GapMind for catabolism of small carbon sources

 

Aligments for a candidate for drdehyd-cytc in Pseudomonas fluorescens FW300-N2E2

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate Pf6N2E2_1903 Putative diheme cytochrome c-553

Query= reanno::WCS417:GFF2133
         (447 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1903 Putative diheme
           cytochrome c-553
          Length = 444

 Score =  625 bits (1612), Expect = 0.0
 Identities = 297/442 (67%), Positives = 347/442 (78%), Gaps = 2/442 (0%)

Query: 8   RTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHS 67
           +T  +L    +V A  L W+V R P +PF  E +  + +  LV RGEYVARLSDCVACHS
Sbjct: 3   KTIKYLLPAGIVVAAGLGWFVNRTPFSPFANEASAPSADAQLVQRGEYVARLSDCVACHS 62

Query: 68  LAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAM 127
               APFAGGLEMATP+G+I+ATNITPDK TGIG YSLADFDRAVR GVA  G RLYPAM
Sbjct: 63  TPKGAPFAGGLEMATPMGSIYATNITPDKQTGIGNYSLADFDRAVRSGVAADGHRLYPAM 122

Query: 128 PYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYA 187
           PYPSY KLSDDD++ALYAFFM G+KPA Q N  S IPWPLNMRWP+ALWN  F     Y 
Sbjct: 123 PYPSYAKLSDDDVRALYAFFMAGVKPAQQQNQQSHIPWPLNMRWPLALWNTAFVDDGAYQ 182

Query: 188 AKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLR 247
           AKP +DALWNRGAYIVQG GHCGSCHTPR L  NEK+LDE+ A FL+G+LLDGWYAPSLR
Sbjct: 183 AKPSEDALWNRGAYIVQGAGHCGSCHTPRSLTMNEKSLDESSATFLSGSLLDGWYAPSLR 242

Query: 248 QDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLP 307
           QDPNTGLGRWSE +IV +LKTGRNAH+VV G+M E FNNSTQ+M D DL AIA YL SLP
Sbjct: 243 QDPNTGLGRWSEQEIVDYLKTGRNAHSVVVGTMAEVFNNSTQYMSDPDLKAIAHYLVSLP 302

Query: 308 GDPQRDGAPWQYQAVAAVQ--DAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAK 365
           GDP+RDG PW+  A  A Q    PGA  Y  +C+SCHG DG GQ  W+PPLAGA+S++ K
Sbjct: 303 GDPKRDGPPWKPAAKLAEQPLSTPGAANYMAKCSSCHGSDGSGQAPWIPPLAGASSSMVK 362

Query: 366 ESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDAN 425
           E A++IN TLNGS+RVVA+G+PD+YRMP +R QLSD E+A+VL++VR++WGN GGAV A+
Sbjct: 363 EGATSINATLNGSERVVANGIPDSYRMPPYRNQLSDQEVADVLTFVRTSWGNQGGAVKAD 422

Query: 426 AVGKLRGHTDPASSSPIILHMR 447
            V +LR  T+PASS+PIIL MR
Sbjct: 423 EVKELRERTNPASSNPIILQMR 444


Lambda     K      H
   0.318    0.133    0.423 

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: 772
Number of extensions: 31
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: 447
Length of database: 444
Length adjustment: 32
Effective length of query: 415
Effective length of database: 412
Effective search space:   170980
Effective search space used:   170980
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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