Align Trehalose permease IIC protein (characterized, see rationale)
to candidate 17782 b3722 fused beta-glucoside-specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= uniprot:A0A1N7UR85 (480 letters) >FitnessBrowser__Keio:17782 Length = 625 Score = 220 bits (560), Expect = 1e-61 Identities = 141/465 (30%), Positives = 241/465 (51%), Gaps = 29/465 (6%) Query: 8 IAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTGGLFQVVI 67 +AR+I+ +GG+DN+ HC TRLR LKD S + L + + +GG FQVVI Sbjct: 4 LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63 Query: 68 GPGEVEKVYAALREQTGLAAATIADVKKKGADKTNAMQRLVRVFSDVFMPILPALIIAGL 127 G V V+ A+ GL A + DK N + R V V S +F P++ + G+ Sbjct: 64 G-NHVADVFLAVNSVAGLDEK--AQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGI 120 Query: 128 LMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSAAKRFGGS 187 L G M A + + T G + ++ ++ F F P ++G++A KRFGG+ Sbjct: 121 LKG----MLALALTFQWTT------EQSGTYLILFSASDALFWFFPIILGYTAGKRFGGN 170 Query: 188 EILGIVLGLMLVHPDLLNAWNYGKAV--AGLDGQSLPYFDIFGWFKIEKVGYQGQILPIL 245 +V+G LVHP +L A+ G+ GLD +P + + Y ++PI+ Sbjct: 171 PFTAMVIGGALVHPLILTAFENGQKADALGLDFLGIP---------VTLLNYSSSVIPII 221 Query: 246 MAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGILITEGVVTL 305 +A++ S++E+ L A +P+AI+ P+ ++V + ++GP++ + LI G + L Sbjct: 222 FSAWLCSILERRLNAWLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWL 281 Query: 306 FDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQGSAAL 365 + P GA+ G + V+ G+H + + + + G + P+++ + +AQ AAL Sbjct: 282 YQAVPAFAGAVMGGFWQIFVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAAL 341 Query: 366 AVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALVGSALGSIFLALNK 425 VF R+A+ K +A ++A+++ FGITEPA++GVNL K+PF A + ALG+ + + Sbjct: 342 GVFLCERDAQKKVVAGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQ 401 Query: 426 VQASAIGVGGLPGFISIVPQ-----SIAVFVIGMVIAMVVPFVLT 465 + + G+ + F+ +P ++ VIG VIA+ FV T Sbjct: 402 TKVYSFGLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAFVGT 446 Lambda K H 0.325 0.141 0.412 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: 761 Number of extensions: 42 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: 480 Length of database: 625 Length adjustment: 36 Effective length of query: 444 Effective length of database: 589 Effective search space: 261516 Effective search space used: 261516 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 (21.6 bits) S2: 53 (25.0 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