GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Dyadobacter tibetensis Y620-1

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_000566685.1:WP_025763135.1
          Length = 384

 Score =  195 bits (496), Expect = 2e-54
 Identities = 142/407 (34%), Positives = 204/407 (50%), Gaps = 55/407 (13%)

Query: 23  IHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVL 82
           I PV   +A+ S +WD  G EY+D  GG AV++ GH HP  +A + EQL K+S     V 
Sbjct: 13  IEPV---KAQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSV- 68

Query: 83  AYEPYIELAEEIAKRVP--GDFPK-KTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAY 139
                I   EE+A ++     +P  K  L  SG+EA ENA+K+A   TGR  V+AFT A+
Sbjct: 69  ----QIPQQEELATKLGTLSGYPDYKLFLCNSGAEANENALKLASFHTGRKKVVAFTKAF 124

Query: 140 HGRTMMTLGLTGKV-----VPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKN 194
           HGRT   +  T        V Y+  +  +P     AL      G++E+            
Sbjct: 125 HGRTAGAVAATDNPSIVAPVNYNEHVSFLPFNDIEALQA----GITEE------------ 168

Query: 195 DAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFA 254
                 +AA+I+E +QG GG  V S  F+Q LR  CD+ G  LI D VQ G GRTG FF+
Sbjct: 169 ------VAAVIVEGIQGVGGIQVCSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFS 222

Query: 255 TEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLK 314
            +  GI PD+ T AK +G GFPI+GV    +   +   G LG T+ G+ +ACAA +AVL 
Sbjct: 223 HQFSGIHPDMMTMAKGMGNGFPIAGVLIAPQFKASF--GLLGTTFGGNHLACAAGIAVLD 280

Query: 315 VFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELV 374
           + ++E+LL+ +  +G  L   + E+        D+RG G M+ IE         P  EL 
Sbjct: 281 IMKDEQLLDNATKIGAYLFHEIEELGG----YKDLRGRGLMIGIEF------DFPVKELR 330

Query: 375 SKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAEC 421
           +K++    E  +     G Y   +R L  + I   + ++ L     C
Sbjct: 331 NKLLF---EHHIFTGVAGAY--TLRLLPSLAISQKEADQFLEAYRSC 372


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: 381
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 426
Length of database: 384
Length adjustment: 31
Effective length of query: 395
Effective length of database: 353
Effective search space:   139435
Effective search space used:   139435
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 24 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