GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Streptacidiphilus oryzae TH49

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_037580293.1 BS73_RS19830 histidinol-phosphate transaminase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>NCBI__GCF_000744815.1:WP_037580293.1
          Length = 361

 Score =  216 bits (550), Expect = 8e-61
 Identities = 141/334 (42%), Positives = 183/334 (54%), Gaps = 11/334 (3%)

Query: 38  KLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSND 97
           KL+SNENP         A   AA E  RYPD     L A LS   GVP   +  G GS  
Sbjct: 36  KLSSNENPYPPLPGVLDAAVAAAGEANRYPDMACAALIAELSGTLGVPESHIATGTGSVG 95

Query: 98  ILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPA-VKYGHDLDAMLAAVSDD 156
           + +    A    G  +VYA  SF  Y + TQ  GAR++ VP      HDLDAM AAV++ 
Sbjct: 96  VAQQLLQATAGPGDEVVYAWRSFEAYPIITQISGARSVRVPLRPDESHDLDAMAAAVNER 155

Query: 157 TRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRY 216
           TRL+F+  PNNPTG  +   ++E FLD+VPR V+VVLDEAY E++  ++  D I   R  
Sbjct: 156 TRLVFLCTPNNPTGNVLRREEIEGFLDRVPRDVLVVLDEAYLEFIRDKEAVDGIEIYRER 215

Query: 217 PNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDK-AF 275
           PN+ V RTFSKA+GLAGLRVG+A+AQ  +   L +   PF V+ LAQ AAI +L  + A 
Sbjct: 216 PNVAVLRTFSKAYGLAGLRVGYAVAQEPVATALRQTAVPFGVSQLAQDAAIVSLRSREAL 275

Query: 276 LEKSAALNAQGYRRLTEAFDKLGLEYVP-SDGNFVLVRVGNDDAAGNRVNLELLKQGVIV 334
           LE+  AL A+   R+ +A    G   VP S  NFV +R+G   AA      E    GV+V
Sbjct: 276 LERVEALVAE-RERVLDALAAQGWPGVPRSQANFVWLRLGERTAAFAAACAE---AGVVV 331

Query: 335 RPVGNYGLPQWLRITIGLPEENEAFIAALERTLA 368
           RP    G    +R++I     N+ F+    R  A
Sbjct: 332 RPFEGEG----VRVSIAERPANDIFLEVASRFAA 361


Lambda     K      H
   0.318    0.135    0.385 

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: 385
Number of extensions: 16
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: 370
Length of database: 361
Length adjustment: 30
Effective length of query: 340
Effective length of database: 331
Effective search space:   112540
Effective search space used:   112540
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: 49 (23.5 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