Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_015817786.1 TERTU_RS04235 histidinol-phosphate aminotransferase family protein
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000023025.1:WP_015817786.1 Length = 352 Score = 143 bits (361), Expect = 6e-39 Identities = 106/361 (29%), Positives = 182/361 (50%), Gaps = 27/361 (7%) Query: 4 KEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQ--QLALY 61 KEH+ ++ Y+P K LD NE S A +EAL I+ +L +Y Sbjct: 5 KEHINRMSAYKPPLDGRDPKQHLLLD------FNERTLPVSAAVEEALVAYIRDGRLQMY 58 Query: 62 PDGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHN 121 P A +++++ V ++ NGSD+ I ++ RA + + P+F Y Sbjct: 59 PAYGDIA--EQIARYARVEADQVMITNGSDQGIDLVIRASSREGDEAIIPGPSFAMYLQC 116 Query: 122 AVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 A +E + + + + L +L I+E+T+++ + +PNNP+GT E++ + Sbjct: 117 AKVENLVIHQPQYTREKGYPLQEVLGLINEKTRLITVANPNNPSGTILPREEIVTLAKAA 176 Query: 182 PSRVLVVLDEAYYEY--VTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADE 239 P V++V DE Y+EY VT D L+++Y N++I RTFSK +G+ +LR+GY I+ Sbjct: 177 PEAVILV-DECYFEYCSVTVAD------LVAQYPNIVITRTFSKTWGIPSLRLGYIISAR 229 Query: 240 NLIRQIEPAREPFNTSRLGQAAAIAALDD----QAFIASCVEQNNAGLQQYYDFAKTHGL 295 I + R P++ ++L A AAL + ++++ ++Q+ L+ Y D + G+ Sbjct: 230 ENILPLLNVRGPYDINQLAIVAIRAALANLDGVESYVDEVMQQSKPRLETYLD---SKGI 286 Query: 296 KCYPSQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAI 355 + +PS NF+ + F P + L G +VR LRIT+GT EQ E +LA+ Sbjct: 287 EYWPSGGNFLWVFFADPVSTEAR-LQAAGILVRPKLDGEGRLGLRITLGTLEQTEHLLAV 345 Query: 356 L 356 L Sbjct: 346 L 346 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: 304 Number of extensions: 19 Number of successful extensions: 4 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: 352 Length adjustment: 29 Effective length of query: 331 Effective length of database: 323 Effective search space: 106913 Effective search space used: 106913 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 10 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