Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate 6937918 Sama_2059 isocitrate dehydrogenase (NADP(+)) (RefSeq)
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__SB2B:6937918
Length = 741
Score = 1041 bits (2692), Expect = 0.0
Identities = 520/737 (70%), Positives = 599/737 (81%)
Query: 2 STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
++P IIYT TDEAPALAT SLLPI++ F +G+ +ETRDISL+GR+IATFPE LTD Q+
Sbjct: 4 NSPTIIYTETDEAPALATLSLLPILQTFAEPAGVKIETRDISLSGRVIATFPEKLTDAQR 63
Query: 62 ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
I D LAELG+LAT P+ANIIKLPNISAS+PQLKA IKELQ QGY +P+YPEEPKTD EK
Sbjct: 64 IGDHLAELGELATKPEANIIKLPNISASIPQLKACIKELQAQGYDIPNYPEEPKTDEEKS 123
Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
+KARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARK+PH MG W++DSKSHV+HM+ GDF
Sbjct: 124 IKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKNPHSMGKWASDSKSHVSHMEAGDF 183
Query: 182 YGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIE 241
YGSE++ + SV I +K G TVLK+ +QAGEIIDS+VMSKNAL F EIE
Sbjct: 184 YGSEQSVTLADADSVSIVHTSKAGVETVLKSGLKLQAGEIIDSAVMSKNALVAFFEREIE 243
Query: 242 DAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLY 301
AK + VLLS+HLKATMMKVSDPIMFG V F+K KHAE +++G DVNNG GD+
Sbjct: 244 AAKAEDVLLSLHLKATMMKVSDPIMFGHAVKVFFKPLFAKHAETFERLGVDVNNGFGDVV 303
Query: 302 ARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 361
A+I++LPEA++ IEADIQAVYA+RP +AMVNSDKGITNLHVPSD+I+DASMPA IR SG
Sbjct: 304 AKIQSLPEAERAAIEADIQAVYAERPAMAMVNSDKGITNLHVPSDIIIDASMPAAIRSSG 363
Query: 362 KMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYG 421
+MWGPDG+L DTK +IPDRCYAGVY I CK HGAFDP TMG++PNVGLMAQKAEEYG
Sbjct: 364 QMWGPDGQLKDTKFMIPDRCYAGVYDATINFCKAHGAFDPRTMGTIPNVGLMAQKAEEYG 423
Query: 422 SHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATN 481
SHDKTF+I DGVV V + +G +L+ +VEAGDI+RMCQ KDAPIQDWVKLAV RAR +
Sbjct: 424 SHDKTFEIAEDGVVTVVNAAGSVLMSHTVEAGDIFRMCQVKDAPIQDWVKLAVRRARLSE 483
Query: 482 TPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISV 541
TPAVFWLD RAHDA++I KVE YL +DTSGL+I I+SPVEAT+FSLAR+++GKDTISV
Sbjct: 484 TPAVFWLDKNRAHDAELIKKVEAYLPQHDTSGLEIHIMSPVEATQFSLARMKDGKDTISV 543
Query: 542 TGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRW 601
TGNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHV+Q E YLRW
Sbjct: 544 TGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVEQVQSENYLRW 603
Query: 602 DSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHF 661
DSLGEFLALAAS EHL KA VLA TLD A GK LD NKSPAR+VG+IDNRGSHF
Sbjct: 604 DSLGEFLALAASFEHLAQTAGVAKAQVLADTLDTAIGKFLDENKSPARRVGQIDNRGSHF 663
Query: 662 YLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTD 721
YLA+YWAQALAAQT D EL A F +A L NE I+ EL QG VD+ GYY P+
Sbjct: 664 YLAMYWAQALAAQTADAELAAHFGQLADKLAANEETILAELIGVQGHSVDLGGYYRPDFA 723
Query: 722 LTSKAIRPSATFNAALA 738
S +RPSAT N ++
Sbjct: 724 KASAVMRPSATLNGLMS 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: 1463
Number of extensions: 46
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: 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 6937918 Sama_2059 (isocitrate dehydrogenase (NADP(+)) (RefSeq))
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.29350.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 1338.3 1.3 0 1338.2 1.3 1.0 1 lcl|FitnessBrowser__SB2B:6937918 Sama_2059 isocitrate dehydrogena
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937918 Sama_2059 isocitrate dehydrogenase (NADP(+)) (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1338.2 1.3 0 0 2 739 .. 2 739 .. 1 741 [] 0.99
Alignments for each domain:
== domain 1 score: 1338.2 bits; conditional E-value: 0
TIGR00178 2 stekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktp 78
++++iiyt tdeap+lat sllpi+++fa++aG+++etrdisl+gr++a+fpe+lt+ q+++d+laelGela+ p
lcl|FitnessBrowser__SB2B:6937918 2 KDNSPTIIYTETDEAPALATLSLLPILQTFAEPAGVKIETRDISLSGRVIATFPEKLTDAQRIGDHLAELGELATKP 78
56789************************************************************************ PP
TIGR00178 79 eaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavke 155
eaniiklpnisas+pqlka+ikelq++Gyd+p+ypeepktdeek+ikary+kikGsavnpvlreGnsdrrapl+vk+
lcl|FitnessBrowser__SB2B:6937918 79 EANIIKLPNISASIPQLKACIKELQAQGYDIPNYPEEPKTDEEKSIKARYDKIKGSAVNPVLREGNSDRRAPLSVKN 155
***************************************************************************** PP
TIGR00178 156 yarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvlskk 232
yark+ph+mG+w+ dskshv+hm+agdfy+se+sv+l a++v i + +k G etvlk+ lkl++ge+ids+v+sk+
lcl|FitnessBrowser__SB2B:6937918 156 YARKNPHSMGKWASDSKSHVSHMEAGDFYGSEQSVTLADADSVSIVHTSKAGVETVLKSGLKLQAGEIIDSAVMSKN 232
***************************************************************************** PP
TIGR00178 233 alvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakiesl 309
alv+f+e eie ak+e+vllslhlkatmmkvsdpi+fGh+v+vf+k fakhae++e lG+dv+nG++d+ aki+sl
lcl|FitnessBrowser__SB2B:6937918 233 ALVAFFEREIEAAKAEDVLLSLHLKATMMKVSDPIMFGHAVKVFFKPLFAKHAETFERLGVDVNNGFGDVVAKIQSL 309
***************************************************************************** PP
TIGR00178 310 paakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyag 386
p+a++ iead+++vy+erp +amv+sdkGitnlhvpsd+i+dasmpa+ir+sG+m+g+dg+lkdtk++ipd++yag
lcl|FitnessBrowser__SB2B:6937918 310 PEAERAAIEADIQAVYAERPAMAMVNSDKGITNLHVPSDIIIDASMPAAIRSSGQMWGPDGQLKDTKFMIPDRCYAG 386
***************************************************************************** PP
TIGR00178 387 vyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqv 463
vy+a i++ck +Gafdp tmGt+pnvGlmaqkaeeyGshdktfei +dGvv vv++ G vl+ + veagdi+rmcqv
lcl|FitnessBrowser__SB2B:6937918 387 VYDATINFCKAHGAFDPRTMGTIPNVGLMAQKAEEYGSHDKTFEIAEDGVVTVVNAAGSVLMSHTVEAGDIFRMCQV 463
***************************************************************************** PP
TIGR00178 464 kdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedt 540
kdapiqdwvklav rarls+tpavfwld++rahd+elikkve yl +hdt+Gl+i+i+spv+at+fsl+r++ G+dt
lcl|FitnessBrowser__SB2B:6937918 464 KDAPIQDWVKLAVRRARLSETPAVFWLDKNRAHDAELIKKVEAYLPQHDTSGLEIHIMSPVEATQFSLARMKDGKDT 540
***************************************************************************** PP
TIGR00178 541 isvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaasle 617
isvtGnvlrdyltdlfpilelGtsakmls+vplm+GGGlfetGaGGsapkhv+q++ en+lrwdslGeflalaas+e
lcl|FitnessBrowser__SB2B:6937918 541 ISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVEQVQSENYLRWDSLGEFLALAASFE 617
***************************************************************************** PP
TIGR00178 618 hvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealt 694
h+a++ g +ka+vladtld a+gk+lde+ksp+r+vG++dnrgs+fyla+ywaq+laaqt d+elaa+f ++a+ l+
lcl|FitnessBrowser__SB2B:6937918 618 HLAQTAGVAKAQVLADTLDTAIGKFLDENKSPARRVGQIDNRGSHFYLAMYWAQALAAQTADAELAAHFGQLADKLA 694
***************************************************************************** PP
TIGR00178 695 kneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnail 739
nee+i ael vqG++vdlgGyy pd ++++v+rpsat+n ++
lcl|FitnessBrowser__SB2B:6937918 695 ANEETILAELIGVQGHSVDLGGYYRPDFAKASAVMRPSATLNGLM 739
*****************************************9876 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.00
//
[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