Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Pf1N1B4_1065 Histidinol-phosphate aminotransferase (EC 2.6.1.9)
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065 Length = 350 Score = 182 bits (463), Expect = 9e-51 Identities = 125/365 (34%), Positives = 187/365 (51%), Gaps = 23/365 (6%) Query: 3 ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASE 62 + F +V+++ PY+ G+ A +VKL +NENP G A AM ++ Sbjct: 2 SKFWSPFVKSLVPYVPGEQPKL---------AKLVKLNTNENPYGPSPKALAAMQTELND 52 Query: 63 -LGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFA 121 L YPD N+ LK A+++ YGV + V LGNGS+++L H ++ Q +++ S++ Sbjct: 53 NLRLYPDPNSDLLKQAVAKYYGVQGNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYS 112 Query: 122 VYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAF 181 Y + G I AV A + I NPN PTG + +E Sbjct: 113 FYPVYC---GLYGIAFDAVPLDEQFQINPADYAKPNGGIIFPNPNAPTGCLLALDAVEQI 169 Query: 182 LDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIA 241 L P VVVV DEAY ++ + +I V RYPNLLV++T SK+ LAGLRVG A+ Sbjct: 170 LKASPDSVVVV-DEAYIDFGGET----AITLVDRYPNLLVTQTLSKSRSLAGLRVGLAVG 224 Query: 242 QPELTDLLNRVRQPFN---VNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLG 298 P+L + L R++ FN ++ LA A AA D+ + +K+ L ++ + G Sbjct: 225 HPDLIEALERIKNSFNSYPLDRLAIVGAAAAFEDREYFDKTCRLVIDSREKVVAQLEAKG 284 Query: 299 LEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEA 358 E +PS NF+ R DAAG + +L ++GVIVR + Q+LRI+IG PE+N+A Sbjct: 285 FEVLPSAANFIFARHPKHDAAG--LAAKLRERGVIVRHFKQERIAQFLRISIGTPEQNQA 342 Query: 359 FIAAL 363 I L Sbjct: 343 LIDGL 347 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: 365 Number of extensions: 21 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: 370 Length of database: 350 Length adjustment: 29 Effective length of query: 341 Effective length of database: 321 Effective search space: 109461 Effective search space used: 109461 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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