GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Sphingopyxis indica DS15

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_089214500.1 CHB69_RS03285 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_900188185.1:WP_089214500.1
          Length = 607

 Score =  159 bits (402), Expect = 2e-43
 Identities = 116/354 (32%), Positives = 173/354 (48%), Gaps = 28/354 (7%)

Query: 14  MEREAAEAGAAVSRMLAANRDAIERVAAR------LRASPPAVVVTCARGSSDHAATYAK 67
           M++E  E    V++ L++    +E+  A       L       +V C  G+S +A   AK
Sbjct: 252 MQKEIFEQPTVVAQTLSSYIRPLEQTVALPQMDFDLSKIDRITIVAC--GTSFYAGMVAK 309

Query: 68  YLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGAFVV 127
           Y  E    VP      S     D  + PG GL L ISQSG++ D LA + H + AG  + 
Sbjct: 310 YWFEQFARVPVDIDVASEFRYRDPVLQPG-GLALFISQSGETADTLAALRHCKAAGQTIA 368

Query: 128 AMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWA---------QD 178
            +VN   S +A  AD+++P  AGPE  VA+TK++ C LA +AAL A  A         ++
Sbjct: 369 VVVNVPTSSMAREADLLLPTHAGPEIGVASTKAFTCQLAVLAALAAHLALKKGKLSADEE 428

Query: 179 EALETAVADLPAQLERAFALDWSAAVTA--LTGASGLFVLGRGYGYGIAQEAALKFKETC 236
             +   + + PA L  A   D   A  A  +  A  +  LGRG  Y +A E ALK KE  
Sbjct: 429 REIVKHLIEAPAALNAALGHDEDIAAMAHLVAPARDVLYLGRGPDYPLALEGALKLKEIS 488

Query: 237 ALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLADPA- 295
            +HAE +++ E++HGP+A++ EA  V+  A S    E     + E  +RG +V+L   A 
Sbjct: 489 YIHAEGYASGEMKHGPIALIDEAVPVIVLAPSGPLFEKTVSNMQEVMARGGKVVLISDAD 548

Query: 296 -ARQAGLPAIA------AHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342
              +AG   +A       HP I P++       +A  +A+A+G D D P +L K
Sbjct: 549 GIAEAGEGCMATIEMPRVHPLIAPLVYAVPVQLLAYHVAVAKGTDVDQPRNLAK 602


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: 447
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: 607
Length adjustment: 33
Effective length of query: 314
Effective length of database: 574
Effective search space:   180236
Effective search space used:   180236
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 24 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