GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  113 bits (282), Expect = 6e-30
 Identities = 74/227 (32%), Positives = 117/227 (51%), Gaps = 29/227 (12%)

Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216
           G  +TL I  + +     LG++  L R S    +R +   +++F+RG PL+  +F+    
Sbjct: 15  GAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFG 74

Query: 217 LPLFLPEGMNF----------------DKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQ 260
           +P  L +  +F                 + L A+I   L   AY+AE+ R G+Q+I +GQ
Sbjct: 75  IPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIERGQ 134

Query: 261 YEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQA 320
            EAA ++G+ + ++M  VILPQA K VIP + N FIA+ KDTSL+ +IG  +L  + +  
Sbjct: 135 MEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNGQLI 194

Query: 321 AADPK-----WLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362
            A        WL   T G+++      I  F +SR   +LER+  TG
Sbjct: 195 IARTYESFAIWL---TVGFIYL-----IMTFTLSRIVDYLERRYKTG 233


Lambda     K      H
   0.330    0.144    0.469 

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: 228
Number of extensions: 11
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: 234
Length adjustment: 26
Effective length of query: 339
Effective length of database: 208
Effective search space:    70512
Effective search space used:    70512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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