GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Desulfoscipio geothermicus DSM 3669

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= uniprot:B2TBJ8
         (250 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  113 bits (282), Expect = 4e-30
 Identities = 68/211 (32%), Positives = 118/211 (55%), Gaps = 10/211 (4%)

Query: 22  TLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLVYYGMGQF 81
           TL +   S+ +G LL L+    R+S   +    A AY+  FRG+PLL+Q+F+VY+G+ + 
Sbjct: 19  TLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFGIPKL 78

Query: 82  GVIRESFL------WPVLRE----PYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAG 131
            +  +SF+       PV        ++ AV++ +L +  Y AEI R G+ ++  GQ+EA 
Sbjct: 79  LMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIERGQMEAA 138

Query: 132 YSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQT 191
            S+G++    +R VI P A ++ +P    E + ++K T+L S++   E+T   Q II +T
Sbjct: 139 RSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNGQLIIART 198

Query: 192 YRTTEVFICAALIYLFLNFVIVRLLGMLETR 222
           Y +  +++    IYL + F + R++  LE R
Sbjct: 199 YESFAIWLTVGFIYLIMTFTLSRIVDYLERR 229


Lambda     K      H
   0.331    0.143    0.431 

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: 122
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: 250
Length of database: 234
Length adjustment: 23
Effective length of query: 227
Effective length of database: 211
Effective search space:    47897
Effective search space used:    47897
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.

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