Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate 642684008 Cphamn1_1515 L-threonine O-3-phosphate decarboxylase (EC 4.1.1.81)
Query= curated2:Q8ESS3 (354 letters) >IMG__ChlphaBS1_FD:642684008 Length = 361 Score = 74.3 bits (181), Expect = 5e-18 Identities = 63/204 (30%), Positives = 102/204 (50%), Gaps = 11/204 (5%) Query: 151 NPNAPTGIFLEIDQIKRILENNPNQVVIIDEAYI----DFALESAVTLVEAFPNLLVIQT 206 NPN PTG + + + P++ IIDEA+I DF S + + AF N++V+ + Sbjct: 149 NPNNPTGSRFPKEVVLALASRFPDKWFIIDEAFIQFVDDFPGASLMNDLRAFKNIIVVSS 208 Query: 207 MSKSRSLAGLRIGFAIGNPELIIGLERIKNSFNSYTVDRLAIAGAIEAIRDKDYFLQTTT 266 ++K +L GLR+G AI +P+ I L K ++V+ +A A A+E + D+ + Sbjct: 209 LTKFYALPGLRLGAAIAHPDTIARLLCFK---TPWSVNAVADAVALELLNAGDFEKEVRR 265 Query: 267 KIIESRSYL-KEQLETRHFDILPSQANFLLVSHK-EVNAEVLYQELKKQGILVRYFQK-P 323 I R+ + K + I ANF L K + + + L L + I VR + P Sbjct: 266 LITHERAKIFKRMKQIPSVSIRGYAANFFLARWKCDSSLDELLTYLMENNIFVRDCRNFP 325 Query: 324 GLEN-FLRISIGTPAQIEKLLKKI 346 GLE+ + R +I P + E LLK + Sbjct: 326 GLEDKYFRFAIRKPEENEYLLKHL 349 Lambda K H 0.318 0.138 0.393 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: 310 Number of extensions: 16 Number of successful extensions: 2 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: 354 Length of database: 361 Length adjustment: 29 Effective length of query: 325 Effective length of database: 332 Effective search space: 107900 Effective search space used: 107900 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: 49 (23.5 bits)
This GapMind analysis is from Jul 25 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