Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_077278775.1 B1C78_RS08600 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_002000365.1:WP_077278775.1 Length = 399 Score = 348 bits (894), Expect = e-100 Identities = 177/380 (46%), Positives = 245/380 (64%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVF +++LKAKAR +G D+ID GMGNPD TP+ +VD + Q H Y Sbjct: 7 RIKRLPPYVFNIVNDLKAKARARGEDIIDFGMGNPDQPTPKHIVDKLCEVAQRDDTHRYS 66 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G RRAIT WY R+ V LDP++EA+ +GSKEGL+HLA+A + PGD VLVP+PA Sbjct: 67 MSRGIPRLRRAITRWYKDRFNVDLDPETEAIVTIGSKEGLAHLALATLGPGDAVLVPNPA 126 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G VIAG + + L P D+ +L ++ + K+L ++P+NPT Sbjct: 127 YPIHPYGCVIAGADIRHVPLTPGVDFFAELEKAIQDSWPRPKMLVLSFPANPTAQCVELG 186 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE+++ AR+Y I +VHDL YAE+ FDGY+ S+L++ GAKD+ VEF++LSK+YNM GW Sbjct: 187 FFEKVIDIAREYGIWVVHDLAYAEITFDGYRAPSILQVSGAKDVAVEFYSLSKSYNMPGW 246 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF+ GN ++ L +K+ LDYG F +Q A+ AL+ P + +++Q Y++RRD L Sbjct: 247 RVGFMCGNPKLVAALGRIKSYLDYGTFTPIQVASIAALEGPQDCVGQIRQLYQSRRDVLC 306 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 GL LGW V K KATM++W P V MGS +F+ LL+ V +PG FG G+ Y Sbjct: 307 DGLNALGWVVEKPKATMFVWAPIPEQYVHMGSLEFSKKLLKDAKVAASPGVGFGSYGDQY 366 Query: 368 VRISLIADCDRLGEALDRIK 387 VR LI + R +A+ IK Sbjct: 367 VRFGLIENEHRTRQAVRGIK 386 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: 486 Number of extensions: 17 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: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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 Jul 25 2024. The underlying query database was built on Jul 25 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