Align Permease IIC component (characterized, see rationale)
to candidate BWI76_RS27750 BWI76_RS27750 PTS lactose/cellobiose family transporter subunit IIC
Query= uniprot:A0A0H2UNC6 (448 letters) >FitnessBrowser__Koxy:BWI76_RS27750 Length = 441 Score = 207 bits (528), Expect = 4e-58 Identities = 139/453 (30%), Positives = 232/453 (51%), Gaps = 49/453 (10%) Query: 7 LFGFLENHVMGPMGKLAQFKVVRAITAAGMAAVPFTIVGSMFLVFSILPQAFSFWPIVAD 66 + +E + G+L Q K V AI AA+PF I+GS LVF P F P + Sbjct: 8 MIAVIEQSITPLAGRLGQQKYVIAIRDGFTAALPFMIIGSFMLVFIFPP----FSPDTTN 63 Query: 67 IFSASFDKFTSLY----MVANYATMGSLSLYFVLSLAYELTKIYAEEEELNMNPLNGALL 122 F+ + F+ Y M+ +MG ++ + + + L + + ++P+ LL Sbjct: 64 GFARGWLDFSQQYREQLMLPFNLSMGVMTFFISVGIGASLGR------QFQLDPVMSGLL 117 Query: 123 ALMAFVMTVPQIIFDGGMMKTVTSLKEGAVIADGWAMGNVVARF-GTTGIFTAIIMAIVT 181 A MAF++ +A +A G + ++ GIFTA+I AI + Sbjct: 118 AFMAFLL-----------------------VAAPYADGKISTQYLSGQGIFTALITAIYS 154 Query: 182 VLIYRMCVKHNWVIKMPEAVPEGVSRGFTALVPGFVVAFVVIFINGLLVAM-GTDIFKVI 240 +Y ++N I++P+ VP GV+R F L+P VV + +N + A G + + I Sbjct: 155 TRVYAWLKQNNITIRLPKEVPTGVARSFEILIPVLVVIATLHPLNLFIEAQTGMILPQAI 214 Query: 241 AIPFGFVSNLTNSWIGLMIIYLLTQLLWIVGIHGANIVFAFVSPIALANMAEN----AAG 296 + + ++S +++ L+ Q+ W GIHG+ IV ++P +AN++ N AAG Sbjct: 215 MHLLEPLVSASDSLPAILLSVLMCQIFWFAGIHGSLIVTGIMNPFWMANLSANQAALAAG 274 Query: 297 G---HFAVAGEFSNMFVIAGGSGATLGLCLYIAFASKSEQLKAIGRASVVPALFNINEPL 353 H + G F + +++ GG G+TL L ++ S+ L+ IG+ +VP+ FNINEP+ Sbjct: 275 AALPHVYLQG-FWDHYLLIGGVGSTLPLA-FLLLRSRVTHLRTIGKMGIVPSFFNINEPI 332 Query: 354 IFGLPIIYNPALAIPFILAPMVTATIYYVANSLNFIKPIIAQVPWPTPVGIGA-FLGTAD 412 +FG PII NP + IPF+ PM+ A + Y A L ++ +++ PW TP IGA + Sbjct: 333 LFGAPIIMNPMMFIPFVFVPMINAVLAYGATRLGWLSQVVSLTPWTTPAPIGASWAANWT 392 Query: 413 LRAVLVALVCAFAAFLVYLPFIRVYDQKLVKEE 445 L V++ L+C + L+YLPF+R Y++ L+K E Sbjct: 393 LSPVVMCLICMVMSALIYLPFLRAYERSLMKTE 425 Lambda K H 0.329 0.142 0.426 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: 572 Number of extensions: 25 Number of successful extensions: 6 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: 448 Length of database: 441 Length adjustment: 32 Effective length of query: 416 Effective length of database: 409 Effective search space: 170144 Effective search space used: 170144 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: 51 (24.3 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