Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate AZOBR_RS08675 AZOBR_RS08675 histidinol phosphate aminotransferase
Query= reanno::azobra:AZOBR_RS20485 (364 letters) >FitnessBrowser__azobra:AZOBR_RS08675 Length = 361 Score = 308 bits (790), Expect = 1e-88 Identities = 159/359 (44%), Positives = 223/359 (62%), Gaps = 6/359 (1%) Query: 9 APRPGILDIAPYVGG----EHAGHIRLASNEGALGPSPRAVEAYRAAAGELHRYPDGGSA 64 +PRPGI I PY + A + L+ LGP +A+ AYR A ++HRYPD Sbjct: 5 SPRPGIGQIKPYRPARPPEDGAAWVDLSLTVNPLGPGKKALTAYRHMAAQIHRYPDWSQD 64 Query: 65 KLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAKSVGA 124 +LR AIA R+ LDA + C GSDE+I L+ +A+ GPGDEVL +HG+ + ++ GA Sbjct: 65 RLRHAIARRYDLDAGHITCANGSDEMIHLVTQAFTGPGDEVLCHEHGYRGFMKAIRAAGA 124 Query: 125 TPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPENAILV 184 TPV A E +L DV++++ +T+L F+ANPNNPTGTYI ++ + RL AGLP + +LV Sbjct: 125 TPVIAAERDLVVDVEAMIDRANEKTKLCFLANPNNPTGTYIPSEMVLRLRAGLPSHTLLV 184 Query: 185 IDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADVLNRV 244 +D+AYA+Y ++YS G E+V+ NV+M RTFSK+ L +R+GWAY PAG+ + +N+ Sbjct: 185 LDSAYADYCRRDNYSDGTEIVENSDNVLMVRTFSKLHGLAGLRVGWAYGPAGVIEAVNQT 244 Query: 245 RGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNFVLVD 304 RGPFNV AAQ A AA+ DT E + +HN W W ++ LG++ +PSV NF+L Sbjct: 245 RGPFNVGIAAQAAAEAAVGDTEHEEATFAHNSSWLPWLSHELEQLGVRVYPSVCNFILAR 304 Query: 305 FAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKDFLA 363 T +A L RGILV+ YGL CLR+T+G E E R +V AL + L+ Sbjct: 305 I--PTDPSLGVQAVLDHLARRGILVKPTQDYGLADCLRITVGREDENRALVAALGEILS 361 Lambda K H 0.319 0.136 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: 405 Number of extensions: 20 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: 364 Length of database: 361 Length adjustment: 29 Effective length of query: 335 Effective length of database: 332 Effective search space: 111220 Effective search space used: 111220 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: 49 (23.5 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