GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Mucilaginibacter mallensis MP1X4

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate WP_091369124.1 BLU33_RS03105 L-fucose:H+ symporter permease

Query= SwissProt::P11551
         (438 letters)



>NCBI__GCF_900105165.1:WP_091369124.1
          Length = 410

 Score =  273 bits (698), Expect = 7e-78
 Identities = 154/416 (37%), Positives = 235/416 (56%), Gaps = 23/416 (5%)

Query: 16  KDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYF 75
           K A     Y +    + +LF LW +A  L D+L   FQ    ++   +GL+Q + +  Y 
Sbjct: 4   KPAFTEPKYRVILFFVTALFMLWGIAITLGDVLNRHFQNVLHISKSHSGLVQLSIFGAYA 63

Query: 76  IIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLE 135
           ++ IPAG+ MK+  YK GI+ GLFLYA GA LF PAA+ +++  F + LFI+A GL  LE
Sbjct: 64  VMGIPAGLFMKRFGYKKGILLGLFLYAFGAFLFVPAADAVSFDFFRIALFILACGLATLE 123

Query: 136 TAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPE 195
           T A+PFV  LG + +   R+N +Q FN  G +I    G   IL      S D        
Sbjct: 124 TVAHPFVAALGDQRTSDQRINFSQAFNGLGGVIGPTLGGYFILKGQQIHSND-------- 175

Query: 196 QLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHS--DAKQGSFSASL-S 252
                    +++V+  Y+II ++++L+ +L +  K P L   ++   D +    +  +  
Sbjct: 176 ---------LIAVKYLYVIIGSVIVLIGVLFLFLKVPHLTHAHNEVIDYENAEGNKKIEK 226

Query: 253 RLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGR 312
           +L   +H+ +AV+AQF  V AQ   W+Y I Y   E+  ++   AA + + +M+   IGR
Sbjct: 227 KLIHQKHYVFAVVAQFFNVAAQGGTWAYFINYG-HEMVHLSDERAAYFFSLSMIMLMIGR 285

Query: 313 FTGTWLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLG 372
           FTGT+L+   AP+++L+ +A   + +CLI A   G +  IAL   + F SI +PTIFSLG
Sbjct: 286 FTGTFLMRYIAPYRLLSIFAAANIVMCLIVAQGAGWLSFIALLFINFFFSIMFPTIFSLG 345

Query: 373 IKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428
           +KNLG  T+ GSSFIVM +IGGG+  P+MG +  A  +I  A  +P +C+ VIF+F
Sbjct: 346 LKNLGGKTQQGSSFIVMGVIGGGLFPPLMGLI--ANHDIAAAYYLPIICYIVIFLF 399


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: 485
Number of extensions: 25
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: 410
Length adjustment: 32
Effective length of query: 406
Effective length of database: 378
Effective search space:   153468
Effective search space used:   153468
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 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