GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Klebsiella michiganensis M5al

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Koxy:BWI76_RS14020
          Length = 461

 Score =  232 bits (592), Expect = 2e-65
 Identities = 150/415 (36%), Positives = 224/415 (53%), Gaps = 31/415 (7%)

Query: 30  RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFT--HTAYQIVPYQGY 87
           +AE   L D + + Y D  AG   L  GH HP V+Q+I + +      HT     P +  
Sbjct: 47  KAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTTPLKD- 105

Query: 88  VTLAERINALVPIQGLNKTALFT--TGAEAVENAIKIARAHTGRPGVIAFSGAFHGRTLL 145
              +E + +L+P +G      FT  +GA+AVE A+K+A+ +TGR  VI+FSG +HG T  
Sbjct: 106 -RFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFSGGYHGMTHG 164

Query: 146 GMALTGKVAPYKIGFGPFPSDIYHAPFPSALH---GVSTERALQALEGLFKTDIDPA--- 199
            +++TG ++P     G  P ++   P+P       G+  E  ++AL   F+  I+     
Sbjct: 165 ALSVTGNLSPKAAVNGMMP-EVQFMPYPHQYRCPLGIGGEAGVKALTYYFENLINDVESG 223

Query: 200 --RVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSH 257
             + AA+I+E VQGEGG   AP ++++ +R V  +HGI+LI DEVQ GF RTGK FA  H
Sbjct: 224 VRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAGFARTGKFFAFEH 283

Query: 258 HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIE 317
             +EPD+I M+K++ GG+PL AV G     DA  PG   GT+ GN LA+A     +  ++
Sbjct: 284 AGIEPDIIVMSKAVGGGLPL-AVLGIKKQFDAWEPGHHTGTFRGNQLAMATGLTTLRHLK 342

Query: 318 EEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEF-----------CDPATG 366
           + K+ +++A+ G+ L+  L   +K  P +  VRGLG M+  E            C PA G
Sbjct: 343 DNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGLMIGIEIVKPNEAPDHMGCYPADG 402

Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
           + SA     +Q +  EAGL+L   G +G V+R L  L I  A+ +       QAL
Sbjct: 403 ELSA----LLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELEIFFDKFEQAL 453


Lambda     K      H
   0.321    0.136    0.400 

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: 473
Number of extensions: 21
Number of successful extensions: 5
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: 423
Length of database: 461
Length adjustment: 32
Effective length of query: 391
Effective length of database: 429
Effective search space:   167739
Effective search space used:   167739
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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