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_110806485.1 C8J30_RS14070 5-dehydro-2-deoxygluconokinase
Query= reanno::Caulo:CCNA_01356 (642 letters) >NCBI__GCF_003217355.1:WP_110806485.1 Length = 638 Score = 658 bits (1698), Expect = 0.0 Identities = 353/631 (55%), Positives = 417/631 (66%), Gaps = 5/631 (0%) Query: 6 KTLDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLLTRVGA 65 KTLD+I +GR+ VDLYG QVGGRLEDMGSF KY+GGSPTN A G ARLGL++ L+TRVG Sbjct: 2 KTLDVITIGRAGVDLYGTQVGGRLEDMGSFQKYIGGSPTNIACGTARLGLRSALITRVGD 61 Query: 66 DHMGRFIREQLEREGVDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMALEPSD 125 +HMGRFIREQL REGVDV GV +DP+RLTALVILGIRD FPLIFYRENCADMAL +D Sbjct: 62 EHMGRFIREQLGREGVDVRGVKTDPERLTALVILGIRDEEQFPLIFYRENCADMALCEAD 121 Query: 126 VDEAWFAQAGAVLINGTHLSQPNVYETSLKAARAVKAAGGRVAFDIDYRPVLWGLTGKDA 185 ++E + A+A +VL GTHLS P LKA + G + A DIDYRP LWG+ G A Sbjct: 122 IEEGFIAEARSVLATGTHLSHPRTEAAVLKALALARKHGAKTALDIDYRPNLWGVAGHGA 181 Query: 186 GENRFVENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDTIAALRAIRRASDALLVCKR 245 GE+RFVE+ +VTAKL + L DLIVGTEEE HI GGSTDTIAALRA+R S+A LVCKR Sbjct: 182 GESRFVESAKVTAKLLGTLHLFDLIVGTEEEFHIAGGSTDTIAALRAVRAVSNATLVCKR 241 Query: 246 GPEGCVAFPGAIPDALDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVETCCEWG 305 G +G VAF G IPD+LD+G S GF +EVFNVLGAGD F +G L+GWL E+ E+ Sbjct: 242 GAKGAVAFEGTIPDSLDDGQSGPGFPIEVFNVLGAGDGFFSGLLKGWLDGEAWPRALEYA 301 Query: 306 NACGAIVVSRHGCTPAMPTWIELQAFLSERERPFRLREDAELEHIHWATTRERVYDELTV 365 NACGA VSRHGCTPA P+ EL+ FL LR DAELE +HWATTR+ + + V Sbjct: 302 NACGAFAVSRHGCTPAYPSLEELKFFLRRGVVRPDLRNDAELEQVHWATTRKGDWSTMRV 361 Query: 366 LAIDHRSQFEDLIAETGGDAERIPDFKRLALRAVQMVAGRDETRFGMLLDGRFGFEALAE 425 A DHR Q E L G A++ FK L L A + V G +G+L D R G +AL Sbjct: 362 FAFDHRMQLEQL---PGFTADKGSRFKELCLAAAREVQG-GRPGYGILCDNRIGRKALHA 417 Query: 426 AADHDYWIARPIELPKSRPLEFECSADVATELLE-WPLNQVVKCLAFYHPDDESDLRERQ 484 A+ WI RP E P SRPLE E LE W VVK L F HPDD DLR Q Sbjct: 418 ASGTGLWIGRPCEWPGSRPLELEPELGPDCGGLENWARENVVKVLVFCHPDDAPDLRRAQ 477 Query: 485 ERQLLRLADACRKTRHELLLELILPRGMSSDSRTVARAIRRLYALGIRPDWWKLEPLTDP 544 E +++RL A R+ R E LLE+I + T A IR+ YA G+ PDWWKLEP+ Sbjct: 478 EAEVVRLYTAARRNRLEFLLEIIPSKVGPVTETTTATLIRQFYAAGVCPDWWKLEPMATR 537 Query: 545 DAWREIEIAIAENDPLCRGVVLLGLSAPEAELVASFEVVAPFPIVKGFAVGRTIFYDVAR 604 AW AI ENDP RG+V+LGL APE +L SF + A FP+VKGFAVGRTIF VAR Sbjct: 538 AAWAAACAAIEENDPHTRGIVVLGLDAPEEDLAESFAIAAGFPLVKGFAVGRTIFGVVAR 597 Query: 605 AWLSNQIDDDAAVTALAAKFKVLVDAWRRLR 635 AW + D AV +A ++ L W R R Sbjct: 598 AWFEGDLGDAEAVAEMARRYARLCTVWDRAR 628 Lambda K H 0.322 0.138 0.419 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: 1139 Number of extensions: 41 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: 642 Length of database: 638 Length adjustment: 38 Effective length of query: 604 Effective length of database: 600 Effective search space: 362400 Effective search space used: 362400 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 WP_110806485.1 C8J30_RS14070 (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.2133368.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-127 409.2 0.0 7.4e-126 405.5 0.0 2.0 2 NCBI__GCF_003217355.1:WP_110806485.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217355.1:WP_110806485.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.5 0.0 7.4e-126 7.4e-126 2 309 .] 4 328 .. 3 328 .. 0.99 2 ! 1.5 0.1 0.0074 0.0074 261 288 .. 520 547 .. 518 553 .. 0.94 Alignments for each domain: == domain 1 score: 405.5 bits; conditional E-value: 7.4e-126 TIGR04382 2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 ld+itiGR+gvDly++q+g +led+ sf+ky+GGsp+Nia+g+arlGl++alit+vgd+++Grf+re+l reg NCBI__GCF_003217355.1:WP_110806485.1 4 LDVITIGRAGVDLYGTQVGGRLEDMGSFQKYIGGSPTNIACGTARLGLRSALITRVGDEHMGRFIREQLGREG 76 8************************************************************************ PP TIGR04382 75 vdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreav 147 vd+++v+td+e++t+lv+l+i+d+++fpl+fYRen+aD+al+ +d++e +iaea+ +l +gt+ls++++++av NCBI__GCF_003217355.1:WP_110806485.1 77 VDVRGVKTDPERLTALVILGIRDEEQFPLIFYRENCADMALCEADIEEGFIAEARSVLATGTHLSHPRTEAAV 149 ************************************************************************* PP TIGR04382 148 lkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEfeiaagekdd 208 lkal la+k+g+k++lDiDYRp+lW+ ++++++a+l l+++d+i+GteeEf+ia g++d+ NCBI__GCF_003217355.1:WP_110806485.1 150 LKALALARKHGAKTALDIDYRPNLWGvaghgagesrfvESAKVTAKLLGTLHLFDLIVGTEEEFHIAGGSTDT 222 ************************************************************************* PP TIGR04382 209 eaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasgllygllegedle 276 aa++a+++++++++v+KrG++G+++++++ ++ + +gf++ev++vlGaGD+F+sgll+g+l+ge + NCBI__GCF_003217355.1:WP_110806485.1 223 IAALRAVRAVSNATLVCKRGAKGAVAFEGTipdslDDGQSGPGFPIEVFNVLGAGDGFFSGLLKGWLDGEAWP 295 *****************************9**9**************************************** PP TIGR04382 277 kalelanAagaivvsrlscaeamptleeleefl 309 +ale+anA+ga++vsr++c++a+p+leel+ fl NCBI__GCF_003217355.1:WP_110806485.1 296 RALEYANACGAFAVSRHGCTPAYPSLEELKFFL 328 *****************************9886 PP == domain 2 score: 1.5 bits; conditional E-value: 0.0074 TIGR04382 261 FasgllygllegedlekalelanAagai 288 +a+g++ + + e++++ +++a A++ai NCBI__GCF_003217355.1:WP_110806485.1 520 YAAGVCPDWWKLEPMATRAAWAAACAAI 547 89*************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (638 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: 39.77 // [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