Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 234 bits (598), Expect = 2e-66 Identities = 133/309 (43%), Positives = 185/309 (59%), Gaps = 2/309 (0%) Query: 3 GIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEI 62 GI++ +++K +G+ QA+ D++L +E G V +GPSG GKSTLLR +AGLE SGRI + Sbjct: 2 GIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFL 61 Query: 63 GGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQ 122 GRD T DR + VFQ YAL+ H+TVR+N+ FG+++ + + R+ E ++Q Sbjct: 62 TGRDATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQ 121 Query: 123 LEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQ 182 L DR P QLSGGQRQRVA+ RA+ P V L DEP LDAK+R +R L LH + Sbjct: 122 LTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDE 181 Query: 183 LGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVF 242 + T ++VTHDQ EAM +AD+IVV+N G++EQ+GSP ++Y P + FV FIG + Sbjct: 182 VHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIGPVNVLPN 241 Query: 243 SSDVGLQDISLDASAAFVGCRPEHIEIVPDG-DGHIAATVHVKERLGGESLLYLGLKGGG 301 SS + Q LD V RP IEI D + A + LG E + L+ G Sbjct: 242 SSHI-FQAGGLDTPHPEVFLRPHDIEIAIDPIPETVPARIDRIVHLGWEVQAEVRLEDGQ 300 Query: 302 QIVARVGGD 310 +VA + D Sbjct: 301 VLVAHLPRD 309 Lambda K H 0.320 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: 313 Number of extensions: 12 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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