GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Pseudomonas fluorescens FW300-N2C3

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate AO356_30205 AO356_30205 alcohol dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_30205
          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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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