GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP1 in Corynebacterium deserti GIMN1.010

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 WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter

Query= TCDB::F2HQ25
         (459 letters)



>NCBI__GCF_001277995.1:WP_082353324.1
          Length = 468

 Score =  302 bits (773), Expect = 2e-86
 Identities = 168/456 (36%), Positives = 251/456 (55%), Gaps = 16/456 (3%)

Query: 2   ENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFF 61
           +N        RGL NRH+QLIAI G IGTGLF+G+GKTI + GPSVI  Y +IG  +FF 
Sbjct: 3   DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62

Query: 62  LRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWL 121
           +R +GE+L  + +  S  + V+   G   G+ T W+YW   +   ++++ AI  Y Q+W 
Sbjct: 63  MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122

Query: 122 PQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYS 181
           P++PLWL  ++ + +LF LN    R FGE EFWFA+IK+ AI+ +I     +V   F   
Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAF--- 179

Query: 182 TVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKK 241
               G     +AS +N+ +    FP+G   F+   Q+ +FAF  +E  G  AAET +P+ 
Sbjct: 180 ----GAPNGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPET 235

Query: 242 SLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVV 301
           +LP+AIN IP+RI++FYV AL  IM +  W+ +  D SPFV +F L GI  AA +INFVV
Sbjct: 236 TLPRAINSIPIRIVVFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVV 295

Query: 302 LTSAASALNSSLFSATRNMYSLAQQ---HDKGRLTPFTKLSKAGIPINALYMATALSLLA 358
           +TSAAS+ NS +FS +R +Y L+ +     +  +    ++   G+  + L +  A+ LL 
Sbjct: 296 ITSAASSANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLY 355

Query: 359 PVLTLIPQIKNAFDFAASCTTNLFLVV--YFITLYTYWQYRKSEDYNPKGFLTPKPQITV 416
              T+I     AF    + ++ LF+VV  Y +  Y  ++ R  E +    F  P   +  
Sbjct: 356 AGGTVI----EAFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMA 411

Query: 417 PFIVAIFAIVFASLFFNADTFYPALGAIVWTIFFGL 452
             ++  F  +   L    DT    L   VW I  G+
Sbjct: 412 VVVLVFFVAMLGVLSLETDTRTALLATPVWFIILGV 447


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: 624
Number of extensions: 39
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: 468
Length adjustment: 33
Effective length of query: 426
Effective length of database: 435
Effective search space:   185310
Effective search space used:   185310
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