GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natB in Sinorhizobium meliloti 1021

Align NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SMc01946 SMc01946 leucine-specific binding protein

Query= TCDB::Q55387
         (454 letters)



>FitnessBrowser__Smeli:SMc01946
          Length = 372

 Score = 91.3 bits (225), Expect = 5e-23
 Identities = 98/360 (27%), Positives = 144/360 (40%), Gaps = 47/360 (13%)

Query: 72  PATGDLSSIGQNMPLAVQLAVDTINACGGVNGQDVTVVIEDDQTDPTAGVSAMTKLAEAD 131
           P TG  ++ G  +    + A + INA GG+NG+ + VV+ DD +DP  GVS   K   AD
Sbjct: 32  PLTGPNAAFGAQLQKGAEQAAEDINAAGGINGEQIKVVLGDDVSDPKQGVSVAQKFV-AD 90

Query: 132 QVAGVVGSFASSVSSAAVPIAVRNNIMMISPGSTSPVFTDQAKKGEFKGFW--ARTAPPD 189
            V  VVG F S VS  A  I   N I+ ++P ST+P FT+       +G W   RT   D
Sbjct: 91  GVKFVVGHFNSGVSIPASEIYAENGILQVTPASTNPQFTE-------RGLWNTFRTCGRD 143

Query: 190 TYQAQALAALAKKQGFTDAATVVINN--DYGVGFEKVFVESFTADGGNVTNKDNPVRYDP 247
             Q  A+A       F DA   VI++   YG G      +S    G      +     D 
Sbjct: 144 DQQG-AVAGAYIAANFKDAKVAVIHDKTPYGQGLADETKKSMNEAGVTEALYEGINTGDK 202

Query: 248 KAATLDTEAAQGFANSPDAVAAILYADTGSVLVQSAYRQGLMDGVTLLLTDGVYSPDFVE 307
             + L  +  Q  A         L+ + G ++ Q    QGL    T++  DG+ S +   
Sbjct: 203 DFSALIAKMKQ--AGVSIVYYGGLHTEAGLIMRQMK-DQGLK--ATMMSGDGIVSNELAS 257

Query: 308 KVGKDANGVSLLSGALGTVPGADGKSLEAFTAQWKDATGGKDVTAFVPHTYDATVLMMLA 367
             G        + G L T      KS  A     K    G +  A+  + Y A  ++   
Sbjct: 258 IAG------DAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEAYTLYAYAALQVIAEG 311

Query: 368 AEAAKSNTGAGIQSKIRDVSNGPGEEVTDACEAIAMVREGKDINYQGASGNVDIDENGDV 427
           A+AA +     +   I+  + GP                     ++ A G +  DE GD+
Sbjct: 312 AKAAGNTDPQAVAEAIK--AKGP---------------------FKTAIGELGFDEKGDI 348


Lambda     K      H
   0.313    0.131    0.374 

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: 430
Number of extensions: 21
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: 454
Length of database: 372
Length adjustment: 31
Effective length of query: 423
Effective length of database: 341
Effective search space:   144243
Effective search space used:   144243
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 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