Alignments for a candidate for adhAqn in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Pseudomonas stutzeri RCH2

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 GFF1386 Psest_1423 PQQ-dependent dehydrogenase, methanol/ethanol family

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__psRCH2:GFF1386
          Length = 710

 Score =  451 bits (1159), Expect = e-131
 Identities = 264/689 (38%), Positives = 360/689 (52%), Gaps = 50/689 (7%)

Query: 53  DWLSYGRSYSEQRYSPLDQINTENVGKLKLAWHYDLDTNRGQEGTPLIVNGVMYATTNWS 112
           DWL+YGR++SEQR+SPL  IN ENV  LK  W+  L       GTPL+V+GVMY     +
Sbjct: 44  DWLAYGRTHSEQRFSPLKDINVENVSGLKPEWYAPLPDRSDIVGTPLVVDGVMYYVGEMN 103

Query: 113 KMKALDAATGKLLWSYDPKVPGNIADRGCCDTV---SRGAAYWNGKVYFGTFDGRLIALD 169
           + +A DA TGK+LW YDP+V   I D          +RG + +  K++  T+DGRLIA+ 
Sbjct: 104 RTRAFDARTGKMLWEYDPQVSKEIIDNNMKKVFWKHNRGLSTYGDKLFIATWDGRLIAIT 163

Query: 170 AKTGKLVWSVYTIPKEAQLGHQRSYTVDGAPRIAKGKVLIGNGGAEFGA-RGFVSAFDAE 228
            K GK VW   T        H +   + G P+   GKV +GNGG E G  RG+V+A+D E
Sbjct: 164 RKDGKEVWQTRTFD------HDQPLNITGHPKAFDGKVFVGNGGTELGPMRGYVTAYDTE 217

Query: 229 TGKLDWRFFTVPNPENKPDGAASDDILMSKAYPTWGKNGAWKQQGGGGTVWDSLVYDPVT 288
           TGK  WRF+ VP   N  DG   +D     A  TW   G W + GGGG  W    YD   
Sbjct: 218 TGKQVWRFYIVPG--NPADGF--EDAAQEMAAKTW--TGRWWENGGGGNAWHGWTYDEKY 271

Query: 289 DLVYLGVGNGSPWNYKFRSEGKGDNLFLGSIVAINPDTGKYVWHFQETPMDEWDYTSVQQ 348
           + +  G GNG PWN K RS   GDNLFL S+VA++ DTG+Y WH Q  P D WDY S   
Sbjct: 272 NQLIFGTGNGGPWNIKVRSPDGGDNLFLCSVVAVDADTGEYKWHVQTAPGDTWDYNSNMD 331

Query: 349 IMTLDMPVNGEMRHVIVHAPKNGFFYIIDAKTGKFITGKPYTYENWANGLDPVTGRPNYV 408
           I+  D+ ++G+    ++HAPKNGFFY ID   GK ++ + +T  NW+   D    R    
Sbjct: 332 IVLADLKIDGKDVDAVLHAPKNGFFYTIDRSNGKVLSAEKFTDANWSTKYDLKEQRHIVA 391

Query: 409 PDALWTLTGKPWLGIPGELGGHNFAAMAYSPKTKLVYIPAQQIPLLYDGQKGGFKAYHDA 468
            DA +    K     P   G H++ AM+Y+P+  L +IP   +   +       K  H  
Sbjct: 392 EDARYPDGEKNI--YPSAFGAHSWHAMSYNPELNLAFIPTNHLGNTFKDDGKDTKPGHKM 449

Query: 469 WNLGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGWTVAWDPEKMAPAFTINHKGPWNGGLL 528
            +  L +   G     DP             +G   AWDP K    + +N K PW GG L
Sbjct: 450 ASHKLYLGLTGWELTKDPHE----------SRGSLQAWDPVKNKRVWQVNQKSPWGGGTL 499

Query: 529 ATAGNVIFQGLANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYTANGKQYVAVEVGWGGI 588
            TAGN++FQG  +G   AYDA  G++L+S+     I APP+TY  +GKQ V++ VG GG 
Sbjct: 500 TTAGNLVFQGQPDGMLKAYDARTGDELWSYDVGLGISAPPITYKLDGKQMVSLLVGPGGA 559

Query: 589 YPFLYGGVA----RTSGWT--VNHSRVIAFSLDGKDSLPPKNELGFTPVKPVPTYDEARQ 642
               +GG       + GW   V+  R++ FSLDGK  +P +      P    P  DE  +
Sbjct: 560 LASNFGGSGELGFESHGWKYGVHERRIMTFSLDGKAVIPEQP----APQLAKPIIDEKFE 615

Query: 643 KD--------GYFMYQTFCSACHGDNAISGGVLPDLRWSG--APRGRESFYKLVGRGALT 692
            D        G F  +  C  CHG  A++G   PDLR S      G ++F  +V  GAL 
Sbjct: 616 VDAKKAEAGAGVFA-ENLCVGCHGAGAVAGMKAPDLRESPILLKGGEKAFESVVRGGALL 674

Query: 693 AYGMDRFDTSMTPEQIEDIRNFIVKRANE 721
           A GM +F + +T  ++E IR+F+ ++A +
Sbjct: 675 ANGMPKF-SDLTDAELESIRHFVRRQARD 702


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: 2108
Number of extensions: 188
Number of successful extensions: 18
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: 710
Length adjustment: 40
Effective length of query: 717
Effective length of database: 670
Effective search space:   480390
Effective search space used:   480390
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