Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_022529710.1 L248_RS08240 PTS transporter subunit EIIA
Query= TCDB::Q1LZ59 (655 letters) >NCBI__GCF_000469325.1:WP_022529710.1 Length = 664 Score = 614 bits (1584), Expect = e-180 Identities = 337/677 (49%), Positives = 451/677 (66%), Gaps = 45/677 (6%) Query: 1 MKIQDLLNKDVMLLDLQATTKEAAIDEMVSKLVEQGIVTDFDTFKAGIMNREVQTSTGLG 60 MKIQDLL KD M++DL+ATTKEAAIDEM+ + + G+++D +K I+ RE +++TG+G Sbjct: 1 MKIQDLLIKDAMIMDLKATTKEAAIDEMIDRYAQVGVISDKADYKKHILAREAESTTGIG 60 Query: 61 DGIAMPHSKNKAVKEATVLFAKSNKGVDYEALDGEPVDLFFMIAAPDGANDTHLAALAEL 120 DGIAMPH+K +VK+A VLFAKS++GVD+ ALDG+PV LFFMIAAP GAN+ HL ALA L Sbjct: 61 DGIAMPHAKTDSVKKAAVLFAKSSQGVDFNALDGQPVHLFFMIAAPAGANNEHLQALATL 120 Query: 121 SQYLLKDGFADKLRQVTNPDDVINLFNATEEEKKEATPAAPVADS--------------- 165 S L+ L++ PD+V++LF+A EE KKEA A D+ Sbjct: 121 SSLLINPSLVASLKKADTPDEVLSLFSAAEE-KKEAEDAQEEKDAAATQAAVGNANAAQE 179 Query: 166 ------HDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDI 219 ++VAVTAC TGIAHTYMAE ALK++A +MGV IKVETNG+ G+ ++LTADDI Sbjct: 180 PAGAIKKPYVVAVTACPTGIAHTYMAEAALKEEAKKMGVAIKVETNGSEGIKHRLTADDI 239 Query: 220 KRAKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSS 279 RA GVIIAADK VEM+RF GK LI+RPV +GI KP ELI L K + + +S Sbjct: 240 SRATGVIIAADKKVEMNRFAGKHLINRPVIDGINKPHELIEDTLAEKGPIFQGNGEAAAS 299 Query: 280 EASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYH 339 ++ SE L Y LM+G+S MLPFV+GGGI++ALSFL+++ GV S+ Sbjct: 300 DSDVSESPSLARQAYASLMNGISNMLPFVVGGGIIMALSFLLERIPGVGAKSI------- 352 Query: 340 EIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFG 399 I N +G+AAFGF++PV AAYIA +I ++P L+ GFVAG MA + F+ + Sbjct: 353 -IFTFTNGLGSAAFGFLVPVLAAYIAEAIGDRPALLPGFVAGWMA-SNTGFSVI------ 404 Query: 400 EKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVT 459 AS G+ +GFLG L GGFLAG +ILVLKK +P+SL+G+K + ++P+L +L Sbjct: 405 -----ASKNGV-AGFLGGLVGGFLAGFIILVLKKWFKNLPKSLDGLKPVFIFPILSLLAI 458 Query: 460 GFLMLF-VNIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTS 518 G +M F +N AIN AL +L L + +L+G I+GGMMAIDMGGPFNKAAYVF Sbjct: 459 GLIMYFAINPVFTAINLALIGWLEGLGTTNVILVGTILGGMMAIDMGGPFNKAAYVFSIG 518 Query: 519 TLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFIT 578 ++ G MA+VMAGGMVPPLA+ +AT ++ K+T E +GL++ ++GLSFIT Sbjct: 519 VFMSSPHQTDGR-WMAAVMAGGMVPPLAIALATTIWPKKWTPAERTSGLSDYLLGLSFIT 577 Query: 579 EGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIALTSNPLLYLLYIA 638 EGAIPF A DP R I S I+G+A+ G L G+ + APHGGIF L + PL ++L + Sbjct: 578 EGAIPFAAADPLRVITSSIIGAAIAGGLTQFMGVNVPAPHGGIFAALLANKPLQFILAVV 637 Query: 639 VGAVIAGILFGSLRKVR 655 VG+VI+G++ G +K R Sbjct: 638 VGSVISGVILGLWKKER 654 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: 1169 Number of extensions: 57 Number of successful extensions: 7 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: 664 Length adjustment: 38 Effective length of query: 617 Effective length of database: 626 Effective search space: 386242 Effective search space used: 386242 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 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