Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_013009503.1 DACET_RS00755 class I and II aminotransferase
Query= curated2:A4XMY1 (358 letters) >NCBI__GCF_000025725.1:WP_013009503.1 Length = 323 Score = 106 bits (265), Expect = 7e-28 Identities = 97/350 (27%), Positives = 159/350 (45%), Gaps = 44/350 (12%) Query: 15 GKPISEVKRELGL--EKVIKLASNENPLGPSENVKKAIKESLDDLSLYPDGNCTELKLKL 72 G I EV LG+ V +SN +P +V K+ LS P+ L Sbjct: 7 GGDIHEVANYLGVPASDVYDYSSNVSPYPIDISVDKSA------LSRLPEPYSRTLAKAF 60 Query: 73 AKKLNVKPTQIIFGAGSDEITQLIASIFINPGDNSIMARPSFPRYETVTK-----VMGGI 127 A+K + AG+ E +I IF G ++ + P++ Y+ K V + Sbjct: 61 AEKYGYDEKMVCITAGTTEAIDIICRIFA--GKSACIKNPTYADYKKFCKNNKITVRNSL 118 Query: 128 PIEIPLKNYTHDLEEFSKHINERTRVIWICNPNNPTGTIVKKDELYNFIKSVPSEIAVVV 187 P+E+ +ICNPNNPTG ++ L + K+ PS + V+ Sbjct: 119 PVEL----------------------YFICNPNNPTGQTCPREFLPTYFKTSPSTLFVID 156 Query: 188 DQAYKEYIDDPEYPDAIHWLDEFKNLIVLQTFSKIYGLASLRIGYAIASEEIIEKLNRVR 247 + +ID+P LD N+ +L++FSKIYGL LR+G IA+E++IEK+ Sbjct: 157 ESYMPFHIDEPMQTLMGEKLD---NIAILRSFSKIYGLPGLRLGAVIANEKLIEKMKNQM 213 Query: 248 PPFNVNHVAQIAAIAALDDQEHIEKAKELNKKSLEFFYKSFEEMK-LPYIKSYGNFVMVD 306 P++VN +AQ A + L D + AK LN ++F K E + L + S N++M Sbjct: 214 SPWSVNSLAQSAGLELL-DVDTAPIAKRLNDIKVQFL-KELESIDFLEAVDSDVNYMMCK 271 Query: 307 VTK-DAVEVFKKLLLKGIIVRPGDIFDMPTYIRVTTGLESDNMEFIKALK 355 + + + E+F+ L + +++R F+ V + D ++ALK Sbjct: 272 MKRGTSDELFRHCLNQRVLIRDCSNFEGLDNRHVRFAMADDMSPLLEALK 321 Lambda K H 0.318 0.138 0.392 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: 268 Number of extensions: 14 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: 358 Length of database: 323 Length adjustment: 28 Effective length of query: 330 Effective length of database: 295 Effective search space: 97350 Effective search space used: 97350 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 (21.7 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