Aligments for a candidate for treEIIA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for treEIIA 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)



>lcl|FitnessBrowser__ANA3:7025672 Shewana3_2822 PTS system,
           glucose-like IIB subunint (RefSeq)
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources