Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 3607559 Dshi_0971 ABC transporter related (RefSeq)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Dino:3607559 Length = 334 Score = 290 bits (743), Expect = 3e-83 Identities = 159/340 (46%), Positives = 215/340 (63%), Gaps = 15/340 (4%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 M +I+ + + KSFG +V+ +DL I GEF V VGPSGCGKSTLLR +AGLE SG I Sbjct: 1 MGQIKLNQVTKSFGDVEVIPPLDLTIEDGEFAVFVGPSGCGKSTLLRLIAGLEDITSGHI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 IDGK ++ P R +AMVFQSYALYPHM+V +N+ F +K+ + AE +R++ ++ Sbjct: 61 EIDGKDATNVPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIDEAEQQRRIDAAAKA 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + LDR+P +LSGGQRQRVA+GRA+ R+ LFDEPLSNLDA LR MRLEI LH Sbjct: 121 LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 ++TMIYVTHDQ+EA T+ D+I VL+ G IEQ+G+P E+YH P+N F+A FIGSP+MN Sbjct: 181 KRLETTMIYVTHDQVEAMTMADKIVVLRAGHIEQVGSPLELYHSPRNEFVAGFIGSPKMN 240 Query: 241 FLEGAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQIDISENLGGQQML 300 ++GA A+ +GIRP+ + T E L + ++ ++E+LG L Sbjct: 241 LIKGA-------EAAKHGVATIGIRPE-----HTDVSTTE-GLWEGRVGVAEHLGSDTFL 287 Query: 301 --HGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFD 338 HG + + + VD + L L K H FD Sbjct: 288 HIHGVPDCDPMTVRVDGELPVKHGDKIFLTPQLDKLHKFD 327 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: 293 Number of extensions: 13 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: 334 Length adjustment: 28 Effective length of query: 319 Effective length of database: 306 Effective search space: 97614 Effective search space used: 97614 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