Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__psRCH2:GFF857 Length = 371 Score = 313 bits (801), Expect = 6e-90 Identities = 174/362 (48%), Positives = 225/362 (62%), Gaps = 34/362 (9%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA + +I KS+ + + IDLDI GEF+V VGPSGCGKSTLLR +AGLE SG + Sbjct: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 ID +++ND+ P++R + MVFQSYALYPHMTVAENM FGLKL ++ EI +RV ++E+ Sbjct: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 LQ+ LL+RKPK+LSGGQRQRVA+GR + R+ V LFDEPLSNLDA LR QMR+EI RLH Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 +STMIYVTHDQ+EA TL D+I VL G I Q+G P +YH PKN F+A F+GSP+MN Sbjct: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240 Query: 241 FLEGAVLEKIP----------WPEARKAD---------QILGIRPDAFALNQGPLGTQEV 281 F+E + P +P D LGIRP+ F + Sbjct: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDE------- 293 Query: 282 ALGDF----QIDISENLGGQQMLHGTL--AGNNVRILVDSMDNFSMKQTLPLKIDLTKAH 335 DF QI ++E LG +L+ TL + + + VD + +T + K H Sbjct: 294 --ADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCH 351 Query: 336 LF 337 LF Sbjct: 352 LF 353 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: 334 Number of extensions: 9 Number of successful extensions: 1 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: 371 Length adjustment: 29 Effective length of query: 318 Effective length of database: 342 Effective search space: 108756 Effective search space used: 108756 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