GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Burkholderia phytofirmans PsJN

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  431 bits (1109), Expect = e-125
 Identities = 231/499 (46%), Positives = 336/499 (67%), Gaps = 6/499 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M P++ VK + KRFPGV AL  V  E   GEVHA++GENGAGKSTLMKI+AGVY  D GE
Sbjct: 1   MTPLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGE 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKR--GIFIDYKKMY 118
           I+YEG+ V +  P EA   G+  + QEL +M++L++A+N+F+G E +   G+F+D  K+ 
Sbjct: 61  ILYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLN 120

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
            +A   +     + +DP   +   ++A QQMVEIA+A+   ++VLI+DEPTS+L   E  
Sbjct: 121 AQAHDILAR-MHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIA 179

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           +LF +++ LK++GV II+ISH+++E+ +I D+V+VLRDGEY+ T ++++ T + I+ MMV
Sbjct: 180 ELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMV 239

Query: 239 GRKL-EKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           GR L +    +     GEV LEV  L+ G    +VSF+LR+GEILGFAGL+GAGRTE+  
Sbjct: 240 GRTLTDAAPSQHIANQGEVALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVAR 299

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            +FG  P   GEI ++G +  I +P DA+ +GIG + EDRK+ GL   MS+  N+ + +L
Sbjct: 300 AVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNL 359

Query: 357 DR-IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415
            + +    F+   + ++ A   I    IR     ++V  LSGGNQQK+V+AKWL     +
Sbjct: 360 RKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDV 419

Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475
           L  DEPTRGIDVGAK+EIY+++  LA +G  ++MISSELPE+L+MSDRI VM  G++ G 
Sbjct: 420 LFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGE 479

Query: 476 IDAKEASQEKVMKLAAGLE 494
           + A  A+QE++M+LA   E
Sbjct: 480 LAAAGATQERIMQLATQRE 498


Lambda     K      H
   0.318    0.138    0.385 

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: 636
Number of extensions: 31
Number of successful extensions: 8
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: 494
Length of database: 503
Length adjustment: 34
Effective length of query: 460
Effective length of database: 469
Effective search space:   215740
Effective search space used:   215740
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 (21.7 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:

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