Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_015449052.1 R2APBS1_RS18160 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>NCBI__GCF_000230695.2:WP_015449052.1
Length = 741
Score = 1122 bits (2901), Expect = 0.0
Identities = 564/739 (76%), Positives = 630/739 (85%), Gaps = 2/739 (0%)
Query: 3 TPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKI 62
TP+IIYTLTDEAP LAT SLLPI+ AF G++GI VETRDISLA R+IA FPE L + Q++
Sbjct: 4 TPRIIYTLTDEAPFLATQSLLPIVAAFAGTAGIKVETRDISLAARIIALFPEALKEGQRL 63
Query: 63 SDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDV 122
DDLAELGKLATTP+ANIIKLPNISAS+PQLKAAIKELQ QGY LPDYP+ PK D+EKD+
Sbjct: 64 PDDLAELGKLATTPEANIIKLPNISASMPQLKAAIKELQGQGYALPDYPDAPKDDSEKDI 123
Query: 123 KARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFY 182
+ARYD++KGSAVNPVLREGNSDRRAP SVKNYARKHPHKMGAWS DSK+HVAHM GDFY
Sbjct: 124 RARYDRVKGSAVNPVLREGNSDRRAPASVKNYARKHPHKMGAWSRDSKTHVAHMGGGDFY 183
Query: 183 GSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIED 242
G+EK+ALIG G+V IE KDGS VLK KT++ AGEIID +VMS+ AL FI A+I D
Sbjct: 184 GTEKSALIGQAGNVSIEWFGKDGSHAVLKPKTALLAGEIIDGAVMSRRALAGFIDAQIAD 243
Query: 243 AKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYA 302
AK+QGVL S+HLKATMMKVSDPIMFG V EFY+D L KHA LKQ+GF+ NNGIGDLYA
Sbjct: 244 AKQQGVLFSLHLKATMMKVSDPIMFGVAVGEFYRDVLAKHAAALKQVGFNPNNGIGDLYA 303
Query: 303 RIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGK 362
R+ +LPEA+Q I+AD+ A YAQRP +AMVNSDKGITNLHVPSDVIVDASMPAMIRDSGK
Sbjct: 304 RLGSLPEAQQAAIKADLDAEYAQRPGVAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGK 363
Query: 363 MWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGS 422
MW G+L D KAVIPDR YAGVYQ I+DCK HGAFDP TMGSVPNVGLMAQ AEEYGS
Sbjct: 364 MWNAQGQLQDVKAVIPDRSYAGVYQATIDDCKAHGAFDPATMGSVPNVGLMAQAAEEYGS 423
Query: 423 HDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNT 482
HDKTFQI DGVV+V DE+G +LL+ VEAGDIWRMCQ KDAPI+DWVKLAV+RAR +T
Sbjct: 424 HDKTFQIAGDGVVKVLDEAGTVLLQHDVEAGDIWRMCQTKDAPIRDWVKLAVSRAR--HT 481
Query: 483 PAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVT 542
PAVFWLDPARAHDAQVIAKVERYLKD+DTSGLDIRI+ PV AT+FSL RIR+G DTISVT
Sbjct: 482 PAVFWLDPARAHDAQVIAKVERYLKDHDTSGLDIRIMDPVAATKFSLERIRQGLDTISVT 541
Query: 543 GNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWD 602
GNVLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQFL+E YLRWD
Sbjct: 542 GNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFLQENYLRWD 601
Query: 603 SLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFY 662
SLGEFLALAASLE + + + VLA TLDQA GK LD +KSP+RK+G IDNRGSHFY
Sbjct: 602 SLGEFLALAASLEFVAGRQGSAEVDVLAKTLDQANGKFLDTDKSPSRKLGGIDNRGSHFY 661
Query: 663 LALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDL 722
LALYWAQALAAQ + L+A+F +AKALT++E IV EL QGKP DI GYYHP+
Sbjct: 662 LALYWAQALAAQDVNAALKAKFAPLAKALTEHEATIVDELVRVQGKPADIGGYYHPDLAR 721
Query: 723 TSKAIRPSATFNAALAPLA 741
S A+RPSATFNAALA L+
Sbjct: 722 VSAAMRPSATFNAALALLS 740
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: 1610
Number of extensions: 58
Number of successful extensions: 3
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: 741
Length adjustment: 40
Effective length of query: 701
Effective length of database: 701
Effective search space: 491401
Effective search space used: 491401
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_015449052.1 R2APBS1_RS18160 (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.2995467.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 1322.4 0.3 0 1322.2 0.3 1.0 1 NCBI__GCF_000230695.2:WP_015449052.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015449052.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1322.2 0.3 0 0 4 742 .. 3 739 .. 1 741 [] 0.99
Alignments for each domain:
== domain 1 score: 1322.2 bits; conditional E-value: 0
TIGR00178 4 ekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelak 76
++++iiytltdeap lat sllpiv afa++aGi+vetrdisla+ri+a fpe l e q+++d+laelG+la+
NCBI__GCF_000230695.2:WP_015449052.1 3 QTPRIIYTLTDEAPFLATQSLLPIVAAFAGTAGIKVETRDISLAARIIALFPEALKEGQRLPDDLAELGKLAT 75
4589********************************************************************* PP
TIGR00178 77 tpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrra 149
tpeaniiklpnisas+pqlkaaikelq +Gy+lpdyp+ pk d+ekdi+ary+++kGsavnpvlreGnsdrra
NCBI__GCF_000230695.2:WP_015449052.1 76 TPEANIIKLPNISASMPQLKAAIKELQGQGYALPDYPDAPKDDSEKDIRARYDRVKGSAVNPVLREGNSDRRA 148
************************************************************************* PP
TIGR00178 150 plavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldge 222
p++vk+yarkhphkmG+ws+dsk+hvahm gdfy++eks+l+++a +v ie+ kdG++ vlk+k+ ll+ge
NCBI__GCF_000230695.2:WP_015449052.1 149 PASVKNYARKHPHKMGAWSRDSKTHVAHMGGGDFYGTEKSALIGQAGNVSIEWFGKDGSHAVLKPKTALLAGE 221
************************************************************************* PP
TIGR00178 223 vidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldv 295
+id++v+s++al+ f++++i+dak++gvl+slhlkatmmkvsdpi+fG +v +fy+dv+akha+ l+q+G++
NCBI__GCF_000230695.2:WP_015449052.1 222 IIDGAVMSRRALAGFIDAQIADAKQQGVLFSLHLKATMMKVSDPIMFGVAVGEFYRDVLAKHAAALKQVGFNP 294
************************************************************************* PP
TIGR00178 296 enGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygk 368
+nG++dlya++ slp+a++ i+adl++ y++rp +amv+sdkGitnlhvpsdvivdasmpamir+sGkm+++
NCBI__GCF_000230695.2:WP_015449052.1 295 NNGIGDLYARLGSLPEAQQAAIKADLDAEYAQRPGVAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWNA 367
************************************************************************* PP
TIGR00178 369 dgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvd 441
+g+l+d kavipd+syagvyqa i+dck +Gafdp+tmG+vpnvGlmaq aeeyGshdktf+i dGvv+v d
NCBI__GCF_000230695.2:WP_015449052.1 368 QGQLQDVKAVIPDRSYAGVYQATIDDCKAHGAFDPATMGSVPNVGLMAQAAEEYGSHDKTFQIAGDGVVKVLD 440
************************************************************************* PP
TIGR00178 442 ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdte 514
+ G vll+++veagdiwrmcq kdapi+dwvklav+rar tpavfwldp+rahd+++i+kve+ylkdhdt+
NCBI__GCF_000230695.2:WP_015449052.1 441 EAGTVLLQHDVEAGDIWRMCQTKDAPIRDWVKLAVSRARH--TPAVFWLDPARAHDAQVIAKVERYLKDHDTS 511
*************************************996..7****************************** PP
TIGR00178 515 GldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGs 587
Gldi+i++pv at+fslerir+G dtisvtGnvlrdyltdlfpi+elGtsakmls+vplmaGGGlfetGaGGs
NCBI__GCF_000230695.2:WP_015449052.1 512 GLDIRIMDPVAATKFSLERIRQGLDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGGS 584
************************************************************************* PP
TIGR00178 588 apkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrg 660
apkhvqq+ +en+lrwdslGeflalaasle va ++g + vla+tld+a gk+ld++kspsrk G +dnrg
NCBI__GCF_000230695.2:WP_015449052.1 585 APKHVQQFLQENYLRWDSLGEFLALAASLEFVAGRQGSAEVDVLAKTLDQANGKFLDTDKSPSRKLGGIDNRG 657
************************************************************************* PP
TIGR00178 661 skfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsa 733
s+fyla ywaq+laaq ++ l+a+fa++a+alt++e++iv el vqG++ d+gGyy+pd +++++rpsa
NCBI__GCF_000230695.2:WP_015449052.1 658 SHFYLALYWAQALAAQDVNAALKAKFAPLAKALTEHEATIVDELVRVQGKPADIGGYYHPDLARVSAAMRPSA 730
************************************************************************* PP
TIGR00178 734 tfnaileal 742
tfna+l+ l
NCBI__GCF_000230695.2:WP_015449052.1 731 TFNAALALL 739
*****9866 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (741 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 37.59
//
[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