GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Pf6N2E2_1960 Various polyols ABC transporter, ATP-binding component

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1960
          Length = 365

 Score =  334 bits (856), Expect = 3e-96
 Identities = 179/372 (48%), Positives = 250/372 (67%), Gaps = 22/372 (5%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA + ++ L K +  L ++ GIDLEVKD+EF+  VGPSGCGKST LR+IAGLE+V+ G I
Sbjct: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
           E+ GR + ++ P  R+++MVFQ+YALYPHMTV +N+ F+L +AG    +++ +VAEAA I
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120

Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180
           L+L  LL+R+P QLSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA LR Q R E+ +LH
Sbjct: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
             +QATMIYVTHDQVEAMTL+ ++V++  G IEQ+G+P +++  PA  FVAGF+G+P M 
Sbjct: 181 KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG 240

Query: 241 MEEAVL-----TDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGD 295
             +A +     +  ++ FASG TL L PR  S +  GQ VT G+RP+ +  S  G     
Sbjct: 241 FLQATVHAVHASGVEVRFASGTTL-LIPRDSSALSVGQSVTIGIRPEHLTLSAEG----- 294

Query: 296 ADAVHEIELPVT--ITEPLGNETLVFTQF-NGRDWVSRMLNPRPLRPGEAVPMSFDLARA 352
                  ++PVT  +TE LG++T       +G     R+     +       ++ D+A  
Sbjct: 295 -------QVPVTTDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHC 347

Query: 353 HLFDGETGRALA 364
           HLFD E+G +++
Sbjct: 348 HLFD-ESGLSVS 358


Lambda     K      H
   0.320    0.137    0.397 

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: 365
Number of extensions: 17
Number of successful extensions: 2
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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