GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc03116 SMc03116 alcohol dehydrogenase
          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 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