Align 5-dehydro-2-deoxygluconokinase; EC 2.7.1.92; 2-deoxy-5-keto-D-gluconate kinase; DKG kinase (uncharacterized)
to candidate WP_050654911.1 C1M55_RS10205 5-dehydro-2-deoxygluconokinase
Query= curated2:Q6LK43 (331 letters) >NCBI__GCF_002893965.1:WP_050654911.1 Length = 322 Score = 172 bits (437), Expect = 8e-48 Identities = 115/323 (35%), Positives = 164/323 (50%), Gaps = 18/323 (5%) Query: 9 DRPLDAIVLGRAGVDLYAREANTDMADISGFNKFVGGSAANIAVAISKLGGKVGFIGCVA 68 D P D + +GR+GVD+Y + + D+ F KF+GGSAAN++VA ++LG + I V Sbjct: 3 DAPFDVLAIGRSGVDIYPLQTGVGLEDVETFGKFLGGSAANVSVAAARLGRRAALISGVG 62 Query: 69 DDAFGGYVRGYMTEQGINLDGMMTDNSGSRTSVAFTEM-KPNDCTVLIYRN-KASDLTLK 126 D FG +V + G++ + + NS T V F E+ P+D + YR A DL + Sbjct: 63 SDPFGKFVTRELARLGVD-NRFVVTNSEYPTPVTFCEIFPPDDFPLYFYRKPHAPDLRIT 121 Query: 127 PEQVDPAYIAQSKMLVVTGTALSESPSREATLIAMEHARRSNTVVVLDVDYRPYSWRTDV 186 PE +D + + + T T LSE PSR A A E AR + VLD+DYRP W T Sbjct: 122 PEDIDLDAVRTASLYWSTVTGLSEEPSRSAHFAAWE-ARERRPLTVLDLDYRPMFWSTPQ 180 Query: 187 DASIYYGIAAGLSDIVIGNREEFDMMETVLAPGNTDDDATADRFLRANTQVVIVKAGELG 246 +A+ A + +GNREE + +A G T+ + AD L ++ IVK G G Sbjct: 181 EATTQVQRALAHVTVAVGNREECE-----IAVGETNPNKAADALLDLGVELAIVKQGPKG 235 Query: 247 SKVYCKDGHKFQQGIF----RVEVKKPFGSGDSFAGGLIWTLVNGGELEDGVKHGSAAAA 302 G +Q I V+V G+GDSF G L L+ G LE +++ +AA A Sbjct: 236 VL-----GKTRKQSITVPPNAVDVVNGLGAGDSFGGSLCHGLLAGWPLEKVLRYANAAGA 290 Query: 303 INVSGNSCTEAMPTKEVLFDFIE 325 I S C+ AMPT E + D E Sbjct: 291 IVASRLECSTAMPTAEEVHDLAE 313 Lambda K H 0.317 0.134 0.384 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: 258 Number of extensions: 13 Number of successful extensions: 5 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: 331 Length of database: 322 Length adjustment: 28 Effective length of query: 303 Effective length of database: 294 Effective search space: 89082 Effective search space used: 89082 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_050654911.1 C1M55_RS10205 (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.2754054.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-122 394.1 0.0 2.5e-122 393.9 0.0 1.0 1 NCBI__GCF_002893965.1:WP_050654911.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050654911.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 393.9 0.0 2.5e-122 2.5e-122 2 307 .. 6 310 .. 5 312 .. 0.99 Alignments for each domain: == domain 1 score: 393.9 bits; conditional E-value: 2.5e-122 TIGR04382 2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 +d+++iGR+gvD+y+ q+g+ ledv++f k+lGGs+aN++v+aarlG+++ali+ vg d +G+fv++el+r g NCBI__GCF_002893965.1:WP_050654911.1 6 FDVLAIGRSGVDIYPLQTGVGLEDVETFGKFLGGSAANVSVAAARLGRRAALISGVGSDPFGKFVTRELARLG 78 8************************************************************************ PP TIGR04382 75 vdtshvvtdkeartslvlleikdpdefpllfYRe.naaDlaltvddvdeeliaeakallvsgtalskepsrea 146 vd ++vvt++e+ t+++++ei++pd+fpl+fYR+ +a+Dl +t++d+d ++++ a++ + ++t+ls+epsr+a NCBI__GCF_002893965.1:WP_050654911.1 79 VDNRFVVTNSEYPTPVTFCEIFPPDDFPLYFYRKpHAPDLRITPEDIDLDAVRTASLYWSTVTGLSEEPSRSA 151 **********************************9************************************** PP TIGR04382 147 vlkalelakkagvkvvlDiDYRpvlWkskeeasaalqlvlkkvdviiGteeEfeiaagekddeaaakallelg 219 +++a+e a++++ +vlD+DYRp++W++++ea++++q++l++v+v++G++eE+eia+ge+++++aa+all+lg NCBI__GCF_002893965.1:WP_050654911.1 152 HFAAWE-ARERRPLTVLDLDYRPMFWSTPQEATTQVQRALAHVTVAVGNREECEIAVGETNPNKAADALLDLG 223 ******.****************************************************************** PP TIGR04382 220 aelvvvKrGeeGslvytkdeeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsr 292 +el++vK+G++G+l t++ ++++v++ v+v+++lGaGD+F+++l++gll+g++lek+l++anAagaiv+sr NCBI__GCF_002893965.1:WP_050654911.1 224 VELAIVKQGPKGVLGKTRK-QSITVPPNAVDVVNGLGAGDSFGGSLCHGLLAGWPLEKVLRYANAAGAIVASR 295 ******************9.***************************************************** PP TIGR04382 293 lscaeamptleelee 307 l+c++ampt+ee+++ NCBI__GCF_002893965.1:WP_050654911.1 296 LECSTAMPTAEEVHD 310 ************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (322 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: 26.01 // [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