Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011365674.1 GMET_RS02435 threonine-phosphate decarboxylase
Query= curated2:O27624 (373 letters) >NCBI__GCF_000012925.1:WP_011365674.1 Length = 399 Score = 173 bits (439), Expect = 6e-48 Identities = 115/367 (31%), Positives = 199/367 (54%), Gaps = 27/367 (7%) Query: 19 EPYVPGRSIKEIADAYGLKEDEIIKLGSNENPLGPSPAAVEAMERELESVHRYPESALTD 78 E + G ++ +A G+ DEI+ ++ NPLGP A A+ + + YP+S T+ Sbjct: 3 ETFDHGGTVFAVARQLGVSPDEILDFSASINPLGPPVEARGAVAAAFDRLVHYPDSGATE 62 Query: 79 LREAIADYAGVGMDQVIVGGDGADEIIDVLGRTFLEPGESFVVPMPSYMYYEYTLQAHDA 138 LR+A+A + + + V +G+ E+I ++ R L G ++ P + Y L Sbjct: 63 LRDALARRHHLLPENICVA-NGSTELIYLVPR--LVGGRRGLIVAPPFSEYAKGLS---- 115 Query: 139 RAVHARWDVNENRLDLESV------LDAVDESTR----LVFLCTPNNPTGGLIDKK---D 185 A W+++ LDL L+A+D+ L+FL P NPTG LI ++ + Sbjct: 116 ---RAGWEIDY--LDLSPADCFTLHLEALDQRLAKGCDLLFLANPGNPTGALIPREVIVE 170 Query: 186 IRAVLESTDTLVVVDEAYTEFAGVDN-TDLLPDHENLFILRTFSKVMGLAGMRIGYGLGD 244 + ++ T +V+DEA+ +F ++ TDL+ E +LR+ +K + G+R+GY +G Sbjct: 171 VVSLCRRHGTFLVLDEAFIDFCEEESATDLVVAGEGAVVLRSMTKFYAIPGLRLGYAMGS 230 Query: 245 PQIIEYMHRVKPVFSLTRLSHAAALATIRDRDYIKKSTEYSIKSREYLYSGLKKFPELRV 304 ++I + ++ +S+ L+ AA LA + D +Y ++ RE+L +G+ + P L V Sbjct: 231 EEVIARLSALREPWSVNTLAQAAGLACLADGEYPARTRALVETEREWLSAGIARLPGLAV 290 Query: 305 FRSYANYILIDVRGTGRTAAELSEELLRKGIIVRDCTSFTGLDEYWIRVSVGTLEEDRRF 364 + S ANY+L+ + G TA EL+ LL + +++RDC+SF GL E + RV+V EE+RR Sbjct: 291 YPSAANYLLVRI-DAGPTAPELATRLLAERVLIRDCSSFRGLSERFFRVAVRGTEENRRL 349 Query: 365 LEVLGEL 371 LE+LG + Sbjct: 350 LELLGRV 356 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: 340 Number of extensions: 18 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: 373 Length of database: 399 Length adjustment: 30 Effective length of query: 343 Effective length of database: 369 Effective search space: 126567 Effective search space used: 126567 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: 50 (23.9 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