GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11885 in Rhizobium freirei PRF 81

Align Rhizopine-binding protein (characterized, see rationale)
to candidate WP_037153961.1 RHSP_RS23430 sugar ABC transporter substrate-binding protein

Query= uniprot:A0A0N9WNI6
         (308 letters)



>NCBI__GCF_000359745.1:WP_037153961.1
          Length = 309

 Score =  250 bits (639), Expect = 3e-71
 Identities = 134/301 (44%), Positives = 197/301 (65%), Gaps = 6/301 (1%)

Query: 11  ALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVK 70
           AL+L+++S A  AD RIGVSM      + T +   M   AK+   G+ LQ  DA +DV K
Sbjct: 9   ALALVMSSQAYAAD-RIGVSMGYLTTNFQTLIANGMQDYAKTK--GLDLQVVDAANDVNK 65

Query: 71  QLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK-LPKGVITV 129
           QL QV +F +  V AI+V+PVD+  T  +++ A  AGIPL+YVN +P DL  L K    V
Sbjct: 66  QLDQVRNFAAGGVSAIIVDPVDSDGTPAMSKIAEDAGIPLIYVNIQPTDLSTLGKKQAFV 125

Query: 130 ASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVL--AKYPGIKIDQ 187
            SN+ E+G +Q + +   + GKGD+V+++GDL++ +   RT+ V +VL  +   GIK+ +
Sbjct: 126 GSNETESGTLQTKEVCRMLGGKGDVVVMVGDLSSQAARQRTQDVHDVLKSSDCSGIKVVR 185

Query: 188 EQTGTWSRDKGMTLVNDWLTQGRKFDAIVSNNDEMAIGAAMALKQAGVEKGSVLIAGVDG 247
           EQ G WSR  G  LV++WLT G  F+A+++NNDEMA+GA  A+K AG      ++AG+D 
Sbjct: 186 EQVGNWSRVDGADLVSNWLTSGLTFNAVIANNDEMALGAISAIKNAGGSTDKTIVAGIDA 245

Query: 248 TPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENVDQF 307
           TPD L+A+K GDL V+VFQDA  Q   ++D AVK  K E +++ VW+P++L+T +N+ QF
Sbjct: 246 TPDALQAMKSGDLKVTVFQDAKAQGRGAVDTAVKAIKGEQIDREVWIPFKLVTKDNMVQF 305

Query: 308 K 308
           +
Sbjct: 306 E 306


Lambda     K      H
   0.315    0.130    0.360 

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: 262
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 308
Length of database: 309
Length adjustment: 27
Effective length of query: 281
Effective length of database: 282
Effective search space:    79242
Effective search space used:    79242
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 (21.5 bits)
S2: 48 (23.1 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