GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adhBqn in Pseudomonas putida KT2440

Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate PP_3623 PP_3623 Alcohol dehydrogenase cytochrome c subunit

Query= SwissProt::P0A388
         (468 letters)



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

 Score =  389 bits (1000), Expect = e-113
 Identities = 207/413 (50%), Positives = 262/413 (63%), Gaps = 12/413 (2%)

Query: 23  AQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYG 82
           AQ   AD ALV +G YVARL DCVACH+   G+ +AGGLE+ +P+G I++TNITPD   G
Sbjct: 38  AQATAADPALVSRGEYVARLSDCVACHSLPGGKPFAGGLEMATPLGAIHATNITPDRDSG 97

Query: 83  IGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDK 142
           IG YT A+FD AVR G+   G  LYPAMPYPS+++++ +D++ALYA+FMHGV+P  Q + 
Sbjct: 98  IGNYTLADFDRAVRQGVAPGGRRLYPAMPYPSYAKLSDDDVKALYAFFMHGVQPARQANL 157

Query: 143 QPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGF 202
             DI WPL++RWP+ +W  +F+ +   +T   G D +  RG Y+V GPGHCG+CHTPRG 
Sbjct: 158 GSDIPWPLNLRWPIALWNGLFA-ATTPYTDKAGQDAQWNRGAYIVQGPGHCGSCHTPRGL 216

Query: 203 AMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAV 262
           A  EKALD +G P FLS GA +D W APSLR D   GLGRWSE +I  FLK+GR  H+ V
Sbjct: 217 AFNEKALDDSGKP-FLS-GALLDGWYAPSLRADHNTGLGRWSEAEIAQFLKTGRNRHAVV 274

Query: 263 FGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGN--YTYDPSTANMLASGNTASV 320
           +G M +    STQ+  DDDL AIA YLKSLP  P   G   +    S A  L S      
Sbjct: 275 YGSMTEAFNNSTQFMHDDDLAAIAHYLKSLPGDPQRDGAPWHYQAESLATRLDS------ 328

Query: 321 PGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPS 380
           PGA TYV  CA CH  DG G A   PPLAG    + +   S +N+  +G     +   P 
Sbjct: 329 PGARTYVTRCASCHGLDGKGQAEWMPPLAGATSALAKESASAINITLNGSQRVVAAGVPD 388

Query: 381 AVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTGAPVSSS 433
           A  MP   + LS Q+IADV++F+RT+WGN+  G V A  V KLR    P SSS
Sbjct: 389 AYRMPALREQLSDQEIADVLSFVRTAWGNQG-GAVDAQAVGKLRGHTDPASSS 440


Lambda     K      H
   0.317    0.134    0.425 

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: 687
Number of extensions: 30
Number of successful extensions: 4
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: 468
Length of database: 447
Length adjustment: 33
Effective length of query: 435
Effective length of database: 414
Effective search space:   180090
Effective search space used:   180090
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 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