GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Rhizorhabdus wittichii RW1

Align TreV, component of Trehalose porter (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  124 bits (311), Expect = 2e-33
 Identities = 76/230 (33%), Positives = 124/230 (53%), Gaps = 12/230 (5%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           + +  + K YG    +  ++  +  GE  VI GPSG GKSTL++ + G+E  D+G +I  
Sbjct: 2   IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEG-VIRI 60

Query: 63  GADITDKPPEKR-------NVAMVFQNYALYPNMSVRDNIAF-PLKMRGMKKEEIIERVE 114
           G D  +  P++R        V MVFQ++ L+P++++ +N A  P+K+RG+ ++       
Sbjct: 61  GED--EVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALAR 118

Query: 115 KAAKLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGE 174
           +  + + I++  DK   Q+SGGQQQR A+ARA+   P   L DEP S LDA +       
Sbjct: 119 ELLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDI 178

Query: 175 LKRIQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYP 224
           +K +  E   T + VTH+   A  +ADRI  +  G+  +   P+  +  P
Sbjct: 179 MKALATE-GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227


Lambda     K      H
   0.318    0.137    0.385 

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: 184
Number of extensions: 12
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: 324
Length of database: 241
Length adjustment: 26
Effective length of query: 298
Effective length of database: 215
Effective search space:    64070
Effective search space used:    64070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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