Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_013537347.1 THEAM_RS02990 succinyldiaminopimelate transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000185805.1:WP_013537347.1 Length = 387 Score = 234 bits (597), Expect = 3e-66 Identities = 133/382 (34%), Positives = 215/382 (56%), Gaps = 12/382 (3%) Query: 12 IQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYPP 71 I++L Y RL+ K + + +G+ L D G G+P TP + +A I+A+ P+ YP Sbjct: 5 IRELKSYPMDRLNRAKEEIKRKGLKLFDFGTGDPKEPTPSFIREALIRAV--PEVSQYPT 62 Query: 72 FEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGD---VVLVPS 128 +G R A W RR+GV L+P++E +P GSKE + HL + ++ V+ + Sbjct: 63 VKGRKELREAAAGWVKRRFGVELNPEAEVIPTAGSKEAIFHLPLVFIEAESDKRKVVFGT 122 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 PAYP + RG + AGG H + LK E ++L+ L +P + + +I++ NYP NPTGA+AP Sbjct: 123 PAYPVYLRGTLFAGGEPHPVELKFEENFLLRLDKLPRSLLEETRIVWINYPHNPTGASAP 182 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 +FEE+ R++ I+L D CY ++ F P S+L++ K+ + FH+LSK M Sbjct: 183 LSYFEEVYGICREHGIILCSDECYVDIYFT-EPPPSVLQV--GKEGVLAFHSLSKRSGMT 239 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAA-LQTAAETALQLPDIYLHEVQQRYRTRRD 307 G+R GFV G+ ++Q LK +G+ + AA TA D ++ E ++ ++ + Sbjct: 240 GYRSGFVAGDGKLVQ--EYLKYRSSFGVASQDFVQAAATAAWSDDGHVEERRRIFKEKAK 297 Query: 308 FLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 + E+G + +AT YLWVK P G+ +AL+LL+ G+VV+PG FG GEG+ Sbjct: 298 VFSEFFKEIGLEFLPAEATFYLWVKTPKGVSGEKYALHLLKY-GIVVSPGEFFGRGGEGF 356 Query: 368 VRISLIADCDRLGEALDRIKQA 389 RI+L+ EA++ ++A Sbjct: 357 FRIALVPTLSECKEAVEVWRRA 378 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: 448 Number of extensions: 22 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: 403 Length of database: 387 Length adjustment: 31 Effective length of query: 372 Effective length of database: 356 Effective search space: 132432 Effective search space used: 132432 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