Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate HSERO_RS12125 HSERO_RS12125 5-dehydro-2-deoxygluconokinase
Query= reanno::HerbieS:HSERO_RS12125 (657 letters) >FitnessBrowser__HerbieS:HSERO_RS12125 Length = 657 Score = 1316 bits (3407), Expect = 0.0 Identities = 657/657 (100%), Positives = 657/657 (100%) Query: 1 MQATHTPSTSTPRRFAADRRLDLICIGRLAVDLYAQQVGAPLSDVSSFAKYLGGSSANIA 60 MQATHTPSTSTPRRFAADRRLDLICIGRLAVDLYAQQVGAPLSDVSSFAKYLGGSSANIA Sbjct: 1 MQATHTPSTSTPRRFAADRRLDLICIGRLAVDLYAQQVGAPLSDVSSFAKYLGGSSANIA 60 Query: 61 FGCARLGLKSAMLARIGDEANGQFLKAELAAEGCDVSHVTVDPQRLTALVMLGLKDKDSF 120 FGCARLGLKSAMLARIGDEANGQFLKAELAAEGCDVSHVTVDPQRLTALVMLGLKDKDSF Sbjct: 61 FGCARLGLKSAMLARIGDEANGQFLKAELAAEGCDVSHVTVDPQRLTALVMLGLKDKDSF 120 Query: 121 PLIFYRDNCADMALAPEDIDEAFIASSKALLITGTHFSTPQVHRSSSLALQYARRHNVRT 180 PLIFYRDNCADMALAPEDIDEAFIASSKALLITGTHFSTPQVHRSSSLALQYARRHNVRT Sbjct: 121 PLIFYRDNCADMALAPEDIDEAFIASSKALLITGTHFSTPQVHRSSSLALQYARRHNVRT 180 Query: 181 VLDIDYRPVLWGLTSKGDGETRFIASDGVTQHLQGILPQFDLVVGTEEEFMIAGGSTDIM 240 VLDIDYRPVLWGLTSKGDGETRFIASDGVTQHLQGILPQFDLVVGTEEEFMIAGGSTDIM Sbjct: 181 VLDIDYRPVLWGLTSKGDGETRFIASDGVTQHLQGILPQFDLVVGTEEEFMIAGGSTDIM 240 Query: 241 AALRAVRALCAATLVVKRGPLGCVVLHGAIPERLDDGFHYRGVQVEVLNVLGAGDAFISG 300 AALRAVRALCAATLVVKRGPLGCVVLHGAIPERLDDGFHYRGVQVEVLNVLGAGDAFISG Sbjct: 241 AALRAVRALCAATLVVKRGPLGCVVLHGAIPERLDDGFHYRGVQVEVLNVLGAGDAFISG 300 Query: 301 FLKGWLNEEDDEHCCRYANACGALVVSRHACAPAMPGPIELDYFLQHAHRLQRPDRDAHL 360 FLKGWLNEEDDEHCCRYANACGALVVSRHACAPAMPGPIELDYFLQHAHRLQRPDRDAHL Sbjct: 301 FLKGWLNEEDDEHCCRYANACGALVVSRHACAPAMPGPIELDYFLQHAHRLQRPDRDAHL 360 Query: 361 QRLHRVVSRRRHWDEVNVFAFDHRNQFFELAVEAGVSQDKLPALKRLLVEAVAQTEAKLG 420 QRLHRVVSRRRHWDEVNVFAFDHRNQFFELAVEAGVSQDKLPALKRLLVEAVAQTEAKLG Sbjct: 361 QRLHRVVSRRRHWDEVNVFAFDHRNQFFELAVEAGVSQDKLPALKRLLVEAVAQTEAKLG 420 Query: 421 LQGKTGVLIDDRYGQDALNAATGRGWWVGRAVELPLSNPLEFDFGRSIGTHLQTWPQEQV 480 LQGKTGVLIDDRYGQDALNAATGRGWWVGRAVELPLSNPLEFDFGRSIGTHLQTWPQEQV Sbjct: 421 LQGKTGVLIDDRYGQDALNAATGRGWWVGRAVELPLSNPLEFDFGRSIGTHLQTWPQEQV 480 Query: 481 VKCLVQFHPDEQVEKRLEQEAQIRALYQAVQRSGHELLLEIIPSKTLPQEEDTVLRALKR 540 VKCLVQFHPDEQVEKRLEQEAQIRALYQAVQRSGHELLLEIIPSKTLPQEEDTVLRALKR Sbjct: 481 VKCLVQFHPDEQVEKRLEQEAQIRALYQAVQRSGHELLLEIIPSKTLPQEEDTVLRALKR 540 Query: 541 LYNLDIYPEWWKLESMSARQWEAIDALIAERDPYCRGVVLLGLAAPVSELAAGFAASRHS 600 LYNLDIYPEWWKLESMSARQWEAIDALIAERDPYCRGVVLLGLAAPVSELAAGFAASRHS Sbjct: 541 LYNLDIYPEWWKLESMSARQWEAIDALIAERDPYCRGVVLLGLAAPVSELAAGFAASRHS 600 Query: 601 KTCRGFMVGRTIFHESSRAWLQGRIDDATLIAQVRTTFEELIGLWRASRVTPAREAA 657 KTCRGFMVGRTIFHESSRAWLQGRIDDATLIAQVRTTFEELIGLWRASRVTPAREAA Sbjct: 601 KTCRGFMVGRTIFHESSRAWLQGRIDDATLIAQVRTTFEELIGLWRASRVTPAREAA 657 Lambda K H 0.322 0.137 0.414 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: 1492 Number of extensions: 20 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: 657 Length of database: 657 Length adjustment: 38 Effective length of query: 619 Effective length of database: 619 Effective search space: 383161 Effective search space used: 383161 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 (21.9 bits) S2: 54 (25.4 bits)
Align candidate HSERO_RS12125 HSERO_RS12125 (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.21677.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-128 412.9 0.0 6.6e-128 412.3 0.0 1.3 1 lcl|FitnessBrowser__HerbieS:HSERO_RS12125 HSERO_RS12125 5-dehydro-2-deoxyg Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS12125 HSERO_RS12125 5-dehydro-2-deoxygluconokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.3 0.0 6.6e-128 6.6e-128 2 309 .] 21 345 .. 20 345 .. 0.99 Alignments for each domain: == domain 1 score: 412.3 bits; conditional E-value: 6.6e-128 TIGR04382 2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvree 69 ldli+iGR++vDlyaqq+ga+l+dv+sfakylGGs+aNia+g+arlGlk+a+++++gd++ G+f+++e lcl|FitnessBrowser__HerbieS:HSERO_RS12125 21 LDLICIGRLAVDLYAQQVGAPLSDVSSFAKYLGGSSANIAFGCARLGLKSAMLARIGDEANGQFLKAE 88 8******************************************************************* PP TIGR04382 70 leregvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgta 137 l++eg+d+shv+ d++++t+lv+l++kd+d+fpl+fYR+n+aD+al+++d+de++ia++kall++gt+ lcl|FitnessBrowser__HerbieS:HSERO_RS12125 89 LAAEGCDVSHVTVDPQRLTALVMLGLKDKDSFPLIFYRDNCADMALAPEDIDEAFIASSKALLITGTH 156 ******************************************************************** PP TIGR04382 138 lskepsreavlkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdvii 193 +s++++++++ al++a++++v++vlDiDYRpvlW+ +++ ++++lq +l+++d+++ lcl|FitnessBrowser__HerbieS:HSERO_RS12125 157 FSTPQVHRSSSLALQYARRHNVRTVLDIDYRPVLWGltskgdgetrfiASDGVTQHLQGILPQFDLVV 224 ******************************************************************** PP TIGR04382 194 GteeEfeiaagekddeaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlG 256 GteeEf ia g++d +aa++a+++l+a+++vvKrG+ G++v++++ ++ ++++g++vevl+vlG lcl|FitnessBrowser__HerbieS:HSERO_RS12125 225 GTEEEFMIAGGSTDIMAALRAVRALCAATLVVKRGPLGCVVLHGAiperlDDGFHYRGVQVEVLNVLG 292 ********************************************9*********************** PP TIGR04382 257 aGDaFasgllygllegedlekalelanAagaivvsrlscaeamptleeleefl 309 aGDaF+sg+l+g+l++ed e+++++anA+ga+vvsr++ca+amp el+ fl lcl|FitnessBrowser__HerbieS:HSERO_RS12125 293 AGDAFISGFLKGWLNEEDDEHCCRYANACGALVVSRHACAPAMPGPIELDYFL 345 *************************************************9996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (657 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 19.78 // [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