Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 337 bits (865), Expect = 8e-97 Identities = 226/631 (35%), Positives = 337/631 (53%), Gaps = 48/631 (7%) Query: 1 MKIQDLLNKDVMLLDLQATTKEAAIDEMVSKLVEQGIVTDFDTFKAGIMNREVQTSTGLG 60 M + L ++D + L+ + T++E AI + +L G ++ + F + RE T LG Sbjct: 21 MNLTTLTHRDALCLNARFTSREEAIHALTQRLAALGKISSTEQFLEEVYRRESLGPTALG 80 Query: 61 DGIAMPHSKNKAVKEATVLFAKSNKGVDYEALDG-EPVDLFFMIAAPDG-ANDTHLAALA 118 +G+A+PH K AVKEA A ++ + +E +DG E VDL ++A P A TH+ L Sbjct: 81 EGLAVPHGKTAAVKEAAFAVATLSEPLQWEGVDGPEAVDLVVLLAIPPNEAGTTHMQLLT 140 Query: 119 ELSQYLLKDGFADKLRQVTNPDDVINLFNATEEEKKEATPAAPVADSHDFLVAVTACTTG 178 L+ L D +++ T PD++++ ++K P+A +++ +V VTAC G Sbjct: 141 ALTTRLADDEIRARIQSATTPDELLSAL----DDKGGTQPSASFSNAPT-IVCVTACPAG 195 Query: 179 IAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAV-EMDR 237 IAHTYMA E L+K ++GV + VE GA+G+ +LTAD + A I AA+ A+ E +R Sbjct: 196 IAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFAAEVAIKESER 255 Query: 238 FNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHL 297 FNG P +S PVAE I+ E LI L K +D + + + K+ + + + L Sbjct: 256 FNGIPALSVPVAEPIRHAEALIQQALTLKR----SDETRTVQQDTQPVKS-VKTELKQAL 310 Query: 298 MSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGF-M 356 +SG+S +P ++ GG ++A++ L+ Q G+ + ++ ++G G M Sbjct: 311 LSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDL----FNEENSWLWMYRKLGGGLLGILM 366 Query: 357 IPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLG 416 +PV AAY AYS+A+KP L GF AG LA N + SGFLG Sbjct: 367 VPVLAAYTAYSLADKPALAPGFAAG------LAANMIG-----------------SGFLG 403 Query: 417 ALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-NIPMAAINT 475 A+ GG +AG ++ +K L + G + LYP+LG L G LMLFV P+A IN Sbjct: 404 AVVGGLIAGYLMRWVKNHLRLSSK-FNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINN 462 Query: 476 ALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMAS 535 +L +L LSG +A+LLG I+G M + D+GGP NKAAY F + G + AS Sbjct: 463 SLTAWLNGLSGSNALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGVY--GPYAIFAS 520 Query: 536 VMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPS 595 V MV V +T+L F + E + G + ++GL+ ITEGAIP DP R I S Sbjct: 521 VK---MVSAFTVTASTMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGS 577 Query: 596 FIVGSAVTGALVGLSGIKLMAPHGGIFVIAL 626 F++GS VTGA+VG I L P GIF + L Sbjct: 578 FVLGSMVTGAIVGAMNIGLSTPGAGIFSLFL 608 Lambda K H 0.320 0.137 0.381 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: 934 Number of extensions: 41 Number of successful extensions: 10 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: 655 Length of database: 658 Length adjustment: 38 Effective length of query: 617 Effective length of database: 620 Effective search space: 382540 Effective search space used: 382540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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