GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Rhizobium etli CFN 42

Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_020922288.1 RHE_RS18500 TRAP transporter large permease subunit

Query= reanno::SB2B:6938090
         (466 letters)



>NCBI__GCF_000092045.1:WP_020922288.1
          Length = 497

 Score =  175 bits (444), Expect = 3e-48
 Identities = 134/460 (29%), Positives = 214/460 (46%), Gaps = 51/460 (11%)

Query: 6   LFLTLFLCMLLGMPIAIALGFSSMLTILL------FSNDSLASVALKLYEATSEHYTLLA 59
           +FL + + ML G P+A +L    M   ++      FS   L ++ L+ +   S    LLA
Sbjct: 11  MFLGMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFGIVSNDL-LLA 69

Query: 60  IPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAI 119
           IPFF L  A L   G+A  +++      G I GGLA A ++   +  A++G+  A+V  +
Sbjct: 70  IPFFTLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITGTVAASVITM 129

Query: 120 GSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPG 179
           G I +  M+R GY  + A GVI  SGT+  +IPPS+V++V A     S   M++  + P 
Sbjct: 130 GVISLPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGDMYLGAIGPS 189

Query: 180 LLMGVL--LMVAIYIVARIKNLPSRP--FPGVKALSLSSAKAMG---GLALIFIVLGSIY 232
           +L   +  L V +  + R K++P  P    G    +L     MG    + LIF+VLG+I+
Sbjct: 190 ILQVTIFVLFVLVMSIVRPKSMPPLPKEVRGDFNWALLVKVLMGMVPSIVLIFLVLGTIF 249

Query: 233 GGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIK 292
            G+A+PTEA A+  V A L+A    R   PL                             
Sbjct: 250 MGLATPTEAGALGVVGAMLLAAMNRRLTWPL----------------------------- 280

Query: 293 TPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLI 352
                 IR  +     ++ M++ I+  +  F+ V         I   + G    P GFLI
Sbjct: 281 ------IREAMTSTTHITSMVVMILIGSTCFSLVFQGMDGSRWIEHMLSGIPGGPVGFLI 334

Query: 353 IVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLN 412
            VN+ +     F++   I  I+ P+L P+A  LGID I  G+++ VNM+   + PP G  
Sbjct: 335 FVNIFIFVLAFFLDFFEIAFIVIPMLAPVASSLGIDLIWFGVLICVNMQTSFMHPPFGFA 394

Query: 413 LFVTAGITGRSI--GWVIHACLPWLLLLLGFLVLITYVPQ 450
           LF    I  + +    +    LPW+ + +  + ++ + PQ
Sbjct: 395 LFYLRSIASKDVKTSDIYMGALPWVGMQIILVAIVIFWPQ 434


Lambda     K      H
   0.329    0.144    0.424 

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: 664
Number of extensions: 40
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 466
Length of database: 497
Length adjustment: 34
Effective length of query: 432
Effective length of database: 463
Effective search space:   200016
Effective search space used:   200016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 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