Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate GFF2791 PGA1_c28340 isocitrate dehydrogenase [NADP]
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__Phaeo:GFF2791
Length = 790
Score = 809 bits (2089), Expect = 0.0
Identities = 422/738 (57%), Positives = 528/738 (71%), Gaps = 7/738 (0%)
Query: 2 STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
STP I+YT+ DEAP LA+ SLLPII++F ++G++V T+DISLAGR++ATFPE L+D Q+
Sbjct: 57 STPDILYTIVDEAPELASASLLPIIRSFAAAAGVSVGTKDISLAGRILATFPEALSDAQR 116
Query: 62 ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
S+DLAELG+L TP+AN+IKLPNISASVPQL AAI ELQ QG+ +PDYP +P TD EK+
Sbjct: 117 QSNDLAELGQLVKTPEANVIKLPNISASVPQLTAAIAELQAQGFGIPDYPADPATDAEKE 176
Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
++ARYD IKGSAVNPVLREGNSDRRA +VKN+A+ +PH MG WSADSK+ V+ M DF
Sbjct: 177 IRARYDTIKGSAVNPVLREGNSDRRAAKAVKNFAQNNPHSMGKWSADSKTKVSSMLGNDF 236
Query: 182 YGSEKAALIGAP--GSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAE 239
Y +E +A I A G+ KIE + KDG+ TVLK ++ G + D++ MS AL +F+
Sbjct: 237 YANEVSATISAAQAGTAKIEFVGKDGAVTVLKDSWPLEEGTVADATFMSAKALSSFLKDA 296
Query: 240 IEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
IED K G + S+H+KATMMKVSDPI+FG V + K ++ G N+G+G
Sbjct: 297 IEDTKADGTMFSLHMKATMMKVSDPIIFGHAVKAWLGPVWDKFGAEIEAAGGSANSGLGA 356
Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
+ A I LP I+A+I A+ RP + MV+SDKGITNLHVPSDVI+DASMPA+IR
Sbjct: 357 VLATIDGLPNGDA--IKAEIAAL--DRPSMYMVDSDKGITNLHVPSDVIIDASMPAVIRA 412
Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
GK W G DT VIPDRCY+ VY I K +GA D TT GSV NVGLMAQKAEE
Sbjct: 413 GGKGWDEAGNKGDTNCVIPDRCYSTVYDESINFFKANGALDVTTAGSVANVGLMAQKAEE 472
Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
YGSH TF+ PADG +R+ +G+ L VEAGDIWR C K API++W++LA++R R
Sbjct: 473 YGSHPTTFEAPADGTIRIVLANGETLHAHEVEAGDIWRSCTVKKAPIENWIELAMDRQRL 532
Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
T + A+FWLD RAHDA++I V L+ S L +I++P EAT SL I GKD+I
Sbjct: 533 TGSEAIFWLDENRAHDAELIKYVTPALEAAGKSDL-FQIMAPREATAQSLKTITAGKDSI 591
Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
++TGNVLRDYLTDLFPI+ELGTSAKMLSIV LM+GGGLFETGAGGSAPKHVQQ +EE +L
Sbjct: 592 AITGNVLRDYLTDLFPILELGTSAKMLSIVKLMNGGGLFETGAGGSAPKHVQQLVEENHL 651
Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
RWDS+GEF AL SL L ++ N KA VL + + AT ILD+N+SP+RKVGE DNR S
Sbjct: 652 RWDSMGEFCALGESLNFLADSKGNAKAGVLGAAAEAATQGILDHNRSPSRKVGEPDNRAS 711
Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
H++ A YWA+ALAAQ +D EL A F IA L E I+ ELA QGK VD+ GY+H +
Sbjct: 712 HYWFARYWAEALAAQGDDAELAAHFAPIAAELAAKEEAILSELAEVQGKAVDLGGYFHAD 771
Query: 720 TDLTSKAIRPSATFNAAL 737
T+ +RPSAT N +
Sbjct: 772 PVKTAAVMRPSATLNGII 789
Lambda K H
0.315 0.131 0.374
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: 1396
Number of extensions: 46
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: 741
Length of database: 790
Length adjustment: 40
Effective length of query: 701
Effective length of database: 750
Effective search space: 525750
Effective search space used: 525750
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 (21.5 bits)
S2: 55 (25.8 bits)
Align candidate GFF2791 PGA1_c28340 (isocitrate dehydrogenase [NADP])
to HMM TIGR00178 (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/TIGR00178.hmm
# target sequence database: /tmp/gapView.31630.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00178 [M=744]
Accession: TIGR00178
Description: monomer_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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1071.8 1.5 0 1071.6 1.5 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2791 PGA1_c28340 isocitrate dehydroge
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2791 PGA1_c28340 isocitrate dehydrogenase [NADP]
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1071.6 1.5 0 0 5 739 .. 58 789 .. 53 790 .] 0.99
Alignments for each domain:
== domain 1 score: 1071.6 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpea 80
++ i+yt+ deap la+ sllpi+++faa+aG++v t+dislagrila+fpe l++ q+ +++laelG+l ktpea
lcl|FitnessBrowser__Phaeo:GFF2791 58 TPDILYTIVDEAPELASASLLPIIRSFAAAAGVSVGTKDISLAGRILATFPEALSDAQRQSNDLAELGQLVKTPEA 133
578************************************************************************* PP
TIGR00178 81 niiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavkey 156
n+iklpnisasvpql+aai elq++G+ +pdyp++p td+ek+i+ary+ ikGsavnpvlreGnsdrra +avk++
lcl|FitnessBrowser__Phaeo:GFF2791 134 NVIKLPNISASVPQLTAAIAELQAQGFGIPDYPADPATDAEKEIRARYDTIKGSAVNPVLREGNSDRRAAKAVKNF 209
**************************************************************************** PP
TIGR00178 157 arkhphkmGewsadskshvahmdagdfyaseksvlldaae..evkieliakdGketvlkaklklldgevidssvls 230
a+++ph+mG+wsadsk++v+ m +dfya+e s+++ aa+ kie++ kdG +tvlk++ +l++g v d++++s
lcl|FitnessBrowser__Phaeo:GFF2791 210 AQNNPHSMGKWSADSKTKVSSMLGNDFYANEVSATISAAQagTAKIEFVGKDGAVTVLKDSWPLEEGTVADATFMS 285
************************************98762269******************************** PP
TIGR00178 231 kkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyaki 306
+kal+ fl++ ied+k++g ++slh+katmmkvsdpi+fGh+v+++ v+ k+++ +e++G ++ Gl++++a i
lcl|FitnessBrowser__Phaeo:GFF2791 286 AKALSSFLKDAIEDTKADGTMFSLHMKATMMKVSDPIIFGHAVKAWLGPVWDKFGAEIEAAGGSANSGLGAVLATI 361
**************************************************************************** PP
TIGR00178 307 eslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipds 382
+ lp++ + i+a++ + +rp + mvdsdkGitnlhvpsdvi+dasmpa+ira+Gk +++ g++ dt+ vipd+
lcl|FitnessBrowser__Phaeo:GFF2791 362 DGLPNG--DAIKAEIAAL--DRPSMYMVDSDKGITNLHVPSDVIIDASMPAVIRAGGKGWDEAGNKGDTNCVIPDR 433
******..99***99875..8******************************************************* PP
TIGR00178 383 syagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiw 458
+y+ vy++ i++ k nGa+d tt G+v nvGlmaqkaeeyGsh tfe +adG++r+v ++Ge l +eveagdiw
lcl|FitnessBrowser__Phaeo:GFF2791 434 CYSTVYDESINFFKANGALDVTTAGSVANVGLMAQKAEEYGSHPTTFEAPADGTIRIVLANGETLHAHEVEAGDIW 509
**************************************************************************** PP
TIGR00178 459 rmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfsleri 534
r c vk api++w+ la+ r rl+g a+fwld++rahd+elik v l+ + l qi+ p +at sl+ i
lcl|FitnessBrowser__Phaeo:GFF2791 510 RSCTVKKAPIENWIELAMDRQRLTGSEAIFWLDENRAHDAELIKYVTPALEAAGKSDL-FQIMAPREATAQSLKTI 584
**************************************************99998888.7**************** PP
TIGR00178 535 rrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGefl 610
+ G+d+i++tGnvlrdyltdlfpilelGtsakmls+v lm+GGGlfetGaGGsapkhvqql+eenhlrwds+Gef
lcl|FitnessBrowser__Phaeo:GFF2791 585 TAGKDSIAITGNVLRDYLTDLFPILELGTSAKMLSIVKLMNGGGLFETGAGGSAPKHVQQLVEENHLRWDSMGEFC 660
**************************************************************************** PP
TIGR00178 611 alaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasf 686
al++sl+ +a ++gn+ka vl+ + +aat+ +ld+++spsrkvGe dnr s++++a+ywa++laaq +d+elaa+f
lcl|FitnessBrowser__Phaeo:GFF2791 661 ALGESLNFLADSKGNAKAGVLGAAAEAATQGILDHNRSPSRKVGEPDNRASHYWFARYWAEALAAQGDDAELAAHF 736
**************************************************************************** PP
TIGR00178 687 asvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnail 739
a++a l+ +ee i +ela+vqG+avdlgGy+++d +t +v+rpsat+n i+
lcl|FitnessBrowser__Phaeo:GFF2791 737 APIAAELAAKEEAILSELAEVQGKAVDLGGYFHADPVKTAAVMRPSATLNGII 789
**************************************************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (790 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 11.00
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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