GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Rhizorhabdus wittichii RW1

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  154 bits (388), Expect = 3e-42
 Identities = 87/222 (39%), Positives = 129/222 (58%), Gaps = 6/222 (2%)

Query: 9   INKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVT 68
           + K+YG   AL +++LD+  GE +V  GPSG GKSTL+R + GLE    G I IG  +V 
Sbjct: 7   VGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVR 66

Query: 69  ----TVEPADRDLAMVFQSYALYPHMTVRENMEFG-MKVNGFEPDLRKERIAEAARVLQL 123
                ++     + MVFQ + L+PH+T+ EN     MKV G   D  +    E    +++
Sbjct: 67  PDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRI 126

Query: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183
            D  D+ P QLSGGQ+QR AI RA+   P + LFDEP S LDA++  ++   ++ L  + 
Sbjct: 127 ADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE- 185

Query: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKP 225
           G TM+ VTH+   A  +AD+I+ ++ G+I + GSP D +  P
Sbjct: 186 GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227


Lambda     K      H
   0.320    0.139    0.396 

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: 222
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: 338
Length of database: 241
Length adjustment: 26
Effective length of query: 312
Effective length of database: 215
Effective search space:    67080
Effective search space used:    67080
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: 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