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_1497 Choline dehydrogenase (EC 1.1.99.1)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1497
          Length = 526

 Score =  311 bits (796), Expect = 5e-89
 Identities = 201/551 (36%), Positives = 300/551 (54%), Gaps = 36/551 (6%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           FD+I++GAG+AGC+LA+RL      RVLL+EAG    + ++ +P  ++  I   R+ W +
Sbjct: 3   FDHIIIGAGSAGCVLAHRL-VRAGRRVLLLEAGPTHEHPFVRMPAAFVRVIGTERS-WDY 60

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            +EP P  NGR +  P+G+ LGG SS+N M+Y+RGQA DYD W +  G   W W + LP 
Sbjct: 61  ASEPQPHANGRRMHVPQGRMLGGGSSLNAMVYIRGQAADYDSWRD-AGCTGWGWSDVLPA 119

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           F+R E + R      A P     HG  G  ++ + R +  + A F  AA +AG+P   DF
Sbjct: 120 FVRAESNERY-----AGP----LHGRDGPLQVSEPRFRHPLSAAFVAAAQQAGLPANPDF 170

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275
           N  +  GV  ++     G R + +  +L  V +   L V     V ++   +G     R 
Sbjct: 171 NGTEQAGVGFYQSTTFRGERGSTAATYLAAVRRDERLAVRTGVHVRRILVEAG-----RA 225

Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
            GV    AG+        +V+LSAGA+ SPQLL LSGIGP   L +  IPV AD  GVG+
Sbjct: 226 VGVEFMEAGQLQQVRCAQDVLLSAGALASPQLLMLSGIGPGEDLHKLGIPVHADSAGVGQ 285

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGK------AKIGLEYILKRSGPMSMAPSQLCI 389
           N QDHL++ S+Y    A+T   +  SL+G+       + GL++ L RSG ++    +   
Sbjct: 286 NYQDHLEV-SVY----ARTRRPI--SLLGQDQGLRALRHGLQWQLLRSGLLTSNVVESGG 338

Query: 390 FTRSSKEYEHPNLEYHVQPLSL-EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448
           F   +     P++++HV P+ + +   +PL     ++ + C L P SRGTV ++S +P  
Sbjct: 339 FV-DTLGTGRPDVQFHVLPVLVGDVEREPLPGH-GLSINPCFLRPQSRGTVSLRSPDPAH 396

Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQ-SDEDLARLAG 507
                   L  + D       +++ R I   PA A+    E  PG +   SD  +     
Sbjct: 397 PILFDAGALRVQADVDTLVRGVKLARRILRAPALAEVVEHELLPGAEATLSDAQVEAHVR 456

Query: 508 DIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMI 567
               T++HP GT +MG   D  +VVD+HLRVRGV GLRV DAS+MPT+ SGNTN+PT+M+
Sbjct: 457 SHAKTVYHPAGTCRMG--GDATSVVDTHLRVRGVAGLRVCDASVMPTLPSGNTNAPTIML 514

Query: 568 AEKAAGWILKS 578
           AE+ A ++L++
Sbjct: 515 AERCAEFVLQA 525


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: 875
Number of extensions: 48
Number of successful extensions: 9
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: 526
Length adjustment: 36
Effective length of query: 543
Effective length of database: 490
Effective search space:   266070
Effective search space used:   266070
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