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_807 Various polyols ABC transporter, ATP-binding component

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_807
          Length = 367

 Score =  325 bits (833), Expect = 1e-93
 Identities = 174/363 (47%), Positives = 236/363 (65%), Gaps = 13/363 (3%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA + +K L K +    ++ GIDLEV DREF+  VGPSGCGKST LR+IAGLEEVS G I
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVSDGTI 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
           E+ GR + ++ P  R+++MVFQ+YALYPHM+V +NM F+L +AG P  E++ +V EAA I
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVPKAEVEKKVNEAARI 120

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

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
             +QATMIYVTHDQVEAMTL+D++V++  G IEQVG+P +++ +PA  FVAGF+G+P M 
Sbjct: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240

Query: 241 MEEAVLT----DGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDA 296
             +  +T     G        T    PR  + +  G  VT G+RP+ +    +    GD 
Sbjct: 241 FLKGKVTGLDSQGCEVLLDAGTRINLPRSGANLSVGGAVTLGIRPEHL----NLAQPGDC 296

Query: 297 DAVHEIELPVTITEPLGNETLV-FTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLF 355
                +++   ++E LG++T       +G     R+      R GE + +  D    HLF
Sbjct: 297 ----TLQVTADVSERLGSDTFCHVVTASGEALTMRVRGDLASRFGEQLSLHLDAEHCHLF 352

Query: 356 DGE 358
           D E
Sbjct: 353 DAE 355


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: 376
Number of extensions: 10
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: 367
Length adjustment: 30
Effective length of query: 335
Effective length of database: 337
Effective search space:   112895
Effective search space used:   112895
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