GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Herbaspirillum seropedicae SmR1

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate HSERO_RS24000 HSERO_RS24000 choline dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS24000
          Length = 539

 Score =  694 bits (1791), Expect = 0.0
 Identities = 343/541 (63%), Positives = 409/541 (75%), Gaps = 11/541 (2%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DYI++GAGTAGC++ANRLS     +VLLIEAG +D+Y WIHIPVGYLYCINNPRTDW F
Sbjct: 7   YDYIIIGAGTAGCVMANRLSRKTGKKVLLIEAGAKDDYIWIHIPVGYLYCINNPRTDWMF 66

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
           RTE D GLNGRSLIYPRGK LGGCSSINGM+Y+RGQARDYD WA++TGDD+WRW N LP 
Sbjct: 67  RTEADAGLNGRSLIYPRGKVLGGCSSINGMIYMRGQARDYDHWADVTGDDSWRWQNVLPL 126

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           F + ED Y L  G        +FHG GGEWR+EKQRL+W +L  F  AA E G+P+  DF
Sbjct: 127 FKKSED-YHLGAG--------QFHGAGGEWRVEKQRLRWDILDAFRDAAAENGIPKVEDF 177

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275
           N GDNEG   F+VNQ+ G RWNASKAFLR   + GNLT+   + V +L    GE   P C
Sbjct: 178 NCGDNEGCGYFDVNQKRGVRWNASKAFLRPAMKDGNLTIMTGSHVSRLRMEQGEQG-PVC 236

Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
            GV     G      A+ E +L AGAIGSP +LQ+SGI   ALL +H IPVV  LPGVGE
Sbjct: 237 TGVEFTGGGSAWFAEAK-ETILCAGAIGSPHILQMSGIADPALLQQHQIPVVHALPGVGE 295

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395
           NLQDHLQ+R ++KV GAKTLN MA++L+GK +IGL+Y+  +SGPMSMAPSQL  F +S  
Sbjct: 296 NLQDHLQMRMVFKVNGAKTLNAMASTLVGKMQIGLQYLFTQSGPMSMAPSQLGAFAKSDA 355

Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455
           +    NL+YHVQPLSLE FG PLH FPA TASVCNL PTSRG VR+ SG+   AP I+ N
Sbjct: 356 QQASANLQYHVQPLSLEKFGDPLHAFPAFTASVCNLRPTSRGHVRLASGDHALAPRITTN 415

Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515
           YLSTEED +VAA++LR+TR IA+ PA ++Y PEE+KPG  Y+++EDL R AG++GTTIFH
Sbjct: 416 YLSTEEDLKVAANALRLTRRIAASPALSRYRPEEYKPGAHYETEEDLYRAAGEVGTTIFH 475

Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575
           PVGT +MGR DD MAVVD+  RVRGV GL V DAS+MP+ITSGNTNSPT+MIAEK A  +
Sbjct: 476 PVGTCRMGRSDDAMAVVDAQGRVRGVGGLSVADASVMPSITSGNTNSPTVMIAEKVASSL 535

Query: 576 L 576
           L
Sbjct: 536 L 536


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: 939
Number of extensions: 33
Number of successful extensions: 3
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: 539
Length adjustment: 36
Effective length of query: 543
Effective length of database: 503
Effective search space:   273129
Effective search space used:   273129
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