Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate AZOBR_RS10995 AZOBR_RS10995 isocitrate dehydrogenase
Query= BRENDA::B7GQR3 (406 letters) >FitnessBrowser__azobra:AZOBR_RS10995 Length = 407 Score = 602 bits (1551), Expect = e-177 Identities = 288/405 (71%), Positives = 341/405 (84%), Gaps = 1/405 (0%) Query: 1 MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60 M KIKV VVELDGDEMTR+IW+ IKD+LILPYLDV+L YYDL +E+RD+TDD+VT+++ Sbjct: 1 MTKIKVANPVVELDGDEMTRIIWQFIKDKLILPYLDVDLKYYDLSVENRDKTDDRVTVES 60 Query: 61 AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120 A+AI+++ VGVKCATITPDEARV EF LKKMWKSPNGTIRNILGGT+FREPIV SNVPR Sbjct: 61 ANAIKQYGVGVKCATITPDEARVTEFNLKKMWKSPNGTIRNILGGTVFREPIVCSNVPRY 120 Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180 VPGWTKPI++ RHAFGDQYKATDF VPG G+LT+ + P+ G EPI+ VY++ G VA Sbjct: 121 VPGWTKPIIIGRHAFGDQYKATDFVVPGKGKLTIKWVPEGGGEPIEQEVYDFPASG-VAM 179 Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240 YN+++SI GFA + F YGL R YPVYLSTKNTILKAYDG+FKDIF +VF+ Y ++ Sbjct: 180 GMYNLDESIEGFAHSSFMYGLERGYPVYLSTKNTILKAYDGRFKDIFQKVFDEHYAAQFK 239 Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300 GL YEHRLIDDMVAS+LKW GG++WACKNYDGDVQSD VAQGFGSLGLMTSVL+TPDG Sbjct: 240 AKGLVYEHRLIDDMVASALKWEGGFVWACKNYDGDVQSDIVAQGFGSLGLMTSVLITPDG 299 Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360 +TVE+EAAHGTVTRHYR QKG++TSTNPIASI+AWT GL +R D TP+V FA+TLE Sbjct: 300 KTVEAEAAHGTVTRHYREHQKGKETSTNPIASIYAWTQGLAYRGKFDNTPDVVKFAETLE 359 Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405 +V V+TVE G MTKDLA+LIGPD+PWL T F++ LDENL K +A Sbjct: 360 RVCVETVESGFMTKDLAILIGPDQPWLTTKQFLDKLDENLQKKMA 404 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: 689 Number of extensions: 23 Number of successful extensions: 2 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: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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 AZOBR_RS10995 AZOBR_RS10995 (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.1031.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-224 729.7 0.1 4.1e-224 729.5 0.1 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS10995 AZOBR_RS10995 isocitrate dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS10995 AZOBR_RS10995 isocitrate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 729.5 0.1 4.1e-224 4.1e-224 1 408 [. 2 404 .. 2 405 .. 0.99 Alignments for each domain: == domain 1 score: 729.5 bits; conditional E-value: 4.1e-224 TIGR00127 1 kkikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynva 69 +kikvanpvveldgdemtriiw+ ikdklilpyl++dlkyydlsve+rd+t+d+vt+++a+aik+y+v+ lcl|FitnessBrowser__azobra:AZOBR_RS10995 2 TKIKVANPVVELDGDEMTRIIWQFIKDKLILPYLDVDLKYYDLSVENRDKTDDRVTVESANAIKQYGVG 70 69******************************************************************* PP TIGR00127 70 vkcatitpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqy 138 vkcatitpdearv ef+lkkmwkspngtirnilggtvfrepi++ ++pr vp+w+kpiiigrhafgdqy lcl|FitnessBrowser__azobra:AZOBR_RS10995 71 VKCATITPDEARVTEFNLKKMWKSPNGTIRNILGGTVFREPIVCSNVPRYVPGWTKPIIIGRHAFGDQY 139 ********************************************************************* PP TIGR00127 139 katdvvvpgpgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklply 207 katd+vvpg+gkl + ++p++g+e+++ +vyd++ +g va++myn desie+fa++s+ le+++p+y lcl|FitnessBrowser__azobra:AZOBR_RS10995 140 KATDFVVPGKGKLTIKWVPEGGGEPIEQEVYDFPASG-VAMGMYNLDESIEGFAHSSFMYGLERGYPVY 207 **********************************998.******************************* PP TIGR00127 208 lstkntilkkydgrfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvq 276 lstkntilk ydgrfkdifq+v++++y +f+a+g+ yehrliddmva alk +gg+++a+knydgdvq lcl|FitnessBrowser__azobra:AZOBR_RS10995 208 LSTKNTILKAYDGRFKDIFQKVFDEHYAAQFKAKGLVYEHRLIDDMVASALKWEGGFVWACKNYDGDVQ 276 ********************************************************************* PP TIGR00127 277 sdivaqgfgslglmtsvlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakl 345 sdivaqgfgslglmtsvl+tpdgktveaeaahgtvtrhyr++qkg+etstn+iasi+aw++gl+ r+k+ lcl|FitnessBrowser__azobra:AZOBR_RS10995 277 SDIVAQGFGSLGLMTSVLITPDGKTVEAEAAHGTVTRHYREHQKGKETSTNPIASIYAWTQGLAYRGKF 345 ********************************************************************* PP TIGR00127 346 dntaelvkfaeilesatietveegimtkdlalilkksklersayltteefldaveerlkkkle 408 dnt+++vkfae+le +++etve+g+mtkdla++++ + +ltt++fld+++e+l+kk++ lcl|FitnessBrowser__azobra:AZOBR_RS10995 346 DNTPDVVKFAETLERVCVETVESGFMTKDLAILIGPD----QPWLTTKQFLDKLDENLQKKMA 404 **********************************999....89*****************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (409 nodes) Target sequences: 1 (407 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: 7.50 // [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