Align ABC transporter (characterized, see rationale)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >MicrobesOnline__882:208681 Length = 349 Score = 287 bits (734), Expect = 4e-82 Identities = 162/354 (45%), Positives = 221/354 (62%), Gaps = 16/354 (4%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M + LD V++ G +R + DVS E+ G+ +V +GPSGCGKST LRLIAGL+S+ G + Sbjct: 1 MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 LI GR V +L P +R + MVFQSYAL+PH++V DNI FGL + K ++R+ + +I Sbjct: 61 LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEI 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 L L KLL+RKP ELSGGQ+QRVA+GRA+ E + L DEPLSNLDA LR +MR EI L Sbjct: 121 LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQ 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 LG TM+YVTHDQ EAM++AD+I+++ GGR+ Q +P E+Y RPA+ F F+G+P MN Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMN 240 Query: 241 FLSARLQTPGETSLVDTLVWGITSLPFDSSNLA--AGTPLSLGIRPEHVSLKAADGTAGV 298 + RLQ + GI S + AG LGIRPEH+ + D Sbjct: 241 LV--RLQGNDD---------GIRVAGSRSGRVTCHAGADCMLGIRPEHI--RIVDDGWRA 287 Query: 299 VVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDA 352 VV +VEYLGS + + G +E + V+ G + L +++H+FDA Sbjct: 288 VVESVEYLGSNSVLSCRVGSEELSVVVHGVT-DTVVGAEIYLHCPEEHVHIFDA 340 Lambda K H 0.320 0.137 0.394 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: 309 Number of extensions: 12 Number of successful extensions: 2 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: 381 Length of database: 349 Length adjustment: 30 Effective length of query: 351 Effective length of database: 319 Effective search space: 111969 Effective search space used: 111969 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