GapMind for catabolism of small carbon sources

 

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

Align TreV, component of Trehalose porter (characterized)
to candidate Pf1N1B4_3027 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3027
          Length = 372

 Score =  232 bits (592), Expect = 9e-66
 Identities = 121/281 (43%), Positives = 186/281 (66%), Gaps = 7/281 (2%)

Query: 1   MTVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60
           + V+  ++ +++G+   ++ ++  I+ GEFF +LGPSG GK+T L+++AG E+   G I 
Sbjct: 30  LAVQFTNVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIR 89

Query: 61  ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120
             GA+    PP +R+V  VFQ+YAL+P+M+V DN+A+ LK++G+ K E  +R E+A  ++
Sbjct: 90  IHGAEAAGLPPYQRDVNTVFQDYALFPHMNVLDNVAYGLKVKGVGKTERQKRAEEALDMV 149

Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180
            +    ++K  Q+SGGQ+QRVALARA+V  P   LLDEPL  LD ++R   +GELK++Q+
Sbjct: 150 ALGGYGERKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQR 209

Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNF 240
           +L  TFI+VTHDQ EALS++DR+A+ +KG+ EQV  P+ LY  P T +VA+FVG    N 
Sbjct: 210 QLGITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATTFVAEFVG--TSNV 267

Query: 241 LPGELMKE---KAQEIGFRPEWVEVGKGNLSCMVESVEASG 278
           + G+L ++     Q    RPE V   +G L+     +E SG
Sbjct: 268 IRGDLAQQLSGNPQPFSIRPEHVRFAEGPLAS--HEIEVSG 306


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: 297
Number of extensions: 10
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: 372
Length adjustment: 29
Effective length of query: 295
Effective length of database: 343
Effective search space:   101185
Effective search space used:   101185
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