GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Methanococcus aeolicus Nankai-3

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_052287789.1 MAEO_RS01500 ABC transporter ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_000017185.1:WP_052287789.1
          Length = 383

 Score =  106 bits (264), Expect = 1e-27
 Identities = 77/260 (29%), Positives = 132/260 (50%), Gaps = 28/260 (10%)

Query: 52  NVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKV 111
           NV    GN  I+   N+VS  V  GEI+ ++G SG GKTTL+  I   ++      SG +
Sbjct: 6   NVSKKMGNQNIL---NNVSLQVHDGEIMVLLGPSGCGKTTLLKIIAGLLKQD----SGNI 58

Query: 112 IFNGMDIFSMTIDEFRK-LLWKDISYVPQASQNALNPVLPISEIFYHEAISHG----EAD 166
           I N   I      E     +++D +  P  +               ++ I+ G    +  
Sbjct: 59  IINNNIINDFPSKERNMGFVFQDYALFPHKN--------------VYDNIAFGLKLRKVP 104

Query: 167 KKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSAL 226
           +  +  + +E+++++ +D  +  K+   QLSGG KQRV +A +L+++P ++L+DEP SAL
Sbjct: 105 ENEINIKINEIMEILEIDHLKDKKIP--QLSGGQKQRVALARALVIDPDVLLLDEPLSAL 162

Query: 227 DMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKS 286
           D + +E L + +K I   +GVT +YVTHD+     + + + VM  G + +  K ++I   
Sbjct: 163 DPILREKLREELKTILNTLGVTGIYVTHDLTEAMILGDNVAVMNNGIIQQIEKPDDIFYH 222

Query: 287 PLNPYTSLLVSSIPSLKGEV 306
           P N + +  V     LKG +
Sbjct: 223 PKNEFVAEFVGVKNILKGRI 242


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: 368
Number of extensions: 21
Number of successful extensions: 2
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: 362
Length of database: 383
Length adjustment: 30
Effective length of query: 332
Effective length of database: 353
Effective search space:   117196
Effective search space used:   117196
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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