Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2C3

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate AO356_20105 AO356_20105 acylaldehyde oxidase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_20105
          Length = 771

 Score =  354 bits (908), Expect = e-101
 Identities = 258/771 (33%), Positives = 392/771 (50%), Gaps = 73/771 (9%)

Query: 13  NLSRRRFL-ASTAVGALVIG--FGLP--LGAGRVQAATSAERGT--QVPAFLEIRPDGTV 65
           NLSRR FL  ++A G LV+   +GLP      +   A     G       ++ I  DG+V
Sbjct: 12  NLSRRGFLKGASATGVLVLAATWGLPDAFAEEKKFGAEGMPHGAVDDPKVYVSIASDGSV 71

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

Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185
             Y  MRR GA AR ML  A A QW VPVGE   Q  +V+H  SGR LGYGELA++A  +
Sbjct: 128 HWYEPMRRCGAAARTMLELAAAAQWKVPVGECHAQLHKVLHQPSGRELGYGELAAAASAL 187

Query: 186 PVPDPASITLRDPSQFRWIGKPVKR-LDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLG 244
            VP   S+ L+ PS+FR+IGK   R +D  D   G+A++  D+  D ML+A +   P  G
Sbjct: 188 AVPARDSLRLKQPSEFRYIGKEASRAIDGADIVNGRAVFGADVHFDGMLYAVIARPPVYG 247

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

Query: 295 EAAADSALRVMPADFSSDKHR-EFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQY 353
           +           A + S  +R E  AA   P +   + GD+  AL  A + +EA+Y+  +
Sbjct: 308 DGP--------NAGYDSIAYRKELEAAALKPGKVVRSSGDLDDALAKADSTLEASYYLPH 359

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

Query: 414 RHFLYDSANPYPQAIALAKAV-SRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPV 472
           R    D      +A  LAK    + +++ W+RE++        ++    +A L+  G+P 
Sbjct: 419 RKSKPDFV---VEAAVLAKEFPGQAVRVQWTREDDIHHSYFHTVSAEYLKAGLNQDGMPS 475

Query: 473 AIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSV 532
                +     T   A     +       G++  +YAIPN R+          +G++RSV
Sbjct: 476 GWLHRTVAPSITALFAPGMTHEAPFEIGMGVTNMAYAIPNLRLENPEAVAHARVGWYRSV 535

Query: 533 GNSLNDFFYESFLDELADKGGHDPYELRLHLLR-------------------------DN 567
            N  + F  +SF+DELA K G DP + ++ LL                          D 
Sbjct: 536 SNIPHGFAIQSFIDELAHKAGQDPLKYQVKLLGPDRKIDPRTLSEEWNYGESPERYPIDT 595

Query: 568 PRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSI-ENGKVKV 626
            R+ T+L+ A + + GW R     E    R  G+A+   F ++ AA+ EV + ++G V V
Sbjct: 596 ARIRTVLETAAK-AAGWGR-----ELPKGRGLGLAVHYSFVTYVAAVLEVEVKDDGTVIV 649

Query: 627 HDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPI----L 682
           H    A+D G  +NP  + +Q  GA  +GL   ++ E  + DGK +  N+ +Y +    L
Sbjct: 650 HKADIAVDCGPQINPERIRSQFEGACVMGLGNAMVGEISFKDGKVQQDNFHMYEVARMSL 709

Query: 683 APAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           AP ++A VH+        +GG+GEP +P +APA+ NA+   TGQR+R+LP+
Sbjct: 710 APKEVA-VHLVTPPGEVPLGGVGEPGVPPIAPALCNAIFAATGQRIRNLPV 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: 1381
Number of extensions: 72
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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, or view the source code.

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