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) (EC 1.1.5.5) (characterized)
to candidate GFF2017 Psest_2060 PQQ-dependent dehydrogenase, methanol/ethanol family

Query= BRENDA::Q44002
         (739 letters)



>FitnessBrowser__psRCH2:GFF2017
          Length = 592

 Score =  339 bits (869), Expect = 3e-97
 Identities = 219/611 (35%), Positives = 299/611 (48%), Gaps = 67/611 (10%)

Query: 8   KRRSLSRTLTAGTICAALISGYATMASADDGQGATGEAIIHADDHPGNWMTYGRTYSEQR 67
           K   L +      +CAA+        S+      T + I++        +T G     QR
Sbjct: 2   KHTGLRKPFALTALCAAVAM------SSLHAWAVTDQEILNDAKSTDQIVTNGMGLQGQR 55

Query: 68  YSPLDQINRSNVGNLKLAWYLDL--DTNRGQEGTPLVIDGVMYATTNWSMMKAVDAATGK 125
           YS LD +N +N+  L+  W   L  +  RGQE  PL+ DGVMY T ++S + AVDA TGK
Sbjct: 56  YSTLDALNANNINQLRPVWGFSLGGEKQRGQEAQPLIKDGVMYITGSYSRVYAVDARTGK 115

Query: 126 LLWSYDPRVPGNIADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIP 185
            LW YD R+P  I    CCD +NRG A ++  V FGT D +L+AL+  TGK+VW      
Sbjct: 116 ELWQYDARLPDGIMP--CCDVINRGVALYDDLVIFGTLDAKLVALNKDTGKVVWKKTVAD 173

Query: 186 PEAELGKQRSYTVDGAPRIAKGRVIIGNGGSEFGARGFVTAFDAETGKVDWRFFTAPNPK 245
            +A       Y++  AP I KG++I G  G EFG  G + A++ + G++ W   T P  +
Sbjct: 174 YKA------GYSLTAAPLIVKGKLITGVSGGEFGVVGKIEAYNPKNGELLW---TRPTVE 224

Query: 246 NEPDHTASDS------VLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGN 299
               +   D       +   +A +TW P   W  + GG   W    YDP  D +  G GN
Sbjct: 225 GHMGYVWKDGKKVESGISGGEAGKTW-PGDLW--KTGGAAPWLGGYYDPDTDSLLFGTGN 281

Query: 300 GSPWNYKYRSEGKGDNLFLGSIVALKPETGEYVWHFQETPMDQWDFTSVQQIMTLDLPIN 359
            +PWN   R    GDNL+  S +AL P  G   WHFQ TP D WD+  V ++++ D    
Sbjct: 282 PAPWNSHLRP---GDNLYSSSRLALDPNDGSIKWHFQTTPHDGWDYDGVNELVSFDYQEG 338

Query: 360 GETRHVIVHAPKNGFFYIIDAKTGEFISGKNYV-YVNWASGLDPKTGRPIYNP------- 411
           G+T      A +NGFFY++D   G+FI G  +V  + WA GLD K GRPIY+        
Sbjct: 339 GKTIKAAGTADRNGFFYVLDRTNGKFIRGFPFVDKITWAKGLD-KNGRPIYDDANRPGSP 397

Query: 412 -DALYTLTGKEWYGIPGDLGGHNFAAMAFSPKTGLVYIPAQQVPFLYTNQVGGFTPHPDS 470
            DA     GK     P  LGG N+  MA+S  TGL Y+P+ +                D 
Sbjct: 398 NDA--GAQGKTVTVAPSFLGGKNWMPMAYSQDTGLFYVPSNEWSM-------------DI 442

Query: 471 WNLGLDMNK------VGIPDSPEAKQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPWNGGI 524
           WN G    K       G    P        D  G + A DP+   E WR  +  P  GG+
Sbjct: 443 WNEGTAYKKGAAYLGAGFTIHP-----LNDDYIGVLRAIDPKTGKEVWRYKNYAPLWGGV 497

Query: 525 LATGGDLLFQGLANGEFHAYDATNGSDLFHFAADSGIIAPPVTYLANGKQYVAVEVGWGG 584
           LAT G+L+F G   G   A+DA  G  L+ F   SG+I  PVT+  +G+QYV+V  GWGG
Sbjct: 498 LATKGNLVFTGNPEGYLMAFDAKTGKKLYEFNTGSGVIGSPVTWEMDGEQYVSVLSGWGG 557

Query: 585 IYPFFLGGLAR 595
             P + G +A+
Sbjct: 558 AVPLWGGEVAK 568


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: 1908
Number of extensions: 182
Number of successful extensions: 21
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: 592
Length adjustment: 38
Effective length of query: 701
Effective length of database: 554
Effective search space:   388354
Effective search space used:   388354
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 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