Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_052367784.1 U743_RS08890 threonine-phosphate decarboxylase CobD
Query= curated2:Q311Z4 (383 letters) >NCBI__GCF_000733765.1:WP_052367784.1 Length = 343 Score = 72.4 bits (176), Expect = 2e-17 Identities = 84/283 (29%), Positives = 125/283 (44%), Gaps = 29/283 (10%) Query: 86 VSAIARSFG--VAAESVVTGNGSDEVIDLIIRVKARPGKHNIVAFNPCFSMYELQTRFCG 143 + AIAR + AA V GS I L+ R++A PG+ + A P ++ + R G Sbjct: 55 LDAIAREWAGAPAAAGCVALPGSQAAIQLLPRLRA-PGRVGVSA--PGYAEHAHWWRAAG 111 Query: 144 VEFRQVPLRADFSFDYDAFVGAADADTAVAFITTPDNPSGYCPPVEEIIDLARRLPS-SC 202 E + +DA A D A+ +I P+NP+G C + + + RRL Sbjct: 112 HEV--------VALAHDAAEDALDELDALVWIH-PNNPTGLCLSRQTLCEWHRRLARRGG 162 Query: 203 LLVVDEAYMDFADDPAAHSVLPHLTEFPNVAVLRTFSKSYGLAGLRLGFGVMHPALADYV 262 LV+DEA++D P + L T + VLR+ K +GLAGLR GF PAL D + Sbjct: 163 WLVLDEAFVD----PTPEASLVVDTGPDGLIVLRSTGKFFGLAGLRGGFCFGPPALCDEL 218 Query: 263 KRVRLPFSINILAEYAGIAALQDTTFHAQTLRVTREGRTYLTGALTEAGCTVYPSAANFI 322 + P++++ A + AL D + T L L G V A F Sbjct: 219 EAQLGPWAVSHPARWVLARALADRDWQHATREALAAQAAALDAVLQRHGLIVAGGTALF- 277 Query: 323 MFALPENCPH-DARAVFEALLRRGIIIRPLSSYNLPQCLRVSI 364 CPH A A+ + L R+GI+ R ++ P LR + Sbjct: 278 -----RYCPHPQAAAIQDRLARQGILSR---TFEEPPALRFGL 312 Lambda K H 0.322 0.137 0.405 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: 359 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: 383 Length of database: 343 Length adjustment: 29 Effective length of query: 354 Effective length of database: 314 Effective search space: 111156 Effective search space used: 111156 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