GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1903
          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.

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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