GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malEIICBA in Shewanella oneidensis MR-1

Align Maltose/Maltotriose PTS transporter, MalT (Shelburne et al., 2008) 631aas (68% identical to 4.A.1.1.11 from S. mutans (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= TCDB::Q48WG5
         (631 letters)



>lcl|FitnessBrowser__MR1:200788 SO1623 PTS system, glucose-specific
           IIBC component (NCBI ptt file)
          Length = 499

 Score =  153 bits (386), Expect = 2e-41
 Identities = 126/419 (30%), Positives = 199/419 (47%), Gaps = 56/419 (13%)

Query: 41  VLESPALNTGVFVGIIAGFVGATAYNKYYNYRKLPEVLTFFNGKRFVPFVVILRSIFVAL 100
           VL    L+TG+  G++ G V   A  ++  Y +LP + +FF G+R    ++I  ++ +  
Sbjct: 126 VLGMETLDTGIAGGMLIGGVTCFAV-RWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGY 184

Query: 101 ILVVVWPVIQSGINSFGMWIASSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPMNYTAL 160
           +L  +WP +   I     W    +   P +A  +YG LERLL+P GLHH+   P      
Sbjct: 185 VLAHIWPSLSLLIERVSDWAVYQK---PAIAFGVYGALERLLIPLGLHHIWNAPFYLEV- 240

Query: 161 GGTYEVMTGAAAGTKVFGQDPLWLAWVTDLVHLKGSDASAYSHLMDSVTPARFKVGQMIG 220
            G Y++         V G+   +LA      +L G                    G +I 
Sbjct: 241 -GQYQLQDAEV----VRGEVARYLAGDPQAGNLAG--------------------GYLIK 275

Query: 221 ATGTLMGVALAMYRNVDADKKHTYKMMFISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYA 280
             G L   ALA++R  D  +++    + +SAAAA +LTGVTEP+E+ FMF A  L++++ 
Sbjct: 276 MWG-LPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPLLFLIHV 334

Query: 281 LVQGASF---AMADLVNLRVHSFGNIELLTRTPMALKAGLGMDVINFVWVSVLFAVIMYF 337
           ++ G ++    M D+ +  V S G ++      ++   G       F  +  L AVI Y 
Sbjct: 335 MLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGW------FAVLGPLTAVIYYI 388

Query: 338 IADMMIKKMHLATAGRLGNYDADILGDRNTQTRPTQVADSNSQVVQIVNLLGGAGNIDDV 397
           +    I   +L T GRL             Q+  T+   S   +  I+  LGG  NI ++
Sbjct: 389 LFRGSILAFNLKTPGRL-------------QSDGTK--GSKESLRAIIAALGGRDNIVEL 433

Query: 398 DACMTRLRVTVKDPAKVGAEDDWKKAGAIGLIQKGNGVQAVYGPKADILKSDIQDLLDS 456
           +AC+TRLR++V  P  V  +    + GA G+I  G GVQ VYG KA+ L+  +Q  LD+
Sbjct: 434 NACLTRLRLSVHSPELVN-KVRLSQLGAKGVIVMGKGVQIVYGTKAETLRKVLQRYLDT 491


Lambda     K      H
   0.322    0.137    0.396 

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: 638
Number of extensions: 29
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: 631
Length of database: 499
Length adjustment: 36
Effective length of query: 595
Effective length of database: 463
Effective search space:   275485
Effective search space used:   275485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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