GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dddA in Phaeobacter inhibens BS107

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF3501 PGA1_c35540 alcohol dehydrogenase AlkJ

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



>lcl|FitnessBrowser__Phaeo:GFF3501 PGA1_c35540 alcohol dehydrogenase
           AlkJ
          Length = 538

 Score =  332 bits (850), Expect = 3e-95
 Identities = 207/546 (37%), Positives = 288/546 (52%), Gaps = 31/546 (5%)

Query: 37  DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCI-NNPR-TDWR 94
           DY++VG G+AG  LA+RLS DP   V L+EAGGR +   +  P   +  +   P+  +W 
Sbjct: 4   DYVIVGGGSAGSTLASRLSEDPDVTVCLLEAGGRGDGLLVRAPAAVVAMLPGRPKINNWA 63

Query: 95  FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154
           + T P PGLNGR    PRGK LGG S+IN MLY+RG ++DYD WA L G + W W + LP
Sbjct: 64  YETVPQPGLNGRRGYQPRGKGLGGSSAINAMLYIRGHSKDYDEWAAL-GCEGWDWQSVLP 122

Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214
            F + E++ R D+           HG  G  ++  Q+    +   F  A     +    D
Sbjct: 123 YFRKSENNERGDDA---------LHGAAGPLQVSNQKSPRPITDAFVKAGRSLQIRHRED 173

Query: 215 FNRGDNEGVDAFEVNQ-----RSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGE 269
           FN GDNEG+  ++V Q     R+G R +A+ A+L  V  R NLTV    Q   + F   E
Sbjct: 174 FNSGDNEGIGHYQVTQFHRDDRNGERCSAAAAYLHPVMDRPNLTVITRAQASSVAF---E 230

Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329
           G   R  GV   + G+  +  AR EV+LS GA  SPQLLQLSG+G    +  H I +V +
Sbjct: 231 GK--RAVGVRYSQGGRAHMVRARREVILSGGAFNSPQLLQLSGVGRPDDICPHGIDMVHE 288

Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389
           LPGVG+NLQDHL     YK +            +   +    +     G ++   ++   
Sbjct: 289 LPGVGQNLQDHLDFTLAYKSRDRDNFGISLPGSVSLLRHIWNWRKTGRGMIATPFAEGAA 348

Query: 390 FTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQA 449
           F ++    +  +++ H     ++   + LH     +  +C L P SRG+V + S +P+ A
Sbjct: 349 FLKTDPNKKRADVQLHFVISIVDDHARKLHMGHGFSCHICVLRPKSRGSVGLNSADPKAA 408

Query: 450 PAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509
           P I P +L+  ED  V    +R TR I +    A Y   E    +    + D A L   I
Sbjct: 409 PRIDPQFLADPEDLAVLIKGVRKTRQIMAAEPLAGYVHRE----LFINGEPDDAALEQHI 464

Query: 510 ---GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566
                TI+HPVGT KMG   DP++VVD  LRV G+ GLRVVDAS+MP +  GNTN+PT+M
Sbjct: 465 RARADTIYHPVGTCKMG--TDPLSVVDPSLRVHGLQGLRVVDASVMPRLIGGNTNAPTIM 522

Query: 567 IAEKAA 572
           IAEKAA
Sbjct: 523 IAEKAA 528


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: 957
Number of extensions: 51
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: 538
Length adjustment: 36
Effective length of query: 543
Effective length of database: 502
Effective search space:   272586
Effective search space used:   272586
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 preprint 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