Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_048061097.1 MTH_RS07600 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000008645.1:WP_048061097.1 Length = 366 Score = 213 bits (541), Expect = 8e-60 Identities = 127/372 (34%), Positives = 211/372 (56%), Gaps = 20/372 (5%) Query: 1 MRIKEHLKQLKPYQPGKPIEAVKSEYGL--DKVVKLASNENPYGCSEAAKEALHHEIQQL 58 ++I+ + ++PY PG+ I+ + YGL D+++KL SNENP G S AA EA+ E++ + Sbjct: 2 VKIRNKINDIEPYVPGRSIKEIADAYGLKEDEIIKLGSNENPLGPSPAAVEAMERELESV 61 Query: 59 ALYPDGYSAALRTRLSKHLNVSETSLIFG-NGSDEIIQIICRAFLNDKTNTVTAAPTFPQ 117 YP+ LR ++ + V +I G +G+DEII ++ R FL + V P++ Sbjct: 62 HRYPESALTDLREAIADYAGVGMDQVIVGGDGADEIIDVLGRTFLEPGESFVVPMPSYMY 121 Query: 118 YKHNAVIEGAEVREIALRPDGSH---DLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGEL 174 Y++ ++ + R + R D + DL+++L+A+DE T++V++C+PNNPTG + ++ Sbjct: 122 YEYT--LQAHDARAVHARWDVNENRLDLESVLDAVDESTRLVFLCTPNNPTGGLIDKKDI 179 Query: 175 LAFLERVPSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGY 234 A LE + LVV+DEAY E+ ++ LL + NL ILRTFSK GLA +R+GY Sbjct: 180 RAVLESTDT--LVVVDEAYTEFAGVDN----TDLLPDHENLFILRTFSKVMGLAGMRIGY 233 Query: 235 GIADENLIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYD-FAKTH 293 G+ D +I + + F+ +RL AAA+A + D+ +I E + + Y K Sbjct: 234 GLGDPQIIEYMHRVKPVFSLTRLSHAAALATIRDRDYIKKSTEYSIKSREYLYSGLKKFP 293 Query: 294 GLKCYPSQTNFVLIDFK---RPADELFQALLEKGYIVRSGNALGFPTS--LRITIGTKEQ 348 L+ + S N++LID + R A EL + LL KG IVR + +R+++GT E+ Sbjct: 294 ELRVFRSYANYILIDVRGTGRTAAELSEELLRKGIIVRDCTSFTGLDEYWIRVSVGTLEE 353 Query: 349 NEEILAILAEIL 360 + L +L E++ Sbjct: 354 DRRFLEVLGELV 365 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: 324 Number of extensions: 21 Number of successful extensions: 7 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: 366 Length adjustment: 29 Effective length of query: 331 Effective length of database: 337 Effective search space: 111547 Effective search space used: 111547 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 Apr 09 2024. The underlying query database was built on Apr 09 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