GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtrB in Echinicola vietnamensis KMM 6221, DSM 17526

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit

Query= TCDB::P74224
         (445 letters)



>lcl|FitnessBrowser__Cola:Echvi_3627 Echvi_3627 TRAP transporter,
           DctM subunit
          Length = 431

 Score =  186 bits (473), Expect = 1e-51
 Identities = 134/437 (30%), Positives = 216/437 (49%), Gaps = 20/437 (4%)

Query: 10  MMFVGALVFLGCGYPVAFSLGGVAILFAIIG-AALGSFDPIFLSAMPQRIFGIMANGTLL 68
           ++ +  +  +G G PVA+SLG  ++L  ++  AA+ S     ++ + QR+   + + +LL
Sbjct: 8   ILVLSFITLMGLGVPVAWSLGFSSLLTLMVTVAAVPS-----MTTIAQRMGAGLNSFSLL 62

Query: 69  AIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVA 128
           AIPFFI  G ++ + GIA +L+     + G L GGL    ++   +  A  G   A   A
Sbjct: 63  AIPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASA 122

Query: 129 MGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLA-DQLGVSVGDLFIGSLL 187
           +G I    M   GY KEL   V V S T G +IPPS VLIV +    GVS+  LF+   +
Sbjct: 123 LGGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYI 182

Query: 188 PGLMMAGSFALYVLIIAWL--KPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVL 245
           PGL M     L +L  A+   K  L    P   + +G      ++     P L L+++V+
Sbjct: 183 PGLFMG---LLLMLTAAYFIKKKKLPAGEPTSFKELG------KVFFSAAPSLTLLVIVI 233

Query: 246 GSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAF 305
           G I  G+ + TEA A+  +  + L+ F   L  + L  +   +   T++V +++  S A 
Sbjct: 234 GGIVMGVFTATEASAIAVLYCLGLSFFYGELKPRDLPAILLKSSATTAVVAMLIATSMAM 293

Query: 306 SLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAE 365
           S V    +  + +  +L +L   +   L I  + +  +G F+D      I  P+F PV  
Sbjct: 294 SWVMSSEDIPQSISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVT 353

Query: 366 ALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLV 425
            L +D + +G+I+  NL     TPP G  LF   GVA  S++   + +  +PF    ++ 
Sbjct: 354 ELGIDPVHFGIIMVLNLCIGLCTPPVGSVLFIGVGVAKTSIS--NVVKPLLPFFIAMIIG 411

Query: 426 LLLIIIFPALINWLPSL 442
           L +I I+P L  WLPSL
Sbjct: 412 LAVITIWPQLTLWLPSL 428


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: 493
Number of extensions: 28
Number of successful extensions: 5
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: 431
Length adjustment: 32
Effective length of query: 413
Effective length of database: 399
Effective search space:   164787
Effective search space used:   164787
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 Sep 17 2021. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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