Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 284 bits (727), Expect = 2e-81 Identities = 155/350 (44%), Positives = 216/350 (61%), Gaps = 2/350 (0%) Query: 8 DLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNV 67 +++ G +L ++L+I GEF+V +G SGCGKSTLL IAGL + DG + I R V Sbjct: 8 NVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLIDGRRV 67 Query: 68 TWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLL 127 EP++RG+GMVFQSYALYP M+V N+SFGLK+AK A + +RV + ++ILQ+ LL Sbjct: 68 NDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQLDKLL 127 Query: 128 KRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTM 187 +RKP ELSGGQRQRVA+GRA+ R+ D+ LFDEPLSNLDA LR ++R EI RLH L +TM Sbjct: 128 QRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRLGSTM 187 Query: 188 IYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVE 247 IYVTHDQ+EA+TLAD+I V+ G I+Q+ P +Y P + FVAGF+GSP MNF + Sbjct: 188 IYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFLPARLH 247 Query: 248 PKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDIE 307 S + + + + + L G + LG+RPEH+ + A+ V Sbjct: 248 SPGETSQIDSPLLGMTPLPFDS-AHLAVGSPLTLGIRPEHMSLKAAQGSAGVGVVGVVGV 306 Query: 308 EPMGADNLLWL-TFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAE 356 E +G++ + L + + + R + G V L G +FDA+ Sbjct: 307 EYLGSETYVHLESGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDAD 356 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: 410 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: 384 Length adjustment: 30 Effective length of query: 331 Effective length of database: 354 Effective search space: 117174 Effective search space used: 117174 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