Aligments for a candidate for dddA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for dddA in Pseudomonas putida KT2440

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PP_0056 PP_0056 choline dehydrogenase

Query= metacyc::MONOMER-15202
         (579 letters)



>FitnessBrowser__Putida:PP_0056
          Length = 550

 Score =  615 bits (1587), Expect = e-180
 Identities = 323/544 (59%), Positives = 380/544 (69%), Gaps = 21/544 (3%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           FDY+VVGAG AGCLLANRLSADP+ RVLL+EAGGRDNY WIHIPVGYLYCI NPRTDW F
Sbjct: 10  FDYVVVGAGPAGCLLANRLSADPSCRVLLLEAGGRDNYPWIHIPVGYLYCIGNPRTDWCF 69

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
           +TE  PGL GR+L YPRGK LGGCSSINGM+Y+RGQA DYD WA   G+D W W + LP 
Sbjct: 70  KTEAQPGLGGRALGYPRGKVLGGCSSINGMIYMRGQAADYDHWAA-QGNDGWAWKDVLPL 128

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           F   E+H+          +H   HG  GEWR+E+QR  W +L  F  AA ++G+ +  DF
Sbjct: 129 FKASENHFA------GASEH---HGAEGEWRVERQRYSWPILDAFRDAAEQSGIGKVDDF 179

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQV--LKLDFASGEGSEP 273
           N GDN+G   F+VNQRSG RWNASKAFLR ++ R NLTV    QV  + LD       + 
Sbjct: 180 NTGDNQGCGYFQVNQRSGVRWNASKAFLRPIKDRANLTVLTGVQVDQVLLDNTRARAVKA 239

Query: 274 RCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGV 333
              G   E A       AR E++L AGA+GSP +LQ SGIGP  LL    I V  D+PGV
Sbjct: 240 LWQGAWHEFA-------ARREIILCAGAVGSPGILQRSGIGPRQLLESLGIGVRHDMPGV 292

Query: 334 GENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRS 393
           G NLQDHLQ+R IY+++  +TLN MANSL GK  +GL Y+  RSGP++MAPSQL  F RS
Sbjct: 293 GGNLQDHLQLRLIYQIRNTRTLNQMANSLWGKMGMGLRYLYDRSGPLAMAPSQLGAFVRS 352

Query: 394 SKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAIS 453
           S E    NL+YHVQPLSLE FG+PLH FPA TASVCNL P SRG + I S +    P I 
Sbjct: 353 SPEQATANLQYHVQPLSLERFGEPLHQFPAFTASVCNLRPASRGRIDICSTDMNSTPRID 412

Query: 454 PNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTI 513
           PNYLS  +D +VAAD++R+TR I   PA A ++P+E+ PG   QS+EDL   AG IGTTI
Sbjct: 413 PNYLSAPQDLRVAADAIRLTRRIVQAPALAAFEPKEYLPGPALQSEEDLFEAAGKIGTTI 472

Query: 514 FHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAG 573
           FHPVGT +MG  +  M VVD+ LRV G+ GLRV DASIMP ITSGNT SPTLMIAEKAA 
Sbjct: 473 FHPVGTCRMG--NGAMDVVDNQLRVHGIPGLRVADASIMPQITSGNTCSPTLMIAEKAAQ 530

Query: 574 WILK 577
            ILK
Sbjct: 531 LILK 534


Lambda     K      H
   0.318    0.135    0.418 

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: 949
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: 579
Length of database: 550
Length adjustment: 36
Effective length of query: 543
Effective length of database: 514
Effective search space:   279102
Effective search space used:   279102
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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