GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Caldicellulosiruptor kronotskyensis 2002

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013429768.1 CALKRO_RS03695 aspartate kinase

Query= BRENDA::Q9WZ17
         (739 letters)



>NCBI__GCF_000166775.1:WP_013429768.1
          Length = 409

 Score =  345 bits (886), Expect = 2e-99
 Identities = 187/400 (46%), Positives = 270/400 (67%), Gaps = 4/400 (1%)

Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399
           +VV K+GG +++D E++ + A + I   + G K VVV+SA GDTTD LIE AK I+ENP 
Sbjct: 3   IVVQKYGGTSVADKERIFRAARRAISEYEKGNKVVVVVSAQGDTTDELIEKAKEINENPS 62

Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459
            RE+D+LLSTGE  S+ALM++A+ K GY  IS TG Q  I TD  Y +ARII+I+++ + 
Sbjct: 63  KREMDMLLSTGEQISIALMAMAIEKLGYPVISLTGWQAGIKTDSHYSNARIIEIDSERLQ 122

Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519
           R L +  I VVAGFQGI +  DITTLGRGGSD TA+ALA +L AD CE+Y DVDGVYTAD
Sbjct: 123 RELDKRNIVVVAGFQGINKYDDITTLGRGGSDTTAVALAAALKADKCEIYTDVDGVYTAD 182

Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIWE 579
           PRIV +A  +KE+S++EM+EL+  GA+VL  R+ E A+KY + ++++++  +  GT++ E
Sbjct: 183 PRIVPNASKLKEISYDEMLELATLGAKVLHNRSVELAKKYNIPLVVRSSFNDNEGTIVKE 242

Query: 580 GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYN 639
              VE  +V  V  +  +A+V +  V + PG A +I   L++  +N+D+I+Q +   +  
Sbjct: 243 VNSVEKLLVSGVACDKDIARVAVIGVENVPGKAFQIFSLLAKENINVDIILQSIGREKTK 302

Query: 640 TVAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696
            ++F V +S L K  +D+L        AK+I     +AKVSIVG  + + P ++A +FE 
Sbjct: 303 DISFTVSKSNL-KQTLDVLTKNLHIIGAKDITYADNVAKVSIVGAGMVNNPGVAAMMFEA 361

Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736
           L + GINI+MIS S  +ISV+ID K  E AV+AIH +F+L
Sbjct: 362 LYDAGINIEMISTSEIKISVLIDEKDAEKAVRAIHDKFKL 401


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: 754
Number of extensions: 39
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: 739
Length of database: 409
Length adjustment: 36
Effective length of query: 703
Effective length of database: 373
Effective search space:   262219
Effective search space used:   262219
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 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