GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Desulfarculus baarsii DSM 2075

Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_013258997.1 DEBA_RS10935 aconitate hydratase

Query= SwissProt::Q9ZNE0
         (418 letters)



>NCBI__GCF_000143965.1:WP_013258997.1
          Length = 639

 Score =  200 bits (509), Expect = 9e-56
 Identities = 142/420 (33%), Positives = 206/420 (49%), Gaps = 14/420 (3%)

Query: 1   MGQTLAEKILS-HKVGRPVRAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVS 59
           M +TLA KI+  H V    + GE + + +DQ +  D+         E L    R    VS
Sbjct: 1   MAKTLARKIIEEHLVEGRCQPGEEIGLRIDQTLTQDATGTLAALEFEAL-GLERVRTEVS 59

Query: 60  I-VIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWVVVGS 118
           +  +DH    ++ +     + +R    R+G+     G G+CHQ+ +     +PG  ++GS
Sbjct: 60  VSYVDHNILQSDFKNPDDHRFLRSIAARYGLWFSPPGNGICHQLHMLN-FGRPGATLLGS 118

Query: 119 DSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDAALEM 178
           DSH+   G +G    G G  D+A A A    +L  P+ + V   G+L   V AKD  LE+
Sbjct: 119 DSHTPHGGGLGMLAMGAGGLDVAAAMAGQPFFLTYPKVLGVRLSGKLSPWVGAKDVILEL 178

Query: 179 VRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGEILEMY--- 235
           +R L+ +G     VE H   G   L+  +R  + N+  E GA +  V PS E  + +   
Sbjct: 179 LRRLSVKGGLGYVVEYHG-PGVTGLSVLQRAAITNMGAELGATSS-VFPSDEKTKAFLTA 236

Query: 236 --RVPDW--LYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQVFIGT 291
             R   W  +  D  A Y K  EIDL+AL P  + P   D V  V ++    V+QV +G+
Sbjct: 237 QGRADAWREMSADDGAVYDKLEEIDLAALEPLAACPSSPDAVRPVRELAEVAVEQVIVGS 296

Query: 292 CTNGRIEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPG 351
           C  G  EDL   A  L+G+ +AP + L V P S Q L +   +G LL +LEAG  +   G
Sbjct: 297 CGGGSYEDLMTIAMALKGKALAPGLNLSVNPGSRQALAQVTANGALLDMLEAGVRLHQAG 356

Query: 352 CGPCMGRHMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEEL 411
           C  C+G      A G   V T  RNF GR G  D  +YL  P VAAA+A+AG+L  P ++
Sbjct: 357 CLGCIGMSQAP-ATGAASVRTFPRNFPGRSGTKDDRVYLTGPEVAAATALAGHLADPRQV 415


Lambda     K      H
   0.318    0.135    0.393 

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: 606
Number of extensions: 45
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: 418
Length of database: 639
Length adjustment: 35
Effective length of query: 383
Effective length of database: 604
Effective search space:   231332
Effective search space used:   231332
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