GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Acidovorax sp. GW101-3H11

Align TreV, component of Trehalose porter (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4785
          Length = 334

 Score =  247 bits (631), Expect = 3e-70
 Identities = 127/301 (42%), Positives = 196/301 (65%), Gaps = 4/301 (1%)

Query: 2   TVELIDIVKKYGK----NIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKG 57
           ++ L +I K+YG     N VI+G+  +++ GEF VI+GPSG GKSTLL+++AG+E++  G
Sbjct: 3   SLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEISGG 62

Query: 58  KIIADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAA 117
           ++      + D  P +R++AMVFQNYALYP+M+  +N+A+ LK+  + K+EI  RV+KAA
Sbjct: 63  ELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDKAA 122

Query: 118 KLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKR 177
           K+L +  +L++K  ++SGGQ+QRVA+ RAIVR P  FL DEPLSNLDA++R   R E+++
Sbjct: 123 KILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEIQK 182

Query: 178 IQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFP 237
           + +EL  T ++VTHDQ EA++LA R+ +++ G  EQ   P+ +Y  P T +VA F+G  P
Sbjct: 183 LHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGSPP 242

Query: 238 MNFLPGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVEASGESRYLICNFKNNNITILSQ 297
           MN L      +    +G RPE ++V     +  VE+VE  G  R +        + +  +
Sbjct: 243 MNLLKNAPGAQPGTILGIRPEHLDVRSEGWAVTVETVELLGAERLIYGRINGEQVIVRVE 302

Query: 298 E 298
           E
Sbjct: 303 E 303


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: 285
Number of extensions: 14
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: 334
Length adjustment: 28
Effective length of query: 296
Effective length of database: 306
Effective search space:    90576
Effective search space used:    90576
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: 49 (23.5 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