GapMind for catabolism of small carbon sources

 

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

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 200661 SO1490 alcohol dehydrogenase II (NCBI ptt file)

Query= metacyc::STM4044-MONOMER
         (382 letters)



>FitnessBrowser__MR1:200661
          Length = 382

 Score =  340 bits (872), Expect = 4e-98
 Identities = 181/382 (47%), Positives = 249/382 (65%)

Query: 1   MSFMLALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMS 60
           M+    +P +++ G GA+ D +  +    + +ALIVTD  LV +GL+  +   L ++ ++
Sbjct: 1   MAAKFFIPSVNVLGKGAVDDAIGDIKTLGFKRALIVTDKPLVNIGLVGEVAEKLGQNGIT 60

Query: 61  YHLFDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYS 120
             +FD V PNPT   V+ G A  ++ +CD++I+ GGGSP D AK + ++  N G    Y 
Sbjct: 61  STVFDGVQPNPTVGNVEAGLALLKANQCDFVISLGGGSPHDCAKGIALVATNGGSIKDYE 120

Query: 121 GVGKVKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVML 180
           G+ K     +PLVAINTTAGTA+EMT   +I D AR +K  I+D +  P ++V+D  +ML
Sbjct: 121 GLDKSTKPQLPLVAINTTAGTASEMTRFCIITDEARHIKMAIVDKHTTPILSVNDPELML 180

Query: 181 EIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEARE 240
           + PAS+TAATGMDALTHAVEAYVS+ A+P+TDA A++AI LI   L  AV  G ++EARE
Sbjct: 181 KKPASLTAATGMDALTHAVEAYVSIAANPITDACAIKAIELIQGNLVNAVKQGQDIEARE 240

Query: 241 QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFA 300
           QMA+ Q+LAGMAFN+A LG VHA+AHQ G  ++LPHGVCNA+LLP V+ +N      R  
Sbjct: 241 QMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNALLLPHVQEYNAKVVPHRLK 300

Query: 301 RIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADP 360
            IA+AMGV+   M+DE  +  AI AI+TLS  V IPE  + LGV  EDI    D AL D 
Sbjct: 301 DIAKAMGVDVAKMTDEQGAAAAITAIKTLSVAVNIPENLTLLGVKAEDIPTLADNALKDA 360

Query: 361 CAPCNPRTASRDEVRGLYLEAL 382
           C   NP+ A+  E+  ++  AL
Sbjct: 361 CGFTNPKQATHAEICQIFTNAL 382


Lambda     K      H
   0.317    0.133    0.384 

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: 409
Number of extensions: 19
Number of successful extensions: 1
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 (21.7 bits)
S2: 50 (23.9 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