GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Burkholderia phytofirmans PsJN

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__BFirm:BPHYT_RS07695
          Length = 411

 Score =  223 bits (569), Expect = 6e-63
 Identities = 148/405 (36%), Positives = 217/405 (53%), Gaps = 34/405 (8%)

Query: 27  VAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEP 86
           V +R   S VWD +GR+YIDFAGGIAV   GH HP+++  + EQ GKL H        EP
Sbjct: 25  VPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHIG-NGYTNEP 83

Query: 87  YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR-AATGRAG-----VIAFTGAYH 140
            + LA+ +       F  +     SG+EA E A+K+AR  A  R G     +I+FT ++H
Sbjct: 84  VLRLAKRLEDLT---FADRAFFANSGAEANEAALKLARRVAFDRHGADKYEIISFTQSFH 140

Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQD 200
           GRT  T+ + G+   YS G G +P GI         H    D     IE + K  A    
Sbjct: 141 GRTFFTVSVGGQP-KYSEGFGPVPAGI--------THLPYND-----IEAVKK--AIGAQ 184

Query: 201 IAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGI 260
             A+I+EP+QGEGG      +F++ LR  CDQHG LLI DEVQTG GR+G F+A ++ G+
Sbjct: 185 TCAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGV 244

Query: 261 VPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEK 320
            PD+ T AK++G GFPI  +    E+      G  G TY G+P+  A A  V+++  + K
Sbjct: 245 TPDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPK 304

Query: 321 LLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVR 380
           LLE  ++  E LK  L ++  +  +  +VRG G ++  EL    +  K  A+     V  
Sbjct: 305 LLEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAEL---NEAFKGRAK---DFVTA 358

Query: 381 AREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425
           A + G+I+L  G   +V+RF+  + +P   + +G   LA+  + +
Sbjct: 359 AGQHGVIMLMAGP--DVLRFVPSLIMPLDDMNEGFERLAKAIESI 401


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: 432
Number of extensions: 17
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: 426
Length of database: 411
Length adjustment: 32
Effective length of query: 394
Effective length of database: 379
Effective search space:   149326
Effective search space used:   149326
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