GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Azospirillum thiophilum BV-S

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_045583256.1 AL072_RS15665 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>NCBI__GCF_001305595.1:WP_045583256.1
          Length = 369

 Score =  192 bits (488), Expect = 1e-53
 Identities = 120/365 (32%), Positives = 187/365 (51%), Gaps = 8/365 (2%)

Query: 7   LTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGG 66
           ++ V+A A  AG  +AQ  +V IG     +G  A  G+ +  GAR A+ ++NA+G  +G 
Sbjct: 6   ISFVSATALLAGFGTAQADIV-IGLGTATTGPVAALGEQSVYGARQAVADINAKGGVLGQ 64

Query: 67  KKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTG 126
           K +   L   DDA DP+Q  A A +    +VA VVGHL SG +IPA+ VY + G+  VT 
Sbjct: 65  KLV---LKVGDDACDPRQAVAVANQFVREQVAAVVGHLCSGASIPAADVYQEEGMVMVTP 121

Query: 127 AATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFK 186
            ATNP LT  G+   FR+   D+  G     Y  +T K K +A++DD+ AYG+G+ADV  
Sbjct: 122 TATNPLLTAKGHPNIFRVCGRDDQQGVVAGTYLAETFKGKNIAVLDDKQAYGKGLADVVV 181

Query: 187 KTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMG 246
           +T    G KV      T    DF A++T++K K  +A++YGG  P+ G ++RQ ++ G+ 
Sbjct: 182 ETLAKAGGKVAYRGSVTAGERDFSALVTSLKDKGVEAVYYGGYHPELGLIVRQAQEQGL- 240

Query: 247 NVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQV 306
             ++  GDG+   E   +   A   G         S A  P      A +      +   
Sbjct: 241 KPQFIAGDGLNNQEYWSITGPA---GEGTLYTDSPSAASDPKAQELIASFKTAGLPEPGN 297

Query: 307 YSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYV 366
           ++ Y+Y A  +I   +++A SV+       L   S + V   + F+  G++  P   +YV
Sbjct: 298 FAFYSYAAVQVIAQGLQKAGSVNGTKLAAALHSGSHETVVGPVEFDKKGDITKPNYVMYV 357

Query: 367 YKDGK 371
           + +GK
Sbjct: 358 WSNGK 362


Lambda     K      H
   0.315    0.131    0.375 

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: 388
Number of extensions: 21
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: 375
Length of database: 369
Length adjustment: 30
Effective length of query: 345
Effective length of database: 339
Effective search space:   116955
Effective search space used:   116955
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: 49 (23.5 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