT 353


Lambda     K      H
   0.320    0.135    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: 394
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 369
Length of database: 360
Length adjustment: 29
Effective length of query: 340
Effective length of database: 331
Effective search space:   112540
Effective search space used:   112540
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