Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate HSERO_RS15835 HSERO_RS15835 aspartate aminotransferase
Query= BRENDA::W0PFQ7 (399 letters) >FitnessBrowser__HerbieS:HSERO_RS15835 Length = 405 Score = 512 bits (1319), Expect = e-150 Identities = 253/398 (63%), Positives = 306/398 (76%), Gaps = 1/398 (0%) Query: 3 TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62 +LF+A+E+APRDPILG+ E YNAD K NLGVGVYYDDNGK+PLL+ V++AE + Sbjct: 8 SLFSAIEMAPRDPILGVTEAYNADQNPAKTNLGVGVYYDDNGKVPLLECVKKAEAELAAK 67 Query: 63 HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122 A R YLPI+G+ Y++ QEL+FG S V+T+ RA+T QALGGTGALK+GADFLK P Sbjct: 68 LAPRTYLPIDGLATYDRAVQELVFGAGSAVVTEKRAITVQALGGTGALKLGADFLKHFSP 127 Query: 123 DST-VYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLH 181 T V+ISDPSWENHRALFE AGFKV Y YYD AT G+NF G ++K M GS+++LH Sbjct: 128 AGTEVWISDPSWENHRALFEMAGFKVNAYPYYDPATRGVNFAGMLDALKTMKSGSVVLLH 187 Query: 182 ACCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSM 241 ACCHNPTG D + +QW Q+ +V R LVPFLD+AYQGFG G+ ED VVR FA+ G + Sbjct: 188 ACCHNPTGADLTDDQWTQVIEVVTSRGLVPFLDMAYQGFGDGIAEDGQVVRRFAEAGGPL 247 Query: 242 FISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQIL 301 F+S+SFSKSFSLYGERVGAL++ +S +EA+RVLSQ+KRV+RTNYSNPP HGG VVA L Sbjct: 248 FVSNSFSKSFSLYGERVGALSIAAASAEEAARVLSQLKRVVRTNYSNPPIHGGQVVATAL 307 Query: 302 NTPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQV 361 +PEL WE ELA+MR RIREMR+ L KL DF+FV+ QRGMFSYSGLTK QV Sbjct: 308 ASPELRKLWEDELAEMRVRIREMRQLLVAKLKEKAPGHDFDFVIKQRGMFSYSGLTKAQV 367 Query: 362 ERLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAVL 399 +RLR E IYAV++GRICVAALN++NID VV AIA VL Sbjct: 368 DRLRNEFSIYAVDTGRICVAALNTKNIDVVVDAIAKVL 405 Lambda K H 0.318 0.134 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: 468 Number of extensions: 15 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: 399 Length of database: 405 Length adjustment: 31 Effective length of query: 368 Effective length of database: 374 Effective search space: 137632 Effective search space used: 137632 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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