GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Salinicoccus carnicancri Crm

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_017548761.1 C792_RS14385 homoserine dehydrogenase

Query= BRENDA::D8WXQ1
         (432 letters)



>NCBI__GCF_000330705.1:WP_017548761.1
          Length = 408

 Score =  307 bits (786), Expect = 4e-88
 Identities = 165/376 (43%), Positives = 241/376 (64%), Gaps = 7/376 (1%)

Query: 4   IQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLTTN 63
           +++ LLGLGTVG+GVV ++ ++++K+    G  + +  +LV D+NKKR   +D A +T +
Sbjct: 1   MKIALLGLGTVGTGVVDVLGSNREKIAGLTGESLTISHVLVNDINKKRSSGLDGAVITDD 60

Query: 64  ADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASANG 123
              I++D  ID+VIEVMGGIE T+N L   L +  HV++ANKD++A +  EL+  A+ N 
Sbjct: 61  IGKIMEDDTIDIVIEVMGGIERTKNILKAFLEKGVHVISANKDMLAQHIDELVETANENN 120

Query: 124 CDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKEA 183
             L YEASVAGGIP++  +   L S++ITK+MGI+NGTTNYIL+KM+  G +Y++ L +A
Sbjct: 121 AQLLYEASVAGGIPVIHGIEHSLNSNQITKVMGILNGTTNYILSKMTIDGWSYDQALDDA 180

Query: 184 QELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQLG 243
           +E GYAEADP +DVEG+DA RK+ +L+ L +   +D+  V V GI+ +   DI+Y  +  
Sbjct: 181 KEKGYAEADPTNDVEGIDAQRKIVLLSRLAYGRTVDIGTVPVSGISGVDIADIEYAAREN 240

Query: 244 YTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGAGS 303
            T+KL+G +      + +SV+P LL   H LA VN E NAV+V G AVGE MFYGPGAGS
Sbjct: 241 LTLKLLGKSEFRDGALSISVEPVLLPSDHQLAGVNYEKNAVFVNGNAVGEAMFYGPGAGS 300

Query: 304 LPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVGVFA 363
           L TA+AVVSDL+ V+++            P   +   G +E Y      + +K   G   
Sbjct: 301 LETASAVVSDLINVVRSRSGRHKNFAPDMPAAMENGIGMNEYY------IRMKGS-GADD 353

Query: 364 NITSIFSEHSVSFEKI 379
           N+T+   E S+ F +I
Sbjct: 354 NLTAALDEMSLRFSRI 369


Lambda     K      H
   0.316    0.134    0.368 

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: 458
Number of extensions: 20
Number of successful extensions: 1
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: 432
Length of database: 408
Length adjustment: 32
Effective length of query: 400
Effective length of database: 376
Effective search space:   150400
Effective search space used:   150400
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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