GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Paraburkholderia bryophila 376MFSha3.1

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_02718 H281DRAFT_02718 Glycine/D-amino acid oxidase (deaminating)

Query= BRENDA::Q8U022
         (378 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02718 H281DRAFT_02718
           Glycine/D-amino acid oxidase (deaminating)
          Length = 466

 Score =  104 bits (260), Expect = 4e-27
 Identities = 62/200 (31%), Positives = 101/200 (50%), Gaps = 2/200 (1%)

Query: 2   IGIIGGGIIGVATAYELAKLGEEVVVFEKRYFGSGSTFRCASGIRAQFTDEANIKLMKYS 61
           + +IGGGI+GV+TAYELA+ G +VV+ EK   G   + R    +R Q  D   + L   S
Sbjct: 43  VAVIGGGIVGVSTAYELARRGVQVVLLEKGVIGGEQSGRNWGWVRQQNRDLYELPLAMQS 102

Query: 62  IERWKTLSEELGHNIMFQQTGYLFLATTEEEVEAFKKNIKLQNKFGVPTRLITPEEAKEI 121
           + RW+ LS ELG +I F++ G L+    + +V  ++  I    + G  + +++  E    
Sbjct: 103 LRRWEELSGELGEDIGFRRAGILYGTELQSDVAQWESWIARAREIGFNSEILSARELAAR 162

Query: 122 VPPLNADAFLAGAWNPEDGKASPFHTLYAYKKAGERLGVKFYEYTKVVGIEKD-GSKWKI 180
           +P   A  +  G W+  DG+A P     A  +  +RLG + ++   V  ++   G    I
Sbjct: 163 IPSGRA-RWAGGLWSITDGRAEPSKAAPAIARGAQRLGARVFQNCAVRSLDMSAGRVGGI 221

Query: 181 KTTRGEFKVDIIINATNAWA 200
            T RG    D ++ A  AW+
Sbjct: 222 WTERGRLAADTVVLAGGAWS 241



 Score = 46.6 bits (109), Expect = 1e-09
 Identities = 30/106 (28%), Positives = 48/106 (45%), Gaps = 14/106 (13%)

Query: 275 EFVKEVLKWAVKIIPALKHVHVVRQWAGHYAKTPDKNPAIGMIE--ENFYVAVGFSGHGF 332
           E+++  L+   ++ P L  + +   WAG    TPD  P I  ++      +A GFSGHGF
Sbjct: 364 EWLERGLRNVARVFPELSGLRIAHAWAGAIDTTPDLVPIISKVDAKPGLVIASGFSGHGF 423

Query: 333 MMAPAVAQALAEKIVEGKTKVPLDWEWFDPWRFERGELRASAFQIG 378
            + P  A  LA ++V  +             +F+ G  R + F  G
Sbjct: 424 GLGPG-AGLLASRLVMNEAP-----------QFDMGPYRLTRFSDG 457


Lambda     K      H
   0.318    0.137    0.420 

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: 436
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 378
Length of database: 466
Length adjustment: 32
Effective length of query: 346
Effective length of database: 434
Effective search space:   150164
Effective search space used:   150164
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, 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