Alignments for a candidate for adhAqn in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Cupriavidus basilensis 4G11

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 RR42_RS11485 RR42_RS11485 dehydrogenase

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__Cup4G11:RR42_RS11485
          Length = 580

 Score =  351 bits (900), Expect = e-101
 Identities = 223/616 (36%), Positives = 309/616 (50%), Gaps = 65/616 (10%)

Query: 16  LLSCAAALAFSAAVPVAFAQEDTGTAITSSDNGGHPGDWLSYGRSYSEQRYSPLDQINTE 75
           L +  A+L   AAV  A  + D  +          PGD LS+G     QR+S L++INT+
Sbjct: 10  LAATTASLVAQAAVTDAMIENDAKS----------PGDVLSWGMGPQGQRFSTLNRINTK 59

Query: 76  NVGKLKLAWHYDL--DTNRGQEGTPLIVNGVMYATTNWSKMKALDAATGKLLWSYDPKVP 133
           N+ +L  AW +    +  RGQE  PLI +G M+ T ++S++ ALD  TG  LW Y+ ++P
Sbjct: 60  NISQLVPAWSFSFGGEKQRGQEAQPLIHDGKMFVTASYSRIYALDLKTGTKLWKYEHRLP 119

Query: 134 GNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVYTIPKEAQLGHQRS 193
             I    CCD V+RGAA ++  V FGT D +L+ALD KTGK+VW      KE    +   
Sbjct: 120 EGIMP--CCDVVNRGAALYDNLVIFGTLDAQLVALDQKTGKVVW------KEKIEDYAAG 171

Query: 194 YTVDGAPRIAKGKVLIGNGGAEFGARGFVSAFDAETGKLDWRFFTVPNP---ENKPDGAA 250
           Y+   AP I KG VL G  G EFG  G V A DA+TG++ W    V      +   DG  
Sbjct: 172 YSYTAAPLIVKGMVLTGISGGEFGVVGRVEARDAKTGQMVWSRPVVEGHMGYKYDKDGNK 231

Query: 251 SDDILMSKAYPTWGKNGAWKQQGGGGTVWDSLVYDPVTDLVYLGVGNGSPWNYKFRSEGK 310
           +++ +      +W     WK   GG   W    YDP T L Y G GN  PWN   R   K
Sbjct: 232 TENGVTGTQNASW-PGETWKT--GGAATWLGGTYDPQTGLAYFGTGNPGPWNSHMR---K 285

Query: 311 GDNLFLGSIVAINPDTGKYVWHFQETPMDEWDYTSVQQIMTLDMPVNGEMRHVIVHAPKN 370
           GDNL+  S VA++P TGK VWH+Q TP D WD+  V + +T D     + + +   A +N
Sbjct: 286 GDNLYSASTVALDPATGKIVWHYQNTPNDGWDFDGVNEFVTFDQ----DGKRLGGKADRN 341

Query: 371 GFFYIIDAKTGKFITGKPYTYE-NWANGLDPVTGRPNYVPDALWTLTGKPWLG------- 422
           GFFY+ DA +GK +   P+  +  WA+ +D  TGRPN + ++     G P  G       
Sbjct: 342 GFFYVNDATSGKLVNAFPFVKKITWASSIDLKTGRPNMIAESR---PGDPAAGGDPKKGQ 398

Query: 423 ----IPGELGGHNFAAMAYSPKTKLVYIPAQQIPLLYDGQKGGFKAYHDAWNLGLDMNKI 478
                PG LGG N   MAYSP+T L Y+PA +  +             D WN  +   K 
Sbjct: 399 SVFAAPGFLGGKNQQPMAYSPQTGLFYVPANEWGM-------------DIWNEPVGYKKG 445

Query: 479 GLFDDNDPEHVAAKKDFLKVLKGWTVAWDPEKMAPAFTINHKGPWNGGLLATAGNVIFQG 538
             F           +D++  L+    A +P+     + + +  P  GG++ TAG ++F G
Sbjct: 446 AAFLGAGFTIHPLNEDYIGSLR----AINPKTGKIEWEVKNYAPLWGGVMTTAGGLVFWG 501

Query: 539 LANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYTANGKQYVAVEVGWGGIYPFLYGGVAR 598
              G   A DA  G +L+ F   S ++APPVT+   G+QYVAV  GWGG  P   G VA+
Sbjct: 502 TPEGYLKAADAKTGKELWKFQTGSGVVAPPVTWEEGGEQYVAVVSGWGGAVPLWGGEVAK 561

Query: 599 TSGWTVNHSRVIAFSL 614
              +      V  F L
Sbjct: 562 RVNFLEQGGSVWVFKL 577


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: 1789
Number of extensions: 174
Number of successful extensions: 26
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: 580
Length adjustment: 38
Effective length of query: 719
Effective length of database: 542
Effective search space:   389698
Effective search space used:   389698
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