GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Rhizobium freirei PRF 81

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_086005351.1 RHSP_RS08730 sugar ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_000359745.1:WP_086005351.1
          Length = 477

 Score =  350 bits (897), Expect = e-101
 Identities = 191/474 (40%), Positives = 293/474 (61%), Gaps = 3/474 (0%)

Query: 28  VDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIG 87
           ++  +RRG +  LLGENGAGKSTL+K L GVY    G I L G+A  P+N   A+  GI 
Sbjct: 1   MNLKVRRGRVHTLLGENGAGKSTLMKILAGVYKPTSGEILLAGKAYQPQNPRDARGHGIS 60

Query: 88  TVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASYGFSLDVREPLNRFS 147
            V+QE++L  N+SVA N+F   EP RFG +R + +  +A  L+   G  ++V   +   S
Sbjct: 61  IVFQELSLCRNLSVAQNIFASHEPSRFGFVRDRVLVAKAEALIEDLGLPVNVHAKVGDLS 120

Query: 148 VAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQ 207
           +A +Q+V I + + L A V+ILDEPT+SL   E E+LF ++ +L+ RG ++I+++H +++
Sbjct: 121 IAQRQLVEIAKGLSLPADVIILDEPTSSLSDSEAEILFSIIERLKARGKAIIYISHRMEE 180

Query: 208 VYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL-DTHALQRAGRTLLSDKPVAA 266
           + ++SD ITV+R+G +V   E  E    +L+ +M+GRE+ D +  + A R   S  PV A
Sbjct: 181 IMRLSDDITVIRDGEYVTTTEKSETSIDKLIALMVGREMQDIYPPRVAPRPAESTAPVLA 240

Query: 267 FKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNL 326
            KN    G      ++V+PGE+VGL GL+GSGR++  + +FG++  + G   + GKP  L
Sbjct: 241 TKNLTVPGKFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGMERPE-GQIFLDGKPLTL 299

Query: 327 RSPHQASVLGIGFCPEDRKTDGIIAAASVRENI-ILALQAQRGWLRPISRKEQQEIAERF 385
            SP  A   GI F  E+RK +G++ A SV  N+ ++AL+   G    +    ++  A+  
Sbjct: 300 ASPSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRGSAERAAAKAE 359

Query: 386 IRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLI 445
           + +L I+  S +     LSGGNQQK++L++WL  RP+ LILDEPTRG+DVGA  EI R+I
Sbjct: 360 VLRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDVGAKFEIYRII 419

Query: 446 ETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAIA 499
             L A+G A+L++SSEL E++G +DRV +M +R   A +    L+   +M   A
Sbjct: 420 RELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPETVMTYAA 473


Lambda     K      H
   0.321    0.138    0.391 

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: 576
Number of extensions: 22
Number of successful extensions: 7
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: 500
Length of database: 477
Length adjustment: 34
Effective length of query: 466
Effective length of database: 443
Effective search space:   206438
Effective search space used:   206438
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:

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