GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Klebsiella michiganensis M5al

Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BWI76_RS05995 BWI76_RS05995 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q8DQI1
         (386 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS05995 BWI76_RS05995 branched-chain
           amino acid ABC transporter substrate-binding protein
          Length = 378

 Score =  184 bits (467), Expect = 4e-51
 Identities = 117/366 (31%), Positives = 188/366 (51%), Gaps = 22/366 (6%)

Query: 34  NSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGIDGKQIEVVDKDNKSET 93
           +S +   IKIG     SG+L+ YG   QKG  + +  I      +G  ++++  D+KS+ 
Sbjct: 22  SSAQAAEIKIGVVLPLSGALSGYGQPSQKGLDI-IQSITPTLK-NGDTVKLIVIDDKSDK 79

Query: 94  AEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLTKGQDYLF 153
            EAA+    LV+  KV AV+G  TS  T A    A  +  PL+S +AT D +T+   Y+ 
Sbjct: 80  VEAANAMQRLVSSDKVDAVIGEVTSSNTLAMTKIADDSKTPLVSSTATNDRVTRNHPYVS 139

Query: 154 IGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKGIAKSFRESY---KGEIVADET 210
              F DSFQG + +N  S  L AK   +  D+++DY+ G+AK+FR  +    G I  +  
Sbjct: 140 RVCFSDSFQGVVGANLASRDLKAKTAAIVFDSSNDYSVGLAKAFRTQFLKNGGTIPIEVQ 199

Query: 211 FVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGDGFNGEEFV 270
              G  DF+A L  +K K+ D I +P YY E   I  QA+ +G+ KP+VGGDG   ++  
Sbjct: 200 APGGSKDFKAQLASVKAKNVDMIYMPIYYTEGALIAVQAKQLGLSKPVVGGDGLAADQVF 259

Query: 271 QQATAEKASNIYFISGFSTTVEVSAKAK-------AFLDAYRAKYNEEPSTFAALAYDSV 323
                +       ++G+ TT   S  AK        F+ A+ AKY +   T+ A+A D+ 
Sbjct: 260 FDVGKDA------VNGYMTTDYYSPNAKEQTPAGEVFIKAWEAKYQQPTHTWGAMAADAY 313

Query: 324 HLVANAAKGAKNSGE---IKNNLAKTKDFEGVTGQTSFDADHNTVKTAYMMTMNNGKVEA 380
           +++ NA     +  +   +   +  TKDF+GVTG  +   + + +++A +  + +GK+  
Sbjct: 314 NVIINAMNQCSDPHDRVCVNEKIRATKDFQGVTGTLTLQ-NGDAIRSAVINEVKDGKLAF 372

Query: 381 AEVVKP 386
             VV P
Sbjct: 373 RTVVNP 378


Lambda     K      H
   0.310    0.126    0.337 

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: 330
Number of extensions: 15
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: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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