Alignments for a candidate for adhAqn in Billgrantia desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Billgrantia desiderata SP1

Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate WP_086511538.1 BZY95_RS19425 methanol/ethanol family PQQ-dependent dehydrogenase

Query= BRENDA::Q44002
         (739 letters)



>NCBI__GCF_002151265.1:WP_086511538.1
          Length = 607

 Score =  296 bits (759), Expect = 2e-84
 Identities = 190/560 (33%), Positives = 282/560 (50%), Gaps = 44/560 (7%)

Query: 47  IHADDHPGNWMTYGRTYSEQRYSPLDQINRSNVGNLKLAWYLDLDTNRGQEGTPLVI-DG 105
           +    +P  W T    Y   R+S LDQINR NV  L+  W       RG EG PL + DG
Sbjct: 27  LELQQNPEYWATQLGNYQGNRFSELDQINRDNVSELRSVWQFSTGVLRGHEGGPLYVGDG 86

Query: 106 VMYATTNW-SMMKAVDAAT-GKLLWSYDPRVPGNIADKGCCDTVNRGAAYWNGKVYFGTF 163
            +Y  T + + + A+D    G+++WSY+P     +    CCDTVNRG AY +G+++ G  
Sbjct: 87  RLYIHTPFPNKVFALDLEDEGRVVWSYEPDQDSRVIPVMCCDTVNRGLAYADGRLFLGQA 146

Query: 164 DGRLIALDAKTGKLVWSVNTIPPEAELGKQRSYTVDGAPRIAKGRVIIGNGGSEFGARGF 223
           D  LIALDA++G+L+W V+    +  +G+  + +    P +    VI+G  G E+G RG 
Sbjct: 147 DNTLIALDAESGELLWDVSN--GDHTVGETNTMS----PLVVHDMVIVGISGGEYGIRGH 200

Query: 224 VTAFDAETGKVDWR-FFTAPNPKN--EPDHTASDSVLMNKA---YQTWSPTGAWTRQGGG 277
           +TA++ ETG++ WR + T P+ +   +P+ T      + +A     TW P   W R  GG
Sbjct: 201 MTAYNVETGEMVWRGYSTGPDDEVLIDPETTLMLGEPIGEADLGVSTW-PEDEWER--GG 257

Query: 278 GTVWDSIVYDPVADLVYLGVGNGSPWNYKYRS-EGK-GDNLFLGSIVALKPETGEYVWHF 335
           G  W  + YDP  DL+Y G GN   WN   R+ +G+  DN +  ++ A  P  G   W +
Sbjct: 258 GAPWGWVTYDPDLDLIYYGTGNPGTWNPDQRAVDGEPADNKWAITVFARDPNDGSVKWVY 317

Query: 336 QETPMDQWDFTSVQQIMTLDLPINGETRHVIVHAPKNGFFYIIDAKTGEFISGKNYV-YV 394
           Q+ P D+WD+  V +   +D+   GE R  +    + GF +++D +TGE +  + +    
Sbjct: 318 QKVPFDEWDYDGVNENQLIDVEFEGEERKGLAIIDRTGFGFLLDRETGELLVAEKFAPET 377

Query: 395 NWASGLDPKTGRPIYNPDALYTLTGKEWYGI------PGDLGGHNFAAMAFSPKTGLVYI 448
           NWA   D +TGRP  N D  Y+ T ++   +      P  +G  N    A+SP+TGL+Y 
Sbjct: 378 NWADSYDMETGRPNVNED--YS-TFRQGVNVNTTDICPTAMGAKNMQPSAYSPRTGLIYA 434

Query: 449 PAQQVPFLY----TNQVGGFTPHPDSWNLGLDMNKVGIPDSPEAKQAFVKDLKGWIVAWD 504
              ++   Y    T  V G  P+     +G  +  +  P     +   ++   G  +AWD
Sbjct: 435 GINRICMNYEPYETEYVAG-QPY-----VGATLTMMPAP----TENGQMEGRMGSFIAWD 484

Query: 505 PQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANGEFHAYDATNGSDLFHFAADSGIIAP 564
           P      W VD +     G LAT GDL F G   G   A D  NG +L+ F   SGII  
Sbjct: 485 PVAGETVWEVDERFAVWSGALATAGDLAFYGTLEGHVKAVDIENGEELWRFKTPSGIIGN 544

Query: 565 PVTYLANGKQYVAVEVGWGG 584
             T++  GKQYVAV  G GG
Sbjct: 545 VNTFMHEGKQYVAVLSGVGG 564


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: 1665
Number of extensions: 139
Number of successful extensions: 15
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: 739
Length of database: 607
Length adjustment: 39
Effective length of query: 700
Effective length of database: 568
Effective search space:   397600
Effective search space used:   397600
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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