Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate HSERO_RS15835 HSERO_RS15835 aspartate aminotransferase
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS15835 Length = 405 Score = 417 bits (1072), Expect = e-121 Identities = 210/398 (52%), Positives = 271/398 (68%), Gaps = 2/398 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F ++ DPIL + E + D K NL +G+YY+++G +P L+ V +AEA L A+ Sbjct: 9 LFSAIEMAPRDPILGVTEAYNADQNPAKTNLGVGVYYDDNGKVPLLECVKKAEAELAAKL 68 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 YLP++GL Y A+ L+FGA V+ ++R T+Q LGG+GALK+GADFLK + P Sbjct: 69 -APRTYLPIDGLATYDRAVQELVFGAGSAVVTEKRAITVQALGGTGALKLGADFLKHFSP 127 Query: 121 E-SGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179 + VW+SDP+WENH A+F AGF+V+ YP+YD AT GV F +L LKT+ + S+VLLH Sbjct: 128 AGTEVWISDPSWENHRALFEMAGFKVNAYPYYDPATRGVNFAGMLDALKTMKSGSVVLLH 187 Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239 CCHNPTGADLT+DQW VIE++ +R L+PFLD+AYQGFG G+ ED +R A AG P Sbjct: 188 ACCHNPTGADLTDDQWTQVIEVVTSRGLVPFLDMAYQGFGDGIAEDGQVVRRFAEAGGPL 247 Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299 VSNSFSK FSLYGERVG LS+ AE A RVL QLK VR NYS+PP G QVVA L Sbjct: 248 FVSNSFSKSFSLYGERVGALSIAAASAEEAARVLSQLKRVVRTNYSNPPIHGGQVVATAL 307 Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359 L+ W E+ EMR RI MRQ LV L + P +FD+++ QRGMFSY+GL+ AQV Sbjct: 308 ASPELRKLWEDELAEMRVRIREMRQLLVAKLKEKAPGHDFDFVIKQRGMFSYSGLTKAQV 367 Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 DRLR EF +Y + +GR+CVA LNT N+ V A A V+ Sbjct: 368 DRLRNEFSIYAVDTGRICVAALNTKNIDVVVDAIAKVL 405 Lambda K H 0.320 0.135 0.401 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: 410 Number of extensions: 11 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: 397 Length of database: 405 Length adjustment: 31 Effective length of query: 366 Effective length of database: 374 Effective search space: 136884 Effective search space used: 136884 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: 50 (23.9 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