GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Mucilaginibacter mallensis MP1X4

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_091372396.1 BLU33_RS11040 L-fucose:H+ symporter permease

Query= uniprot:A0A1I2JXG1
         (442 letters)



>NCBI__GCF_900105165.1:WP_091372396.1
          Length = 444

 Score =  249 bits (636), Expect = 1e-70
 Identities = 141/412 (34%), Positives = 227/412 (55%), Gaps = 6/412 (1%)

Query: 27  MAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLV 86
           ++  ++T +F +WG    +NDILI      F+L+  +A L+Q  F+  YF +++P+GL++
Sbjct: 21  VSFSLVTMLFLIWGIPNNMNDILIKQFMKSFELSRTQAGLIQSAFYMGYFFLAVPSGLIM 80

Query: 87  ARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALL 146
            +  YK G++AGL +  +G   FWPAA    Y  FL ALFV+A+G+T L+  AN ++  L
Sbjct: 81  KKYSYKTGLIAGLLLFALGCCLFWPAAIAGKYGLFLFALFVIASGLTFLETGANIFIVKL 140

Query: 147 GPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIA--KLSPAEQVAYRVQE 204
           G  +SA  RL  +QA N +G  L    G + ILS    +  +IA  KLS  E   Y  QE
Sbjct: 141 GSSQSAERRLNFSQAFNPIGAVLGVLIGTIFILSGIEHNPVKIAVMKLS-GEYQHYLKQE 199

Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI 264
              V  PYL LA    L ++ +   + P  T++ ++ +    +    L++PH   GVL+ 
Sbjct: 200 TMRVVTPYLVLAAFAVLWSILLMFTKFPKGTDELKEETQAPANAKELLKYPHFYKGVLSQ 259

Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRK 324
           FFY G +    SF + Y+   D     E+ A  ++    +   +GRF  + ++  +SP K
Sbjct: 260 FFYCGAQTCTWSFFIQYVQ--DYTGEPEKIAGYFLTGTLVAFGLGRFSATYIMRYVSPGK 317

Query: 325 LLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSL 384
           L+ I+  IN+ALV+  ++  G V ++++     F S+M+PT F+L I  +G       S+
Sbjct: 318 LMGIYGVINIALVVIAILFPGVVGVWAIFFTSFFMSLMYPTNFALSIRSLGNNAKIGGSI 377

Query: 385 LIMAIVGGAIVPFVQGLFADHI-GVQHAFFLPLLCYAYIVFYGLYGSRIKSD 435
           ++MAIVGGA  P + GL A+    +  A  +PL+CY YI +Y   GS+I ++
Sbjct: 378 MVMAIVGGAFFPPIMGLIAESAKSMAVAMVIPLICYLYIAYYAFRGSKIPNE 429


Lambda     K      H
   0.327    0.140    0.414 

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: 504
Number of extensions: 28
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: 442
Length of database: 444
Length adjustment: 32
Effective length of query: 410
Effective length of database: 412
Effective search space:   168920
Effective search space used:   168920
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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