GapMind for catabolism of small carbon sources

 

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

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

Query= TCDB::F2HQ24
         (457 letters)



>NCBI__GCF_001277995.1:WP_082353324.1
          Length = 468

 Score =  325 bits (832), Expect = 3e-93
 Identities = 178/443 (40%), Positives = 263/443 (59%), Gaps = 12/443 (2%)

Query: 14  RGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLYQ 73
           RGL NRH+QLIAI G IGTGLF+G+GK+I + GPS+I VY IIG +++ ++RA+GE+L  
Sbjct: 13  RGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFVMRAMGELLLA 72

Query: 74  DPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTEV 133
           + N  S  + VS  LG   G+   W+Y    +   MA+++AI  Y  +W P++P+W+  V
Sbjct: 73  NLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWWPEIPLWLPGV 132

Query: 134 FVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHY--HTGTDTVSVTN 191
             +++L  LN    + FGE EFWF +IKIVAI+ LI     ++ + +    GT T S  N
Sbjct: 133 LTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAPNGT-TASFNN 191

Query: 192 ITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLF 251
           + +   FFPNG++ F   FQ+ +FAFV +E  G  AAET +P  TL +AIN IPIRIV+F
Sbjct: 192 LIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAINSIPIRIVVF 251

Query: 252 YVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFSIT 311
           YV AL  IM +  W ++  D SPFV +F L GI  AA ++NFVV+TSAAS+ NS +FS +
Sbjct: 252 YVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASSANSGIFSTS 311

Query: 312 RNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPA---ISNSFVFI 368
           R LY LS        K +   SK  VP   L F+ L ++  P + ++ A   +  +F  I
Sbjct: 312 RMLYGLSL--EGAAPKRWGVLSKRQVPARGLTFSVLCLI--PAVGLLYAGGTVIEAFTLI 367

Query: 369 TSVATNLFLVVYLMTLITYLKYRKSSD--FDPKGFVLPAAHIFIPLAIAGFVLIFISLFC 426
           T+V++ LF+VV+   L+ Y+ YR+ +    +   F +P   +   + +  FV +   L  
Sbjct: 368 TTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVVVLVFFVAMLGVLSL 427

Query: 427 FKDTIVPAIGSVIWVLIFGLFTF 449
             DT    + + +W +I G+  F
Sbjct: 428 ETDTRTALLATPVWFIILGVGWF 450


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: 548
Number of extensions: 30
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: 457
Length of database: 468
Length adjustment: 33
Effective length of query: 424
Effective length of database: 435
Effective search space:   184440
Effective search space used:   184440
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