GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Rhizorhabdus wittichii RW1

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate WP_012050679.1 SWIT_RS22755 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HXN5
         (842 letters)



>NCBI__GCF_000016765.1:WP_012050679.1
          Length = 759

 Score =  280 bits (715), Expect = 3e-79
 Identities = 212/635 (33%), Positives = 302/635 (47%), Gaps = 35/635 (5%)

Query: 209 FAG-QVASVDSLVGIMGLGVAEQ---DEVEVICRGEDSEAALGALLAALASATAGAPKDA 264
           FAG  +   +  VG++ +   +Q   D+VE+         AL  +   LA   AGA    
Sbjct: 117 FAGVPIVRRERAVGVLAVQHRDQRRFDDVEI--------EALQTVAMVLAELIAGAGLID 168

Query: 265 PRAIAPGEPARPAAVAGTLAGVCASPGLASG-PLARLGAISLPADDGRHRPEEQHLALDQ 323
                PG        A  LAG+    G+A G  +     I +          E+H  +  
Sbjct: 169 EGV--PGSKGTRDNGAVRLAGLKLVEGMARGRAVYHQPRIEIEHTVAEDIEVERHRVIS- 225

Query: 324 ALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHR 383
           A  ++RD ++   ++A  G       + + +     D G +   +  ID G+ A  A  R
Sbjct: 226 AFSKMRDQIERMTREADFGAGGEHQDVLAMYKMFAYDEGWIRRINEAIDSGLTAEAAIER 285

Query: 384 AIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL---LGDTAPLRVPAGAIVAAREITP 440
             Q     ++ +G+ LLA+R +DL DL  R+LR++   LG  A L +   +I+ AR + P
Sbjct: 286 VQQRTRMRMREIGDPLLADRMHDLEDLSNRLLRIVSGQLGTAAQLGLRHDSILIARNLGP 345

Query: 441 SDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQG 500
           ++L         G+ + EG  T+HV I+AR+ G+P L  +      + EG  ++LD   G
Sbjct: 346 AELLEYDRRRLKGVVLEEGSLTAHVTIVARAMGVPVLGRVKDVRRMIGEGDTLLLDGTAG 405

Query: 501 RLELSPDARRLEQVALQVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAE 558
            + +  +A   E  A +      Q+RR +  A R+  A TRD  RIE+  N     + A 
Sbjct: 406 SVVVRANATMEE--AFEAKMMVGQKRRAEFAAMRDLPARTRDDLRIELMVNAGLRDDMAA 463

Query: 559 AFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLD 618
               GADG+GL RTEF FL     P  E Q   Y++VLDA G R VI RT+D+GGDK L 
Sbjct: 464 LDVTGADGIGLFRTEFQFLVSATLPQRERQLRLYRDVLDAAGDRPVIFRTVDIGGDKALP 523

Query: 619 YLPL---PVEENPALGLRGIHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDELR 675
           YL       EENPALG R I LG  R  L+  Q RAL+         ++ PMVSE  E  
Sbjct: 524 YLKAGDDADEENPALGWRAIRLGLERDALMKVQARALIEAAAGRTLNVMFPMVSEPWEFE 583

Query: 676 -------AIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQ 728
                  A R+ + +     G+      G M+EVP+ A   D L    DFLSIGTNDL+Q
Sbjct: 584 EAVALFDAQRKWIHDHGR--GVPNAIRYGTMLEVPALAESLDMLLPRLDFLSIGTNDLTQ 641

Query: 729 YALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGL 788
           +  A DR +  LA+R D L PA+LR I +        G  +GVCG +   PL    L+GL
Sbjct: 642 FLFAADRANPKLAERYDWLSPAILRFIGRVTRQTRAAGVPIGVCGEMGGRPLEAMALIGL 701

Query: 789 GVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALL 823
           G++ LS+ P  VG +K  +R LDA   R      L
Sbjct: 702 GIDRLSITPAAVGPVKAMIRSLDAKALREAMDGFL 736


Lambda     K      H
   0.319    0.136    0.390 

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: 1394
Number of extensions: 84
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: 842
Length of database: 759
Length adjustment: 41
Effective length of query: 801
Effective length of database: 718
Effective search space:   575118
Effective search space used:   575118
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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