Alignments for a candidate for mglA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Burkholderia phytofirmans PsJN

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate BPHYT_RS32815 BPHYT_RS32815 sugar ABC transporter

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__BFirm:BPHYT_RS32815
          Length = 519

 Score =  377 bits (969), Expect = e-109
 Identities = 212/500 (42%), Positives = 311/500 (62%), Gaps = 11/500 (2%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GSI 70
           L+ MRGI K+F GVKALD ++L V P     L GENGAGKSTL+K L G+Y   +  G I
Sbjct: 5   LMTMRGIVKAFSGVKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDGEI 64

Query: 71  VFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMYQD 129
           +++G+ +   S ++    GI ++HQEL LV + SV +N++LG   T  G  ++   MYQ 
Sbjct: 65  IWEGEPLKAASVRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMYQR 124

Query: 130 TKAIFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHL 188
              +  EL I  I+    V        Q+IEIAKA +  AK++I+DEP+SSLT  E+  L
Sbjct: 125 ADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIRIL 184

Query: 189 FTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGR 248
             I+R LK RG   VYISHK++E+  +CD I+++RDG+ +AT+P+  L  D+II++MVGR
Sbjct: 185 LDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMVGR 244

Query: 249 SLNQRFPDKENKPGDVILEVRHLTSL-----RQPSIRDVSFDLHKGEILGIAGLVGAKRT 303
            +   FP + +  GDVI E RH+T       R+  + DVSF L  GEILG+AGLVGA RT
Sbjct: 245 EIKNLFPREPHPIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGLVGAGRT 304

Query: 304 DIVETLFGIRE-KSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNS 362
           ++++ +FG     S  T+ + GK +      +AI  G  +V E+R+  GI   L +G N 
Sbjct: 305 ELMQAIFGAYPGVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPGLSVGHNI 364

Query: 363 LISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLL 422
            ++ ++ + +  G +D++         +  + V+       I SLSGGNQQK ++ R LL
Sbjct: 365 TLAVLQRFASG-GRIDSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKAVLTRMLL 423

Query: 423 TQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482
           T P++L+LDEPTRG+DVGAK+EIY+LI +LA++G  I+++SSE+PE+LGI+DR+LV+  G
Sbjct: 424 TNPKVLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVLVIGEG 483

Query: 483 LVSGIVDTKTTTQNEILRLA 502
            + G       TQ +IL  A
Sbjct: 484 ELRGDFVNDGLTQEDILSAA 503



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 60/257 (23%), Positives = 121/257 (47%), Gaps = 26/257 (10%)

Query: 8   PSGEYLLEMRGI---NKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQ 64
           P G+ + E R +   + + P  K +++V+  +R   I  + G  GAG++ L++ +FG Y 
Sbjct: 256 PIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGLVGAGRTELMQAIFGAYP 315

Query: 65  KDS-GSIVFQGKEVDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLG---RYPTK 117
             S  ++V  GK +   +  +A+  GI MV ++     +V   SV  N+ L    R+ + 
Sbjct: 316 GVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPGLSVGHNITLAVLQRFASG 375

Query: 118 GMFVDQDKMYQDTKAIFDELDIDID--------PRARVGTLSVSQMQMIEIAKAFSYNAK 169
           G          D+ A  D ++ ++         P   + +LS    Q   + +    N K
Sbjct: 376 GRI--------DSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKAVLTRMLLTNPK 427

Query: 170 IVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIA 229
           ++I+DEPT  +       ++ +I +L +RG  IV +S ++ E+  + D + ++ +G+   
Sbjct: 428 VLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVLVIGEGELRG 487

Query: 230 TQPLEGLDMDKIIAMMV 246
               +GL  + I++  +
Sbjct: 488 DFVNDGLTQEDILSAAI 504


Lambda     K      H
   0.319    0.137    0.388 

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: 627
Number of extensions: 25
Number of successful extensions: 9
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: 506
Length of database: 519
Length adjustment: 35
Effective length of query: 471
Effective length of database: 484
Effective search space:   227964
Effective search space used:   227964
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 (21.7 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources