Alignments for a candidate for dddA in Halioglobus japonicus S1-36

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Halioglobus japonicus S1-36

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_084200303.1 C0029_RS03565 choline dehydrogenase

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



>NCBI__GCF_002869505.1:WP_084200303.1
          Length = 536

 Score =  604 bits (1558), Expect = e-177
 Identities = 312/548 (56%), Positives = 387/548 (70%), Gaps = 14/548 (2%)

Query: 33  THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTD 92
           T  +DYI++GAGTAGC+LANRLSADP  +VLL+EAGG+D+Y WI+IPVGYL+ I NPRTD
Sbjct: 2   TQTYDYIIIGAGTAGCVLANRLSADPETQVLLLEAGGKDDYFWINIPVGYLFTIGNPRTD 61

Query: 93  WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152
           W F TEPD GLNGRSL Y RGK LGGCSSIN M+Y+RGQ  DYD WA   G+  W W + 
Sbjct: 62  WCFETEPDDGLNGRSLGYARGKVLGGCSSINAMVYMRGQQYDYDQWAA-AGNQGWGWKDV 120

Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212
           LP F + E +    + G ++     FHG  GE R+E++R+ W +L  +  AA E G+PR 
Sbjct: 121 LPVFKQSESY----QHGASE-----FHGDQGELRVEERRVSWDILDAWRDAAAETGIPRI 171

Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272
            ++NRGDN G   F++NQR G R +A+ AFL  V+ R NLT+     V  L+  S +  +
Sbjct: 172 EEYNRGDNFGTAYFQMNQRKGQRCSAAHAFLHPVKDRPNLTIKTQAMVHGLELDSSD-DK 230

Query: 273 PRCCGVTVERA-GKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLP 331
            R  GV      G+  +  AR EV+L+AG+IGSPQLLQLSGIGP  LL +H I V  +L 
Sbjct: 231 LRATGVKARIGKGEAQIFKARKEVILAAGSIGSPQLLQLSGIGPRPLLEKHGIEVRQELI 290

Query: 332 GVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFT 391
           GVGENLQDHLQIR++Y+V    TLNT+ +SL GK K+GL+Y+L R+GP++M PSQL  F 
Sbjct: 291 GVGENLQDHLQIRTVYRVSNTTTLNTLYHSLWGKLKMGLQYLLFRTGPLTMPPSQLGAFA 350

Query: 392 RSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPA 451
           +S      P+LE+HVQPLSL+ FG PLH F AIT SVCNL PTSRG V I+S +P  AP 
Sbjct: 351 KSDSNLATPDLEWHVQPLSLDKFGDPLHTFDAITPSVCNLRPTSRGHVHIRSPDPEAAPE 410

Query: 452 ISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGT 511
           I  NYLSTE DR+ A + L+ TR I +  A   + PEE KPG   +++EDLAR AGD+GT
Sbjct: 411 IKLNYLSTEADRKAAVEGLKFTRRIMASDAMKPFSPEELKPGPNIETEEDLARAAGDLGT 470

Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571
           TIFHPVGT KMGR  DPMAVVD  LRV GV GLRVVDASIMPTI SGNTN+PT+MIAE+ 
Sbjct: 471 TIFHPVGTCKMGR--DPMAVVDERLRVHGVAGLRVVDASIMPTIVSGNTNAPTVMIAEQG 528

Query: 572 AGWILKSQ 579
           A +IL  +
Sbjct: 529 AAFILSEK 536


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: 917
Number of extensions: 31
Number of successful extensions: 5
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: 536
Length adjustment: 36
Effective length of query: 543
Effective length of database: 500
Effective search space:   271500
Effective search space used:   271500
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources