Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate 3606735 Dshi_0166 aminotransferase class I and II (RefSeq)
Query= curated2:A5FVN2 (364 letters) >FitnessBrowser__Dino:3606735 Length = 318 Score = 70.9 bits (172), Expect = 5e-17 Identities = 64/203 (31%), Positives = 91/203 (44%), Gaps = 22/203 (10%) Query: 158 NPNNPTGSLVPASDVSRLRAELPPDVLLVLDAAYAEYVERADYDPGVELVDSGQNTVMTR 217 +PNNP G L A ++ RA L VLD ++ + A P + + TV+ + Sbjct: 132 HPNNPNGRLWQAEEIPTDRA------LTVLDESFCDIAPEASLMP----LAARPRTVILK 181 Query: 218 TFSKMFGLGGVRLGWAYAPLAIVDVLNRTRMPFNVSGPAAAAGIAALAEPGWVERCRNHN 277 +F K +GL G+RLG+A + L P+ VSGPA G AL + GW + R Sbjct: 182 SFGKFWGLAGLRLGFAIGQAETLAPLRDRIGPWAVSGPALRVGALALRDAGWAAKTRARL 241 Query: 278 TRARTELAARIERAGFRVWPSEANFLLADLETADRAAAADTHLRSRGIIVRQVAAYGLP- 336 R L A + G+ V F L D T D +AA D R RQ+ P Sbjct: 242 DRDAARLDALAKGFGWSVTGGTGLFRLYD--TPDASAAQDRLAR------RQIWTRRFPY 293 Query: 337 --QCLRITI-GTDEECSTVADAL 356 + LR+ + GT+ + VA AL Sbjct: 294 SDRWLRLGLPGTEADWGRVARAL 316 Lambda K H 0.320 0.136 0.405 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: 14 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: 364 Length of database: 318 Length adjustment: 28 Effective length of query: 336 Effective length of database: 290 Effective search space: 97440 Effective search space used: 97440 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 (21.8 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