Alignments for a candidate for adhAqn in Pandoraea thiooxydans ATSB16

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Pandoraea thiooxydans ATSB16

Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate WP_047215054.1 PATSB16_RS15940 PQQ-dependent dehydrogenase, methanol/ethanol family

Query= BRENDA::Q44002
         (739 letters)



>NCBI__GCF_001931675.1:WP_047215054.1
          Length = 575

 Score =  295 bits (755), Expect = 4e-84
 Identities = 189/597 (31%), Positives = 279/597 (46%), Gaps = 42/597 (7%)

Query: 18  AGTICAALISGYATMASADDGQGATGEAIIHADDHPGNWMTYGRTYSEQRYSPLDQINRS 77
           AG + A+ ++  A  A   D    T + +  A   PG W+TY R+Y+ Q  SPL QIN +
Sbjct: 15  AGVLLASGLAIGAASAQTADYPAVTYDRLTSAQADPG-WLTYYRSYTGQSNSPLKQINTA 73

Query: 78  NVGNLKLAWYLDL--DTNRGQEGTPLVIDGVMYATTNWSMMKAVDAATGKLLWSYDPRVP 135
              +L+  W      +  +G E TP+V    M+ TT    + A DA TGK LW+YDP++ 
Sbjct: 74  TAKDLQQVWSYKFPAELQQGFEATPIVNGNYMFVTTPKDHVYAFDAKTGKELWTYDPKLT 133

Query: 136 GNIADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIPPEAELGKQRS 195
                  CCD VNRG A +   VY     G+++ALDA++GK+VW      P         
Sbjct: 134 SLSFKTACCDVVNRGVALYGKNVYVAMLSGQVVALDAQSGKVVWEKQLFEPGI------G 187

Query: 196 YTVDGAPRIAKGRVIIGNGGSEFGARGFVTAFDAETGKVDWRFFTAPNPKNEPDHTASDS 255
           Y    AP   K  +I+G+ G E+GARGF+ A +   G++ W+ +T P P           
Sbjct: 188 YAFTLAPLALKDSIIVGSSGGEYGARGFIAALNPANGEIQWKRWTVPAPN---------- 237

Query: 256 VLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPWNYKYRSEGKGDN 315
               K   TW P G +  Q  G   W +  YD   + ++ GVGN  PW    R    G N
Sbjct: 238 ---EKGGNTW-PNGMY--QHAGSPAWLTGTYDVKTNTLFWGVGNPGPWLADMR---PGKN 288

Query: 316 LFLGSIVALKPETGEYVWHFQETPMDQWDFTSVQQIMTLDLPINGETRHVIVHAPKNGFF 375
           L+  S++AL P  G+  WHFQ T  D WD+  V   +  ++   G+    I+HA +NG+ 
Sbjct: 289 LYSDSLLALDPANGDLKWHFQYTSHDTWDYDGVNTPVLANITYKGKHYEAIIHADRNGYI 348

Query: 376 YIIDAKTGEFISGKNYVYVNWASGLDPKTGRPIYNPDALYTLTGKEWYGIPGDLGGHNFA 435
           + ID   G+ I  K +V     +G     G PI N    Y   G      P  LGG N+ 
Sbjct: 349 HAIDRTNGKLIYAKPFVKATSVTGY-TAAGVPIQN-QKHYPKVGTTIETCPSFLGGKNWW 406

Query: 436 AMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDSWNLGLDMNKVGIPDSPEAKQAFVKD 495
           ++++ P T L ++P+       + +         ++  GL     G    PE       +
Sbjct: 407 SVSYDPTTHLAFVPSLHACMTMSGKA-------VTYMQGLPYLGEGFEIRPEPGSKGYGE 459

Query: 496 LKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANGEFHAYDATNGSDLFHF 555
           L+    A D     + W    K PWNGG+ +T G L+F G  NG  +A+D  NG  L+  
Sbjct: 460 LQ----AIDVNTGKKVWSHWSKLPWNGGVASTAGGLVFSGSLNGHLYAFDQKNGKVLWES 515

Query: 556 -AADSGIIAPPVTYLANGKQYVAVEVGWGGIYPFFLGGLARTSGWTVNHSRIIAFSL 611
               SG+IA P  +  +G +YVAV  G+GG  P + G +A+ +        +  F+L
Sbjct: 516 PQLASGVIAQPSVFEVDGTEYVAVLAGYGGANPIWGGPMAKIAEHVPRGGTLYVFAL 572


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: 1693
Number of extensions: 149
Number of successful extensions: 23
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: 739
Length of database: 575
Length adjustment: 38
Effective length of query: 701
Effective length of database: 537
Effective search space:   376437
Effective search space used:   376437
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 24 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 2024 update 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