GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Thiohalospira halophila HL 3

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_093428089.1 BM272_RS07150 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_900112605.1:WP_093428089.1
          Length = 610

 Score =  143 bits (360), Expect = 1e-38
 Identities = 103/307 (33%), Positives = 159/307 (51%), Gaps = 21/307 (6%)

Query: 55  ARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLA 114
           A G+S HA   A+Y +E + GVP  S  ++    Y  PV   + L + ISQSG++ D LA
Sbjct: 301 ACGTSYHAGMVARYWLEAVAGVP-CSVEVANEFRYRRPVVRPDTLVVTISQSGETADTLA 359

Query: 115 TVEH-QRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVA 173
            +   + + G+  +A+ N  +S L   +++V+  +AGPE  VA+TK++   L A+  L  
Sbjct: 360 ALRDIKARVGSRALAICNVPESSLVRESELVLMTRAGPEIGVASTKAFTTQLTALLLLTL 419

Query: 174 AWAQDEALET--------AVADLPAQLERAFALDWSAAVTALTGAS---GLFVLGRGYGY 222
           A A+   L          A+ +LP ++ERA  L+ +    A   A     LF LGRG  Y
Sbjct: 420 ALARRNGLPAEREAEYVAALEELPRRIERALELNDAIDALAADFADKHHSLF-LGRGPLY 478

Query: 223 GIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEF 282
            +A E ALK KE   +HAE++ A E++HGP+A+V     V+A A +D   E ++  + E 
Sbjct: 479 PVAMEGALKLKEISYIHAEAYPAGELKHGPLALVDGEMPVIAIAPNDDLLEKLKSNLQEV 538

Query: 283 RSRGAE-VLLADPAARQ------AGLPAIAAHPAIEPILIVQSFYKMANALALARGCDPD 335
           R+RG   V+ AD AA           P   +H  I P++       +A  +A+ +G D D
Sbjct: 539 RARGGRLVVFADTAAGMDDGEGVRTFPLEHSHELIAPVVYTVPLQLLAYHVAVIKGTDVD 598

Query: 336 SPPHLNK 342
            P +L K
Sbjct: 599 QPRNLAK 605


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: 400
Number of extensions: 23
Number of successful extensions: 5
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: 610
Length adjustment: 33
Effective length of query: 314
Effective length of database: 577
Effective search space:   181178
Effective search space used:   181178
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