GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natF in Rhodobacter viridis JA737

Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate WP_110804792.1 C8J30_RS05885 amino acid ABC transporter substrate-binding protein

Query= uniprot:Q31RP1
         (359 letters)



>NCBI__GCF_003217355.1:WP_110804792.1
          Length = 338

 Score =  309 bits (791), Expect = 8e-89
 Identities = 151/320 (47%), Positives = 213/320 (66%), Gaps = 3/320 (0%)

Query: 41  SNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYRS 100
           S S L+ V+ARG+L+CGV   L GF   D+ GNY G DV  CKA+AAA+  DP  ++Y++
Sbjct: 21  SASTLDDVKARGQLICGVNPGLTGFGAPDANGNYQGFDVAACKAVAAAVLGDPMKVQYKA 80

Query: 101 LDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQSL 160
           L    RF ALASGEVD+L+RN+TWT  RD +    L+F    +YDGQG MV ++ G+ S 
Sbjct: 81  LTGETRFTALASGEVDMLARNSTWTFGRDTELA--LDFVAVNYYDGQGFMVNKSLGVSSA 138

Query: 161 QDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRSQ 220
           ++  G ++CV+TGTT+E+NLAD  +   + Y  +   +       +  G C+  T+D S 
Sbjct: 139 KELDGATVCVQTGTTTEMNLADYFKSNNMTYTPVNIADDAEGQQKFLAGACDSYTTDASG 198

Query: 221 LAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQAN 280
           LAA R T+ +A    +L  +ISKEPL+ A  + D+ W D+V+W   A + AEE+GIT+AN
Sbjct: 199 LAASRATMPNAADIVILPEIISKEPLALAVRHGDNNWGDIVRWSFYALVAAEEYGITKAN 258

Query: 281 IDQFKTS-KNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLKL 339
           +++   S +NPEIRR LGLEG++G+++GL NDFA RAI A GNYGEI+E N+G  + + L
Sbjct: 259 LEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAIMASGNYGEIFEANIGASTSIGL 318

Query: 340 NRGLNQLYKNGGLLYSPPFR 359
            RGLN  +  GGL+Y+PPFR
Sbjct: 319 ARGLNAQWTQGGLMYAPPFR 338


Lambda     K      H
   0.317    0.134    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: 318
Number of extensions: 10
Number of successful extensions: 3
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: 359
Length of database: 338
Length adjustment: 29
Effective length of query: 330
Effective length of database: 309
Effective search space:   101970
Effective search space used:   101970
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 (21.6 bits)
S2: 49 (23.5 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