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.18578.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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 10.45
//
[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