GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AO356_00010 AO356_00010 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00010
          Length = 365

 Score =  343 bits (880), Expect = 4e-99
 Identities = 181/360 (50%), Positives = 247/360 (68%), Gaps = 5/360 (1%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  L +++++K +  + +I GIDL++K+ EFVVFVGPSGCGKSTLLR+IAGLE++T G +
Sbjct: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            +DG  + +V P+KR +AMVFQ+YALYPHMTV  N++F + +A E K +++R+V  AA +
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L+L   LDR PK LSGGQRQRVAIGRAI RNPK+FLFDEPLSNLDAALRV TR+E+++L 
Sbjct: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           + +   TMIYVTHDQVEAMTLA ++VVL+AG IEQ+G+PLELY  PANLFVA F+G+P M
Sbjct: 181 KEL-QATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKM 239

Query: 241 NVIPATITAT-GQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299
             + AT+ A       V  A G ++ +   ++A   G++ + G+RPE L +      L  
Sbjct: 240 GFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEGQVLV- 298

Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQS 359
            T  + E LG  T  ++  +   E +  ++ G   V    +   T D A  HLFD +G S
Sbjct: 299 -TTDVTERLGSDTFCHV-NVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFDESGLS 356


Lambda     K      H
   0.320    0.137    0.387 

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: 352
Number of extensions: 12
Number of successful extensions: 4
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: 362
Length of database: 365
Length adjustment: 29
Effective length of query: 333
Effective length of database: 336
Effective search space:   111888
Effective search space used:   111888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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