GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Phyllobacterium leguminum ORS 1419

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_110754457.1 C7477_RS17345 choline dehydrogenase

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



>NCBI__GCF_003217235.1:WP_110754457.1
          Length = 555

 Score =  364 bits (934), Expect = e-105
 Identities = 213/540 (39%), Positives = 305/540 (56%), Gaps = 11/540 (2%)

Query: 37  DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRFR 96
           D++++G+G+AG  LA RLS +  + V++IE GG D   +I +P    + +N    DW F 
Sbjct: 4   DFVIIGSGSAGSALAYRLSENGKHSVIVIEFGGSDIGPFIQMPAALSFPMNMATYDWGFA 63

Query: 97  TEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPDF 156
           +EP+P L GRSL+ PRGK +GG SSINGM+Y+RG ARD+D WAE +G   W + + LP F
Sbjct: 64  SEPEPHLGGRSLVTPRGKVIGGSSSINGMVYVRGHARDFDHWAE-SGARGWAFADVLPYF 122

Query: 157 MRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDFN 216
            R E+ +  + GG  +     + G  G   +++   K  +   F  A  +AG   T D+N
Sbjct: 123 KRMENAHFHENGGGGENG---WRGTDGPLHVQRGSRKNPLFHAFVEAGSQAGFQVTEDYN 179

Query: 217 RGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRCC 276
               EG  A E     G RW+A+ A+L+    R N+ +       K+   +G     R  
Sbjct: 180 GEKQEGFGAMEQTIYRGRRWSAANAYLKPALNRQNVRLVRGL-ARKVVIENG-----RAT 233

Query: 277 GVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGEN 336
           GV V   G+  V  AR EV++SA +I SP+LL LSGIGP A L E  + V+AD PGVG+N
Sbjct: 234 GVEVATGGRIRVARARREVIISASSINSPKLLMLSGIGPAAHLKERGVTVIADRPGVGQN 293

Query: 337 LQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSKE 396
           LQDHL++    +     TL +  N L  KA+IG +++  ++G  +    +   F RS   
Sbjct: 294 LQDHLEVYIQQECIQPITLYSKLN-LFSKARIGAQWLFFKTGDGATNHFESAAFVRSKPG 352

Query: 397 YEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPNY 456
            E+P+++YH  P+++   G+   +     A V  +   SRG+V ++S +P++ P I  NY
Sbjct: 353 VEYPDIQYHFLPVAIRYDGKAAAESHGFQAHVGPMRSKSRGSVTLRSADPKEKPVIRFNY 412

Query: 457 LSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFHP 516
           +S  +D       +R+TR I  Q AF  Y   E +PG   QSDE++         + FHP
Sbjct: 413 MSHPDDWADFRHCVRLTREIFGQAAFDPYRGREIQPGADVQSDEEIDDFIRAHVESAFHP 472

Query: 517 VGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWIL 576
            GTAKMG  DDPMAVVD   RV GV GLRV D+SI P IT+GN N P++M+ EKAA  IL
Sbjct: 473 CGTAKMGSVDDPMAVVDPECRVIGVEGLRVADSSIFPRITNGNLNGPSMMVGEKAADHIL 532


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: 952
Number of extensions: 53
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 579
Length of database: 555
Length adjustment: 36
Effective length of query: 543
Effective length of database: 519
Effective search space:   281817
Effective search space used:   281817
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 24 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