GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Rhizorhabdus wittichii RW1

Align ABC transporter (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  145 bits (366), Expect = 1e-39
 Identities = 93/242 (38%), Positives = 139/242 (57%), Gaps = 18/242 (7%)

Query: 4   LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDS------ICG 57
           + +  V K  GG   LR+VSL++A GE +V  GPSG GKSTL+R I GL++        G
Sbjct: 2   IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIG 61

Query: 58  GDLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFG----LKLAKTDKTSLRER 113
            D +   RRV  L+     VGMVFQ + L+PH+++ +N +        LA+    +L   
Sbjct: 62  EDEVRPDRRV--LQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARE 119

Query: 114 VLKTAQIL-QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQM 172
           +L+  +I  Q DK     P +LSGGQ+QR A+ RA+A +P+I+LFDEP S LDA + V+ 
Sbjct: 120 LLERVRIADQADKY----PAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEM-VKE 174

Query: 173 RNEIARLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAG 232
             +I +     G TM+ VTH+   A  +AD+I+ ++ G++ + GSPR+ +  P       
Sbjct: 175 VLDIMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRA 234

Query: 233 FL 234
           FL
Sbjct: 235 FL 236


Lambda     K      H
   0.320    0.137    0.394 

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: 209
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: 381
Length of database: 241
Length adjustment: 27
Effective length of query: 354
Effective length of database: 214
Effective search space:    75756
Effective search space used:    75756
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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