GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Dechlorosoma suillum PS

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Dsui_0415 Dsui_0415 oligopeptide/dipeptide ABC transporter, ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__PS:Dsui_0415
          Length = 326

 Score =  172 bits (437), Expect = 9e-48
 Identities = 103/313 (32%), Positives = 171/313 (54%), Gaps = 5/313 (1%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           ++ + +L V ++   +R   A+N VS  + +GE+LG++GESGSGK+  +  +LR      
Sbjct: 5   LVSIQDLTVQFN--GARRASALNQVSLELGQGEVLGLLGESGSGKSVTLRTLLRLHPERH 62

Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164
              +G++  +G D+ ++   E  +     +S V Q    A +PV  I +        H  
Sbjct: 63  TRTAGRIRVDGQDVLALRGRELDRYRGGTVSMVFQEPGLAFDPVYTIGQQISEAVRVHEG 122

Query: 165 ADKKRVIERASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223
            D+     RA  +L+ V +  AR     YP +LSGGM+QR MIAL+L   PKL+L DEPT
Sbjct: 123 VDQATAAARALAMLERVQIPQARRRFDAYPHELSGGMRQRAMIALALACKPKLLLADEPT 182

Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283
           +ALD   Q  +L L++ + +E G+++++VTHDI    ++A+R+ VMY G ++E+G   ++
Sbjct: 183 TALDATVQIQILLLLRELQRETGMSVIFVTHDIGAAVEVADRIAVMYAGRIVEQGPVGQL 242

Query: 284 IKSPLNPYT-SLLVSSIPSLKGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEEL 341
           ++ P +PYT  LL +++        +  +P   P L +   GC F  RCS A  RC  ++
Sbjct: 243 VRQPCHPYTRGLLAATVGHEHRGRPLEAIPGSPPDLAALPPGCSFAPRCSHASERCHRDI 302

Query: 342 PEIRLVYDRKVRC 354
           P +     R + C
Sbjct: 303 PPLEQQGARTLAC 315


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: 225
Number of extensions: 6
Number of successful extensions: 4
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: 326
Length adjustment: 29
Effective length of query: 333
Effective length of database: 297
Effective search space:    98901
Effective search space used:    98901
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 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