Align histidine transaminase (EC 2.6.1.38) (characterized)
to candidate WP_078428542.1 BK574_RS10305 threonine-phosphate decarboxylase CobD
Query= BRENDA::Q8R5Q4 (351 letters) >NCBI__GCF_002019605.1:WP_078428542.1 Length = 360 Score = 159 bits (402), Expect = 1e-43 Identities = 107/330 (32%), Positives = 181/330 (54%), Gaps = 20/330 (6%) Query: 30 NETPFELPEEVMKNIGDIVKSIHVNIYPDPTAEKLREELARYCSVTPKNIFVGNGSDEII 89 N P +P V +++I YPDP A +LRE+LA +V+ + VGNG+ E+I Sbjct: 31 NVNPLGVPRVVRDRWNQYIEAI--TTYPDPHASQLREKLANDLNVSIDQLIVGNGAAELI 88 Query: 90 HLIMLAFVDKGDTVLYPHPSFAMYSIYSKIAGANEIAVNLNEDYTYN--VERFAEAVERY 147 LI F K VL P+F+ Y I L ++ +++ VE EA+ Sbjct: 89 LLIANYFRKK--RVLIVEPTFSEYRDACLTYDCEIIRYQLLQESSWDIQVESLLEAINGV 146 Query: 148 KPKLVFLCNPNNPTGSVIDEEDIIRIIEKARG---IVIVDEAYFEFYGK--TLVPYIDRF 202 ++FLC+PNNPTG+ I+ +I++ +AR VI+DEA+++F + +++PYI+ F Sbjct: 147 D--ILFLCHPNNPTGTTIERSTLIQVFSRAREKNVTVIIDEAFYDFCTENVSVIPYIEEF 204 Query: 203 ENLIVLRTLSKAFGIAGLRVGYALSNGEIVKYLNLVKSPYNLNSLSQRIALEVLKSGV-L 261 NL+VLR+L+K + I LR+GY ++ E V L + P+++N ++Q++ L+ + Sbjct: 205 HNLVVLRSLTKMYAIPSLRLGYVVARKEFVSELKKFQQPWSVNGMAQQVGLDCISDEEHA 264 Query: 262 KERVNYIINEREKLVKELNKINGIKVYPSHANFVLCKFENAND----VHKRLVERGILVR 317 + +I ER+++ K L+ I G +V PS NF L K + N+ + L+ G++ R Sbjct: 265 IDTKTFIREERKRMFKLLSDI-GYEVSPSVVNFYLLKPKGTNEDLTPLITFLIRNGVIPR 323 Query: 318 NFSNVKGLEGT-LRITVSSSDANDYLINAL 346 + N GLEG +R+ + + ND L++ L Sbjct: 324 HTYNFLGLEGKYIRLAIKTRQDNDLLLSVL 353 Lambda K H 0.319 0.138 0.389 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: 301 Number of extensions: 17 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: 351 Length of database: 360 Length adjustment: 29 Effective length of query: 322 Effective length of database: 331 Effective search space: 106582 Effective search space used: 106582 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: 49 (23.5 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