Alignments for a candidate for HSERO_RS05250 in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Streptacidiphilus oryzae TH49

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_084703851.1 BS73_RS06830 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000744815.1:WP_084703851.1
          Length = 559

 Score =  320 bits (821), Expect = 7e-92
 Identities = 191/510 (37%), Positives = 286/510 (56%), Gaps = 22/510 (4%)

Query: 23  IALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLD 82
           ++LR + K +  V  LD  + EL  G++  ++GENGAGKSTLM +LSG     +G+I + 
Sbjct: 15  VSLRGISKSYGPVKVLDLPELELRHGQIVGVVGENGAGKSTLMGVLSGTVTPTTGEITVS 74

Query: 83  GKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAM-------------G 129
           G+ +    P  AQ LG+ ++ QE  L+  +S A+N+ +GR P++               G
Sbjct: 75  GRRLHAGRPDHAQQLGVALVAQEFPLVGRMSVAENLLLGRRPQREAAEQREDGAEARTGG 134

Query: 130 L---FIDEDELNRQAAAIFARMRLD-MDPSTPVGELTVARQQMVEIAKALSFDSRVLIMD 185
           L     D     R+A  +   + +  +D   PV  L+V  +QMVEIAKA      VLI+D
Sbjct: 135 LRRWLFDRAGTRREARRLLGDVGVTGVDVDRPVERLSVPLRQMVEIAKAWGRSPLVLILD 194

Query: 186 EPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQ 245
           EPT++L   E   +  + R   A G  +++I H++DE++ I+DRV V+R G+ +A +  +
Sbjct: 195 EPTSSLGPVEAERVLALARRHAADGGAVLFIGHRLDEVQAISDRVLVLRSGRLVADLTPE 254

Query: 246 ETSMDTIISMMVGRALDGEQRIPPDTSRND----VVLEVRGLNRGRAIRDVSFTLRKGEI 301
           E + + +I  MVG  L      PP +   D     VL+VRGL     +  V   +R GEI
Sbjct: 255 EATEERLIREMVGSELAAVDISPPPSVAEDGTDGAVLQVRGLTAD-GLGPVDLDVRAGEI 313

Query: 302 LGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFG 361
           +G AGLMG+GR+ +   +FGA P   G I + G +     PA+AVA G+G + EDRK   
Sbjct: 314 VGVAGLMGSGRSRLLHTVFGAQPRTGGRIRLAGREFTPGHPAEAVAAGVGLVPEDRKLQS 373

Query: 362 LAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQ 421
           L     V+ N  L+++ R +  G +  RA R  A+  V  L ++  S EQ    LSGGNQ
Sbjct: 374 LLPDHPVRWNATLATLRRISPRGVLTPRADRAHARRIVGDLGVRLHSAEQPISGLSGGNQ 433

Query: 422 QKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRM 481
           QK+V  +WL     +L  DEPTRG+DVGAK+EIY+L+D  A+ G A++  SSEL E+L +
Sbjct: 434 QKVVFGRWLAARPRLLLLDEPTRGVDVGAKAEIYRLIDEAAKDGLAVLAASSELEELLWI 493

Query: 482 SHRVLVMCEGRITGELARADATQEKIMQLA 511
            HR++VM  GR+  ++ R   ++E IM  A
Sbjct: 494 CHRIVVMAGGRVVADIPRERFSKELIMTAA 523



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 60/229 (26%), Positives = 108/229 (47%), Gaps = 10/229 (4%)

Query: 44  ELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIH 103
           ++ AGE+  + G  G+G+S L+  + G   R  G I L G+      P +A A G+G++ 
Sbjct: 307 DVRAGEIVGVAGLMGSGRSRLLHTVFGAQPRTGGRIRLAGREFTPGHPAEAVAAGVGLVP 366

Query: 104 QELNLMNHL-------SAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPST 156
           ++  L + L       +A         PR  +    D     R    +  R+        
Sbjct: 367 EDRKLQSLLPDHPVRWNATLATLRRISPRGVLTPRADRAHARRIVGDLGVRLH---SAEQ 423

Query: 157 PVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYI 216
           P+  L+   QQ V   + L+   R+L++DEPT  ++    AE++R+I +    G+ ++  
Sbjct: 424 PISGLSGGNQQKVVFGRWLAARPRLLLLDEPTRGVDVGAKAEIYRLIDEAAKDGLAVLAA 483

Query: 217 SHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQ 265
           S +++EL  I  R+ VM  G+ +A +P +  S + I++   G A+  EQ
Sbjct: 484 SSELEELLWICHRIVVMAGGRVVADIPRERFSKELIMTAAAGSAVRAEQ 532


Lambda     K      H
   0.320    0.135    0.372 

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: 732
Number of extensions: 32
Number of successful extensions: 7
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: 520
Length of database: 559
Length adjustment: 35
Effective length of query: 485
Effective length of database: 524
Effective search space:   254140
Effective search space used:   254140
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 24 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 2024 update 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