Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate SMc04396 SMc04396 periplasmic binding protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__Smeli:SMc04396 Length = 414 Score = 227 bits (579), Expect = 4e-64 Identities = 132/360 (36%), Positives = 196/360 (54%), Gaps = 11/360 (3%) Query: 7 AAALGATAALPFGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSGGT 66 A L ATAA +A ++EV HWWTSGGEAAA+ L K ++ G W D +AG GGT Sbjct: 12 ALMLAATAA-----RAAENVEVLHWWTSGGEAAALDVLKKDLESKGISWTDMPVAGGGGT 66 Query: 67 -ARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSLLDS 125 A ++ +R+T G+ A Q G + + G + +L ++A KE W ++V P++L Sbjct: 67 EAMTVLRARVTAGNAPTAVQML-GFDILDWAKEGALGNLDEVAAKEGWDKVV-PAALQQF 124 Query: 126 CTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEKAGIVPLAVGG 185 +G APVN+HS W+W++ AA +AG + P W+E +A ++ GI P+A GG Sbjct: 125 SKYDGHWIAAPVNVHSTNWVWINKAALDKAGAKEPTTWEELIALLDKFKEQGITPIAHGG 184 Query: 186 QPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARR-MSKGTNVQ 244 QPWQ FD +++++ G + +++ F D G ++ + F R + + + Sbjct: 185 QPWQDATIFDAVVLSL-GNDFYKQAFIDLDPAALGGDKMKEAFDRMTKLRSYVDDNFSGR 243 Query: 245 DWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDAFYFP 304 DWN A+ MVI KAG Q MGDWA+GEF A + G D+ C+ G ++ D F Sbjct: 244 DWNLASAMVIENKAGLQFMGDWAKGEFLKAKKVPGTDFVCMRFPGTQGSVTFNSDQFAM- 302 Query: 305 LLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKGLDILAKGN 364 E+K AQ +AS + P Q AFN+ KGS+P R DV + C KKG+ LA+ N Sbjct: 303 FKVSEDKVPAQLQMASAIESPAFQSAFNVVKGSVPARTDVPDTDFDACGKKGIKDLAEAN 362 Lambda K H 0.315 0.131 0.389 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: 502 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 411 Length of database: 414 Length adjustment: 31 Effective length of query: 380 Effective length of database: 383 Effective search space: 145540 Effective search space used: 145540 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 (21.6 bits) S2: 50 (23.9 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