GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Rhizobium etli CFN 42

Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate WP_020922288.1 RHE_RS18500 TRAP transporter large permease subunit

Query= TCDB::Q8YSQ7
         (445 letters)



>NCBI__GCF_000092045.1:WP_020922288.1
          Length = 497

 Score =  470 bits (1210), Expect = e-137
 Identities = 233/430 (54%), Positives = 317/430 (73%)

Query: 10  PVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLL 69
           P MF G ++ +  G+PVAFSL  V + FG++GI  G F   FL A+P R FGI++N  LL
Sbjct: 9   PAMFLGMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFGIVSNDLLL 68

Query: 70  AIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVA 129
           AIP+F  MGA+LE+ G+AE LLE  G L G + GGLA AV+LVGA+L A TG VAA+V+ 
Sbjct: 69  AIPFFTLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITGTVAASVIT 128

Query: 130 MGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIP 189
           MG+ISLPIMLRYGY+  LATGVIAASGT+ Q+IPPS+VLVVL DQLG SVGD+++G++ P
Sbjct: 129 MGVISLPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGDMYLGAIGP 188

Query: 190 GLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSI 249
            ++  + F L VL+++ +RP   P LP +VR     AL  +V+  M+P ++LI LVLG+I
Sbjct: 189 SILQVTIFVLFVLVMSIVRPKSMPPLPKEVRGDFNWALLVKVLMGMVPSIVLIFLVLGTI 248

Query: 250 FFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLV 309
           F G ATPTEAGA+G  GA+ LAA N + T   +R+   +T  ITSMVV ILIGST FSLV
Sbjct: 249 FMGLATPTEAGALGVVGAMLLAAMNRRLTWPLIREAMTSTTHITSMVVMILIGSTCFSLV 308

Query: 310 FRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLG 369
           F+G++G +++  +L+ +PGG +GFL      +F+L FF+DFFEIAFIVIP+  PVA  LG
Sbjct: 309 FQGMDGSRWIEHMLSGIPGGPVGFLIFVNIFIFVLAFFLDFFEIAFIVIPMLAPVASSLG 368

Query: 370 IDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLL 429
           IDL+W+GV++  N+QTSF+ PPFGFALFYLR +A  +V TSDIY G +P++ +Q++++ +
Sbjct: 369 IDLIWFGVLICVNMQTSFMHPPFGFALFYLRSIASKDVKTSDIYMGALPWVGMQIILVAI 428

Query: 430 IIIFPGIVSF 439
           +I +P  V++
Sbjct: 429 VIFWPQSVTY 438


Lambda     K      H
   0.331    0.149    0.437 

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: 745
Number of extensions: 30
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: 445
Length of database: 497
Length adjustment: 33
Effective length of query: 412
Effective length of database: 464
Effective search space:   191168
Effective search space used:   191168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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