GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Pseudomonas fluorescens FW300-N1B4

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf1N1B4_1127 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127
          Length = 326

 Score =  171 bits (433), Expect = 3e-47
 Identities = 102/298 (34%), Positives = 163/298 (54%), Gaps = 13/298 (4%)

Query: 63  IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122
           ++A+N VSF +E G+ L ++GESG GK+TL  A+     P     SG +   G ++    
Sbjct: 27  VRALNGVSFELEAGKTLAVVGESGCGKSTLARALTLIEEPS----SGSLKIAGQEVAGAD 82

Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182
             + RK L KD+  V Q+   +LNP   + +      + +         E+   ++K VG
Sbjct: 83  KAQ-RKQLRKDVQMVFQSPYASLNPRQKVGDQLAEPLLINTNLSASERREKVQAMMKQVG 141

Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242
           L P    + YP   SGG +QR+ +A +++L PK+++ DEPTSALD+  Q  +L L  ++ 
Sbjct: 142 LRPEHYQR-YPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQVLNLFMDLQ 200

Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIPSL 302
           QE     V+++H++  +  +A+ ++VMY G  +E G  E+I   PL+PYT  L+S+ P++
Sbjct: 201 QEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGPKEDIYTRPLHPYTQALLSATPTI 260

Query: 303 -----KGEVKVINVPLDEPLVSKEKGCPFLARCSKAFGRCKEELPEIRLVYDRKVRCH 355
                K ++K++   L  PL +   GC F  RC  A  RC  E P +RLV  R+V CH
Sbjct: 261 HPDPTKPKIKIVG-ELPNPL-NPPSGCAFHKRCPYATDRCTTEEPLLRLVDTRQVACH 316


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: 267
Number of extensions: 10
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