GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Amycolatopsis halophila YIM 93223

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_000504245.1:WP_034272173.1
          Length = 393

 Score =  261 bits (667), Expect = 3e-74
 Identities = 152/373 (40%), Positives = 205/373 (54%), Gaps = 17/373 (4%)

Query: 19  NYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSR 78
           NY    + L RG+G  V+D DGN YLD +   +  + GH HP ++ A+ EQ   L  TS 
Sbjct: 14  NYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGHTSN 73

Query: 79  AFHND---QLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEI 135
            + N     LA    +IA L+G  KVL  NSGAEAVE+AIK  R  G         ++++
Sbjct: 74  LYINPVALSLAETLLDIAGLSG--KVLFCNSGAEAVEAAIKITRLTG---------KSKL 122

Query: 136 IVCADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEP 195
           + C   FHGRT+G +  +  P  R  F P  PG   +PFGD AALE A+  +T A  VEP
Sbjct: 123 VACDGGFHGRTMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEP 182

Query: 196 IQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLG 255
           + GE GV+  P G+    RE+ TA   +LVLDE+QTG+GR G   A Q  G+  DV  L 
Sbjct: 183 VLGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLA 242

Query: 256 KALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAAR 315
           K L GG  P+ AV+   +    L+PGQHG+TFGGNP+ACA   A +R + E+G++++   
Sbjct: 243 KGLGGGL-PLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVET 301

Query: 316 QGARLLEGLKDIRANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375
            G  L  G++ +    V EVRG GL+  + L      A     A Q  G L        I
Sbjct: 302 LGKDLAAGVRKLDHPLVSEVRGAGLLQGIGLTKPV--APTVATAAQRAGYLINPVQPDVI 359

Query: 376 RIAPPLVITSDEV 388
           R+APPL+IT  +V
Sbjct: 360 RLAPPLIITERQV 372


Lambda     K      H
   0.319    0.136    0.405 

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: 436
Number of extensions: 17
Number of successful extensions: 5
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: 404
Length of database: 393
Length adjustment: 31
Effective length of query: 373
Effective length of database: 362
Effective search space:   135026
Effective search space used:   135026
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