GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucP in Sphingomonas koreensis DSMZ 15582

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate Ga0059261_2650 Ga0059261_2650 glucose/galactose transporter

Query= SwissProt::P11551
         (438 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_2650 Ga0059261_2650
           glucose/galactose transporter
          Length = 425

 Score =  214 bits (545), Expect = 4e-60
 Identities = 139/415 (33%), Positives = 224/415 (53%), Gaps = 10/415 (2%)

Query: 23  SYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAG 82
           SY    ALL SLFF+W     +N+ LLP  +  F L   +  LI+S ++  YF+  IP+ 
Sbjct: 18  SYRRALALLASLFFMWGFITVINNTLLPHLRSVFDLDYTRTTLIESVWFIAYFVASIPSA 77

Query: 83  ILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFV 142
            L++++ Y+  ++ GL + A G+A    AA I +Y + L  LF+IA+G+  L+ AANP+V
Sbjct: 78  RLIERIGYQRSLVAGLLVMAAGSAGMMLAASIPSYGVTLAMLFVIASGITLLQVAANPYV 137

Query: 143 TVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKH 202
            V+G   +   RLNL Q  NS G ++A  FG  LIL      + +    ++  +  A   
Sbjct: 138 AVVGRPETASSRLNLVQAMNSAGTMLAPAFGAWLILGRSKGGTSEAGTVLTQAERFADAQ 197

Query: 203 SLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIRHWRW 262
           S++L    PY ++   ++++AL+I     PA+ +     AK+   + S   L + R+  +
Sbjct: 198 SVIL----PYGLVAVALVMLALVIACFPLPAMGAATRRLAKEERRNHS---LWKHRNLVF 250

Query: 263 AVLAQFCYVGAQTACWSYLIRYAVE-EIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISR 321
            V A F Y+ A+    +  + +  + +I  +T   A +YLT        GRF G+ L+ R
Sbjct: 251 GVPAIFIYLIAEIGVANLFVNFVSQPDIANLTHEQAGHYLTFLWGGMMAGRFAGSALMQR 310

Query: 322 FAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTK 381
           F    VLA +A+ A A+ L++ FA G   + AL L   F SI +PTIF+LGI+ LG  T+
Sbjct: 311 FDAAHVLAVFAIGAFAVMLVATFATGPTAMWALILVGFFHSIMFPTIFTLGIRGLGPLTE 370

Query: 382 YGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFARFRSQTA 436
            GS  ++M I GG +V  V G+++D  G +  + L+ A C   +  +A + S+TA
Sbjct: 371 EGSGLLIMAIAGGALVI-VQGWLADQWG-LQLSFLLTAACEVYVLFYALWGSRTA 423


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: 424
Number of extensions: 25
Number of successful extensions: 3
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: 425
Length adjustment: 32
Effective length of query: 406
Effective length of database: 393
Effective search space:   159558
Effective search space used:   159558
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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