GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Rhizorhabdus wittichii RW1

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  121 bits (303), Expect = 2e-32
 Identities = 79/199 (39%), Positives = 107/199 (53%), Gaps = 8/199 (4%)

Query: 24  LQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEG-PGAER--- 79
           L  V   +    FV ++G SG GK+TLL+ +  L    +G + ++G  V   P AE    
Sbjct: 17  LDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELRRR 76

Query: 80  -GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRG-FEQHFPKQLS 137
            G VFQ   LFP +++ +N+    R +G+P  ++  R A  +  V L   F +  P QLS
Sbjct: 77  IGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAERRPAQLS 136

Query: 138 GGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDID 197
           GG  QR   ARALA  P I+LMDEPFGALD  TR  +      + EA   T L VTHD+ 
Sbjct: 137 GGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVTHDMA 196

Query: 198 EAIFMANRVAVFSARPGRI 216
           EA+ +A+RV V     GRI
Sbjct: 197 EALLLADRVIVIG--EGRI 213


Lambda     K      H
   0.322    0.136    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: 148
Number of extensions: 12
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: 259
Length of database: 252
Length adjustment: 24
Effective length of query: 235
Effective length of database: 228
Effective search space:    53580
Effective search space used:    53580
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 (21.9 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