GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Rhodanobacter denitrificans FW104-10B01

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_021560695.1:WP_027489558.1
          Length = 408

 Score =  232 bits (591), Expect = 2e-65
 Identities = 149/408 (36%), Positives = 219/408 (53%), Gaps = 33/408 (8%)

Query: 26  VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85
           +V +  + + VWD EGR+Y+DF  GIAV   GH  P ++AA+  Q  KL H+   V   E
Sbjct: 25  LVLDHGKGARVWDTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQAHKLWHSS-NVFYTE 83

Query: 86  PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR---AATGRAG----VIAFTGA 138
           P + LAEE+       F ++  L  SG+EA E A+K+ R   AA GRA     ++ F G+
Sbjct: 84  PPLRLAEELVHA--SGFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERRVIVTFNGS 141

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198
           +HGRT+ T+  T +   Y  G   +P G FR L         + +   ++E  F      
Sbjct: 142 FHGRTLATVTATAQA-KYQQGYEPLPEG-FRYL---------DFNDAEALEATFAAG--- 187

Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258
            D+AA+++EPVQGEGG    +  F++R+R LCDQH  LL+ DE+Q G GRTGT FA    
Sbjct: 188 -DVAAVMLEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHD 246

Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318
            +VPD+ T AK++GGGFPI  +    ++ + +  G  G T+ G+P+A A A   L     
Sbjct: 247 HVVPDIVTLAKALGGGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALAKLSS 306

Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378
             +L   +     L+AGL  I  + ++  +VRG G M+   L    D +K  A     ++
Sbjct: 307 PAVLMNVERQANDLRAGLARINHELQLFAEVRGRGLMIGAVL---ADAYKGKA---GAVL 360

Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDELA 426
             A  +GL+LL  G   +V+RF+ P+TI D +L  GLA L     + A
Sbjct: 361 DHAATRGLLLLQAGP--DVLRFVPPLTITDEELADGLARLHAALSDFA 406


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: 424
Number of extensions: 14
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: 408
Length adjustment: 31
Effective length of query: 395
Effective length of database: 377
Effective search space:   148915
Effective search space used:   148915
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 Apr 09 2024. 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