GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fcbT3 in Rhizobium leguminosarum bv. trifolii WSM1325

Align FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate WP_012759004.1 RLEG_RS18145 TRAP transporter large permease subunit

Query= TCDB::Q9RBQ9
         (439 letters)



>NCBI__GCF_000023185.1:WP_012759004.1
          Length = 497

 Score =  228 bits (582), Expect = 3e-64
 Identities = 128/428 (29%), Positives = 215/428 (50%), Gaps = 9/428 (2%)

Query: 13  GTTVLLFLGLPVAYSFFAIN----VVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLF 68
           G  + +  G PVA+S  A+     ++G      G+  L  L       +++  L  IP F
Sbjct: 14  GMIIFMLYGFPVAFSLAAVGLFFAIIGIVTGHFGEVFLQALPLRFFGILSNDLLLAIPFF 73

Query: 69  ILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLM 128
             MG +L   GLA+  ++G  K+   +PG LA   ++ G    AI+G+  A+   +G + 
Sbjct: 74  TFMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITGTVAASVITMGMIS 133

Query: 129 LPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLA 188
           LP+ML  GY P+L  G I A G +  +IPPS + V+L    G S+  + +G + P +L  
Sbjct: 134 LPIMLRYGYNPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGDMYLGAIGPSILQV 193

Query: 189 ISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVL---PLSLIFVAIVAVISGGV 245
             FV +I+  + +RP+S P     V RG   W  LV  ++   P  ++   ++  I  G+
Sbjct: 194 TIFVLFILVMSIIRPKSMPPLPKEV-RGDFNWALLVKVLMGMVPSIVLIFLVLGTIFMGL 252

Query: 246 ATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFS 305
           ATPTEA A+G    + +  M R L W  + +A+  T  I+ M++ I++ +T FS V    
Sbjct: 253 ATPTEAGALGVVGAIVLAAMNRRLTWPLIREAMASTTHITSMVVMILIGSTCFSLVFQGM 312

Query: 306 GATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQI 365
             +  I  ++      P G +  +   +  L  F+D   +  + +P   P+  SLGID I
Sbjct: 313 DGSRWIEHMLWGIPGGPVGFLIFVNIFIFVLAFFLDFFEIAFIVIPMLAPVASSLGIDLI 372

Query: 366 WFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFW 425
           WFGV+  + MQ   + PP G  L+ ++ +A K +    ++  A+P+VG+   ++ ++ FW
Sbjct: 373 WFGVLICVNMQTSFMHPPFGFALFYLRSIASKDVKTSDIYMGALPWVGMQLILVAIVIFW 432

Query: 426 P-GIATWL 432
           P  +  WL
Sbjct: 433 PQSVTYWL 440


Lambda     K      H
   0.329    0.143    0.433 

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: 633
Number of extensions: 40
Number of successful extensions: 2
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: 439
Length of database: 497
Length adjustment: 33
Effective length of query: 406
Effective length of database: 464
Effective search space:   188384
Effective search space used:   188384
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: 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