Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate SMc04323 SMc04323 aminotransferase
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__Smeli:SMc04323 Length = 408 Score = 300 bits (767), Expect = 7e-86 Identities = 174/404 (43%), Positives = 241/404 (59%), Gaps = 12/404 (2%) Query: 4 LSWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREK 63 L W F + R++AS IRELLKL RP I+SFAGG+P PELFP + EA A I Sbjct: 2 LDWESIFATRSSRMKASEIRELLKLLDRPDIISFAGGIPDPELFPNDAFREAYAEIFGGP 61 Query: 64 GE-VALQYSPTEGYAPLRAFVAEW-----IGVRPEEVLITTGSQQALDLVGKVFLDEGSP 117 ALQYS +EGY PLR ++A I + + IT+GSQQ LD +GK+FL Sbjct: 62 SVGAALQYSISEGYRPLREWLAGQMAALGIPASVDNIFITSGSQQGLDYLGKLFLSPKDT 121 Query: 118 VLLEAPSYMGAIQAFRLQGPRFLTV-PAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPT 176 L+ P+Y+GA+QAF P + + PAG P A R +F YL F NPT Sbjct: 122 ALVTWPTYLGALQAFNAYEPSYDQLNPAGNRTPAAYAQAAAEAGGRVKFAYLSADFANPT 181 Query: 177 GGLTPLPARKRLLQMVMERGLVVVEDDAYREL-YFGEARLPSL-FELAREAGYPGV--IY 232 G R+R+L++ E + ++ED AY+ L Y GEA P L E+AR+ IY Sbjct: 182 GETVGRAGRERVLELAEELDIAIIEDAAYQSLRYDGEAIPPILALEIARKGDINSTRTIY 241 Query: 233 LGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLER 292 GSFSK L+PGLRV + A ++KLV KQ ADLH+ +NQM + + + GF E++ + Sbjct: 242 CGSFSKTLAPGLRVGWICAAEPVIRKLVLMKQAADLHSSTINQMAIATVAERGFEEQVAK 301 Query: 293 VRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALE-ENVAF 351 + + YR++ AML AL++ +P V +T+P+GGMF+W+ LPKG L ++++ VAF Sbjct: 302 IHKAYRQRRDAMLSALEKYMPAGVTWTKPEGGMFIWVTLPKGSDGAELLAKSIQTAKVAF 361 Query: 352 VPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLLA 395 VPG FFA+G GENTLRLS++ + I EG+RRLG ++G +A Sbjct: 362 VPGRAFFADGSGENTLRLSFSCANDRMIDEGIRRLGDLVRGEVA 405 Lambda K H 0.320 0.139 0.401 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: 471 Number of extensions: 28 Number of successful extensions: 6 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: 397 Length of database: 408 Length adjustment: 31 Effective length of query: 366 Effective length of database: 377 Effective search space: 137982 Effective search space used: 137982 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