Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 353246 BT3720 putative aspartate aminotransferase (NCBI ptt file)
Query= BRENDA::Q8TQ40 (389 letters) >FitnessBrowser__Btheta:353246 Length = 383 Score = 178 bits (452), Expect = 2e-49 Identities = 121/380 (31%), Positives = 187/380 (49%), Gaps = 12/380 (3%) Query: 9 RINALPPYLFAAIDEAKDEMIAKGVDVIDLGVGDPDLPTHPHIVEAMREAVCDPKTHQYP 68 ++ + ++ + E +E+ +GVDVI L VG+PD + EA + A TH Y Sbjct: 7 QVEQMTSFIVMDVLERANELQKQGVDVIHLEVGEPDFDVPACVAEAAKAAYDRHLTH-YT 65 Query: 69 SYAGMPEFREAAAEWCKKYKGIELDPATEVLSLIGSKEAVAHIPLAFVNPGDVVLYTDPG 128 G PE R A + ++ G+ +DP V++ GS ++ + + N V+ ++PG Sbjct: 66 HSLGDPELRREIAAFYQREYGVTVDPDCIVVTS-GSSPSILLVLMLLCNSDSEVILSNPG 124 Query: 129 YPVYKIGTLFAGGEPYSLPLKAENSFLPDLDSIPADILKRAKLFFFNYPNNPTSATADMK 188 Y Y+ L A +P +PL EN D+++I + F N P NPT D Sbjct: 125 YACYRNFVLAAQAKPVLVPLSEENGLQYDIEAIRKCVTPHTAGIFINSPMNPTGMLLDES 184 Query: 189 FFEKVVEFCKKNDIIAVHDNAYSQMVYDGYDAPSFLAAEGAMDIGIELYSHSKTYNMTGW 248 F V + + D Y +VY+G A S L D L SK + MTG Sbjct: 185 FLRSVASL----GVPIISDEIYHGLVYEGR-AHSILEYT---DKAFVLNGFSKRFAMTGL 236 Query: 249 RLGFAVGSKALIKGLGKVKSNVDSGVFDAIQIAGIAALSSSQACVDDTNKIYEERRNVLI 308 RLG+ + K+ ++ L K++ N+ Q AGIAAL + + V+ +IY+ERR +I Sbjct: 237 RLGYLIAPKSCMRSLQKLQQNLFICASSIAQQAGIAALRQADSDVERMKQIYDERRRYMI 296 Query: 309 EGLTAMGLEVK-PPKATFYVWAPVPTGFT-SIEFAKLLLEEAGIVATPGVGFGDAGEGYV 366 L MG E+K P+ FY++A T S FA +LE A + TPG+ FG GEGYV Sbjct: 297 SRLREMGFEIKVEPQGAFYIFADARKFTTDSYRFAFDVLENAHVGITPGIDFGTGGEGYV 356 Query: 367 RFALTKPVERIKEAVERMKK 386 RF+ +E I+E ++R+ + Sbjct: 357 RFSYANSLESIREGLDRISQ 376 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: 357 Number of extensions: 20 Number of successful extensions: 5 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: 383 Length adjustment: 30 Effective length of query: 359 Effective length of database: 353 Effective search space: 126727 Effective search space used: 126727 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