Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 299 bits (765), Expect = 9e-86 Identities = 174/374 (46%), Positives = 232/374 (62%), Gaps = 16/374 (4%) Query: 1 MTSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 M +VS+R + + + ++L+I GEF+V +G SGC KST L IAGL D+S G+ Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119 I+I +R V PKDRGI MVFQ+YALYP TV N++FGLK+ K P EI++RV+ A+E Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179 L+I LL RKP E+SGGQRQRVA+GRA+VR DVFLFDEPLSNLDAKLR +R++I +L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 HQSLKN-----TMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI 234 H+SLK TMIYVTHDQ EALTL DRI V+ G I Q+ P +YN P N FVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 235 GSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTR--LQPG---QKVVLGLRPEHVK 289 GSPS+N + + R +V IA V H++ L G + V G+RPEH+ Sbjct: 241 GSPSINLIDTAIRKNNERLYVE---IAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHIS 297 Query: 290 VDEARDGEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYP--PGSTVRLSFDM 347 + D T + V+ + E MG++ L+ G+ + R+ Q P G T+R + + Sbjct: 298 LASDDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRFNLNT 357 Query: 348 GVASIFDAESENRL 361 +FD +EN L Sbjct: 358 AFCHVFDFYNENNL 371 Lambda K H 0.320 0.137 0.392 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: 355 Number of extensions: 10 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: 361 Length of database: 376 Length adjustment: 30 Effective length of query: 331 Effective length of database: 346 Effective search space: 114526 Effective search space used: 114526 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: 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