GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Clostridium kluyveri DSM 555

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_012101484.1 CKL_RS05440 homoserine dehydrogenase

Query= BRENDA::D8WXQ1
         (432 letters)



>NCBI__GCF_000016505.1:WP_012101484.1
          Length = 433

 Score =  359 bits (921), Expect = e-103
 Identities = 188/430 (43%), Positives = 285/430 (66%), Gaps = 4/430 (0%)

Query: 1   MEAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQL 60
           M+ +++ L+GLG VG+GV  I+++++ ++M + G  V+V KILV++ +KKRDV+V    +
Sbjct: 1   MKKVKIALMGLGNVGTGVWMILDSNKKEIMKRSGYDVEVAKILVRNKDKKRDVEVPEEII 60

Query: 61  TTNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAAS 120
           TT+ +DIL+D  I +VIEVMGGIE  + Y+LK +   KH+VTANK L+A  G EL   A 
Sbjct: 61  TTDFNDILEDDSIKIVIEVMGGIEPAKEYMLKCMDRNKHIVTANKMLIATEGDELFEKAH 120

Query: 121 ANGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVL 180
             G    YEASVAGGIPI++ + + L +++I +  GIVNGTTNYIL+KM      ++  L
Sbjct: 121 DKGVVFNYEASVAGGIPIIKGIEESLTANKIEEFYGIVNGTTNYILSKMQLERLNFDVAL 180

Query: 181 KEAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGK 240
           K+AQ++GYAEADP SD+EG DA  K+AIL++L F  K+D+++V  EGIT+I   D++Y K
Sbjct: 181 KQAQDMGYAEADPTSDIEGFDAQYKLAILSSLAFGTKVDVNNVYREGITKIESIDMKYAK 240

Query: 241 QLGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPG 300
           +    +KL+ IA     K+E+ VQPT++   HPLA+V D +NA+++ G AVG+ MFYG G
Sbjct: 241 KFDMVIKLLAIAKESNGKLELKVQPTMIPKEHPLANVYDSFNAIFIKGNAVGDLMFYGRG 300

Query: 301 AGSLPTATAVVSDLVGVMK-NMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEV 359
           AGSLPT +AVV D+V +++ N+ +      A    + ++++   E +SKF++R+ V D+ 
Sbjct: 301 AGSLPTGSAVVGDIVAILRSNVDVANYSHIAQNDLWHREIQNISESHSKFYIRITVIDQP 360

Query: 360 GVFANITSIFSEHSVSFEKILQMPLKEN--GLAEIVLVTHQASLQDYEDILVKLRDLNAV 417
           GV   IT+I  +++VS   ++Q   +EN  G   IVL TH+ S  D    + +L +L  V
Sbjct: 361 GVLGEITTILGKYNVSLRSVIQKG-EENSKGQVTIVLFTHKTSEADVSSAIEELMNLKPV 419

Query: 418 HEIKSSYRVE 427
             I +  R+E
Sbjct: 420 ITIDNVIRIE 429


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: 451
Number of extensions: 22
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: 432
Length of database: 433
Length adjustment: 32
Effective length of query: 400
Effective length of database: 401
Effective search space:   160400
Effective search space used:   160400
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 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