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.17643.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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 13.17
//
[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