GapMind for catabolism of small carbon sources

 

Alignments 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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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