GapMind for catabolism of small carbon sources

 

Aligments for a candidate for serP in Burkholderia phytofirmans PsJN

Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease

Query= TCDB::F2HQ24
         (457 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS07280 BPHYT_RS07280 amino acid
           permease
          Length = 466

 Score =  214 bits (546), Expect = 4e-60
 Identities = 124/395 (31%), Positives = 203/395 (51%), Gaps = 5/395 (1%)

Query: 7   EENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRA 66
           E  K  QRGL    + +IAI G IGTGLFLG+G +I   GPS++  Y I   +  +L+  
Sbjct: 13  EREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALLLMGC 72

Query: 67  IGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDL 126
           + EM    P   SF  +   Y+    G+ ++++Y   +VF    E+ AI  Y+ +W P +
Sbjct: 73  LAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAV 132

Query: 127 PIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDT 186
           P W   V     L  +N+++ K FG  E+ F M+KIVAI+G IL    ++F        T
Sbjct: 133 PGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVFG--APADST 190

Query: 187 VSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPI 246
           +   N T    FFP G+   + +  + +F+++S+E I + A E  +P+  + +A      
Sbjct: 191 IGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMF 250

Query: 247 RIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSA 306
           R+V FY+  L  +++I  W     D+SPFV +     +  AA ++NFV+L +A SA+NS 
Sbjct: 251 RLVFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNSQ 310

Query: 307 LFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAISNSFV 366
           L+  TR ++SLS+       +     +  GVPV AL  +++ I     ++++     SFV
Sbjct: 311 LYITTRMMFSLSRAGYAP--RKLGALNGKGVPVAALWLSTIGIALATVLNVVYP-DASFV 367

Query: 367 FITSVATNLFLVVYLMTLITYLKYRKSSDFDPKGF 401
            + SV+    +  +LM  +T+  +R      P  F
Sbjct: 368 LMMSVSMFGAMFTWLMIFVTHFFFRHRHQGAPLAF 402


Lambda     K      H
   0.330    0.144    0.431 

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: 569
Number of extensions: 35
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: 457
Length of database: 466
Length adjustment: 33
Effective length of query: 424
Effective length of database: 433
Effective search space:   183592
Effective search space used:   183592
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 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