Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_078429378.1 BK574_RS16655 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_002019605.1:WP_078429378.1 Length = 390 Score = 345 bits (884), Expect = 2e-99 Identities = 165/374 (44%), Positives = 236/374 (63%) Query: 15 LPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYPPFEG 74 LP FA L ++G D+I+LG GNPD TP +V + +A PK H YPPF G Sbjct: 13 LPKQYFASLVAKVGALVKEGADIINLGQGNPDQPTPDHIVKSLKEAADLPKYHKYPPFRG 72 Query: 75 TASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPAYPAH 134 + A+ +Y R YGV +DP+ E L G K GL ++ +NPGDV LVP P YP + Sbjct: 73 YRFLKEAVAEFYQREYGVDIDPEKEVCVLFGGKGGLVEISQCMLNPGDVTLVPDPGYPDY 132 Query: 135 FRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPREFFEE 194 + G +AGG + + L+ N++L D I E+ +KAK+++ NYP+NPTGATA + F++E Sbjct: 133 WSGVALAGGQMEMMPLQENNNFLPDYQVISEDAKKKAKLMFLNYPNNPTGATASKAFYDE 192 Query: 195 IVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGWRVGF 254 V FAR++++ +VHD Y + FDG +P S L+ GAK++G+E +TLSKTYNMAGWRV F Sbjct: 193 TVTFARQHDLCVVHDFAYGGIGFDGQKPVSFLQSEGAKEVGIEIYTLSKTYNMAGWRVAF 252 Query: 255 VVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLIQGLG 314 VGN VI+ L + ++ +F A+Q AA TAL P + E+ ++Y RR+ LI+GL Sbjct: 253 AVGNASVIEMLNLYQDHMYVSLFGAIQKAAATALLSPQTCVDELVKKYEGRRNVLIEGLQ 312 Query: 315 ELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYVRISLIA 374 +GWDV + + W+ CP GM S +FA LL + + V PG FG +GEGYVR+ L+ Sbjct: 313 SIGWDVKAPNGSFFAWLPCPEGMSSEEFADILLYKAHIAVAPGRGFGESGEGYVRVGLLE 372 Query: 375 DCDRLGEALDRIKQ 388 + DRL EA++RI++ Sbjct: 373 EEDRLKEAVERIRK 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: 477 Number of extensions: 29 Number of successful extensions: 1 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: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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