Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_012283451.1 HM1_RS11010 L-threonine-O-3-phosphate decarboxylase
Query= curated2:A5CZ78 (359 letters) >NCBI__GCF_000019165.1:WP_012283451.1 Length = 374 Score = 139 bits (351), Expect = 9e-38 Identities = 116/345 (33%), Positives = 173/345 (50%), Gaps = 23/345 (6%) Query: 28 EVVKLDANENPYGFPPEVLTAILSEVGSREFSRYPDAAAGRLRESLAGYTGVDPENIMVG 87 E++ L AN N G P V AI+ + + YPD RL E+LA + V PE+I G Sbjct: 30 EILDLSANINFLGLSPLVRQAIVESID--QVVHYPDPKCRRLIEALADHLTVPPESICAG 87 Query: 88 NGADELILNIMLTFGTGAKFAIATPTFSMYGIHGRIASCEKVEVPR-LDG---FRVDVEA 143 NGA +L L+ L + I P F Y + + V VP LD FR+DVEA Sbjct: 88 NGAVDL-LDHWLHAVQARRVLIPEPGFGQY--ERAVVAQGGVAVPLPLDEKRQFRLDVEA 144 Query: 144 MKRAAGEPGVKIAVICTPNNPTGNATPPEEIEEIL---KSTGAIVVVDEAYAEF--GGR- 197 K+A E G A++CTP+NP G +E + +L +S+ ++VDE++ +F GR Sbjct: 145 WKKALREEGCDTAILCTPHNPAGWVWTEKEKQAVLAHLESSPVRLLVDESFLDFLPDGRA 204 Query: 198 -SCIPLLNRYPNLVILRTFSKAFALAGLRVGYLLAGRPVINELLKVKQPYNLNAFSQAAA 256 SC P + L +L + +K FA+ GLR+G L+ +I ++ + P+ +N +QAA Sbjct: 205 LSCCPQASENDRLAVLYSLTKFFAIPGLRLGALITDSDIIKGIVARRDPWVVNQLAQAAG 264 Query: 257 RVVMENLPPFKERIKKILEERERLFTELSALPGVEAFPSQANFILFRTPMPAGEVYG--- 313 + + ++ +++ +ER LF +LS LPG+ PS +NF L G Sbjct: 265 VAALADRDYHQKTWEQLPQERNYLFEQLSKLPGLTPLPSDSNFSLLYVAESGISSTGWTE 324 Query: 314 GLLERGVLVRNVDGPGLS---RCLRVAVGTAEENRLFIEKLGEVL 355 L RG+LVRN + LS R LR+AV IE + VL Sbjct: 325 RLRRRGILVRNCN-TFLSLGERYLRLAVRDKAATDRLIEAMRAVL 368 Lambda K H 0.319 0.139 0.401 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: 248 Number of extensions: 8 Number of successful extensions: 3 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: 359 Length of database: 374 Length adjustment: 30 Effective length of query: 329 Effective length of database: 344 Effective search space: 113176 Effective search space used: 113176 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 (21.7 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