Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate BWI76_RS20495 BWI76_RS20495 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__Koxy:BWI76_RS20495 Length = 412 Score = 360 bits (925), Expect = e-104 Identities = 182/394 (46%), Positives = 253/394 (64%), Gaps = 6/394 (1%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI +LPPYVF ELK AR +G D+ID MGNPDGATP +V+ Q P HGY Sbjct: 12 RIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQRPDTHGYS 71 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G RRAI+ WY RY V +DP+SEA+ +GSKEGL+HL +A ++ GD VLVP+P+ Sbjct: 72 TSRGIPRLRRAISRWYQERYNVEIDPESEAIVTIGSKEGLAHLMLATLDHGDTVLVPNPS 131 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G VIAG V S+ L D+ +L E K K++ +PSNPT E Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVEGVDFFNELERAIRESYPKPKMMILGFPSNPTAQCVELE 191 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE++VA A++Y++L+VHDL YA++ +DG++ S++++PGA+D+ VEF TLSK+YNMAGW Sbjct: 192 FFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPGARDVAVEFFTLSKSYNMAGW 251 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 R+GF+VGN+ ++ L +K+ DYG F LQ AA AL+ + ++ ++Y+ RRD L+ Sbjct: 252 RIGFMVGNKTLVNALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYKRRRDVLV 311 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GL E GW V KA+MY+W K P MGS +FA LLQ V V+PG FG G+ + Sbjct: 312 KGLHEAGWMVECPKASMYVWAKIPEQYAAMGSLEFAKKLLQDAKVCVSPGIGFGDYGDTH 371 Query: 368 VRISLIADCDRLGEALDRIKQAGIRYRPEALVSA 401 VR +LI + DR+ +A+ IK +R + L+ A Sbjct: 372 VRFALIENRDRIRQAVRGIKS---MFRADGLLPA 402 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: 482 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: 412 Length adjustment: 31 Effective length of query: 372 Effective length of database: 381 Effective search space: 141732 Effective search space used: 141732 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