Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 144 bits (362), Expect = 5e-39 Identities = 83/244 (34%), Positives = 133/244 (54%), Gaps = 15/244 (6%) Query: 1 MSELQLSDVRKSYGGLE--VIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSG 58 MS LQL + K + + +K + ++I+ G VG +G GK+TLL++IAGLE G Sbjct: 1 MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60 Query: 59 DLTIDDVRM----NDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRV 114 ++ + + + ++R + ++FQ YAL+P MT+ EN+ AL +I Sbjct: 61 EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQI---- 116 Query: 115 NEAAHILELGALLDR---KPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVH 171 A L L L D P QLS GQRQR A+ RA+ PK+ L D+P +LD + Sbjct: 117 --AMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNE 174 Query: 172 MRIEIARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVA 231 + +I + K T + +H +A++LAD I ++ G+++QVG+P+++Y PAN +VA Sbjct: 175 ISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVA 234 Query: 232 GFIG 235 F G Sbjct: 235 NFFG 238 Lambda K H 0.321 0.139 0.396 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: 286 Number of extensions: 8 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: 358 Length of database: 345 Length adjustment: 29 Effective length of query: 329 Effective length of database: 316 Effective search space: 103964 Effective search space used: 103964 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: 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