Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 171 bits (434), Expect = 2e-47 Identities = 97/275 (35%), Positives = 158/275 (57%), Gaps = 14/275 (5%) Query: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 S L + GI+K+F + + ++ + + + G +VG +G GK+TLL +IAGL+ P + Sbjct: 2 SLLQLHGISKKFPQTKQFA--VKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDK 59 Query: 63 GEIRIGGKNVVG----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118 GEI G+ +V +P R++ ++FQ YAL+P +++ +N+ AL + RQ Sbjct: 60 GEIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQES--RNARQIA 117 Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178 +D +A + + P QLS GQRQR A+ RALA +P+L L D+P +LD + + E+ Sbjct: 118 MDSLA-LAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEIS 176 Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATF 238 +I+ + +A+GIT++ +H +A++L IA++ G++QQ+GTP EIY +PAN YVA F Sbjct: 177 EDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANF 236 Query: 239 IGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSAN 273 G LL G + A P P SA+ Sbjct: 237 FGKRN-ELLATPTEDGFY----AGFGFIPHPDSAS 266 Lambda K H 0.318 0.135 0.388 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: 245 Number of extensions: 9 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: 355 Length of database: 345 Length adjustment: 29 Effective length of query: 326 Effective length of database: 316 Effective search space: 103016 Effective search space used: 103016 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 (21.7 bits) S2: 49 (23.5 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