Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_012967290.1 KVAR_RS04245 threonine-phosphate decarboxylase
Query= reanno::Miya:8500145 (387 letters) >NCBI__GCF_000025465.1:WP_012967290.1 Length = 358 Score = 118 bits (295), Expect = 3e-31 Identities = 104/358 (29%), Positives = 168/358 (46%), Gaps = 16/358 (4%) Query: 36 GLSIDEIRDRYGLA--HVIKLASNENPLGTSPVVQHALRHKADLAFRYAQSGNPRLTAAI 93 G +I E G+A ++ ++N NPLG ++ A+ A RY +L A+ Sbjct: 9 GGNIREAAALLGIAPGELLDFSANINPLGMPASLRQAIVDNPGCAERYPDVEYQQLHQAL 68 Query: 94 AAHHGVPAERVVAGNGSDEIIDLIVRVRAVPGVHNVVAFNPCFSIYELQTRLAGVEFRQA 153 AAHH +PA ++AGNG E I +V V+ P F+ Y + E + Sbjct: 69 AAHHQLPAAHILAGNGETESIFTLVHGLKPRRAMIVI---PGFAEYRRALQTVDCELVEY 125 Query: 154 PLAADFSFD-WDGLMALVDDATAVVFVTTPDNPSGFCPPVADLERLAHALPA-GCLLVVD 211 L + D ++ + A +F+ TP+NP+G P LE +A A L++D Sbjct: 126 ALRECDGWQLTDAILDALTPALDCLFLCTPNNPTGLLPERGLLEAIAQRCRALNISLILD 185 Query: 212 EAYMDFCGDESAHSLLARVDEFPNLAVLRTFSKSFGLAGLRLGYGI-LPVQLADYLRRVR 270 EA++DF D+ + + + P++ VLR+ +K + + GLRLGY + Q LR + Sbjct: 186 EAFLDFIPDQP--GFIPLLAQHPHVWVLRSLTKFYAIPGLRLGYLLNADAQAVARLRERQ 243 Query: 271 LPFSVNILAEEAGLAALADDVFRTETLRVISEGRAALTEGLTAL-GCHVYPSKANFVMFR 329 +P+S+N A AG L D ++ T + + E A L + G V+P +AN++ R Sbjct: 244 MPWSINAYAALAGEIILQDRAYQRATWQWLQEEGARFCSRLKEITGLTVWPGRANYLFLR 303 Query: 330 PAPTCKSAAHLFEELLRRGIIIRPLKSY-GLPD-LLRVSVGSPDENAAFLKAAGEIMA 385 + L LLR+ ++IR +Y GL RV++ S EN L A +A Sbjct: 304 ---CDRQGLDLQYALLRQHVLIRSCANYPGLDSRYFRVAIRSASENDQLLAALRRALA 358 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: 335 Number of extensions: 19 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: 387 Length of database: 358 Length adjustment: 30 Effective length of query: 357 Effective length of database: 328 Effective search space: 117096 Effective search space used: 117096 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