GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Herbaspirillum seropedicae SmR1

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS05195 HSERO_RS05195 xylose ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__HerbieS:HSERO_RS05195
          Length = 518

 Score =  696 bits (1795), Expect = 0.0
 Identities = 347/505 (68%), Positives = 418/505 (82%)

Query: 3   NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62
           + ILEMR I K+FPGVKAL NVNL V+EGEIHA+VGENGAGKSTLMKVLSGVYP G+Y G
Sbjct: 2   SNILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSG 61

Query: 63  EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122
           +I Y+G VR F+ I DSE +GIIIIHQELALVPLLS+ EN+FLGNE A  GVI W+Q++ 
Sbjct: 62  DIVYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNEQARGGVIDWEQSYV 121

Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182
           R +ELL KVGLKESP T + D+GVGKQQL+EIAKALSK VKLLILDEPTASLNESDS+AL
Sbjct: 122 RAKELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDAL 181

Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242
           L LL+E + QG+ SI+I+HKLNE+ KVAD ITVLRDG TV T DC  E ISED II++MV
Sbjct: 182 LELLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHMV 241

Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302
           GR++ DRYP RD  IGE I EV++W  +H  H DR  + D+N++VR GE+VGIAGLMGAG
Sbjct: 242 GREMADRYPQRDPQIGEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGAG 301

Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362
           RTE A S+FG++YG +ITG   + GK VD+ST+ KAI  G+AYVTEDRK  GLVL ++I 
Sbjct: 302 RTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKAIAKGIAYVTEDRKGDGLVLEEDIK 361

Query: 363 HNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422
            N +LANL GVS+ ++ID+ +E K+A+DF+ ++RIR S + Q+ VNLSGGNQQKVVLSKW
Sbjct: 362 KNISLANLGGVSERTVIDEAREYKIAADFKQQMRIRCSSVLQKVVNLSGGNQQKVVLSKW 421

Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482
           LFS P+VLILDEPTRGIDVGAK+EIY II++LAA+GK ++MISSEMPELLG CDRIYVMN
Sbjct: 422 LFSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELLGMCDRIYVMN 481

Query: 483 EGRIVAELPKGEASQESIMRAIMRS 507
           EG+ V  LPK EA+QE+IMRAIMR+
Sbjct: 482 EGQFVGHLPKAEATQENIMRAIMRN 506


Lambda     K      H
   0.316    0.135    0.374 

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: 787
Number of extensions: 23
Number of successful extensions: 5
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: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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 (21.6 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