Aligments for a candidate for dddA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for dddA in Pseudomonas fluorescens FW300-N2E3

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AO353_26740 AO353_26740 choline dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_26740
          Length = 550

 Score =  617 bits (1592), Expect = 0.0
 Identities = 319/542 (58%), Positives = 384/542 (70%), Gaps = 17/542 (3%)

Query: 35  AFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWR 94
           A+DYIVVGAG AGCLLANRLSA+P +RVLL+EAGGRDNY WIHIPVGYLYCI NPRTDW 
Sbjct: 7   AYDYIVVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLYCIGNPRTDWC 66

Query: 95  FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154
           F+TE   GL GRSL YPRGK LGG SSINGM+Y+RGQA DYD WA   G+  W W++ LP
Sbjct: 67  FKTEAQTGLQGRSLSYPRGKVLGGSSSINGMIYMRGQAGDYDRWAA-EGNPGWSWNDVLP 125

Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214
            F + E+H+  D           FHG  GEWR+E+QRL W +L  F +AA ++G+    D
Sbjct: 126 LFKQSENHFAGDSA---------FHGAAGEWRVERQRLSWPILDAFRSAAEQSGIASVDD 176

Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274
           FN+GDNEG   F+VNQ++G RWNA+KAFL+ V  R NLTV  S  V ++   +G  S   
Sbjct: 177 FNQGDNEGCGYFQVNQKAGVRWNAAKAFLKPVRHRPNLTVLTSVDVDRVLLENGRASR-- 234

Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334
              V+    G+  +  AR E++LSAG++GSP +LQ SGIGP  LL    I V  +L GVG
Sbjct: 235 ---VSARWQGQVNIFAARREIILSAGSVGSPSILQRSGIGPGDLLKRLGIGVAHELNGVG 291

Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394
            NLQDHLQ+R IYK++ A+TLN +A SL GK  +GL Y+  RSGP+SMAPSQL  F RS 
Sbjct: 292 RNLQDHLQLRLIYKLENARTLNQIAGSLWGKIGMGLRYLYDRSGPLSMAPSQLGAFARSG 351

Query: 395 KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISP 454
            E    NLEYHVQPLSLE FG+PLH FPA TASVC+L P SRG V I+S +P+Q P I P
Sbjct: 352 PEQTSANLEYHVQPLSLERFGEPLHAFPAFTASVCDLRPQSRGRVEIRSADPQQPPLIQP 411

Query: 455 NYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIF 514
           NYLS  ED +VAA+++R+TR I + PA   ++P E+ PG   QS+E L   A  IGTTIF
Sbjct: 412 NYLSHPEDLRVAAEAIRLTRRIVAAPALQPFNPVEYLPGAALQSEEQLHEAAARIGTTIF 471

Query: 515 HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGW 574
           HPVGT +MG D D  AVVD+ LRV G+ GLR+ DASIMP ITSGNT SPTLMIAEKAA  
Sbjct: 472 HPVGTCRMGNDAD--AVVDAQLRVHGIPGLRIADASIMPHITSGNTCSPTLMIAEKAAQL 529

Query: 575 IL 576
           IL
Sbjct: 530 IL 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: 941
Number of extensions: 39
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: 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