Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_007679744.1 BN137_RS02915 PTS beta-glucoside transporter subunit IIABC
Query= TCDB::P08722 (625 letters) >NCBI__GCF_000319285.1:WP_007679744.1 Length = 619 Score = 691 bits (1783), Expect = 0.0 Identities = 344/620 (55%), Positives = 455/620 (73%), Gaps = 9/620 (1%) Query: 4 LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63 LA+ I+A VGG +NI S++HCATRLRF+LKD+ KA A LK PG+IMVV SGGQFQVVI Sbjct: 6 LAQDILARVGGKENISSVIHCATRLRFRLKDDRKADAPGLKAHPGVIMVVVSGGQFQVVI 65 Query: 64 GNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILKG 123 GNHV DV+LAV AG+ + QA ++ +GNLL R + ++SGIFTP IG++AA+GILKG Sbjct: 66 GNHVHDVWLAVRREAGITDDGAQAEDDGPRGNLLARLIDIVSGIFTPFIGVLAASGILKG 125 Query: 124 MLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALVH 183 +LALA+ +W SGTY I F+ASDALF+FFP++LGYTAGK+FGGNPF M IGGAL H Sbjct: 126 LLALAVVCRWIDPASGTYKIWFAASDALFFFFPLVLGYTAGKKFGGNPFITMTIGGALTH 185 Query: 184 PLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAIK 243 P++++AFE Q+A AL FLG+PV NYSSSVIPII +AW+ LE++ N LP A+K Sbjct: 186 PVMISAFEASQQAGALADSFLGVPVIWFNYSSSVIPIILAAWVSCWLEKQGNRLLPCAMK 245 Query: 244 NFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVMF 303 NFFTPLLCL V P+TFL++GP++TW+S+++A GY ++Y P AGA G WQ+ V+F Sbjct: 246 NFFTPLLCLGVTVPLTFLVIGPVATWLSQMLANGYQFIYTFAPWLAGAATGALWQVCVIF 305 Query: 304 GLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAALTS 363 GLHWGLVPL +NN VLG+D+++P+L+PA+M QVGAAL VFL RDA++K++AGS+ Sbjct: 306 GLHWGLVPLMVNNIAVLGHDSLLPMLLPAVMGQVGAALAVFLRSRDARQKMLAGSSVTAG 365 Query: 364 LFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIPSTG 423 +FGITEPAVYGVNLP + PF+ C +GA+G I+G + T+VYSFG +IFT Q IP G Sbjct: 366 IFGITEPAVYGVNLPLRRPFIFGCAAGAVGGAIVGLSSTQVYSFGFANIFTIAQMIPPDG 425 Query: 424 IDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPEQGGICSPM 483 ++ T+W + G + A+ A G ++ + A GA + T P Q +P+ Sbjct: 426 VNATLWGGLFGTLSALVLA-CGLTLIAGLPA------GAKEANTGSQNVP--QNAALAPL 476 Query: 484 TGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVE 543 +G ++ L +V D TFASGLLG+G AI+PS +VR+P AG +ASLF T HAIG+ D+G+E Sbjct: 477 SGTVLALDNVPDPTFASGLLGQGAAIIPSDNQVRAPFAGVVASLFETRHAIGLAGDNGME 536 Query: 544 ILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNSDDF 603 +LIHVGIDTVKL+G+ F+AHV VGD+VN GD LI FD AI +AG+DLTTP++ISNSD + Sbjct: 537 LLIHVGIDTVKLEGQLFTAHVRVGDRVNPGDLLIEFDRQAIIDAGYDLTTPIIISNSDSY 596 Query: 604 TDVLPHGTAQISAGEPLLSI 623 V +SAG PLL++ Sbjct: 597 GAVTTVAATAVSAGMPLLTV 616 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: 1330 Number of extensions: 81 Number of successful extensions: 2 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: 619 Length adjustment: 37 Effective length of query: 588 Effective length of database: 582 Effective search space: 342216 Effective search space used: 342216 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