Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate HSERO_RS17020 HSERO_RS17020 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__HerbieS:HSERO_RS17020 Length = 406 Score = 303 bits (775), Expect = 7e-87 Identities = 162/350 (46%), Positives = 225/350 (64%), Gaps = 3/350 (0%) Query: 14 GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPK 73 G VL L+L I GEF+VLLG SGCGKST+L IAGL D+S G + I V + Sbjct: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74 Query: 74 DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSE 133 +R + MVFQ+YALYP M+V N++FGL+ K P AEI++RV+ + +L ++ LL+RKP Sbjct: 75 ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134 Query: 134 LSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHD 193 +SGGQ+QR AI RA+++ VFLFDEPLSNLDAKLR++LR +IKRLHQ L+ T +YVTHD Sbjct: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194 Query: 194 QIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRS 253 Q+EA+TLADR+ +M+ G I Q P +Y P NLF AGFIG+P+MNF G V+ +DG+ Sbjct: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254 Query: 254 FVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDIE--EPMG 311 F+ + +T +RL+ V L +RP+HV++ R+ + V +E E +G Sbjct: 255 FIETAHQRWALTG-ERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILG 313 Query: 312 ADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENRL 361 AD LL Q+++ + R PG+T+ L+ D +FD ES L Sbjct: 314 ADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENL 363 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: 427 Number of extensions: 14 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: 406 Length adjustment: 30 Effective length of query: 331 Effective length of database: 376 Effective search space: 124456 Effective search space used: 124456 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