Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate PP_4011 PP_4011 isocitrate dehydrogenase, NADP(+)-specific
Query= SwissProt::Q02NB5 (418 letters) >FitnessBrowser__Putida:PP_4011 Length = 418 Score = 761 bits (1964), Expect = 0.0 Identities = 375/418 (89%), Positives = 396/418 (94%) Query: 1 MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60 MGYQKI+VP G KITVNAD SL+VP +PIIP+IEGDGIGVD+SPVMIKVVDAAV+KAY Sbjct: 1 MGYQKIKVPTDGTKITVNADHSLNVPDHPIIPYIEGDGIGVDVSPVMIKVVDAAVQKAYG 60 Query: 61 GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120 G+RKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL Sbjct: 61 GKRKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120 Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180 RQQLDLYVC RPV WF+GVPSPVKKPGDVDMVIFRENSEDIYAG+EWKAGSPEA KVIKF Sbjct: 121 RQQLDLYVCLRPVLWFQGVPSPVKKPGDVDMVIFRENSEDIYAGIEWKAGSPEANKVIKF 180 Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240 L EEMGV KIRF ++CGIG+KPVS+EGTKRLVRKALQY VDNDR S+TLVHKGNIMKFTE Sbjct: 181 LKEEMGVTKIRFDQDCGIGVKPVSKEGTKRLVRKALQYVVDNDRESLTLVHKGNIMKFTE 240 Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300 GAFKDWGYEVARDEFGAELLDGGPWM+FKNPKTG+ V+VKD IADAMLQQILLRPAEYDV Sbjct: 241 GAFKDWGYEVARDEFGAELLDGGPWMKFKNPKTGREVIVKDAIADAMLQQILLRPAEYDV 300 Query: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLIL 360 IATLNLNGDYLSDALAAEVGGIGIAPGANLSD+VAMFEATHGTAPKYAGQDKVNPGS+IL Sbjct: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGQDKVNPGSVIL 360 Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLM+GA L+S S FGD MI M Sbjct: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMEGAKLVSSSGFGDEMIKHM 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: 766 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 PP_4011 PP_4011 (isocitrate dehydrogenase, NADP(+)-specific)
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.20369.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-226 737.6 0.9 2.2e-226 737.4 0.9 1.0 1 lcl|FitnessBrowser__Putida:PP_4011 PP_4011 isocitrate dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4011 PP_4011 isocitrate dehydrogenase, NADP(+)-specific # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 737.4 0.9 2.2e-226 2.2e-226 2 416 .. 3 418 .] 2 418 .] 0.99 Alignments for each domain: == domain 1 score: 737.4 bits; conditional E-value: 2.2e-226 TIGR00183 2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekay 75 ++k+k+p++G kit++++ l+vp++piipyieGdGiGvd+ p +ikv+daav+kay+g++kiaw+evyaGeka+ lcl|FitnessBrowser__Putida:PP_4011 3 YQKIKVPTDGTKITVNADhSLNVPDHPIIPYIEGDGIGVDVSPVMIKVVDAAVQKAYGGKRKIAWMEVYAGEKAT 77 78*************865279****************************************************** PP TIGR00183 76 elygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlv 150 ++y+++++lp++tlda+++y v+ikGplttpvGgGirslnvalrq+ldlyvclrpv +++gvpspvk+p +vd+v lcl|FitnessBrowser__Putida:PP_4011 78 QVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVLWFQGVPSPVKKPGDVDMV 152 *************************************************************************** PP TIGR00183 151 ifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksv 225 ifren+ediyaGiew++gs ea+k+ikflk+e++v+kir+ +d+GiG+kp+s+egtkrlvrka++y ++nd++s+ lcl|FitnessBrowser__Putida:PP_4011 153 IFRENSEDIYAGIEWKAGSPEANKVIKFLKEEMGVTKIRFDQDCGIGVKPVSKEGTKRLVRKALQYVVDNDRESL 227 *************************************************************************** PP TIGR00183 226 tlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydvia 300 tlvhkGnimkfteGafkdwGye+a++efg+e+++ ++w k knp++G++++vkd iada+lqqil+rp+eydvia lcl|FitnessBrowser__Putida:PP_4011 228 TLVHKGNIMKFTEGAFKDWGYEVARDEFGAELLDGGPWMKFKNPKTGREVIVKDAIADAMLQQILLRPAEYDVIA 302 *************************************************************************** PP TIGR00183 301 tmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadl 375 t+nlnGdylsdalaa vGG+GiapGan++d+va+feathGtapkyaG+dkvnpgsvils++++l+++Gw+eaadl lcl|FitnessBrowser__Putida:PP_4011 303 TLNLNGDYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGQDKVNPGSVILSAEMMLRHMGWTEAADL 377 *************************************************************************** PP TIGR00183 376 ivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416 i+k+ + aia+k+vtyd++rlm+gak v +s f++++++++ lcl|FitnessBrowser__Putida:PP_4011 378 IIKGTNGAIAAKTVTYDFERLMEGAKLVSSSGFGDEMIKHM 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.44 // [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