GapMind for catabolism of small carbon sources

 

Alignments 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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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