Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= uniprot:Q6MNM2 (347 letters) >MicrobesOnline__882:207786 Length = 397 Score = 163 bits (412), Expect = 8e-45 Identities = 93/264 (35%), Positives = 150/264 (56%), Gaps = 17/264 (6%) Query: 21 GID---LDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKINDIEP----- 72 G+D D+ GE +V++G SG GKSTL+R L L +GT+++DG+ + + Sbjct: 42 GVDRASFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRR 101 Query: 73 -QNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKP 131 + R MVFQ++AL+PH TV +N FGL+ + AE ++ E + + +P Sbjct: 102 LRQRSFGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRP 161 Query: 132 KELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVT 191 +LSGG +QRV L RALS ++L DE S LD +R M+ E+ RL + + T+++++ Sbjct: 162 AQLSGGMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFIS 221 Query: 192 HDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN--FLEGAVLEK 249 HD EA LGDRI +++DG + QIGTP +I P + ++A F+G ++ G+V+++ Sbjct: 222 HDLDEALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVTKVLTAGSVMKR 281 Query: 250 IPWPEARKADQILGIRPDAFALNQ 273 +A +LGI AL + Sbjct: 282 ------SEAVAVLGIDGPRTALRK 299 Lambda K H 0.318 0.136 0.383 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: 269 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: 347 Length of database: 397 Length adjustment: 30 Effective length of query: 317 Effective length of database: 367 Effective search space: 116339 Effective search space used: 116339 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 (21.7 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