Align Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate Ac3H11_2062 ABC-type sugar transport system, periplasmic component
Query= TCDB::Q72KX2 (414 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2062 Length = 416 Score = 171 bits (432), Expect = 5e-47 Identities = 129/412 (31%), Positives = 197/412 (47%), Gaps = 24/412 (5%) Query: 6 LAIGMVLGLSALAQGGKLEIFSWW-AGDEGPALEALIRLYKQKYPGVEVINATVTGGAGV 64 +A+G+ +SA A G++E+ +W +G E ++ L ++ + K G + V GG G Sbjct: 10 VAVGLAAAMSASA--GEVEVLHYWTSGGEAKSVAELKKIMQGK--GHTWRDFAVAGGGGD 65 Query: 65 NARAVLKTRMLGGDPPDTFQVHAGMELIGTWVVANRMEDLSALFRQEGWLQAFPKGLIDL 124 +A VLK+R++ G+PP Q I W + ++ L + E W + PK + D+ Sbjct: 66 SAMTVLKSRVISGNPPSAAQTKG--PAIQEWASEGVLANMDTLAKAEKWDELLPKVVADV 123 Query: 125 ISYKGGIWSVPVNIHRSNVMWYLPAKLKEWGVNP-PRTWDEFLATCQTLKQKGLEAPLAL 183 + YKG + PVN+HR N MW LK+ GV P+TWDEF A LK GL Sbjct: 124 MKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHG 183 Query: 184 GENWTQQHLWESVALAVLGPDDWNN--LWNGKLKFTDPKAVRAWEVFGRVLDCANKDAAG 241 G+NW +ESV L V G + + + T ++ E F R+ + A G Sbjct: 184 GQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPG 243 Query: 242 LSWQQAVDRVVQGKAAFNVMGDWAAGYMTTTLKLKPGTDFAWAPSPGTQGVFMMLSDSFG 301 W A ++QGKA F +MGDWA G K PG DF A +PG+ F DSF Sbjct: 244 RDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGK-APGKDFLCAAAPGSANAFTFNVDSFI 302 Query: 302 L--PKGAKNRQNAINWLRLVGSKEGQDTFNPLKGSIAARLDSDPSKYNAYGQSAMRDW-- 357 L K A ++ + + S Q+ FN KGSI R K++ +++ +D+ Sbjct: 303 LFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVD 362 Query: 358 --RSNRIVGSLVHG-AVAPESFMSQFGTVMEIFLQTRNPQ--AAANAAQAIA 404 +S +V S HG A+AP + G + ++ Q N + A+A + IA Sbjct: 363 TAKSGGLVPSAAHGMAIAP----ATEGAIKDVVSQFWNDDKVSVADAMKKIA 410 Lambda K H 0.319 0.134 0.429 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: 577 Number of extensions: 35 Number of successful extensions: 6 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: 414 Length of database: 416 Length adjustment: 31 Effective length of query: 383 Effective length of database: 385 Effective search space: 147455 Effective search space used: 147455 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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