Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate GFF835 HP15_814 aspartate aminotransferase
Query= BRENDA::Q8TQ40 (389 letters) >FitnessBrowser__Marino:GFF835 Length = 416 Score = 158 bits (400), Expect = 2e-43 Identities = 114/367 (31%), Positives = 171/367 (46%), Gaps = 7/367 (1%) Query: 28 MIAKGVDVIDLGVGDPDLPTHPHIVEAMREAVCDPKTHQYPSYAGMPEFREAAAEWCKKY 87 M A DVI L +G PDLPT H+++A +A+ +T Y AG+PE A ++ K Sbjct: 52 MAATMKDVIHLSIGQPDLPTPKHVIDAYIDALNAGQTG-YTMDAGLPELLVALRDYYGKR 110 Query: 88 KGIELDPATEVLSLIGSKEAVAHIPLAFVNPGDVVLYTDPGYPVYKIGTLFAGGEPYSLP 147 +L +L G+ EA+ A PG + TDP + +Y GGE + Sbjct: 111 YNRKLT-RDNILITSGATEAMYLAISATSAPGRQFIVTDPSFLLYAPLIRMNGGEVKFVQ 169 Query: 148 LKAENSFLPDLDSIPADILKRAKLFFFNYPNNPTSATADMKFFEKVVEFCKKNDIIAVHD 207 +AEN+ D D + + R N PNNPT A E ++E C I D Sbjct: 170 TRAENNHQLDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVETILEECAYRGIQVYAD 229 Query: 208 NAYSQMVYDGYDAPSFLAAEGAMDIGIELYSHSKTYNMTGWRLGFAVGSKALIKGLGKVK 267 Y +++D D S L +D + + S SKTY+M G R+G+ + S+A IK L + Sbjct: 230 EVYDHLIFDDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVGWVIASQAAIKSLRRFH 289 Query: 268 SNVDSGVFDAIQIAGIAALSSSQACVDDTNKIYEERRNVLIEGLTAMG-LEVKPPKATFY 326 S Q AG+AAL+ Q CV D IY ERR+ ++E + + P F+ Sbjct: 290 MFTTSVANTPSQFAGVAALTGDQQCVRDMVDIYRERRDKVVELVDQTPYMTGYKPGGAFF 349 Query: 327 VWAPVPTGFTSIEFAKLLLEEAGIVATPGVGFGDAGEGYVRFALTKPVERIKEAVER--- 383 + +P + A +L+E G+ PG FG+ VR + + E+++EA +R Sbjct: 350 AFPDLPPHVDGSDLALRMLKETGVCMVPGDAFGEGCTNAVRISFSTTCEKLEEAFDRVIP 409 Query: 384 -MKKLQF 389 M K QF Sbjct: 410 WMAKQQF 416 Lambda K H 0.319 0.137 0.409 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: 390 Number of extensions: 14 Number of successful extensions: 3 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: 389 Length of database: 416 Length adjustment: 31 Effective length of query: 358 Effective length of database: 385 Effective search space: 137830 Effective search space used: 137830 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 (21.7 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