Alignments for a candidate for sdh in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Pseudomonas fluorescens FW300-N2C3

Align Glycerol dehydrogenase large subunit; EC 1.1.99.22; D-arabitol dehydrogenase large subunit; ARDH; D-sorbitol dehydrogenase subunit SldA; SLDH; Gluconate/polyol dehydrogenase large subunit (uncharacterized)
to candidate AO356_30385 AO356_30385 quinoprotein glucose dehydrogenase

Query= curated2:Q8KIL1
         (740 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30385
          Length = 811

 Score =  519 bits (1337), Expect = e-151
 Identities = 288/700 (41%), Positives = 397/700 (56%), Gaps = 30/700 (4%)

Query: 49  TENSPKSQSYFAGPSPYA------PQAPGVNAANLPDIESIDPSQVPAMAPQQSANPARG 102
           T   P+    FAG    A        A G +A + P +     SQ PA  PQ  AN  R 
Sbjct: 130 TRKLPRGWPSFAGGLVAAIALGSVSHAFGPDAPDFPMLRRGVQSQAPAKLPQPLANNERT 189

Query: 103 DWVAYGRDDHQTRYSPLSEITPENASKLKVAFVYHTGSYPRPGQVNKWAAETTPIKVGDG 162
           DW AYG D   TR+SPL++I   N SKL    V+     P  G +N  A E TPI +G  
Sbjct: 190 DWQAYGNDQGGTRFSPLADIDTTNVSKL--VKVWEADMAPVNGDLN--AIEGTPIMMGSS 245

Query: 163 LYTCSAMNDIIKLDPATGKQIWRRNVDVKYHSIPYTAA-CKGVTYFTSSVVPEGQP-CHN 220
           LY C   N I   D  TGK++WRR++    + +P +   C+GV Y+    VP+    C  
Sbjct: 246 LYACDGNNGIHAFDAETGKELWRRDIS---NGVPQSGKPCRGVAYYK---VPDANGFCSE 299

Query: 221 RLIEGTLDMRLIAVDAETGDFCPNFGHGGQVNLMQGLGESVPGFVSMTAPPPVINGVVVV 280
           R+   + +  L+A+DA+TG++CP FG+ G V+L +G+     G   +++ P VI G +VV
Sbjct: 300 RIYAPSHNPTLVALDAKTGEYCPGFGNNGAVDLTKGVAPYPHGLFYVSSAPQVIRGKIVV 359

Query: 281 NHEVLDGQRRWAPSGVIRGYDAESGKFVWAWDVNNSDDHSQPTGNRHYSRGTPNSWATMT 340
              + DGQ    PSGVIR +DA +G+  WA+D    +    P   ++Y+  TPNSWA ++
Sbjct: 360 GGGIPDGQYWGGPSGVIRAFDAVTGELAWAFDAGAPNRLGLPPEGQYYTPSTPNSWAPIS 419

Query: 341 GDNEEGLVYVPTGNSAADYYSALRSDAENKVSSAVVAIDVKTGSPRWVFQTAHKDVWDYD 400
            D + GLVY+P GN+  D Y   R   +  +SSAV+A+D +TG  RW FQ  H D+WDYD
Sbjct: 420 ADEKLGLVYLPVGNATPDAYGGQRRPYDEDISSAVIALDAETGRLRWKFQATHHDIWDYD 479

Query: 401 IGSQATLMDMPGPDGQTVPALIMPTKRGQTFVLDRRTGKPILPVEERPAPSPGVIPGDPR 460
           + SQ TL++ P   G   PALI PTKRG+ FVLDR TG+PI  VEE+P P   +  G+  
Sbjct: 480 VASQPTLLNWPTAKGMR-PALIQPTKRGEIFVLDRETGEPIKAVEEQPVPQRDIAKGEWL 538

Query: 461 SPTQPWSVGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYVGEFTPPSVDKPWIEYP 520
           SPTQP SV +PA R P L+E DMWG +PIDQ+ CRI F+++ Y G+FTP ++DK  +  P
Sbjct: 539 SPTQPASVELPAFRGPQLREKDMWGATPIDQMVCRIMFKQSRYEGQFTPITLDKNVLIDP 598

Query: 521 GYNGGSDWGSMSYDPQSGILIANWNITPMYDQLVTRKKADSLGLMPIDDPNFKPG-GGGA 579
           G  GG +W  +S D   G++I NW   P   +LVTR++A              PG   G 
Sbjct: 599 GSMGGVNWNGISLDVDRGLMIVNWTQVPDRIELVTREEATQRNF------RIAPGLDAGG 652

Query: 580 EGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGP 639
           +    M  TPYG     F  Q  G+ CN PP+G+I A+D+  G K++W  P G+ R  GP
Sbjct: 653 QAEQPMLDTPYGAYRVNFLSQ-LGIPCNAPPWGLIGAVDLVSG-KLIWSKPFGSPRDIGP 710

Query: 640 WGLPTGLPWEIGTPNNGGSVVTGGGLIFIGAATDNQIRAIDEHTGKVVWSAVLPGGGQAN 699
           +GLPT +   IGTP  GG+V T GGL+FIG A ++  RA+D  TG+ +WS+ L     A 
Sbjct: 711 FGLPTLVSIPIGTPTAGGAVTTRGGLVFIGGAAEHTFRALDAATGRELWSSRLATSANAT 770

Query: 700 PMTYEA--NGHQYVAIMAGGHHFMMTPVSDQLVVYALPDA 737
           PMTY +  +G Q+V +  GG     T    +LV +A+PD+
Sbjct: 771 PMTYRSPVSGRQFVVVAEGGRPHYRTKPGSKLVAFAIPDS 810


Lambda     K      H
   0.315    0.135    0.430 

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: 2166
Number of extensions: 155
Number of successful extensions: 12
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: 740
Length of database: 811
Length adjustment: 41
Effective length of query: 699
Effective length of database: 770
Effective search space:   538230
Effective search space used:   538230
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 (21.5 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