Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate CCNA_01124 CCNA_01124 histidinol-phosphate aminotransferase
Query= curated2:A7HCR6 (364 letters) >FitnessBrowser__Caulo:CCNA_01124 Length = 347 Score = 130 bits (326), Expect = 7e-35 Identities = 101/322 (31%), Positives = 164/322 (50%), Gaps = 21/322 (6%) Query: 37 SNENALGPSPLAL-AAAREACAKVHLYPDGSAYLLRNAIAAKLGVPPEEVMVGNGSNELI 95 +NEN LGPS A A AR A G LL IAA+ G+ PE + V GS+E + Sbjct: 5 ANENPLGPSKAACDAIARVAPLGGRYDLTGETELLTKTIAAQSGLKPEFIAVYAGSSEPL 64 Query: 96 ELLVRTFVLDGEEVLTSAQSFVAYKLAAHEHGRTLVEAPMKGRFHYDLDALRKLLSRRTK 155 V F + +T+ S+ A AA +++ P+ F +D+ A+ + Sbjct: 65 HYSVLAFTSPTKSFVTADPSYEAGMFAARTSQAKIIKTPLTSAFAHDVKAM-VAADAQAG 123 Query: 156 LVFLANPDNPTGTWFTEAELTPFLDAVPKDTLVVLDEAYVEYVDAPGFQDGLALRRKYPN 215 ++++ NP+NPTGT T+ ++ L+ P +++++DEAY+ D P D L L + + Sbjct: 124 VIYICNPNNPTGTLTTKKDIVWALENKPAGSILLVDEAYIHLTDEP---DTLDLVAQGKD 180 Query: 216 VVVLRTFSKIYGLAGMRLGYGLARPEVVEYVDRVRPPFNTN---LVAQAAGAAALGDSAH 272 ++VLRTFSKIYG+AG+R G+ RP+++ + PF N + AA A+L D Sbjct: 181 LIVLRTFSKIYGMAGIRCGFAAGRPDLLAKL----KPFGQNAMPITGSAAARASLEDPKL 236 Query: 273 VAKSRALVLEERPFLAKGLAALG-AIVVPSQGNFVLADFPGRTGKDLFEAL-LREGVIAR 330 V + R ++ + R L G ++ Q N + D GR G+ + A+ R +I R Sbjct: 237 VPERRKMIGDTRRDTIAWLKTNGYKVIGDPQTNCFMID-TGRNGRAVMAAMKARNVMIGR 295 Query: 331 --PVAGYGFPSALRITVGLRRE 350 P+ +P+A+R++VG E Sbjct: 296 TWPI----WPNAVRVSVGTPEE 313 Lambda K H 0.320 0.138 0.399 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: 272 Number of extensions: 10 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: 364 Length of database: 347 Length adjustment: 29 Effective length of query: 335 Effective length of database: 318 Effective search space: 106530 Effective search space used: 106530 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 (21.8 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