Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 371 bits (952), Expect = e-107 Identities = 208/365 (56%), Positives = 252/365 (69%), Gaps = 14/365 (3%) Query: 1 MTS-VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 MTS VS RDLS+ FGAV VL LNLDI GEFLVLLG+SGCGKSTLLN IAGL + ++GQ Sbjct: 9 MTSHVSARDLSVRFGAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQ 68 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119 I+I D NVTW EPKDRG+ MVFQSYALYP+MTV NL+FGL++ K+P AE +K V A+ Sbjct: 69 IWINDENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVDEAAR 128 Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179 +LQ++ LL R+P ELSGGQRQRVAIGRALVR VDVFLFDEPLSNLDAKLR+ELRVE+KRL Sbjct: 129 VLQLEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVELKRL 188 Query: 180 HQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 HQ L TMIYVTHDQ+EALTLADRIAVMK GV+QQL P IY P N +VA F+G PSM Sbjct: 189 HQELGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSM 248 Query: 240 NFFRGEVEPKDGRSFVRAGGIAFD---VTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296 NF G V + G +A D + + PA PG +V +G+RPEHV A Sbjct: 249 NFVNG-VVTESGAIQTEDFELALDQCNLASTPA-----PGTEVEIGIRPEHVHPANAGG- 301 Query: 297 EPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAE 356 V + E +G++ L+W S+ +R G VR++ G S+F A+ Sbjct: 302 ---FMLDVGMVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAK 358 Query: 357 SENRL 361 + R+ Sbjct: 359 TGLRI 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: 396 Number of extensions: 16 Number of successful extensions: 3 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: 363 Length adjustment: 29 Effective length of query: 332 Effective length of database: 334 Effective search space: 110888 Effective search space used: 110888 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