GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Bacteroides thetaiotaomicron VPI-5482

Align TreV, component of Trehalose porter (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  218 bits (555), Expect = 2e-61
 Identities = 115/264 (43%), Positives = 172/264 (65%), Gaps = 3/264 (1%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           +E+  + K +G    ++ +T  ++ GEF  ILGPSG GK+TLL+++AG +   +G+I   
Sbjct: 10  IEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRIS 69

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G +IT  PP KR V  VFQ YAL+P+++V DNIAF LK++   K+ I ++V+ A K++G+
Sbjct: 70  GKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGM 129

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
           ++   + V  +SGGQQQRVA+ARAIV  P   LLDEPL+ LD ++R   + ELK + K L
Sbjct: 130 TDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSL 189

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
             TF+YVTHDQ+EAL+L+D I ++ +GK +Q+  P  +Y  P   +VA F+GE   N L 
Sbjct: 190 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNILN 247

Query: 243 GELMKEK-AQEIGFRPEWVEVGKG 265
           G ++ +K  +  G   E V+ G G
Sbjct: 248 GTMIHDKLVRFCGTEFECVDEGFG 271


Lambda     K      H
   0.318    0.137    0.385 

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: 368
Number of extensions: 20
Number of successful extensions: 1
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: 324
Length of database: 463
Length adjustment: 30
Effective length of query: 294
Effective length of database: 433
Effective search space:   127302
Effective search space used:   127302
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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