Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Ac3H11_3720 Uncharacterized PLP-dependent aminotransferase YfdZ
Query= curated2:Q5P791 (356 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3720 Length = 408 Score = 86.3 bits (212), Expect = 1e-21 Identities = 98/316 (31%), Positives = 142/316 (44%), Gaps = 36/316 (11%) Query: 34 HPYGPSPRALAAIRAEASDALRLYPDPHA-------DRLKAAIA----TRFGVE---PRE 79 +P G +P + A E + PD H RL+ AI+ R+ V+ E Sbjct: 45 NPDGATPPHIVAKLTEVAQR----PDTHGYSASKGIPRLRRAISHWYKDRYAVDIHPDTE 100 Query: 80 VFVGNGSDEVLAHAFMALLKHERPLRFPDISYSFYPVYCGLYGIAFETVPL--DDDFAIR 137 V GS E LAH +A L + PD SY + + G +VP+ D DF Sbjct: 101 AIVTIGSKEGLAHLMLATLDRGDTVLVPDPSYPIHIYGAVIAGADIRSVPVAPDVDFFAE 160 Query: 138 PDDYLPHGSVAAGGIIFPNPNAPTGRLMPLSDIERIVA--GNPQCVVVIDEAYVD--FGG 193 + + +IF P+ PT + + LS ER++A +VV D AY D + G Sbjct: 161 LEKAIRGSYPKPKMMIFGFPSNPTAQCVELSFFERVIALAKKHDILVVHDLAYADIVYDG 220 Query: 194 ESAIPLVRHHPNLLVVQ----TLSKSRSLAGLRVGFAVGNPDLIEALDRVKDSFNSYPLD 249 A P + P V TLSKS ++AG RVGF VGNPDL+ AL R+K S++ Y Sbjct: 221 YRA-PSIMEVPGAKDVAVEFFTLSKSYNMAGWRVGFMVGNPDLVAALARIK-SYHDYGTF 278 Query: 250 RLAIAGGVAAIE-DEEHFQRTRMAVIATRERLSADLASLGFDV-LPSAANFVFTR--HPH 305 +AA+E D++ + R+ L L G+ V P A+ +++ R P+ Sbjct: 279 TPLQVAAIAALEGDQQCVKDIAAQYQRRRDVLYKGLTEAGWAVDCPKASMYIWARIPEPY 338 Query: 306 RDAG--ELAAQLRRRA 319 R G E A QL +A Sbjct: 339 RALGSLEFARQLLDKA 354 Lambda K H 0.323 0.140 0.417 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: 415 Number of extensions: 21 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: 356 Length of database: 408 Length adjustment: 30 Effective length of query: 326 Effective length of database: 378 Effective search space: 123228 Effective search space used: 123228 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: 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