Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_057508605.1 ABB28_RS10585 aminotransferase
Query= curated2:Q67KI2 (361 letters) >NCBI__GCF_001431535.1:WP_057508605.1 Length = 373 Score = 155 bits (391), Expect = 2e-42 Identities = 117/332 (35%), Positives = 166/332 (50%), Gaps = 9/332 (2%) Query: 33 VKLNQNENPLGPSPRAVAAARAAMAQVHTYPEGTARRLRERLAQMWNLPADWFLIGNGSD 92 + LN NE P GPSP A AAR ++A Y A LR+ A L + GS Sbjct: 47 ILLNFNECPYGPSPAAQQAARDSVAASGRYQFALASELRDAFAHGEQLDPKQVRLFPGSS 106 Query: 93 EVFRLLAEVYLEPGDRVVVPEPSFAAYRFVAELMGAEVVAVPL-AGWTMDLPAMAEAAAR 151 E A ++ P +V +P+F +A GA V + L A D+ AM +AA + Sbjct: 107 EPLNRAALLWTGPEAALVTADPTFETLGEMAAARGALVHRIALRADGAHDVRAMVDAARQ 166 Query: 152 GAK-LLFLCRPNNPTGTVFAEADLRAALERVPPSTLVVVDEAYREFDE-TPFDSRALVQD 209 L+++C PNNPTG++ ADL L P +T V++DEAY ++ E A +D Sbjct: 167 QPTGLIYICNPNNPTGSITPRADLDWLLANKPAATRVLLDEAYLQYSEQASLAGEAGKRD 226 Query: 210 YPNVVIARTFSKIYGMAGFRLGYGVMRPEVLAPLYTARD-PFSVNGLAVAAGLAALDDVE 268 ++++ RTFSK+YGMAG RLG + P LA L T D P V A+AAGLA+L D Sbjct: 227 --DLIVLRTFSKLYGMAGLRLGVAIAAPARLAELATLGDNPLPVP--ALAAGLASLRDPL 282 Query: 269 HVERTRALTREGKAYLYAAFQRLGLGYVPSEANFVLFDAGRPAAEVFDALLRRGVLVRPC 328 V + R + + A + G +PSEAN + D GR AE A+ +GV++ Sbjct: 283 LVPQRRLQNAQVRQATIAWLGKRGFACIPSEANCFMVDVGRNGAEWVAAMKAQGVVIGRS 342 Query: 329 GSFGLPDHLRVTVGTPEQNRRFVEALKAALGE 360 P +RVTVG+ + RF +A G+ Sbjct: 343 WPI-WPQRVRVTVGSEAEMERFRDAFAIVAGQ 373 Lambda K H 0.322 0.138 0.408 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: 316 Number of extensions: 16 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: 361 Length of database: 373 Length adjustment: 30 Effective length of query: 331 Effective length of database: 343 Effective search space: 113533 Effective search space used: 113533 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 (21.9 bits) S2: 49 (23.5 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