Alignments for a candidate for adhAqn in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Klebsiella michiganensis M5al

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 BWI76_RS04950 BWI76_RS04950 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= SwissProt::P28036
         (738 letters)



>FitnessBrowser__Koxy:BWI76_RS04950
          Length = 796

 Score =  161 bits (408), Expect = 1e-43
 Identities = 183/689 (26%), Positives = 264/689 (38%), Gaps = 143/689 (20%)

Query: 18  AGTICAALISG-YATMASADDGQGATGEAIIHADDHP---------GNWMTYGRTYSDQR 67
           AG + A LISG   T A  +D Q   G   + AD  P         G+W  YGR    QR
Sbjct: 122 AGLVVALLISGGILTWAGFNDPQEVNGT--LSADATPAAPISEVADGDWSAYGRNQEGQR 179

Query: 68  YSPLDQINRSNVGNLKLAWY-----LDLDTNRGQ---EGTPLVIDGVMYATTNWSMMKAV 119
           YSPL QIN  NV NLK AW      L    + G+   E TP+ +   +Y  T    + A+
Sbjct: 180 YSPLKQINADNVKNLKEAWVFRTGDLKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFAL 239

Query: 120 DAATGKLLWSYDPRVPGNIADKGCCDTVNRGAAYWNGK---------------VYFGTFD 164
           DAATGK  W +DP++    AD        RG +Y   K               +     D
Sbjct: 240 DAATGKEKWHFDPQLN---ADPSFQHVTCRGVSYHEAKADNAPADVVADCPRRIILPVND 296

Query: 165 GRLIALDAKTGKLVWS-----VNTIPPEAELGKQRSYTVDGAPRIAKGRVIIGNGGSE-F 218
           GRL A++A+TGKL  S     +  +     +     Y     P I    ++I    ++ F
Sbjct: 297 GRLFAINAETGKLCESFANKGILNLQTNMPVTTPGMYEPTSPPIITDKTIVIAGAVTDNF 356

Query: 219 GAR---GFVSAFDAETGKVDWRFFTVPNPKNEPDAASDSVLMNKAYQTWSPTGAWTRQGG 275
             R   G +  FD  TGK+ W F   P  K +P+A  D       +   SP         
Sbjct: 357 STREPSGVIRGFDVNTGKLLWAFD--PGAK-DPNAIPDD---EHHFTLNSPNS------- 403

Query: 276 GGTVWDSIVYDPVADLVYLGVGNGSP--WNYKYRSEGKGDNLFLGSIVALKPETGEYVWH 333
               W    YD   DLVYL +G  +P  W      E      +  SIVAL   TG+  W 
Sbjct: 404 ----WAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPE---QERYASSIVALNATTGKLAWS 456

Query: 334 FQETPMDQWDFTSDQQIMTLDLPINGETRHVIVHARKNGFFYIIDAKTGEFI--SGKNYV 391
           +Q    D WD     Q    D+ +NG+T  VI    K G  +++D + GE +  + +  V
Sbjct: 457 YQTVHHDLWDMDMPSQPTLADIDVNGKTVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPV 516

Query: 392 YVNWASGLDPKTGRPI----YNPDALYTLTGKEWYG------------------------ 423
               A G      +P     + P     LTG + +G                        
Sbjct: 517 PQGAAKGDYVAKTQPFSDLSFRPKK--DLTGADMWGATMFDQLVCRVIFHQLRYEGIFTP 574

Query: 424 --------IPGDLGGHNFAAMAFSPKTGLVYIPAQQVPFLY------------------- 456
                    PG+LG   +  ++  P   +       +PF+                    
Sbjct: 575 PSEQGTLVFPGNLGMFEWGGISVDPNRQVAIANPMALPFVSKLIPRGPGNPMEQPKDAKG 634

Query: 457 TNQVGGFTPH---PDSWNLGLDMNKVGIP-DSPEAKQAFVKDLKGWIVAWDPQ----KQA 508
           +    G  P    P    L   ++  G+P   P        DLK   V W  +    + +
Sbjct: 635 SGTEAGIQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDS 694

Query: 509 EAWRVDHKGPWNGGI------LATGGDLLFQG-LANGEFHAYDATNGSDLFHFAADSGII 561
             + +  K P+  G+      ++T G++LF G  A+    AY+ +NG  L+     +G  
Sbjct: 695 LPFPMPVKLPFTMGMPMLGGPISTAGNVLFIGATADNYLRAYNMSNGEKLWQARLPAGGQ 754

Query: 562 APPVTYLANGKQYVAVEVGWGGIYPFFLG 590
           A P+TY  NGKQYV +  G  G +   +G
Sbjct: 755 ATPMTYEVNGKQYVVISAGGHGSFGTKMG 783


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: 2086
Number of extensions: 168
Number of successful extensions: 19
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 2
Length of query: 738
Length of database: 796
Length adjustment: 41
Effective length of query: 697
Effective length of database: 755
Effective search space:   526235
Effective search space used:   526235
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: 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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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