Alignments for a candidate for asp-kinase in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Heliobacterium modesticaldum Ice1; ATCC 51547

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012282995.1 HM1_RS08710 homoserine dehydrogenase

Query= BRENDA::Q9WZ17
         (739 letters)



>NCBI__GCF_000019165.1:WP_012282995.1
          Length = 429

 Score =  207 bits (528), Expect = 7e-58
 Identities = 140/427 (32%), Positives = 223/427 (52%), Gaps = 12/427 (2%)

Query: 20  VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79
           + VG+ GLGTVGG   RIL+ R  +I +R+G    + KV+ R+  K   + V    +  +
Sbjct: 5   IMVGLLGLGTVGGGTLRILQNRVEDIAQRLGRPVQVKKVLVRNLHKPRPVVVDPALLTDN 64

Query: 80  FDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137
             D++ + ++  VVE +GG   A+D ++ AL+ G+ VVT NK+L++ +G E  +  + ++
Sbjct: 65  PADILEDPEISIVVELMGGIHPALDYIKSALKAGKNVVTANKDLMAVHGRELFDLAEAKE 124

Query: 138 LF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVLKEA 194
           L   FEASV GGIPII  L+  L   ++  ++GI+NGTTN+ILT+M++ G  F EVLKEA
Sbjct: 125 LDLEFEASVAGGIPIIRPLKVCLAANRIEELKGIINGTTNFILTKMTQEGSDFGEVLKEA 184

Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254
           Q LGYAEADPT D+EG D A K++++A +       +N V  EGIT++    ++   + G
Sbjct: 185 QALGYAEADPTADVEGLDAARKLAIVASIAFNSRITLNDVYVEGITKVTARDIQYARQMG 244

Query: 255 KKLKLIGELDFSTNRYEVRLREVTPED--PFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312
             +KL+G       + E R+      D  P   V+   NAI V  D  G+ +  GRGAG 
Sbjct: 245 YTIKLLGIAKEIDGKVEARVHPAMIPDCHPLAAVNDAFNAIFVKGDAVGETMFYGRGAGD 304

Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVK 372
            PT SAV+ D+  VA+  + G   + S             V  + ++  K   R     K
Sbjct: 305 MPTGSAVVGDIIDVARNIIKGHTGRISCTCYH-----QKPVRPIGEIVCKYFLRLVVTEK 359

Query: 373 PVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISF 432
           P V+ +  G   D  + +   I +       +++L T  ++   L           ++  
Sbjct: 360 PGVLAAIAGVFGDQGVSIQTLIQQETIGDSAEIVLVTHPVREDNLQMALKILSDMPSVER 419

Query: 433 TGNQLKI 439
            GN +++
Sbjct: 420 VGNVIRV 426



 Score = 26.6 bits (57), Expect = 0.003
 Identities = 13/40 (32%), Positives = 19/40 (47%)

Query: 605 VPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTVAFI 644
           V +KPGV A I       GV+I  +IQ    G+   +  +
Sbjct: 356 VTEKPGVLAAIAGVFGDQGVSIQTLIQQETIGDSAEIVLV 395


Lambda     K      H
   0.318    0.137    0.377 

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: 741
Number of extensions: 33
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 739
Length of database: 429
Length adjustment: 36
Effective length of query: 703
Effective length of database: 393
Effective search space:   276279
Effective search space used:   276279
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: 53 (25.0 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis