GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Sphingopyxis indica DS15

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate WP_089214098.1 CHB69_RS00850 MFS transporter

Query= SwissProt::P11551
         (438 letters)



>NCBI__GCF_900188185.1:WP_089214098.1
          Length = 457

 Score =  169 bits (429), Expect = 1e-46
 Identities = 131/448 (29%), Positives = 208/448 (46%), Gaps = 45/448 (10%)

Query: 19  GQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIP 78
           G   + +  FA +  LFF W    +L D L+   +  FTL++ +A L  SAF+  Y ++ 
Sbjct: 12  GGRSTALAAFAAVTVLFFAWGFITSLIDPLVAAVKGIFTLSDAEAQLSASAFFIAYGVMS 71

Query: 79  IPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAA 138
            PA  L+ ++     I+  L     G  +   AA +  Y L L+GLF++A+G+  L+ AA
Sbjct: 72  FPAAALIARVHSVPSILIALATMVGGCLVMLAAANLAVYPLVLLGLFMLASGITVLQVAA 131

Query: 139 NPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLS 198
           NP    LG     HFRL L+QTFNSFG  I  + G  L L  V  +   V+ +       
Sbjct: 132 NPLAAALGDPKRSHFRLTLSQTFNSFGTFIGPLIGAHLFLQGVEVKEGAVVTE------- 184

Query: 199 AYKHSLVLSVQTPYMIIVAIVLLVALLIMLTK---FPALQSDNHSDAKQGSF----SASL 251
           A +   +  + + Y  I  ++  + L   +++     A+       A+   F     A  
Sbjct: 185 AVRKQALAGIDSAYFWICGLIAALFLFFWISRRIVDAAVPPPPLGTARANIFELMGEAFA 244

Query: 252 SRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEE-------------IPGMTAGF-- 296
           SR AR+       LA F YVGA+ A  + +  +   +             + G T G   
Sbjct: 245 SRWARL-----GALAIFLYVGAEVAIGTQMALFLNSDAVWGQSDAPFGVPLLGFTMGSDG 299

Query: 297 ---AANYLTGTMVCFF-----IGRFTGTWLISRFAPHKVLAAYALIAMALCLISAFAGG- 347
               +    G  V F+     +GR  G+ L++R +  K+LA +  IA  LCL     GG 
Sbjct: 300 VAGVSLQEAGKAVAFYWGGAMVGRAIGSLLLARVSATKLLATFTAIACGLCLYVVTVGGA 359

Query: 348 HVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDA 407
             G +AL +   F SI +P IF+L ++  G   +  S  +   I+GG  +  ++G +SDA
Sbjct: 360 TAGFVALAI-GLFNSIMFPVIFTLTLERAGARAEATSGLLCTAIVGGAAIPVLVGSLSDA 418

Query: 408 AGNIPTAELIPALCFAVIFIFARFRSQT 435
            G   TA ++PALC+A++  FA   ++T
Sbjct: 419 WG-YGTALILPALCYALLCAFALAAART 445


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: 459
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: 457
Length adjustment: 33
Effective length of query: 405
Effective length of database: 424
Effective search space:   171720
Effective search space used:   171720
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