Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_084275315.1 B8779_RS04270 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_900176045.1:WP_084275315.1 Length = 368 Score = 242 bits (618), Expect = 1e-68 Identities = 145/358 (40%), Positives = 210/358 (58%), Gaps = 15/358 (4%) Query: 1 MRIKEHLKQLKPYQPGKPIEAVKSEYGLDK--VVKLASNENPYGCSEAAKEALHHEIQQL 58 MR E+L++LK Y+ GKPIE V EYG+D+ ++KLASNENPYG S + + ++ Sbjct: 1 MRFNENLQRLKTYEAGKPIELVVREYGIDEKDIIKLASNENPYGTSPKVVKKVQENAHKM 60 Query: 59 ALYPDGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQY 118 LYPD L+ L+K VS +I G GSD++++ RA LN+ T+ + + TF Y Sbjct: 61 YLYPDDSMYELKAALAKRFGVSAEEIIIGAGSDQVLEFCARAVLNEHTSVLMSKITFAMY 120 Query: 119 KHNAVIEGAEV-REIALRPDGSHDLDAMLEAIDEQT-QVVWICSPNNPTGTYTSEGELLA 176 + A+ +G+++ R R HDLD + + +V IC+PNNPTG + L + Sbjct: 121 EIYALQQGSKIIRSSCYR----HDLDEFYDLYQKHNPSIVHICTPNNPTGDAIDKEYLYS 176 Query: 177 FLERVPSRVLVVLDEAYYEYVTAEDYPETVP---LLSKYSNLMILRTFSKAYGLAALRVG 233 FLE+V LVV+D AY EY +D + +P L++ Y N + L TFSKAYGL +RVG Sbjct: 177 FLEKVKDP-LVVVDGAYMEYAAYKDPKKLIPPRELIAMYPNAIYLGTFSKAYGLGGMRVG 235 Query: 234 YGIADENLIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTH 293 YGIA + +I+Q+ R PFN + L AA AL D+ F+ +E+N A + ++ FA + Sbjct: 236 YGIAQKEIIQQLYKLRPPFNITTLSLLAATEALKDEEFVQRAIEKNFAQMDRFIHFAMQN 295 Query: 294 GLKCYPSQTNFV--LIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQN 349 L+ S TNF+ L+ A +L ALL +G IVR ++ G +LRITIGT EQN Sbjct: 296 ELEFIDSYTNFITYLLPQNINAKDLANALLRRGIIVRDLSSYGM-NALRITIGTPEQN 352 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: 374 Number of extensions: 19 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 360 Length of database: 368 Length adjustment: 29 Effective length of query: 331 Effective length of database: 339 Effective search space: 112209 Effective search space used: 112209 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