GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Chryseobacterium viscerum 687B-08

Align Glucose/galactose porter (characterized)
to candidate WP_109739303.1 C1634_RS24670 L-fucose:H+ symporter permease

Query= TCDB::P0C105
         (412 letters)



>NCBI__GCF_002899945.2:WP_109739303.1
          Length = 414

 Score =  237 bits (604), Expect = 5e-67
 Identities = 135/410 (32%), Positives = 218/410 (53%), Gaps = 18/410 (4%)

Query: 11  LHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGA 70
           ++T   ++K Y   L  +  LFF W     + D+L  H +NV +++ ++S L+Q   FGA
Sbjct: 1   MNTTKFTEKKYYVVLAFVISLFFFWAIALTMGDVLNKHFQNVLKISKSESGLVQLSIFGA 60

Query: 71  YFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTI 130
           Y ++ +PAG  +KR  YK G+++GL + A+G  LFIPAA+   +  F  ALFVLA G+  
Sbjct: 61  YALMGIPAGLFMKRFGYKLGVILGLSLFALGSFLFIPAANQISFNFFRIALFVLAMGMAT 120

Query: 131 LQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNAEADAV 190
           L+  A+P+V  LG  +T+  R+   Q+FN LG  + P+ G   I   +     +   D+V
Sbjct: 121 LETVAHPFVAALGNEKTSDQRVNFAQSFNGLGAIIGPLLGGFFIFGRS--GLEDNSLDSV 178

Query: 191 RFPYLLLALAFTVLAIIFAILKPP---DVQEDEPALSDKKEG----------SAWQYRHL 237
           +  Y  + +    + IIF+ +K P   D    E  +SD ++G            ++ RH 
Sbjct: 179 KNLYTWIGIVILTITIIFSFIKVPSLKDTHAGEIQISDSEKGVEADVSDPHAPLYKQRHF 238

Query: 238 VLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM 297
           +   I  F  + A+    ++ +N+  +     L E  A+++ +      M+GRF+G+  M
Sbjct: 239 IFAVIAQFFNIAAQGGTWAYFINYGVEK--MNLPEIQASYYFSLSMAMMMIGRFVGTFLM 296

Query: 298 RYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSH 357
           ++I   K LA      I+L  I   + G ++  S++ + LF S+M+PTIFSL L  LGS 
Sbjct: 297 KFIAPNKLLAIFTACNIVLCLIISQSFGWVSFMSLILLNLFLSVMYPTIFSLGLKRLGSK 356

Query: 358 TSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGL 407
             Q S  L +A+ GGAI P + G +A+    H A+L+PIICYA I  + L
Sbjct: 357 VPQASSFLVMAMFGGAIFPPLMGKIAEKDIAH-AYLLPIICYAVILLFAL 405


Lambda     K      H
   0.328    0.141    0.420 

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: 499
Number of extensions: 24
Number of successful extensions: 6
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: 412
Length of database: 414
Length adjustment: 31
Effective length of query: 381
Effective length of database: 383
Effective search space:   145923
Effective search space used:   145923
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: 50 (23.9 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