GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dddA in Pseudomonas fluorescens FW300-N2C3

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AO356_21730 AO356_21730 choline dehydrogenase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21730 AO356_21730 choline
           dehydrogenase
          Length = 547

 Score =  628 bits (1619), Expect = 0.0
 Identities = 318/541 (58%), Positives = 393/541 (72%), Gaps = 17/541 (3%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DY++VGAG AGCLLANRLSA+P +RVLL+EAGGRDNY WIHIPVGYL+CI NPRTDW F
Sbjct: 8   YDYVIVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLFCIGNPRTDWCF 67

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
           +TE  PGL GR+L YPRGK LGGCSSINGM+Y+RGQA DYDGWA   G+  W W++ LP 
Sbjct: 68  KTEAQPGLQGRALSYPRGKVLGGCSSINGMIYMRGQAADYDGWAA-EGNPGWAWEDVLPL 126

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           F + E+H+     G ++     FHG GGEWR+E+QRL W +L  F +AA ++G+P   DF
Sbjct: 127 FRQSENHF----AGASE-----FHGVGGEWRVERQRLSWPILDAFRSAAEQSGIPNVDDF 177

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275
           N GDNEG   F+VNQ++G RWNA+KAFL+ V QR NLTV    +V ++        + R 
Sbjct: 178 NGGDNEGCGYFQVNQKAGVRWNAAKAFLKPVRQRANLTVLTDVEVDRVLLR-----DDRA 232

Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
             V+    GK +   AR E+VL AGA+GSP +LQ SGIGP +LL    I V  +LPGVG 
Sbjct: 233 HAVSARWQGKGMTFKARKEIVLCAGAVGSPGILQRSGIGPRSLLQRLGIGVTHELPGVGG 292

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395
           NLQDHLQ+R IY+++ A+TLN +A +L GK  +GL Y+  RSGP+SMAPSQL  F RS  
Sbjct: 293 NLQDHLQLRLIYQLENARTLNQIAGTLWGKMGMGLRYLYDRSGPLSMAPSQLGAFARSGP 352

Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455
           E    NLEYHVQPLSLE FG+PLH FPA TASVC+L P SRG V I+S +P +AP I PN
Sbjct: 353 EQTSANLEYHVQPLSLERFGEPLHSFPAFTASVCDLRPQSRGRVDIRSADPHEAPLIQPN 412

Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515
           YLS  ED +VAAD++R+TR I + PA + + P E+ PG   Q++E+L + A  IGTTIFH
Sbjct: 413 YLSHPEDLRVAADAIRLTRRIVAAPALSAFKPVEYLPGPSLQTEEELHQAAARIGTTIFH 472

Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575
           PVGT +MG+D D  AVVD+ LRV G+ GLR+ DASIMP ITSGNT SPTLMIAEKAA  +
Sbjct: 473 PVGTCRMGQDRD--AVVDAQLRVHGIKGLRIADASIMPRITSGNTCSPTLMIAEKAAQMM 530

Query: 576 L 576
           L
Sbjct: 531 L 531


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: 929
Number of extensions: 37
Number of successful extensions: 6
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: 547
Length adjustment: 36
Effective length of query: 543
Effective length of database: 511
Effective search space:   277473
Effective search space used:   277473
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 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