Align L-lysine 2,3-aminomutase; LAM; EC 5.4.3.2 (characterized)
to candidate PfGW456L13_4924 Lysine 2,3-aminomutase (EC 5.4.3.2)
Query= SwissProt::Q8PYC9 (419 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4924 Length = 446 Score = 105 bits (262), Expect = 3e-27 Identities = 68/228 (29%), Positives = 115/228 (50%), Gaps = 13/228 (5%) Query: 110 ITHRYPDRVLFL--ISNRCGMYCRHCTRKRR-VGNREHDYSEKAIREGIEYIRMHHEVRD 166 I H+Y + VLF C YC C R + +G E ++ + +E + Y+R+H EV D Sbjct: 130 IQHKYRETVLFFPGAGQTCHAYCTFCFRWAQFIGEEELKFNARESQELVSYLRVHTEVTD 189 Query: 167 VLLSGGDALLVSDERLDWLLGELFSIPHVEIVRLGTRAPVTLPQRI-----TPELCEILG 221 VL++GGD ++++ L + L +PH++ +R+GT++ PQR PEL E+ Sbjct: 190 VLITGGDPMIMNTRSLAGYIEPLLDLPHLKNIRIGTKSVAYWPQRFVSDKDAPELLELFQ 249 Query: 222 KYPSVWLNT----HFNHPKEITPE-AKKAMNMLACAGIPLGNQSVLLRRVNDCPVIIKNL 276 + + N H+NHP EI A++A+ + G + Q+ ++R VN+ P L Sbjct: 250 RIVAAGKNLSIMGHYNHPVEIRQVIARQAIERIRSTGATVRMQAPVIRHVNENPADWAAL 309 Query: 277 CHELLKIKTRPYYLYQCDLSFGLEHFRTSVARGIEIIEMLRGHTSGLA 324 E +++ PYY++ + +F +AR EI + SGLA Sbjct: 310 WTEGVRLGAVPYYMFVERDTGPSHYFEMPLARAFEIFQAAYRTVSGLA 357 Lambda K H 0.320 0.138 0.426 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: 451 Number of extensions: 22 Number of successful extensions: 2 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: 419 Length of database: 446 Length adjustment: 32 Effective length of query: 387 Effective length of database: 414 Effective search space: 160218 Effective search space used: 160218 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: 51 (24.3 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