GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Acidovorax sp. GW101-3H11

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ac3H11_3320 Choline dehydrogenase (EC 1.1.99.1)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3320
          Length = 562

 Score =  778 bits (2008), Expect = 0.0
 Identities = 387/555 (69%), Positives = 439/555 (79%), Gaps = 11/555 (1%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           FD I++G GTAG LLANRLSAD  +RVLLIEAG +D+YHWIHIPVGYLYCI NPRTDW +
Sbjct: 6   FDTIIIGGGTAGALLANRLSADGRHRVLLIEAGRKDDYHWIHIPVGYLYCIGNPRTDWLY 65

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            TEPD GLNGR+L YPRGKTLGGCSSINGM+Y+RGQARDYD WAELTGD  WRWDN LP 
Sbjct: 66  NTEPDTGLNGRTLRYPRGKTLGGCSSINGMIYMRGQARDYDQWAELTGDAGWRWDNALPY 125

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHG-----GEWRIEKQRLKWQVLADFATAAVEAGVP 210
           F RHEDH+RLD+ G A+ +  + HG+      GEWR+EKQRL+W VL  FA AA +AG+P
Sbjct: 126 FRRHEDHWRLDQPGSANENFKRLHGNKATGSTGEWRVEKQRLRWDVLDAFAHAAQQAGIP 185

Query: 211 RTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGV-EQRGNLTVWHSTQVLKLDFASGE 269
            T DFN G NEGV  FEVNQ+SGWRWN +KAFLR     R N  +W S Q  KL   +  
Sbjct: 186 ATDDFNGGSNEGVGYFEVNQKSGWRWNTAKAFLRPTCYGRPNFEMWTSAQAAKLVVETQP 245

Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329
               RC GV V    + V   A  EV+LSAGA+ SPQLLQLSGIGP ALL +H I V  D
Sbjct: 246 DGSKRCTGVMVWDGQEMVTAQATGEVILSAGAVNSPQLLQLSGIGPAALLRQHGIDVAVD 305

Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389
           LPGVG NLQDHLQIR+++KV+G +TLNTMANSL+GKAKIGLEY LKRSGPMSMAPSQL  
Sbjct: 306 LPGVGANLQDHLQIRAVFKVQGVQTLNTMANSLVGKAKIGLEYALKRSGPMSMAPSQLGA 365

Query: 390 FTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQA 449
           FTRSS +  +PN+EYHVQPLSL+AFG+PLH FPA TASVCNLNPTSRGTV IKS + + A
Sbjct: 366 FTRSSADQPYPNIEYHVQPLSLDAFGEPLHSFPAFTASVCNLNPTSRGTVNIKSADFKTA 425

Query: 450 PAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509
           PAI+PNYLST EDRQVAADSLRVTR I +QPA AKY PEE+KPGVQ++SDEDLARLAGDI
Sbjct: 426 PAIAPNYLSTPEDRQVAADSLRVTRRIVAQPALAKYRPEEWKPGVQFESDEDLARLAGDI 485

Query: 510 GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRG-----VTGLRVVDASIMPTITSGNTNSPT 564
            TTIFHPVGT KMG D DPMAV+D+ +RVR      V GLRVVDA  MPTITSGNTNSPT
Sbjct: 486 ATTIFHPVGTTKMGLDGDPMAVLDAQMRVRDGRGGVVAGLRVVDAGAMPTITSGNTNSPT 545

Query: 565 LMIAEKAAGWILKSQ 579
           LM+AEKAA WI+ ++
Sbjct: 546 LMMAEKAAEWIIAAR 560


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: 1052
Number of extensions: 27
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: 562
Length adjustment: 36
Effective length of query: 543
Effective length of database: 526
Effective search space:   285618
Effective search space used:   285618
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