Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011318570.1 AVA_RS08955 threonine-phosphate decarboxylase CobD
Query= curated2:Q67KI2 (361 letters) >NCBI__GCF_000204075.1:WP_011318570.1 Length = 367 Score = 137 bits (346), Expect = 3e-37 Identities = 109/340 (32%), Positives = 165/340 (48%), Gaps = 21/340 (6%) Query: 32 LVKLNQNENPLGPSPRAVAAARAAMAQVHTYPEGTARRLRERLAQMWNLPADWFLIGNGS 91 +V + + +PLGP A+AA ++ ++ + YP+ LR L LP +W L GNGS Sbjct: 24 IVDFSASISPLGPPQSAIAAIQSQISNLRHYPDPDYSELRLALGHFHQLPLEWILPGNGS 83 Query: 92 DEVFRLLAEVYLEPGDRVVVPEPSFAAYRFVAELMGAEVVAVPLA-------GWTMDLPA 144 E+ L + V++ P+F Y A V+ PL G L Sbjct: 84 AELLTLAGRELAQLAATVLIT-PAFGDYYRTLRAYHARVLEFPLVSVESRVLGTECHLTQ 142 Query: 145 M--AEAAARGAKLLFLCRPNNPTGTVFAEADLRAALERVPPSTLVVVDEAYREFDETPFD 202 + + L L P+NPTG +F + LE+ LVVVDEA+ +F P + Sbjct: 143 LHTQHSGLSTNYALLLNNPHNPTGKLFTREAILPLLEQF---ALVVVDEAFMDF-VPPDE 198 Query: 203 SRAL---VQDYPNVVIARTFSKIYGMAGFRLGYGVMRPEVLAPLYTARDPFSVNGLAVAA 259 ++L V +YPN+VI R+ +K Y + G RLGY + P+ L RDP+ VN LA AA Sbjct: 199 EQSLIPVVAEYPNLVILRSLTKFYSLPGLRLGYAIAHPDRLQKWQLWRDPWPVNTLAAAA 258 Query: 260 GLAALDDVEHVERTRALTREGKAYLYAAFQRL-GLGYVPSEANFVLFDAGRPAAEVFDAL 318 +AAL+D E +T + L+ + GL S ANF+L + + + E+ L Sbjct: 259 AIAALEDREFQVQTWQWLPPAREELFQGLTAIPGLTPQASAANFLLVETQQSSLELQQKL 318 Query: 319 LRR-GVLVRPCGSF-GLPDH-LRVTVGTPEQNRRFVEALK 355 L++ +L+R C SF L D R+ V + N+R +ALK Sbjct: 319 LQQHQILIRDCLSFKELGDRFFRLAVRSHTDNQRLTKALK 358 Lambda K H 0.322 0.138 0.408 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: 13 Number of successful extensions: 4 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: 361 Length of database: 367 Length adjustment: 29 Effective length of query: 332 Effective length of database: 338 Effective search space: 112216 Effective search space used: 112216 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