Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_007474130.1 CMTB2_RS03835 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000170735.1:WP_007474130.1 Length = 358 Score = 209 bits (531), Expect = 1e-58 Identities = 122/361 (33%), Positives = 204/361 (56%), Gaps = 12/361 (3%) Query: 5 EHLKQLKPYQPGKPIEAVKSEYGL--DKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62 E L+QLK Y+ GKPIE V EYG+ ++KLASNENPYG S E + + YP Sbjct: 3 ESLEQLKTYEAGKPIELVVREYGIKPQNIIKLASNENPYGPSPKVIEKVKKNAHLMHRYP 62 Query: 63 DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNA 122 D L+ L+K ++ ++I G GSD++++ K + A TF Y+ + Sbjct: 63 DDSFYELKEGLAKKFDIKSKNIIIGAGSDQVLEFAIHGVKPKKV--LMAGITFAMYEIYS 120 Query: 123 VIEGAEVREIALRPDGSHDLDAMLEAID-EQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 GA++ + +H+L+ E E+ +++++C PNNP G + E+ F+E++ Sbjct: 121 KQVGADILKTKTP---THNLEEFYEIYKKEKPEIIFLCIPNNPLGECLNSNEVFDFIEKI 177 Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPL--LSKYSNLMILRTFSKAYGLAALRVGYGIADE 239 L+++D AY E+ + +D + + + KY N++ TFSKAYGL +RVGYGI++E Sbjct: 178 DEETLIIIDGAYQEFASFKDKNKEIKPKDILKYKNVLYTGTFSKAYGLGGMRVGYGISNE 237 Query: 240 NLIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYP 299 +I+ + R PFN S L A+I +L D+ ++ +E N +Q+Y DFA + L+ Sbjct: 238 FIIKNLHKLRPPFNISILSLIASIESLKDKDWVRMGIENNFKEMQKYIDFANENNLEYIE 297 Query: 300 SQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359 S TNF+++ + + ++ LL+KG I+R + GF +++RITIG +N+ +L L E+ Sbjct: 298 SFTNFIVL-YINNSTKVANELLKKGIIIRDMASYGF-SAIRITIGKPSENDILLKNLREL 355 Query: 360 L 360 + Sbjct: 356 I 356 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: 349 Number of extensions: 18 Number of successful extensions: 5 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: 358 Length adjustment: 29 Effective length of query: 331 Effective length of database: 329 Effective search space: 108899 Effective search space used: 108899 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