GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Tistlia consotensis USBA 355

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  362 bits (929), Expect = e-104
 Identities = 196/509 (38%), Positives = 307/509 (60%), Gaps = 10/509 (1%)

Query: 14  ASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ 73
           A+   + P++ LR V +RFPGVLALD   F+L  GEVH L GENGAGKST++ +++G  +
Sbjct: 15  AAPLPAAPLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALR 74

Query: 74  RDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFID 133
              G+    G+PVE+     A+ LGI  + QE +L+  ++  +N+F+G E  + +GL +D
Sbjct: 75  PSEGEFRFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTR-LGL-LD 132

Query: 134 EDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193
              L+ +A AI  R+   + P   V  LT A QQMVEIAKA   +  VLI+DEPTA+L  
Sbjct: 133 RRALHDRADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTE 192

Query: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253
            E A+LF++I  ++AQGVG++YI+H++ E+R+I DR++V+RDG+Y+ATV  Q T    ++
Sbjct: 193 RETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELV 252

Query: 254 SMMVGRALD---GEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGA 310
            +M GR  D    + R  P     +++   R      ++ + S ++  GEI+G AGL+G+
Sbjct: 253 RLMTGRVYDELFPKVRFKPG---RELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGS 309

Query: 311 GRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQA 370
           G++EVARA FG + +  G + + G +   + P   +  G  Y+  DR+  GL +   V+ 
Sbjct: 310 GKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRE 369

Query: 371 NIALSS--MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428
           N++L S  +  F     +D+R   +  +    QL ++ P +E+     SGGNQQK+++AK
Sbjct: 370 NVSLPSLTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAK 429

Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488
              R   +  FDEPT G+DVG +  IY+ +  L E G  I++ISS+LPEVL +S+R  V 
Sbjct: 430 SRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVF 489

Query: 489 CEGRITGELARADATQEKIMQLATQRESA 517
             GR+  ELA  + T+EK++    +R++A
Sbjct: 490 YRGRVQAELAGDEITEEKVLSHFFERDAA 518


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: 604
Number of extensions: 34
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: 520
Length of database: 518
Length adjustment: 35
Effective length of query: 485
Effective length of database: 483
Effective search space:   234255
Effective search space used:   234255
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 Apr 09 2024. 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