GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Methanobacterium veterum MK4

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_048081181.1 EJ01_RS06730 ABC transporter ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_000745485.1:WP_048081181.1
          Length = 566

 Score =  128 bits (321), Expect = 4e-34
 Identities = 91/253 (35%), Positives = 146/253 (57%), Gaps = 13/253 (5%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           +++V NL+  Y   N   IKA+ND++  VE+GEI+GIIG SGSGKT+L+  ILR + P  
Sbjct: 1   MIKVENLSKTYKIENGGEIKALNDINLNVEEGEIVGIIGMSGSGKTSLLR-ILRGVEP-- 57

Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQAS-----QNAL-NPVLPISEIFY-H 157
              SGK+  +G+++   +   +   L K  +   Q S     + AL N V  ++   Y  
Sbjct: 58  -FDSGKITLDGIEVSPDSSPYYFAKLKKATAIHLQRSFGLWGETALQNVVRKLAGAKYGD 116

Query: 158 EAISHGEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217
           E++   +       ++A E+L++VGL     +  +   LSGG KQR+++A  L   PK++
Sbjct: 117 ESLQDVDDAVAEFGDQAKEILEIVGL--GHKINHFAPVLSGGEKQRLIMARQLAKKPKVL 174

Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277
           L+DEP +      ++ +L  IKNIN+E+GVTIV V+H       +++RL++M  G +++E
Sbjct: 175 LLDEPATMSCPRTKQEILDAIKNINKELGVTIVLVSHLPEVHRYLSDRLVLMENGEIIDE 234

Query: 278 GKTEEIIKSPLNP 290
           G TEEII   + P
Sbjct: 235 GSTEEIITKFMEP 247



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 73/292 (25%), Positives = 136/292 (46%), Gaps = 57/292 (19%)

Query: 45  ILEVHNLN---VIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIR 101
           I++V++L+    +   GN+  IK   DV+F ++KGEI+ +IG SG+GKT L+  I     
Sbjct: 264 IIKVNDLDKRFFLLKGGNTLQIK---DVNFDIKKGEIVSLIGPSGAGKTVLLRMIAGLDA 320

Query: 102 PPGKIISGKVIFNGMDIFSMTIDEF---RKLLW-----------------------KDIS 135
           P    I  K+  N +D+  + ++     RKL +                       KD  
Sbjct: 321 PDSGSILFKLDDNWVDMQDLGLERMNVRRKLGFMHQEFALTHYATIKDQIAARLGVKDEH 380

Query: 136 YVPQASQNA---------LNPVLPISEIFYHEAISHGEADKKR---------------VI 171
            + +A + A         L+ +  ++++  HEA +  E  + +               V 
Sbjct: 381 VISKARKTAEELGISDKILDVLYQLTDLPEHEAKARLEKIELKPDILDLLFPKFPDTEVR 440

Query: 172 ERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQ 231
           + A  + K + L P  +L    ++LSGG K R  +AL L   P ++++DEP   LD +  
Sbjct: 441 KYAEPIFKALDL-PLDILDRCSYELSGGQKVRATLALVLTSKPDVLILDEPFGDLDPITL 499

Query: 232 ELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283
            ++   +K IN+E   TI+ V+H +  I ++  R +++  G ++ +G  +++
Sbjct: 500 RIVSNSLKRINKEFNTTILMVSHHVDFIREVTTRAIMIEDGKLVGDGDPQKL 551


Lambda     K      H
   0.319    0.138    0.391 

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: 441
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 362
Length of database: 566
Length adjustment: 33
Effective length of query: 329
Effective length of database: 533
Effective search space:   175357
Effective search space used:   175357
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: 51 (24.3 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