Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 323 bits (827), Expect = 6e-93 Identities = 182/362 (50%), Positives = 231/362 (63%), Gaps = 11/362 (3%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 MT V++ +G V V+ ++L ID GEF V +G SGCGKSTLL IAGL + S G I Sbjct: 1 MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I DR+VT + DRG+ MVFQSYALYP MTVE N+ FGLK+ P +I ++V AS I Sbjct: 61 HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L++ LKRKP LSGGQRQRVAIGRA+VR +VFLFDEPLSNLDA+LR ++RVEI RLH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + + TMIYVTHDQ+EA+TLAD+I V+++G ++Q+ PM +Y P+N FVAGFIGSPSMN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300 F G V+ A PA G KV+LGLRP+H+ V A Sbjct: 241 FLEGTVQGDGVVVPALENRRVATSVALPA-----DGSKVLLGLRPQHLSVTAA-----DS 290 Query: 301 QAVVDIEEPMGADNLLWL-TFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESEN 359 V+D+ E +G + +L T G+ + V G P G+ V L FD A IFD +E Sbjct: 291 SLVLDLRERLGGVSYDYLSTPTGEKLIVETRGDEALPEGTAVALGFDDADAYIFDGATEQ 350 Query: 360 RL 361 RL Sbjct: 351 RL 352 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: 343 Number of extensions: 11 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: 353 Length adjustment: 29 Effective length of query: 332 Effective length of database: 324 Effective search space: 107568 Effective search space used: 107568 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