Alignments for a candidate for adhAqn in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1752 Quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.99.8)

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1752
          Length = 726

 Score =  595 bits (1533), Expect = e-174
 Identities = 321/719 (44%), Positives = 439/719 (61%), Gaps = 33/719 (4%)

Query: 16  LLSCAAALAFSAAVPVAFAQEDTGTA----ITSSDNGGHPGDWLSYGRSYSEQRYSPLDQ 71
           L S A AL  S A   A A E         + ++D    PG+W+S GR+Y EQRYSPL +
Sbjct: 21  LKSLAGALLLSLATASALASETPANVDSQRLIAADK--EPGNWMSTGRTYDEQRYSPLKR 78

Query: 72  INTENVGKLKLAWHYDLDTNRGQEGTPLIVNGVMYATTNWSKMKALDAATGKLLWSYDPK 131
           I+ +NVG+L LAW Y LD +RG E TP++V+GVMY T  +S + ALDA  GKL+W YDP+
Sbjct: 79  ISDQNVGQLGLAWSYKLDLDRGVEATPIVVDGVMYTTGPFSVVYALDARNGKLIWKYDPQ 138

Query: 132 VPGNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVYTIPKEAQLGHQ 191
              N A   CCD V+RG A W GKVY G  DGRL A+DAKTG+  WSV T     +  H+
Sbjct: 139 SDRNRAGEACCDAVNRGVAVWKGKVYVGVLDGRLEAIDAKTGQRAWSVDT-----RADHK 193

Query: 192 RSYTVDGAPRIAKGKVLIGNGGAEFGARGFVSAFDAETGKLDWRFFTVPNPENKPDGAAS 251
           RSYT+ GAPR+  GKV+IGNGGAEFG RG+V+A+DAETGK  WRF+TVP     P     
Sbjct: 194 RSYTITGAPRVVNGKVVIGNGGAEFGVRGYVTAYDAETGKQAWRFYTVPGDPKLPP---- 249

Query: 252 DDILMSKAYPTWGKNGAWKQQGGGGTVWDSLVYDPVTDLVYLGVGNGSPWNYKFRSEGKG 311
           +D  M+ A  TW    A+ +QGGGGT WDS  +DP  +L+Y+GVGNGS W+ K+RS+ KG
Sbjct: 250 EDKGMAIAAKTW-HGDAFVEQGGGGTAWDSFAFDPDLNLLYIGVGNGSLWDPKWRSQAKG 308

Query: 312 DNLFLGSIVAINPDTGKYVWHFQETPMDEWDYTSVQQIMTLDMPVNGEMRHVIVHAPKNG 371
           DNLFL SIVA+N DTG+YVWH+Q TP D WDYT+ Q ++  ++P++G+ R V++ APKNG
Sbjct: 309 DNLFLSSIVAVNADTGEYVWHYQTTPGDAWDYTATQHMILAELPIDGKPRKVLMQAPKNG 368

Query: 372 FFYIIDAKTGKFITGKPYTYENWANGLDPVTGRPNYVPD--ALWTLTGKPWLGIPGELGG 429
           FFY+ID  TG+ ++ K    ++W  G+D  TGRP  V D  A +   GK  L  P   G 
Sbjct: 369 FFYVIDRATGQLLSAKGIVPQSWTKGMDMKTGRP-IVDDENAAYWKDGKRKLVTPAFWGA 427

Query: 430 HNFAAMAYSPKTKLVYIPAQQIPLLYDGQKGGFKAYHDAWNLGLDMNKIGLFDDNDPEHV 489
           H++  M+Y+P T LVYIPA  +   Y+      K      N    M ++GL     PE+V
Sbjct: 428 HDWQPMSYNPNTGLVYIPAHIMSAYYEHIPEAPKR-----NPFKSMYQLGLRTGMMPENV 482

Query: 490 AAKKDFLKVLKGWT---VAWDPEKMAPAFTINHKGPWNGGLLATAGNVIFQGLANGEFHA 546
                 L++ KGW+   +AWDP K  PA+ + +   +NGG L+TAGN++F+G A+G   A
Sbjct: 483 ---DGLLEMAKGWSGKLIAWDPVKQQPAWEVPYVTIFNGGTLSTAGNLVFEGSADGRVIA 539

Query: 547 YDATNGNDLYSFPAQSAIIAPPVTYTANGKQYVAVEVGWGGIYPFLYGGVARTSGWTVNH 606
           Y A  G  L+  PA S ++A P+TY+ +G+QYV    GWGG +    G ++  +G     
Sbjct: 540 YAADTGKKLWEQPAASGVMAAPITYSVDGEQYVTFMAGWGGAFSTFAGALSLRAG-VQPF 598

Query: 607 SRVIAFSLDGKDSLPPKNELGFTPVKPVPTYDEARQKDGYFMYQTFCSACHGDNAISGGV 666
           S+V+ + + G   L        TP  P  + D A  + G  +Y  +CS CHG +A+SGGV
Sbjct: 599 SQVLTYKIGGTAKLQEPAPRPDTPKPPALSTDTAAIEAGGKLYDGYCSQCHGIHAVSGGV 658

Query: 667 LPDLRWSGAPRGRESFYKLVGRGALTAYGMDRFDTSMTPEQIEDIRNFIVKRANESYDD 725
           LPDLR    P   + F  ++  G +   GM  F  + TPEQ++ I  +++KRA++  D+
Sbjct: 659 LPDLR-KLTPEKHQMFLGILFGGRVPD-GMPSFADAFTPEQVDQIHQYLIKRAHDLQDE 715


Lambda     K      H
   0.317    0.136    0.435 

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: 2198
Number of extensions: 155
Number of successful extensions: 19
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: 757
Length of database: 726
Length adjustment: 40
Effective length of query: 717
Effective length of database: 686
Effective search space:   491862
Effective search space used:   491862
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: 55 (25.8 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