GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_02718
          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 (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:

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. 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:

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:

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