GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Desulforamulus ruminis DSM 2154

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013842892.1 DESRU_RS14810 aspartate kinase

Query= BRENDA::Q9WZ17
         (739 letters)



>NCBI__GCF_000215085.1:WP_013842892.1
          Length = 404

 Score =  340 bits (872), Expect = 8e-98
 Identities = 177/398 (44%), Positives = 260/398 (65%), Gaps = 3/398 (0%)

Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399
           +VV KFGG+++ D E++++VA ++++  + G + VV +SAMGDTTD LI L K +  NP 
Sbjct: 2   LVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLMKQVTNNPP 61

Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459
            RE+D+LLSTGE  S+AL+++A+R  G   +S TG Q+ I TD  +  A+I+ I T  + 
Sbjct: 62  EREMDMLLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIETGRVR 121

Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519
             L Q  + VVAGFQG+   GDITTLGRGGSD TA+ALA +L AD+CE++ DVDGVYT D
Sbjct: 122 EELNQGRVVVVAGFQGVNPDGDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTTD 181

Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIWE 579
           PR+V +AR +  +S++EM+EL+  GAQVL  R+ E A++YG+ + ++ +     GT++ E
Sbjct: 182 PRVVPEARKLSHISYDEMLELASLGAQVLHPRSVELAKQYGIPLHVRTSFNHMEGTIVEE 241

Query: 580 GTKVEN-PIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638
              +EN P+V  V  +  +AK+ L DVPDKPGVA  I + LS+  +N+DMIIQ       
Sbjct: 242 APDMENAPVVSGVAHDYNVAKIGLFDVPDKPGVAKTIFKALSKQSINVDMIIQSAMRNNM 301

Query: 639 NTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696
           N + F      L K    I+ ++     K    ++ +AKVSIVG  + S P ++A +FE 
Sbjct: 302 NDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDEDVAKVSIVGAGMISHPGVAADMFEA 361

Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734
           LA+EGIN++MI+ S  ++S +I     E AVKA+H +F
Sbjct: 362 LADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKF 399


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: 710
Number of extensions: 35
Number of successful extensions: 4
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: 404
Length adjustment: 35
Effective length of query: 704
Effective length of database: 369
Effective search space:   259776
Effective search space used:   259776
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: 52 (24.6 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