GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Klebsiella michiganensis M5al

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Koxy:BWI76_RS11670
          Length = 406

 Score =  198 bits (503), Expect = 3e-55
 Identities = 135/375 (36%), Positives = 197/375 (52%), Gaps = 25/375 (6%)

Query: 71  GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130
           G  + L D QG+E+ID  GG  +  +GH +P +V A+  Q  K         +     LA
Sbjct: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPVLRLA 87

Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGA 187
           K L   T       FFCNSG E+ EAALKLA+ Y   R    K   +A   AFHG++L  
Sbjct: 88  KQLIDATFADRV--FFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFT 145

Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247
           +SA  +  + + F PL P  +H  + ++++ +  ++      D+  AVI+EP+QGEGGV+
Sbjct: 146 VSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALID------DNTCAVIVEPMQGEGGVV 199

Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307
                +L  +R+LCD   AL+I DEVQTG+GRTG+++A  H  V PD+L  AKALGGG  
Sbjct: 200 PADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGG-F 258

Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367
           PIGA +A+E   SV+      H TT+GGNPLACA A      +  + +    +Q+     
Sbjct: 259 PIGALLASERCASVM--TVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFC 316

Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG-----YNFASEMFRQRVLVAGTLNNA 422
           +    +   Y  L +E RG G+L+     D   G      N A+E     +L+AG    A
Sbjct: 317 ERLNAINARY-GLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEE-GLMILIAG----A 370

Query: 423 KTIRIEPPLTLTIEQ 437
             +R  P L ++ ++
Sbjct: 371 NVVRFAPALIISEDE 385


Lambda     K      H
   0.320    0.135    0.393 

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: 417
Number of extensions: 20
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: 459
Length of database: 406
Length adjustment: 32
Effective length of query: 427
Effective length of database: 374
Effective search space:   159698
Effective search space used:   159698
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 (21.8 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