Align ABC transporter (characterized, see rationale)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= uniprot:A0A166QFW2 (381 letters) >MicrobesOnline__882:207786 Length = 397 Score = 163 bits (413), Expect = 7e-45 Identities = 100/293 (34%), Positives = 154/293 (52%), Gaps = 7/293 (2%) Query: 23 SLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEP------RERG 76 S ++ GE VV +G SG GKSTL+R + L G + +DGR V + R+R Sbjct: 47 SFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRRLRQRS 106 Query: 77 VGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKELSG 136 GMVFQ++AL+PH +V N +FGL+ + + + + + + L + +P +LSG Sbjct: 107 FGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRPAQLSG 166 Query: 137 GQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHDQVE 196 G +QRV + RA++ +PDILL DE S LD +R M++E+ RL D L T+++++HD E Sbjct: 167 GMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFISHDLDE 226 Query: 197 AMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETSLVD 256 A+ L D+IV++ G V Q+G+P ++ PA +VA F+G + + + V Sbjct: 227 ALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVTKVLTAGSVMKRSEAVA 286 Query: 257 TL-VWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVVVTAVEYLGS 308 L + G + A T L R V L AD A + V LGS Sbjct: 287 VLGIDGPRTALRKMRRNAIATLFVLDERHRLVGLITADDAARLAAEGVRELGS 339 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: 312 Number of extensions: 16 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: 397 Length adjustment: 30 Effective length of query: 351 Effective length of database: 367 Effective search space: 128817 Effective search space used: 128817 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