Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate HSERO_RS12570 HSERO_RS12570 isocitrate dehydrogenase
Query= BRENDA::O53611
(745 letters)
>FitnessBrowser__HerbieS:HSERO_RS12570
Length = 742
Score = 1111 bits (2873), Expect = 0.0
Identities = 546/738 (73%), Positives = 630/738 (85%), Gaps = 1/738 (0%)
Query: 6 PTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTEEQRVP 65
PTIIYTLTDEAP LAT++ LPIV+ F AGI + SDISVAARILAEFP+YLT+EQ+VP
Sbjct: 6 PTIIYTLTDEAPYLATHSLLPIVKKFTAAAGIDVVESDISVAARILAEFPEYLTDEQKVP 65
Query: 66 DNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQEKAIK 125
DNLA LG LTQ PD NIIKLPNISAS+ QL AAI+ELQ +GY +PDYP +P T++EKA++
Sbjct: 66 DNLAALGALTQSPDANIIKLPNISASILQLQAAIRELQSRGYKLPDYPENPTTEEEKALQ 125
Query: 126 ERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRHGDFYA 185
+RYA+ GSAVNPVLR+GNSDRRAP AVK YARKHPHSM +WSMASRTHVAHM GDFYA
Sbjct: 126 KRYAKVTGSAVNPVLREGNSDRRAPNAVKNYARKHPHSMAKWSMASRTHVAHMHGGDFYA 185
Query: 186 GEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEEQMQDA 245
GEKS+TLD+A +V+M+L+ KSG+TIVLKP++ L G++IDSMFMSKKALC +YEEQMQDA
Sbjct: 186 GEKSLTLDKAVDVKMDLVTKSGETIVLKPKISLQAGEIIDSMFMSKKALCAYYEEQMQDA 245
Query: 246 FETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLSDLYSK 305
FET ++ S+HVKATMMKVSHPIVFGHAVR +YKD F KH +LF ++GVN NNG+S +Y K
Sbjct: 246 FETDLLLSVHVKATMMKVSHPIVFGHAVRTYYKDTFTKHAKLFAEIGVNPNNGMSGVYEK 305
Query: 306 IESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIRAGGKM 365
I +LP +++ E++ DL RP LAMVDSA+GI+N H+P+DVIVDASMPAMIRAGGKM
Sbjct: 306 INTLPDAKKAEVLADLKADEAKRPRLAMVDSAKGITNLHAPNDVIVDASMPAMIRAGGKM 365
Query: 366 YGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAEEYGSH 425
+ A GK +DTKA+ PESTF+RIYQE+INFCKTNG FDPTTMGTVPNVGLMAQ+AEEYGSH
Sbjct: 366 WNAAGKTEDTKALLPESTFARIYQEMINFCKTNGAFDPTTMGTVPNVGLMAQKAEEYGSH 425
Query: 426 DKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRARISGM 485
DKTFEI + GVA IV + G+VLL +NVE GDIWRMC VKDA +RDWVKLAVTRAR+SGM
Sbjct: 426 DKTFEIAQAGVARIVTL-DGQVLLEQNVEEGDIWRMCQVKDAAVRDWVKLAVTRARLSGM 484
Query: 486 PVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLDTIAAT 545
P +FWLDPYRPHE ELIKKV TYLKDHD G DIQIMSQVR+MRYT ER++RGLDTI+ T
Sbjct: 485 PAVFWLDPYRPHEAELIKKVNTYLKDHDLTGADIQIMSQVRAMRYTLERVIRGLDTISVT 544
Query: 546 GNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEENHLRWD 605
GNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGM+ETGAGGSAPKHV+QLV ENHLRWD
Sbjct: 545 GNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVGENHLRWD 604
Query: 606 SLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNRGSQFY 665
SLGEFLAL E++GIKTGN +AK+L KTLDAA GKLLDN+KSPS KTGELDNRGS FY
Sbjct: 605 SLGEFLALAVSIEEVGIKTGNSKAKILAKTLDAATGKLLDNNKSPSPKTGELDNRGSHFY 664
Query: 666 LAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYAPDSDM 725
LA+YWAQELAAQ DD +LA+ FA LA L +NE IV EL VQG+ VDIGGYY PD +
Sbjct: 665 LALYWAQELAAQKDDAELAKQFAPLAKALAENEQKIVEELNSVQGKQVDIGGYYLPDREK 724
Query: 726 TTAVMRPSKTFNAALEAV 743
T AVMRPS T N ALE +
Sbjct: 725 TFAVMRPSATLNQALETL 742
Lambda K H
0.317 0.134 0.388
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: 1513
Number of extensions: 37
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: 745
Length of database: 742
Length adjustment: 40
Effective length of query: 705
Effective length of database: 702
Effective search space: 494910
Effective search space used: 494910
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 (21.7 bits)
S2: 55 (25.8 bits)
Align candidate HSERO_RS12570 HSERO_RS12570 (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.24210.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 1341.9 2.8 0 1341.7 2.8 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS12570 HSERO_RS12570 isocitrate dehydro
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS12570 HSERO_RS12570 isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1341.7 2.8 0 0 3 742 .. 3 742 .] 1 742 [] 1.00
Alignments for each domain:
== domain 1 score: 1341.7 bits; conditional E-value: 0
TIGR00178 3 tekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalae 70
t +++iiytltdeap lat+sllpivk f+a+aGi+v +dis+a+rilaefpeylt+eqkv+d+la
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 3 TGNPTIIYTLTDEAPYLATHSLLPIVKKFTAAAGIDVVESDISVAARILAEFPEYLTDEQKVPDNLAA 70
7789**************************************************************** PP
TIGR00178 71 lGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnp 138
lG l++ p+aniiklpnisas+ ql+aai+elq++Gy+lpdype+p+t+eek++++ryak+ Gsavnp
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 71 LGALTQSPDANIIKLPNISASILQLQAAIRELQSRGYKLPDYPENPTTEEEKALQKRYAKVTGSAVNP 138
******************************************************************** PP
TIGR00178 139 vlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakd 206
vlreGnsdrrap avk+yarkhph+m +ws++s++hvahm+ gdfya+eks++ld+a +vk++l++k+
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 139 VLREGNSDRRAPNAVKNYARKHPHSMAKWSMASRTHVAHMHGGDFYAGEKSLTLDKAVDVKMDLVTKS 206
******************************************************************** PP
TIGR00178 207 GketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvr 274
G+++vlk+k++l++ge+ids+++skkal++++ee+++da+e+++lls+h+katmmkvs+pivfGh+vr
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 207 GETIVLKPKISLQAGEIIDSMFMSKKALCAYYEEQMQDAFETDLLLSVHVKATMMKVSHPIVFGHAVR 274
******************************************************************** PP
TIGR00178 275 vfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitn 342
++ykd+f+kha+l+ ++G++ +nG++ +y ki++lp+akk e+ adl++ ++rp lamvds+kGitn
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 275 TYYKDTFTKHAKLFAEIGVNPNNGMSGVYEKINTLPDAKKAEVLADLKADEAKRPRLAMVDSAKGITN 342
******************************************************************** PP
TIGR00178 343 lhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvp 410
lh+p dvivdasmpamira+Gkm+++ gk +dtka+ p+s++a++yq++i++ck+nGafdpttmGtvp
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 343 LHAPNDVIVDASMPAMIRAGGKMWNAAGKTEDTKALLPESTFARIYQEMINFCKTNGAFDPTTMGTVP 410
******************************************************************** PP
TIGR00178 411 nvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtr 478
nvGlmaqkaeeyGshdktfei ++Gv+r+v +G+vlle++ve+gdiwrmcqvkda ++dwvklavtr
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 411 NVGLMAQKAEEYGSHDKTFEIAQAGVARIVTLDGQVLLEQNVEEGDIWRMCQVKDAAVRDWVKLAVTR 478
******************************************************************** PP
TIGR00178 479 arlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGn 546
arlsg+pavfwldp+r+h++elikkv++ylkdhd +G diqi+s+v+a+r++ler+ rG dtisvtGn
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 479 ARLSGMPAVFWLDPYRPHEAELIKKVNTYLKDHDLTGADIQIMSQVRAMRYTLERVIRGLDTISVTGN 546
******************************************************************** PP
TIGR00178 547 vlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaa 614
+lrdyltdlfpi+elGtsakmls+vplmaGGG+fetGaGGsapkhvqql+ enhlrwdslGeflala
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 547 ILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVGENHLRWDSLGEFLALAV 614
******************************************************************** PP
TIGR00178 615 slehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkel 682
s+e+v++ktgn+kak+la+tldaatgklld++ksps k+Geldnrgs+fyla ywaqelaaq +d+el
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 615 SIEEVGIKTGNSKAKILAKTLDAATGKLLDNNKSPSPKTGELDNRGSHFYLALYWAQELAAQKDDAEL 682
******************************************************************** PP
TIGR00178 683 aasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
a++fa++a+al++ne+kiv+el++vqG+ vd+gGyy pd ++t +v+rpsat+n++le+l
lcl|FitnessBrowser__HerbieS:HSERO_RS12570 683 AKQFAPLAKALAENEQKIVEELNSVQGKQVDIGGYYLPDREKTFAVMRPSATLNQALETL 742
*********************************************************976 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (742 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 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 11.69
//
[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