Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011973901.1 MAEO_RS06050 pyridoxal phosphate-dependent aminotransferase
Query= curated2:A9AA96 (371 letters) >NCBI__GCF_000017185.1:WP_011973901.1 Length = 375 Score = 117 bits (294), Expect = 4e-31 Identities = 113/370 (30%), Positives = 173/370 (46%), Gaps = 30/370 (8%) Query: 25 EIARNYGIDPEKIIKLGSNENPWGCSPKIAE---KLMDEVSKLHQYPQPINPELMEEISK 81 EI + + + + I LG E + I E K +DE K H P PEL E IS Sbjct: 13 EIRKIFNMATKDSINLGIGEPDFDTPQHIVEGAKKALDE-GKTHYTPNNGIPELREAISH 71 Query: 82 FTKMPVE-----NIIVGGDGADEVIDNIMRILIDEDDEVIIPIPTFTQYAISAKIHGANI 136 K+ N I+ GA E + + L+++ DEV+I P F Y ++ NI Sbjct: 72 KLKIDNNLDVDANNIITTCGASEALMLSLMTLVNKGDEVLISNPGFVSYNSLTQLCEGNI 131 Query: 137 KWAKFDEENGFKLDAESVLNNITEKTKAIFLCTPNNPTGNVIPTEDIK---KIVESTDAL 193 K DE+ F +D E V N+IT KTK I L +P NPTG V+ +IK I E + + Sbjct: 132 IPMKLDEK--FNIDIEEVKNSITNKTKCIMLNSPANPTGKVMDKSEIKAICDIAEDNNII 189 Query: 194 VMIDHAY--IEYSKEEYDLTNWALKYDNVLVLRTFSKVFGLAGQRVGY-GVT---SKK-- 245 ++ D Y I Y K+ Y + DN +++ FSK + G R+GY G+ +KK Sbjct: 190 IISDEIYEKIIYDKKHYSPMEFT---DNCILINGFSKSHAMTGWRIGYIGINENLNKKYD 246 Query: 246 LVDYMMRIKP--IFSLTRASQVSAITALQ-DKEFFKKCLKEGIESREEIYNGLKKFKQLE 302 L++ M +I T +Q A+ AL + + L E R+ + NGLK +L Sbjct: 247 LIENMTKIHQYGFACATSFAQYGALEALTGSQNCVNEMLNEFRRRRDLMVNGLKNTFKLT 306 Query: 303 VYPTEANYMLVKVKNGMNSSEFCEALLKKGVIVRDCYSFEGLEPYYFRVSIGT-FEENER 361 V P A Y+ V+ N E + L++ ++ +F Y R S T +E+ E+ Sbjct: 307 V-PDGAFYVFPNVEEYDNGMEISQKLIENNILCVPGIAFGSGGENYVRFSYATKYEDIEK 365 Query: 362 FLKIMSEIVE 371 L+I++ + E Sbjct: 366 ALEIINNLFE 375 Lambda K H 0.317 0.136 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: 364 Number of extensions: 20 Number of successful extensions: 2 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: 371 Length of database: 375 Length adjustment: 30 Effective length of query: 341 Effective length of database: 345 Effective search space: 117645 Effective search space used: 117645 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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