Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate 642684274 Cphamn1_1781 L-alanine aminotransferase apoenzyme (EC 2.6.1.2)
Query= curated2:A8HZS2 (378 letters) >IMG__ChlphaBS1_FD:642684274 Length = 405 Score = 75.9 bits (185), Expect = 2e-18 Identities = 56/176 (31%), Positives = 86/176 (48%), Gaps = 11/176 (6%) Query: 84 KAMGID--PDRIICGAGSDEILNLIAHAYVGPGDEAIHCAHGFLVYK--IATLGAGGVPV 139 + GID PD II +G+ E +L+ A + PGDE + + G+ +Y IA L A +P Sbjct: 91 RCRGIDTTPDNIIVTSGASEAADLVCTAMLNPGDEVLCPSPGYPLYSAIIAKLNARELPY 150 Query: 140 VVPDREDLQMDVDAIIGAVTERTRVIFLANPNNPTGTYLPFNEVRRL-HAALPPNVLLVL 198 + D + I +T RT+++ + NPNNPTG P N +R L A +L++ Sbjct: 151 KLDPENSWLPDPEDIERRITSRTKILVVINPNNPTGELYPLNVLRSLADIARRHRLLIIS 210 Query: 199 DAAYSEYVRRNDYETGLELALSAEN---VIMCRTFSKIHGLAALRIGWAVASEAVI 251 D Y + V E + LA AE+ +I + SK RIGW + +V+ Sbjct: 211 DEVYHKLVYE---EVHIPLASLAEDDVAIITIDSLSKNLMAPGWRIGWLAITNSVL 263 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: 356 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: 378 Length of database: 405 Length adjustment: 31 Effective length of query: 347 Effective length of database: 374 Effective search space: 129778 Effective search space used: 129778 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 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