GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Lactobacillus shenzhenensis LY-73

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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