Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate GFF5184 PS417_26550 ABC transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_771 (304 letters) >FitnessBrowser__WCS417:GFF5184 Length = 300 Score = 335 bits (858), Expect = 1e-96 Identities = 171/271 (63%), Positives = 202/271 (74%) Query: 24 AELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQLKIVEAIKKDLDMPN 83 A L GTL KI + +ITLG+RDAS+PFSY+ D SGKP+GYS ++ KIVE I++ + Sbjct: 24 APLDGTLGKIASAKSITLGYRDASVPFSYVGDNSGKPMGYSVELASKIVERIQQKTGVAT 83 Query: 84 LQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVGIFEIGTKLLSKKDSAY 143 L VKYNLVTSQTRIPLVQNGTVD+ECGST ERQ+QV FS G + +LL+ KDS Sbjct: 84 LNVKYNLVTSQTRIPLVQNGTVDLECGSTGVTAERQKQVAFSYGFIYVKGQLLTAKDSGI 143 Query: 144 KDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESFQMLETGRAVAFMMD 203 K F DL GKNVVTTAGTT+ER LKS NA+ + M VISAKDHGE+F+MLETGRA AF MD Sbjct: 144 KGFPDLAGKNVVTTAGTTNERFLKSYNAEHKTNMFVISAKDHGEAFKMLETGRAAAFYMD 203 Query: 204 DALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAVDDAIIATYKSGEINKI 263 DALL GE AKAK P +W V G QS EIY CM+RK D F V++ + Y+SGEIN I Sbjct: 204 DALLYGERAKAKDPHNWVVVGEEQSREIYSCMLRKDDPQFLAVVNETLGDLYRSGEINGI 263 Query: 264 YEKWFMQPIPPKGLNLMFPMSEELKALIANP 294 Y++WF PIPPKGLNL FPM+ ELKA+IA P Sbjct: 264 YQRWFESPIPPKGLNLEFPMTRELKAIIAKP 294 Lambda K H 0.315 0.131 0.365 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: 285 Number of extensions: 9 Number of successful extensions: 1 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: 304 Length of database: 300 Length adjustment: 27 Effective length of query: 277 Effective length of database: 273 Effective search space: 75621 Effective search space used: 75621 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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