Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_011936990.1 GURA_RS00215 threonine-phosphate decarboxylase CobD
Query= reanno::Miya:8500145 (387 letters) >NCBI__GCF_000016745.1:WP_011936990.1 Length = 357 Score = 171 bits (432), Expect = 4e-47 Identities = 123/342 (35%), Positives = 181/342 (52%), Gaps = 18/342 (5%) Query: 51 VIKLASNENPLGTSPVVQHALRHKADLAFRYAQSGNPRLTAAIAAHHGVPAERVVAGNGS 110 ++ +++ NPLG +PVV+ AL D Y S L+ A+AA HG+ + NGS Sbjct: 24 ILDFSASINPLGMAPVVKEALLSSLDRLMHYPDSDAVELSRAVAAFHGLDEASICVSNGS 83 Query: 111 DEIIDLIVRVRAVPGVHNVVAFNPCFSIYELQTRLAGVEFRQAPLAAD--FSFDWDGLMA 168 E+I L+ R+ V G ++ P FS Y G E LAA FS L Sbjct: 84 TELIYLLPRL--VKGKRALIVA-PAFSEYANALAREGWEIAYLDLAAHDGFSLSLQALEE 140 Query: 169 LVDDATAVVFVTTPDNPSGFCPPVADLERL-AHALPAGCLLVVDEAYMDFCGDESAHSLL 227 + + +F+ P NP+G P A +E++ A G LV+DEA+MDFC +ESA L+ Sbjct: 141 RLAEGFDALFLCNPGNPTGKLLPPATIEKVCALCRSNGTFLVLDEAFMDFCEEESAKHLI 200 Query: 228 ARVDEFPNLAVLRTFSKSFGLAGLRLGYGILPVQLADYLRRVRLPFSVNILAEEAGLAAL 287 + VLR+ +K F + GLRLGY + + L +R P+SVN A+ AG+AAL Sbjct: 201 VKGGG----VVLRSLTKFFAIPGLRLGYALGSASVIAGLAALREPWSVNTPAQAAGIAAL 256 Query: 288 ADDVFRTETLRVISEGRAALTEGLTAL-GCHVYPSKANFVM--FRPAPTCKSAAHLFEEL 344 +D +R T+R ++ RA L GL AL GC YP+ AN+++ + P SAA L E L Sbjct: 257 SDHDYRQRTMRFVAAERAFLAAGLAALAGCKPYPAAANYLLVEIKGGP---SAADLRERL 313 Query: 345 LRRGIIIRPLKSY-GLPD-LLRVSVGSPDENAAFLKAAGEIM 384 L RGI+IR ++ GL D RV+V +EN ++ +++ Sbjct: 314 LGRGILIRDCSTFHGLDDRFFRVAVRGREENERLVEQLAKVL 355 Lambda K H 0.322 0.138 0.413 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: 344 Number of extensions: 20 Number of successful extensions: 5 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: 387 Length of database: 357 Length adjustment: 30 Effective length of query: 357 Effective length of database: 327 Effective search space: 116739 Effective search space used: 116739 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 Jul 26 2024. The underlying query database was built on Jul 25 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