GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Amycolatopsis halophila YIM 93223

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000504245.1:WP_034272173.1
          Length = 393

 Score =  249 bits (636), Expect = 9e-71
 Identities = 148/349 (42%), Positives = 200/349 (57%), Gaps = 15/349 (4%)

Query: 8   LRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDE 67
           L LVRG+G  V+D  G  YLDL+ GI VN LGHAHP  V  +S Q+  +     ++ +  
Sbjct: 20  LELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGHTSNLYINPV 79

Query: 68  REEMLEELSHWVDYE-YVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLS 126
              + E L         V   NSG EAVEAAIK  RL TG+S++VA    FHGRT+G+LS
Sbjct: 80  ALSLAETLLDIAGLSGKVLFCNSGAEAVEAAIKITRL-TGKSKLVACDGGFHGRTMGALS 138

Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFVK 186
            T +   RE F PL+PG  H+PF +  A + A+  +TAAV  EP+ GEGG+VPA + F++
Sbjct: 139 VTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPVLGEGGVVPAPDGFLR 198

Query: 187 TLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL--- 242
             R++    GALL+ DEVQ+G+ R G + A +  GV PD++T+ KG+G G P+   +   
Sbjct: 199 AAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAKGLGGGLPLGAVIGIG 258

Query: 243 -TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRL---VEKAGEKF----MEFSGERV 294
            T   +  G+HG+TFGGNP+AC A    +R +R   L   VE  G+       +     V
Sbjct: 259 QTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLGKDLAAGVRKLDHPLV 318

Query: 295 VKTRGRGLMIGIVLRRP-AGNYVKALQERGILVNTAGNRVIRLLPPLII 342
            + RG GL+ GI L +P A     A Q  G L+N     VIRL PPLII
Sbjct: 319 SEVRGAGLLQGIGLTKPVAPTVATAAQRAGYLINPVQPDVIRLAPPLII 367


Lambda     K      H
   0.320    0.140    0.410 

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: 363
Number of extensions: 16
Number of successful extensions: 7
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: 362
Length of database: 393
Length adjustment: 30
Effective length of query: 332
Effective length of database: 363
Effective search space:   120516
Effective search space used:   120516
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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