GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Amycolatopsis halophila YIM 93223

Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase

Query= BRENDA::Q93R93
         (395 letters)



>NCBI__GCF_000504245.1:WP_034272173.1
          Length = 393

 Score =  301 bits (771), Expect = 2e-86
 Identities = 173/371 (46%), Positives = 217/371 (58%), Gaps = 2/371 (0%)

Query: 24  YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83
           Y    L +VRG GA V+DA+GN Y+D VGG  V  LGH +P VVEAV  Q  TL      
Sbjct: 15  YGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGHTSNL 74

Query: 84  LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143
              P+      TL  I      +V   NSG EA EAA+K  R  TG+ K VA   GF GR
Sbjct: 75  YINPVALSLAETLLDIAGLS-GKVLFCNSGAEAVEAAIKITRL-TGKSKLVACDGGFHGR 132

Query: 144 TMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPA 203
           TMG+LSVT +P  REPF PL+  V  +P+ D  AL+ AVD +TAAV +EPV GEGGV PA
Sbjct: 133 TMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPVLGEGGVVPA 192

Query: 204 TPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLG 263
              FLRAAREI    GALL+LDE+QTG+GR G  FAF+  G+ PD++TLAK LGGG+PLG
Sbjct: 193 PDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAKGLGGGLPLG 252

Query: 264 VAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRA 323
             +   +    +  G HGTTFGGNP+A AAG A IR +    L +    LG      +R 
Sbjct: 253 AVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLGKDLAAGVRK 312

Query: 324 IPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLVIEKEDL 383
           +  P + EVRG GL+ G+ L +  AP +A   +    L     P VIR  PPL+I +  +
Sbjct: 313 LDHPLVSEVRGAGLLQGIGLTKPVAPTVATAAQRAGYLINPVQPDVIRLAPPLIITERQV 372

Query: 384 ERVVEAVRAVL 394
              + A+ A L
Sbjct: 373 ADFLAALPAAL 383


Lambda     K      H
   0.319    0.137    0.403 

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: 411
Number of extensions: 16
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: 395
Length of database: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
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 (21.7 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