GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Mycolicibacterium vanbaalenii PYR-1

Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_049778231.1 MVAN_RS16610 acetylornithine transaminase

Query= uniprot:A0A806JQF3
         (400 letters)



>NCBI__GCF_000015305.1:WP_049778231.1
          Length = 379

 Score =  611 bits (1576), Expect = e-180
 Identities = 300/378 (79%), Positives = 336/378 (88%), Gaps = 2/378 (0%)

Query: 19  MMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGH 78
           MMNNYGTPP+ALA GDGAVVTDVDG+ Y+DLLGGIAVNVLGHRHPAVIEAVTRQM+TLGH
Sbjct: 1   MMNNYGTPPLALAGGDGAVVTDVDGKAYLDLLGGIAVNVLGHRHPAVIEAVTRQMNTLGH 60

Query: 79  TSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRLTGRTKLVAAHDA 138
           TSNLYATEPG+ALAE LV LLGA    + FFCNSG EANEAAFK++RLTGRTK+VAA  A
Sbjct: 61  TSNLYATEPGVALAESLVGLLGAP--AKAFFCNSGTEANEAAFKITRLTGRTKVVAAEGA 118

Query: 139 FHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHTAAVFLEPIMGESG 198
           FHGRTMGSLALTGQP+K+ PF PLPG VTHV YGD+D L   VDD TAAVFLEPIMGE G
Sbjct: 119 FHGRTMGSLALTGQPSKRAPFEPLPGGVTHVPYGDIDELRRVVDDQTAAVFLEPIMGEGG 178

Query: 199 VVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITPDVVTLAKGLGGG 258
           VVVPPAGYL AAR+ITA  GALLVLDEVQTG+GRTGAF+AHQHDGITPD+VTLAKGLGGG
Sbjct: 179 VVVPPAGYLVAAREITAAHGALLVLDEVQTGVGRTGAFYAHQHDGITPDIVTLAKGLGGG 238

Query: 259 LPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGLVRRAEVLGKSLRH 318
           LPIGACLA+G  A+LLTPGLHGSTFGGNPVC AAALAVL+VLA +GLV RA+VLGK++ H
Sbjct: 239 LPIGACLAIGDTADLLTPGLHGSTFGGNPVCTAAALAVLKVLADEGLVERADVLGKTIAH 298

Query: 319 GIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAAAPDVIRLAPPLIIA 378
           G+E+LGHPL+DHVRGRGLL GI LTA  AK  E  AR+AG+LVNAAAP ++RLAPPL+I 
Sbjct: 299 GVESLGHPLVDHVRGRGLLRGIVLTADAAKPVETAAREAGFLVNAAAPAIVRLAPPLVIT 358

Query: 379 EAQLDGFVAALPAILDRA 396
           EAQ++ F++ALPAILD+A
Sbjct: 359 EAQVETFLSALPAILDKA 376


Lambda     K      H
   0.320    0.136    0.399 

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: 610
Number of extensions: 25
Number of successful extensions: 2
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: 400
Length of database: 379
Length adjustment: 30
Effective length of query: 370
Effective length of database: 349
Effective search space:   129130
Effective search space used:   129130
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 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