Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 291 bits (746), Expect = 1e-83 Identities = 161/351 (45%), Positives = 224/351 (63%), Gaps = 7/351 (1%) Query: 8 DLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNV 67 +++ G + +L ++L+I GEF+V +G SGCGKSTLL IAGL + G + I R V Sbjct: 8 NVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRV 67 Query: 68 TWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLL 127 EP++RG+GMVFQSYALYP M+V N+SFGLK+AK + +RV + ++ILQ+ LL Sbjct: 68 NDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLL 127 Query: 128 KRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTM 187 +RKP ELSGGQRQRVA+GRA+ R+ D+ LFDEPLSNLDA LR ++R EI RLH L +TM Sbjct: 128 QRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTM 187 Query: 188 IYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVE 247 IYVTHDQ+EA+TLAD+I V+ G ++Q+ P +Y P + FVAGF+GSP MNF ++ Sbjct: 188 IYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQ 247 Query: 248 PKDGRSFVRAGGIAFDVTAYP-AHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDI 306 S V + + +T+ P + L G + LG+RPEHV + +A DG T VV Sbjct: 248 TPGETSLVDT--LVWGITSLPFDSSNLAAGTPLSLGIRPEHVSL-KAADG--TAGVVVTA 302 Query: 307 EEPMGADNLLWL-TFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAE 356 E +G++ + L T + + R + G V L D+ +FDA+ Sbjct: 303 VEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353 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: 386 Number of extensions: 13 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: 381 Length adjustment: 30 Effective length of query: 331 Effective length of database: 351 Effective search space: 116181 Effective search space used: 116181 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 Apr 09 2024. 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