GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Shewanella sp. ANA-3

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)

Query= TCDB::Q8GBT6
         (403 letters)



>FitnessBrowser__ANA3:7025672
          Length = 452

 Score =  219 bits (558), Expect = 1e-61
 Identities = 139/383 (36%), Positives = 205/383 (53%), Gaps = 23/383 (6%)

Query: 18  LPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNMALLFAVGIAIGFAKKSD 77
           +PAA +++ L  + +   P  P  +T +   M A G  I   M +LFAV +AIGF +   
Sbjct: 1   MPAAGVMLGLTVSPI---PFMPEVLTVL---MLAVGKLIFAIMPILFAVAVAIGFCR-DQ 53

Query: 78  GSTALAAVVGYLVFKNVLATFTDK-NLPQVAKAVDGKVVMVDAPVDAKVLGGVVMGLVVA 136
           G  A  AV GY V    LA   D   LP        ++++    +D  + GG+++G V  
Sbjct: 54  GIAAFTAVFGYGVMTATLAALADLYQLPT-------QLLLGMETLDTGIAGGMLIGGVTC 106

Query: 137 LLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVLGTGLHNFGEWLV-G 195
              +     +LP    FF GRR   +L     + +G +  ++WP L   +    +W V  
Sbjct: 107 FAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQ 166

Query: 196 SGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEYEGKS-----GDIARFLAGDPTAGQ 250
             A+  G++G   R LIP+G+HH+ N+  + + G+Y+ ++     G++AR+LAGDP AG 
Sbjct: 167 KPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQNSEVVRGEVARYLAGDPQAGN 226

Query: 251 FMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTGVTEPIEFTFMFIA 310
              G+  I M+ LPAA LAI  CA P  R  V G+M S A  S++TGVTEPIEF FMF+A
Sbjct: 227 LAGGYL-IKMWGLPAAALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVA 285

Query: 311 PVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPWGLALVGVCFAALY 370
           P L+ IH +L+G++  +   L +     FS G VDF L   ++ N      +G   A +Y
Sbjct: 286 PFLFLIHVLLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVFLGPLTAVIY 345

Query: 371 YVVFRFAITKFNLPTPGR-ESDE 392
           Y++FR +I  FNL TPGR E DE
Sbjct: 346 YLLFRGSILAFNLKTPGRLEPDE 368


Lambda     K      H
   0.328    0.143    0.441 

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: 482
Number of extensions: 25
Number of successful extensions: 5
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: 403
Length of database: 452
Length adjustment: 32
Effective length of query: 371
Effective length of database: 420
Effective search space:   155820
Effective search space used:   155820
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 (21.7 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