Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate CCNA_02244 CCNA_02244 aminotransferase class I family protein
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__Caulo:CCNA_02244 Length = 425 Score = 305 bits (781), Expect = 2e-87 Identities = 175/400 (43%), Positives = 240/400 (60%), Gaps = 18/400 (4%) Query: 6 WSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREK-- 63 W+ F + R++AS IRELLKL +P ILSFAGG+P P LFP +E + IL + Sbjct: 23 WAGRFSERMSRVRASEIRELLKLLDQPDILSFAGGIPDPGLFPAQEIQKGYDAILADPVL 82 Query: 64 GEVALQYSPTEGYAPLRAFVAE-----WIGVRPEEVLITTGSQQALDLVGKVFLDEGSPV 118 ALQYS +EGY PLR ++AE + P+ +++T GSQQALDL+GK+FL +G V Sbjct: 83 SRQALQYSVSEGYLPLRQWIAERMTRDGMPCGPDNIMLTAGSQQALDLIGKLFLTKGDTV 142 Query: 119 LLEAPSYMGAIQAFRLQGPRFLTVP--AGEEGPDLDALEEVLKRERPRFL-YLIPSFQNP 175 ++ P+Y+GA+QAF P +L +P A +G D AL + PR L Y +P F NP Sbjct: 143 MVARPTYLGALQAFNGYEPAYLDLPETALSQGVDEAAL---MAGRAPRPLGYFVPDFANP 199 Query: 176 TGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLF--ELAREAGYPGV--I 231 TG L R+ LL M + +VED AYREL F P++ ++ R G + Sbjct: 200 TGVSLTLAEREALLAMADRLDMTLVEDAAYRELRFAGEATPTVLGLDITRSGGIDNARTL 259 Query: 232 YLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLE 291 +LG+ SK LSP LR+ + ++KLV KQGADLH +NQM+ H + EG+ + L Sbjct: 260 FLGTLSKTLSPALRIGWVCGPKAVIEKLVLLKQGADLHVSTINQMVAHRAVTEGYDQHLH 319 Query: 292 RVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRAL-EENVA 350 R+R Y KA+ ML AL+R +PK V ++ P+GGMFVW++LP+G+ L RA+ EE VA Sbjct: 320 RLRGAYGAKARVMLAALERTMPKGVTWSHPEGGMFVWIDLPEGIDGAALLARAIEEERVA 379 Query: 351 FVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGRAL 390 FVPG PFFA N +RLSY+ I EGV+RL R + Sbjct: 380 FVPGAPFFAENQTPNAIRLSYSLPTDAQIEEGVQRLARLI 419 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: 479 Number of extensions: 23 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: 425 Length adjustment: 31 Effective length of query: 366 Effective length of database: 394 Effective search space: 144204 Effective search space used: 144204 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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