GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Cupriavidus basilensis 4G11

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate RR42_RS14425 RR42_RS14425 leucine ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Cup4G11:RR42_RS14425
          Length = 371

 Score =  183 bits (464), Expect = 8e-51
 Identities = 126/379 (33%), Positives = 195/379 (51%), Gaps = 17/379 (4%)

Query: 1   MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60
           M L    ++  A A  A  A+A  + +KI    P+SG+ A YG   + GA  AIE++NA 
Sbjct: 1   MTLSRLTSISLATALCALGAAANAETIKIAIAGPMSGSVAQYGDMVKAGALTAIEQINAA 60

Query: 61  GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120
           G   G K   FE+V  DDA +PKQ  A A K+   K+  V+GH+ SG+TIPAS +Y + G
Sbjct: 61  GGAGGNK---FEVVMMDDACEPKQAVAVANKIVSQKIHYVIGHVCSGSTIPASDIYENEG 117

Query: 121 IPHVTGAATNPNLTK-PGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQ 179
           I  VT +AT P LT+    K  FR I  D+  G   A Y +  +K K VAI+ D+ +YGQ
Sbjct: 118 IVMVTPSATAPQLTENKKRKFIFRTIGRDDQQGPAAAQYIITKIKPKKVAILHDKQSYGQ 177

Query: 180 GVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQ 239
           G+A   KK   A  + V   +      +D+ A++T +K++  D +++GG  P+ G +LRQ
Sbjct: 178 GIASSVKKDLEAAKIPVAVFEGVNAGDSDYSAVITKLKSQGVDFVYFGGYHPEMGLLLRQ 237

Query: 240 MEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKA----K 295
             + G+    + G +G+   ++  + AGA + G ++      S A        KA    K
Sbjct: 238 AREQGV-KATFMGPEGVGNKDVTAI-AGASSEGMLVTLPADFS-ADPSNAALVKAFADKK 294

Query: 296 YDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNG 355
            DA  P Q   Y+     A  +I DA+  A S DP      + K++F+     + ++  G
Sbjct: 295 RDANGPFQMPAYA-----AVQIIGDAIAGAKSTDPTKVAAYMHKNAFQTPIGKVEYDAQG 349

Query: 356 EMKNPAITLYV-YKDGKKT 373
           ++K+    ++  +KD  KT
Sbjct: 350 DLKSFKFVVFTWHKDATKT 368


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: 371
Number of extensions: 18
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: 371
Length adjustment: 30
Effective length of query: 345
Effective length of database: 341
Effective search space:   117645
Effective search space used:   117645
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: 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