GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Burkholderia phytofirmans PsJN

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate BPHYT_RS32815 BPHYT_RS32815 sugar ABC transporter

Query= SwissProt::P37388
         (513 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS32815 BPHYT_RS32815 sugar ABC
           transporter
          Length = 519

 Score =  556 bits (1432), Expect = e-163
 Identities = 286/502 (56%), Positives = 371/502 (73%), Gaps = 3/502 (0%)

Query: 4   LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63
           L+ M+ I K F  VKA+D + L +  GE V LCGENG+GKSTLMKVL G+YP G+++GEI
Sbjct: 5   LMTMRGIVKAFSGVKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDGEI 64

Query: 64  IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEIT-HNGIMDYDLMTLR 122
           I+ GE ++A+ +RDTER GI IIHQEL LV EL+V ENIFLGNEIT   G M+Y  M  R
Sbjct: 65  IWEGEPLKAASVRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMYQR 124

Query: 123 CQKLLAQVSLS-ISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSIL 181
             +LL ++ +S I+    V + G G QQL+EIAKALNK+ +LLILDEP++SLT  E  IL
Sbjct: 125 ADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIRIL 184

Query: 182 LDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGR 241
           LDI+RDL++ G+AC+YISHKL+EV A+ DTI VIRDG+H+ T     ++ D II++MVGR
Sbjct: 185 LDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMVGR 244

Query: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301
           E+  L+P EPH  GD I    H+T +   N   KRVNDVSF L+ GEILG+AGLVGAGRT
Sbjct: 245 EIKNLFPREPHPIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGLVGAGRT 304

Query: 302 ETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNI 361
           E +Q +FG +PG  E  + +DGK + IR    AI  GI MVPEDRKR GIVP ++VG NI
Sbjct: 305 ELMQAIFGAYPGVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPGLSVGHNI 364

Query: 362 TLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLL 421
           TLA L +F  G  ++D AAE   I   +++L V+ + P L+I  LSGGNQQKA+L R LL
Sbjct: 365 TLAVLQRFASG-GRIDSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKAVLTRMLL 423

Query: 422 LNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEG 481
            NP++LILDEPTRG+D+GAKYEIYKLI QL Q+G++++++SSELPEVLG+SDRVLV+ EG
Sbjct: 424 TNPKVLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVLVIGEG 483

Query: 482 KLKANLINHNLTQEQVMEAALR 503
           +L+ + +N  LTQE ++ AA+R
Sbjct: 484 ELRGDFVNDGLTQEDILSAAIR 505



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 58/233 (24%), Positives = 121/233 (51%), Gaps = 6/233 (2%)

Query: 274 IKRVNDVSFSLKRGEILGIAGLVGAGRTETIQCLFGVWP-GQWEGKIYIDGKQVDIRNCQ 332
           +K ++ +  ++  GE +G+ G  GAG++  ++ L GV+P G W+G+I  +G+ +   + +
Sbjct: 18  VKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDGEIIWEGEPLKAASVR 77

Query: 333 QAIAQGIAMVPEDRKRDGIVPVMAVGKNITLAALNKFTGGISQLDDAAEQKCILESIQQL 392
                GI ++ ++     +VP ++V +NI L       GG  +++ AA  +   E +++L
Sbjct: 78  DTERAGIIIIHQELM---LVPELSVAENIFLGNEITLPGG--RMNYAAMYQRADELLREL 132

Query: 393 KVKTSSPDLAIGRLSGGNQQKAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLV 452
            +   +    +    GG+QQ   +A+ L    ++LILDEP+  +       +  ++  L 
Sbjct: 133 GISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIRILLDIVRDLK 192

Query: 453 QQGIAVIVISSELPEVLGLSDRVLVMHEGKLKANLINHNLTQEQVMEAALRSE 505
           ++G+A + IS +L EV  + D + V+ +G+  A      LT ++++   +  E
Sbjct: 193 RRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMVGRE 245


Lambda     K      H
   0.319    0.137    0.391 

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: 753
Number of extensions: 25
Number of successful extensions: 8
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: 513
Length of database: 519
Length adjustment: 35
Effective length of query: 478
Effective length of database: 484
Effective search space:   231352
Effective search space used:   231352
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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