Align Melibiose permease; Melibiose transporter MelY (characterized)
to candidate BWI76_RS00610 BWI76_RS00610 MFS transporter
Query= SwissProt::P96517 (425 letters) >FitnessBrowser__Koxy:BWI76_RS00610 Length = 421 Score = 692 bits (1785), Expect = 0.0 Identities = 330/408 (80%), Positives = 372/408 (91%) Query: 1 MNTTTCTHKDNPNFWIFGLFFFLYFFIMATCFPFLPIWLSDIIGLNKTHTGIVFSCISLS 60 MN T CTHK+NPNFWIFGLFFFLYFFIMATCFPFLPIWLSD+IGLNKT TGIVFS +SL Sbjct: 1 MNPTVCTHKNNPNFWIFGLFFFLYFFIMATCFPFLPIWLSDVIGLNKTETGIVFSSLSLF 60 Query: 61 AIAFQPVLGVISDKLGLKKHLLWIISVLLFLFAPFFLYVFAPLLKTNIWLGALSGGLYIG 120 AI FQP+LGVISDKLGLKKHL+WI++VLL L APFFLYVFAPLLKTNIWLGALSGG YIG Sbjct: 61 AICFQPILGVISDKLGLKKHLMWIVTVLLVLIAPFFLYVFAPLLKTNIWLGALSGGAYIG 120 Query: 121 FVFSAGSGAIEAYIERVSRNSAFEYGKARMFGCLGWGLCASTGGILFGIDPSYVFWMGSA 180 FVFSAG+GA+EAYIERVSRNS FEYGKAR FGCLGW LCA+T G+LF ++P +VFWMGSA Sbjct: 121 FVFSAGAGAMEAYIERVSRNSGFEYGKARTFGCLGWALCATTAGMLFSVNPEWVFWMGSA 180 Query: 181 AALLLMLLLVVAKPKPNQTAQVMNALGANQPQITAKKVFNLFRQRRMWMFILYVIGVACV 240 AAL+L++L+ +AKP+ +QTAQVM++LGAN+ + K +FRQR+MWMFILYVIGVACV Sbjct: 181 AALVLVVLVAIAKPQASQTAQVMDSLGANRSSVDLKTAVRMFRQRKMWMFILYVIGVACV 240 Query: 241 YDVFDQQFATFFKTFFATPQEGTRAFGFATTAGEICNAIIMFCSPWIINRIGAKNTLLIA 300 YDVFDQQFATFFK+FFATP+ GTRAFGFATTAGEICNAIIMF SPWIINRIGAKNTLLIA Sbjct: 241 YDVFDQQFATFFKSFFATPESGTRAFGFATTAGEICNAIIMFSSPWIINRIGAKNTLLIA 300 Query: 301 GLIMATRIIGSSFATTAVEVIALKMLHALEVPFLLVGAFKYITGVFDTRLSATIYLIGFQ 360 G++MA R+IGSSFATTA EV+ALKMLHALEVPFLLVGAFKYITGVFD RLSATIYL+GFQ Sbjct: 301 GMVMAARMIGSSFATTAAEVVALKMLHALEVPFLLVGAFKYITGVFDVRLSATIYLVGFQ 360 Query: 361 FAKQSAAIFLSAFAGNMYDRIGFQETYLMLGCFVLAITVVSAFTLSSR 408 F+KQ AAIFLSAFAGNMYDRIGFQ+TY++LG L +T++SAFTLS + Sbjct: 361 FSKQVAAIFLSAFAGNMYDRIGFQDTYMILGGIALTVTLISAFTLSGK 408 Lambda K H 0.331 0.142 0.444 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: 727 Number of extensions: 28 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 421 Length adjustment: 32 Effective length of query: 393 Effective length of database: 389 Effective search space: 152877 Effective search space used: 152877 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 50 (23.9 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