GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Escherichia coli BW25113

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate 17519 b3458 leucine transporter subunit (NCBI)

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Keio:17519
          Length = 369

 Score =  169 bits (427), Expect = 1e-46
 Identities = 111/351 (31%), Positives = 177/351 (50%), Gaps = 7/351 (1%)

Query: 8   TVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGK 67
           T++A + A A   +A    +K+  V  +SG  A +G    NGAR AI+++NA+G   G K
Sbjct: 7   TIIAGMIALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGDK 66

Query: 68  KIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGA 127
            +  E    DDA DPKQ  A A K+ +  +  V+GHL S +T PAS +Y D GI  ++  
Sbjct: 67  LVGVEY---DDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPG 123

Query: 128 ATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKK 187
           ATNP LT+ GY+   R    D++ G   A Y ++T+K + +AII D+  YG+G+A   + 
Sbjct: 124 ATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQD 183

Query: 188 TATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGN 247
              A    VV     T    DF A++  +K +N D ++YGG  P+ G MLRQ   +G+  
Sbjct: 184 GLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGL-K 242

Query: 248 VKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVY 307
            ++ G +G+  + ++ +A  A   G ++             G     K D K P+   V+
Sbjct: 243 TQFMGPEGVGNASLSNIAGDAAE-GMLVTMPKRYDQDPANQGIVDALKADKKDPSGPYVW 301

Query: 308 SPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMK 358
              TY A   +  A++R  S +P     +L  +    V   + ++  G++K
Sbjct: 302 --ITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLK 350


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: 342
Number of extensions: 16
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: 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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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