Alignments for a candidate for dddA in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Sinorhizobium medicae WSM419

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_028053538.1 SMED_RS24235 GMC family oxidoreductase N-terminal domain-containing protein

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



>NCBI__GCF_000017145.1:WP_028053538.1
          Length = 533

 Score =  437 bits (1123), Expect = e-127
 Identities = 239/545 (43%), Positives = 321/545 (58%), Gaps = 14/545 (2%)

Query: 32  NTHAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRT 91
           N   FDYIVVGAG++GC +A RLS D   RV L+EAG +D   WIH+P+GY   + + R 
Sbjct: 2   NEAQFDYIVVGAGSSGCTVAARLSEDGRFRVALVEAGPKDTSPWIHLPLGYGKTMWDERI 61

Query: 92  DWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDN 151
           +W+  TEPDP +NGR + +PRGK LGGCS+ING++ +RGQA DYD WA   GD  W + N
Sbjct: 62  NWKLYTEPDPNMNGRRIYWPRGKVLGGCSAINGLIAIRGQAEDYDDWARYGGDQ-WNYRN 120

Query: 152 CLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPR 211
            LP F + E        G A+P+   FHG  G   +   R +  ++  F  +A + G+P 
Sbjct: 121 VLPHFRKSESF-----AGAANPE---FHGKHGPICVAPIRHRHPLIDAFIGSANQLGIPC 172

Query: 212 TRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGS 271
             DFN    EGV  + +  R+G R +A+  +LR  ++R NLT+     V K+ F   EG 
Sbjct: 173 NDDFNGPSQEGVGYYSLTTRNGMRSSAAVGYLRPAKRRSNLTIVTEALVTKVRF---EGR 229

Query: 272 EPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLP 331
             R  G+     G+K+   AR  V+LSAGA+ +P L+ LSGIGP A L  H I VVAD+P
Sbjct: 230 --RAQGIDYTTNGRKMSMNARRGVILSAGAVHTPHLMMLSGIGPAAHLKAHGIDVVADMP 287

Query: 332 GVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFT 391
           GVG NL+DHLQ+R IY+     T N   NSL GK KIGL+++L R+GP+++  +Q  +F 
Sbjct: 288 GVGANLRDHLQLRLIYRCNRPITTNDELNSLTGKVKIGLQWLLTRTGPLAVGINQGGLFA 347

Query: 392 RSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPA 451
           R   +   P++++HV  LS +  G  +H F   T SVC L P S GT+R+   +P   P 
Sbjct: 348 RVMPDATRPDVQFHVATLSADMAGGKVHPFSGFTMSVCQLRPESHGTIRLACADPTTPPL 407

Query: 452 ISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGT 511
           I  NYL  E DRQ+A   +R+ R IA     ++    E  PG    S E +   A   G 
Sbjct: 408 IHANYLDAELDRQIAIGGIRLARRIARTGPLSQLVTREELPGESVDSKEGILDFARQNGA 467

Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571
           TIFHP  T +MG+DDD  AVV   L+VRG  GL + D S+MPTI SGNTN P +MI EK 
Sbjct: 468 TIFHPTSTCRMGQDDDADAVVRPDLKVRGFDGLWIADCSVMPTIVSGNTNLPAIMIGEKL 527

Query: 572 AGWIL 576
           +  IL
Sbjct: 528 SSSIL 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: 804
Number of extensions: 33
Number of successful extensions: 4
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: 533
Length adjustment: 36
Effective length of query: 543
Effective length of database: 497
Effective search space:   269871
Effective search space used:   269871
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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