Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate N515DRAFT_3749 N515DRAFT_3749 L-lysine 2,3-aminomutase (EC 5.4.3.2)
Query= SwissProt::Q9XBQ8 (416 letters) >FitnessBrowser__Dyella79:N515DRAFT_3749 Length = 336 Score = 166 bits (419), Expect = 1e-45 Identities = 95/274 (34%), Positives = 142/274 (51%), Gaps = 4/274 (1%) Query: 69 PNDPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMY 128 P DP+DP+ Q +P EL +A + DP+ + GL H+Y R LL+ + C++ Sbjct: 65 PGDPDDPLLLQVLPQLAELEQAPGYVADPVGDLAAREAQGLLHKYEGRALLIASGSCAVN 124 Query: 129 CRHCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKL 188 CR+C RR F ++ + KA+D++R + +++LSGGD L ++ LE + L Sbjct: 125 CRYCFRRHFP-YGEEMAAAGQWRKALDHLRQDASIAELILSGGDPLSLATPKLEELSRGL 183 Query: 189 REIPHVEIVRIGSRTPVVLPQRITPELVNMLKKYHPVW--LNTHFNHPNEITEESTRACQ 246 +P V +RI +R PVVLP+RI + P+ + H NH NE AC+ Sbjct: 184 AALPQVTRLRIHTRLPVVLPERIDAAFLAWFAAL-PLQKVVVLHANHANEFDAAVDDACR 242 Query: 247 LLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVS 306 L +AG L NQSVLL+ +ND + EL +L V PYY++Q D G HF + Sbjct: 243 RLREAGATLLNQSVLLKNINDDADTLSELSERLFAAGVLPYYLHQLDRVQGSAHFEVDDA 302 Query: 307 KGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKTPV 340 + ++E +RG GY VP V + G K PV Sbjct: 303 RARALVEAIRGRLPGYLVPKLVREMEGDASKRPV 336 Lambda K H 0.320 0.138 0.422 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: 17 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: 416 Length of database: 336 Length adjustment: 30 Effective length of query: 386 Effective length of database: 306 Effective search space: 118116 Effective search space used: 118116 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