GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Azospirillum brasilense Sp245

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate AZOBR_RS09675 AZOBR_RS09675 glucosamine--fructose-6-phosphate aminotransferase

Query= reanno::Korea:Ga0059261_1644
         (347 letters)



>FitnessBrowser__azobra:AZOBR_RS09675
          Length = 608

 Score =  132 bits (332), Expect = 2e-35
 Identities = 97/313 (30%), Positives = 153/313 (48%), Gaps = 26/313 (8%)

Query: 51  VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110
           +V C  G++ +A   AKY  ETL  +P      S     +AP+ P  G+ L ISQSG++ 
Sbjct: 296 IVAC--GTAYYAGVVAKYWFETLARLPVEVDIASEFRYREAPL-PEGGVALFISQSGETL 352

Query: 111 DLLATVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAA 170
           D L  + + ++ G  ++++VN  +S +A  +D V+   AGPE  VA+TK++   L  +A 
Sbjct: 353 DTLEALRYCKRQGQKILSIVNVPESTIARESDAVLYTMAGPEIGVASTKAFTTQLTTLAC 412

Query: 171 L---------VAAWAQDEALETAVADLPAQLERAFALDWSAAVTA--LTGASGLFVLGRG 219
           L         V    + + +  A+ ++PA+     A D      A  +  A  +  LGRG
Sbjct: 413 LAVTVGHARGVIPAERMQQIAQALREVPARAADVLAHDERLHELAQEVAEARDVLYLGRG 472

Query: 220 YGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETV 279
             Y +A E ALK KE   +HAE ++A E++HGP+A++ E+  V+    SD   E     V
Sbjct: 473 AMYPLALEGALKLKEISYIHAEGYAAGELKHGPIALIDESVPVIVLVPSDNLFEKTVSNV 532

Query: 280 AEFRSRGAEVL----------LADPAARQAGLPAIAAHPAIEPILIVQSFYKMANALALA 329
            E  +R  +VL          L+D       LP  A  P + P+L       +A  +A+ 
Sbjct: 533 QEVCARSGKVLLIADKKGIDKLSDKVRWSLELP--ACDPLVAPLLYAIPVQLLAYHVAVL 590

Query: 330 RGCDPDSPPHLNK 342
           +G D D P +L K
Sbjct: 591 KGTDVDQPRNLAK 603


Lambda     K      H
   0.317    0.128    0.360 

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: 398
Number of extensions: 23
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: 347
Length of database: 608
Length adjustment: 33
Effective length of query: 314
Effective length of database: 575
Effective search space:   180550
Effective search space used:   180550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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