GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Shewanella oneidensis MR-1

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 201293 SO2136 aldehyde-alcohol dehydrogenase (NCBI ptt file)

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>FitnessBrowser__MR1:201293
          Length = 866

 Score =  199 bits (507), Expect = 2e-55
 Identities = 140/389 (35%), Positives = 207/389 (53%), Gaps = 31/389 (7%)

Query: 8   IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67
           +PS       SL  A+  ++D    R LIVTD  L   G   +  K L+ + + + ++  
Sbjct: 456 LPSSIYFRRGSLPIALEELSDK--KRALIVTDPFLFNQGYCDETLKILKAQGLETEVFYE 513

Query: 68  TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGI-----------ALVAANGGD 116
            + +PT   V  G K+      D +I+LGGGSP D AK I           A +A    D
Sbjct: 514 VEADPTLATVRQGAKVANSFKPDVIIALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMD 573

Query: 117 IRDYEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVND 176
           IR           +  M+AI TT+GT SE+T F ++TDE    K  I D  +TP +++ D
Sbjct: 574 IRKRIYKFPKMGVKATMVAIPTTSGTGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVD 633

Query: 177 SSLMIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSN 236
            +L++ MPKSLTA  G+DA+THA+EAYVS+ A   +D  AL+A+ ++ + LP A + G+ 
Sbjct: 634 PNLVMDMPKSLTAFGGIDAITHALEAYVSVMANEYSDGQALQALDLLCKYLPDAYQLGAA 693

Query: 237 AK-AREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFN--- 292
           +  ARE +     +AG+AF NA LG  H+MAH+LG  ++L HG+ NA+L+ +V  FN   
Sbjct: 694 SPIAREKVHNGATIAGIAFANAFLGICHSMAHKLGAEFHLAHGLANALLISNVIRFNATD 753

Query: 293 --SKVAA--------ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRD 342
             +K AA        A  R  A A  + + G +DA+  E  +  I +L K + IPA +++
Sbjct: 754 LPTKQAAFSQYDRPKALCRYAAIADHLALGGNSDAQKVEKLLEKIEQLKKTLGIPASIQE 813

Query: 343 LNVKEEDFA----VLATNALKDACGFTNP 367
             V E DF     +LA +A  D C   NP
Sbjct: 814 AGVNEADFLAKLDMLAEDAFDDQCTGANP 842


Lambda     K      H
   0.318    0.131    0.373 

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: 650
Number of extensions: 27
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: 383
Length of database: 866
Length adjustment: 36
Effective length of query: 347
Effective length of database: 830
Effective search space:   288010
Effective search space used:   288010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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