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 WP_004121794.1 RHSP_RS20075 5-dehydro-2-deoxygluconokinase
Query= reanno::Smeli:SMc01165 (650 letters) >NCBI__GCF_000359745.1:WP_004121794.1 Length = 644 Score = 893 bits (2308), Expect = 0.0 Identities = 442/635 (69%), Positives = 517/635 (81%), Gaps = 4/635 (0%) Query: 13 AGAKP---LDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGTARLGLKSAL 69 +GA+P LD+ITIGR+SVDLYGQQIG++LED+ASFAKSVGGCP NI++GTARLGLKS L Sbjct: 6 SGAEPEARLDVITIGRSSVDLYGQQIGSKLEDIASFAKSVGGCPANIAIGTARLGLKSGL 65 Query: 70 LTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLLFYRDNCADN 129 +TRVGDEQMGRFIREQ REGV GI TD ERLTAL +L+VE + P++FYR +CAD Sbjct: 66 ITRVGDEQMGRFIREQAAREGVAVDGIATDKERLTALVLLAVEAEGVSPMIFYRSDCADM 125 Query: 130 ALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFDIDYRPNLWG 189 AL EDDI E FI+S+ AVLV+GTHF+KPN +AAQRKAIRIAK +G +++FDIDYRPNLWG Sbjct: 126 ALNEDDIDESFIKSSNAVLVSGTHFSKPNTEAAQRKAIRIAKANGRKVIFDIDYRPNLWG 185 Query: 190 LAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAALKTIRSLSKA 249 LAGH G RY+ SDRVS+ +K L DCDLIVGTEEE++IASG D+L ALK IR LS A Sbjct: 186 LAGHAEGFERYVKSDRVSSKMKETLPDCDLIVGTEEEIMIASGADDVLGALKEIRRLSSA 245 Query: 250 TIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLRGWLTGEPHA 309 IVLKRG MGCIVY+GPISDDLE GIVG+GFPIEV+NVLGAGDAFMSGFLRG+L GEP Sbjct: 246 VIVLKRGAMGCIVYEGPISDDLEAGIVGEGFPIEVFNVLGAGDAFMSGFLRGYLRGEPLK 305 Query: 310 TSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHVHWATTRR-R 368 TSATWANACGAFAVSRLLC+PE PTW EL +FL+ GSK +ALRKDEAINH+HWATTRR Sbjct: 306 TSATWANACGAFAVSRLLCSPEYPTWAELDFFLKTGSKHRALRKDEAINHIHWATTRRSE 365 Query: 369 DIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFGMLIDDKYG 428 +IPLLMALA+DHRSQL + + +I AFK LAV+AAA VA GRSG+GMLID+++G Sbjct: 366 EIPLLMALAIDHRSQLVSVCDELGIGHDKIVAFKQLAVEAAARVADGRSGYGMLIDERFG 425 Query: 429 RDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLSFYHPDDPA 488 RDA + A WIG+P+ELPGS+PL FEFSQD+GS+LV+WP+ HCIK L FYHPDDP Sbjct: 426 RDAFFDAATKNFSWIGRPVELPGSKPLRFEFSQDIGSQLVEWPLSHCIKCLCFYHPDDPK 485 Query: 489 ELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAGLKPDWWKL 548 ELK Q KLR+ FEAARKVGRE+L+EIIA K+G L D TIP ALEELY G+KPDWWKL Sbjct: 486 ELKEEQQEKLRTLFEAARKVGRELLVEIIASKNGPLTDDTIPTALEELYALGIKPDWWKL 545 Query: 549 EPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVKGFAVGRTI 608 EPQ S AW IDAVI DPLCRG+VLLGLEAP E L F A + +VKGFAVGRTI Sbjct: 546 EPQESTTAWKKIDAVIAKNDPLCRGIVLLGLEAPAEELIRSFEATLAAPSVKGFAVGRTI 605 Query: 609 FADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQ 643 F+DAA+AWL+G M DE+A++DMA +F+ L WL+ Sbjct: 606 FSDAARAWLSGGMNDEEAIADMAGRFRQLTAAWLK 640 Lambda K H 0.320 0.136 0.407 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: 1219 Number of extensions: 52 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: 650 Length of database: 644 Length adjustment: 38 Effective length of query: 612 Effective length of database: 606 Effective search space: 370872 Effective search space used: 370872 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: 54 (25.4 bits)
Align candidate WP_004121794.1 RHSP_RS20075 (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.2734548.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-120 386.8 0.0 5.2e-120 386.3 0.0 1.2 1 NCBI__GCF_000359745.1:WP_004121794.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359745.1:WP_004121794.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.3 0.0 5.2e-120 5.2e-120 2 309 .] 14 338 .. 13 338 .. 0.99 Alignments for each domain: == domain 1 score: 386.3 bits; conditional E-value: 5.2e-120 TIGR04382 2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 ld+itiGR++vDly+qqig++led+ sfak++GG+paNia+g+arlGlk++lit+vgd+q+Grf+re+ +reg NCBI__GCF_000359745.1:WP_004121794.1 14 LDVITIGRSSVDLYGQQIGSKLEDIASFAKSVGGCPANIAIGTARLGLKSGLITRVGDEQMGRFIREQAAREG 86 8************************************************************************ PP TIGR04382 75 vdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreav 147 v ++++ tdke++t+lvll ++ + +p++fYR+++aD+al+ dd+de +i++++a+lvsgt++sk+++++a+ NCBI__GCF_000359745.1:WP_004121794.1 87 VAVDGIATDKERLTALVLLAVEAEGVSPMIFYRSDCADMALNEDDIDESFIKSSNAVLVSGTHFSKPNTEAAQ 159 ************************************************************************* PP TIGR04382 148 lkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEfeiaagekdd 208 ka+++ak++g kv++DiDYRp+lW+ +++++s ++++ l+++d+i+GteeE+ ia+g++d NCBI__GCF_000359745.1:WP_004121794.1 160 RKAIRIAKANGRKVIFDIDYRPNLWGlaghaegferyvKSDRVSSKMKETLPDCDLIVGTEEEIMIASGADDV 232 ************************************************************************* PP TIGR04382 209 eaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasgllygllegedle 276 a+k++++l+ +++v+KrG+ G++vy++ e + +gf++ev++vlGaGDaF+sg+l+g+l+ge+l+ NCBI__GCF_000359745.1:WP_004121794.1 233 LGALKEIRRLSSAVIVLKRGAMGCIVYEGPisddlEAGIVGEGFPIEVFNVLGAGDAFMSGFLRGYLRGEPLK 305 ****************************9999999999*********************************** PP TIGR04382 277 kalelanAagaivvsrlscaeamptleeleefl 309 +++++anA+ga++vsrl c++++pt++el+ fl NCBI__GCF_000359745.1:WP_004121794.1 306 TSATWANACGAFAVSRLLCSPEYPTWAELDFFL 338 *****************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (644 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: 44.70 // [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