Align glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate 14808 b0678 glucosamine-6-phosphate deaminase (NCBI)
Query= BRENDA::P0A759 (266 letters) >FitnessBrowser__Keio:14808 Length = 266 Score = 543 bits (1398), Expect = e-159 Identities = 266/266 (100%), Positives = 266/266 (100%) Query: 1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQ 60 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQ Sbjct: 1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQ 60 Query: 61 VSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQ 120 VSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQ Sbjct: 61 VSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQ 120 Query: 121 YEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQ 180 YEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQ Sbjct: 121 YEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQ 180 Query: 181 VPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCD 240 VPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCD Sbjct: 181 VPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCD 240 Query: 241 EPSTMELKVKTLRYFNELEAENIKGL 266 EPSTMELKVKTLRYFNELEAENIKGL Sbjct: 241 EPSTMELKVKTLRYFNELEAENIKGL 266 Lambda K H 0.320 0.135 0.405 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: 372 Number of extensions: 7 Number of successful extensions: 1 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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: 47 (22.7 bits)
Align candidate 14808 b0678 (glucosamine-6-phosphate deaminase (NCBI))
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00502.hmm # target sequence database: /tmp/gapView.20088.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00502 [M=259] Accession: TIGR00502 Description: nagB: glucosamine-6-phosphate deaminase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-148 478.2 0.0 3.3e-148 478.0 0.0 1.0 1 lcl|FitnessBrowser__Keio:14808 b0678 glucosamine-6-phosphate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14808 b0678 glucosamine-6-phosphate deaminase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.0 0.0 3.3e-148 3.3e-148 1 259 [] 1 259 [. 1 259 [. 1.00 Alignments for each domain: == domain 1 score: 478.0 bits; conditional E-value: 3.3e-148 TIGR00502 1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglse 79 m+l++l+t+e+++k+aar+i+++in+fkp+a+rpfvlGl+tGgtP+++yk+l+e++kag+vsfk+vvtfn+deyvgl++ lcl|FitnessBrowser__Keio:14808 1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPK 79 9****************************************************************************** PP TIGR00502 80 ehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiafnePgsslesrtr 158 ehPesy+sfm++nff+h+di +enin+lnGna+d++aecr+yeeki+s+Gki+lf++G+G+dGhiafneP+ssl+srtr lcl|FitnessBrowser__Keio:14808 80 EHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTR 158 ******************************************************************************* PP TIGR00502 159 vktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvtisalqlhkkviv 237 +ktlt+dt++ansrff++dvn+vPk+altvG++t+ld++ev++lv G++ka a++++veg+vn+++tis+lqlh k+i+ lcl|FitnessBrowser__Keio:14808 159 IKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIM 237 ******************************************************************************* PP TIGR00502 238 vadeeaaqelkvktlkyfnele 259 v+de +++elkvktl+yfnele lcl|FitnessBrowser__Keio:14808 238 VCDEPSTMELKVKTLRYFNELE 259 ********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (266 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.20 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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