GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_21730
          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:

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