Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 270 bits (691), Expect = 4e-77 Identities = 163/371 (43%), Positives = 216/371 (58%), Gaps = 51/371 (13%) Query: 30 GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVAPA 89 G VL GI+L++ DGEF++ VGPSGCGKSTLLR +AGLE + G +++ V + Sbjct: 45 GEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAK 104 Query: 90 KRGIAMVFQSYALYPHLTVKDNMGLGLKQAG---------------VPK---------AE 125 R IAMVFQSYALYPHL+V DN+ GL++ G +PK A Sbjct: 105 ARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEAR 164 Query: 126 IEEKVAKAAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALR 185 I+ +V + A ML L+ L R+P +LSGGQ+QRVA+GRAI R P++FL DEPLSNLDA LR Sbjct: 165 IKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLR 224 Query: 186 VNTRLEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLF 245 TR +I L R L T +YVTHDQ EAMT+ D+I VLN G ++QV SP+E+Y+RPAN F Sbjct: 225 AETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRF 284 Query: 246 VAGFIGSPQMNFIEAA------------------------KLGDGEAKTIGIRPEHIGL- 280 VA FIGSP MN I +L DG+ +GIRPEH+ + Sbjct: 285 VAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVG 344 Query: 281 SRESGDWKGKVIHVEHLGADTIIYIESETVGL-LTVRLFGEHRYATDDIVHATPVIGSMH 339 + S + V VE LG+DT I E + G+ + RL + + D + T +H Sbjct: 345 AAASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQIH 404 Query: 340 RFDAD-GRVIK 349 FD + G+ I+ Sbjct: 405 LFDLETGKAIR 415 Lambda K H 0.320 0.137 0.393 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: 357 Number of extensions: 11 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: 352 Length of database: 417 Length adjustment: 30 Effective length of query: 322 Effective length of database: 387 Effective search space: 124614 Effective search space used: 124614 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 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