GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Sulfurivirga caldicuralii DSM 17737

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  117 bits (292), Expect = 3e-31
 Identities = 72/203 (35%), Positives = 117/203 (57%), Gaps = 7/203 (3%)

Query: 37  VLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELTSDLKNIDKV 96
           VL+ ++L +HR ER+ I G SGSGKST++  +  L+    G++++ G +  S L    + 
Sbjct: 24  VLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLG-QPFSKLGEAARG 82

Query: 97  R---SEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKIPEQAQK 153
           R     +G V+Q  +L P LT  EN+ + P+ +R+  +  A + A+  L+ V +  +   
Sbjct: 83  RLRNRHMGFVYQFHHLLPELTAEENVMM-PLLIRRESEATARDKALALLDAVGLSRRTAH 141

Query: 154 YPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQLAEE-GMTMLC 212
            P +LSGG++QRVA+AR+L  +P  +L DEPT  LD    ++VL  M  L +  G  +L 
Sbjct: 142 KPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTALLV 201

Query: 213 VTHEMGFAQAVANRVIFMADGQI 235
           VTH++  A A  +R + + DG I
Sbjct: 202 VTHDVNIA-ARMDRTLTLRDGMI 223


Lambda     K      H
   0.320    0.134    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: 143
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: 263
Length of database: 227
Length adjustment: 24
Effective length of query: 239
Effective length of database: 203
Effective search space:    48517
Effective search space used:    48517
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: 46 (22.3 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