Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_010627814.1 BZY95_RS15605 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::Q02NB5 (418 letters) >NCBI__GCF_002151265.1:WP_010627814.1 Length = 418 Score = 726 bits (1874), Expect = 0.0 Identities = 354/418 (84%), Positives = 382/418 (91%) Query: 1 MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60 MGYQKI VP G+KITVNAD +L+VP NPIIPFIEGDGIGVD++P M +DAAV+KAY Sbjct: 1 MGYQKIVVPEGGEKITVNADNTLNVPNNPIIPFIEGDGIGVDVTPAMKIAIDAAVQKAYN 60 Query: 61 GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120 GERKI WMEVYAGEKATQVYD DTWLP+ETL+AV++YVVSIKGPLTTPVGGGIRSLNVAL Sbjct: 61 GERKIHWMEVYAGEKATQVYDADTWLPEETLEAVQEYVVSIKGPLTTPVGGGIRSLNVAL 120 Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180 RQ+LDLYVC RPVRWFEGVPSPVKKP DVDMVIFRENSEDIYAG+EWKAG+PEA+KVIKF Sbjct: 121 RQKLDLYVCLRPVRWFEGVPSPVKKPADVDMVIFRENSEDIYAGIEWKAGTPEADKVIKF 180 Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240 L EEMGV IRF ENCGIG+KPVS+EGTKRLVR+ALQY VDNDR S+TLVHKGNIMKFTE Sbjct: 181 LREEMGVTNIRFPENCGIGVKPVSEEGTKRLVRQALQYTVDNDRESLTLVHKGNIMKFTE 240 Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300 G+FKDWGYEVA+ EFGAELLDGGPWMQFKNPKTGKN+VVKDVIADAMLQQILLRPAEYDV Sbjct: 241 GSFKDWGYEVAKQEFGAELLDGGPWMQFKNPKTGKNIVVKDVIADAMLQQILLRPAEYDV 300 Query: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLIL 360 IATLNLNGDYLSDALAAEVGGIGIAPGANL+D+VAMFEATHGTAPKYAGQDKVNPGS+IL Sbjct: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLADAVAMFEATHGTAPKYAGQDKVNPGSVIL 360 Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418 SAEMMLRHMGW EAADL++KG AIA VTYDF RLMD A LL CSEFG A+ M Sbjct: 361 SAEMMLRHMGWVEAADLVLKGMEKAIAKGEVTYDFHRLMDNAKLLKCSEFGQAVADNM 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: 742 Number of extensions: 21 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 WP_010627814.1 BZY95_RS15605 (NADP-dependent 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.9810.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-228 744.2 1.0 2.1e-228 744.0 1.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_010627814.1 BZY95_RS15605 NADP-dependent iso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_010627814.1 BZY95_RS15605 NADP-dependent isocitrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 744.0 1.0 2.1e-228 2.1e-228 2 416 .. 3 418 .] 2 418 .] 0.99 Alignments for each domain: == domain 1 score: 744.0 bits; conditional E-value: 2.1e-228 TIGR00183 2 eekvkppeeGekitlk.ngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevy 69 ++k+++pe Gekit++ ++ l+vpnnpiip+ieGdGiGvd++pa++ +daav+kay+ge+ki w+evy lcl|NCBI__GCF_002151265.1:WP_010627814.1 3 YQKIVVPEGGEKITVNaDNTLNVPNNPIIPFIEGDGIGVDVTPAMKIAIDAAVQKAYNGERKIHWMEVY 71 789***********9736789************************************************ PP TIGR00183 70 aGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvp 138 aGeka+++y+ +++lpe+tl+a++ey v+ikGplttpvGgGirslnvalrq+ldlyvclrpvr+++gvp lcl|NCBI__GCF_002151265.1:WP_010627814.1 72 AGEKATQVYDADTWLPEETLEAVQEYVVSIKGPLTTPVGGGIRSLNVALRQKLDLYVCLRPVRWFEGVP 140 ********************************************************************* PP TIGR00183 139 spvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtk 207 spvk+p +vd+vifren+ediyaGiew++g+ ea k+ikfl++e++v++ir+pe++GiG+kp+seegtk lcl|NCBI__GCF_002151265.1:WP_010627814.1 141 SPVKKPADVDMVIFRENSEDIYAGIEWKAGTPEADKVIKFLREEMGVTNIRFPENCGIGVKPVSEEGTK 209 ********************************************************************* PP TIGR00183 208 rlvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkiv 276 rlvr+a++y+++nd++s+tlvhkGnimkfteG+fkdwGye+ak+efg+e+++ ++w + knp++Gk+iv lcl|NCBI__GCF_002151265.1:WP_010627814.1 210 RLVRQALQYTVDNDRESLTLVHKGNIMKFTEGSFKDWGYEVAKQEFGAELLDGGPWMQFKNPKTGKNIV 278 ********************************************************************* PP TIGR00183 277 vkdriadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapky 345 vkd+iada+lqqil+rp+eydviat+nlnGdylsdalaa vGG+GiapGan++d va+feathGtapky lcl|NCBI__GCF_002151265.1:WP_010627814.1 279 VKDVIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANLADAVAMFEATHGTAPKY 347 ********************************************************************* PP TIGR00183 346 aGldkvnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaive 414 aG+dkvnpgsvils++++l+++Gw eaadl+ k++ekaia+ evtyd++rlmd ak +kcsef++a+ + lcl|NCBI__GCF_002151265.1:WP_010627814.1 348 AGQDKVNPGSVILSAEMMLRHMGWVEAADLVLKGMEKAIAKGEVTYDFHRLMDNAKLLKCSEFGQAVAD 416 *******************************************************************99 PP TIGR00183 415 nl 416 n+ lcl|NCBI__GCF_002151265.1:WP_010627814.1 417 NM 418 98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.08 # Mc/sec: 1.95 // [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