GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_3308
          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.

Links

Downloads

Related tools

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