GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manMFS in Pseudomonas fluorescens GW456-L13

Align D-mannose and D-mannitol transporter (characterized)
to candidate PfGW456L13_2130 Hexuronate transporter

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2130
          Length = 436

 Score =  217 bits (552), Expect = 6e-61
 Identities = 134/408 (32%), Positives = 209/408 (51%), Gaps = 18/408 (4%)

Query: 6   RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65
           R  I+++LF+  VINYLDRS LS+AAP +  D G+    +G+IFS+F   YAA    GGW
Sbjct: 19  RFFIMVLLFITVVINYLDRSNLSIAAPALTSDLGIDPIHVGLIFSAFGWTYAAMQIPGGW 78

Query: 66  AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWY 125
             DR   +    +A++LWS+ + +      F +L ++R+  G  E P     S++V  W+
Sbjct: 79  LVDRVPPRILYSVALLLWSVATVMLGFAGSFIALFVLRMAVGALEAPAYPINSRVVTTWF 138

Query: 126 TPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKE 185
             + RA AIG   SG  +G A   PV+ ++   +GW + F+    +G+VWA +W+   +E
Sbjct: 139 PERERATAIGFYTSGQFVGLAFLTPVLAWLQHEFGWHMVFVTTGAVGIVWAVIWYAVYRE 198

Query: 186 RPEGEGAEDI---LRAEGQGEL---AAQPVFPLRFYLKQPTVLFTS-------LAFFSYN 232
             + +GA D    L  EG G +   A Q     +F      ++ T        L  F  N
Sbjct: 199 PRDFKGANDAEIDLIREGGGLVDIQAEQARVKAKFSWTDLGIVLTKRKLWGIYLGQFCLN 258

Query: 233 YTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFS 292
            TL+FFLTWFP+YL    G++     +   +P++  F+G+   GF SDF+ ++   + F+
Sbjct: 259 STLWFFLTWFPTYLVKYRGMDFIKSGLLASLPFLAAFIGVLCSGFFSDFLIRRGYTVGFA 318

Query: 293 RKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVG 352
           RK+ +++ LL     I    + +T  P VI      FF     +I W+++    PA  +G
Sbjct: 319 RKLPIISGLLISTSIIGANFVEST--PLVIAFLALAFFGNGLASITWSLVSTLAPARLLG 376

Query: 353 GVSGFMHFLANTSGIVGPTLTGFLVQFTG-SFTSAFLLAGLLTVIGAV 399
              G  +F+ N S I  P + GFL   TG SF  A     +L +IGA+
Sbjct: 377 LTGGVFNFIGNLSAIATPIVIGFLA--TGDSFAPAITYISVLALIGAL 422


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: 603
Number of extensions: 34
Number of successful extensions: 3
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: 436
Length adjustment: 32
Effective length of query: 398
Effective length of database: 404
Effective search space:   160792
Effective search space used:   160792
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:

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