GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0085 in Microvirga lotononidis WSM3557

Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_009763321.1 MICLODRAFT_RS18455 TAXI family TRAP transporter solute-binding subunit

Query= reanno::psRCH2:GFF85
         (317 letters)



>NCBI__GCF_000262405.1:WP_009763321.1
          Length = 327

 Score =  168 bits (425), Expect = 2e-46
 Identities = 119/329 (36%), Positives = 176/329 (53%), Gaps = 17/329 (5%)

Query: 1   MRLTKR----LGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNKIDG 56
           M+LT+R    +GL   AA+     A   AP F  I TGGT+G YYP+G  ++   +    
Sbjct: 3   MKLTRRELAKIGLGLGAASVLGRGAFAQAPAFFRIGTGGTAGTYYPVGGLIANAISNPPQ 62

Query: 57  AKTSVQATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYN 116
              + QA+  SV N+N + +G  E  F+  D    A+ G      K  ++ LR +A  Y 
Sbjct: 63  LVLTAQASNGSVANVNSIVSGALESGFTQADVAYWAYTGTGLFEGKGKIEDLRLLANLYP 122

Query: 117 NYIQIVASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYA 176
             I +VA+  + IK++ DLKGKR+S+  P SGT ++AR I    G+   D+ + +FL   
Sbjct: 123 ESIHLVAAKSANIKSVADLKGKRVSMDEPGSGTLVDARIILAGWGIKESDV-KADFLKPN 181

Query: 177 ESVELIKNRQLDATLQSSGLGMAAIRDLAST------MPVTFVEIPAEVVEKIESDAYLA 230
           ++ E +++  LDA     G   +AI +LA+T      +P+   E  A+ + K +   + A
Sbjct: 182 QAAERMRDGGLDAFFFVGGYPTSAITELAATGGGVDLVPLAGPE--ADAIRK-QYSFFAA 238

Query: 231 GVIPAGTYDGQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDN--LAALGNAHSAAKD 288
             IPAGTY    A V T+A+    VT  KV D V Y++ K ++ +   AAL   H+  K 
Sbjct: 239 DEIPAGTYKDVSA-VKTLAVGAQWVTSAKVPDAVVYEVVKGLWGDKTRAALDAGHAKGKM 297

Query: 289 IKLENATKNLPIPLHPGAERFYKEAGVLK 317
           I+ ENA     IP+H GAERFYKEAG+LK
Sbjct: 298 IRKENALAGAGIPIHAGAERFYKEAGLLK 326


Lambda     K      H
   0.314    0.131    0.359 

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: 246
Number of extensions: 14
Number of successful extensions: 3
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: 317
Length of database: 327
Length adjustment: 28
Effective length of query: 289
Effective length of database: 299
Effective search space:    86411
Effective search space used:    86411
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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