GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ketodeoxyribonate-cleavage in Azospirillum brasilense Sp245

Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate AZOBR_RS27000 AZOBR_RS27000 3-keto-5-aminohexanoate cleavage protein

Query= reanno::Burk376:H281DRAFT_00641
         (312 letters)



>FitnessBrowser__azobra:AZOBR_RS27000
          Length = 316

 Score =  427 bits (1099), Expect = e-124
 Identities = 205/306 (66%), Positives = 252/306 (82%), Gaps = 2/306 (0%)

Query: 6   RKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGRPTPSP 65
           +KVIISCA+TG+ H P+MS+ LP+TP++I +Q + AA+AGAAI+HLHARDP  G+PTP P
Sbjct: 10  KKVIISCALTGSIHTPTMSDALPVTPDEIVEQGVGAAEAGAAILHLHARDPRTGQPTPDP 69

Query: 66  EIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFSIHPVA 125
            +F  F+P + ++TDAV+NITTGGS  MT++ERLA P  ARPEMCSLNMGSMNF I P+A
Sbjct: 70  AVFMQFLPRLKQSTDAVLNITTGGSLNMTVQERLAAPLQARPEMCSLNMGSMNFGIFPLA 129

Query: 126 AKISSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGES-GTRFEFECYDVGHLYNLAH 184
            +   W++ WE+ Y+   +D IFRNTFRDI  IL  LGE  GTRFEFECYDVGHLYNLAH
Sbjct: 130 DRYQGWKHDWEEPYLRSTDDFIFRNTFRDIAYILEHLGEGCGTRFEFECYDVGHLYNLAH 189

Query: 185 FVDQGLVKPPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLGAGRHQMPL 244
           FVD+GLVKPPFF+Q++FGILGG+GA+  N++ MR TADRLFG + Y +SVL AGRHQ+P 
Sbjct: 190 FVDRGLVKPPFFVQTIFGILGGIGAEQRNLVFMRETADRLFGTD-YEWSVLAAGRHQIPF 248

Query: 245 VTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPADARKMLGL 304
            TM+A+MGGNVRVGLEDS+YL+KG  A  +A+QV KIRRILEELSLE+ATPA+AR ML L
Sbjct: 249 TTMAAVMGGNVRVGLEDSLYLSKGRLARNSAEQVAKIRRILEELSLEVATPAEARAMLAL 308

Query: 305 KGADQV 310
           KGADQV
Sbjct: 309 KGADQV 314


Lambda     K      H
   0.321    0.137    0.400 

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: 337
Number of extensions: 14
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: 312
Length of database: 316
Length adjustment: 27
Effective length of query: 285
Effective length of database: 289
Effective search space:    82365
Effective search space used:    82365
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 (21.9 bits)
S2: 48 (23.1 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