Alignments for a candidate for adhAqn in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Pseudomonas putida KT2440

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 PP_2674 PP_2674 quinoprotein ethanol dehydrogenase

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__Putida:PP_2674
          Length = 631

 Score =  333 bits (853), Expect = 2e-95
 Identities = 220/623 (35%), Positives = 314/623 (50%), Gaps = 63/623 (10%)

Query: 6   LTPIKVTKKRLLSCAAALAFSAAVPVAFAQEDTGTAITSSDNGGH---PGDWLSYGRSYS 62
           L+P+ ++ + LL   +    + A   +      G  +T  D         D L YG   +
Sbjct: 9   LSPLALSVRVLLMAGSLALGNVATAASTPAAPAGKNVTWEDIANDHLTTQDVLQYGMGTN 68

Query: 63  EQRYSPLDQINTENVGKLKLAWHYDL--DTNRGQEGTPLIVNGVMYATTNWSKMKALDAA 120
            QR+SPL Q+N +NV KL  AW Y    +  RGQE   ++ +GV+Y T ++S++ ALDA 
Sbjct: 69  AQRWSPLAQVNDKNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTGSYSRVFALDAK 128

Query: 121 TGKLLWSYDPKVPGNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVY 180
           TGK LW+Y+ ++P NI  R CCD V+RGAA +  K+YFGT D R+IALD +TGK+VW+  
Sbjct: 129 TGKRLWTYNHRLPDNI--RPCCDVVNRGAAIYGDKIYFGTLDARVIALDKRTGKVVWN-- 184

Query: 181 TIPKEAQLG-HQRSYTVDGAPRIAK----GKVLI--GNGGAEFGARGFVSAFDAETGKLD 233
                 + G H   YT+ GAP + K    GKVL+  G+ G EFG  G + A D +TG+  
Sbjct: 185 -----KKFGDHSAGYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLFARDPDTGEEV 239

Query: 234 WRFFTVPNPENKPDGAASDDILMSKAYPTW--------GKNGAWKQQGGGGTVWDSLVYD 285
           W    V     + +G  S      KA P+W        GK  AW    GGG  W S  +D
Sbjct: 240 WMRPFVEGHMGRLNGKDSTPTGDVKA-PSWPDDPTTETGKVEAWSH--GGGAPWQSASFD 296

Query: 286 PVTDLVYLGVGNGSPWNYKFRSEGKG-----DNLFLGSIVAINPDTGKYVWHFQETPMDE 340
           P T+ + +G GN  PWN   R+   G     D+L+    V ++P TG+  W +Q TP D 
Sbjct: 297 PETNTIIVGAGNPGPWNTWARTSKDGNPHDFDSLYTSGQVGVDPSTGEVKWFYQHTPNDA 356

Query: 341 WDYTSVQQIMTLDMP-VNGEMRHVIVHAPKNGFFYIIDAKTGKFITGKPYTYE-NWANGL 398
           WD++   +++  D    NG +     HA +NGFFY++D   GK     P+     WA+ +
Sbjct: 357 WDFSGNNELVLFDYKDKNGNVVKATAHADRNGFFYVVDRNNGKLQNAFPFVDNITWASHI 416

Query: 399 DPVTGRPNYVPDAL------WTLTGKPWLGIPGELGGHNFAAMAYSPKTKLVYIPAQQIP 452
           D  TGRP   P             GKP    P  LGG N+  MAYS  T L YIP  Q  
Sbjct: 417 DLKTGRPVENPGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTGLFYIPGNQWK 476

Query: 453 LLYDGQKGGFKAYHDAWNLGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGWTVAWDPEKMA 512
             Y  ++  +K       +G  + +  ++DD    HV   +           A DP    
Sbjct: 477 EEYWTEEVNYKKGSAYLGMGFRIKR--MYDD----HVGTLR-----------AMDPTTGK 519

Query: 513 PAFTINHKGPWNGGLLATAGNVIFQGLANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYT 572
             +      P   G+LAT GN++F G  +G F A+DA  G +L+ F   S I++PP+T+ 
Sbjct: 520 LVWEHKEHLPLWAGVLATKGNLVFTGTGDGFFKAFDAKTGKELWKFQTGSGIVSPPITWE 579

Query: 573 ANGKQYVAVEVGWGGIYPFLYGG 595
            +G+QY+ V VG+GG  P L+GG
Sbjct: 580 QDGEQYIGVTVGYGGAVP-LWGG 601


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: 2011
Number of extensions: 184
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: 757
Length of database: 631
Length adjustment: 39
Effective length of query: 718
Effective length of database: 592
Effective search space:   425056
Effective search space used:   425056
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.

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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