GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artQ in Cupriavidus basilensis 4G11

Align arginine/ornithine transport protein (characterized)
to candidate RR42_RS31740 RR42_RS31740 ABC transporter permease

Query= CharProtDB::CH_107317
         (229 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS31740 RR42_RS31740 ABC
           transporter permease
          Length = 222

 Score =  119 bits (299), Expect = 4e-32
 Identities = 79/217 (36%), Positives = 119/217 (54%), Gaps = 15/217 (6%)

Query: 9   IVDGAWLTLQLALLSMLLAIVLGLLGAAFRLSPVRWLAW--CGDLYATVVRGIPDLVLIL 66
           +V GA +T+++   +++L  V+GLL    RL P R + +  C   Y T +RG P LV + 
Sbjct: 15  LVRGAGVTVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLC-TAYVTAIRGTPLLVQLF 73

Query: 67  LIFYGGQGLLNWVAPQLGYDDYIDLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQGE 126
           L+F+G         PQ      I L  FV GV  LG   GAY+SE  RGA  ++ KGQ E
Sbjct: 74  LLFFG--------LPQFD----ILLPAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQME 121

Query: 127 AGYGYGMSHRQVFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQASD 186
           A    GMS  Q    + +PQ I   IP   N ++ L+K +AL+S++ + D+M + ++   
Sbjct: 122 AARSIGMSSGQAMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKIIS 181

Query: 187 ATREPFTYYLAVAGLYLLVTSVSLLLLRLLERRYSVG 223
            +      YLA+A +YLL+TS + L LR +E+R  +G
Sbjct: 182 VSYRSLEVYLAIALVYLLLTSAAGLFLRHMEQRLRMG 218


Lambda     K      H
   0.328    0.144    0.442 

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: 115
Number of extensions: 7
Number of successful extensions: 2
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: 229
Length of database: 222
Length adjustment: 22
Effective length of query: 207
Effective length of database: 200
Effective search space:    41400
Effective search space used:    41400
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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