GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_3623
          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.

Links

Downloads

Related tools

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