Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate 8499892 DvMF_0657 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__Miya:8499892 Length = 297 Score = 143 bits (360), Expect = 5e-39 Identities = 96/280 (34%), Positives = 147/280 (52%), Gaps = 9/280 (3%) Query: 14 VNGWLFVAPALGLITLFMVYPIAWSLWMSF-QSGRG-MTLKFAGFANIVRLWNDPVFIKA 71 ++ WL + PAL I F YP + SF GRG +F G + L D VF KA Sbjct: 14 IHAWLLLLPALAFIAAFTHYPAVNTFIHSFFLDGRGGAPAQFVGLEHYQYLLEDEVFRKA 73 Query: 72 LTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMF 131 L N + + +P+ I LA+ +A L+N L G+ V R F+P V ++A + ++ + Sbjct: 74 LVNNLLFASGTIPLSIGLAMTMAFLVN-AGLAGQSVLRLCYFVPTVLPMIAVANIWLFFY 132 Query: 132 ATD-GIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKS 190 + G++ A+GLA + WL A VI W+ G+ MIFYLAALQ I S Sbjct: 133 TPEYGLLEQIRGALGLAG--VNWLGSESTALPCVIAVAVWKDAGFFMIFYLAALQQIPPS 190 Query: 191 IYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNAT 250 + E A ++G + IPLL P LF V +TI ++ D ++ LT+ GGP+NA+ Sbjct: 191 LGEAAMLEGASRLYYYRRVVIPLLMPTTLFVLVNATINAFRMVDHLFVLTQ--GGPNNAS 248 Query: 251 LTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQF 290 L YIY ++F++ + GY A ++ V++ +AL + QF Sbjct: 249 SLLLYYIYEVSFKYW-DTGYGAALTMVLLGFLALASIGQF 287 Lambda K H 0.330 0.142 0.447 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: 249 Number of extensions: 13 Number of successful extensions: 4 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: 298 Length of database: 297 Length adjustment: 26 Effective length of query: 272 Effective length of database: 271 Effective search space: 73712 Effective search space used: 73712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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