Align Glucosamine-6-phosphate deaminase 1; GlcN6P deaminase 1; GNPDA 1; Glucosamine-6-phosphate isomerase 1; EC 3.5.99.6 (characterized)
to candidate WP_003465244.1 J416_RS03835 glucosamine-6-phosphate deaminase
Query= SwissProt::O35000 (242 letters) >NCBI__GCF_000359605.1:WP_003465244.1 Length = 241 Score = 261 bits (668), Expect = 7e-75 Identities = 122/237 (51%), Positives = 164/237 (69%) Query: 1 MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQN 60 M +++ Y+++S A + DT++ LGLATGGTP+GTY+QL++ HQ S+Q+ Sbjct: 1 MNIIQATNYQDMSNQTAELIIDTVRNNDYVTLGLATGGTPKGTYQQLVKDHQLNQTSYQH 60 Query: 61 ITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLV 120 +TT NLDEY G+ DPNSY +YM+ FF +D IPNG A+DL EC RYE+ + Sbjct: 61 VTTFNLDEYVGMRPTDPNSYRYYMDQYFFDEVDIPEQNIHIPNGMAEDLPRECARYEKQI 120 Query: 121 DSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKAL 180 D D+Q+LGIG+NGHIGFNEPGT+F+S THVV L TR+ANAR+F +D VP A+ Sbjct: 121 DDTNGIDLQILGIGKNGHIGFNEPGTAFESTTHVVELAHSTRKANARFFNHLDDVPTHAI 180 Query: 181 TMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREA 237 TMGI TI+ SK+ILLL SG+ KAEA+RKL+ + E PAS L HS+VT++ D+ A Sbjct: 181 TMGIATIMKSKQILLLASGEDKAEAIRKLIHEEVDEHMPASVLRHHSNVTIIADQNA 237 Lambda K H 0.316 0.133 0.375 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: 208 Number of extensions: 9 Number of successful extensions: 2 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: 242 Length of database: 241 Length adjustment: 23 Effective length of query: 219 Effective length of database: 218 Effective search space: 47742 Effective search space used: 47742 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)
Align candidate WP_003465244.1 J416_RS03835 (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.272145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-96 307.2 1.5 4.6e-96 307.1 1.5 1.0 1 NCBI__GCF_000359605.1:WP_003465244.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359605.1:WP_003465244.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 307.1 1.5 4.6e-96 4.6e-96 1 244 [. 1 238 [. 1 241 [] 0.98 Alignments for each domain: == domain 1 score: 307.1 bits; conditional E-value: 4.6e-96 TIGR00502 1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 m ++++++y+++s+ +a+ i++++++ +d + lGlatGgtP g+y+ql+++++ ++ s+++v+tfnlde NCBI__GCF_000359605.1:WP_003465244.1 1 MNIIQATNYQDMSNQTAELIIDTVRN--ND---YVTLGLATGGTPKGTYQQLVKDHQLNQTSYQHVTTFNLDE 68 89**********************99..33...468************************************* PP TIGR00502 74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146 yvg+ + +P+sy ++m + ff+ +di ++ni+i+nG a+dl ec rye++i++ +idl++lGiG++Ghi+f NCBI__GCF_000359605.1:WP_003465244.1 69 YVGMRPTDPNSYRYYMDQYFFDEVDIPEQNIHIPNGMAEDLPRECARYEKQIDDTNGIDLQILGIGKNGHIGF 141 ************************************************************************* PP TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219 nePg+ +es t+v++l+++t+ an+rff+ ++ vP +a+t+Gi ti++sk++lll+sG++kaea++kl+ + NCBI__GCF_000359605.1:WP_003465244.1 142 NEPGTAFESTTHVVELAHSTRKANARFFN-HLDDVPTHAITMGIATIMKSKQILLLASGEDKAEAIRKLIHEE 213 ****************************9.9****************************************** PP TIGR00502 220 vnedvtisalqlhkkvivvadeeaa 244 v+e +++s+l+ h++v+++ad++a NCBI__GCF_000359605.1:WP_003465244.1 214 VDEHMPASVLRHHSNVTIIADQNAL 238 **********************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (259 nodes) Target sequences: 1 (241 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: 22.31 // [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