Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate PP_1676 PP_1676 subunit of adenosylcobinamide-phosphate synthase beta component
Query= curated2:Q67KI2 (361 letters) >FitnessBrowser__Putida:PP_1676 Length = 330 Score = 79.3 bits (194), Expect = 1e-19 Identities = 69/221 (31%), Positives = 102/221 (46%), Gaps = 14/221 (6%) Query: 108 RVVVPEPSFAAYRFVAELMGAEVVAVPLAGWTMDLPAMAEAAARGAKLLFLCRPNNPTGT 167 RV V P +A + + + G +++A+ A EAA G +L L PNNPTG Sbjct: 88 RVGVLTPCYAEHPYAWQRAGHQLLALD--------EAQVEAALDGLDVLVLVNPNNPTGQ 139 Query: 168 VFAEADLRAALERVPP-STLVVVDEAYREFDETPFDSRALVQDYPNVVIARTFSKIYGMA 226 + L A R+ ++VDEA+ D TP DS + P +++ R+F K +G+A Sbjct: 140 RVSRERLLAWHARLAARGGWLLVDEAF--MDNTPADSVVDCAERPGLIVLRSFGKFFGLA 197 Query: 227 GFRLGYGVMRPEVLAPLYTARDPFSVNGLAVAAGLAALDDVEHVERTRALTREGKAYLYA 286 G RLG+ +L L P++VNG A+L D E +R +A R A Sbjct: 198 GVRLGFVAAEHSLLLRLAELLGPWTVNGPTRVLAQASLSD-ETAQRAQA-QRCAAASQRL 255 Query: 287 AFQRLGLGYVPS-EANFVLFDAGRPAAEVFDALLRRGVLVR 326 A G PS + + AA + + L RRG+LVR Sbjct: 256 AHVLRSAGLAPSGGCDLFQYVRSEHAARLHEFLARRGILVR 296 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: 274 Number of extensions: 16 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: 361 Length of database: 330 Length adjustment: 29 Effective length of query: 332 Effective length of database: 301 Effective search space: 99932 Effective search space used: 99932 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