GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Shewanella sp. ANA-3

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)

Query= CharProtDB::CH_001857
         (699 letters)



>FitnessBrowser__ANA3:7025672
          Length = 452

 Score =  297 bits (760), Expect = 8e-85
 Identities = 178/496 (35%), Positives = 277/496 (55%), Gaps = 44/496 (8%)

Query: 23  LPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQIVFDNLPLLFAVGVAIG 82
           +PAAG++L +         +  + F+     +++  +M + G+++F  +P+LFAV VAIG
Sbjct: 1   MPAAGVMLGL--------TVSPIPFMP----EVLTVLMLAVGKLIFAIMPILFAVAVAIG 48

Query: 83  LANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAKFFTENHPAYVNMLGIPTL 142
                G+A   A+ GY VM  +++A L     +P+                  +LG+ TL
Sbjct: 49  FCRDQGIAAFTAVFGYGVMTATLAA-LADLYQLPTQL----------------LLGMETL 91

Query: 143 ATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPIVTSISALILGLIMLVIWPP 202
            TG+ GG+++G +          I LP    FF G+R   ++    A+ LG I+  +WPP
Sbjct: 92  DTGIAGGMLIGGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPP 151

Query: 203 IQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFYSPFWYEFFSYKSAAGEIIR 262
           +   +   S   V   P +A  ++G +ER LIP GLHHI+ +PF+ E   Y+    E++R
Sbjct: 152 LSLLIERVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQNSEVVR 211

Query: 263 GDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAALAIYHEAKPQNKKLVAGIMGSAA 322
           G+   ++A       L  G      Y   M+GLPAAALAI+  A+P  +  VAGIM SAA
Sbjct: 212 GEVARYLAGDPQAGNLAGG------YLIKMWGLPAAALAIWRCAEPSERNRVAGIMLSAA 265

Query: 323 LTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQLLNVKIGMTFSGGLIDYFLFG 382
             S+LTG+TEP+EF+F+FVAP LF IH L +GL++ V  +L++   + FS GL+D+ L  
Sbjct: 266 AASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLF 325

Query: 383 ILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTPGREDAAEETAAPGKTGEAGDLP 442
            L   T W++ +  G   AVIYY  FR +I  FNLKTPGR +       P +   A +  
Sbjct: 326 SLSRNTGWFVFL--GPLTAVIYYLLFRGSILAFNLKTPGRLE-------PDEPHGAKESL 376

Query: 443 YEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQLGASGVLEVGNNIQAIFGPR 502
             I+ A+G +ENI  L+AC+TRLR++V+  + V+K RL QLGA GV+ +G  +Q ++G +
Sbjct: 377 RAIIAALGGRENIVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGKGVQVVYGTK 436

Query: 503 SDGLKTQMQDIIAGRK 518
           ++ L+  +Q  +  R+
Sbjct: 437 AETLRKVLQRYLDTRR 452


Lambda     K      H
   0.323    0.141    0.412 

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: 750
Number of extensions: 32
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: 699
Length of database: 452
Length adjustment: 36
Effective length of query: 663
Effective length of database: 416
Effective search space:   275808
Effective search space used:   275808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 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