GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Rhodanobacter denitrificans 2APBS1

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_000230695.2:WP_015448118.1
          Length = 255

 Score =  138 bits (347), Expect = 2e-37
 Identities = 85/233 (36%), Positives = 128/233 (54%), Gaps = 11/233 (4%)

Query: 11  KRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVL-- 68
           KRYG ++ L+ + +A  +G    L+GSSG GKST+L ++ GL  P  G + +  R +   
Sbjct: 19  KRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRS 78

Query: 69  GVHPKDRDIAMVFQSYALYPNLSVARNIGF-----GLEMRRVPQAEHDKAVRDTARLLQI 123
            V P  R +  V Q   L+P+L+   N+       G    R+ Q    +A +  A     
Sbjct: 79  DVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQ----RAEQLAALTHLP 134

Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183
             +L+R P++LSGGQRQRVA+ RAL+ +P   L DEPL  LD  +R E++ ELK++   L
Sbjct: 135 TGVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQL 194

Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGS 236
             TV+ VTHD  EA   A R+ ++R G + Q     ++ +RPA  +V  FV +
Sbjct: 195 GKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAA 247


Lambda     K      H
   0.320    0.136    0.385 

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: 212
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: 360
Length of database: 255
Length adjustment: 27
Effective length of query: 333
Effective length of database: 228
Effective search space:    75924
Effective search space used:    75924
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 Sep 24 2021. 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