GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Sinorhizobium meliloti 1021

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate SMc03116 SMc03116 alcohol dehydrogenase

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



>FitnessBrowser__Smeli:SMc03116
          Length = 531

 Score =  665 bits (1715), Expect = 0.0
 Identities = 339/541 (62%), Positives = 395/541 (73%), Gaps = 17/541 (3%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           FDYI+VGAG+AGC+LANRLS DP  RVLL+EAGG DNYHWIHIPVGYLYCINNPRTDW F
Sbjct: 4   FDYIIVGAGSAGCVLANRLSEDPDRRVLLLEAGGSDNYHWIHIPVGYLYCINNPRTDWCF 63

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            T  + GLNGRSL YPRGK LGGCSSINGM+Y+RGQARDYD W +L G   W W++ LP 
Sbjct: 64  TTAAEEGLNGRSLGYPRGKVLGGCSSINGMIYMRGQARDYDLWRQL-GCPGWSWNDVLPF 122

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           F + E+HYR   G D        HG  GEWR+EK R++W VL  F  AA EAG+P T DF
Sbjct: 123 FRKSENHYR---GAD------DMHGASGEWRVEKARVRWAVLDAFQKAATEAGIPETDDF 173

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275
           NRG+NEG   F+VNQRSG RWN +KAFL+    R NLT+     V +L    G     R 
Sbjct: 174 NRGNNEGSGYFDVNQRSGIRWNTAKAFLKPARNRRNLTILTKAHVRRLILEDG-----RV 228

Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
            GV  +  G      AR E VLSAGAIGSP +L+LSGIG   +L E+ I V  +LP VGE
Sbjct: 229 AGVEFQHDGTVKSARARRETVLSAGAIGSPHILELSGIGRPDVLHENGIEVRHELPSVGE 288

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395
           NLQDHLQ+R  YKV G  TLN  A SL GKA IGLEY+++RSGPM+MAPSQL IFTRS  
Sbjct: 289 NLQDHLQLRLAYKVTGVPTLNEKATSLFGKAAIGLEYLVRRSGPMAMAPSQLGIFTRSGP 348

Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455
           E E P+L+YHVQP++LE FG+P+H FPA+TASVCNL P SRG+V +K  +   AP I P 
Sbjct: 349 EKETPDLQYHVQPVTLEKFGEPVHPFPAVTASVCNLRPESRGSVHLKGPDFAAAPDIRPR 408

Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515
           YL+ E DR VA  S+R+TR I +QPAFA+Y P EFKPG  YQ+DE+L R AGDIGTTIFH
Sbjct: 409 YLTAEADRDVAVKSIRLTRRIVAQPAFARYKPVEFKPGPDYQTDEELKRAAGDIGTTIFH 468

Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575
           PVGT +MG   DP +VVD  LR+RG+ GLR+ DASIMPTITSGNTNSPT+MIAEKAA  I
Sbjct: 469 PVGTCRMG--SDPDSVVDPELRLRGIAGLRIADASIMPTITSGNTNSPTIMIAEKAAEMI 526

Query: 576 L 576
           L
Sbjct: 527 L 527


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: 940
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: 531
Length adjustment: 36
Effective length of query: 543
Effective length of database: 495
Effective search space:   268785
Effective search space used:   268785
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