GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS32815
          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:

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