GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas fluorescens FW300-N2E3

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10500
          Length = 390

 Score =  233 bits (594), Expect = 8e-66
 Identities = 141/394 (35%), Positives = 213/394 (54%), Gaps = 36/394 (9%)

Query: 25  PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84
           PV   R + +++WD  G EY+D   G+AV + GH +P++ AA+ EQ G+L HT       
Sbjct: 16  PVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLLHTSNMF--- 72

Query: 85  EPYIELAEEIAKRVPG-DFPKKTLLVTSGSEAVENAVKIARAATG-----RAGVIAFTGA 138
             +IE  E++++R+      ++     SG+EA E A+K+AR         +  V+    +
Sbjct: 73  --HIEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANARHVAQPQVLVMENS 130

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198
           +HGRT+ TL  TG          LMPG +           V  D+    IE I K  AQ 
Sbjct: 131 FHGRTLATLAATGNPAVQRGFEPLMPGFL----------RVPYDN----IEEIRKVAAQS 176

Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258
            DI A+++EPVQGEGG +  S  ++Q LR LCD+H  L++ DEVQTG GRTG +F  +  
Sbjct: 177 PDIVAVLVEPVQGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHA 236

Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318
           GIVPD+ T AK++G GFPI     + +  +  +PG    T+ G+P+AC     VL + E 
Sbjct: 237 GIVPDVITLAKALGNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMER 296

Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378
           + + +R+   G RL A L+E    H  +  +RGLG MV IEL      ++  AELV + +
Sbjct: 297 DHIPQRAATSGRRLLAALQEALGNHSEVVSIRGLGLMVGIEL------NRQCAELVGRAL 350

Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412
               ++ LI ++ GT    +R L P+   D+Q++
Sbjct: 351 --DEQRLLITVTRGT---TLRLLPPLICEDSQID 379


Lambda     K      H
   0.319    0.137    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: 359
Number of extensions: 17
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: 426
Length of database: 390
Length adjustment: 31
Effective length of query: 395
Effective length of database: 359
Effective search space:   141805
Effective search space used:   141805
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: 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