Alignments for a candidate for adhAqn in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Pseudomonas putida KT2440

Align Alcohol dehydrogenase (quinone), dehydrogenase subunit; ADH; Alcohol dehydrogenase (quinone), acceptor subunit; Alcohol dehydrogenase (quinone), subunit I; Ethanol:Q2 reductase; G3-ADH subunit I; Quinohemoprotein alcohol dehydrogenase; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate PP_2679 PP_2679 quinoprotein ethanol dehydrogenase

Query= SwissProt::P28036
         (738 letters)



>FitnessBrowser__Putida:PP_2679
          Length = 595

 Score =  344 bits (883), Expect = 7e-99
 Identities = 211/587 (35%), Positives = 301/587 (51%), Gaps = 48/587 (8%)

Query: 21  ICAALISGYATMASADDGQGATGEAIIHADDHPGNWMTYGRTYSDQRYSPLDQINRSNVG 80
           + A L++G A  A        + E I+    +P   +T G     QRYSPLD +N +NV 
Sbjct: 16  LSAMLLAGAAHAA-------VSNEEILQDPKNPQQIVTNGLGVQGQRYSPLDLLNVNNVK 68

Query: 81  NLKLAWYLDL--DTNRGQEGTPLVIDGVMYATTNWSMMKAVDAATGKLLWSYDPRVPGNI 138
            L+  W      +  RGQ+  PL+ DGVMY T ++S + AVDA TGK LW YD R+P +I
Sbjct: 69  ELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLWQYDARLPDDI 128

Query: 139 ADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIPPEAELGKQRSYTV 198
             + CCD +NRG A +   V+FGT D +L+AL+  TGK+VWS            +  Y++
Sbjct: 129 --RPCCDVINRGVALYGNLVFFGTLDAKLVALNKDTGKVVWSKKVAD------HKEGYSI 180

Query: 199 DGAPRIAKGRVIIGNGGSEFGARGFVSAFDAETGKVDWRFFTVPNPKN----EPDAASDS 254
             AP I  G++I G  G EFG  G + A++ E G++ W   TV         +  A  + 
Sbjct: 181 SAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENG 240

Query: 255 VLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPWNYKYRSEGKGDN 314
           +   +A +TW P   W  + GG   W    YDP  +L+  G GN +PWN   R    GDN
Sbjct: 241 ISGGEAGKTW-PGDLW--KTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRP---GDN 294

Query: 315 LFLGSIVALKPETGEYVWHFQETPMDQWDFTSDQQIMTLDLPINGETRHVIVHARKNGFF 374
           L+  S +AL P+ G   WHFQ TP D WDF    ++++ +    G+       A +NGFF
Sbjct: 295 LYSSSRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFF 354

Query: 375 YIIDAKTGEFISGKNYV-YVNWASGLDPKTGRPIYNPDALYTLTGKEWYG-----IPGDL 428
           Y++D   G+FI G  +V  + WA+GLD K GRPIYN  +     G E  G      P  L
Sbjct: 355 YVLDRTNGKFIRGFPFVDKITWATGLD-KDGRPIYNDASRPGAPGSEAKGSSVFVAPAFL 413

Query: 429 GGHNFAAMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDSWNLGLDMNK-VGIPDSPEA 487
           G  N+  MA++  TGL Y+P+        N+ G      D WN G+   K      +   
Sbjct: 414 GAKNWMPMAYNKDTGLFYVPS--------NEWG-----MDIWNEGIAYKKGAAFLGAGFT 460

Query: 488 KQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANGEFHAYDATN 547
            +   +D  G + A DP    E WR  +  P  GG+L T G+L+F G   G   A++A  
Sbjct: 461 IKPLNEDYIGVLRAIDPVSGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKT 520

Query: 548 GSDLFHFAADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFLGGLAR 594
           G  ++ F   SG++  PVT+  +G+QYV+V  GWGG  P + G +A+
Sbjct: 521 GDKVWEFQTGSGVLGSPVTWEMDGEQYVSVVSGWGGAVPLWGGEVAK 567


Lambda     K      H
   0.318    0.137    0.440 

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: 1809
Number of extensions: 166
Number of successful extensions: 17
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: 738
Length of database: 595
Length adjustment: 38
Effective length of query: 700
Effective length of database: 557
Effective search space:   389900
Effective search space used:   389900
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 (21.7 bits)
S2: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources