GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Klebsiella michiganensis M5al

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BWI76_RS07260 BWI76_RS07260 branched chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__Koxy:BWI76_RS07260
          Length = 385

 Score =  208 bits (530), Expect = 2e-58
 Identities = 126/367 (34%), Positives = 201/367 (54%), Gaps = 11/367 (2%)

Query: 5   TQRLSRLFAAMAIAGFAS---YSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQIN 61
           T ++S L AA+ ++GFAS   +S A++T+ I LAGP+TGP A+ G     GA +AI+ IN
Sbjct: 3   TVKISALSAAILLSGFASSAAWSAASETVIIGLAGPLTGPSARIGKDLENGAQLAIDDIN 62

Query: 62  KAGGVNGAQLEGVIY-----DDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIY 116
           K     G +   V +     DD  DP+ AVAVA ++V+ GV  VVGH  + ++ PA  +Y
Sbjct: 63  KQHPTIGGK--AVTFKLQSEDDQSDPRTAVAVAQRLVDSGVAGVVGHWNTGTSIPAARVY 120

Query: 117 EDEGVLMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQ 176
            D G+  + P AT    T +G+   FR +G D+  G  AG++  +  K K IAV+ D+  
Sbjct: 121 HDAGIAQVAPVATGHAYTKQGFDTSFRVMGHDDDGGQFAGQYAVQTLKAKRIAVIDDRTA 180

Query: 177 YGEGIATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLL 236
           +G+G+A E  K++E  GI +   + ++    DF+A+++ ++      ++FGG   +   L
Sbjct: 181 FGQGLADEFIKSLEVQGINIVDRQYVDDKTVDFSAVLTAIRSKNADLIFFGGVDSQAAPL 240

Query: 237 LRQAKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLP-RAFEQDPKNKALIDAFKAK 295
            R+ KQ G++A  MG  G  +     +A    +G++A  P    E+ P  KA   A++++
Sbjct: 241 ARRIKQLGMNATLMGAGGFVSQTFLQLAQKEGDGVVALEPGLPVERMPGGKAFEQAYQSR 300

Query: 296 NQDPSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKN 355
                 +    AY A  V+   +EKA   DP     ALRA  +   TG + FD++G+LK+
Sbjct: 301 YHTHIELHAPFAYDATRVLVAAMEKADSVDPADYLPALRAINYAGVTGQIAFDKEGNLKS 360

Query: 356 FDFTVYE 362
             FTVY+
Sbjct: 361 PTFTVYK 367


Lambda     K      H
   0.316    0.133    0.377 

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: 369
Number of extensions: 18
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: 373
Length of database: 385
Length adjustment: 30
Effective length of query: 343
Effective length of database: 355
Effective search space:   121765
Effective search space used:   121765
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: 41 (21.6 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