Alignments for a candidate for dddA in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Sphingomonas histidinilytica UM2

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_079649446.1 B5X82_RS17375 choline dehydrogenase

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



>NCBI__GCF_900167915.1:WP_079649446.1
          Length = 561

 Score =  346 bits (888), Expect = 1e-99
 Identities = 222/563 (39%), Positives = 301/563 (53%), Gaps = 44/563 (7%)

Query: 37  DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRD--------------NYHWIHIPVGY 82
           DY+++GAG+AGC+LANRLSAD  ++V+++EAG  D              N + IH+P G+
Sbjct: 16  DYVIIGAGSAGCVLANRLSADGRHKVVVLEAGADDRPTRNLSDPAQAIANIN-IHMPAGF 74

Query: 83  LYCINNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELT 142
              + +P+ +W + T+PDPG  GR   +PRGK LGG SSINGML++RG   DY GW +L 
Sbjct: 75  TRMLKDPKVNWNYMTDPDPGTEGRQHSFPRGKVLGGSSSINGMLWVRGLPEDYQGWRQL- 133

Query: 143 GDDAWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFAT 202
           G D W WD+  P F R E  +   +  +A P         G   +    +K  +L     
Sbjct: 134 GCDGWSWDDVEPYFRRIEHQHGEGQISEAQP---------GPLHVSDVPIKHAMLDVMTR 184

Query: 203 AAVEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLK 262
           A  EAG P + D N    EGV    +N R+G R +A+ A+L    +R NLTV       +
Sbjct: 185 AFEEAGAPVSTDLNGTTREGVARVRLNARNGVRVSAAVAYLHPAMKRPNLTVQLRAHATR 244

Query: 263 LDFASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEH 322
           L F   EG   +  GV   + G +    AR EV+LS GAI SPQLL+LSGIG    L   
Sbjct: 245 LLF---EGR--KAIGVEYVQGGVRKQVRARREVILSGGAINSPQLLELSGIGDGERLRAL 299

Query: 323 AIPVVADLPGVGENLQDHLQIRSIYKVK-GAKTLNTMANS--LIGKAKIGLEYILKRSGP 379
            I V+ D P VGENLQDH       ++K G+   N ++    L+G+    L Y   RSG 
Sbjct: 300 GIDVLVDRPRVGENLQDHYAAMVRARMKPGSAGFNELSRGVRLMGQL---LRYAFTRSGL 356

Query: 380 MSMAPSQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHD------FPAITASVCNLNP 433
           +++  S L  F +S    + P++++   P +++  G   H        P +T     + P
Sbjct: 357 LALGGSNLTAFLKSDPALDLPDIQFFASPATVDFEGLAKHGTMSMERAPGMTVGGYVMRP 416

Query: 434 TSRGTVRIKSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPG 493
            S G++ I S + R  P+I PNYL+ E DR+    SLR  R I   PA A Y   E  PG
Sbjct: 417 RSHGSIHITSPDYRDHPSIKPNYLADEADRRAQIASLRWARRIMHSPALAPYFDHELTPG 476

Query: 494 VQYQSDEDLARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMP 553
            + QSDE L   A   G+T +H   T  MG   D  AVV   LRV G+  LRVVDAS+MP
Sbjct: 477 AEVQSDEALLAFARASGSTGYHQSCTCAMGPGAD--AVVSPTLRVNGIERLRVVDASVMP 534

Query: 554 TITSGNTNSPTLMIAEKAAGWIL 576
            I SGNT++ T+MIAEKAA  IL
Sbjct: 535 NIVSGNTHAATVMIAEKAADLIL 557


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: 968
Number of extensions: 44
Number of successful extensions: 8
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: 561
Length adjustment: 36
Effective length of query: 543
Effective length of database: 525
Effective search space:   285075
Effective search space used:   285075
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