Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_011972972.1 MAEO_RS01250 histidinol-phosphate aminotransferase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000017185.1:WP_011972972.1 Length = 371 Score = 203 bits (517), Expect = 5e-57 Identities = 125/369 (33%), Positives = 205/369 (55%), Gaps = 14/369 (3%) Query: 2 RIKEHLKQLKPYQPGKPIEAVKSEYGL--DKVVKLASNENPYGCSEAAKEALHHEIQQLA 59 +I+ +K+ K Y PGK E + Y + D+++KL SNENP+G S KE + E+ + Sbjct: 6 KIRHIVKEFKAYVPGKSKEEIARNYNINPDEIIKLGSNENPWGSSPKIKEEILKELPNIH 65 Query: 60 LYPDGYSAALRTRLSKHLNVSETSLIFG-NGSDEIIQIICRAFLNDKTNTVTAAPTFPQY 118 YP+ + L LSK N+ + +++ G +G+DEII + R ++ + PTF QY Sbjct: 66 QYPEPVNPILMEELSKFTNIPKENIVVGGDGADEIIDTMMRILIDKDDEVIIPIPTFTQY 125 Query: 119 KHNAVIEGAEVR--EIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLA 176 + +A I GA ++ + D D+D++L I ++T+++++C+PNNPTG + ++ Sbjct: 126 RISAKIYGANIKYAKFDKEKDFKLDVDSVLNNITDKTKIIFLCTPNNPTGNIIDKKDIEK 185 Query: 177 FLERVPSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGI 236 + + LV++D AY EY + E+Y T L KY N++ILRTFSK +GLA R+GYGI Sbjct: 186 IINSTDA--LVMIDHAYIEY-SKEEYDLTEFAL-KYDNVLILRTFSKVFGLAGQRIGYGI 241 Query: 237 ADENLIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKT-HGL 295 + ++ + + F+ +RL Q AI AL D+ F ++ Y+ K L Sbjct: 242 TSKKIVDYMMRVKPIFSITRLSQICAITALRDKEFFEKSKNDGIKSMEILYNGLKEFKEL 301 Query: 296 KCYPSQTNFVLIDFKR--PADELFQALLEKGYIVRSGNAL-GFPTS-LRITIGTKEQNEE 351 K YPS+ N++L++ K + E LL++G IVR + G +R+ IGT E++ Sbjct: 302 KVYPSEANYLLVEVKNGMSSGEFCVELLKRGVIVRDCKSFEGLDGEYVRVAIGTFEEDRR 361 Query: 352 ILAILAEIL 360 L IL EI+ Sbjct: 362 FLEILKEIV 370 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: 337 Number of extensions: 17 Number of successful extensions: 6 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: 371 Length adjustment: 30 Effective length of query: 330 Effective length of database: 341 Effective search space: 112530 Effective search space used: 112530 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