Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate 3607126 Dshi_0548 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::O51924 (295 letters) >FitnessBrowser__Dino:3607126 Length = 288 Score = 157 bits (397), Expect = 3e-43 Identities = 92/279 (32%), Positives = 155/279 (55%), Gaps = 7/279 (2%) Query: 15 KLGYLMILPLLTVVLVFIILPVMGTFWISLH-RDVTFIPEKPFVGLRNYLRVLSAREFWY 73 K + I P + + + I P++ W SLH ++T + F+GL NY VL+ FW Sbjct: 8 KTVFAFIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQ 67 Query: 74 STFVTVSFSFVSVSLETILGLSFALILNER--LKGRGVLRAIVLIPWAVPTIISARTWEL 131 + T ++ L+ LGL AL+L++ + + R +++P A + ++ Sbjct: 68 AMGRTFFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQV 127 Query: 132 MYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAIPQD 191 M+N +G+ N +LG + +NW+G P +AF I+ DVW+ TPF+ L+LLAGL +P + Sbjct: 128 MFNQKFGVVN---QLLGGADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGE 184 Query: 192 LYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTS 251 + EAA ++ S + + + LP L P L+ LILRT D L++FD+++ LT GGPG +T Sbjct: 185 VEEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEF 244 Query: 252 ISLLAFNYYNLG-DYGIGSAISILTFVLVLSFTIVYLKV 289 ISL+ G D G+ SA +I+ ++ + +Y++V Sbjct: 245 ISLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYIRV 283 Lambda K H 0.329 0.145 0.439 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: 266 Number of extensions: 18 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: 295 Length of database: 288 Length adjustment: 26 Effective length of query: 269 Effective length of database: 262 Effective search space: 70478 Effective search space used: 70478 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