Align glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_007706747.1 AFK65_RS05930 glucosamine-6-phosphate deaminase
Query= BRENDA::P0A759 (266 letters) >NCBI__GCF_001277175.1:WP_007706747.1 Length = 266 Score = 486 bits (1251), Expect = e-142 Identities = 236/266 (88%), Positives = 250/266 (93%) Query: 1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQ 60 MRLIPL T +QVGKWAARHIV RIN F PTADRPFVLGLPTGGTP+ YKAL+EMHKAGQ Sbjct: 1 MRLIPLATPQQVGKWAARHIVKRINDFNPTADRPFVLGLPTGGTPLEAYKALIEMHKAGQ 60 Query: 61 VSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQ 120 VSFKHVVTFNMDEYVGLPK+HPESY+SFM+RNFF+HVDIP ENINLL+GNAPDIDAECR+ Sbjct: 61 VSFKHVVTFNMDEYVGLPKDHPESYHSFMYRNFFEHVDIPEENINLLDGNAPDIDAECRR 120 Query: 121 YEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQ 180 YEEKIR+YGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFF DVNQ Sbjct: 121 YEEKIRAYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFGGDVNQ 180 Query: 181 VPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCD 240 VPKYALTVGVGTLLDA+EVMILVLG KA ALQAAVEG VNHMWTISCLQLHPKA++VCD Sbjct: 181 VPKYALTVGVGTLLDAQEVMILVLGHVKAQALQAAVEGNVNHMWTISCLQLHPKAVIVCD 240 Query: 241 EPSTMELKVKTLRYFNELEAENIKGL 266 EPSTMELKVKTL+YF ELEAENIK L Sbjct: 241 EPSTMELKVKTLKYFTELEAENIKDL 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: 344 Number of extensions: 10 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 WP_007706747.1 AFK65_RS05930 (glucosamine-6-phosphate deaminase)
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.286106.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-143 462.5 0.0 2e-143 462.3 0.0 1.0 1 NCBI__GCF_001277175.1:WP_007706747.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001277175.1:WP_007706747.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.3 0.0 2e-143 2e-143 1 259 [] 1 259 [. 1 259 [. 1.00 Alignments for each domain: == domain 1 score: 462.3 bits; conditional E-value: 2e-143 TIGR00502 1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 m+l++l t ++++k+aar+i+++in+f+p+a+rpfvlGl+tGgtP++ yk+lie++kag+vsfk+vvtfn+de NCBI__GCF_001277175.1:WP_007706747.1 1 MRLIPLATPQQVGKWAARHIVKRINDFNPTADRPFVLGLPTGGTPLEAYKALIEMHKAGQVSFKHVVTFNMDE 73 9************************************************************************ PP TIGR00502 74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146 yvgl+++hPesyhsfmy+nff+h+di +enin+l+Gna+d++aecrryeeki+ +Gki+lf++G+G+dGhiaf NCBI__GCF_001277175.1:WP_007706747.1 74 YVGLPKDHPESYHSFMYRNFFEHVDIPEENINLLDGNAPDIDAECRRYEEKIRAYGKIHLFMGGVGNDGHIAF 146 ************************************************************************* PP TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219 neP+ssl+srtr+ktlt+dt++ansrff+gdvn+vPk+altvG++t+ld++ev++lv G+ ka+a++++veg+ NCBI__GCF_001277175.1:WP_007706747.1 147 NEPASSLASRTRIKTLTHDTRVANSRFFGGDVNQVPKYALTVGVGTLLDAQEVMILVLGHVKAQALQAAVEGN 219 ************************************************************************* PP TIGR00502 220 vnedvtisalqlhkkvivvadeeaaqelkvktlkyfnele 259 vn+++tis+lqlh k+++v+de +++elkvktlkyf+ele NCBI__GCF_001277175.1:WP_007706747.1 220 VNHMWTISCLQLHPKAVIVCDEPSTMELKVKTLKYFTELE 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 24.52 // [ok]
This GapMind analysis is from Sep 24 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