GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Azospirillum brasilense Sp245

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 AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__azobra:AZOBR_RS06625
          Length = 511

 Score =  305 bits (781), Expect = 2e-87
 Identities = 175/505 (34%), Positives = 285/505 (56%), Gaps = 17/505 (3%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P LE + ++K F   HA + VS+    G +H ++GENGAGKST+M I+ G    D G I+
Sbjct: 6   PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTIL 65

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            +GR V    P +A+ AGI  V Q   ++D  +V EN+ +G E    +     +   E  
Sbjct: 66  VDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAEGGVTLAAGMARARTELT 125

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           +  ++ +G+E+D +  +G+  +  QQ VEI +A+Y+ A +LILDEPT  LT +ET+ LF 
Sbjct: 126 RLARD-YGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDHLFR 184

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           ++++L+E+G  ++ I+H+L EI E+ D V+V+R G+ +   +    ++E++ E+MVGRK+
Sbjct: 185 ILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGRKV 244

Query: 243 EKFYIKEAHEPGEVVLEVKNL------SGERFENVSFSLRRGEILGFAGLVGAGRTELME 296
                K    PG  VLEV  L        ER + +  ++R GEI+G AG+ G G++EL+E
Sbjct: 245 LLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQSELLE 304

Query: 297 TIFGFRPKRGGEIYIEGKRVEIN------HPLDAIEQGIGLVPEDRKKLGLILIMSIMHN 350
            + G RP   G + + G+ +           L A+  G+G VPEDR+++GL+        
Sbjct: 305 ALAGMRPPAEGSVRLRGEELTATPDRFTARGLRAL--GVGHVPEDRQRVGLVTGFEAQEC 362

Query: 351 VSLPSL-DRIKKGPFISFKREK-ELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKW 408
             L    D    G  +  +R   +     +  +D+RP  P       SGGNQQK+VLA+ 
Sbjct: 363 AILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVLARE 422

Query: 409 LALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMS 468
           +   P +L++ +PTRG+D+GA   I+R +  L  +G  ++++S EL E+  +SDRI VM 
Sbjct: 423 MERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILVMF 482

Query: 469 FGKLAGIIDAKEASQEKVMKLAAGL 493
            G+L G +   EA + ++  + AG+
Sbjct: 483 DGRLVGEVAPGEADERRLGLMMAGV 507


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: 657
Number of extensions: 42
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: 494
Length of database: 511
Length adjustment: 34
Effective length of query: 460
Effective length of database: 477
Effective search space:   219420
Effective search space used:   219420
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.

Links

Downloads

Related tools

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