Alignments for a candidate for adhAqn in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Pseudomonas simiae WCS417

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 GFF3412 PS417_17460 quinonprotein alcohol dehydrogenase

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__WCS417:GFF3412
          Length = 615

 Score =  325 bits (834), Expect = 3e-93
 Identities = 219/607 (36%), Positives = 312/607 (51%), Gaps = 66/607 (10%)

Query: 21  AALAFSAAVPVAFAQEDTGTAITSSDNGGHPGDWLSYGRSYSEQRYSPLDQINTENVGKL 80
           +A+ F+AA P    +  T   I +        D L YG   + QR+SPL Q+N +NV KL
Sbjct: 13  SAVTFAAAEPAKPTRTVTWEDIANDHLTTQ--DVLQYGMGTNAQRWSPLAQVNDKNVFKL 70

Query: 81  KLAWHYDL--DTNRGQEGTPLIVNGVMYATTNWSKMKALDAATGKLLWSYDPKVPGNIAD 138
             AW Y    +  RGQE   ++ +GV+Y T ++S++ ALDA TGK LW+Y+ ++P NI  
Sbjct: 71  TPAWSYSFGDEKQRGQESQAIVSDGVVYVTGSYSRVFALDAKTGKRLWTYNHRLPDNI-- 128

Query: 139 RGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVYTIPKEAQLG-HQRSYTVD 197
           R CCD V+RGAA +  K+YFGT D RLIALD  TGK+VW+        + G H   YT+ 
Sbjct: 129 RPCCDVVNRGAAIFGDKIYFGTLDARLIALDKNTGKVVWN-------KKFGDHAAGYTLT 181

Query: 198 GAPRIAK----GKVLI--GNGGAEFGARGFVSAFDAETGKLDWRFFTVPNPENKPDGAAS 251
           GAP + K    GKVL+  G+ G EFG  G + A D +TG+  W    V     + +G  S
Sbjct: 182 GAPVLIKDKVSGKVLLIHGSSGDEFGVVGQLFARDPDTGEEVWMRPFVEGHMGRLNGKDS 241

Query: 252 DDILMSKAYPTW--------GKNGAWKQQGGGGTVWDSLVYDPVTDLVYLGVGNGSPWNY 303
                 KA P+W        GK  AW    GGG  W S  +D  T+ + +G GN  PWN 
Sbjct: 242 TPTGDVKA-PSWPDDPTTETGKVEAWSH--GGGAPWQSASFDAETNTIIVGAGNPGPWNT 298

Query: 304 KFRSEGKG-----DNLFLGSIVAINPDTGKYVWHFQETPMDEWDYTSVQQIMTLDMP-VN 357
             R+   G     D+L+    V ++P TG+  W +Q TP D WD++   +++  D    +
Sbjct: 299 WARTAKDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDAWDFSGNNELVLFDYKDKD 358

Query: 358 GEMRHVIVHAPKNGFFYIIDAKTGKFITGKPYTYE-NWANGLDPVTGRP------NYVPD 410
           G++     HA +NGFFY++D   GK     P+     WA+ +D  TGRP           
Sbjct: 359 GKVVKATGHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHIDLKTGRPVENEGQRPAKP 418

Query: 411 ALWTLTGKPWLGIPGELGGHNFAAMAYSPKTKLVYIPAQQIPLLYDGQKGGFKAYHDAWN 470
                 GKP    P  LGG N+  MAYS  T L YIP  Q    Y  ++  +K       
Sbjct: 419 LPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWKEEYWTEEVNYKKGSAYLG 478

Query: 471 LGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGWT--VAWDPEKMAPAFTINHKGPWNGGLL 528
           +G  + +  ++DD    HV      L+ +   T  V W+ ++  P +          G+L
Sbjct: 479 MGFRIKR--MYDD----HVGT----LRAMNPTTGKVVWEHKEALPLWA---------GVL 519

Query: 529 ATAGNVIFQGLANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYTANGKQYVAVEVGWGGI 588
           AT GN++F G  +G F A+DA  G +L+ F   S I++PP+T+  +G+QYV V VG+GG 
Sbjct: 520 ATKGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWEQDGEQYVGVTVGYGGA 579

Query: 589 YPFLYGG 595
            P L+GG
Sbjct: 580 VP-LWGG 585


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: 1955
Number of extensions: 184
Number of successful extensions: 24
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: 615
Length adjustment: 39
Effective length of query: 718
Effective length of database: 576
Effective search space:   413568
Effective search space used:   413568
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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