Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Pf1N1B4_3710 L-threonine 3-O-phosphate decarboxylase (EC 4.1.1.81)
Query= curated2:B7L9P8 (356 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3710 Length = 330 Score = 68.6 bits (166), Expect = 2e-16 Identities = 59/185 (31%), Positives = 88/185 (47%), Gaps = 17/185 (9%) Query: 77 QVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVECRTVPTLENWQLD 136 QVL G+ I+LL R GK +L P Y ++ + G R V E Sbjct: 66 QVLPVAGSQMAIQLLPR-LRRAGKVGVL--SPCYAEHAEAWRRNGYIVREVLESE----- 117 Query: 137 LQGISDKLDGVKVVYVCSPNNPTGQLINPQ---DFRTLLELTRGKAIVVADEAYIEFCPQ 193 + LD + V+ V +PNNPTG + P D+ L G +V DEA+++ P Sbjct: 118 ---VDFFLDSLDVLVVVNPNNPTGLSLTPARLLDWHARLAQRGGWLVV--DEAFMDNTPH 172 Query: 194 ASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAPYPLSTPVADIA 253 SLA + A L +LR+ K F LAG+R GF LA +++ LL + + P+ +S P + Sbjct: 173 LSLAPF-ANQIGLIVLRSFGKFFGLAGVRLGFVLAERKLLKLLAEQVGPWAVSGPTRVLG 231 Query: 254 AQALS 258 L+ Sbjct: 232 QACLT 236 Lambda K H 0.319 0.135 0.395 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: 264 Number of extensions: 13 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: 356 Length of database: 330 Length adjustment: 29 Effective length of query: 327 Effective length of database: 301 Effective search space: 98427 Effective search space used: 98427 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