Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 200 bits (508), Expect = 6e-56 Identities = 105/238 (44%), Positives = 150/238 (63%), Gaps = 5/238 (2%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 ++LT + K +G + LS +NLDIQ+GE+I +GPSG GK+TLLR+IAGLE G + Sbjct: 3 IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFG 62 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQ----AEIDAAVEAAAE 119 V V R + VFQ+YAL+ HMTV +N++F L++ K Q AEI V E Sbjct: 63 NRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHLLE 122 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 +QLG R P+ LSGGQ+QR+A+ R++ P+V L DEP LDA +R R + L Sbjct: 123 MVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSL 182 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGS 237 + + + T V+VTHDQ EA+ L+ R+VV++ G I QV +P+ELY +P + FV F+G+ Sbjct: 183 HDEL-KFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN 239 Lambda K H 0.316 0.135 0.379 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: 19 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: 373 Length of database: 376 Length adjustment: 30 Effective length of query: 343 Effective length of database: 346 Effective search space: 118678 Effective search space used: 118678 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 (21.6 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