GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Rhizobium freirei PRF 81

Align ABC transporter permease (characterized, see rationale)
to candidate WP_004107282.1 RHSP_RS00675 sugar ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>NCBI__GCF_000359745.1:WP_004107282.1
          Length = 295

 Score =  253 bits (647), Expect = 3e-72
 Identities = 123/268 (45%), Positives = 176/268 (65%)

Query: 17  PAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVALKNLGIFGV 76
           P ++       G M W+  LS T S ++P+  + G AQY +L++  RW  +L+N+ IFG 
Sbjct: 17  PTWIAAIFVYIGTMAWSVRLSFTDSTIIPSSNYVGFAQYAKLFKNSRWLASLENVLIFGA 76

Query: 77  GYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLNPGLGIEKMV 136
            YVGG L +G VLA  LD+K+R E   RTI+LYP A+SFVVTG  W+W+LNP  GI+  V
Sbjct: 77  LYVGGCLALGFVLAAALDRKVRFESVFRTIFLYPYAMSFVVTGLIWQWMLNPTFGIQATV 136

Query: 137 RDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKAAQVDGAS 196
           R  G+  F F W+V+ +MAIY VV AG+WQ AG  M + L+G+RGI +   KAAQ+DG  
Sbjct: 137 RALGWQGFVFDWIVNRDMAIYTVVFAGVWQGAGLVMVIALSGMRGISEEQWKAAQIDGIP 196

Query: 197 LPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPATFMYTMSFS 256
           + RIY+ I+LP L P   ++ M+LS   IK++DL++A T GGPG++T+VPA F+    F 
Sbjct: 197 VWRIYFSIILPQLGPALAASGMLLSMGVIKTYDLIVAQTGGGPGYSTEVPAKFIMDNLFE 256

Query: 257 RGQIGLGAASATMMLATVAALVIPYLYS 284
           R  +GL +A AT+++ +V   V P+ Y+
Sbjct: 257 RQNLGLASAGATVLVLSVVMAVAPFRYA 284


Lambda     K      H
   0.327    0.141    0.451 

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: 332
Number of extensions: 14
Number of successful extensions: 1
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: 293
Length of database: 295
Length adjustment: 26
Effective length of query: 267
Effective length of database: 269
Effective search space:    71823
Effective search space used:    71823
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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