Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_026127539.1 D471_RS0108560 putative succinyldiaminopimelate transaminase DapC
Query= curated2:Q51687 (367 letters) >NCBI__GCF_000341125.1:WP_026127539.1 Length = 393 Score = 63.5 bits (153), Expect = 9e-15 Identities = 81/272 (29%), Positives = 110/272 (40%), Gaps = 30/272 (11%) Query: 44 GPSDKAREAMIRAAHGLHRYP-NTDHAGLRGAIGEVHG------LDPD-RIICGVGSDEI 95 GP A G+++YP + LR A+ LDPD + VG+ Sbjct: 41 GPRSLLEAATGHILDGVNQYPPGSGRPELRRAVSRYRARHYGIELDPDSEVYVTVGATAG 100 Query: 96 IHFLCQAYAGPGTEVLFTEHGFLMYRISAHAAGAIPVQVA-----ERDRVT-DIDALIAG 149 I A G EV+ E + Y AG + VA ER T D D L A Sbjct: 101 IAASLLALVERGDEVVVFEPMYDSYAAMISLAGGVRRPVALRPDPERGAFTFDPDELRAA 160 Query: 150 ATPRTRLIFVANPNNPTGTMVGLPELERLARAVPQ--AILVVDAAYAEYVGDYDGGAELA 207 PRTR+I V P+NPTGT+ ELE +A+ + + + D Y D LA Sbjct: 161 VGPRTRVIIVNTPHNPTGTVFTAEELETIAQVCREHDLLALTDEVYEFLTFDGLPHVPLA 220 Query: 208 TRLPNVFMTRTFS-----KIYGLGGLRVGWGYGPREIVDVLNRIRGPFNLS-NVALEGAE 261 T LP + RT S K++ + + GW GP +V + + S N AL+ A Sbjct: 221 T-LPGM-RERTLSVSSVGKMFAVTAWKTGWVMGPEPLVRAVRTVNQFLTFSANGALQLAI 278 Query: 262 AAMRDRE------HIARCQAENARMRAWLAEA 287 A D E A QA+ R+ A L A Sbjct: 279 ADAIDHEGAWIESQRASLQAKRDRLAAGLVRA 310 Lambda K H 0.320 0.137 0.408 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: 338 Number of extensions: 22 Number of successful extensions: 1 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: 367 Length of database: 393 Length adjustment: 30 Effective length of query: 337 Effective length of database: 363 Effective search space: 122331 Effective search space used: 122331 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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