GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP1 in Escherichia coli BW25113

Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate 18233 b4208 D-alanine/D-serine/glycine transporter (NCBI)

Query= TCDB::F2HQ25
         (459 letters)



>FitnessBrowser__Keio:18233
          Length = 470

 Score =  328 bits (842), Expect = 2e-94
 Identities = 181/446 (40%), Positives = 263/446 (58%), Gaps = 14/446 (3%)

Query: 11  QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70
           +R L NRHIQLIAI G IGTGLF+G+GKTI + GPS+IF Y++IG  +FF +R +GE+L 
Sbjct: 20  RRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELLL 79

Query: 71  NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130
           ++    SF +F +   G   GYFT W+YW   V   ++++ AI  Y QFW P +  W+  
Sbjct: 80  SNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVAS 139

Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190
           + ++ LL  LN    + FGE EFWFAMIK+ AI+ +IV  +++VA +F   T +      
Sbjct: 140 LAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGV------ 193

Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250
             AS +++++    FP G   F    Q+ +FAF  +E +G TAAET +P+KSLP+AIN I
Sbjct: 194 -EASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSI 252

Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310
           P+RI++FYV AL+ IM++  W  +  +KSPFV +F L+G+  AA++INFVVLTSAAS+ N
Sbjct: 253 PIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSAN 312

Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLTLI--PQIK 368
           S +FS +R ++ LAQ+    +   F KLSK  +P   L   + + LL  V+ L   P + 
Sbjct: 313 SGVFSTSRMLFGLAQEGVAPK--AFAKLSKRAVPAKGLTF-SCICLLGGVVMLYVNPSVI 369

Query: 369 NAFDFAASCTTNLFLVVYFITLYTYWQYRKSED--YNPKGFLTPKPQITVPFIVAIFAIV 426
            AF    + +  LF+ V+ I L +Y  YRK     +    +  P  ++     +A F  V
Sbjct: 370 GAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFV 429

Query: 427 FASLFFNADTFYPALGAIVWTIFFGL 452
              L    DT    L   +W I  GL
Sbjct: 430 VVLLTLEDDTRQALLVTPLWFIALGL 455


Lambda     K      H
   0.329    0.141    0.434 

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: 637
Number of extensions: 32
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: 459
Length of database: 470
Length adjustment: 33
Effective length of query: 426
Effective length of database: 437
Effective search space:   186162
Effective search space used:   186162
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:

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