GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Alicycliphilus denitrificans K601

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_000204645.1:WP_013518270.1
          Length = 398

 Score =  218 bits (554), Expect = 3e-61
 Identities = 136/400 (34%), Positives = 215/400 (53%), Gaps = 37/400 (9%)

Query: 25  PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84
           P+  ER +   VWDV G++Y+D  GGIAV   GH HP+++ A+QEQ+ KL HT       
Sbjct: 20  PIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIHTSNYY--- 76

Query: 85  EPYIELAEEIAKRVPGDFPK-KTLLVTSGSEAVENAVKIARAATGRAGV-----IAFTGA 138
             ++   EE+A+ + G           +G EA E A+KIAR      G+     + +  A
Sbjct: 77  --HVPGQEELARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVDKGIEKPEIVVYDHA 134

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198
           +HGR++ T+  TG     + G G +  G  R +AP ++  + E             +  P
Sbjct: 135 FHGRSIATMTATGNPKVRN-GFGPLLEGFIR-VAPNDIEALQE-----------ATEGNP 181

Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258
            ++ A+++EP+QGEGG +     ++Q++R LCD +G LL+ DEVQ G GRTG +FA +  
Sbjct: 182 -NVVAVLMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLDEVQAGMGRTGKWFAHQWA 240

Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318
           GIVPD+ T AK +G G P+  V       + + PG  G T+ G+P+A  A +  +++ EE
Sbjct: 241 GIVPDVMTLAKGLGSGVPVGAVLAHGAASEVLKPGNHGSTFGGNPLAMRAGVETIRIMEE 300

Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378
           E LL+ +  VG  LKAGL++       + +VRG G ++ +EL       +P   L+    
Sbjct: 301 EGLLQNAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVEL------DRPCGVLID--- 351

Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAIL 418
            RA + GL+L    T   VIR +  +T+  A+ ++ +A+L
Sbjct: 352 -RAAQAGLLL--SVTADRVIRLVPALTLTRAEADEIVALL 388


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: 414
Number of extensions: 20
Number of successful extensions: 3
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: 398
Length adjustment: 31
Effective length of query: 395
Effective length of database: 367
Effective search space:   144965
Effective search space used:   144965
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