GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cimA in Desulfovibrio vulgaris Hildenborough

Align 2-isopropylmalate synthase / (R)-citramalatesynthase; EC 2.3.1.182; EC 2.3.3.13 (characterized, see rationale)
to candidate 408370 DVUA0016 homocitrate synthase

Query= uniprot:D4GSQ2
         (512 letters)



>lcl|MicrobesOnline__882:408370 DVUA0016 homocitrate synthase
          Length = 384

 Score =  197 bits (501), Expect = 6e-55
 Identities = 133/367 (36%), Positives = 199/367 (54%), Gaps = 18/367 (4%)

Query: 17  VQLLDTTLRDGEQAPGVSLTPTQKADIARALDRAEVDYIEAGSACTGPGERE---TIKRV 73
           V L+D+TLR+G QA GV      +  I + +  + V   EAG A    G+ +   T++  
Sbjct: 22  VMLIDSTLREGAQAYGVYFDAADRESILQGVAASGVTEAEAGWA----GQDDLAATLRLG 77

Query: 74  TSLGLDATVTSFARGVKNDVDLALDCDVDGVTLVVPASDRHVESKVGTTREDVVETTDEL 133
             +     +  + R    D+D A +     V + VP+SD H+  ++G  R++V++    +
Sbjct: 78  ARVAPSLRLAVWCRCCTADLDKAAEAGARRVHIGVPSSDAHMRLRLGMGRDEVLQRVTTV 137

Query: 134 VAYAKDHGLWVEVIG-EDGSRAAPEFLESLARASHDAGADRFCFADTVGHTSPEHTYEVV 192
           + +A   G     +G ED  RAAP+ LE+LAR +   GA R   +DTVG  +P+    +V
Sbjct: 138 LEHAAHLGFLHVTLGLEDAGRAAPDLLEALARTAARTGAHRLRCSDTVGLLTPDGMVRLV 197

Query: 193 --SRLSELGPTSTHTHDDLGLAMANVHASLAAGADLVHTTVNGIGERAGNVALEEVAIAL 250
             +R +   P + H H+DLGLA AN  A+L AGAD    ++ G+GERAG    EE+A AL
Sbjct: 198 LLARRASALPVAVHCHNDLGLATANALAALDAGADGADVSLLGLGERAGITRAEELAAAL 257

Query: 251 DHCYDVESVKLDELYALAQKVAQATGVSLPPNKAVVGQNAFTHESGIHTDGTLKDDAMYE 310
                 ES +LD L  + +++A +  + LPP+ AV G+N F  ESG+H  G  +D A++E
Sbjct: 258 VVLRG-ESYRLDMLRGVCRRLAASLEMRLPPHWAVAGENLFAVESGVHLHGVQRDPALFE 316

Query: 311 PYPPETVGRERRLVLGKHAGRAGVKAALDEHGV----DATDEEVAAVVERVKELGDRGKR 366
           P+PP  VG ERRL +G   G AGV A    HG+    DA    V AV ++   L   G+ 
Sbjct: 317 PFPPALVGAERRLGVGGKCGSAGVAAMAHSHGLTLQGDALRRHVRAVRDKACSL---GRP 373

Query: 367 VTDADLL 373
           +TDA+ L
Sbjct: 374 LTDAEFL 380


Lambda     K      H
   0.312    0.129    0.361 

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: 498
Number of extensions: 30
Number of successful extensions: 5
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: 512
Length of database: 384
Length adjustment: 32
Effective length of query: 480
Effective length of database: 352
Effective search space:   168960
Effective search space used:   168960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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 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