Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 301 bits (771), Expect = 2e-86 Identities = 163/355 (45%), Positives = 219/355 (61%), Gaps = 13/355 (3%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA +Q +KK FGS +++G+D+DIA GEF VLVGPSGCGKSTLLR LAGLE G I Sbjct: 1 MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 I G +N+++P++RDIAMVFQ+YALYPHMTV +NM F L L A + +RV + +++ Sbjct: 61 LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + LLDR P++LSGGQRQRVA+GRA+ R V LFDEPLSNLDA LR QMR EIK LH Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 K+T IYVTHDQ+EA T+ D+I V++DG++EQ G P ++Y P N F+A FIGSP MN Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240 Query: 241 FLEGAVLEKIPWPEARKADQILGIRPDAFAL--NQGPLGT-----QEVALG------DFQ 287 F+ + E AD P AL N G T + +++G + Sbjct: 241 FIPATLRRNATGAEVEFADGTRVPAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQGIATK 300 Query: 288 IDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342 + + E G + ++ + +F + L D ++ HLFD ++G Sbjct: 301 VIVVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFDAESG 355 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: 345 Number of extensions: 9 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: 347 Length of database: 361 Length adjustment: 29 Effective length of query: 318 Effective length of database: 332 Effective search space: 105576 Effective search space used: 105576 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