GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1D in Desulfoscipio geothermicus DSM 3669

Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= uniprot:A0A0H3PA28
         (219 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  112 bits (279), Expect = 8e-30
 Identities = 72/221 (32%), Positives = 115/221 (52%), Gaps = 22/221 (9%)

Query: 13  LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWMLAA 72
           + QG  +TL+I + +  I  + G    +++    ++ +FLA  Y+D FR TPLL+ +   
Sbjct: 12  IFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIV 71

Query: 73  CFVLPVF-----------FGQFPQA--------FWGTIGFSLYTSSVMAEIIRGGLNSIP 113
            F +P             +G  P A            I  SL + + +AEI R G+ SI 
Sbjct: 72  YFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIE 131

Query: 114 KGQFEAAYSQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNS 173
           +GQ EAA S G      + Y+ILPQ F+++IP L ++ +  +KDT+ L+ +G AELT N 
Sbjct: 132 RGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNG 191

Query: 174 KTILAKLTSFEEILAMIGVVAGIYFIICFSLSMLVRYYAKK 214
           + I+A+     E  A+   V  IY I+ F+LS +V Y  ++
Sbjct: 192 QLIIART---YESFAIWLTVGFIYLIMTFTLSRIVDYLERR 229


Lambda     K      H
   0.331    0.144    0.428 

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: 152
Number of extensions: 9
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: 219
Length of database: 234
Length adjustment: 22
Effective length of query: 197
Effective length of database: 212
Effective search space:    41764
Effective search space used:    41764
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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.

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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