GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Rhizorhabdus wittichii RW1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_012050591.1 SWIT_RS22335 ATP-binding cassette domain-containing protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_000016765.1:WP_012050591.1
          Length = 211

 Score =  122 bits (306), Expect = 8e-33
 Identities = 76/182 (41%), Positives = 106/182 (58%), Gaps = 9/182 (4%)

Query: 35  VGPSGCGKSTLLRVISGLEDATAGEISIGGQT----VTTTPPAKRGIAMVFQSYALYPHL 90
           +GPSG GK+++LR ++GLE   AG I + G+      T  PP +R +  VFQ   L PHL
Sbjct: 32  LGPSGSGKTSILRALAGLE-RIAGTIIVDGEVWQDGATFLPPERRRVGYVFQGAGLLPHL 90

Query: 91  SVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVR 150
           SV  N+A A   ER+      AR A  +R   +   LDRRP+ LSGG+ QR  I RA++ 
Sbjct: 91  SVAANLAYA---ERRAGPGRFARDAIVART-GIAPLLDRRPASLSGGEAQRAGIARALLG 146

Query: 151 EPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDG 210
           +P+L L DEPLS LD   R +    +  L  +++  + +VTHD  EA  LA + + LRDG
Sbjct: 147 QPRLLLLDEPLSALDTDARADLLDWLDDLLAEIAIPVFHVTHDHAEAARLAARTIRLRDG 206

Query: 211 RI 212
           R+
Sbjct: 207 RV 208


Lambda     K      H
   0.320    0.137    0.391 

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: 180
Number of extensions: 8
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: 331
Length of database: 211
Length adjustment: 25
Effective length of query: 306
Effective length of database: 186
Effective search space:    56916
Effective search space used:    56916
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