Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Synpcc7942_1109 Synpcc7942_1109 threonine phosphate decarboxylase
Query= curated2:Q67KI2 (361 letters) >FitnessBrowser__SynE:Synpcc7942_1109 Length = 357 Score = 125 bits (314), Expect = 2e-33 Identities = 108/338 (31%), Positives = 162/338 (47%), Gaps = 14/338 (4%) Query: 31 DLVKLNQNENPLGPSPRAVAAARAAMAQVHTYPEGTARRLRERLAQMWNLPADWFLIGNG 90 DL+ + + NPLGP + + YP+ R+LRE +A+ + DW L GNG Sbjct: 23 DLLDFSASLNPLGPPAWLATWLQQHYTHLIAYPDPQYRQLREAIARHHDCDPDWILPGNG 82 Query: 91 SDEVFRLLAEVYLEPGDRVVVPEPSFAAYRFVAELMGA--EVVAVPL--AGWTMDLPAMA 146 + E+ A L V++ P+F Y +G +A+PL L + Sbjct: 83 AAELLTWAARD-LAACREVLLLGPAFRDYERALTAVGVPWRRLALPLDRPASLATLRGLL 141 Query: 147 EAAARGAKLLFLCRPNNPTGTVFAEADLRAALERVPPSTLVVVDEAYREFDETPFD--SR 204 E L + P+NPTG ++ DL L+R LVV DEA+ +F T D + Sbjct: 142 EPQLTPETGLLINNPHNPTGWLWPLRDLWPLLQRC---RLVVADEAFLDFLPTAADWSLQ 198 Query: 205 ALVQDYPNVVIARTFSKIYGMAGFRLGYGVMRPEVLAPLYTARDPFSVNGLAVAAGLAAL 264 + ++VI R+ +K Y +AG RLGY + P+ L RDP+SVNGLA A G L Sbjct: 199 PCLAQSRSLVIVRSLTKFYSLAGLRLGYAIAHPDRLESWQQWRDPWSVNGLAAALGPELL 258 Query: 265 DDVEHVERTRALTREGKAYLYAAFQRL-GLGYVPSEANFVLFDAGRPAAEVFDALLRR-G 322 D + T +A L + + GL +PS+ANF+L A + + LL++ Sbjct: 259 ADHDFQAATWNWLPPARAALASGLASIPGLRVLPSQANFLLVQAEDSILPLQERLLQQHR 318 Query: 323 VLVRPCGSF-GLPDH-LRVTVGTPEQNRRFVEALKAAL 358 +L+R C SF L D RV V + +N+R +EA+ A L Sbjct: 319 LLIRDCLSFTELGDRWFRVAVRSSAENQRLLEAIAAEL 356 Lambda K H 0.322 0.138 0.408 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: 302 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: 361 Length of database: 357 Length adjustment: 29 Effective length of query: 332 Effective length of database: 328 Effective search space: 108896 Effective search space used: 108896 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 09 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