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_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  153 bits (386), Expect = 6e-42
 Identities = 90/224 (40%), Positives = 124/224 (55%), Gaps = 9/224 (4%)

Query: 4   LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63
           +  D+V K   G  +L DVSL I  G FV  VG SG GK+TLL+ I  L  I  G + I+
Sbjct: 2   ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61

Query: 64  GRRV--NDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQIL 121
           GR V    +    R +G VFQ   L+PHMSV +N++   +L    +    ER  + A++L
Sbjct: 62  GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPR---EERAARVAELL 118

Query: 122 QLDKL----LQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIA 177
            L  L     +R+P +LSGGQ QRV   RA+A  P I+L DEP   LD   R ++     
Sbjct: 119 DLVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYR 178

Query: 178 RLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPREL 221
            LH+ +G T + VTHD  EA+ LAD+++V+  GR+     PR L
Sbjct: 179 ALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRAL 222



 Score = 23.5 bits (49), Expect = 0.007
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 207 LNGGRVEQVGSPRELYERPA 226
           L+GG+ ++VG  R L  RPA
Sbjct: 135 LSGGQAQRVGFARALAARPA 154


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: 216
Number of extensions: 7
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 381
Length of database: 252
Length adjustment: 27
Effective length of query: 354
Effective length of database: 225
Effective search space:    79650
Effective search space used:    79650
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.

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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