GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Sulfurivirga caldicuralii DSM 17737

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= SwissProt::P54537
         (240 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  133 bits (335), Expect = 3e-36
 Identities = 81/203 (39%), Positives = 120/203 (59%), Gaps = 7/203 (3%)

Query: 16  VLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIKDTEITK---PKTNT 72
           VLK +S  +   E VA++G SGSGKST L  L  L++P  G + +     +K        
Sbjct: 24  VLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLGQPFSKLGEAARGR 83

Query: 73  LKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDLLRKVGLFEKRND 132
           L+ R ++G V+Q  HL P  T  EN+M  P+ +++ES+  A++KA  LL  VGL  +   
Sbjct: 84  LRNR-HMGFVYQFHHLLPELTAEENVMM-PLLIRRESEATARDKALALLDAVGLSRRTAH 141

Query: 133 YPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMKELVET-GMTMVI 191
            P+ LSGG++QRVA+ARAL   PD +L DEPT  LD    ++VL +M +L +  G  +++
Sbjct: 142 KPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTALLV 201

Query: 192 VTHEMGFAKEVADRVLFMDQGMI 214
           VTH++  A  + DR L +  GMI
Sbjct: 202 VTHDVNIAARM-DRTLTLRDGMI 223


Lambda     K      H
   0.317    0.134    0.368 

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: 129
Number of extensions: 10
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: 240
Length of database: 227
Length adjustment: 23
Effective length of query: 217
Effective length of database: 204
Effective search space:    44268
Effective search space used:    44268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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