Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_086509941.1 BZY95_RS10840 threonine-phosphate decarboxylase
Query= curated2:Q4FSH2 (380 letters) >NCBI__GCF_002151265.1:WP_086509941.1 Length = 366 Score = 152 bits (384), Expect = 1e-41 Identities = 105/362 (29%), Positives = 187/362 (51%), Gaps = 20/362 (5%) Query: 26 PYQTGKPIEELTREYGV---SDVVKLASNENPIGCSPHVTLAITEQIGQLSRYPDGNGYY 82 P G+P E+L +G+ S+V+ ++N NP+G P + + + +L+ YPD + Sbjct: 5 PSHGGRP-EQLLPRFGLAGDSEVIDFSANLNPLGPPPWLAQRLAACVTELAVYPDPDYCE 63 Query: 83 LKQALADFNDVNVDQITLGNGSDDLLDILARSFV--GADDAIVYSQYAFVVYSMLAKMQG 140 + A+A + Q+ L NG + + + A G A + Q F Y + G Sbjct: 64 ARDAIAMSEGLGPKQVRLTNGGAEAIFLAAALLARQGVRRAAIV-QPTFGEYERACRHYG 122 Query: 141 AM--DVEVPAQRFGHDLKAMSQAIENNSNTKIVFIANPNNPTGTQLEHGELREFVASVPS 198 VE+ F D +A+ + +F+ PNNPTGT +E G + +A+ S Sbjct: 123 IAVEHVELAPGSFALDEARADEAMRD---VGALFLCRPNNPTGTLIERGVVERLLATGRS 179 Query: 199 -SVLVVLDEAYIEY-SPESNNRALLDEFDNVVIVRTFSKAYGLAGLRVGYALSSAAVADL 256 ++V+DEA++++ +P+ LL FDN++++R+ +K Y + GLR+GY L SAA + Sbjct: 180 HGAMLVVDEAFVDFVTPDERLTPLLARFDNLLLLRSMTKLYAIPGLRLGYLLGSAAAVNA 239 Query: 257 LNRIRQPFNVSRVALAAAAAALADQDFIEKTRLINDEQMHWLEKQFDALGLGFIKSHANF 316 + ++ P++V+ +A A LAD+D++ +TR D + WL+ + ALGL + SHANF Sbjct: 240 IAELQPPWSVNALAAGLVAPLLADRDYLARTRAWLDAERPWLQGELAALGLDVVPSHANF 299 Query: 317 IMVEIAVEMEDTNAA---VIYQALLEQGVIVRQLEVY-GLYN-WLRISVGVAEDNMRLID 371 ++ A ++D + + L G++VR + GL WLR++V +N L++ Sbjct: 300 LLFRDA-RLQDARGGSMPALLEHLARGGILVRHTHHFIGLEGAWLRVAVRSRPENRALVE 358 Query: 372 TL 373 + Sbjct: 359 AI 360 Lambda K H 0.318 0.134 0.372 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: 265 Number of extensions: 11 Number of successful extensions: 3 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: 380 Length of database: 366 Length adjustment: 30 Effective length of query: 350 Effective length of database: 336 Effective search space: 117600 Effective search space used: 117600 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 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