Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >FitnessBrowser__Keio:17340 Length = 367 Score = 135 bits (340), Expect = 1e-36 Identities = 74/209 (35%), Positives = 124/209 (59%), Gaps = 7/209 (3%) Query: 16 WNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWFY 75 W G+ +TL + +G+ G + G LLAL R SH ++ ++ ++ ++R +PL+ V+ Sbjct: 156 WGGLTLTLIIASVGIAGALPWGILLALGRRSHMPIVRILSVIFIEFWRGVPLITVLFMSS 215 Query: 76 LAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAKALGMG 135 + +P + E T I +V ++F++AY E+VR G+Q++PKGQ AA++L +G Sbjct: 216 VMLPLFM----AEGTSIDKLIRALVGVILFQSAYVAEVVRGGLQALPKGQYEAAESLALG 271 Query: 136 YGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVD-FLNATRASGD--IIGRA 192 Y + L+ILPQA + + P L+ I LF+DTSLV +GL D F + +A+ D +G + Sbjct: 272 YWKTQGLVILPQALKLVIPGLVNTIIALFKDTSLVIIIGLFDLFSSVQQATVDPAWLGMS 331 Query: 193 NEFLIIAGLVYFTISFAASRLVKRLQKRF 221 E + A L+Y+ F+ SR + L+KRF Sbjct: 332 TEGYVFAALIYWIFCFSMSRYSQYLEKRF 360 Lambda K H 0.331 0.143 0.425 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: 217 Number of extensions: 12 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: 223 Length of database: 367 Length adjustment: 26 Effective length of query: 197 Effective length of database: 341 Effective search space: 67177 Effective search space used: 67177 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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