Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 311 bits (798), Expect = 1e-89 Identities = 176/369 (47%), Positives = 244/369 (66%), Gaps = 34/369 (9%) Query: 1 MAKIQFSNIKKSFGSADV--LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58 MA ++ N++KS+G++ + LK I L I GEFL+LVGPSGCGKSTL+ +AGLE+ G Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 TISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEIS 118 I +DG+ I+ P++RDIAMVFQSYALYP M+V +N+ FGLK++ + AA+I + V ++ Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 119 ELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKR 178 +LLQI+ LL+RKP +LSGGQ+QRVA+GRAL+R+ + LFDEPLSNLDA LR +MR EIK Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 179 LHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPE 238 +H K+T +YVTHDQ+EA TLGD++AV+KDGVI+Q GTP EIY+ P N F+A+FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 239 MNFLEGAVLEK----------------IPWP-----EARKADQILGIRPDAFALNQGPLG 277 MNF+ + ++ +P P R + ILGIRP+ L P G Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGL--APAG 298 Query: 278 TQEVALGDFQIDISENLGGQQMLHGTLAGNNV----RILVDSMDNFSMKQTLPLKIDLTK 333 + + +L I++ E G ++ TL N V R+ D + +TL L+ D + Sbjct: 299 SADFSLA-VDIEVVEPTGPDTLVVFTL--NQVKACCRLAPDQAPR--VGETLNLQFDPRR 353 Query: 334 AHLFDKKTG 342 A LFD +TG Sbjct: 354 ALLFDAQTG 362 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: 360 Number of extensions: 11 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: 390 Length adjustment: 30 Effective length of query: 317 Effective length of database: 360 Effective search space: 114120 Effective search space used: 114120 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