Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 299 bits (765), Expect = 8e-86 Identities = 170/354 (48%), Positives = 225/354 (63%), Gaps = 21/354 (5%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA+I+ ++ K +G+ +VL+ I+LDI GEF+VLVGPSGCGKSTLLR +AGLE SG Sbjct: 1 MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 IDG+++ND+ P++RDIAMVFQSYALYPHM VA NMGF ++++ A E RV +E Sbjct: 61 EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + L+DR PK LSGGQRQRVA+GRA+ R LFDEPLSNLDA LR +MRLEI RLH Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 +TMIYVTHDQ+EA TL DRI VL G I+Q+G+P E+Y RP N F+A FIGSP MN Sbjct: 181 KQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMN 240 Query: 241 FL------------EGAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQI 288 L G +L + A + LGIRP+ + + P +A+ Sbjct: 241 ILPVSGAASGVMATNGMMLTLDHMHDTAAAVE-LGIRPEHLDVVE-PGEGHLIAVA---- 294 Query: 289 DISENLGGQQMLHGTLAGNNVRILVDSMDNFSMK--QTLPLKIDLTKAHLFDKK 340 D+ E LG ++ + G ++V N ++ + L L++ AH+FD + Sbjct: 295 DVVERLGSDTNIYAKVDGLG-PLMVRKHGNVPVRSGERLGLRVQAQNAHIFDDR 347 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: 317 Number of extensions: 14 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: 355 Length adjustment: 29 Effective length of query: 318 Effective length of database: 326 Effective search space: 103668 Effective search space used: 103668 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