Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_093396405.1 BM091_RS13065 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_900114975.1:WP_093396405.1 Length = 388 Score = 412 bits (1059), Expect = e-120 Identities = 190/386 (49%), Positives = 267/386 (69%) Query: 6 ITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPK 65 I A+R+++LPPY+F LD L+ + R QG+D+ID G+G+PD TP +V+A +A++DP Sbjct: 3 IERAERLKKLPPYLFKELDRLRDEVRAQGVDIIDFGVGDPDLPTPDHIVEALKKAVEDPS 62 Query: 66 NHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVL 125 H YP + G FR + WY +R+GV LDP E + L+GSKEG++H+ +A++NPGD+ L Sbjct: 63 THRYPSYSGMNDFRDCVARWYKKRFGVDLDPAREVIVLIGSKEGIAHIPLAFINPGDLAL 122 Query: 126 VPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGA 185 VP+PAYP + G + AGG + + L END+L DL AIPE+VA KA++++ NYP+NPT A Sbjct: 123 VPTPAYPVYHTGTIFAGGESYFMPLLEENDFLPDLNAIPEDVAEKARMMFINYPNNPTSA 182 Query: 186 TAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTY 245 A +FF +V FAR Y I++ HD Y+ELAFDGY+P S L++ GAK++G+EFH+LSKTY Sbjct: 183 VAEEDFFRRVVDFARTYNIIVCHDAAYSELAFDGYKPMSFLQVEGAKEVGIEFHSLSKTY 242 Query: 246 NMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTR 305 NM GWR+GF VGN VIQGL +K+N+D G F A+Q A AL+ + E + Y+ R Sbjct: 243 NMTGWRLGFAVGNAEVIQGLGQVKSNIDSGAFNAVQMAGIAALEGDQTCVEENCRIYKER 302 Query: 306 RDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGE 365 RD L+ GL G KAT Y+W + P STDF++ LL++ G+V TPGN FG GE Sbjct: 303 RDVLVAGLRSAGLKPIVPKATFYVWCRIPENTTSTDFSMRLLKEAGIVTTPGNGFGEPGE 362 Query: 366 GYVRISLIADCDRLGEALDRIKQAGI 391 GYVR +L +R+ EA++RIK+ G+ Sbjct: 363 GYVRFALTVPVERIEEAIERIKKLGV 388 Lambda K H 0.321 0.140 0.427 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: 490 Number of extensions: 21 Number of successful extensions: 1 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: 403 Length of database: 388 Length adjustment: 31 Effective length of query: 372 Effective length of database: 357 Effective search space: 132804 Effective search space used: 132804 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 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