GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HP1174 in Bacteroides thetaiotaomicron VPI-5482

Align Glucose/galactose porter (characterized)
to candidate 353142 BT3616 fucose permease (NCBI ptt file)

Query= TCDB::P0C105
         (412 letters)



>lcl|FitnessBrowser__Btheta:353142 BT3616 fucose permease (NCBI ptt
           file)
          Length = 418

 Score =  238 bits (607), Expect = 2e-67
 Identities = 150/417 (35%), Positives = 225/417 (53%), Gaps = 27/417 (6%)

Query: 18  QKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLP 77
           +  Y   L  +  LFF+W   + L   +I  L    +LN  ++   +  ++ AYFI  +P
Sbjct: 3   KNTYTIPLALVFSLFFLWAISSNLLPTMIRQLMKTCELNTFEASFTETAYWLAYFIFPIP 62

Query: 78  AGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANP 137
               +KR SYK GI+ GL++AA+G  LF PAA  + Y  +L   F++A+G+  L+ AANP
Sbjct: 63  IAMFMKRYSYKAGIIFGLLLAAVGGLLFFPAAMLKEYWAYLCIFFIIATGMCFLETAANP 122

Query: 138 YVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILS--------------AATDATV 183
           YVT+LG PETA  RL L Q+FN LG  +A +F + LILS                  A +
Sbjct: 123 YVTVLGAPETAPRRLNLAQSFNGLGAFIAAMFLSKLILSGTHYTRETLPVDYPGGWQAYI 182

Query: 184 NAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQED--EPALSDKKEG----SAWQYRHL 237
             E DA++ PYL+LAL    +A++F   K P + ++  EPA S KKE        +  HL
Sbjct: 183 QLETDAMKLPYLILALLLLAIAVVFVFSKLPKIGDEGAEPA-SGKKEKLIDFDVLKRSHL 241

Query: 238 VLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM 297
             G I  F Y G + ++ S  + +    T AGL E  A      +    ++GR+IG+  M
Sbjct: 242 RWGVIAQFFYNGGQTAINSLFLVYCC--TYAGLPEDTATTFFGLYMLAFLLGRWIGTGLM 299

Query: 298 -RYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGS 356
            ++   G  L + A + I+L  + +   G I ++++LAI  F SIM+PT FSLAL GLG+
Sbjct: 300 VKFRPQGMLLVY-ALMNILLCGVVMLWGGMIGLYAMLAISFFMSIMYPTQFSLALKGLGN 358

Query: 357 HTSQGSGILCLAIVGGAIVPLIQGAL--ADAIGIHLAFLMPIICYAYIAFYGLIGSK 411
            T  GS  L +AIVG A +P +       +    ++A+ +P+IC+A+ A+YG  G K
Sbjct: 359 QTKSGSAFLVMAIVGNACLPQLTAYFMHVNEHIYYVAYGIPMICFAFCAYYGWKGYK 415


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: 533
Number of extensions: 34
Number of successful extensions: 5
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: 418
Length adjustment: 31
Effective length of query: 381
Effective length of database: 387
Effective search space:   147447
Effective search space used:   147447
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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