Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_072907619.1 BUB13_RS07935 threonine-phosphate decarboxylase
Query= reanno::Miya:8500145 (387 letters) >NCBI__GCF_900142125.1:WP_072907619.1 Length = 352 Score = 144 bits (363), Expect = 4e-39 Identities = 110/355 (30%), Positives = 177/355 (49%), Gaps = 16/355 (4%) Query: 36 GLSIDEIRDRYGLAH--VIKLASNENPLGTSPVVQHALRHKADLAFRYAQSGNPRLTAAI 93 G +D GL+ + +++ NPLGT P V+ AL + Y + L A + Sbjct: 7 GGGVDAAMSELGLSRQQIDDFSASINPLGTPPEVRRALADALERIGDYPEIDATSLRADL 66 Query: 94 AAHHGVPAERVVAGNGSDEIIDLIVRVRAVPGVHNVVAFNPCFSIYELQTRLAGVEFRQA 153 AA H +P + ++ G+GS E+I L+ RV + PCFS Y R A Sbjct: 67 AAFHHLPEKNLLPGSGSTELIYLLPRVFK---PRRALLVQPCFSEYAPALRQADCSIDTV 123 Query: 154 PLAAD--FSFDWDGLMALVDDATAVVFVTTPDNPSGFCPPVADLERLAHALPAGCLLVVD 211 L A+ F+F + +++ + T +V + P NP+G L LA L LVVD Sbjct: 124 SLVAEEGFAFSIEAVLSALQPDTDLVLLANPGNPTGVAIDPCQLVSLATQL-GDRRLVVD 182 Query: 212 EAYMDFCGDESAHSLLARVDEFPNLAVLRTFSKSFGLAGLRLGYGILPVQLADYLRRVRL 271 EA++DFC S HS+L +V + NL VLR+ +K + + G+R+GY + L + Sbjct: 183 EAFIDFC---SQHSVLPQVTQLANLLVLRSMTKFYAIPGVRVGYLAASQADIELLSAGKE 239 Query: 272 PFSVNILAEEAGLAALADDVFRTETLRVISEGRAALTEGLTALGCHVYPSKANFVMFRPA 331 P++++ LA AG A LA ++ +TLR+I + R L GL ALG V+ S+ N+++ + Sbjct: 240 PWTLSNLAIAAGKACLAATGYQQQTLRLIPQLRDELARGLEALGIKVFTSETNYLLCQMP 299 Query: 332 PTCKSAAHLFEELLRRGIIIRPLKSYGLPD--LLRVSVGSPDENAAFLKAAGEIM 384 P + L ++GI+IR + D RV+V S D N+ L + +++ Sbjct: 300 PGIGAP---INALRQQGILIRGCGDFAPLDDSFFRVAVLSADANSRLLTSLEKLL 351 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: 309 Number of extensions: 17 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: 352 Length adjustment: 30 Effective length of query: 357 Effective length of database: 322 Effective search space: 114954 Effective search space used: 114954 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 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