Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 286 bits (732), Expect = 7e-82 Identities = 165/370 (44%), Positives = 218/370 (58%), Gaps = 27/370 (7%) Query: 18 IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITEVTPAKRDL 77 ++ GI+LE+ D EF+V VGPSGCGKSTLLRL+AGLE S G I++ R + + RD+ Sbjct: 49 VLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDI 108 Query: 78 AMVFQTYALYPHMSVRKNMSFALDLAG---------------VDKKL---------VESK 113 AMVFQ+YALYPH+SV N++F L G + K L ++ + Sbjct: 109 AMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRR 168 Query: 114 VSEAARILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMR 173 V E A +L+L LL+R+PKQLSGGQ+QRVA+GRAI RNP++FL DEPLSNLDA LR + R Sbjct: 169 VREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETR 228 Query: 174 LELARLHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGF 233 ++ L ++L T +YVTHDQ EAMT+ D++ VLN G ++QV SPLE+Y +PAN FVA F Sbjct: 229 AQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQF 288 Query: 234 LGTPKMGFLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASP 293 +G+P M + VT + TL L G V LGIRPEHLE+ + Sbjct: 289 IGSPPMNLI--PVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGAA 346 Query: 294 GQTTLTVTADVGERLGSDTF-CHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLF 352 L +T E LGSDTF + +G + R+ Q G+ L L P HLF Sbjct: 347 ASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLF 406 Query: 353 DTDGVAVARP 362 D + RP Sbjct: 407 DLETGKAIRP 416 Lambda K H 0.319 0.136 0.384 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: 409 Number of extensions: 16 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: 367 Length of database: 417 Length adjustment: 31 Effective length of query: 336 Effective length of database: 386 Effective search space: 129696 Effective search space used: 129696 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