GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Dyella japonica UNC79MFTsu3.2

Align ornithine aminotransferase; EC 2.6.1.13 (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase

Query= CharProtDB::CH_122124
         (454 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3308 N515DRAFT_3308
           acetylornithine/N-succinyldiaminopimelate
           aminotransferase
          Length = 411

 Score =  250 bits (638), Expect = 7e-71
 Identities = 154/400 (38%), Positives = 222/400 (55%), Gaps = 19/400 (4%)

Query: 33  YHPLPVVFARAQGTSVWDPEGRHYLDFLSAYSAVNQ-GHCHPKLVAALVDQASRLTLSSR 91
           Y P  VV    +G  VWD EGR Y+D L A  AVN  GH  P LV ALV QA +L  SS 
Sbjct: 22  YRPREVVLDHGKGARVWDTEGRDYVD-LGAGIAVNALGHQDPDLVDALVTQARKLWHSSN 80

Query: 92  AFYNDVFPKFAEMVTKYFGF-DMVLPMNTGAEAVETGIKIARKWGYKVKGIPENEAIILS 150
            FY +     AE + +  GF + V   N+G EA E  IK+ RKW    KG    + +IL+
Sbjct: 81  VFYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKLVRKWAAS-KGRAPEQRVILT 139

Query: 151 AENNFHGRTMAAISLSSDPESRENYGPYVPNIGCTIPGTEKPITYNDKAALREAFEKAGS 210
              +FHGRT+AA++ ++ P+ +ENY P        +PG  + + +ND A L  AF  A  
Sbjct: 140 FRGSFHGRTLAAVTATAQPKYQENYEP--------LPGGFRYLDFNDVAGLEAAF--AQG 189

Query: 211 NLAAFLVEPIQGEAGIIVPDDDYLQLARSLCDQHNVLLICDEIQTGIARTGKLLCHEWSG 270
           ++AA ++EP+QGE G++     +++ AR LCD H  LL+ DEIQ G+ RTG L  H   G
Sbjct: 190 DVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDG 249

Query: 271 IKPDMVLLGKAISGGMYPVSCVLGRKDVMLTVEPGTHGSTYGGNPLACAVAIRALEVVQE 330
           + PD+V L KA+  G +P+  +L    V   ++ G HG+T+GGNP+A AVA  AL  +  
Sbjct: 250 VTPDIVTLAKALGCG-FPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLAS 308

Query: 331 ENMVERAEKLGQAFRSGLEAIQN--PIIQTVRGKGLLNAIVIDESKTNGHTAWDLCMLMK 388
             ++    K  QA R GL AI     +   VRG+GL+   V+ E+      A ++     
Sbjct: 309 AELMANVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKG--RAGEVLDHAA 366

Query: 389 EKGLLAKPTHQNIIRLAPPLVITEEEIAKALEIIKAAVAE 428
             GLL      +++R  PPL IT+ ++A+ L  ++AA+A+
Sbjct: 367 AHGLLVLQAGPDVLRFVPPLNITDADLAEGLARLRAALAD 406


Lambda     K      H
   0.316    0.133    0.392 

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: 408
Number of extensions: 25
Number of successful extensions: 6
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: 454
Length of database: 411
Length adjustment: 32
Effective length of query: 422
Effective length of database: 379
Effective search space:   159938
Effective search space used:   159938
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 (21.6 bits)
S2: 51 (24.3 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 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