GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Phaeacidiphilus oryzae TH49

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

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



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  223 bits (567), Expect = 8e-63
 Identities = 127/323 (39%), Positives = 187/323 (57%), Gaps = 25/323 (7%)

Query: 4   IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63
           +++  + K +G+  A+  ++L I  G F   +G SGCGK+T LR ++GLE  ++GRI +G
Sbjct: 19  LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78

Query: 64  GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123
            +DVT  +P  R +  VFQ+YAL+PH+ + EN+ FG++  G      K+ + +   +++L
Sbjct: 79  DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRSV--KKPVEDMLDLVEL 136

Query: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183
                RKP QLSGGQ+QR+A+ RA++  P V L DEPL  LD KLR QM++EL+ +  ++
Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196

Query: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIG-----SPA 238
           G T ++VTHDQ EAMTMAD I V+N GRIEQ+GSP +LY  PN+ FVA F+G     +  
Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGT 256

Query: 239 MNVFSSD---VGLQDISLDASAA---------FVGCRPEHIEI------VPDGDGHIAAT 280
           +   S D   V     SL   AA          +G RPE + I      VP G  H+   
Sbjct: 257 VESVSGDVVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLTGK 316

Query: 281 VHVKERLGGESLLYLGLKGGGQI 303
           V     +G  +   + L  G ++
Sbjct: 317 VTDASFIGVSTQYLVELPSGEEL 339


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: 315
Number of extensions: 13
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: 338
Length of database: 386
Length adjustment: 29
Effective length of query: 309
Effective length of database: 357
Effective search space:   110313
Effective search space used:   110313
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 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