Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate H281DRAFT_01451 H281DRAFT_01451 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Burk376:H281DRAFT_01451 Length = 415 Score = 357 bits (915), Expect = e-103 Identities = 189/369 (51%), Positives = 247/369 (66%), Gaps = 10/369 (2%) Query: 3 SVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFI 62 +V+VR+L++ G TV++ L+LD+ GEF+VLLG SGCGKSTLL+ IAGL+DV+DG I I Sbjct: 47 NVAVRNLTIRLGGNTVIENLDLDVQPGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEI 106 Query: 63 KDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQ 122 ++TW +PKDR I +VFQSYALYP M+VE+NLSF L++ P AEI +RV RA+E+LQ Sbjct: 107 AGEDMTWADPKDRRIALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARAAEMLQ 166 Query: 123 IQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQS 182 + PLLKRKP++LSGGQRQRVAIGRA+VR+ DVFLFDEPLSNLDAKLR+ELR E+K+LHQ Sbjct: 167 LGPLLKRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQR 226 Query: 183 LKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFF 242 L TMIYVTHDQ+EA+ LA R+AVM+ G IQQ P +Y P NLFVA F+G+P+MN Sbjct: 227 LGATMIYVTHDQVEAMMLATRMAVMRGGAIQQFGTPAEVYARPANLFVATFLGTPAMNLV 286 Query: 243 RGEVEPKDGRSFVRAGGIAFDVTAY----------PAHTRLQPGQKVVLGLRPEHVKVDE 292 G +E +DG DV+ Y P P + VLG+R E V++ Sbjct: 287 NGTLEQRDGALHFCTEQWRLDVSNYAFVDRSGESQPQSQPQSPPRPCVLGVRAEDVRIGP 346 Query: 293 ARDGEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASI 352 + A + + EPMG ++WL + G ++ + PG T+ S D S+ Sbjct: 347 TQGEGAGEHAKISLVEPMGNHRVVWLDYHGVQIASIDQSKTPVMPGDTLAFSLDSTHVSL 406 Query: 353 FDAESENRL 361 FDA S RL Sbjct: 407 FDAASGARL 415 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: 432 Number of extensions: 15 Number of successful extensions: 2 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: 415 Length adjustment: 30 Effective length of query: 331 Effective length of database: 385 Effective search space: 127435 Effective search space used: 127435 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