Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_010530816.1 ON01_RS09560 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000224785.1:WP_010530816.1 Length = 368 Score = 365 bits (937), Expect = e-105 Identities = 185/359 (51%), Positives = 244/359 (67%), Gaps = 1/359 (0%) Query: 1 MRIKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLAL 60 M+ K+ LK++ PYQPGK E VK EYGL+++VKLASNENP+G S + L + L + Sbjct: 1 MKSKQILKEMTPYQPGKQTEEVKKEYGLNRIVKLASNENPFGYSRKVDDYLSGQKPALNI 60 Query: 61 YPDGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKH 120 YPDGY++ LRT L L VSE LIFGNG+DE++QII RA+L NTV AAPTFPQYKH Sbjct: 61 YPDGYTSKLRTALVNKLEVSEHQLIFGNGTDEVVQIIGRAYLYPGVNTVMAAPTFPQYKH 120 Query: 121 NAVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLER 180 NA+IEGAEV+E+ +G HDL MLE ID+ T VVW+CSPNNPTG +L FL + Sbjct: 121 NALIEGAEVKEVPTI-NGYHDLQGMLEVIDDNTNVVWLCSPNNPTGALIPRDDLYEFLGK 179 Query: 181 VPSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADEN 240 PS +LVVLDEAY+EY ++ P+ + L +Y NL++LRTFSKAYGLA LR+GYGIA+E Sbjct: 180 CPSDILVVLDEAYFEYADSQKQPDVLQHLHQYKNLVVLRTFSKAYGLAGLRIGYGIANEE 239 Query: 241 LIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPS 300 LI +++ R PFNTS + Q AAIAALDD F+ + +NN Q + F + G Y S Sbjct: 240 LIPRLDVVRGPFNTSSIAQQAAIAALDDDEFLKDSISRNNKIKQSFEQFLNSIGWPFYDS 299 Query: 301 QTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359 QTNF+L+ + F L E G+IVR LG ++R+TIGT++ +E+ +L ++ Sbjct: 300 QTNFLLVSTPISGKKAFHFLQENGFIVRPVEGLGSSETIRVTIGTEKDMQELQDVLYQL 358 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: 387 Number of extensions: 13 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: 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 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