Alignments for a candidate for rhaD in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaD in Sinorhizobium medicae WSM419

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate YP_001325917.1 Smed_0223 short chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>NCBI__GCF_000017145.1:YP_001325917.1
          Length = 699

 Score = 1323 bits (3423), Expect = 0.0
 Identities = 659/699 (94%), Positives = 678/699 (96%)

Query: 1   MLDKHQGARLANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLT 60
           ML K QGARLANLWDDGKAAGMTEPE+LLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLT
Sbjct: 1   MLGKQQGARLANLWDDGKAAGMTEPERLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLT 60

Query: 61  GEIVEVLWVKGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLN 120
           GE+VEVLWVKGSGGDVGTIKMDGF+TLYMDKLRAL+GIYRGVEFEDEM GYLPHCTFNLN
Sbjct: 61  GEMVEVLWVKGSGGDVGTIKMDGFATLYMDKLRALEGIYRGVEFEDEMFGYLPHCTFNLN 120

Query: 121 PRAASIDTPLHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYEL 180
           PRAASIDTPLHAYVPK HVDHMHPDAIIAIAASKNS+ELTSKIFG EIGWLPWKRPGYEL
Sbjct: 121 PRAASIDTPLHAYVPKVHVDHMHPDAIIAIAASKNSKELTSKIFGTEIGWLPWKRPGYEL 180

Query: 181 GLWLEKFCQENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPAFGG 240
           GLWLE+FC+ENP+ARGVVLESHGLFTWGDTAK+AYETTIEIINRAIAWFETENTGPAFGG
Sbjct: 181 GLWLERFCRENPEARGVVLESHGLFTWGDTAKQAYETTIEIINRAIAWFETENTGPAFGG 240

Query: 241 RSKPVLAAADRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTS 300
            +KP LA  +R AIA+KLMPVIRGLIS  ESKVGHFDDS+AVLDFVTST+LEPLAALGTS
Sbjct: 241 PAKPALAGGERVAIARKLMPVIRGLISGAESKVGHFDDSEAVLDFVTSTNLEPLAALGTS 300

Query: 301 CPDHFLRTKIRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDP 360
           CPDHFLRTKIRPL+VDFDPAQPD+  TLAGLPEAIATYRADYAAYY+RCKRADSPA+RDP
Sbjct: 301 CPDHFLRTKIRPLIVDFDPAQPDLEKTLAGLPEAIATYRADYAAYYDRCKRADSPAIRDP 360

Query: 361 NAVVYLVPGVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWL 420
           NAVVYL+PGVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWL
Sbjct: 361 NAVVYLLPGVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWL 420

Query: 421 LEEAKLQRMPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTE 480
           LEEAKLQRMPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDE ALEAAQ E
Sbjct: 421 LEEAKLQRMPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDERALEAAQNE 480

Query: 481 LSTRYGKDFVRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALW 540
           LS RYGKDFVRSVNMNVT EAAV SGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALW
Sbjct: 481 LSNRYGKDFVRSVNMNVTDEAAVASGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALW 540

Query: 541 NKNMDILATGYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLA 600
           NKNMDILATGYFLVSREAFRIFRNQK GGNVVFVASKNGLAASPGASAYCTAKAAEIHLA
Sbjct: 541 NKNMDILATGYFLVSREAFRIFRNQKTGGNVVFVASKNGLAASPGASAYCTAKAAEIHLA 600

Query: 601 RCLALEGASAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKL 660
           RCLALEGASAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAY MDVDELEAHYRERSMLKL
Sbjct: 601 RCLALEGASAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYNMDVDELEAHYRERSMLKL 660

Query: 661 SVFPEDIAEAIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699
           SVFPEDIAEAIYFLASDMSAKSTGNIVNVDAGNAQSFTR
Sbjct: 661 SVFPEDIAEAIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699


Lambda     K      H
   0.317    0.133    0.393 

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: 1547
Number of extensions: 37
Number of successful extensions: 1
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: 699
Length of database: 699
Length adjustment: 39
Effective length of query: 660
Effective length of database: 660
Effective search space:   435600
Effective search space used:   435600
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: 54 (25.4 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 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