Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate GFF835 HP15_814 aspartate aminotransferase
Query= curated2:A8HZS2 (378 letters) >FitnessBrowser__Marino:GFF835 Length = 416 Score = 89.7 bits (221), Expect = 1e-22 Identities = 81/272 (29%), Positives = 125/272 (45%), Gaps = 26/272 (9%) Query: 34 AAGVEKVFKLSSNETPLGPSPK--------AIAAFQSAGTNLQDYPDGSSTALREAIGKA 85 AA ++ V LS + L P+PK A+ A Q+ T P+ ALR+ GK Sbjct: 53 AATMKDVIHLSIGQPDL-PTPKHVIDAYIDALNAGQTGYTMDAGLPE-LLVALRDYYGKR 110 Query: 86 MG--IDPDRIICGAGSDEILNLIAHAYVGPGDEAIHCAHGFLVYKIATLGAGGVPVVVPD 143 + D I+ +G+ E + L A PG + I FL+Y GG V Sbjct: 111 YNRKLTRDNILITSGATEAMYLAISATSAPGRQFIVTDPSFLLYAPLIRMNGGEVKFVQT 170 Query: 144 REDL--QMDVDAIIGAVTERTRVIFLANPNNPTGTYLPFNEVRR-LHAALPPNVLLVLDA 200 R + Q+D D +I A+ RT + L NPNNPTG P + V L + + D Sbjct: 171 RAENNHQLDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVETILEECAYRGIQVYADE 230 Query: 201 AYSEYVRRN-DYETGLELALSAENVIMCRTFSKIHGLAALRIGWAVASEAVIDALNRIRG 259 Y + + D+ + L ++ +N++ +FSK + +A LR+GW +AS+A I +L R Sbjct: 231 VYDHLIFDDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVGWVIASQAAIKSLRR--- 287 Query: 260 PFNM------NAPAIAAGAAAILDAEHVERSI 285 F+M N P+ AG AA+ + R + Sbjct: 288 -FHMFTTSVANTPSQFAGVAALTGDQQCVRDM 318 Lambda K H 0.318 0.134 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: 334 Number of extensions: 17 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: 378 Length of database: 416 Length adjustment: 31 Effective length of query: 347 Effective length of database: 385 Effective search space: 133595 Effective search space used: 133595 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: 50 (23.9 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