Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate SMc00480 SMc00480 isocitrate dehydrogenase
Query= BRENDA::B7GQR3 (406 letters) >FitnessBrowser__Smeli:SMc00480 Length = 404 Score = 609 bits (1571), Expect = e-179 Identities = 297/405 (73%), Positives = 343/405 (84%), Gaps = 2/405 (0%) Query: 1 MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60 MAKIKV VVELDGDEMTR+IW+ IKD+LI PYLD++L+YYDLG+E+RD TDDQVTIDA Sbjct: 1 MAKIKVANPVVELDGDEMTRIIWQFIKDKLIHPYLDLDLEYYDLGVENRDATDDQVTIDA 60 Query: 61 AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120 A+AI+KH VGVKCATITPDE RV+EF LKKMWKSPNGTIRNILGG IFREPI+ NVPRL Sbjct: 61 ANAIKKHGVGVKCATITPDEGRVEEFKLKKMWKSPNGTIRNILGGVIFREPIICKNVPRL 120 Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180 VPGWTKPI+V RHAFGDQY+ATDFK PG G+L++ F +DG + I+H VY+ GVA Sbjct: 121 VPGWTKPIIVGRHAFGDQYRATDFKFPGKGKLSIKFVGEDG-QTIEHDVYD-APGAGVAL 178 Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240 YN+++SI FARA FNYGL R PVYLSTKNTILKAYDG+FKDIF +VF+ E+ ++ Sbjct: 179 AMYNLDESITEFARASFNYGLQRKVPVYLSTKNTILKAYDGRFKDIFQKVFDEEFAAQFK 238 Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300 L YEHRLIDDMVAS+LKW GGY+WACKNYDGDVQSD VAQGFGSLGLMTSVLMTPDG Sbjct: 239 AEKLWYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDG 298 Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360 +TVE+EAAHGTVTRHYR+ QKGE+TSTN IASIFAWT GL HRA LDG E+ F++TLE Sbjct: 299 KTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNAELAKFSETLE 358 Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405 +V VDTVE G MTKDLA+LIGPD+PWL T GF++ +DENL KA+A Sbjct: 359 RVCVDTVESGFMTKDLALLIGPDQPWLSTTGFLDKIDENLRKAMA 403 Lambda K H 0.318 0.136 0.416 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: 694 Number of extensions: 26 Number of successful extensions: 4 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: 406 Length of database: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate SMc00480 SMc00480 (isocitrate dehydrogenase)
to HMM TIGR00127 (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/TIGR00127.hmm # target sequence database: /tmp/gapView.8181.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00127 [M=409] Accession: TIGR00127 Description: nadp_idh_euk: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-217 708.1 0.1 1.5e-217 707.9 0.1 1.0 1 lcl|FitnessBrowser__Smeli:SMc00480 SMc00480 isocitrate dehydrogenas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc00480 SMc00480 isocitrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 707.9 0.1 1.5e-217 1.5e-217 2 408 .. 3 403 .. 2 404 .] 0.99 Alignments for each domain: == domain 1 score: 707.9 bits; conditional E-value: 1.5e-217 TIGR00127 2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkcatit 76 kikvanpvveldgdemtriiw+ ikdkli pyl+ldl+yydl+ve+rdat+d+vt daa+aikk++v+vkcatit lcl|FitnessBrowser__Smeli:SMc00480 3 KIKVANPVVELDGDEMTRIIWQFIKDKLIHPYLDLDLEYYDLGVENRDATDDQVTIDAANAIKKHGVGVKCATIT 77 9************************************************************************** PP TIGR00127 77 pdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvpgpgkl 151 pde rv+efklkkmwkspngtirnilgg +frepii+k++prlvp+w+kpii+grhafgdqy+atd+ pg+gkl lcl|FitnessBrowser__Smeli:SMc00480 78 PDEGRVEEFKLKKMWKSPNGTIRNILGGVIFREPIICKNVPRLVPGWTKPIIVGRHAFGDQYRATDFKFPGKGKL 152 *************************************************************************** PP TIGR00127 152 klvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkydgrfkdif 226 + ++ +d +++++ vyd ++ g valamyn desi +fa+as++ l++k+p+ylstkntilk ydgrfkdif lcl|FitnessBrowser__Smeli:SMc00480 153 SIKFVGED-GQTIEHDVYDAPGAG-VALAMYNLDESITEFARASFNYGLQRKVPVYLSTKNTILKAYDGRFKDIF 225 *****987.58999*******998.************************************************** PP TIGR00127 227 qevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmtsvlvtpdgkt 301 q+v+++++ +f+a ++wyehrliddmva alk ggy++a+knydgdvqsdivaqgfgslglmtsvl+tpdgkt lcl|FitnessBrowser__Smeli:SMc00480 226 QKVFDEEFAAQFKAEKLWYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDGKT 300 *************************************************************************** PP TIGR00127 302 veaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatietveegimtkdla 376 veaeaahgtvtrhyr++qkgeetstnsiasifaw+rgl++rakld +ael+kf+e+le ++++tve+g+mtkdla lcl|FitnessBrowser__Smeli:SMc00480 301 VEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNAELAKFSETLERVCVDTVESGFMTKDLA 375 *************************************************************************** PP TIGR00127 377 lilkksklersayltteefldaveerlkkkle 408 l+++ + +l+t fld+++e+l+k ++ lcl|FitnessBrowser__Smeli:SMc00480 376 LLIGPD----QPWLSTTGFLDKIDENLRKAMA 403 ****99....89****************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (409 nodes) Target sequences: 1 (404 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.36 // [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