GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Sulfuricurvum kujiense DSM 16994

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_013460368.1 SULKU_RS07600 homocitrate synthase

Query= curated2:O26819
         (496 letters)



>NCBI__GCF_000183725.1:WP_013460368.1
          Length = 371

 Score =  266 bits (679), Expect = 1e-75
 Identities = 141/364 (38%), Positives = 223/364 (61%), Gaps = 2/364 (0%)

Query: 7   DTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITSEGLRA 66
           DTTLRDGEQ P V+   EEKLRIA  +DA GAD +E G A     ERE I+++ + GL+A
Sbjct: 6   DTTLRDGEQAPYVAFNTEEKLRIATLLDACGADELEIGIAAMGAKEREDIKELLNLGLKA 65

Query: 67  EICSFARAVREDIDAAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAVDCTEYAVDH 126
            + ++ R   ED+DA++SC V +V L +P SDL +  K   ++ +VL +       A   
Sbjct: 66  RMMTWNRMKLEDLDASLSCGVQAVDLSIPISDLLIGVKFGGSKIKVLNELERVVTAATRE 125

Query: 127 GILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEFYRGLSELG- 185
           G+ V +  EDS+R ++ F+R +   G E GA R   CDT+G++TP ++Y+  + L +L  
Sbjct: 126 GLFVCIGGEDSSRGELSFMRDVMELGRECGAGRFRYCDTIGVMTPTQTYQAVKELCDLNL 185

Query: 186 APLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEEVVVALKSLYDVDT 245
            P+ +H HNDFGLA AN+L+G+ AGA  ++ T+ G+GERAGNA+ E+++++LK LY    
Sbjct: 186 LPIEMHTHNDFGLANANALSGIDAGAISMNTTVIGLGERAGNASFEQILMSLKHLYGESR 245

Query: 246 SINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADGVLKKAETYEPITPEMV 305
           +++  +L    + VA    + L  N  I+GE  FAHESGIHADG++K +  YEP   + V
Sbjct: 246 AVDPLLLRSLVQSVADAANINLSANAPIIGERIFAHESGIHADGMMKDSHAYEPYEAKEV 305

Query: 306 GHGRGFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTLGDMGKCVTDV-DLQAIA 364
           G    F +GKH G+  +R  L  +G+   +  L ++  +++ +    K V ++ +L+++ 
Sbjct: 306 GLTSSFPIGKHSGSATIRYHLARMGISADNSILGDLLPKIREIVTSRKRVLEIGELKSLY 365

Query: 365 EDVL 368
           +D +
Sbjct: 366 QDAV 369


Lambda     K      H
   0.317    0.135    0.373 

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: 452
Number of extensions: 21
Number of successful extensions: 2
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: 496
Length of database: 371
Length adjustment: 32
Effective length of query: 464
Effective length of database: 339
Effective search space:   157296
Effective search space used:   157296
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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