Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate HSERO_RS07015 HSERO_RS07015 isocitrate dehydrogenase
Query= SwissProt::Q02NB5 (418 letters) >FitnessBrowser__HerbieS:HSERO_RS07015 Length = 418 Score = 636 bits (1640), Expect = 0.0 Identities = 301/418 (72%), Positives = 361/418 (86%) Query: 1 MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60 M YQ IQVPA G KIT NAD +L+VP NPIIP+I GDG+GVD++PVM+KVV+AAVEKAY Sbjct: 1 MSYQHIQVPAEGRKITANADDTLNVPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYG 60 Query: 61 GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120 G RKI WME+YAGEKAT++Y D WLP+ETL ++ Y+V+IKGPL+TPVGGGIRSLNVA+ Sbjct: 61 GARKIHWMEIYAGEKATRLYGPDVWLPEETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAM 120 Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180 RQQLDLYVC RPVR+F+GVPSP+++P DMVIFRENSEDIYAG+EW AG+PE K+I Sbjct: 121 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDL 180 Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240 LT EMGVKK+RF E+ +GIKPVS+EGT+RLVR+A+QYA+D+D+ SVTLVHKGNIMKFTE Sbjct: 181 LTREMGVKKLRFPESSALGIKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTE 240 Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300 GAF+DWGY +A EFGAEL+D GPWM+ KNPKTG+ +++KD I DA QQ+L+RPAEY V Sbjct: 241 GAFRDWGYALAAREFGAELIDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSV 300 Query: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLIL 360 IATLNLNGDY+SDA+AA+VGGIGIAPGAN+SDSVA+FEATHGTAPKYAG+D VNPGS IL Sbjct: 301 IATLNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSIL 360 Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418 SAEMMLRHMGW EAADLII ++++K VTYDF RL++GAT +SCS FG+ MI M Sbjct: 361 SAEMMLRHMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 Lambda K H 0.317 0.135 0.397 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: 636 Number of extensions: 15 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: 418 Length of database: 418 Length adjustment: 32 Effective length of query: 386 Effective length of database: 386 Effective search space: 148996 Effective search space used: 148996 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate HSERO_RS07015 HSERO_RS07015 (isocitrate dehydrogenase)
to HMM TIGR00183 (icd: isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))
# 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/TIGR00183.hmm # target sequence database: /tmp/gapView.18736.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00183 [M=417] Accession: TIGR00183 Description: prok_nadp_idh: isocitrate dehydrogenase, NADP-dependent 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-219 713.4 0.1 4.7e-219 713.2 0.1 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS07015 HSERO_RS07015 isocitrate dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS07015 HSERO_RS07015 isocitrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 713.2 0.1 4.7e-219 4.7e-219 2 416 .. 3 418 .] 2 418 .] 0.99 Alignments for each domain: == domain 1 score: 713.2 bits; conditional E-value: 4.7e-219 TIGR00183 2 eekvkppeeGekitlk.ngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfev 68 ++++++p+eG+kit + ++ l+vpnnpiipyi GdG+Gvd++p + kv++aavekay+g +ki w+e+ lcl|FitnessBrowser__HerbieS:HSERO_RS07015 3 YQHIQVPAEGRKITANaDDTLNVPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIHWMEI 70 6789**********9725789*********************************************** PP TIGR00183 69 yaGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykg 136 yaGeka++lyg + +lpe+tl ++k+y vaikGpl+tpvGgGirslnva+rq+ldlyvclrpvry+kg lcl|FitnessBrowser__HerbieS:HSERO_RS07015 71 YAGEKATRLYGPDVWLPEETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAMRQQLDLYVCLRPVRYFKG 138 ******************************************************************** PP TIGR00183 137 vpspvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpisee 204 vpsp++epek+d+vifren+ediyaGiewa+g+ e++kli l e++vkk+r+pe+s +Gikp+s+e lcl|FitnessBrowser__HerbieS:HSERO_RS07015 139 VPSPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALGIKPVSRE 206 ******************************************************************** PP TIGR00183 205 gtkrlvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeG 272 gt+rlvr+ai+yai++dk svtlvhkGnimkfteGaf+dwGy+la +efg+e+i++++w +lknp++G lcl|FitnessBrowser__HerbieS:HSERO_RS07015 207 GTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAELIDDGPWMRLKNPKTG 274 ******************************************************************** PP TIGR00183 273 kkivvkdriadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathG 340 + i++kd i+da++qq+l+rp+ey+viat+nlnGdy+sda+aa+vGG+GiapGan++d+va+feathG lcl|FitnessBrowser__HerbieS:HSERO_RS07015 275 RAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHG 342 ******************************************************************** PP TIGR00183 341 tapkyaGldkvnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsef 408 tapkyaG+d vnpgs ils++++l+++Gw eaadli++a++k+++sk+vtyd+arl++ga++v cs f lcl|FitnessBrowser__HerbieS:HSERO_RS07015 343 TAPKYAGKDYVNPGSSILSAEMMLRHMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSCSGF 410 ******************************************************************** PP TIGR00183 409 aeaivenl 416 +e+++en+ lcl|FitnessBrowser__HerbieS:HSERO_RS07015 411 GEVMIENM 418 *******8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (418 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.40 // [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