GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate RR42_RS21085 RR42_RS21085 3-isopropylmalate dehydratase

Query= uniprot:LEUC_DESVH
         (419 letters)



>FitnessBrowser__Cup4G11:RR42_RS21085
          Length = 435

 Score =  296 bits (758), Expect = 8e-85
 Identities = 175/424 (41%), Positives = 239/424 (56%), Gaps = 11/424 (2%)

Query: 4   TLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSF-RAMGAKRVFDKDRVAL 62
           TLAQK++ R         G IV CRV + +++D + P  +    R +GAK V+D +R  +
Sbjct: 13  TLAQKLVARAAGLERVTPGTIVTCRVDLAMSHDSSGPRRVAPLLRELGAK-VWDPERYVV 71

Query: 63  VMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGA 122
           V DH+ P  D EA   V+ TR++ RE  + H+ +G   G+ H +LPE G V PG  +VG 
Sbjct: 72  VTDHYLPAADPEAQAIVRFTRDWVREARLPHFIDGE--GICHLVLPEHGHVLPGRFIVGG 129

Query: 123 DSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLILTL 182
           DSH+ T G  GA+  G+G+T++AG +A GE W +VP TIR  + G L A V AKD++L L
Sbjct: 130 DSHSPTGGAFGAYMFGIGATEMAGVLATGEIWLRVPHTIRLQWDGKLSAGVCAKDIMLFL 189

Query: 183 IGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTTAG 242
            G +G+DG  Y A+E+ G A+ AL ++ RMT+ NM+ E G + GL A DA T  +   AG
Sbjct: 190 CGRLGLDGGRYEAIEYTGEAVTALPMQERMTLTNMSAELGAQTGLIAPDATTRAWLAQAG 249

Query: 243 ----RTGDTAFS---ADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQV 295
               +    A S   ++ GA       FD   + P VA PH P N  PV +     V   
Sbjct: 250 VPAAKLDAIALSHWRSEPGAPVLASHRFDAAALAPQVAAPHSPANTGPVDQAAGQRVDIA 309

Query: 296 VIGSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIV 355
            +G+CT  ++ DLR AA+VLRGR+V+  V   V PA+    RQA  EG +   ++AG  +
Sbjct: 310 YLGACTGAKLEDLRMAASVLRGRRVAPGVTLQVAPASLRDQRQAESEGTLAILLDAGAQL 369

Query: 356 GPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITD 415
            P  C  C G          RAIA+T RNF GRMG   S V+L+ P T AA AVTG ITD
Sbjct: 370 LPNACNACAGYGPSRFPANSRAIASTARNFAGRMGESGSAVWLASPLTVAACAVTGSITD 429

Query: 416 PSTL 419
           P  L
Sbjct: 430 PRGL 433


Lambda     K      H
   0.320    0.136    0.401 

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: 519
Number of extensions: 17
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: 419
Length of database: 435
Length adjustment: 32
Effective length of query: 387
Effective length of database: 403
Effective search space:   155961
Effective search space used:   155961
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 (21.8 bits)
S2: 51 (24.3 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 (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