GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Lactobacillus shenzhenensis LY-73

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_040534573.1 L248_RS03250 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_000469325.1:WP_040534573.1
          Length = 604

 Score =  119 bits (298), Expect = 2e-31
 Identities = 97/307 (31%), Positives = 143/307 (46%), Gaps = 25/307 (8%)

Query: 55  ARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLA 114
           A G+S HA      L E + G+P A A L+    Y  P+   +   L +SQSG++ D   
Sbjct: 299 AAGTSYHAGLVGARLFEEVAGLP-AEAYLASEFGYHMPLLSQHPFFLLLSQSGETADSRE 357

Query: 115 TVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAA 174
            +   +K G  V+ M N   S L+  AD  + L AGPE +VA+TK+Y   +   A L  A
Sbjct: 358 VLVKVKKMGYPVLTMTNTAGSTLSREADYTMLLHAGPEIAVASTKAYTAQIGVQAVLAKA 417

Query: 175 W--------AQDEALETAVADLPAQLERAFALDWSAAVTALTGA-----SGLFVLGRGYG 221
                    A D AL   ++   A ++    +D    +  L G         F +GRG  
Sbjct: 418 LGMYRQQPAANDFALRHQLSIAAAGMQTL--VDEKDQIKNLVGQYMPDQHDAFYIGRGAD 475

Query: 222 YGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAE 281
           Y ++ EAALK KE   +H E F+A E++HG +A++ E   VLAF + D      R  + E
Sbjct: 476 YPLSLEAALKLKEVSYVHTEGFAAGELKHGTIALISEDTPVLAFITDDATAAHTRSNLQE 535

Query: 282 FRSRGAEVL------LADPAARQAGLPAIAAHPAIEPILIVQSFYKMANALALARGCDPD 335
             +RGA  L      LA+P      LP +   P +  ++ +     +A   AL +G D D
Sbjct: 536 TEARGAHTLSIVSEHLAEPTDNIV-LPDV--DPRLSALVGIIPAQLIAYYTALGKGLDVD 592

Query: 336 SPPHLNK 342
            P +L K
Sbjct: 593 KPRNLAK 599


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: 367
Number of extensions: 15
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: 347
Length of database: 604
Length adjustment: 33
Effective length of query: 314
Effective length of database: 571
Effective search space:   179294
Effective search space used:   179294
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