GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Rhodobacter viridis JA737

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_110804641.1 C8J30_RS05120 hypothetical protein

Query= reanno::Smeli:SMc02875
         (294 letters)



>NCBI__GCF_003217355.1:WP_110804641.1
          Length = 493

 Score =  139 bits (349), Expect = 2e-37
 Identities = 97/277 (35%), Positives = 143/277 (51%), Gaps = 14/277 (5%)

Query: 6   IGIDGGGTSCRAAVAALDGRILGRGKAGAANILTDPETALQNITDAARDAFGDAGLDPAG 65
           + IDGGG+ CRAA+    G+ L R + G ANI +D +TAL ++ + A    GD  LD   
Sbjct: 223 LAIDGGGSGCRAALCDDAGQELARAEGGPANIASDFDTALASLRELALRMIGDRPLDQV- 281

Query: 66  IGASRAIVGVAGHNVGDAVHYVKRRLPFAQADIESDGLIALQGALGDGDGAVAILGTGTI 125
               RA++GVAG N+  A   ++  LPF +A +  D   +L+GALGD DG +A +GTG++
Sbjct: 282 ----RAVLGVAGANLSGAGPRLEAALPF-RAKVVQDVTTSLRGALGDADGIMAAIGTGSV 336

Query: 126 YIARRGDEVSYVGGWGFTIGDHGSGARIGHALLQESLLAYDGIHQGSGVTDAVLAEFNDD 185
           +  + G EV  +GGWGF +GD  SGA +G  +L       DG    S +  AVL +    
Sbjct: 337 FARQVGGEVKAIGGWGFRLGDEASGAWMGRLMLNRITRMLDGYAPLSPLAKAVLDDLGGG 396

Query: 186 PRDIVDFARLAKPGEFGRYAPRVFEFAERGDPVAISLLKAAAATVDEALDVVVSRGSEKL 245
           P  +V F     P +      R+    E  DP++  +L    A +  A+ ++ +     +
Sbjct: 397 P-GLVAFTLKKTPADHALLVHRMAAALE--DPLSRQVLTETRAELRAAIGLLQTDPPLPV 453

Query: 246 CLLGGLAPLYRRWLADRHQPRFVEARADALTGAVALA 282
             LGGL P     LA    PR  E    +L GA+A+A
Sbjct: 454 VWLGGLGPT----LALTDWPR-TEPLGSSLDGAMAMA 485


Lambda     K      H
   0.320    0.139    0.410 

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: 21
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: 294
Length of database: 493
Length adjustment: 30
Effective length of query: 264
Effective length of database: 463
Effective search space:   122232
Effective search space used:   122232
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 (21.8 bits)
S2: 50 (23.9 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