Align MalG, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 8500163 DvMF_0921 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q97UG3 (323 letters) >FitnessBrowser__Miya:8500163 Length = 284 Score = 103 bits (257), Expect = 5e-27 Identities = 93/298 (31%), Positives = 144/298 (48%), Gaps = 22/298 (7%) Query: 1 MKVSKYYNRIRKALF--NNKFILAGIVIILVDFAIGIVGAFWTPYPVS--ETFGISLPPS 56 M + ++ R LF + + G+ ++L A ++ + P+ + I PPS Sbjct: 1 MSAADLFSPRRWLLFWTRHPMLATGLSLVLAMSAAALLAPWIAPHDPTALNLTAILQPPS 60 Query: 57 SAHILGTDEFGHDVLSVMMASTLTSLIVG-ISVGALIAIISTLIGLFGGYYGGKISGVII 115 SAH LGTD G DVLS M+ SL VG +SVG +A I +GL GY+GG +I+ Sbjct: 61 SAHPLGTDALGRDVLSRMLHGARVSLWVGFVSVGISVA-IGLALGLAAGYFGGLADELIM 119 Query: 116 DILTITALTIPGVILLVIIEAYFRAASSTINITLSYIIVVIGLAITSWAFGAKQIRAQVL 175 + I L P L++ + A+ + +L I+ VIGL TSW A+ +RA+ L Sbjct: 120 RCVDI-MLCFPSFFLILAVIAF-------LEPSLLNIMAVIGL--TSWMGVARLVRAETL 169 Query: 176 SISKRDYIIASRLIGEKSWRIIFNQILPSILPLTVAQFLFGVLYGILSLITAEFWGV-LP 234 S+ +RD+I A+RL G RI+ +LP+ + + GV IL+ F G+ + Sbjct: 170 SLRERDFIAAARLAGAGPVRILCLHVLPNAVAPVLVSATLGVAGAILTESALSFLGLGVQ 229 Query: 235 TNINNLGTMLFFISSNGAYLSNQWWWIL-GAIIPIMVLGAGLGILNIGIDEFIDPRLK 291 + + G ML + W + G I + VLG L L + + +DPRLK Sbjct: 230 PPMPSWGNML--LEGKDVLEIAPWLSVFPGCAILLTVLGYNL--LGESLRDLLDPRLK 283 Lambda K H 0.326 0.144 0.427 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: 210 Number of extensions: 13 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: 323 Length of database: 284 Length adjustment: 27 Effective length of query: 296 Effective length of database: 257 Effective search space: 76072 Effective search space used: 76072 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 (21.6 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