GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrB in Rhizobium etli CFN 42

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate WP_020922288.1 RHE_RS18500 TRAP transporter large permease subunit

Query= TCDB::P74224
         (445 letters)



>NCBI__GCF_000092045.1:WP_020922288.1
          Length = 497

 Score =  474 bits (1221), Expect = e-138
 Identities = 232/440 (52%), Positives = 322/440 (73%), Gaps = 1/440 (0%)

Query: 1   MVDYDWLGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFG 60
           M D+  + P MF+G ++F+  G+PVAFSL  V + F IIG   G F   FL A+P R FG
Sbjct: 1   MFDFGIIPPAMFLGMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFG 60

Query: 61  IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTG 120
           I++N  LLAIPFF  +G++LER G+AE LLE  G + G + GGLA AVILVG +L A TG
Sbjct: 61  IVSNDLLLAIPFFTLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITG 120

Query: 121 VVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGD 180
            VAA+V+ MG+ISLPIMLRYGYS  LA+GVI ASGT+ Q+IPPS+VL+VLADQLG SVGD
Sbjct: 121 TVAASVITMGVISLPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGD 180

Query: 181 LFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVL 240
           +++G++ P ++    F L+VL+++ ++P   P LP EVR      L  +++  M+P +VL
Sbjct: 181 MYLGAIGPSILQVTIFVLFVLVMSIVRPKSMPPLPKEVRGDFNWALLVKVLMGMVPSIVL 240

Query: 241 ILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILL 300
           I LVLG+IF G+A+PTEAGA+G +GA+ LA  N+RL W  + E   +T  ITSMV++IL+
Sbjct: 241 IFLVLGTIFMGLATPTEAGALGVVGAMLLAAMNRRLTWPLIREAMTSTTHITSMVVMILI 300

Query: 301 GSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLF 360
           GST FSLVF+G++G R++  +L+ +PGG +GFL    I IF+L FF+DFFEIAFIV+P+ 
Sbjct: 301 GSTCFSLVFQGMDGSRWIEHMLSGIPGGPVGFLIFVNIFIFVLAFFLDFFEIAFIVIPML 360

Query: 361 KPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIG 420
            PVA +L +DLIW+GV++  N+QTSF+ PPFGFALFYLR +A   + T  IY GA+P++G
Sbjct: 361 APVASSLGIDLIWFGVLICVNMQTSFMHPPFGFALFYLRSIASKDVKTSDIYMGALPWVG 420

Query: 421 LQVLVLLLIIIFPALIN-WL 439
           +Q++++ ++I +P  +  WL
Sbjct: 421 MQIILVAIVIFWPQSVTYWL 440


Lambda     K      H
   0.331    0.148    0.443 

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: 754
Number of extensions: 36
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