GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treC in Echinicola vietnamensis KMM 6221, DSM 17526

Align trehalose-6-P hydrolase (TreA;BlTreA;BLi00797;BL03069) (EC 3.2.1.93) (characterized)
to candidate Echvi_2850 Echvi_2850 Glycosidases

Query= CAZy::AAU39732.1
         (562 letters)



>FitnessBrowser__Cola:Echvi_2850
          Length = 519

 Score =  243 bits (621), Expect = 1e-68
 Identities = 172/542 (31%), Positives = 251/542 (46%), Gaps = 90/542 (16%)

Query: 5   ENPWWKKAVVYQIYPKSFKDTTGNGVGDIRGIIEKLDYIKELACDVIWLTPIYQSPQNDN 64
           +N W +  + Y+I+ +SF DT G+G+GDI G+ +KLD+++EL  + IW  P+  SP    
Sbjct: 31  KNYWPEAGITYEIFIQSFYDTDGDGIGDINGVTKKLDHVQELGANAIWFMPLMPSPSYHK 90

Query: 65  GYDISDYYSIHEEYGTMADFEELLEEAHKRGIKVIMDLVVNHTSTEHRWFKEAASGKENL 124
            YD++DY +IH +YGTM DF+++L+EAHKR IKV++D+++NHTS EH WF+EA  G++N 
Sbjct: 91  -YDVTDYKAIHPDYGTMDDFKQMLDEAHKRDIKVVIDMIINHTSDEHPWFQEAKKGRDNP 149

Query: 125 YRDFYIWK---------DMKPNGAPPTNWESKFGGSAWEFHAESGQYYLHLYDVTQADLN 175
           YRD+Y+W          D K       N         W    +   YY   +     DLN
Sbjct: 150 YRDYYVWAQYDTIQDYLDKKVVTLDSDNIRQ------WHDPGQGDDYYYGFFTGDMPDLN 203

Query: 176 WENEAVRKKVYEMMHFWF-EKGIDGFRLDVINVISKDQRFPDDDEGDGRRFYTDGPRVHE 234
           ++N  VR+++YE+  +W  E G+DGFRLD    I     +PDD   D   F+       E
Sbjct: 204 FDNPKVREEIYEIGRYWLAEVGVDGFRLDAAKHI-----YPDDRAADSHEFW------EE 252

Query: 235 FLNEMNREVFSKYDSMTVGEMSSTTIADCIRYTNPESRELDMVFNF---HHLKADYPNGE 291
           F  EM +    K D   VGE     + D      P    L  +FNF   + L   Y   +
Sbjct: 253 FRAEMEK---VKPDVYLVGE-----VYDMKEVVAPYLTGLRALFNFDFHYTLLEAYKKED 304

Query: 292 KWALA--DFDFLKLKKILSEWQTEMNKGGGWNALFWCNHDQPRIVSRYGDDGKYRKKSAK 349
              LA    D L     +++           +A    NHDQPR+++  G      K++  
Sbjct: 305 GMLLAKKQHDILAFYNGITD--------DFIDATISSNHDQPRLLNELGKSKDKLKQAIA 356

Query: 350 MLATAIHMLQGTPYIYQGEELGMTNPKFDDISLYRDVESLNMYRILKEAGKPEAEIIEIL 409
           +L T    + G PYIY GEE+GM   K D         ++    +   A + E     I 
Sbjct: 357 ILMT----MPGAPYIYYGEEIGMLGKKPD--------PNIREPFLWDVAEQDEGRTKWIT 404

Query: 410 KAKSRDNSRTPVQWNGEENAGFTAGTPWIPVPDNYKEINAEEALNDPDSIFYHYKKLNEL 469
            A S DN+ TP+    E                            D DS F HYK++ +L
Sbjct: 405 PAFSTDNTVTPLAIQKE----------------------------DADSYFNHYKRVIQL 436

Query: 470 RKEFDIITTGDYQLILED-DQELYAYLRNGADEKLLVINNFYGKETEFQLPDDIDIEGYD 528
           R     +  G  +L  E   + + AY R   +++L V +N   K  E  LP   D E Y 
Sbjct: 437 RNTHPALAIGSLELPAEKYPKAVMAYQRKTGEQELYVFHNLGKKSVEIPLPQGFDREVYH 496

Query: 529 AK 530
            K
Sbjct: 497 LK 498


Lambda     K      H
   0.317    0.137    0.424 

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: 983
Number of extensions: 55
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: 562
Length of database: 519
Length adjustment: 35
Effective length of query: 527
Effective length of database: 484
Effective search space:   255068
Effective search space used:   255068
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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