Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate WP_011610169.1 TERY_RS01355 pyridoxal phosphate-dependent aminotransferase
Query= curated2:Q3AAT6 (362 letters) >NCBI__GCF_000014265.1:WP_011610169.1 Length = 390 Score = 112 bits (279), Expect = 2e-29 Identities = 94/327 (28%), Positives = 159/327 (48%), Gaps = 28/327 (8%) Query: 46 VAAAIKEAVDK--VNYYPDGGAFRLKEKIAAKYG------VTPDNIILGNGSDELVMFLA 97 + A ++A+D Y P G +L+E IA K +NII+ NG + L Sbjct: 48 IKVAAQKALDSGYTKYGPAAGEPKLREAIAHKLSQENGLNYKAENIIVTNGGKHSLFNLM 107 Query: 98 MALIDPGDEAIMPVPSFPRYEPVVTMMNG---IAREIPLKEHRLDLKTMAEAVNEKTRLV 154 +ALI+PGDE I+P P + Y +V + G I P +++ + + +++ +KT+L Sbjct: 108 LALIEPGDEVIIPAPYWLSYPEMVKLAGGEPIILTTDPETGYKVTPEQLRQSITDKTKLF 167 Query: 155 YLCNPNNPTGTYITKGELEEFLE-RVPEEVVVVLDEAY----FEFARLFNDYPDGLNFFK 209 L +P+NPTG E++ E V ++++VV DE Y ++ A + FK Sbjct: 168 VLNSPSNPTGMVYQPAEIKALAEVLVEKDILVVSDEIYEKIIYDDAEHLSIGAVNSEIFK 227 Query: 210 KRPNTVVLRTFSKAYGLAGLRVGYGFAPENLAKAINSLR--PPFNVNFLAQMAAVAALDD 267 NT++ F+KAY + G R+GY AP L A ++ NV AQ A+AAL+ Sbjct: 228 ---NTIISNGFAKAYSMTGWRIGYLAAPVELINATVKIQGHSTSNVCTFAQYGAIAALES 284 Query: 268 EEYVREVVKNTDEGKKFLYQEIIRM--GLS-YIPSAANFLMIKTEK--PSALVFRELL-- 320 + E ++ ++ + ++++ G+S P A ++ + K S+L F L Sbjct: 285 SQDCVEQMRQAFAKRRKIIYDLLKTLPGISCNQPEGAFYMFVNISKISSSSLEFCNALLE 344 Query: 321 KRGVIVRSGDIFGMDDWIRVTVGTPVQ 347 + V V G FG DD IR++ T ++ Sbjct: 345 DQNVAVIPGIAFGADDHIRISYATDLE 371 Lambda K H 0.319 0.139 0.399 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: 322 Number of extensions: 16 Number of successful extensions: 4 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: 362 Length of database: 390 Length adjustment: 30 Effective length of query: 332 Effective length of database: 360 Effective search space: 119520 Effective search space used: 119520 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 (21.7 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