Alignments for a candidate for adhBqn in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhBqn in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03306 H281DRAFT_03306 Cytochrome c, mono- and diheme variants

Query= SwissProt::P0A388
         (468 letters)



>FitnessBrowser__Burk376:H281DRAFT_03306
          Length = 434

 Score =  365 bits (937), Expect = e-105
 Identities = 197/435 (45%), Positives = 264/435 (60%), Gaps = 15/435 (3%)

Query: 1   MINRLKVTFSAAAFSLLAGTALAQTPD-------ADSALVQKGAYVARLGDCVACHTALH 53
           M+ R K+   A    L A T    T +       A +ALV +G Y+A+  DC  CHTA+ 
Sbjct: 1   MMRRFKLIVLAGTAMLGAFTTPCVTAEPAGASDPALAALVARGEYLAKASDCAGCHTAVG 60

Query: 54  GQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYP 113
           GQ+Y GGL + SP GTI S+NITPD  YGIG Y++ +F  +VR G+      LYPAMPY 
Sbjct: 61  GQAYGGGLGLTSPFGTIMSSNITPDRRYGIGAYSYEDFARSVREGVSPGNKRLYPAMPYA 120

Query: 114 SFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPA 173
           SFS+M+ +DM+ALYAYFMHGVKP  +P     +++P + RW L  W++ F+P+ + + P 
Sbjct: 121 SFSKMSDDDMRALYAYFMHGVKPAPEPAPPTKLAFPFNQRWVLYFWQLAFAPT-EPYRPK 179

Query: 174 PGTDPEIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLR 233
            G D +  RG +LV GPGHCGACHTPRG   QE+  D +  P +L+GG   DNW  P+L 
Sbjct: 180 AGRDAQWNRGAFLVQGPGHCGACHTPRGPGFQERGYDES-SPMYLTGGVN-DNWFGPNLT 237

Query: 234 NDPVVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLP 293
            DP  GLGR  E D+  FLK+G       FG M + V  STQY TD+D  A+A Y+KSLP
Sbjct: 238 GDPGSGLGRIGEKDLAAFLKTGHGAGLVAFGSMVEQVEDSTQYLTDEDALAMAHYVKSLP 297

Query: 294 PVPPSQGNYTYDPSTANMLASGNTASVP---GADTYVKECAICHRNDGGGVARMFPPLAG 350
              PS G+Y           +GN    P   GA  Y+  CA CH   G G+  +FP LAG
Sbjct: 298 AQKPS-GSYEPHAQPDLPTRNGNRVDAPQSVGARVYISFCARCHGVQGAGMPNVFPRLAG 356

Query: 351 NPVVVTENPTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNK 410
           NP V+TE+ TSL+ ++  GG  P +   P   AMPG++++L+  Q+A+V+++IRTSWGN 
Sbjct: 357 NPSVITEDTTSLIRLMVEGGNSPATISGPPRQAMPGFAQTLTNAQMANVLSWIRTSWGND 416

Query: 411 APGTVTAADVTKLRD 425
           A   VTA D+  LR+
Sbjct: 417 A-RPVTANDIQSLRE 430


Lambda     K      H
   0.317    0.134    0.425 

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: 742
Number of extensions: 40
Number of successful extensions: 5
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: 468
Length of database: 434
Length adjustment: 33
Effective length of query: 435
Effective length of database: 401
Effective search space:   174435
Effective search space used:   174435
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: 51 (24.3 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