Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_034632185.1 G496_RS0103180 histidinol-phosphate transaminase
Query= curated2:Q311Z4 (383 letters) >NCBI__GCF_000429985.1:WP_034632185.1 Length = 515 Score = 221 bits (562), Expect = 5e-62 Identities = 122/369 (33%), Positives = 198/369 (53%), Gaps = 4/369 (1%) Query: 13 PEAVTAIRPEVAAFKPYAPGLSIDEIKERYGLSQVVKMASNENPLGTSPLVQQTLRTHAD 72 P + ++ E +A K S K+RYG+++ + + SN NP+G S V + + Sbjct: 150 PVSTAEVKAEYSAPKTIKKSASASSFKKRYGITKEIDLYSNSNPIGVSKAVSLAMERMST 209 Query: 73 LAFRYVQSGNPRLVSAIARSFGVAAESVVTGNGSDEVIDLIIRVKARPGKHNIVAFNPCF 132 + ++ L +A+ V +V S E++DL++R+ PG+ +I++++ Sbjct: 210 CCNAFEENNIDSLKFGLAKRHDVNENQIVIATASIEILDLLLRISVTPGRDHILSYSNGL 269 Query: 133 SMYELQTRFCGVEFRQVPLRADFSFDYDAFVGAADADTAVAFITTPDNPSGYCPPVEEII 192 Y CGVE ++ +F D V A+ +TA IT PD PSGY EEI Sbjct: 270 PEYSSVAALCGVELLRLRRGRNFMPPLDQLVAQANDNTAAVLITNPDIPSGYGIAGEEIA 329 Query: 193 DLARRLPSSCLLVVDEAYMDFADDPAAHSVLPHLTEFPNVAVLRTFSKSYGLAGLRLGFG 252 + LP LL+VDE ++F+ ++ L +L + PN+ VLR+FS S+GL GLRLG+G Sbjct: 330 TMVNLLPDRTLLIVDERSVEFSWPEDDYTALHYLNKAPNLIVLRSFSWSFGLRGLRLGYG 389 Query: 253 VMHPALADYVKRVRLPFSINILAEYAGIAALQDTTFHAQTLRVTREGRTYLTGALTEAGC 312 +M+ +LA ++ RLP I+ + AG+AAL + F+ T+ + +GR + L +AGC Sbjct: 390 IMNSSLARKLEDSRLPIPISPVNVGAGLAALNHSEFYYSTIALIIKGRERMEKGLQDAGC 449 Query: 313 TVYPSAANFIMFALPENCPHDARAVFEALLRRGIIIRPLSSYNLPQCLRVSIGNRHENEL 372 TVYP +NF+MF++P A +E +L RG+ +R L + LP + SIGN N Sbjct: 450 TVYPGQSNFVMFSVPV----AANTFYEEMLARGLHVRKLDEFGLPDLMTASIGNNSRNRT 505 Query: 373 FIAQFKELL 381 F+A ++L Sbjct: 506 FLAAVNDIL 514 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: 468 Number of extensions: 11 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: 515 Length adjustment: 32 Effective length of query: 351 Effective length of database: 483 Effective search space: 169533 Effective search space used: 169533 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: 51 (24.3 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