GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gadh2 in Pseudomonas putida KT2440

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate PP_3623 PP_3623 Alcohol dehydrogenase cytochrome c subunit

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



>lcl|FitnessBrowser__Putida:PP_3623 PP_3623 Alcohol dehydrogenase
           cytochrome c subunit
          Length = 447

 Score =  400 bits (1028), Expect = e-116
 Identities = 211/405 (52%), Positives = 268/405 (66%), Gaps = 12/405 (2%)

Query: 15  AAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPDK 74
           A A A  AD  ALV +GEY+AR  DCVACH+   GKPFAGGL M TP+G I++TNITPD+
Sbjct: 36  ADAQATAADP-ALVSRGEYVARLSDCVACHSLPGGKPFAGGLEMATPLGAIHATNITPDR 94

Query: 75  -TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVAR 133
            +GIG+Y+  DFD+AVR GVA GG  LYPAMP+PSYA++SD D++ALYA+FM GV P  +
Sbjct: 95  DSGIGNYTLADFDRAVRQGVAPGGRRLYPAMPYPSYAKLSDDDVKALYAFFMHGVQPARQ 154

Query: 134 DNQDSDIPWPLSMRWPLSIWRWMFAPSVETP-APAAGSDPVISRGAYLVEGLGHCGACHT 192
            N  SDIPWPL++RWP+++W  +FA +  TP    AG D   +RGAY+V+G GHCG+CHT
Sbjct: 155 ANLGSDIPWPLNLRWPIALWNGLFAAT--TPYTDKAGQDAQWNRGAYIVQGPGHCGSCHT 212

Query: 193 PRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSD 252
           PR L   EKAL  S G  FLSG A L+GW A SLR DH  GLG WSE ++ QFLKTGR+ 
Sbjct: 213 PRGLAFNEKALDDS-GKPFLSG-ALLDGWYAPSLRADHNTGLGRWSEAEIAQFLKTGRNR 270

Query: 253 RSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKD-QPHQYDKQVAQALWNGDD 311
            + V+G M++   +S Q+M D DL AIA YLKSLP +  +D  P  Y    A++L    D
Sbjct: 271 HAVVYGSMTEAFNNSTQFMHDDDLAAIAHYLKSLPGDPQRDGAPWHYQ---AESLATRLD 327

Query: 312 SKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSA 371
           S PGA  Y+  CA+CH  DG G     P LAG     + ++ S I+I L G         
Sbjct: 328 S-PGARTYVTRCASCHGLDGKGQAEWMPPLAGATSALAKESASAINITLNGSQRVVAAGV 386

Query: 372 PSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
           P  + MPA   +LSDQE+ADV++F+R++WGNQ  AV    V  LR
Sbjct: 387 PDAYRMPALREQLSDQEIADVLSFVRTAWGNQGGAVDAQAVGKLR 431


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: 639
Number of extensions: 34
Number of successful extensions: 6
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: 447
Length adjustment: 32
Effective length of query: 402
Effective length of database: 415
Effective search space:   166830
Effective search space used:   166830
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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