Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034283552.1 BA81_RS15550 PTS transporter subunit EIIC
Query= TCDB::P08722 (625 letters) >NCBI__GCF_000691165.1:WP_034283552.1 Length = 632 Score = 435 bits (1119), Expect = e-126 Identities = 248/632 (39%), Positives = 369/632 (58%), Gaps = 17/632 (2%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 +LA I+ VGG +N+VS CATRLR LK + E + PG+I VVE+GGQFQVV Sbjct: 9 KLAEDILEAVGGEENVVSAARCATRLRLVLKRSNPKAKEAVNAMPGVITVVENGGQFQVV 68 Query: 63 IGNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILK 122 IG HV +V+ +S+ L + ++ N++KG +LNR + +S +F P + ++AA GIL+ Sbjct: 69 IGQHVGEVYEHFSSLVQL-QPSEDDQVNENKGTVLNRVIATMSAVFAPFVYILAAAGILQ 127 Query: 123 GMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALV 182 G L L + ++GTY + S A F F PI + TA K F N + A+ ALV Sbjct: 128 GALILINLLFPSFSKTGTYEVFSFISWAPFTFLPIFIAITAAKHFKTNMYIAVACTAALV 187 Query: 183 HPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAI 242 P G+ A G+ FLGI ++ Y+SSV+P +F W+ S +ER LN + + Sbjct: 188 SPAWTEIA--GRVASGEGVTFLGIALSETVYTSSVLPPLFLVWILSYVERFLNKRIHEVV 245 Query: 243 KNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVM 302 K F P +C++V+ P+T LL+GPLST + IA GY L + VPA AGA++GGFWQ+ V+ Sbjct: 246 KPLFVPFICMVVMVPLTILLIGPLSTAGANGIANGYNVLAENVPALAGAIIGGFWQVLVI 305 Query: 303 FGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAALT 362 FG+HWG+ P+ + NF G D+ A++AQVGA LGV L R+ + + V SA +T Sbjct: 306 FGVHWGITPMVLANFEQYGRDSFQAYQTIAVIAQVGAVLGVILKARNRETRKVGVSAGIT 365 Query: 363 SLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSF-GLPSIFTFMQTIPS 421 LFGITEPA+YGV L K PF+ CISGA+GA + +++ GLP T + I S Sbjct: 366 GLFGITEPAIYGVTLRFKKPFIFGCISGAVGAIAASFFTPYYFAYAGLPGPLTIVNGISS 425 Query: 422 TGIDFTVWASVIGGVIAIGCAFVGTVMLHFI------TAKRQPAQGAPQEKTPEVITPP- 474 DF S+IG +I + A + V+L + T ++ + +++ E + Sbjct: 426 ---DFP--TSIIGILIGVAIALILPVVLIQMFGYGEDTVEQTAGATSDKDQVGEKMNASM 480 Query: 475 -EQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHA 533 + I +P+ G+++PL V D F+SG +GKG AI P+ ++ +P G + L T HA Sbjct: 481 NNEETIPAPLAGKVLPLSEVPDAVFSSGAMGKGFAIEPTDNKLYAPFDGSVVMLAPTKHA 540 Query: 534 IGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTT 593 IG+ S+ GVE+L+HVGIDTV LDG F+ H+ G KV GD L++FD AI G T Sbjct: 541 IGLRSEFGVELLVHVGIDTVSLDGSAFTLHIKEGSKVKKGDLLMTFDQEAIESKGLKTIT 600 Query: 594 PVLISNSDDFTDVLPHGTAQISAGEPLLSIIR 625 PV+I+N+ + DV+ + + + +++I++ Sbjct: 601 PVIITNTQAYEDVIVQEQSTCQSTDVMITIVK 632 Lambda K H 0.324 0.141 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: 1082 Number of extensions: 72 Number of successful extensions: 4 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: 625 Length of database: 632 Length adjustment: 38 Effective length of query: 587 Effective length of database: 594 Effective search space: 348678 Effective search space used: 348678 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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