GapMind for Amino acid biosynthesis

 

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

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1410 N515DRAFT_1410
           methionine aminotransferase
          Length = 381

 Score =  271 bits (693), Expect = 2e-77
 Identities = 164/389 (42%), Positives = 218/389 (56%), Gaps = 13/389 (3%)

Query: 4   SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63
           ++L    TT+F+ MS LA    AVNLGQGFPD + P  + +A   A+A G NQY PG G 
Sbjct: 5   TKLPKVGTTIFSVMSQLAVEHQAVNLGQGFPDFEPPQALREAIARAMAEGRNQYAPGIGL 64

Query: 64  APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123
             LR  IA +  R +G   D   EV VT GATEA+ AA+  +V  G EV++ +P YDSY 
Sbjct: 65  PTLREQIALKTERMYGRRIDAAGEVTVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYE 124

Query: 124 PVVAMAGAHRVTVPL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182
           PV+ + GA  V +PL VP    F +D   +R AVTPRTR ++INSPHNP+GAVLSA +L 
Sbjct: 125 PVIELQGAKAVHIPLTVPS---FGVDWQRVRDAVTPRTRMILINSPHNPSGAVLSAADLD 181

Query: 183 AIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIG 242
            +A I     +VV++DEVYEH+VFD A H  +     +A R+I +SS  K ++CTGWK+G
Sbjct: 182 QLAAIVRDTEIVVLSDEVYEHIVFDGALHQSVLRHAELAARSIVVSSFGKTYHCTGWKLG 241

Query: 243 WACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGL 302
           +A  PA L A  R   QYL++    P Q A A  + +       L    +A+RDR  A +
Sbjct: 242 YAVAPAALSAEFRKVHQYLTFCTFHPAQVAFAEFMASTPEHYLELPAFYQAKRDRFRALI 301

Query: 303 TEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQ 362
               F + D  G YF   D   +  +    FC  L ++ GVAAIP++ F + A       
Sbjct: 302 APSRFKLLDVPGGYFQLVDYSAIRDEPDVTFCEWLVKQGGVAAIPLAPFYETAPD----- 356

Query: 363 ADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391
                 LVR  F K D T+D A  RL  L
Sbjct: 357 ----TRLVRLCFAKSDATMDAAAERLCKL 381


Lambda     K      H
   0.321    0.135    0.405 

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: 397
Number of extensions: 15
Number of successful extensions: 3
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: 397
Length of database: 381
Length adjustment: 30
Effective length of query: 367
Effective length of database: 351
Effective search space:   128817
Effective search space used:   128817
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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