Align Lactose permease; Lactose-proton symport (characterized)
to candidate BWI76_RS15425 BWI76_RS15425 MFS transporter
Query= SwissProt::P02920 (417 letters) >FitnessBrowser__Koxy:BWI76_RS15425 Length = 416 Score = 522 bits (1345), Expect = e-153 Identities = 245/395 (62%), Positives = 320/395 (81%) Query: 8 NFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLS 67 NF F LFFFFY+FIM AYFPFFP+WL ++NH++K++TGI+F+ ISLF+++FQP+FGL+S Sbjct: 13 NFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQPVFGLIS 72 Query: 68 DKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEA 127 DKLGLRK+LLW IT +L++FAPFFIF+F PLLQ NI+ G++VGG+YLG F++G+ AVEA Sbjct: 73 DKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIIAGALVGGVYLGIVFSSGSGAVEA 132 Query: 128 FIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALILAVLLFFA 187 +IE+VSR + FE+G+ R+ GCVGWALCASI GI+F+I+ FW+ SG ALIL VLL+ + Sbjct: 133 YIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALILGVLLWVS 192 Query: 188 KTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFF 247 K ++ +SA V +A+GAN AFS++ A EL R P+ W +YV+GV+ YDVFDQQFANFF Sbjct: 193 KPESSNSAEVIDALGANRQAFSMRTAAELLRMPRFWGFIIYVVGVASVYDVFDQQFANFF 252 Query: 248 TSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSS 307 FF++ ++GT VFG+VTT GELLNA IMF AP IINRIG KNALL+AG IMSVRI+GSS Sbjct: 253 KGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIMSVRILGSS 312 Query: 308 FATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSV 367 FATSA+EV+ILK LHMFE+PFLLVG FKYI+S F + SAT++L+ F KQL+ + +S Sbjct: 313 FATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFNPKLSATLFLIGFNLSKQLSGVVLSA 372 Query: 368 LAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSG 402 G MY+++GF AYL+LG + L FT+IS+FTL G Sbjct: 373 WVGRMYDTVGFHQAYLILGCITLSFTVISLFTLKG 407 Lambda K H 0.334 0.147 0.460 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: 620 Number of extensions: 22 Number of successful extensions: 1 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: 417 Length of database: 416 Length adjustment: 31 Effective length of query: 386 Effective length of database: 385 Effective search space: 148610 Effective search space used: 148610 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: 39 (21.6 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