GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate Echvi_3909 Echvi_3909 Fucose permease

Query= SwissProt::P11551
         (438 letters)



>FitnessBrowser__Cola:Echvi_3909
          Length = 469

 Score =  225 bits (574), Expect = 2e-63
 Identities = 150/472 (31%), Positives = 226/472 (47%), Gaps = 84/472 (17%)

Query: 14  VDKDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFY-- 71
           V+ D+GQ   Y+ P  L+  LFF+W     +NDIL+P  QQ FTL N+QA LIQ+AF+  
Sbjct: 15  VEFDSGQQ--YLGPLFLVTMLFFMWGFITCMNDILIPHLQQVFTLQNWQAMLIQTAFFGA 72

Query: 72  -----FGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFI 126
                 GY++I I  G  + ++ YK GII GL + A+G   F+PAA ++++  FL  LF+
Sbjct: 73  YFFISLGYYLISITKGDPIGRIGYKNGIILGLVISAVGCLFFYPAASLVSFGFFLFALFV 132

Query: 127 IAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQ 186
           +A+G+  L+ AANP+VT+LG  S    RLN+ Q FNS G  IA + G  LI   +     
Sbjct: 133 LASGITILQIAANPYVTILGKPSGASSRLNMTQAFNSLGTTIAPLIGGYLIFGAI----- 187

Query: 187 DVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGS 246
                     +SA       SV+ PY+ +   +LL+AL+  L K P + S     +  G+
Sbjct: 188 ------GDVDISAD------SVKMPYVALALTLLLIALIFKLFKLPEIGSQGVIISDSGA 235

Query: 247 FSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYA-VEEIPGMTAGFAANYLTGTM 305
                    + RH    + A F YVG +    S LI +A + EI G+    A++YL    
Sbjct: 236 L--------KHRHLMLGIGAIFAYVGGEVTVGSNLINFARLPEIAGLDEAEASHYLALFW 287

Query: 306 VCFFIGRFTG-------------------------------------------------T 316
               +GRF G                                                  
Sbjct: 288 GGAMVGRFFGAVALADFKHNLNRFLIIGAITAISYVTIYYVYGGEMALYALAFIGLNIVV 347

Query: 317 WLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNL 376
            +I +F P++ L  + +  + L +I     G + L ++     F SI +PTIFSL IK L
Sbjct: 348 IIIGQFIPNRTLWLFGITGIGLLVIGLLTSGQLALWSIVALGLFNSIMFPTIFSLAIKGL 407

Query: 377 GQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428
           G+ T   SS +VM I+GG IV  + G ++D +G++  + L+P  C+  I  +
Sbjct: 408 GKYTAQASSLLVMAIVGGAIVPLLQGLLADISGSVQLSFLVPLACYLYIVFY 459


Lambda     K      H
   0.329    0.140    0.425 

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: 495
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 438
Length of database: 469
Length adjustment: 33
Effective length of query: 405
Effective length of database: 436
Effective search space:   176580
Effective search space used:   176580
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