Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate SMc04396 SMc04396 periplasmic binding protein
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__Smeli:SMc04396 Length = 414 Score = 380 bits (977), Expect = e-110 Identities = 196/413 (47%), Positives = 256/413 (61%), Gaps = 3/413 (0%) Query: 4 MTKIAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGG 63 MT A A+ LAA + +A VEVLH+WTSGGEA ++ LKK ++ KG +W D VAGGG Sbjct: 5 MTTTAVAALMLAATAARAAENVEVLHWWTSGGEAAALDVLKKDLESKGISWTDMPVAGGG 64 Query: 64 GDSAMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADV 123 G AMTVL++RV +GN P+A Q G I +WA EG L N+D +A E WD+++P + Sbjct: 65 GTEAMTVLRARVTAGNAPTAVQMLGFDILDWAKEGALGNLDEVAAKEGWDKVVPAALQQF 124 Query: 124 MKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHG 183 KY G ++AAPVNVH NW+W + AL KAG A P TW+E A DK K G+ P+AHG Sbjct: 125 SKYDGHWIAAPVNVHSTNWVWINKAALDKAG-AKEPTTWEELIALLDKFKEQGITPIAHG 183 Query: 184 GQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPG 243 GQ WQD T F++VVL +G FY+ A + LD AL D MK++ + +++ Y D G Sbjct: 184 GQPWQDATIFDAVVLSLGN-DFYKQAFIDLDPAALGGDKMKEAFDRMTKLRSYVDDNFSG 242 Query: 244 RDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFIL 303 RDWNLA+AM+I+ KAG Q MGDWAKGEFL A K PG DF+C PG+ + TFN D F + Sbjct: 243 RDWNLASAMVIENKAGLQFMGDWAKGEFLKAKKVPGTDFVCMRFPGTQGSVTFNSDQFAM 302 Query: 304 FKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDT 363 FK+ + AQ +AS+I SPAFQ FN+ KGS+P R P FD C K KD + Sbjct: 303 FKVSEDKV-PAQLQMASAIESPAFQSAFNVVKGSVPARTDVPDTDFDACGKKGIKDLAEA 361 Query: 364 AKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKTK 416 +G L S AHG A A + AI DVV++ +N + S + +AA K Sbjct: 362 NTNGTLFGSMAHGHANPAAVKNAIYDVVTRQFNGELNSEEAVTELVAAVEAAK 414 Lambda K H 0.315 0.128 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: 550 Number of extensions: 32 Number of successful extensions: 4 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: 416 Length of database: 414 Length adjustment: 31 Effective length of query: 385 Effective length of database: 383 Effective search space: 147455 Effective search space used: 147455 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