GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Pedobacter sp. GW460-11-11-14-LB5

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease

Query= SwissProt::P11551
         (438 letters)



>FitnessBrowser__Pedo557:CA265_RS08575
          Length = 422

 Score =  308 bits (788), Expect = 3e-88
 Identities = 170/413 (41%), Positives = 252/413 (61%), Gaps = 7/413 (1%)

Query: 17  DAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFI 76
           D+   + Y++PF L+ SLFFLW +A+NL+ IL+P  ++A  L N Q+ LI ++ +F YF+
Sbjct: 6   DSSSGKKYLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFL 65

Query: 77  IPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLET 136
           + IPAG+++KK  YKA +I+GL  +A GA LF PAA  ++Y  FL+ LFII  GL  LET
Sbjct: 66  MAIPAGMILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLET 125

Query: 137 AANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQ 196
           +ANP+  VLG  +    RLNLA +FN   A++A + G   ILS   H  ++ L  M+   
Sbjct: 126 SANPYAAVLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEE-LAAMTDAG 184

Query: 197 LSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLAR 256
            ++Y      SV+TPY+ +  ++L++A +      P +++ +     +GSF  +L    R
Sbjct: 185 RNSYFLEEAASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKSIDGEAKGSFFGAL----R 240

Query: 257 IRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGT 316
            +H +WAV+AQF YVGAQ    S+ IR A ++  G     AA+YL    + F +GRF GT
Sbjct: 241 HKHLKWAVVAQFFYVGAQVCVTSFFIRMA-QQGGGFDEKTAASYLAIYGLLFTVGRFAGT 299

Query: 317 WLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNL 376
            ++   + HK+LA YA+I++ LCL++    G   + AL     FMSI +PTIF+LGI  +
Sbjct: 300 AILQFVSSHKLLAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALGIDGI 359

Query: 377 GQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAG-NIPTAELIPALCFAVIFIF 428
           G DTK GSS+++M+I+GG I+   MG + D  G NI     IP +CF VI  F
Sbjct: 360 GDDTKPGSSWLIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVILYF 412


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: 475
Number of extensions: 22
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: 438
Length of database: 422
Length adjustment: 32
Effective length of query: 406
Effective length of database: 390
Effective search space:   158340
Effective search space used:   158340
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