Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_078718425.1 B5D49_RS14390 cobyric acid synthase
Query= curated2:Q8TVG3 (391 letters) >NCBI__GCF_900167125.1:WP_078718425.1 Length = 888 Score = 138 bits (348), Expect = 5e-37 Identities = 100/366 (27%), Positives = 164/366 (44%), Gaps = 20/366 (5%) Query: 25 YVPGKSKEEIAREYGIEPDEIVKLGSNENPLGPSPKAVKAAKRELERLHEYPEPLAPPSL 84 Y G +A+ G E E+ ++ NPLGP + R + YP+P + Sbjct: 17 YAHGGDVRVLAQHAGCEVRELDDFSASLNPLGPPSWLERELARAALDVTAYPDPTSRDVC 76 Query: 85 YEAIIDYLADPPYPAGEPVEITREHLVVGGDGADEIIDVLTRVLVDPG-DPVVIPVPTFS 143 A Y P V G+GA + V R V G VIP P+++ Sbjct: 77 LAACELYKVWPTQ-------------VCAGNGASGLFPVAVRAAVRDGFQRAVIPAPSYA 123 Query: 144 QYGISARACGAEVRKPRFDPERGFELDEDSLFEALDREVRLVYLCTPNNPTGNRIRERVV 203 Y + G DPE+GF D L L+ L++LC+PNNPTGN + V Sbjct: 124 DYERACELAGMRTEFFPLDPEQGFAPDFRELESRLNAPA-LIFLCSPNNPTGNVLDATRV 182 Query: 204 RDVVE---ECRGVVLIDHAYVEFADHDYTPLALEYDNVLVLRTCSKALGLAGARVGYGIA 260 R++ E +CR L+D ++ +F + DN+LV+ + +K + G R+G Sbjct: 183 RELAESHPQCR--FLVDESFADFVPGMDRLVRKRPDNLLVIHSLTKFFAIPGLRLGLAFG 240 Query: 261 NPELIEHLHRIKPVFSLTRPSAAAAEATFRDRDYIEKSVRLMIESRKYLYRELRKLDRLT 320 PELI L + +P +S+ + + RD Y + + R+ L L + + Sbjct: 241 APELILPLQKSQPEWSVNVAAQRVGASALRDLPYQAATRAEVQRLREDLELGLGFVPGIR 300 Query: 321 PFPSEANYLLVDVSNTGMNASEFTEELLKRGVIVRDCSSFEGIEPFYVRVSTGTLEEDRK 380 FPS+AN+LL + G N E+LL + + +R C++F G++ Y RV+ T E++++ Sbjct: 301 VFPSQANFLLCRIERLGQNVRPLFEKLLSQRIAIRPCANFRGLDDRYFRVAVRTREQNQR 360 Query: 381 FIEVVK 386 ++ Sbjct: 361 LCNALE 366 Lambda K H 0.318 0.140 0.405 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: 808 Number of extensions: 43 Number of successful extensions: 5 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: 391 Length of database: 888 Length adjustment: 37 Effective length of query: 354 Effective length of database: 851 Effective search space: 301254 Effective search space used: 301254 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: 53 (25.0 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