GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1D in Brucella inopinata BO1

Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease

Query= uniprot:A0A0H3PA28
         (219 letters)



>NCBI__GCF_000182725.1:WP_008511689.1
          Length = 323

 Score = 95.1 bits (235), Expect = 1e-24
 Identities = 73/217 (33%), Positives = 109/217 (50%), Gaps = 14/217 (6%)

Query: 5   FNAQNIEFLM-QGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNT 63
           F A+ I FL+ QG   TL I+  +  I+ +     AI K   + +   L+  Y  +FR  
Sbjct: 109 FIARKISFLITQGTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGL 168

Query: 64  PLLLWMLAACFVLPVF---FGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAA 120
           PLL+ +      LP      G  P    G +  SL   + M EI R G+ SIP GQ EAA
Sbjct: 169 PLLMQIYIIYLGLPQIGYVIGAIPA---GILALSLCYGAYMTEIFRAGIESIPHGQKEAA 225

Query: 121 YSQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKL 180
            + G G   T++ +ILPQ  R IIP   +Q +  +KD++ ++ +G+ EL Y ++T     
Sbjct: 226 TALGLGSAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVART--QGQ 283

Query: 181 TSFEEILAMIGVVAGIYFIICFSL----SMLVRYYAK 213
           T F  I  M+   + IY+I+  S     S + RYYA+
Sbjct: 284 TEFRHI-EMLITASMIYWILSISFEFIQSRIERYYAR 319


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: 201
Number of extensions: 11
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: 219
Length of database: 323
Length adjustment: 25
Effective length of query: 194
Effective length of database: 298
Effective search space:    57812
Effective search space used:    57812
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. 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