GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Shewanella amazonensis SB2B

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 6936101 Sama_0298 ATPase, BadF/BadG/BcrA/BcrD type (RefSeq)

Query= reanno::ANA3:7025966
         (302 letters)



>FitnessBrowser__SB2B:6936101
          Length = 327

 Score =  222 bits (566), Expect = 8e-63
 Identities = 117/282 (41%), Positives = 176/282 (62%), Gaps = 4/282 (1%)

Query: 12  FIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLHGLAQTFASIEASTRQALLDAGMKET 71
           ++G+D GGS CRA +    G VLG GVAG ANP++G++Q+ A+I ++  +AL  A   + 
Sbjct: 39  WVGIDAGGSHCRALLTDDSGQVLGHGVAGPANPVNGVSQSQAAIMSAIDKAL-GAARLDK 97

Query: 72  DSHLLVAGLGLAGVNVPRLYQDVISWQHPFAAMYVTTDLHTACIGAHRGADGAVIITGTG 131
             H L+ G GLAG+++P++ Q +  W HPFAA + TTDLH A +GAH+GADG VII GTG
Sbjct: 98  QYHRLIVGAGLAGLHLPKMQQVMNEWAHPFAAWHTTTDLHVAALGAHQGADGGVIILGTG 157

Query: 132 SCGYAHVGDDSLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTALTEMLLKHFG 191
               A+V    + IGGHGF +    SG+W GL+A + VLL  DG    T+LT  LL+   
Sbjct: 158 FSSLANVKGQQILIGGHGFPINATCSGSWFGLEAVKAVLLDADGIGPGTSLTGKLLQG-- 215

Query: 192 VSDALGIVEHLAGKSSSCYAELARSVLDCANAGDEVARGIVQEGADYISEMARKLFSLNP 251
            ++A+ + E L   +++ +A  A  V + A AGD V+  ++++GA +I+ + R+L +   
Sbjct: 216 -TNAMALAEQLMHANATDFARFAPQVFEQAGAGDAVSLSLIEQGATFINGVIRRLLATGI 274

Query: 252 VRFSMIGGLAEPLQAWLGSDVVAKISETLAPPELGAMYFAQQ 293
              S++GG+A  +Q WL  D+  +I    A PE GA+ FA+Q
Sbjct: 275 DSLSLVGGIAPLMQPWLAPDLSTRIRTAKASPEEGAILFARQ 316


Lambda     K      H
   0.319    0.135    0.400 

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: 307
Number of extensions: 13
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: 302
Length of database: 327
Length adjustment: 27
Effective length of query: 275
Effective length of database: 300
Effective search space:    82500
Effective search space used:    82500
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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