GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_3623
          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:

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