Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_041099774.1 SUTH_RS12925 threonine-phosphate decarboxylase CobD
Query= curated2:Q67KI2 (361 letters) >NCBI__GCF_000828635.1:WP_041099774.1 Length = 332 Score = 64.7 bits (156), Expect = 3e-15 Identities = 71/244 (29%), Positives = 105/244 (43%), Gaps = 25/244 (10%) Query: 103 LEPGDRVVVPEPSFAAYRFVAELMGAEVVAVPLAGWTMDLPAMAEAAARGAKLLFLCRPN 162 L P V V EPS+ + G EV +LP MA A + + PN Sbjct: 83 LRPAGVVAVLEPSYEEHAAAWRAAGHEVRPCSSG----ELPLMAAAV----DAVVIGSPN 134 Query: 163 NPTGTVFAEADLRAALERVPPST-LVVVDEAYREFDETPFDSRALVQ-----DYPNVVIA 216 NP G F L ++ +VVDEA+ + +E S +LV PNVV+ Sbjct: 135 NPAGQRFLRKQLLDMARQLEQRQGWLVVDEAFADAEEK---SESLVDVAGSAAAPNVVVL 191 Query: 217 RTFSKIYGMAGFRLGYGVMRPEVLAPLYTARDPFSV-NGLAVAAGLAALDDVEHVERTRA 275 R+ K +G+AG R+G+ + +L L A P+++ + +AAG A D + + Sbjct: 192 RSLGKFFGLAGARVGFAIAGEAILDSLAEAIGPWAIAHPSRLAAGAALADSDWQCAQRQR 251 Query: 276 LTREGKAYLYAAFQRLGLGYVPSEANFVLFDAGRPAAEVFDALLRRGVLVR-----PCGS 330 L R+G A L+ GLG A F + A A + R+G+L+R Sbjct: 252 LQRDG-ARLHELLAAAGLGESSGTALF-RYLACDDALALHGFFARQGILLRHFARPAAVR 309 Query: 331 FGLP 334 FGLP Sbjct: 310 FGLP 313 Lambda K H 0.322 0.138 0.408 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: 299 Number of extensions: 18 Number of successful extensions: 1 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: 361 Length of database: 332 Length adjustment: 29 Effective length of query: 332 Effective length of database: 303 Effective search space: 100596 Effective search space used: 100596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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