GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Klebsiella michiganensis M5al

Align Glucosamine-6-phosphate deaminase; EC 3.5.99.6; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase (uncharacterized)
to candidate BWI76_RS00120 BWI76_RS00120 glucosamine-6-phosphate deaminase

Query= curated2:Q8ESL6
         (250 letters)



>FitnessBrowser__Koxy:BWI76_RS00120
          Length = 245

 Score =  134 bits (337), Expect = 2e-36
 Identities = 82/245 (33%), Positives = 133/245 (54%), Gaps = 10/245 (4%)

Query: 1   MKIIQTENYQSMSKLASQHVINTIKQLNKPVLGLATGSTPEGLYQHLIKAYRMHQISFAN 60
           MK+I TE+Y  MS +AS HV+  I    +  L +  GSTP+ +Y+HL  A +     ++ 
Sbjct: 1   MKLIVTEDYAEMSLVASHHVLGYITAPRRMNLAVTAGSTPKKMYEHLTAAIKGKSF-YSQ 59

Query: 61  VSTFNLDEYVGLHKEDKNSYHYYMQKFLFNHVDIPYKNIHLPNGIAKDLSVECTSYEDRI 120
              +N DE     ++ +      ++   F    IP +NIH      K        ++ R+
Sbjct: 60  AHYYNFDEIPFRGQDREGVTISNLRSLFFTPAQIPEENIH------KLSHANFIHHDQRL 113

Query: 121 QQAGGIHIQVLGIGRNGHIGFNEPGTS-FESQTHVVDL--DESTRNANARFFDSIDEVPN 177
           Q+ GG+ + V+G+G +GH   N P T+ F   T  V +  D     A+         VP+
Sbjct: 114 QEEGGLDLVVMGLGADGHFCGNLPNTTRFHDATVKVPIVGDLVDLVAHGEMDGDFSAVPD 173

Query: 178 QAITMGIQSIMRAKEILLLVSGSEKAEALEKLVNGNVSEEFPASILQTHQNVKIIADKAA 237
             +TMG +S+M AK +LL+VSG+ KA+AL++++ G VSE  PAS+L+ H ++ I+ADKAA
Sbjct: 174 SYVTMGPKSVMAAKNLLLIVSGAAKAQALKQVIEGEVSERVPASVLKLHPSLVIVADKAA 233

Query: 238 LQDIS 242
             +++
Sbjct: 234 AAELT 238


Lambda     K      H
   0.317    0.132    0.372 

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: 154
Number of extensions: 11
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: 250
Length of database: 245
Length adjustment: 24
Effective length of query: 226
Effective length of database: 221
Effective search space:    49946
Effective search space used:    49946
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 (21.6 bits)
S2: 46 (22.3 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