Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate N515DRAFT_2186 N515DRAFT_2186 alanine-synthesizing transaminase
Query= curated2:Q1AY33 (351 letters) >FitnessBrowser__Dyella79:N515DRAFT_2186 Length = 410 Score = 76.3 bits (186), Expect = 1e-18 Identities = 68/208 (32%), Positives = 100/208 (48%), Gaps = 18/208 (8%) Query: 70 REAVAAANP-----GSDVANVLVGNGSSEVLQNLLMLVERPG-EVLFPWPTFTLYPS--I 121 RE +AA G +V + VGNG SE++ L + +PG EVL P P + L+ + I Sbjct: 76 RETIAAQQRARGARGVEVERIFVGNGVSELIDLSLRALLQPGDEVLLPSPDYPLWSAATI 135 Query: 122 AGTLGLRARRVPLTEEHRVKPEALLSAVTGETRAVILCNPNNPTGT---HLTLEEVSALA 178 R R H P+ + + VT TRA++L NPNNPTG LE + +A Sbjct: 136 LNDGQPRYYRCLAENGHLPDPDEIEALVTARTRAIVLINPNNPTGAVYPRELLERIVRIA 195 Query: 179 DALPEDVLLILDEAYQEFVADPAYHGSHA-LALERPNVAVARTFSKAHGLAGFRVGYGLA 237 + +LL+ DE Y E + D A A +A + P V+ SK H G+RVG+ Sbjct: 196 ER--HHLLLLTDEIYDEILYDGAQFVPLATVAGDVPCVSFG-GLSKVHRACGYRVGWMSL 252 Query: 238 SRE---IADYAERVRFPFSVNLAAQVAA 262 S + DY + ++ ++ L A V A Sbjct: 253 SGDPVRTHDYRDALQLLAALRLCANVTA 280 Lambda K H 0.317 0.133 0.382 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: 321 Number of extensions: 24 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: 351 Length of database: 410 Length adjustment: 30 Effective length of query: 321 Effective length of database: 380 Effective search space: 121980 Effective search space used: 121980 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