Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_008629425.1 C943_RS15090 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>NCBI__GCF_000330725.2:WP_008629425.1
Length = 742
Score = 1056 bits (2731), Expect = 0.0
Identities = 522/735 (71%), Positives = 607/735 (82%)
Query: 3 TPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKI 62
T KI+YTLTDEAPALATYSLLPI+KAFT S+GIAVETRDISL+GR+IA FPE+L Q+I
Sbjct: 5 TAKILYTLTDEAPALATYSLLPIVKAFTHSAGIAVETRDISLSGRIIALFPEFLKPQQRI 64
Query: 63 SDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDV 122
SDDLAELG++A PDANI+KLPNISAS+PQLKAAIKELQ QGY LPDYP++PK++ EKD+
Sbjct: 65 SDDLAELGEIAKQPDANIVKLPNISASIPQLKAAIKELQAQGYALPDYPDDPKSEQEKDI 124
Query: 123 KARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFY 182
K RYDK+KGSAVNPVLREGNSDRRAPL+VK YA+ +PH MG WS+DSK+HVA M GDFY
Sbjct: 125 KGRYDKVKGSAVNPVLREGNSDRRAPLAVKQYAKNNPHSMGKWSSDSKTHVASMSRGDFY 184
Query: 183 GSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIED 242
GSEK+ I + V I+L G+ LK ++QA E+ID++V+S L F+ + D
Sbjct: 185 GSEKSVTIASATKVSIDLHTSAGTKISLKENLALQAEEVIDAAVLSVADLIEFLQQQKAD 244
Query: 243 AKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYA 302
AKKQGVL S+H+KATMMKVSDPI+FG V F+ KH V ++IG DVNNG GDL A
Sbjct: 245 AKKQGVLFSLHMKATMMKVSDPIIFGHAVKVFFAQLFEKHQAVFEKIGVDVNNGFGDLIA 304
Query: 303 RIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGK 362
+++TLPE+++K IE+DI+A A+ P LAMVNSDKGITNLHVPSDVI+DASMPAMIR SG+
Sbjct: 305 KMQTLPESERKAIESDIEATLAEGPDLAMVNSDKGITNLHVPSDVIIDASMPAMIRSSGQ 364
Query: 363 MWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGS 422
MW GKL DTKAVIPDRCYAGVY+ I CK+HGAFDP TMGSVPNVGLMAQKAEEYGS
Sbjct: 365 MWNKAGKLQDTKAVIPDRCYAGVYEETINFCKKHGAFDPATMGSVPNVGLMAQKAEEYGS 424
Query: 423 HDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNT 482
HDKTF+IPADG V VTD SG++L+ V+ GDIWRMCQ KDAPIQDWVKLAVNRARAT
Sbjct: 425 HDKTFEIPADGTVTVTDSSGEVLISHDVKKGDIWRMCQTKDAPIQDWVKLAVNRARATGV 484
Query: 483 PAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVT 542
PAVFWLD RAHDA++I KV++YL D+DT GLDIRILSPV+ATR SL RI+EGKDTISVT
Sbjct: 485 PAVFWLDEKRAHDAELIKKVKKYLGDHDTKGLDIRILSPVDATRLSLERIKEGKDTISVT 544
Query: 543 GNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWD 602
GNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHV+QFLEE +LRWD
Sbjct: 545 GNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVEQFLEENHLRWD 604
Query: 603 SLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFY 662
SLGEFLALA SLEHL + + N +A VLA TLDQ TGK L+ +KSP+R E+DNRGSHFY
Sbjct: 605 SLGEFLALAVSLEHLADTFHNDRAKVLAETLDQGTGKFLEQDKSPSRNAKELDNRGSHFY 664
Query: 663 LALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDL 722
LA+YWA+ALA Q +D EL+ +FT IAKAL +NE KIV EL AQG +DI GYY P+
Sbjct: 665 LAMYWAEALAGQDKDLELKTKFTPIAKALQENEQKIVSELNEAQGVKMDIGGYYKPDESK 724
Query: 723 TSKAIRPSATFNAAL 737
TS A+RPS TFNA L
Sbjct: 725 TSAAMRPSPTFNAIL 739
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: 1488
Number of extensions: 55
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: 741
Length of database: 742
Length adjustment: 40
Effective length of query: 701
Effective length of database: 702
Effective search space: 492102
Effective search space used: 492102
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 WP_008629425.1 C943_RS15090 (NADP-dependent isocitrate dehydrogenase)
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.1606341.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 1329.3 2.3 0 1329.1 2.3 1.0 1 NCBI__GCF_000330725.2:WP_008629425.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330725.2:WP_008629425.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1329.1 2.3 0 0 1 741 [. 1 741 [. 1 742 [] 1.00
Alignments for each domain:
== domain 1 score: 1329.1 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGe 73
m+ ++aki+ytltdeap+latysllpivkaf++saGi+vetrdisl+gri+a fpe+l +q+++d+laelGe
NCBI__GCF_000330725.2:WP_008629425.1 1 MTDKTAKILYTLTDEAPALATYSLLPIVKAFTHSAGIAVETRDISLSGRIIALFPEFLKPQQRISDDLAELGE 73
566789******************************************************************* PP
TIGR00178 74 laktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsd 146
+ak p+ani+klpnisas+pqlkaaikelq++Gy+lpdyp++pk+++ekdik ry+k+kGsavnpvlreGnsd
NCBI__GCF_000330725.2:WP_008629425.1 74 IAKQPDANIVKLPNISASIPQLKAAIKELQAQGYALPDYPDDPKSEQEKDIKGRYDKVKGSAVNPVLREGNSD 146
************************************************************************* PP
TIGR00178 147 rraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklkll 219
rraplavk+ya+++ph+mG+ws dsk+hva m+ gdfy+seksv++ +a++v i+l + G+++ lk++l l+
NCBI__GCF_000330725.2:WP_008629425.1 147 RRAPLAVKQYAKNNPHSMGKWSSDSKTHVASMSRGDFYGSEKSVTIASATKVSIDLHTSAGTKISLKENLALQ 219
************************************************************************* PP
TIGR00178 220 dgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlG 292
++evid++vls l efl+++ +dak++gvl+slh+katmmkvsdpi+fGh+v+vf+++ f kh++++e++G
NCBI__GCF_000330725.2:WP_008629425.1 220 AEEVIDAAVLSVADLIEFLQQQKADAKKQGVLFSLHMKATMMKVSDPIIFGHAVKVFFAQLFEKHQAVFEKIG 292
************************************************************************* PP
TIGR00178 293 ldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkm 365
+dv+nG++dl+ak+++lp+++++ ie+d+e++++e+p+lamv+sdkGitnlhvpsdvi+dasmpamir+sG+m
NCBI__GCF_000330725.2:WP_008629425.1 293 VDVNNGFGDLIAKMQTLPESERKAIESDIEATLAEGPDLAMVNSDKGITNLHVPSDVIIDASMPAMIRSSGQM 365
************************************************************************* PP
TIGR00178 366 ygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvr 438
++k gkl+dtkavipd++yagvy++ i++ckk+Gafdp+tmG+vpnvGlmaqkaeeyGshdktfei+adG+v
NCBI__GCF_000330725.2:WP_008629425.1 366 WNKAGKLQDTKAVIPDRCYAGVYEETINFCKKHGAFDPATMGSVPNVGLMAQKAEEYGSHDKTFEIPADGTVT 438
************************************************************************* PP
TIGR00178 439 vvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdh 511
v+dssGevl+ ++v++gdiwrmcq kdapiqdwvklav+rar++g+pavfwld++rahd+elikkv+kyl dh
NCBI__GCF_000330725.2:WP_008629425.1 439 VTDSSGEVLISHDVKKGDIWRMCQTKDAPIQDWVKLAVNRARATGVPAVFWLDEKRAHDAELIKKVKKYLGDH 511
************************************************************************* PP
TIGR00178 512 dteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGa 584
dt+Gldi+ilspv+atr+sleri++G+dtisvtGnvlrdyltdlfpilelGtsakmls+vplm+GGGlfetGa
NCBI__GCF_000330725.2:WP_008629425.1 512 DTKGLDIRILSPVDATRLSLERIKEGKDTISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGA 584
************************************************************************* PP
TIGR00178 585 GGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeld 657
GGsapkhv+q+ eenhlrwdslGeflala sleh+a + n++akvla+tld+ tgk+l+++kspsr eld
NCBI__GCF_000330725.2:WP_008629425.1 585 GGSAPKHVEQFLEENHLRWDSLGEFLALAVSLEHLADTFHNDRAKVLAETLDQGTGKFLEQDKSPSRNAKELD 657
************************************************************************* PP
TIGR00178 658 nrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlr 730
nrgs+fyla+ywa++la q +d el+ +f+++a+al++ne+kiv+el+++qG +d+gGyy+pd+ +t++++r
NCBI__GCF_000330725.2:WP_008629425.1 658 NRGSHFYLAMYWAEALAGQDKDLELKTKFTPIAKALQENEQKIVSELNEAQGVKMDIGGYYKPDESKTSAAMR 730
************************************************************************* PP
TIGR00178 731 psatfnailea 741
ps tfnaile
NCBI__GCF_000330725.2:WP_008629425.1 731 PSPTFNAILER 741
********985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (742 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 42.51
//
[ok]
This GapMind analysis is from Sep 24 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