GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Sulfurivirga caldicuralii DSM 17737

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= reanno::Smeli:SMc02121
         (258 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  110 bits (274), Expect = 3e-29
 Identities = 72/224 (32%), Positives = 119/224 (53%), Gaps = 17/224 (7%)

Query: 19  IEITNMNKWYGD----FHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGK 74
           +E  N+ K Y D      VL+ ++L + R ER+ + G SGSGKST++  +  L+    G+
Sbjct: 6   LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65

Query: 75  IVVDGIELTNDLKKIDEV------RREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKK 128
           +++ G        K+ E        R +G V+Q  +L P LT  EN  + P+ +R+  + 
Sbjct: 66  VLLLG----QPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEEN-VMMPLLIRRESEA 120

Query: 129 EAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEM 188
            A   A+  L+ V +  +    P +LSGG++QRVA+AR+L   P  +L DEPT  LD   
Sbjct: 121 TARDKALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRS 180

Query: 189 VKEVLDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQI 231
            ++VL  M  L +  G  ++ VTH++  A ++ +R + +  G I
Sbjct: 181 AEQVLSLMDDLNQRFGTALLVVTHDVNIAARM-DRTLTLRDGMI 223


Lambda     K      H
   0.322    0.136    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: 133
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: 258
Length of database: 227
Length adjustment: 23
Effective length of query: 235
Effective length of database: 204
Effective search space:    47940
Effective search space used:    47940
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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