GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Rhizobium freirei PRF 81

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_004124215.1 RHSP_RS23465 sugar ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_000359745.1:WP_004124215.1
          Length = 262

 Score =  342 bits (877), Expect = 5e-99
 Identities = 175/262 (66%), Positives = 210/262 (80%), Gaps = 1/262 (0%)

Query: 1   MSMSQ-PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKP 59
           MS SQ P++ ++ + KHFGS+IAL GVS+ V  GE  CLLGDNGAGKST I T+SGV KP
Sbjct: 1   MSTSQTPIVEVKNLVKHFGSIIALNGVSLSVNAGEVLCLLGDNGAGKSTLINTLSGVFKP 60

Query: 60  TKGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLF 119
           T G+ L EGQP  F  PRDA+ AGIATV+Q LAMIPLMSV+RNFFMG EP++  GP K  
Sbjct: 61  TSGEFLVEGQPRTFNGPRDALDAGIATVYQDLAMIPLMSVTRNFFMGREPLKGFGPFKHM 120

Query: 120 DHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSAL 179
           D D+A+ +T +EMRK+GI++R PDQAVGTLSGGERQ VAIARAV+FGAKVLILDEPTSAL
Sbjct: 121 DMDFASNVTRDEMRKIGIDVREPDQAVGTLSGGERQCVAIARAVYFGAKVLILDEPTSAL 180

Query: 180 GVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEE 239
           GV QT+ VL  ID+VR +G+ V+FITHNVRHA AVG+RFT LNRGKTLGT  + +I  + 
Sbjct: 181 GVAQTSMVLKYIDQVRSKGLGVIFITHNVRHAYAVGNRFTALNRGKTLGTFAKSEIDLDG 240

Query: 240 LQDMMAGGQELATLEGSLGGTV 261
           LQ++MAGG+EL +L   LGGTV
Sbjct: 241 LQNLMAGGKELQSLSEELGGTV 262


Lambda     K      H
   0.321    0.137    0.395 

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: 281
Number of extensions: 7
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: 261
Length of database: 262
Length adjustment: 25
Effective length of query: 236
Effective length of database: 237
Effective search space:    55932
Effective search space used:    55932
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 (21.9 bits)
S2: 47 (22.7 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