Align 5-dehydro-2-deoxygluconokinase; EC 2.7.1.92; 2-deoxy-5-keto-D-gluconate kinase; DKG kinase (uncharacterized)
to candidate WP_084703970.1 BS73_RS11395 5-dehydro-2-deoxygluconokinase
Query= curated2:Q898F0 (339 letters) >NCBI__GCF_000744815.1:WP_084703970.1 Length = 385 Score = 166 bits (421), Expect = 7e-46 Identities = 108/335 (32%), Positives = 165/335 (49%), Gaps = 24/335 (7%) Query: 11 PLDVIPIGRVTIDFNPNEINRPLEESRTFTKYLGGSPGNIAVGLARLGKKVGFLSTVSDD 70 P D+I +GR+ +D P +I PL E TF K+LGGS N+AV ARL ++ +S D Sbjct: 19 PFDLITMGRIGVDIYPLQIGVPLAEVETFGKFLGGSATNVAVAAARLRRRSAVVSRTGAD 78 Query: 71 QFGNFVVNYLKNEGIDISQINRAKNGEKLGLTFTEILSPKESSILMYRKGIA-DLQLSSK 129 FG +V L+ G+D + + +TF EI P + I YR+ A DL++ + Sbjct: 79 PFGEYVHRALREFGVDDRWVTPVQR-YPTPVTFCEIFPPDDFPIWFYRRPKAPDLEIHPE 137 Query: 130 EVSEDYIKSAKAIVISGTALSKSPSREAAFVAL--EYAKKHNTRIIFDLDYREYTWN--- 184 E+ D I+SA I+GT L + PSR A AL A+ +FDLD+R W Sbjct: 138 ELDLDAIRSAGIFWITGTGLCEEPSRTATLAALAARSARPGAGPTVFDLDWRPAFWGGEG 197 Query: 185 ------------CKEEIAIYYSLAARMSDVIMGSREEFNLMEGLISPEESNDKETAERWI 232 E Y A + V +G+ +E + GL P+ AE + Sbjct: 198 GASGDGGEGGARAMAEARPIYREALAHATVAVGNLDEAEVATGLRDPQAC-----AEALL 252 Query: 233 GYGNKIVVIKHGKDGSTAYLHDGTSYKIKPFPVKLLKSFGGGDAYASAFIYGIMEGWDVI 292 G ++ V+K G G A DGT ++ P PV+++ G GDA+ A +G++ GW + Sbjct: 253 ELGAELAVVKQGPKGVLALHRDGTRAQVPPVPVEVVNGLGAGDAFGGALCHGLLAGWPLE 312 Query: 293 DALEFGSASAAMLVASHSCSEAMPKVEEIKQFIKE 327 + + +A+ A++ +CS AMP EEI+Q + E Sbjct: 313 RTVRWANAAGAIVAGRLACSSAMPTPEEIEQRLTE 347 Lambda K H 0.315 0.134 0.381 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: 262 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: 339 Length of database: 385 Length adjustment: 29 Effective length of query: 310 Effective length of database: 356 Effective search space: 110360 Effective search space used: 110360 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 (21.5 bits) S2: 49 (23.5 bits)
Align candidate WP_084703970.1 BS73_RS11395 (5-dehydro-2-deoxygluconokinase)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))
# 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/TIGR04382.hmm # target sequence database: /tmp/gapView.2522704.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04382 [M=309] Accession: TIGR04382 Description: myo_inos_iolC_N: 5-dehydro-2-deoxygluconokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-113 363.8 0.0 4.5e-113 363.6 0.0 1.0 1 NCBI__GCF_000744815.1:WP_084703970.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_084703970.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 363.6 0.0 4.5e-113 4.5e-113 2 307 .. 20 343 .. 19 345 .. 0.97 Alignments for each domain: == domain 1 score: 363.6 bits; conditional E-value: 4.5e-113 TIGR04382 2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 +dlit+GR+gvD+y+ qig++l++v++f k+lGGs++N+av+aarl +++a++++ g+d +G++v+++l+++g NCBI__GCF_000744815.1:WP_084703970.1 20 FDLITMGRIGVDIYPLQIGVPLAEVETFGKFLGGSATNVAVAAARLRRRSAVVSRTGADPFGEYVHRALREFG 92 8************************************************************************ PP TIGR04382 75 vdtshvvtdkeartslvlleikdpdefpllfYRe.naaDlaltvddvdeeliaeakallvsgtalskepsrea 146 vd+++v+ + + t+++++ei++pd+fp++fYR+ +a+Dl+++++++d ++i++a +++++gt+l++epsr+a NCBI__GCF_000744815.1:WP_084703970.1 93 VDDRWVTPVQRYPTPVTFCEIFPPDDFPIWFYRRpKAPDLEIHPEELDLDAIRSAGIFWITGTGLCEEPSRTA 165 **********************************9************************************** PP TIGR04382 147 vlkale..lakkagvkvvlDiDYRpvlWk...............skeeasaalqlvlkkvdviiGteeEfeia 202 +l+al a+ +v+D+D+Rp +W+ + +ea+ ++++l++++v++G+ +E e+a NCBI__GCF_000744815.1:WP_084703970.1 166 TLAALAarSARPGAGPTVFDLDWRPAFWGgeggasgdggeggarAMAEARPIYREALAHATVAVGNLDEAEVA 238 **99871134445568**************************999999999********************** PP TIGR04382 203 agekddeaaakallelgaelvvvKrGeeGslvytkdeeevevkgfkvevlkvlGaGDaFasgllygllegedl 275 g +d++a a+allelgael+vvK+G++G+l++++d+++ +v++++vev+++lGaGDaF+++l++gll+g++l NCBI__GCF_000744815.1:WP_084703970.1 239 TGLRDPQACAEALLELGAELAVVKQGPKGVLALHRDGTRAQVPPVPVEVVNGLGAGDAFGGALCHGLLAGWPL 311 ************************************************************************* PP TIGR04382 276 ekalelanAagaivvsrlscaeamptleelee 307 e+++++anAagaiv+ rl+c+ ampt ee+e+ NCBI__GCF_000744815.1:WP_084703970.1 312 ERTVRWANAAGAIVAGRLACSSAMPTPEEIEQ 343 ******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (385 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: 19.28 // [ok]
This GapMind analysis is from Apr 09 2024. 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