Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_108360051.1 B9Z44_RS01960 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_003063475.1:WP_108360051.1 Length = 394 Score = 154 bits (389), Expect = 4e-42 Identities = 105/331 (31%), Positives = 163/331 (49%), Gaps = 10/331 (3%) Query: 34 ILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE 93 ++ L++G+PDF P + +AA ++ G T Y G LR+RI+ + R G V A Sbjct: 36 MIFLNIGEPDFTAPPLVQEAAARAVHDGVTQYTPALGIPELRERISAWYSTRFGVNVPAR 95 Query: 94 QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRV 153 ++V+ AGA AL L+ GDEV++ +P Y A R V VP + F++ Sbjct: 96 RIVITAGASAALQLACLALIEAGDEVLMPDPSYPCNRHFVSAAEGRAVLVPTTAAERFQL 155 Query: 154 QAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFD 213 AE+V A T +TR + L SP NP+G S+ A+ + DE+Y L +D Sbjct: 156 SAEQVRANWTAQTRGVLLASPSNPTGTSIHPDELRAIHNEVSQRGGTTLIDEIYLGLSYD 215 Query: 214 GEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEF 273 E ++L G+ D+ ++NS SK MTGWR+GW+V P AL +E LA + + Sbjct: 216 -EQFGQSAL-GLDDQIISINSFSKYFNMTGWRLGWLVVPDALVPVVERLAQNLFICASTV 273 Query: 274 IQDAACTALEA-PLPELEAMREAYRRRRDLVIECLADSPGLR-PLRPDGGMFVMVDIRPT 331 Q AA EA + E E R ++ RRD + L ++ GL P+ PDG + D Sbjct: 274 AQHAALACFEAESMAEYERRRAEFKARRDYFVPAL-NALGLNVPVMPDGAFYAWADCTQA 332 Query: 332 G-----LSAQAFADRLLDRHGVSVLAGEAFG 357 + FA ++++ +++ G FG Sbjct: 333 ANKLGVKGSWDFAFEVMNKANLAITPGRDFG 363 Lambda K H 0.322 0.136 0.411 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: 370 Number of extensions: 18 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: 393 Length of database: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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