GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Pseudomonas stutzeri RCH2

Align Probable c4-dicarboxylate-binding protein (characterized, see rationale)
to candidate GFF772 Psest_0786 tripartite ATP-independent periplasmic transporter solute receptor, DctP family

Query= uniprot:Q9HVH5
         (332 letters)



>FitnessBrowser__psRCH2:GFF772
          Length = 341

 Score =  405 bits (1041), Expect = e-118
 Identities = 205/331 (61%), Positives = 252/331 (76%)

Query: 1   MFKPFVGVALAALFAVSAVAHAEDAGPVVIKFSHVVSDDTPKGKGALLFKKLAEERLPGK 60
           +FK  V    AAL    +   A+ A P+VIKF+HVV DDTPKGKGALLF+ L  ERL GK
Sbjct: 11  VFKSLVVAPFAALVLTLSPLIAQAAEPIVIKFAHVVGDDTPKGKGALLFQTLVRERLAGK 70

Query: 61  VKVEVYPNSTLFGDADEIEALRANKVQMLATSLSKFEPYTKQLQVFDLPFLFDDLEALKR 120
           V VEVYPNSTL GDADE++AL  NKVQMLA SLSKF  Y+ +L+VFDLPFLFDD  A+ R
Sbjct: 71  VDVEVYPNSTLVGDADEMQALLDNKVQMLAPSLSKFIEYSPKLEVFDLPFLFDDDAAVAR 130

Query: 121 FQKRDKSRELLRSMAKHGIYGLAYWNNGMKQLSATRELHRPDDAKGLVFRIQPSSVLEAQ 180
           FQKR+ SR+LLRSMA  GIYGLAYWNNG+KQLSA + L  P DA GL FRIQPS VLEAQ
Sbjct: 131 FQKREASRDLLRSMAGRGIYGLAYWNNGLKQLSANQPLQTPADAAGLAFRIQPSPVLEAQ 190

Query: 181 FAMLGATAKQLSYAETLKAMQAGSVQGTENTWSNLAGQKIDSVQPYITETNHGALSYMLI 240
           FA + A A +L ++E  KAMQ+G+VQGTE  WSN+ GQ     Q Y+TETNHG L+YML+
Sbjct: 191 FAAVDAKAVRLPFSEVSKAMQSGTVQGTEGPWSNIRGQNAGLKQSYVTETNHGVLNYMLV 250

Query: 241 TSSAFWTGIPYQTRTELESIVDEVTLVVNKEAEALNQKEREHLLAAGKSRLVSLSAEEHE 300
           T+S FWT IP+  R+ELE+IV EVT  VN EA A+NQ+ERE +LA+G + LV+L+  + +
Sbjct: 251 TNSEFWTSIPFAVRSELENIVLEVTQTVNAEAAAINQREREQILASGNTTLVTLTPAQRQ 310

Query: 301 AWRNAMKPLWKNYEAQIGSDVLRAAQVVNRK 331
           AWR  M+P+WK++EA IG+D++RAA  VNR+
Sbjct: 311 AWRVKMQPVWKSFEAHIGADIMRAALAVNRR 341


Lambda     K      H
   0.316    0.130    0.367 

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: 298
Number of extensions: 10
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: 332
Length of database: 341
Length adjustment: 28
Effective length of query: 304
Effective length of database: 313
Effective search space:    95152
Effective search space used:    95152
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 Apr 09 2024. 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