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 GFF2134 PGA1_c21660 choline dehydrogenase BetA

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



>FitnessBrowser__Phaeo:GFF2134
          Length = 551

 Score =  367 bits (943), Expect = e-106
 Identities = 217/540 (40%), Positives = 303/540 (56%), Gaps = 14/540 (2%)

Query: 37  DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRFR 96
           DY++VGAG+AGC +A RLS +    VL+IE GG D   +I +P    Y +N    DW ++
Sbjct: 4   DYVIVGAGSAGCAMAYRLS-EAGKSVLVIEHGGTDAGPFIQMPGALSYPMNMSMYDWGYK 62

Query: 97  TEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPDF 156
           ++P+P L GR L+ PRGK +GG SSINGM+Y+RG A DY+ WAE +G   W + + LP F
Sbjct: 63  SQPEPHLGGRELVCPRGKVVGGSSSINGMVYVRGHAGDYNHWAE-SGAAGWSYADVLPYF 121

Query: 157 MRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDFN 216
            R E       GGD D     + G  G   + +      + A F  A  +AG P ++D+N
Sbjct: 122 KRMETWDDRGHGGDPD-----WRGTDGPLHVTRGPRDNPLHAAFVKAGEQAGYPVSKDYN 176

Query: 217 RGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRCC 276
               EG    E+    G RW+A+ A+L+   +R N  +  +    K+    G     R  
Sbjct: 177 GEQQEGFGPMEMTVYKGQRWSAANAYLKPALKRDNCEMIRAL-ARKVVIEDG-----RAV 230

Query: 277 GVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGEN 336
           GV VER GK  V  A  EV+L+A ++ SP+LL LSGIGP   LAEH I VV D PGVG+N
Sbjct: 231 GVEVERGGKIEVIRANAEVILAASSLNSPKLLMLSGIGPAKHLAEHGIDVVVDRPGVGQN 290

Query: 337 LQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSKE 396
           LQDHL+    +  K   TL    N L GKA +G +++  ++G  +    +   F RS K 
Sbjct: 291 LQDHLEFYFQFASKQPITLFKYWN-LFGKALVGAQWLFTKTGLGASNQFESAAFIRSDKG 349

Query: 397 YEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPNY 456
            ++P+++YH  P+++   GQ   +     A V  +   SRG V + S +P  AP I  NY
Sbjct: 350 VDYPDIQYHFLPIAVRYDGQAAAEGHGFQAHVGPMRSDSRGEVTLASADPNDAPKILFNY 409

Query: 457 LSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFHP 516
           +STE+D +     +R+TR + +Q A   +   E +PG   QSDE+L     +   + +HP
Sbjct: 410 MSTEKDWEDFRKCIRLTREVFAQDAMKPFVKHEIQPGDALQSDEELNGFIREHVESAYHP 469

Query: 517 VGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWIL 576
            GT KMG  +DPMAVVD   RV GV GLRV D+SI P IT+GN N P++M  EKA+  IL
Sbjct: 470 CGTCKMGAVEDPMAVVDPECRVIGVEGLRVADSSIFPRITNGNLNGPSIMTGEKASDHIL 529


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: 971
Number of extensions: 58
Number of successful extensions: 7
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: 551
Length adjustment: 36
Effective length of query: 543
Effective length of database: 515
Effective search space:   279645
Effective search space used:   279645
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