GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Klebsiella michiganensis M5al

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BWI76_RS07260 BWI76_RS07260 branched chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Koxy:BWI76_RS07260
          Length = 385

 Score =  318 bits (816), Expect = 1e-91
 Identities = 162/366 (44%), Positives = 239/366 (65%), Gaps = 4/366 (1%)

Query: 9   VVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKK 68
           +++  A++A  ++A E V+ IG   P++G  A  GKD ENGA++AI+++N Q  TIGGK 
Sbjct: 14  LLSGFASSAAWSAASETVI-IGLAGPLTGPSARIGKDLENGAQLAIDDINKQHPTIGGKA 72

Query: 69  IKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAA 128
           + F+L +EDD +DP+   A AQ+L D+ VAGVVGH N+GT+IPA++VY+D GI  V   A
Sbjct: 73  VTFKLQSEDDQSDPRTAVAVAQRLVDSGVAGVVGHWNTGTSIPAARVYHDAGIAQVAPVA 132

Query: 129 TNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKT 188
           T    TK G+ T+FR++ +D+  G     YAV TLK K +A+IDDRTA+GQG+AD F K+
Sbjct: 133 TGHAYTKQGFDTSFRVMGHDDDGGQFAGQYAVQTLKAKRIAVIDDRTAFGQGLADEFIKS 192

Query: 189 ATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNV 248
              +G+ +VD Q+  DK  DF A+LTAI++KN D IF+GG+D Q  P+ R+++QLGM N 
Sbjct: 193 LEVQGINIVDRQYVDDKTVDFSAVLTAIRSKNADLIFFGGVDSQAAPLARRIKQLGM-NA 251

Query: 249 KYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYS 308
              G  G  +    +LA   K    V+  E G  + +MPGG A++  Y ++Y    ++++
Sbjct: 252 TLMGAGGFVSQTFLQLA--QKEGDGVVALEPGLPVERMPGGKAFEQAYQSRYHTHIELHA 309

Query: 309 PYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYK 368
           P+ YDAT ++V AM++A+SVDP  Y P L   ++ GVT  IAF+  G +K+P  T+Y   
Sbjct: 310 PFAYDATRVLVAAMEKADSVDPADYLPALRAINYAGVTGQIAFDKEGNLKSPTFTVYKVV 369

Query: 369 DGKKTP 374
           +GK  P
Sbjct: 370 EGKWQP 375


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: 372
Number of extensions: 13
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: 375
Length of database: 385
Length adjustment: 30
Effective length of query: 345
Effective length of database: 355
Effective search space:   122475
Effective search space used:   122475
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