Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E3

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate AO353_01420 AO353_01420 acylaldehyde oxidase

Query= metacyc::MONOMER-20833
         (739 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_01420
          Length = 771

 Score =  335 bits (860), Expect = 4e-96
 Identities = 250/770 (32%), Positives = 379/770 (49%), Gaps = 71/770 (9%)

Query: 13  NLSRRRFLAS-TAVGALVI----GFGLPLGAGRVQAATSAERG--TQVPAFLEIRPDGTV 65
           NLSRR FL   +A GALV+    G+       +   A     G       ++ I  DG+V
Sbjct: 12  NLSRRGFLKGVSATGALVLAASWGWQDAFAEEKKFGAAGMPNGWIDDPKVYVSIAADGSV 71

Query: 66  RLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVR 125
            ++    E GQG  T+++ +V +ELDAD A   V  AP  E    +  G + T GS S+R
Sbjct: 72  TVVCNRSEMGQGVRTSLSMVVADELDADWAMVKVRQAPGDE----VRFGNQDTDGSRSMR 127

Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185
             Y  MRR GA AR ML QA A QW VPVGE   Q  +V+H  +GR LGYG LA +A  +
Sbjct: 128 HWYEPMRRCGAAARTMLEQAAADQWKVPVGECRAQLHKVIHQPTGRELGYGALAVAAGAL 187

Query: 186 PVPDPASITLRDPSQFRWIGKP-VKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLG 244
            VP   S+ L+  S+FR+IGK   K +D  D   G+A+Y  D+  D ML A V      G
Sbjct: 188 AVPARESLRLKQSSEFRYIGKEGTKAIDGADIVNGRAVYGADVHFDGMLFATVARPAVYG 247

Query: 245 MTVGSLRNQS--QVEGMKGVHSVHVLP--------GAVAVVAERWWHAKRAVEAIQVDWQ 294
             V S    +  +V G+  V  +   P        G VAV+A   W A +  EA++++W 
Sbjct: 248 GKVKSFDASAALKVPGVVKVIQIESRPLPSEFQPLGGVAVIASNTWAAIKGREALKIEWD 307

Query: 295 EAAADSALRVMPADFSSDKHR-EFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQY 353
           + A         A + S  +R E  AA   P +   + G++  A+  A + +EA Y+  +
Sbjct: 308 DGA--------NAGYDSIVYRKELEAAALKPGKVVRSTGNIEEAMNSADSSLEAAYYLPH 359

Query: 354 LNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFG 413
           L  + +EP  A+ARF  DG  E W P+QAP + R  IA+R G+   ++T++  LLGG FG
Sbjct: 360 LAQSPMEPMVAVARFK-DGHCEAWAPSQAPQVTRERIAERLGIPFDKVTVNVTLLGGGFG 418

Query: 414 RHFLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVA 473
           R    D       AI   +   + +++ W+RE++        ++    +A+L+  G+P  
Sbjct: 419 RKSKPDFI--LEAAILAKEFPGKAVRVQWTREDDIHCSYFHTVSAEYLKASLNKDGMPSG 476

Query: 474 IEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVG 533
               +     T   A     +       G +  +YAIPN R+          +G++RSV 
Sbjct: 477 WLHRTVAPSITALFAPGMNHEAAFELGMGFTNMAYAIPNVRLENPDAAAHTRVGWYRSVS 536

Query: 534 NSLNDFFYESFLDELADKGGHDPYELRLHLLR-------------------------DNP 568
           N  + F  +SF+DELA K G DP + ++ LL                          D  
Sbjct: 537 NIPHGFAIQSFVDELAHKAGQDPLKYQIKLLGPDRQIDPRTLSEEWNYGESPERYPIDTA 596

Query: 569 RLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSI-ENGKVKVH 627
           RL  +L+ A + +G  ++ P        R  G+A+   F ++ AA+ EV + ++G + VH
Sbjct: 597 RLRGVLETAAKGAGWGRKLP------KGRGLGLAVHYSFVTYVAAVIEVEVKDDGTLIVH 650

Query: 628 DIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPI----LA 683
               A+D G  +NP  + +Q  GA  +GL   +L E  + DGK +  N+ +Y +    LA
Sbjct: 651 KADIAVDCGPQINPERIRSQFEGACVMGLGNAVLGEISFKDGKVQQDNFHMYEVARMSLA 710

Query: 684 PAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           P ++A VH+        +GG+GEP +P +APA+ NA+   TG+R+RSLP+
Sbjct: 711 PKEVA-VHLVTPAGNVPLGGVGEPGVPPIAPALCNAIFAATGKRIRSLPV 759


Lambda     K      H
   0.317    0.134    0.394 

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: 1332
Number of extensions: 66
Number of successful extensions: 10
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: 771
Length adjustment: 40
Effective length of query: 699
Effective length of database: 731
Effective search space:   510969
Effective search space used:   510969
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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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