GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3501
          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:

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