GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pseudomonas putida KT2440

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate PP_2803 PP_2803 1,3-propanediol dehydrogenase

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



>FitnessBrowser__Putida:PP_2803
          Length = 394

 Score =  222 bits (565), Expect = 2e-62
 Identities = 128/325 (39%), Positives = 192/325 (59%), Gaps = 1/325 (0%)

Query: 32  KALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTEELVQKGFAAYQSAECDYI 91
           + LIVTD  +   GLLDS++++LD+  ++Y    ++  NP  + +      Y+    D +
Sbjct: 41  RVLIVTDAGVKAAGLLDSVYASLDKAGIAYEEVADIKANPRSDDINHTAQRYRGTGIDGL 100

Query: 92  IAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLVAINTTAGTAAEMTSNAVI 151
           +A GGGS +D AKA+ +L  + G    Y G   + +A  P+VAI TTAGT +E+T  +VI
Sbjct: 101 LAVGGGSAMDAAKAISLLLTHDGRIEDYEGSFTLTHAIPPIVAIPTTAGTGSEVTCFSVI 160

Query: 152 IDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMDALTHAVEAYVSVGAHPLT 211
            D+AR  K  ++D  I P +A+ D+ +   +P S+ AATGMDALTHA+EAY    A+P++
Sbjct: 161 TDTARHFKMNVLDYRIGPVLALLDSHITDTLPPSIAAATGMDALTHAIEAYTCRVANPIS 220

Query: 212 DANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGAT 271
           D  AL AIRLI+  L  AV +  N  AREQM     +AGMAF +A +G VH ++   G  
Sbjct: 221 DGLALHAIRLISQHLKAAVQEPDNQAAREQMLVASLIAGMAFGNADVGSVHCISEAIGGM 280

Query: 272 HNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETRGMSDEAASQEAINAIRTLSK 331
           ++ PHGV NAI LP V   NR   + R A++A A+G++   +S   A++ A+  +  +SK
Sbjct: 281 YDTPHGVGNAIFLPFVFGHNRDADIVRHAQVAYALGIDPT-LSPVDAAEAAVGHLFQMSK 339

Query: 332 RVGIPEGFSKLGVTKEDIEGWLDKA 356
            +GIP      GV +ED     +K+
Sbjct: 340 DLGIPRFAEVKGVREEDFPTIAEKS 364


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: 411
Number of extensions: 17
Number of successful extensions: 2
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: 394
Length adjustment: 30
Effective length of query: 352
Effective length of database: 364
Effective search space:   128128
Effective search space used:   128128
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