GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Rhizorhabdus wittichii RW1

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  136 bits (342), Expect = 7e-37
 Identities = 82/222 (36%), Positives = 122/222 (54%), Gaps = 9/222 (4%)

Query: 21  LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKD--RD 78
           L ++ L I+ G F+ LVG SG GK+TL+  I  L  I  G I ++  D++     +  R 
Sbjct: 17  LDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELRRR 76

Query: 79  IAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHL----LSRKPG 134
           I  VFQ   L+P MSV +N+A   +++ +P    +E  ARV++LL +  L      R+P 
Sbjct: 77  IGYVFQGIGLFPHMSVAENVALVPRLQGVPR---EERAARVAELLDLVALPADFAERRPA 133

Query: 135 QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTH 194
           QLSGGQ QRV   RALA RP I L DEP   LD   R E+    + +H+ +  T++ VTH
Sbjct: 134 QLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVTH 193

Query: 195 DQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236
           D  EA+ L D+V V+ +G I     P+ + +   +  + + I
Sbjct: 194 DMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEAMI 235


Lambda     K      H
   0.319    0.138    0.393 

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: 189
Number of extensions: 6
Number of successful extensions: 3
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: 386
Length of database: 252
Length adjustment: 27
Effective length of query: 359
Effective length of database: 225
Effective search space:    80775
Effective search space used:    80775
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 (21.7 bits)
S2: 48 (23.1 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