GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Burkholderia phytofirmans PsJN

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS32815 BPHYT_RS32815 sugar ABC transporter

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__BFirm:BPHYT_RS32815
          Length = 519

 Score =  412 bits (1060), Expect = e-119
 Identities = 228/513 (44%), Positives = 329/513 (64%), Gaps = 5/513 (0%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           M   ++ MR I K F GVKAL+ ++L V  GE   L GENGAGKSTLMKVLSGVYP GT+
Sbjct: 1   MTQALMTMRGIVKAFSGVKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTW 60

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVA-SNGVISWQQ 119
           +GEI +EG      ++ D+E  GIIIIHQEL LVP LS+AENIFLGNE+    G +++  
Sbjct: 61  DGEIIWEGEPLKAASVRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAA 120

Query: 120 TFNRTRELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178
            + R  ELL+++G+   +    + + G G QQL+EIAKAL+K  KLLILDEP++SL  S+
Sbjct: 121 MYQRADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSE 180

Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238
              LL+++ + + +G+  + I+HKL+EV  V D I+V+RDG  V T       ++ D II
Sbjct: 181 IRILLDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEP--MRALTTDRII 238

Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298
             MVGR++++ +P    PIG+ I E ++   +   +  R+ ++D++  +R GE++G+AGL
Sbjct: 239 SLMVGREIKNLFPREPHPIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGL 298

Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358
           +GAGRTE   ++FG +Y       V++DGKP+ +     AI AG+  V EDRK  G+V  
Sbjct: 299 VGAGRTELMQAIFG-AYPGVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPG 357

Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
            ++ HN TLA L   +    ID   E+   +    RL +R++       +LSGGNQQK V
Sbjct: 358 LSVGHNITLAVLQRFASGGRIDSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKAV 417

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           L++ L +NP VLILDEPTRG+DVGAKYEIY +I QLA  G  ++M+SSE+PE+LG  DR+
Sbjct: 418 LTRMLLTNPKVLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRV 477

Query: 479 YVMNEGRIVAELPKGEASQESIMRAIMRSGEKN 511
            V+ EG +  +      +QE I+ A +R  +++
Sbjct: 478 LVIGEGELRGDFVNDGLTQEDILSAAIRPVQRS 510


Lambda     K      H
   0.316    0.135    0.374 

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: 658
Number of extensions: 28
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: 512
Length of database: 519
Length adjustment: 35
Effective length of query: 477
Effective length of database: 484
Effective search space:   230868
Effective search space used:   230868
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 (21.6 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