GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS05995
          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:

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