Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_106717290.1 CU100_RS14195 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_003010935.1:WP_106717290.1 Length = 380 Score = 210 bits (534), Expect = 6e-59 Identities = 118/359 (32%), Positives = 187/359 (52%), Gaps = 2/359 (0%) Query: 3 IKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62 +++ + +L PY G + V YG K+ KLASNENP G S + L LYP Sbjct: 8 VRDEVHELAPYNSGLTVREVNERYGPAKIAKLASNENPLGPSPDLDSITMADSDLLRLYP 67 Query: 63 DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNA 122 D LR ++ L+V+ T +I GNGS+E+I IICRA L + VT P+FP ++ A Sbjct: 68 DPAGVELREAIAVALDVASTQIILGNGSEELISIICRAVLRPRDRVVTLYPSFPLHEDYA 127 Query: 123 VIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVP 182 + GA V + ++ + S D+D + I ++V +P NP G++ + EL + Sbjct: 128 ALMGASVERVNVKGNMSVDVDTFEKKIATPARMVIFSNPMNPVGSWLAPAELSRVIAAAD 187 Query: 183 SRVLVVLDEAYYEYVTAEDYPETVPLL-SKYSNLMILRTFSKAYGLAALRVGYG-IADEN 240 L+V+DEAY EY EDY + LL ++LRT SKAYGLA LR+GYG +AD Sbjct: 188 KNTLIVVDEAYAEYAAGEDYVSAIDLLKGSRRPWVVLRTMSKAYGLAGLRIGYGVVADPE 247 Query: 241 LIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPS 300 ++ R PFN + + Q +A+ AL D+ + V + Q+ F + S Sbjct: 248 FRSLLDRVRTPFNVNAIAQVSAVKALADRQHLQRVVTLAASERQRVQAFLLANDWPVAAS 307 Query: 301 QTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359 + NF+ D A + + LL G IV+ G+ T +R+++G+ ++N + ++ + + Sbjct: 308 KGNFLFFDCAGNAADFAEGLLRYGVIVKPWKQAGYETFVRVSVGSPDENNQFMSAVLSL 366 Lambda K H 0.317 0.134 0.382 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: 333 Number of extensions: 15 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: 360 Length of database: 380 Length adjustment: 30 Effective length of query: 330 Effective length of database: 350 Effective search space: 115500 Effective search space used: 115500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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