Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate HSERO_RS15835 HSERO_RS15835 aspartate aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >FitnessBrowser__HerbieS:HSERO_RS15835 Length = 405 Score = 421 bits (1083), Expect = e-122 Identities = 210/397 (52%), Positives = 261/397 (65%), Gaps = 1/397 (0%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F I+ P DPIL + E++ D K NL +G+Y+DD G++P+++ V++AEA L A + Sbjct: 9 LFSAIEMAPRDPILGVTEAYNADQNPAKTNLGVGVYYDDNGKVPLLECVKKAEAELAAKL 68 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFP- 119 PR YLP+ G A Y AVQ LVFG E R TVQ LGG+GAL++GADFLK + P Sbjct: 69 APRTYLPIDGLATYDRAVQELVFGAGSAVVTEKRAITVQALGGTGALKLGADFLKHFSPA 128 Query: 120 DAQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHA 179 +VWISDPSWENHR +FE GF VN YPYYD AT G+ F MLDAL+ + S+VLLHA Sbjct: 129 GTEVWISDPSWENHRALFEMAGFKVNAYPYYDPATRGVNFAGMLDALKTMKSGSVVLLHA 188 Query: 180 CCHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCL 239 CCHNPTG DL DQW Q+I ++ L+PF+DMAYQGFG G+ +D VR G P Sbjct: 189 CCHNPTGADLTDDQWTQVIEVVTSRGLVPFLDMAYQGFGDGIAEDGQVVRRFAEAGGPLF 248 Query: 240 VANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLT 299 V+NSFSK+FSLYGER G LS+ SAEE RVL QL VR NYSNPP HG +VVA L Sbjct: 249 VSNSFSKSFSLYGERVGALSIAAASAEEAARVLSQLKRVVRTNYSNPPIHGGQVVATALA 308 Query: 300 TPALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVD 359 +P LR +WE ELA RI +MR + L G + QRGMF+Y+GLT QVD Sbjct: 309 SPELRKLWEDELAEMRVRIREMRQLLVAKLKEKAPGHDFDFVIKQRGMFSYSGLTKAQVD 368 Query: 360 RLRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 RLR E +Y + +GR+CVA LN +N+ V AIA VL Sbjct: 369 RLRNEFSIYAVDTGRICVAALNTKNIDVVVDAIAKVL 405 Lambda K H 0.323 0.137 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: 446 Number of extensions: 14 Number of successful extensions: 2 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: 400 Length of database: 405 Length adjustment: 31 Effective length of query: 369 Effective length of database: 374 Effective search space: 138006 Effective search space used: 138006 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 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