GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manMFS in Pseudomonas fluorescens FW300-N2E2

Align D-mannose and D-mannitol transporter (characterized)
to candidate Pf6N2E2_3297 D-galactarate permease

Query= reanno::pseudo5_N2C3_1:AO356_28540
         (430 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3297 D-galactarate
           permease
          Length = 454

 Score =  207 bits (527), Expect = 5e-58
 Identities = 128/424 (30%), Positives = 208/424 (49%), Gaps = 23/424 (5%)

Query: 6   RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65
           R LI++MLFL   INY DR+ +++A   +QKD G+    +G IFS+F   Y A    GGW
Sbjct: 10  RYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGW 69

Query: 66  AADRYGAKTTLLLAMVLWSLFS------GLTVLTVGFASLVLIRILFGMGEGPLSVTTSK 119
             DR+G+K    L++  WSLF+      G   ++    +L ++R L G+ E P     ++
Sbjct: 70  LLDRFGSKKIYALSIFTWSLFTVLQGYVGEFGMSTAVVALFMLRFLVGLAEAPSFPGNAR 129

Query: 120 MVNNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVW 179
           +V  W+    R  A     S       +  P++G+I   +GW+  FI++ +IG+V++ +W
Sbjct: 130 IVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYRFGWQHVFIVMGVIGIVFSLIW 189

Query: 180 FKFV---KERPEGEGAE-----------DILRAEGQGELAAQPVFP-LRFYLKQPTVLFT 224
            K +   ++ P    AE           D+ + +G+ + A  P +  +R  L    +L  
Sbjct: 190 LKVIYSPRQHPMINEAEFNHIAANGAMVDMDQDKGKEKKADGPKWDYIRQLLTNRMMLGV 249

Query: 225 SLAFFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFK 284
            L  +  N   +FFLTWFP YL    G+ +        +P + GF+G  LGG ISD++ +
Sbjct: 250 YLGQYCINGITYFFLTWFPVYLVQERGMTILKAGFIASLPAICGFIGGVLGGVISDYLLR 309

Query: 285 KTGRMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQD 344
           K   + F+RK  ++  LL  +  +AC   V   +  V  +ALA FF    GA+ WA++ D
Sbjct: 310 KGHSLTFARKTPIIAGLLVSSSIVAC-NYVDIEWMVVGFMALA-FFGKGVGALGWAVVSD 367

Query: 345 TVPAARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARY 404
           T P    G   G  +   N + I  P + G+++  TGSF  A +  G   ++        
Sbjct: 368 TSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISSTGSFKWALVFVGCNALMAVFSYLVI 427

Query: 405 VKPL 408
           V P+
Sbjct: 428 VGPI 431


Lambda     K      H
   0.329    0.142    0.439 

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: 599
Number of extensions: 42
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: 430
Length of database: 454
Length adjustment: 32
Effective length of query: 398
Effective length of database: 422
Effective search space:   167956
Effective search space used:   167956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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