Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate CA265_RS02350 CA265_RS02350 isocitrate dehydrogenase (NADP(+))
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__Pedo557:CA265_RS02350
Length = 739
Score = 1009 bits (2608), Expect = 0.0
Identities = 503/739 (68%), Positives = 590/739 (79%), Gaps = 2/739 (0%)
Query: 2 STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
+T KIIYT TDEAP LATYSLLPI++AFT S+GI VETRDISLAGR++A FPEYL D QK
Sbjct: 3 NTSKIIYTKTDEAPMLATYSLLPIVQAFTASAGIDVETRDISLAGRILANFPEYLKDDQK 62
Query: 62 ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
I D LAELG LATTP+ANIIKLPNISAS+PQL AI ELQ QG+ +P+YP+ ++D EK
Sbjct: 63 IGDALAELGALATTPEANIIKLPNISASIPQLVGAITELQSQGFAIPNYPDNAQSDEEKA 122
Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
+KA+Y K+ GSAVNPVLREGNSDRRAP +VKNYA+++PH MG WSADSK+ VA M GDF
Sbjct: 123 IKAKYAKVLGSAVNPVLREGNSDRRAPKAVKNYAKQNPHSMGKWSADSKTKVASMTEGDF 182
Query: 182 YGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIE 241
YGSEK+ + KIE +A DG+ T LK + ++AGE+IDSS +S +AL+ F+A EI
Sbjct: 183 YGSEKSTTVAEASQFKIEFVAADGTVTELKGLSPLKAGEVIDSSALSLSALKTFVAKEIA 242
Query: 242 DAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLY 301
+AK GVLLS HLKATMMKVSDPI+FG IV ++ D TK+A++ K++ D NG+GD+Y
Sbjct: 243 EAKAAGVLLSAHLKATMMKVSDPIIFGAIVEVYFADVFTKYADLFKELNIDTRNGLGDVY 302
Query: 302 ARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 361
A+I AKQ E+EA + P LAMVNSDKGITNLHVPSDVIVDASMPAMIR SG
Sbjct: 303 AKIAG--NAKQAEVEAALAQAIENGPALAMVNSDKGITNLHVPSDVIVDASMPAMIRTSG 360
Query: 362 KMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYG 421
+MW GK DT A+IPDR YAGVY I+DCK +GAFD TT+GSVPNVGLMAQKAEEYG
Sbjct: 361 QMWNAAGKAQDTIALIPDRSYAGVYTATIDDCKANGAFDVTTIGSVPNVGLMAQKAEEYG 420
Query: 422 SHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATN 481
SHDKTFQ G +RVTD GK+ +Q VE GDI+RMCQ KDAPIQDWVKLAVNR+R +
Sbjct: 421 SHDKTFQATGSGTIRVTDADGKVFFDQKVEKGDIFRMCQTKDAPIQDWVKLAVNRSRLSE 480
Query: 482 TPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISV 541
TPAVFWLD RAHD ++I KV YLKD+DT+GLDIRIL+P+EAT+F+L RIR+G DTISV
Sbjct: 481 TPAVFWLDENRAHDREIITKVNTYLKDHDTTGLDIRILAPIEATKFTLERIRKGLDTISV 540
Query: 542 TGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRW 601
TGNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKH++QF++EGYLRW
Sbjct: 541 TGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHIEQFIDEGYLRW 600
Query: 602 DSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHF 661
DSLGEFLAL ASLEHL N KA VLA LD+A K L +KSP RK+G IDNRGSHF
Sbjct: 601 DSLGEFLALQASLEHLSQTQNNTKAQVLADALDEANAKFLATDKSPGRKLGTIDNRGSHF 660
Query: 662 YLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTD 721
YLALYWA+ALAAQT+D +LQA+F +AK L NE KI EL AQGKP +I GYY+PN +
Sbjct: 661 YLALYWAEALAAQTKDADLQARFAPLAKTLFANEAKINEELIGAQGKPQNIGGYYNPNDE 720
Query: 722 LTSKAIRPSATFNAALAPL 740
L SKA+RPS T N +LA L
Sbjct: 721 LASKAMRPSETLNTSLASL 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: 1404
Number of extensions: 45
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: 739
Length adjustment: 40
Effective length of query: 701
Effective length of database: 699
Effective search space: 489999
Effective search space used: 489999
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 CA265_RS02350 CA265_RS02350 (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.8314.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 1280.4 4.8 0 1280.2 4.8 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS02350 CA265_RS02350 isocitrate dehydro
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS02350 CA265_RS02350 isocitrate dehydrogenase (NADP(+))
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1280.2 4.8 0 0 4 741 .. 3 738 .. 1 739 [] 0.99
Alignments for each domain:
== domain 1 score: 1280.2 bits; conditional E-value: 0
TIGR00178 4 ekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalael 71
+++kiiyt tdeap+latysllpiv+af+asaGi+vetrdislagrila+fpeyl ++qk++dalael
lcl|FitnessBrowser__Pedo557:CA265_RS02350 3 NTSKIIYTKTDEAPMLATYSLLPIVQAFTASAGIDVETRDISLAGRILANFPEYLKDDQKIGDALAEL 70
569***************************************************************** PP
TIGR00178 72 GelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpv 139
G la+tpeaniiklpnisas+pql+ ai elq++G+++p+yp+++++deek+ika+yak++Gsavnpv
lcl|FitnessBrowser__Pedo557:CA265_RS02350 71 GALATTPEANIIKLPNISASIPQLVGAITELQSQGFAIPNYPDNAQSDEEKAIKAKYAKVLGSAVNPV 138
******************************************************************** PP
TIGR00178 140 lreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdG 207
lreGnsdrrap+avk+ya+++ph+mG+wsadsk++va m++gdfy+seks ++ +a++ kie++a+dG
lcl|FitnessBrowser__Pedo557:CA265_RS02350 139 LREGNSDRRAPKAVKNYAKQNPHSMGKWSADSKTKVASMTEGDFYGSEKSTTVAEASQFKIEFVAADG 206
******************************************************************** PP
TIGR00178 208 ketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrv 275
++t lk +l++gevidss ls +al+ f+++ei++ak+ gvlls+hlkatmmkvsdpi+fG +v v
lcl|FitnessBrowser__Pedo557:CA265_RS02350 207 TVTELKGLSPLKAGEVIDSSALSLSALKTFVAKEIAEAKAAGVLLSAHLKATMMKVSDPIIFGAIVEV 274
******************************************************************** PP
TIGR00178 276 fykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnl 343
+++dvf+k+a+l+++l +d+ nGl+d+yaki+ +ak+ e+ea+l ++ e++p lamv+sdkGitnl
lcl|FitnessBrowser__Pedo557:CA265_RS02350 275 YFADVFTKYADLFKELNIDTRNGLGDVYAKIA--GNAKQAEVEAALAQAIENGPALAMVNSDKGITNL 340
*******************************8..58999***************************** PP
TIGR00178 344 hvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpn 411
hvpsdvivdasmpamir+sG+m+++ gk +dt a+ipd+syagvy a i+dck nGafd tt+G+vpn
lcl|FitnessBrowser__Pedo557:CA265_RS02350 341 HVPSDVIVDASMPAMIRTSGQMWNAAGKAQDTIALIPDRSYAGVYTATIDDCKANGAFDVTTIGSVPN 408
******************************************************************** PP
TIGR00178 412 vGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtra 479
vGlmaqkaeeyGshdktf+ G++rv+d++G+v+++++ve+gdi+rmcq kdapiqdwvklav+r+
lcl|FitnessBrowser__Pedo557:CA265_RS02350 409 VGLMAQKAEEYGSHDKTFQATGSGTIRVTDADGKVFFDQKVEKGDIFRMCQTKDAPIQDWVKLAVNRS 476
******************************************************************** PP
TIGR00178 480 rlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnv 547
rls+tpavfwld++rahd+e+i+kv++ylkdhdt+Gldi+il p++at+f+lerir+G dtisvtGnv
lcl|FitnessBrowser__Pedo557:CA265_RS02350 477 RLSETPAVFWLDENRAHDREIITKVNTYLKDHDTTGLDIRILAPIEATKFTLERIRKGLDTISVTGNV 544
******************************************************************** PP
TIGR00178 548 lrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaas 615
lrdyltdlfpilelGtsakmls+vplm+GGGlfetGaGGsapkh++q+ +e++lrwdslGeflal as
lcl|FitnessBrowser__Pedo557:CA265_RS02350 545 LRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHIEQFIDEGYLRWDSLGEFLALQAS 612
******************************************************************** PP
TIGR00178 616 lehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkela 683
leh++++++n+ka+vlad+ld+a k+l ++ksp rk G +dnrgs+fyla ywa++laaqt+d++l+
lcl|FitnessBrowser__Pedo557:CA265_RS02350 613 LEHLSQTQNNTKAQVLADALDEANAKFLATDKSPGRKLGTIDNRGSHFYLALYWAEALAAQTKDADLQ 680
******************************************************************** PP
TIGR00178 684 asfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailea 741
a+fa++a++l ne+ki +el +qG++ ++gGyy+p+++l++k++rps+t+n+ l++
lcl|FitnessBrowser__Pedo557:CA265_RS02350 681 ARFAPLAKTLFANEAKINEELIGAQGKPQNIGGYYNPNDELASKAMRPSETLNTSLAS 738
******************************************************9986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (739 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: 12.50
//
[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