Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_043743299.1 AMB_RS03135 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>NCBI__GCF_000009985.1:WP_043743299.1
Length = 741
Score = 1117 bits (2890), Expect = 0.0
Identities = 559/741 (75%), Positives = 633/741 (85%), Gaps = 1/741 (0%)
Query: 1 MSTPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQ 60
M+T KII+T DEAPALATYSLLPI++AFTG++G+AVETRDISLAGR+IA FPE LT Q
Sbjct: 1 MTTAKIIWTKVDEAPALATYSLLPIVQAFTGAAGVAVETRDISLAGRIIANFPENLTPAQ 60
Query: 61 KISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEK 120
+I D+LAELG+L P+ANIIKLPN+SASVPQLKAAIKELQ QGYK+PD+PE+PKTD EK
Sbjct: 61 RIGDELAELGELTLKPEANIIKLPNVSASVPQLKAAIKELQSQGYKIPDFPEDPKTDAEK 120
Query: 121 DVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGD 180
++KAR+ K+ GSAVNPVLREGNSDRRA SVK +ARK+PHKMGAW+A S+SHVAHM+ GD
Sbjct: 121 ELKARFGKVLGSAVNPVLREGNSDRRAAASVKAFARKNPHKMGAWAASSQSHVAHMNAGD 180
Query: 181 FYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEI 240
FYGSEK+ + A VKIE KDGS VLKAKT ++AGE+ID++VMS ALR F A +I
Sbjct: 181 FYGSEKSVTVAAATDVKIEFHGKDGSIHVLKAKTKLKAGEVIDAAVMSAKALRAFYAEQI 240
Query: 241 EDAKKQ-GVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
DAK Q G+LLS+HLKATMMKVSDPIMFG V+ F+KD KHA +K +G +VNNG GD
Sbjct: 241 ADAKSQPGLLLSLHLKATMMKVSDPIMFGHAVTVFFKDVFEKHAAAIKDLGVNVNNGFGD 300
Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
L A++ LP AK+ EIEADI+A Y P LAMVNSDKGITNLHVPSDVIVDASMPAMIRD
Sbjct: 301 LIAKLDKLPAAKKAEIEADIKAAYEAGPPLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 360
Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
SG+MWG DGKLHDTKA+IPDRCYA +YQVVI+DCK+HGAFDP TMGSVPNVGLMAQKAEE
Sbjct: 361 SGRMWGTDGKLHDTKAMIPDRCYARMYQVVIDDCKKHGAFDPKTMGSVPNVGLMAQKAEE 420
Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
YGSHDKTF+I ADGVV+V DESG +LLEQ VEAGDI+R CQ KDAPIQDWVKLAV RAR
Sbjct: 421 YGSHDKTFEIAADGVVQVVDESGAVLLEQKVEAGDIFRACQTKDAPIQDWVKLAVTRARL 480
Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
+NTPA+FWLD RAHDAQ+IAKVE+YLKD+DT+GLDI I +P EA SL RIR+G DTI
Sbjct: 481 SNTPAIFWLDKNRAHDAQIIAKVEKYLKDHDTTGLDITIKAPEEAIAVSLERIRKGLDTI 540
Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
SVTGNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQF EEGYL
Sbjct: 541 SVTGNVLRDYLTDLFPILELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFQEEGYL 600
Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
RWDSLGEFLAL SLEHL +KNPKA VLA TLDQA +ILDNN+SPARKVGE+DNRGS
Sbjct: 601 RWDSLGEFLALGVSLEHLAQTFKNPKAQVLADTLDQANARILDNNRSPARKVGELDNRGS 660
Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
HFYLALYWAQALA QT+DKEL A+F +AKALT+NE KI EL AAQGKPVD+ GYY PN
Sbjct: 661 HFYLALYWAQALAEQTKDKELAARFAPLAKALTENEDKINAELIAAQGKPVDMGGYYSPN 720
Query: 720 TDLTSKAIRPSATFNAALAPL 740
TS A+RPSAT NAALA +
Sbjct: 721 DSKTSAAMRPSATLNAALAAI 741
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: 1551
Number of extensions: 59
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: 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_043743299.1 AMB_RS03135 (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.6889.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 1345.7 5.5 0 1345.5 5.5 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043743299.1 AMB_RS03135 NADP-dependent isoci
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743299.1 AMB_RS03135 NADP-dependent isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1345.5 5.5 0 0 5 742 .. 3 741 .] 1 741 [] 0.99
Alignments for each domain:
== domain 1 score: 1345.5 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGe 73
+akii+t deap+latysllpiv+af+++aG++vetrdislagri+a+fpe lt q+++d+laelGe
lcl|NCBI__GCF_000009985.1:WP_043743299.1 3 TAKIIWTKVDEAPALATYSLLPIVQAFTGAAGVAVETRDISLAGRIIANFPENLTPAQRIGDELAELGE 71
58******************************************************************* PP
TIGR00178 74 laktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlre 142
l+ peaniiklpn+sasvpqlkaaikelq++Gy++pd+pe+pktd+ek++kar+ k++Gsavnpvlre
lcl|NCBI__GCF_000009985.1:WP_043743299.1 72 LTLKPEANIIKLPNVSASVPQLKAAIKELQSQGYKIPDFPEDPKTDAEKELKARFGKVLGSAVNPVLRE 140
********************************************************************* PP
TIGR00178 143 GnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketv 211
Gnsdrra ++vk +ark+phkmG+w+a s+shvahm+agdfy+seksv++ aa++vkie+ kdG+ v
lcl|NCBI__GCF_000009985.1:WP_043743299.1 141 GNSDRRAAASVKAFARKNPHKMGAWAASSQSHVAHMNAGDFYGSEKSVTVAAATDVKIEFHGKDGSIHV 209
********************************************************************* PP
TIGR00178 212 lkaklklldgevidssvlskkalvefleeeiedakee.gvllslhlkatmmkvsdpivfGhvvrvfykd 279
lkak+kl++gevid++v+s+kal++f++e+i+dak + g+llslhlkatmmkvsdpi+fGh+v vf+kd
lcl|NCBI__GCF_000009985.1:WP_043743299.1 210 LKAKTKLKAGEVIDAAVMSAKALRAFYAEQIADAKSQpGLLLSLHLKATMMKVSDPIMFGHAVTVFFKD 278
**********************************98759****************************** PP
TIGR00178 280 vfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsd 348
vf kha+ +++lG++v+nG++dl+ak+++lpaakk eiead++++ye +p lamv+sdkGitnlhvpsd
lcl|NCBI__GCF_000009985.1:WP_043743299.1 279 VFEKHAAAIKDLGVNVNNGFGDLIAKLDKLPAAKKAEIEADIKAAYEAGPPLAMVNSDKGITNLHVPSD 347
********************************************************************* PP
TIGR00178 349 vivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaq 417
vivdasmpamir+sG+m+g+dgkl+dtka+ipd++ya++yq+vi+dckk+Gafdp tmG+vpnvGlmaq
lcl|NCBI__GCF_000009985.1:WP_043743299.1 348 VIVDASMPAMIRDSGRMWGTDGKLHDTKAMIPDRCYARMYQVVIDDCKKHGAFDPKTMGSVPNVGLMAQ 416
********************************************************************* PP
TIGR00178 418 kaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpa 486
kaeeyGshdktfei adGvv+vvd+sG vlle++veagdi+r+cq kdapiqdwvklavtrarls+tpa
lcl|NCBI__GCF_000009985.1:WP_043743299.1 417 KAEEYGSHDKTFEIAADGVVQVVDESGAVLLEQKVEAGDIFRACQTKDAPIQDWVKLAVTRARLSNTPA 485
********************************************************************* PP
TIGR00178 487 vfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdl 555
+fwld++rahd+++i+kvekylkdhdt+Gldi i p +a+ slerir+G dtisvtGnvlrdyltdl
lcl|NCBI__GCF_000009985.1:WP_043743299.1 486 IFWLDKNRAHDAQIIAKVEKYLKDHDTTGLDITIKAPEEAIAVSLERIRKGLDTISVTGNVLRDYLTDL 554
********************************************************************* PP
TIGR00178 556 fpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktg 624
fpilelGtsakmls+vplmaGGGlfetGaGGsapkhvqq++ee++lrwdslGeflal+ sleh+a++ +
lcl|NCBI__GCF_000009985.1:WP_043743299.1 555 FPILELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFQEEGYLRWDSLGEFLALGVSLEHLAQTFK 623
********************************************************************* PP
TIGR00178 625 nekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaeal 693
n+ka+vladtld+a ++ld+++sp+rkvGeldnrgs+fyla ywaq+la qt+dkelaa+fa++a+al
lcl|NCBI__GCF_000009985.1:WP_043743299.1 624 NPKAQVLADTLDQANARILDNNRSPARKVGELDNRGSHFYLALYWAQALAEQTKDKELAARFAPLAKAL 692
********************************************************************* PP
TIGR00178 694 tkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
t+ne+ki ael a+qG++vd+gGyy+p++ +t++++rpsat+na+l+a+
lcl|NCBI__GCF_000009985.1:WP_043743299.1 693 TENEDKINAELIAAQGKPVDMGGYYSPNDSKTSAAMRPSATLNAALAAI 741
**********************************************986 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.07
# Mc/sec: 7.67
//
[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