Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_022949065.1 H035_RS0111195 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000421465.1:WP_022949065.1 Length = 394 Score = 358 bits (918), Expect = e-103 Identities = 181/380 (47%), Positives = 250/380 (65%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVF +++LKAK R G D+ID GMGNPD P+ + D ++A Q H Y Sbjct: 6 RIKRLPPYVFNIVNQLKAKQRAAGEDIIDFGMGNPDQPPPRHITDKLVEAAQRETTHRYS 65 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G R+AI +WY +RY V LDP+S+A+ +GSKEGL+HLA+A + PGDVVLVP+PA Sbjct: 66 LSKGIPRLRKAICDWYAQRYDVQLDPESQAIVTIGSKEGLAHLALATLGPGDVVLVPNPA 125 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G VIAG + + L D+ +L ++ + K+L N+P+NPT E Sbjct: 126 YPIHPYGCVIAGADIRHVPLTSGRDFFEELEQAIRDLWPRPKMLILNFPANPTTQCVELE 185 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE +VA AR+Y I LV+D+ YA++ FDGY+ S+L++PGA D+ VEF++LSK+YNM GW Sbjct: 186 FFERVVAIAREYRIWLVNDIAYADIVFDGYKAPSILQVPGAMDMAVEFYSLSKSYNMPGW 245 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF+ GNR ++ L LK+ LDYG+F +Q AA TAL+ P + E++ YR RRD L Sbjct: 246 RVGFMCGNRELVAALGRLKSYLDYGMFTPIQIAAITALEGPQDCVAEIRDMYRRRRDVLC 305 Query: 311 QGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 GL +LGW+V K KATM++W P MGS +F+ LL + V V+PG FG GEG+ Sbjct: 306 DGLMQLGWEVEKPKATMFVWTPIPEPYRAMGSLEFSKKLLLEAKVAVSPGIGFGQYGEGF 365 Query: 368 VRISLIADCDRLGEALDRIK 387 VR LI + R +A+ I+ Sbjct: 366 VRFGLIENEHRTRQAIRGIR 385 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: 470 Number of extensions: 22 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: 403 Length of database: 394 Length adjustment: 31 Effective length of query: 372 Effective length of database: 363 Effective search space: 135036 Effective search space used: 135036 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