Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011189191.1 DP_RS09980 cobyric acid synthase
Query= curated2:Q2RL44 (386 letters) >NCBI__GCF_000025945.1:WP_011189191.1 Length = 853 Score = 135 bits (340), Expect = 4e-36 Identities = 109/362 (30%), Positives = 169/362 (46%), Gaps = 22/362 (6%) Query: 35 IKPYVPGKPIEEVQRELGVKDVIKLASNENPLGPSPDAVQALQEASDRIFLYPDGNCYYL 94 IK G + +++ E + +I ++N NPLGP + + + YPD +C Sbjct: 2 IKRKEHGGNLRKIKAEGAEQKIIDFSANINPLGPPEWLRPVISNELETLIHYPDPDCLEF 61 Query: 95 KEALAAKLGVKQENLIIGNGTDEILKMLAETYINPGDEIVVADPTFSEYEFAAQVMGGRA 154 +A+A G+ ++ ++ GNGT E+L L I P IV+ P++ +Y AA G Sbjct: 62 CQAIAGHHGISEKRVVAGNGTAELLYALLR--IIPSKRIVIPVPSYIDYYHAASQTGQEI 119 Query: 155 IKV---PTRNFRHDLAAMAAAITPRTRLVFVCNPNNPTGTIVGQAALDGFLKQVPPSVLV 211 + V P F+ L + + P L + PNNPTG + L +K + P V Sbjct: 120 VPVELSPENGFQLSLERLKKILRPGD-LALIARPNNPTGLLPDTEQLADIIKSM-PEVWF 177 Query: 212 VLDEAYSDYVTAEHYPNSLAYVRAGR-ANVIILRTFSKIYGLAGLRVGYGVAVPEIIRDL 270 LDEA+ D++ E P+ AGR NVI L + +K Y L GLR+GY E+ L Sbjct: 178 CLDEAFLDFIADE--PSF-----AGRFENVITLNSMTKFYALPGLRLGYCSCSEELKVAL 230 Query: 271 NRVREPFNVNLLAQVAAVAALKDEAHVGKSREVNSEGKDYLYSQFESL-GLKYVPTEANF 329 + P+ VN LAQ DE + +S + + + SL L+ P+ N+ Sbjct: 231 HNALPPWTVNTLAQAVGKRLFADETYRQQSLAYAEAARRDCFQELSSLDALEVFPSRVNY 290 Query: 330 IFVDIQRDSREV---FRQLLQKGVIVRTGDIF-GYD-TFLRVTIGTRRQNETFIRALREI 384 + RD V ++LLQ G +R + F G D ++ RV + T +N F +ALR Sbjct: 291 HLCRL-RDGGAVEPLRKRLLQAGFAIRPCENFSGLDRSYFRVAVRTHEENHLFFQALRTS 349 Query: 385 LA 386 LA Sbjct: 350 LA 351 Lambda K H 0.319 0.137 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: 637 Number of extensions: 30 Number of successful extensions: 6 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: 386 Length of database: 853 Length adjustment: 36 Effective length of query: 350 Effective length of database: 817 Effective search space: 285950 Effective search space used: 285950 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 (21.8 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