GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  134 bits (337), Expect = 4e-36
 Identities = 77/228 (33%), Positives = 131/228 (57%), Gaps = 3/228 (1%)

Query: 3   LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62
           L L+ ++ K+G +  L D++L +Q G   ++LG T  GKT ++  +AG+  P  G +   
Sbjct: 2   LRLEHVTVKLG-EFQLLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFK 60

Query: 63  GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHI 120
            +++  +    R V  VYQ +  +P + V  NI    ++R   +K I +++ E+ + L I
Sbjct: 61  ERNLATLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGI 120

Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180
              L+R+P+ LSGG+QQR ALARAL     ++LLDEPL  LD + +E  +EEL ++    
Sbjct: 121 GHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTL 180

Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVA 228
           ++T ++ T +  EA+ L     V+ +GQ++Q G   E+F+ P +  VA
Sbjct: 181 KTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVA 228


Lambda     K      H
   0.318    0.133    0.375 

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: 201
Number of extensions: 6
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: 363
Length of database: 344
Length adjustment: 29
Effective length of query: 334
Effective length of database: 315
Effective search space:   105210
Effective search space used:   105210
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 (21.7 bits)
S2: 49 (23.5 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