Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_051418774.1 THITH_RS07700 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000227685.2:WP_051418774.1 Length = 373 Score = 346 bits (887), Expect = e-100 Identities = 186/374 (49%), Positives = 249/374 (66%), Gaps = 11/374 (2%) Query: 3 ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASE 62 AS + V+A+ PY GKP++ + RE G+ +A VKLASNENPLG A AM A +E Sbjct: 5 ASLAVAGVQALHPYEPGKPVATLERELGIRDA--VKLASNENPLGPSPKAVAAMQAALAE 62 Query: 63 LGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAV 122 + YPD N F LK AL+ER+ + + VTLGNGSN+ILE+ A A++ G+S VY++++FAV Sbjct: 63 VHIYPDGNGFALKQALAERHRLAPEQVTLGNGSNEILELVARAWLAPGRSAVYSRHAFAV 122 Query: 123 YALATQGLGARAIVVPAVK------YGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGP 176 Y L Q + A A V A+ +GHDL AM A V + TR++F+ANPNNPTGT++ Sbjct: 123 YPLVVQAVSADARVAEALPAGADQPFGHDLGAMAALVDESTRVVFIANPNNPTGTWVGAA 182 Query: 177 KLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRV 236 +LEAF+ VP +VV+DEAY EY+ + D+ WV R+PNL+V+RTFSK GLAGLR+ Sbjct: 183 ELEAFIAGVPEQTLVVVDEAYAEYVEADGYPDTTQWVARFPNLIVTRTFSKIHGLAGLRL 242 Query: 237 GFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDK 296 G++++ P + +LLNRVRQPFNVN LAQAA +AAL D +++S N G R++ Sbjct: 243 GYSVSSPPVAELLNRVRQPFNVNALAQAAGLAALADPEHVQESVRTNRDGLRQVEAGLRD 302 Query: 297 LGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEEN 356 GL ++PS GNF+ V V +LL+QGVIVRPV NYGLP LR+TIG EEN Sbjct: 303 RGLGFIPSVGNFITFDVRQPPGP---VYEQLLRQGVIVRPVANYGLPTHLRVTIGRDEEN 359 Query: 357 EAFIAALERTLAAA 370 F+ AL+ LAAA Sbjct: 360 ARFLQALDAVLAAA 373 Lambda K H 0.318 0.135 0.385 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: 447 Number of extensions: 23 Number of successful extensions: 4 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: 370 Length of database: 373 Length adjustment: 30 Effective length of query: 340 Effective length of database: 343 Effective search space: 116620 Effective search space used: 116620 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 (21.7 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