Align phenylalanine aminotransferase (EC 2.6.1.57) (characterized)
to candidate 201550 SO2406 aspartate aminotransferase (NCBI ptt file)
Query= reanno::Marino:GFF879 (395 letters) >FitnessBrowser__MR1:201550 Length = 396 Score = 400 bits (1029), Expect = e-116 Identities = 198/396 (50%), Positives = 267/396 (67%), Gaps = 3/396 (0%) Query: 1 MFEALQPLPQDPILQLMQTFLEDDRPDKVDLGIGVYKDDAGNTPIMAAVHEAERRLLEGE 60 MF +L +P DPIL L+ + ED P KVDLG+GVYKD AGNTPI+ V +AE+ LE E Sbjct: 1 MFNSLIAMPADPILGLLTQYREDTHPQKVDLGVGVYKDPAGNTPILNCVKKAEKFRLETE 60 Query: 61 TTKSYVGPAGSAGFNSAMAELILGSNSPLVRDGRVSVIQTPGGCGALRMAAEFLRLCKAD 120 TTK Y+GP GS FN+ M EL GS+ + R+ + TPGG GALR+A +F++ C + Sbjct: 61 TTKVYIGPTGSPQFNTLMTELAFGSDHSAIIANRIRTVSTPGGTGALRVAGDFIKRCNPN 120 Query: 121 TKVWVSTPTWANHLPLLGGAGLTIREYPYLNPETLQVDFGAMLETLERADAGDVVLLHGC 180 +WVS PTWANH L AG+T++ YPY + ++ + F ML L + DVVLLH C Sbjct: 121 AVLWVSDPTWANHTGLFEAAGITVKTYPYYDYDSKSLKFDEMLAALSQVSPDDVVLLHAC 180 Query: 181 CHNPSGADLSLAQWQEVTSLIQRKGLLPFVDMAYQGLGEGLDADAAGLRHLASAVPEMLI 240 CHNPSG DL+ QW +V +L + +G P +DMAYQG G+G+D DA G+R +A+AV M++ Sbjct: 181 CHNPSGMDLTTDQWDKVVTLTKEQGFTPLIDMAYQGFGDGVDIDAYGVRKMAAAVDNMIL 240 Query: 241 AASCSKNFGLYRERTGALALVSETATVNAAATSQLLSVIRSHYSMPPAHGASIVETILGD 300 +SCSKNFGLYRER G+ ++V++ A A S LL V+R YSMPPAHGA+IVETILG Sbjct: 241 CSSCSKNFGLYRERIGSCSVVAKDANTANIAQSVLLYVVRCLYSMPPAHGAAIVETILGS 300 Query: 301 DDLRAQWQQELNGMCKRILHLRHAFADALSPVG---DFDFIARQRGMFSFLGISPEQVGR 357 +L +W EL M RI R + L G DF FIARQ+GMFSFLG++PEQV R Sbjct: 301 KELTQEWLDELKVMRDRINGNRAILVEKLKANGVARDFSFIARQKGMFSFLGVNPEQVAR 360 Query: 358 LRKEHGIHMLESSRVNVAGLNDHVLPQVASALREVL 393 L+KE I+M+ SSR+++AG+++ + +A ++ +VL Sbjct: 361 LQKEFSIYMVGSSRISIAGISEDNVDYLAQSIAKVL 396 Lambda K H 0.320 0.136 0.402 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: 384 Number of extensions: 8 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: 395 Length of database: 396 Length adjustment: 31 Effective length of query: 364 Effective length of database: 365 Effective search space: 132860 Effective search space used: 132860 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 Aug 03 2021. The underlying query database was built on Aug 03 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