Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate SMc00042 SMc00042 aminotransferase
Query= BRENDA::O86428 (307 letters) >FitnessBrowser__Smeli:SMc00042 Length = 293 Score = 111 bits (277), Expect = 2e-29 Identities = 87/280 (31%), Positives = 137/280 (48%), Gaps = 12/280 (4%) Query: 13 DGELVQWRDATTHVLTHTLHYGMGVFEGVRAYDTPQGTAIFRLQAHTDRLFDSAHIMNMQ 72 DGE + +H + G VF+G R +D G A L H R+ SA + ++ Sbjct: 16 DGEWLAGNPPLIGPTSHAMWLGSTVFDGARWFD---GIAP-DLDLHCQRVNRSAEALGLK 71 Query: 73 IPYSRDEINEATRAAVRENNLESA-YIRPMVFYGSEGMGLRASGLKVHVIIAAWSWGAYM 131 S +EI V++ + ++A Y++PM ++G G + A + A M Sbjct: 72 PTMSAEEIEGLAWEGVKKFDGKTAIYVKPM-YWGEHGSWSVVAVDPESTRFALCLFEAPM 130 Query: 132 GEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGADEAMMLDPEGY 191 G G + S F R + T AK+ Y N+ L EA S G D A++ D G Sbjct: 131 GNG--HAGSSLTLSPFRRPTLECMPTDAKAGCLYPNNARILNEARSRGFDNALVRDMLGN 188 Query: 192 VAEGSGENIFIIKDGVIYTPEVT-ACLNGITRNTILTLAAEHGFKLVEKRITRDEVYIAD 250 +AE NIF++KDGV++TP L GITR+ ++ L +E GF+++E +T + AD Sbjct: 189 IAETGSSNIFMVKDGVVFTPAANRTFLAGITRSRVMGLLSEAGFEVIETSLTMADFEGAD 248 Query: 251 EAFFTGTAAEVTPIREVDGRKIGAGRRGPVTEKLQKAYFD 290 E F +G ++V P+ ++ R++ A GPVT K + Y D Sbjct: 249 EIFTSGNYSKVLPVTRLEQRELQA---GPVTAKARDLYMD 285 Lambda K H 0.319 0.134 0.394 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: 244 Number of extensions: 14 Number of successful extensions: 4 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: 307 Length of database: 293 Length adjustment: 27 Effective length of query: 280 Effective length of database: 266 Effective search space: 74480 Effective search space used: 74480 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: 48 (23.1 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