GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Rhodanobacter denitrificans 2APBS1

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

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_000230695.2:WP_015448118.1
          Length = 255

 Score =  163 bits (412), Expect = 5e-45
 Identities = 91/229 (39%), Positives = 135/229 (58%), Gaps = 3/229 (1%)

Query: 11  KRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKV--N 68
           KRYG L+ +  + L        AL+G SG GKST LR++ GLE    G +E+ GR +  +
Sbjct: 19  KRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRS 78

Query: 69  DLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL-AHLL 127
           D+ P  R +  V Q   L+PH+T   N+    +  G   E I+ R  + AA+  L   +L
Sbjct: 79  DVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPTGVL 138

Query: 128 ERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATM 187
           ER P++LSGGQRQRVA+ RA++  PD  L DEPL  LD  +R +++ E+K++  ++  T+
Sbjct: 139 ERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLGKTV 198

Query: 188 IYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGS 236
           I VTHD  EA   ++R+V++R G + Q GT  D+  RPA  FV  F+ +
Sbjct: 199 IVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAA 247


Lambda     K      H
   0.320    0.137    0.397 

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: 240
Number of extensions: 9
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: 365
Length of database: 255
Length adjustment: 27
Effective length of query: 338
Effective length of database: 228
Effective search space:    77064
Effective search space used:    77064
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.

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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