GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Echinicola vietnamensis KMM 6221, DSM 17526

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate Echvi_3159 Echvi_3159 Na+/H+-dicarboxylate symporters

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__Cola:Echvi_3159
          Length = 449

 Score =  258 bits (660), Expect = 2e-73
 Identities = 145/404 (35%), Positives = 239/404 (59%), Gaps = 15/404 (3%)

Query: 14  KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVC 73
           K++I +  G+  GLLL    G        I   +  + G +F+  ++M+++PL+  S++ 
Sbjct: 27  KVIIALLLGVGFGLLLSPQNGWISKETADIAGNWLALPGVLFLKLVQMIMIPLIVASIIT 86

Query: 74  GTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGN-----ASLASESMQYS 128
           G  S ++   L +LGG  L ++L TT +++ +    + + +PG      A      +   
Sbjct: 87  GIAS-NDKDSLKKLGGGVLLYFLGTTIVSVSIGTILSQIFRPGRFLHQQALKEHNEITAV 145

Query: 129 AKEAPSLA-------DVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHI-GERGRRV 180
           + + P L+       D + N++P NP+ ++  G ML I+IF +I G A+  +  +  R V
Sbjct: 146 STDEPELSFGVETIPDAISNLLPENPLASMVSGEMLSIVIFTIIIGVAVLSLENDLLRPV 205

Query: 181 AALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHG 240
             L   + EV M VV   M L P  VF LM +L  ++G+ +L  +  Y  +VL+ LLF  
Sbjct: 206 KLLLSAIQEVCMTVVKWSMLLVPIAVFGLMAQLTSSVGLSSLSGLTYYVGVVLLGLLFL- 264

Query: 241 FVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASF 300
            + Y  L+ L    +P+ F++K+RDVQL AFST SS A +P++++ +E +L  D  +++F
Sbjct: 265 VIFYLGLIVLLGKANPMHFLKKIRDVQLLAFSTTSSAAVMPLSLQTAEEKLKVDKTISNF 324

Query: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLV 360
            +P+GAT+NMDGTA+ Q + T+FIAQ +G+++++ +  +V++T   ASIGT  +PG G+V
Sbjct: 325 IIPIGATVNMDGTALYQTITTLFIAQAYGLEMSLLNIIVVIVTIVAASIGTPAIPGGGVV 384

Query: 361 MLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVV 404
           +LA VL  VG+P EGI +I+GV+R+L M RTAVNV GD  A +V
Sbjct: 385 ILASVLGSVGIPAEGIIIIIGVERLLGMFRTAVNVMGDLTACMV 428


Lambda     K      H
   0.325    0.139    0.388 

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: 351
Number of extensions: 17
Number of successful extensions: 4
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: 437
Length of database: 449
Length adjustment: 32
Effective length of query: 405
Effective length of database: 417
Effective search space:   168885
Effective search space used:   168885
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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:

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