Align MalF, component of Maltose/trehalose porter (characterized)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease
Query= TCDB::O51924 (300 letters) >FitnessBrowser__Koxy:BWI76_RS23380 Length = 296 Score = 155 bits (393), Expect = 8e-43 Identities = 95/283 (33%), Positives = 153/283 (54%), Gaps = 12/283 (4%) Query: 21 LGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSARE-FWYS 79 LG I P + ++VF P + +F++S + + F G+ NY +L+ FW S Sbjct: 7 LGLAWISPYIIGLIVFTAFPFVSSFFLSF-TEYDLMSPPVFNGIENYRYMLTEDGLFWKS 65 Query: 80 TFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIIS-ARTWELMY 138 VT ++ F+++ L+ L A +LN +L+G G R IP + + ++ A W ++ Sbjct: 66 MGVTFAYVFLTIPLKLAFALGIAFVLNFKLRGIGFFRTAYYIPSILGSSVAIAVLWRALF 125 Query: 139 NYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLY 198 GL N + +LG PVNWLG P A ++ + VW+ M ++ LA LQ +PQ Y Sbjct: 126 AID-GLLNSFIGVLGFDPVNWLGEPSLALMSVTLLRVWQFGSAM-VIFLAALQNVPQSQY 183 Query: 199 EAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSIS 258 EAA+IDGAS ++ F +T+PL+ PV+ I++T A + F YV+TGGGP +T S Sbjct: 184 EAAMIDGASKWQMFMKVTVPLITPVIFFNFIMQTTQAFQEFTGPYVITGGGPTYSTYLFS 243 Query: 259 L----LAFNYYNLGDYGIGSAISILTFVLVLSFTIVYLKVGRF 297 L AF Y+ D G G+A++ + F++V F + K ++ Sbjct: 244 LYIYDTAFKYF---DMGYGAALAWVLFLVVAVFAAIAFKSSKY 283 Lambda K H 0.329 0.145 0.436 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: 284 Number of extensions: 19 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: 300 Length of database: 296 Length adjustment: 26 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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 (21.8 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