Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012971318.1 ALVIN_RS10590 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000025485.1:WP_012971318.1 Length = 400 Score = 354 bits (908), Expect = e-102 Identities = 179/381 (46%), Positives = 245/381 (64%), Gaps = 3/381 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVF ++ELKA+AR +G D+ID GMGNPD TPQ +VD +++ Q P H Y Sbjct: 10 RIKRLPPYVFNIVNELKAEARARGEDIIDFGMGNPDQGTPQHIVDKLVESAQRPDTHRYS 69 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G RRA+ NWY R+ V LDP+SEA+ +GSKEGL+HLA+A + GD VLVP+PA Sbjct: 70 MSRGIPRLRRAVCNWYRDRFDVHLDPESEAILTIGSKEGLAHLALATMGAGDTVLVPNPA 129 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G +IAG V + L P+ D+ +L ++ K K+L N+P NPT + Sbjct: 130 YPIHPYGFIIAGADVRHVRLTPDVDFFDELQKAIQDSWPKPKMLVLNFPGNPTTQCVELD 189 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FF++++ AR++ I +VHDL Y ++AFDGY+P S+L+IP AKDI VEF TLSK+YNM GW Sbjct: 190 FFQKVIDIAREHGIWVVHDLAYVDIAFDGYKPPSILQIPEAKDIAVEFFTLSKSYNMPGW 249 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF+ GN+ ++ L +K+ LDYG F +Q AA AL+ P + E+ Y++RRD L Sbjct: 250 RVGFMCGNKTLVSALARIKSYLDYGTFTPIQVAAIAALEGPQECVREISDMYQSRRDVLC 309 Query: 311 QGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 GL GW V KATM++W P MGS +F+ LL+ V V PG FG G+ + Sbjct: 310 AGLNAAGWPVEPPKATMFVWAPIPEPYRAMGSLEFSKKLLRDAKVAVAPGIGFGEYGDTH 369 Query: 368 VRISLIADCDRLGEALDRIKQ 388 VR LI + R +A+ IK+ Sbjct: 370 VRFGLIENEHRTRQAIRGIKE 390 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: 514 Number of extensions: 24 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: 400 Length adjustment: 31 Effective length of query: 372 Effective length of database: 369 Effective search space: 137268 Effective search space used: 137268 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