Aligments for a candidate for gadh2 in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh2 in Pseudomonas fluorescens FW300-N2E2

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate Pf6N2E2_1903 Putative diheme cytochrome c-553

Query= metacyc::MONOMER-12746
         (434 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1903
          Length = 444

 Score =  398 bits (1023), Expect = e-115
 Identities = 211/410 (51%), Positives = 269/410 (65%), Gaps = 8/410 (1%)

Query: 17  ANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPDK-T 75
           A+A  AD Q LVQ+GEY+AR  DCVACH+   G PFAGGL M TP+G IY+TNITPDK T
Sbjct: 35  ASAPSADAQ-LVQRGEYVARLSDCVACHSTPKGAPFAGGLEMATPMGSIYATNITPDKQT 93

Query: 76  GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDN 135
           GIG+YS  DFD+AVR GVA  G  LYPAMP+PSYA++SD D++ALYA+FM GV P  + N
Sbjct: 94  GIGNYSLADFDRAVRSGVAADGHRLYPAMPYPSYAKLSDDDVRALYAFFMAGVKPAQQQN 153

Query: 136 QDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHTPRA 195
           Q S IPWPL+MRWPL++W   F       A  +  D + +RGAY+V+G GHCG+CHTPR+
Sbjct: 154 QQSHIPWPLNMRWPLALWNTAFVDDGAYQAKPS-EDALWNRGAYIVQGAGHCGSCHTPRS 212

Query: 196 LTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSA 255
           LTM EK+L  S  + FLSGS  L+GW A SLR D   GLG WSE+++V +LKTGR+  S 
Sbjct: 213 LTMNEKSLDESSAT-FLSGSL-LDGWYAPSLRQDPNTGLGRWSEQEIVDYLKTGRNAHSV 270

Query: 256 VFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDDSKPG 315
           V G M++V  +S QYM+D DL AIA YL SLP +  +D P     + A  L     S PG
Sbjct: 271 VVGTMAEVFNNSTQYMSDPDLKAIAHYLVSLPGDPKRDGP---PWKPAAKLAEQPLSTPG 327

Query: 316 AAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTF 375
           AA Y+  C++CH +DG G     P LAG       +  + I+  L G      +  P ++
Sbjct: 328 AANYMAKCSSCHGSDGSGQAPWIPPLAGASSSMVKEGATSINATLNGSERVVANGIPDSY 387

Query: 376 TMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALRNGDLQSTSN 425
            MP +  +LSDQEVADV+ F+R+SWGNQ  AVK  +V  LR     ++SN
Sbjct: 388 RMPPYRNQLSDQEVADVLTFVRTSWGNQGGAVKADEVKELRERTNPASSN 437


Lambda     K      H
   0.316    0.131    0.404 

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: 615
Number of extensions: 31
Number of successful extensions: 5
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: 434
Length of database: 444
Length adjustment: 32
Effective length of query: 402
Effective length of database: 412
Effective search space:   165624
Effective search space used:   165624
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: 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources