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

GapMind for catabolism of small carbon sources

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

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 H281DRAFT_00328 H281DRAFT_00328 alcohol dehydrogenase (cytochrome c)

Query= SwissProt::P28036
         (738 letters)



>FitnessBrowser__Burk376:H281DRAFT_00328
          Length = 575

 Score =  306 bits (785), Expect = 1e-87
 Identities = 200/610 (32%), Positives = 296/610 (48%), Gaps = 44/610 (7%)

Query: 8   KRRSLS--RTLTAGTICAALIS-GYATMASADDGQGATGEAIIHADDHPGNWMTYGRTYS 64
           K RS+S  R     T  AA++S   AT A ADD    T + +  A   PG W+TY RTY+
Sbjct: 2   KARSISVLRPRALATSVAAVVSLSCATAAFADDYPAVTYDRLSAAQSDPG-WLTYYRTYN 60

Query: 65  DQRYSPLDQINRSNVGNLKLAWYLDL--DTNRGQEGTPLVIDGVMYATTNWSMMKAVDAA 122
            Q +SPL QI+ SNV  LK  W      D  +G E TP+V    ++ TT    + A DAA
Sbjct: 61  GQAHSPLKQIDTSNVKQLKQVWSYKFPADLQQGFEATPIVNGHYLFVTTPKDNVYAFDAA 120

Query: 123 TGKLLWSYDPRVPGNIADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVN 182
           +GK LW ++P++        CCD +NRG A +   VY    +G ++ALDA+TG L W   
Sbjct: 121 SGKQLWKFEPKLGAESFKTACCDVINRGVALYGKNVYVAMLNGEVVALDAQTGSLAWRKT 180

Query: 183 TIPPEAELGKQRSYTVDGAPRIAKGRVIIGNGGSEFGARGFVSAFDAETGKVDWRFFTVP 242
              P         Y    AP    G +++G+ G E+GARGF++A + + G V W+ FTVP
Sbjct: 181 MFEPGV------GYAFSLAPLAIDGALVVGSAGGEYGARGFIAALNPDNGNVLWKRFTVP 234

Query: 243 NPKNEPDAASDSVLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPW 302
                  AA +     K   TW P G   ++ GG   W +  YD  +  +Y GVGN  PW
Sbjct: 235 -------AAGE-----KGANTW-PDG--MQEHGGAPAWLTGTYDAASRTLYWGVGNPGPW 279

Query: 303 NYKYRSEGKGDNLFLGSIVALKPETGEYVWHFQETPMDQWDFTSDQQIMTLDLPINGETR 362
               R    GDNL+  S++AL P+TG+  WH+Q T  D WD+      +  ++    +  
Sbjct: 280 LADLR---PGDNLYSDSLLALDPKTGDLKWHYQYTKHDTWDYDGVNTPVLANIKYQDKNY 336

Query: 363 HVIVHARKNGFFYIIDAKTGEFISGKNYVYVNWASGLDPKTGRPIYNPDALYTLTGKEWY 422
             I+HA +NG+F+ ID  TG+ I  K +V     +G     G P+ +P + Y  TG    
Sbjct: 337 DAIIHADRNGYFHAIDRGTGKLIYAKPFVKATSVTGY-TADGVPVQDP-SKYPKTGTTIE 394

Query: 423 GIPGDLGGHNFAAMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDSWNLGLDMNKVGIP 482
             P  LGG N+ ++++ P   +  +PA       + +         ++  GL     G  
Sbjct: 395 TCPSFLGGKNWWSVSYDPDRQVAIVPALHACMSLSGK-------SVTYMEGLPYLGEGFE 447

Query: 483 DSPEAKQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANGEFHA 542
             PE       +L+    A D     + W    K PWNGG+  T   L F G  +G  +A
Sbjct: 448 IKPEPGSKGYGELQ----AIDVTTGKKMWSYWSKLPWNGGVATTASGLAFSGSLDGHLYA 503

Query: 543 YDATNGSDLFHF-AADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFLGGLARTSGWTVN 601
           +D++ G  L+      SGI+A P  +  +GK+YVA+  G+GG  P + G +A+ +     
Sbjct: 504 FDSSTGKVLWKSPKLASGIVAQPSVFEVDGKEYVAILAGYGGANPIWGGPMAKAAEKIPR 563

Query: 602 HSRIIAFSLD 611
              +  F+L+
Sbjct: 564 GGTLYVFALN 573


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: 1610
Number of extensions: 137
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: 738
Length of database: 575
Length adjustment: 38
Effective length of query: 700
Effective length of database: 537
Effective search space:   375900
Effective search space used:   375900
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 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