GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treV in Pseudomonas fluorescens FW300-N1B4

Align TreV, component of Trehalose porter (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 ABC transporter,
           ATP-binding protein
          Length = 341

 Score =  227 bits (579), Expect = 3e-64
 Identities = 111/242 (45%), Positives = 172/242 (71%), Gaps = 2/242 (0%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           V+L ++ K+YG+   +      +E GEF  +LGPSG GK+T L+++AG  ++  G+I+ D
Sbjct: 4   VQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRIVLD 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G DIT   P  R + +VFQ+YAL+P+M+VRDN+AF L+MR +  +E+ +RV++  KL+ +
Sbjct: 64  GRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKLVRL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
           ++  ++   ++SGGQ+QRVALARA+V  P   LLDEPLSNLDA +R   + E++RIQ+E+
Sbjct: 124 NQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQREV 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
             T + VTHDQ EALS++DR+ ++  G+  Q+  P TLYE+P+T++++ FVG+   N LP
Sbjct: 184 GITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVGK--ANLLP 241

Query: 243 GE 244
           GE
Sbjct: 242 GE 243


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: 282
Number of extensions: 8
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: 341
Length adjustment: 28
Effective length of query: 296
Effective length of database: 313
Effective search space:    92648
Effective search space used:    92648
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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