GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Pseudomonas stutzeri RCH2

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate GFF2099 Psest_2142 tripartite ATP-independent periplasmic transporter solute receptor, DctP family

Query= SwissProt::Q9HU18
         (331 letters)



>FitnessBrowser__psRCH2:GFF2099
          Length = 330

 Score =  417 bits (1072), Expect = e-121
 Identities = 201/324 (62%), Positives = 259/324 (79%), Gaps = 7/324 (2%)

Query: 15  LTVAGIVQA-------ADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKVKVEVYPN 67
           +T+AG++ A       A+PIVIKFSHVVA+ TPKG+GAL+FK+L EERL G+V+VEVYPN
Sbjct: 5   ITLAGVLLALASACAQAEPIVIKFSHVVADDTPKGKGALMFKRLAEERLAGQVRVEVYPN 64

Query: 68  SSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRFQQSPQGK 127
           S+LFGD  E+EAL   +VQ++APSLAKFEQYTK+LQ+FDLPFLFD+I+AV+RFQ+  +GK
Sbjct: 65  STLFGDATELEALRNDEVQLLAPSLAKFEQYTKQLQVFDLPFLFDDIEAVNRFQKRAKGK 124

Query: 128 ELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQFKAVRANP 187
           +LL SM+DK ITGL YWHNGMKQLSA + LR+P DA GL FR+Q S VLE QF  V A+ 
Sbjct: 125 QLLRSMEDKNITGLAYWHNGMKQLSATRMLRQPSDASGLSFRIQPSAVLEAQFGTVGAST 184

Query: 188 RKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVITNTKFWNG 247
           +K+ FA+VY  L+ G V G ENPWSNIYS+KMH VQ YI E+DHGVLDYMV++NT+FW G
Sbjct: 185 QKIPFADVYDALRAGTVQGAENPWSNIYSKKMHTVQPYIIETDHGVLDYMVVSNTRFWMG 244

Query: 248 LPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAEWRKAMQP 307
           +P  +R  L   +DEV+  VN++A+ LN+ D++RI +A TSEI+ L+PE+R  WR+AM+P
Sbjct: 245 MPHKIRFELEAILDEVSFMVNREADELNRADRERIRQAGTSEIVALSPEERERWREAMRP 304

Query: 308 VWKKFEGEIGADLIKAAEAANQAQ 331
           VW++FE  IGAD+IKAAE  N+ Q
Sbjct: 305 VWQQFEPVIGADIIKAAETVNRKQ 328


Lambda     K      H
   0.316    0.132    0.376 

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: 343
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: 331
Length of database: 330
Length adjustment: 28
Effective length of query: 303
Effective length of database: 302
Effective search space:    91506
Effective search space used:    91506
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 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 (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