GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1D in Paraburkholderia bryophila 376MFSha3.1

Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate H281DRAFT_05299 H281DRAFT_05299 amino acid ABC transporter membrane protein 1, PAAT family

Query= uniprot:A0A0H3PA28
         (219 letters)



>FitnessBrowser__Burk376:H281DRAFT_05299
          Length = 216

 Score = 98.6 bits (244), Expect = 8e-26
 Identities = 65/201 (32%), Positives = 108/201 (53%), Gaps = 10/201 (4%)

Query: 14  MQGLFLTLKIALATCIISIV---FGTFLAI----TKNYGDRLSKFLAACYIDIFRNTPLL 66
           +QG+ L L  ALAT  +S+     G F+A+     +   +R ++     Y+  FR  P+L
Sbjct: 8   VQGMPLLLHAALATIGVSLTGLFIGFFVAVGVCAARLSPNRAARRFGGAYVFFFRGVPML 67

Query: 67  LWMLAACFVLPVFFGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFG 126
           + +L   ++LP                SL ++S +AEI+RGG  SIP G  EAA   G  
Sbjct: 68  VQLLLVYYLLPFAGINVSPLVAAISAVSLCSASYIAEILRGGFLSIPPGHIEAARMLGLS 127

Query: 127 KFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEI 186
            F TL  I++PQ FR  +P+L++++V  +K ++ ++ +G+AELT  ++ I A      E 
Sbjct: 128 PFDTLRRILVPQAFRLTLPSLVNEMVLLIKASSLISVVGVAELTRTAQNIAASTYRPLEA 187

Query: 187 LAMIGVVAGIYFIICFSLSML 207
               G+   IYF+IC +L+++
Sbjct: 188 YLAAGL---IYFVICGALALI 205


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: 128
Number of extensions: 6
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 219
Length of database: 216
Length adjustment: 22
Effective length of query: 197
Effective length of database: 194
Effective search space:    38218
Effective search space used:    38218
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: 45 (21.9 bits)

This GapMind analysis is from Sep 17 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