GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Thermocrinis albus DSM 14484

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012992553.1 THAL_RS07720 LL-diaminopimelate aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>NCBI__GCF_000025605.1:WP_012992553.1
          Length = 387

 Score =  303 bits (776), Expect = 6e-87
 Identities = 154/389 (39%), Positives = 236/389 (60%), Gaps = 7/389 (1%)

Query: 5   WMFP-KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPN 63
           W F  ++++LP Y+FA ++  K +   +G D++DLG+G+PD+P  + I+  + +    P 
Sbjct: 2   WSFSQRIQQLPPYLFAQIDRKKREKIAQGADVIDLGVGDPDLPTPEPIVRAMQKAVENPQ 61

Query: 64  VHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVI 123
            H Y + +G+   R+A+ D+YKRR+GVELDPE+  I  IG+KEG +H  LA ++PGD V+
Sbjct: 62  HHRYPSYEGMFSFRQAVSDWYKRRFGVELDPEKEVIALIGSKEGIAHFPLAFVDPGDVVL 121

Query: 124 VPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHN 183
            P+P YP++    I  GG+   +P+  E  F   F     D++K    + K + +++P+N
Sbjct: 122 CPDPAYPVYKIGTIFAGGEPYFLPLKEENGFLPDFRSVPQDVLK----RAKIIWVNYPNN 177

Query: 184 PTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSM 243
           PT++   L+F++E+V+ A Q  I +  D AY+++ F    PPSILQVEGA +VA+E +S+
Sbjct: 178 PTSVTATLDFYKELVEWAHQHNIIVASDLAYSEVYFGEEKPPSILQVEGAKEVAIEFHSL 237

Query: 244 SKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREI 303
           SK F+M GWR+   VGN  LI+ L  +K+ +D G F  IQ A+I AL  P E ++  R+ 
Sbjct: 238 SKTFNMTGWRIGMAVGNRRLIEGLGKVKTNVDSGQFQAIQEAAIAALSLPEEALKPIRDT 297

Query: 304 YRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIG 363
           Y  RR V+ E L  +G EV   + + ++W KVP+  G  S  F   LL E  +  +PG G
Sbjct: 298 YAERRRVMTEALKNIGLEVVPSEATFYLWVKVPK--GYTSAQFVERLLDECAIVCTPGNG 355

Query: 364 FGEYGEGYVRFALVENEHRIRQAVRGIKK 392
           FGE GEGY R +L    HR+ +A   I K
Sbjct: 356 FGEAGEGYFRISLTVPTHRLLEAADRIGK 384


Lambda     K      H
   0.322    0.141    0.425 

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: 466
Number of extensions: 21
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: 402
Length of database: 387
Length adjustment: 31
Effective length of query: 371
Effective length of database: 356
Effective search space:   132076
Effective search space used:   132076
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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