Alignments for a candidate for adhBqn in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhBqn in Acidovorax sp. GW101-3H11

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 Ac3H11_3427 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

Query= SwissProt::Q47945
         (478 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3427
          Length = 1243

 Score =  220 bits (561), Expect = 2e-61
 Identities = 152/428 (35%), Positives = 212/428 (49%), Gaps = 42/428 (9%)

Query: 17   GWKLAAAIGLMAVSFGAAHAQDADEALIKRGEYVARLSDCIACHTALHGQPYAGGLEIKS 76
            GW+ + A  +  V     +A     A I+RG  +A   DC  CHTA  G P  GG  +++
Sbjct: 830  GWRPSIAPVVQTVGASVYNA-----ATIERGRLLAAAGDCAVCHTAPGGTPNTGGRAMET 884

Query: 77   PIGTIYSTNITPDPEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRA 136
            P G IY+TN+TPD E GIG ++   F +A+R+GI + G  +YPA PY  FA++SDDD+ A
Sbjct: 885  PFGKIYTTNLTPDAETGIGQWSFSAFQRAMREGISQGGKHLYPAFPYTSFAKMSDDDLTA 944

Query: 137  MYAFFMHGVKPVALQNKAPDISWPLSMRWPLGMWRAMFVPSMTPGVDKSISDPEVARGEY 196
            +YA+ M     V  +    ++++P S+R  +  W A+F    TP        PE  RG Y
Sbjct: 945  LYAYLM-AQPAVRAEVPKTELTFPFSVRPLMAGWNALF-HDATPFKPDPTRPPEWNRGAY 1002

Query: 197  LVNGPGHCGECHTPRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGR--- 253
            LV G GHCG CHTPR       A G   G A    GA ID W AP+L     TGL +   
Sbjct: 1003 LVQGVGHCGACHTPR------NALGAELGGAAFLSGAMIDGWEAPAL-----TGLSKAPV 1051

Query: 254  -WSEDDIVTFLKSGRI-DHSAVFGGMADVVAYSTQHWSDDDLRATAKYLKSMPAVPEGKN 311
             W+ D +  +L+ G    H +  G MA VV     H  DDD+RA A YL S  A      
Sbjct: 1052 PWTADALYGYLRHGHSPQHGSASGPMAPVVR-ELAHLPDDDIRAMASYLASFTAAEAATQ 1110

Query: 312  LGQDD--------GQTTALLNKGGQGNAGAEVYLHNCAICHMN-DGTGVNRMFPPLAGNP 362
               D          Q  AL  + GQ      ++   CA CH + DG  +  +  PLA N 
Sbjct: 1111 PVSDPQQRAQTAVAQAAALAPQPGQAQ---RLFDGACAACHHDGDGPKLLGVNVPLALNS 1167

Query: 363  VVITDDPTSLANVVAFGGILPPTNSAPSAVAMPGFKNHLSDQEMADVVNFMRKGWGNNAP 422
             + +D P +L  V+  G   P   +A     MPGF + LSD ++ ++  +MR+ +   AP
Sbjct: 1168 NLHSDRPDNLLQVIVHGIREP---AARDIGFMPGFGHALSDAQITELAGYMRQRY---AP 1221

Query: 423  GTVSASDI 430
            G  +  D+
Sbjct: 1222 GRPAWRDV 1229


Lambda     K      H
   0.317    0.134    0.421 

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: 1790
Number of extensions: 121
Number of successful extensions: 9
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: 478
Length of database: 1243
Length adjustment: 41
Effective length of query: 437
Effective length of database: 1202
Effective search space:   525274
Effective search space used:   525274
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