GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Pseudomonas litoralis 2SM5

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  123 bits (308), Expect = 9e-33
 Identities = 82/243 (33%), Positives = 140/243 (57%), Gaps = 17/243 (6%)

Query: 65  AVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMTID 124
           AV+DV+  + +GEI  ++G SGSGK+TL+  IL     P +   G+V+ +G +I ++   
Sbjct: 35  AVDDVTLTINRGEIFALLGGSGSGKSTLLR-ILAGFETPSE---GRVLLDGQNITALPPH 90

Query: 125 EFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVGLD 184
           +      + I+ + Q+   AL P + + +      +   +     + ER +E+LKLV + 
Sbjct: 91  K------RPINMMFQSY--ALFPHMTVEQNIAF-GLKQDKLSNTEISERVAEMLKLVHM- 140

Query: 185 PARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALD-MLNQELLLKLIKNINQ 243
            A+  K  P QLSGG +QRV +A SL   PKL+L+DEP  ALD  L  ++ L+L++ I +
Sbjct: 141 -AKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVE-IIE 198

Query: 244 EMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIPSLK 303
            +GVT + VTHD      +A R+ +M +G++++ G   +I +SP+N + +  V S+   +
Sbjct: 199 RVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGSVNIFE 258

Query: 304 GEV 306
           GE+
Sbjct: 259 GEI 261


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: 9
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: 378
Length adjustment: 30
Effective length of query: 332
Effective length of database: 348
Effective search space:   115536
Effective search space used:   115536
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 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