GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Shewanella amazonensis SB2B

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 6939551 Sama_3639 glucosamine--fructose-6-phosphate aminotransferase (RefSeq)

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



>FitnessBrowser__SB2B:6939551
          Length = 609

 Score =  123 bits (308), Expect = 1e-32
 Identities = 106/356 (29%), Positives = 171/356 (48%), Gaps = 31/356 (8%)

Query: 14  MEREAAEAGAAVSRMLA---ANRDAIE-----RVAARLRASPPAVVVTCARGSSDHAATY 65
           M +E  E   A++R L    AN   ++     + A  L+      ++ C  G+S HA   
Sbjct: 253 MLKEIYEQPRALARTLEGRIANMQVLDSAFGDKAADLLKDIKHVQIIAC--GTSYHAGMT 310

Query: 66  AKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAG-A 124
           A+Y +E   GV       S      + + P N L + ISQSG++ D LA +   ++ G  
Sbjct: 311 ARYWLEQWAGVSCNVEIASEFRYRKSHLFP-NSLLVTISQSGETADTLAALRLAKEMGYQ 369

Query: 125 FVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDE----- 179
             + + NA  S L   +D+   +KAG E  VA+TK++   LA +  L A   ++      
Sbjct: 370 ATLTICNAPGSSLVRESDMAYMMKAGAEIGVASTKAFTVQLAGLLMLTAVIGRNNGMSAE 429

Query: 180 ---ALETAVADLPAQLERAFALDWSAAVTALTGAS---GLFVLGRGYGYGIAQEAALKFK 233
              +L  ++  LPA++E+A  LD + A  A   A     LF LGRG  Y IA E ALK K
Sbjct: 430 LQSSLTQSLQSLPAKVEQALGLDDAIASLAEDFADKHHALF-LGRGDQYPIAMEGALKLK 488

Query: 234 ETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEV-LLA 292
           E   +HAE++++ E++HGP+A++     V+  A ++   E ++  V E R+RG  + + A
Sbjct: 489 EISYIHAEAYASGELKHGPLALIDADMPVIVVAPNNELLEKLKSNVEEVRARGGLMYVFA 548

Query: 293 DPAARQAG------LPAIAAHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342
           D  A  A       +P       + P++       ++  +AL +G D D P +L K
Sbjct: 549 DKDAEFASDDTMKVIPVPHCDEFMAPLIYTIPLQLLSYHVALIKGTDVDQPRNLAK 604


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: 393
Number of extensions: 22
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: 609
Length adjustment: 33
Effective length of query: 314
Effective length of database: 576
Effective search space:   180864
Effective search space used:   180864
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.

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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