GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Burkholderia phytofirmans PsJN

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate BPHYT_RS02510 BPHYT_RS02510 C4-dicarboxylate ABC transporter

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__BFirm:BPHYT_RS02510
          Length = 426

 Score =  533 bits (1372), Expect = e-156
 Identities = 265/419 (63%), Positives = 334/419 (79%)

Query: 1   MKTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTG 60
           MK  + K LY QV+ AI IGI LGHFYP +   MKPLGDGF+KLIKM+I P+IFCTVVTG
Sbjct: 1   MKKPIHKVLYVQVIVAIIIGIALGHFYPNLAVDMKPLGDGFIKLIKMVIGPIIFCTVVTG 60

Query: 61  IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120
           IAGME MK VGR G  ALLYFEIVST AL++GLI  +V++PG G N+DPATLD KAVA Y
Sbjct: 61  IAGMEDMKKVGRVGGKALLYFEIVSTFALVLGLIATHVLKPGVGFNIDPATLDGKAVASY 120

Query: 121 ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIES 180
           A +A  Q  V F+M +IP +++ AFA G ILQ+LL A+LFG  L   G KG+++ + I+ 
Sbjct: 121 AAKAHGQTTVDFLMHLIPDTLVSAFAQGEILQILLIALLFGAVLATAGEKGKVVTSFIDG 180

Query: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGS 240
            S V+FGI+ +I +LAPIGAFGAMAFTIGKYG+G+L+ + +LI  FY+T I+FVV+VLG 
Sbjct: 181 LSHVLFGIVRIITKLAPIGAFGAMAFTIGKYGIGSLLPMLKLIGTFYLTSIVFVVVVLGI 240

Query: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300
           IA+A GF+I +F+ YI+EE+LIVLGTSSSE+ALP+++ K+EKLGC +SVVGLV+PTGYSF
Sbjct: 241 IARAVGFNILRFVAYIKEEMLIVLGTSSSEAALPQLMLKLEKLGCSRSVVGLVVPTGYSF 300

Query: 301 NLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSA 360
           NLDGT+IY+TMA +FIAQATN+ +    Q+TLL V +L+SKGA+GVTG+GFI LAATL+ 
Sbjct: 301 NLDGTNIYMTMAVLFIAQATNTDLTWTQQLTLLAVTMLTSKGASGVTGAGFITLAATLAV 360

Query: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAP 419
           V  +P++G+ LILGIDRFMSE RALTN+VGNGVAT+VV+ W KELD  KL+  L    P
Sbjct: 361 VPTIPLSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNKLNAALRGDVP 419


Lambda     K      H
   0.327    0.142    0.401 

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: 585
Number of extensions: 26
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: 428
Length of database: 426
Length adjustment: 32
Effective length of query: 396
Effective length of database: 394
Effective search space:   156024
Effective search space used:   156024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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