GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Shewanella sp. ANA-3

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 7025499 Shewana3_2653 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__ANA3:7025499
          Length = 335

 Score =  160 bits (405), Expect = 5e-44
 Identities = 100/321 (31%), Positives = 175/321 (54%), Gaps = 12/321 (3%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           +L+V NL +  D  + R+ +A+  VS  +  GEI G++GESGSG++ L  AIL    P  
Sbjct: 3   LLDVRNLTIELDTPHGRV-RALEKVSLTLNAGEIHGLVGESGSGRSLLARAILGIPGPNW 61

Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164
            I + +++++G ++ +MT  E R L+  D++ + Q    +L+P   +          + +
Sbjct: 62  TITADRMMWDGNNLMAMTSKERRNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMPKNPK 121

Query: 165 A----DKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILM 219
           A      K     A + L  VG+ +P +V+  Y ++LS G  Q+VMIA+++   P+L++ 
Sbjct: 122 AYFWQKHKHAKLTAQKWLHKVGIKNPQKVMLSYAWELSEGECQKVMIAMAIANQPRLLIA 181

Query: 220 DEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGK 279
           DEPT+++++  Q  + +L+  +NQ   V+I+ ++H++  +AQ  + L V+Y G VME G 
Sbjct: 182 DEPTNSMELSTQAQIFRLLSQLNQLQNVSILIISHELETLAQWCDHLSVLYCGQVMESGP 241

Query: 280 TEEIIKSPLNPYTSLLVSSIPSLKG----EVKVINVPLDEP-LVSKEKGCPFLARCSKAF 334
           TEE+I  P +PYT  L+ ++P   G    +  +  +P   P L     GC    RC +A 
Sbjct: 242 TEELINQPYHPYTKALLDNMPDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLGPRCPEAQ 301

Query: 335 GRCKEELPEIRLVYDRKVRCH 355
            +C  + P +  + DR   CH
Sbjct: 302 KKCVNQ-PSLSHLRDRYFACH 321


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: 274
Number of extensions: 15
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: 335
Length adjustment: 29
Effective length of query: 333
Effective length of database: 306
Effective search space:   101898
Effective search space used:   101898
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