Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate RR42_RS28800 RR42_RS28800 isocitrate dehydrogenase
Query= BRENDA::O53611
(745 letters)
>FitnessBrowser__Cup4G11:RR42_RS28800
Length = 745
Score = 1224 bits (3167), Expect = 0.0
Identities = 604/744 (81%), Positives = 664/744 (89%)
Query: 1 MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
MS +QPTIIYTLTDEAPLLAT AFLPI+R F PAGI + SDISVA RIL EFP++LTE
Sbjct: 1 MSTQQPTIIYTLTDEAPLLATSAFLPIIRTFTAPAGINVTTSDISVAGRILGEFPEFLTE 60
Query: 61 EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
QRVPDNLAELGRLT PDTNIIKLPNISASV QLV+AIKELQ KGY VPD+P DPKTD
Sbjct: 61 AQRVPDNLAELGRLTLQPDTNIIKLPNISASVHQLVSAIKELQAKGYKVPDFPEDPKTDA 120
Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
EKAI++RY++CLGSAVNPVLR+GNSDRRAP AVK YARK+PHSMGEWSMASRTHVAHM+H
Sbjct: 121 EKAIRQRYSKCLGSAVNPVLREGNSDRRAPAAVKNYARKNPHSMGEWSMASRTHVAHMKH 180
Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
GDFY GEKSMTLDRAR+V+MEL+ KSGKTIVLKP+V L DG++IDSMFMSKKALCDFYEE
Sbjct: 181 GDFYHGEKSMTLDRARDVKMELVTKSGKTIVLKPKVSLLDGEIIDSMFMSKKALCDFYEE 240
Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
QM+DA +TGVM SLHVKATMMKVSHPIVFGHAV+IFYK+AF KH +LFD+LGVNVNNGL
Sbjct: 241 QMEDARKTGVMLSLHVKATMMKVSHPIVFGHAVKIFYKEAFEKHGKLFDELGVNVNNGLV 300
Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
+LY K+ESLP+S+R+EII D+H CHEHRPELAMVDSA+GISN H+P+DVIVDASMPAMIR
Sbjct: 301 NLYDKLESLPSSKREEIIRDMHACHEHRPELAMVDSAKGISNLHAPNDVIVDASMPAMIR 360
Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
GGKM+GADG+ KDTKAV PESTF+RIYQEIINFCKTNG FDP TMGTVPNVGLMAQQAE
Sbjct: 361 IGGKMWGADGRPKDTKAVIPESTFARIYQEIINFCKTNGNFDPVTMGTVPNVGLMAQQAE 420
Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
EYGSHDKTFE+PE G A IVD+ATGEVLL +NVE GDIWRMC VKDAPIRDWVKLAVTRA
Sbjct: 421 EYGSHDKTFEVPEAGEARIVDIATGEVLLVQNVEEGDIWRMCQVKDAPIRDWVKLAVTRA 480
Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
R SGMP +FWLDPYRPHE E+IKKV+TYLKDHDT GLDIQIMSQVR+MRYT ER++RGLD
Sbjct: 481 RNSGMPAIFWLDPYRPHEAEMIKKVETYLKDHDTTGLDIQIMSQVRAMRYTLERVIRGLD 540
Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
TI+ TGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGMYETGAGGSAPKHVKQLVEEN
Sbjct: 541 TISVTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
HLRWDSLGEFLAL E++GIKT NE+AK+L KTLDAA GKLLDN+K+PS KTG+LDNR
Sbjct: 601 HLRWDSLGEFLALAVSLEELGIKTSNEKAKVLAKTLDAATGKLLDNNKNPSPKTGQLDNR 660
Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
GSQFYLAMYWAQELAAQTDD LA FA LA LT NE VIV EL+ VQG+ DIGGYY
Sbjct: 661 GSQFYLAMYWAQELAAQTDDAALAAQFAPLAKQLTDNEQVIVGELSAVQGKQADIGGYYK 720
Query: 721 PDSDMTTAVMRPSKTFNAALEAVQ 744
PD VMRPSKT NAAL AV+
Sbjct: 721 PDFAKLDIVMRPSKTLNAALAAVK 744
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: 1587
Number of extensions: 41
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: 745
Length of database: 745
Length adjustment: 40
Effective length of query: 705
Effective length of database: 705
Effective search space: 497025
Effective search space used: 497025
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 RR42_RS28800 RR42_RS28800 (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.1387.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 1381.3 0.4 0 1381.2 0.4 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS28800 RR42_RS28800 isocitrate dehydrog
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS28800 RR42_RS28800 isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1381.2 0.4 0 0 1 743 [. 1 744 [. 1 745 [] 1.00
Alignments for each domain:
== domain 1 score: 1381.2 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddala 69
mst++++iiytltdeapllat ++lpi+++f+a+aGi+v t+dis+agril efpe+lte q+v+d+la
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 1 MSTQQPTIIYTLTDEAPLLATSAFLPIIRTFTAPAGINVTTSDISVAGRILGEFPEFLTEAQRVPDNLA 69
9******************************************************************** PP
TIGR00178 70 elGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnp 138
elG+l+ p++niiklpnisasv ql++aikelq+kGy++pd+pe+pktd+ek+i++ry+k++Gsavnp
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 70 ELGRLTLQPDTNIIKLPNISASVHQLVSAIKELQAKGYKVPDFPEDPKTDAEKAIRQRYSKCLGSAVNP 138
********************************************************************* PP
TIGR00178 139 vlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdG 207
vlreGnsdrrap+avk+yark+ph+mGews++s++hvahm++gdfy++eks++ld+a++vk+el++k+G
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 139 VLREGNSDRRAPAAVKNYARKNPHSMGEWSMASRTHVAHMKHGDFYHGEKSMTLDRARDVKMELVTKSG 207
********************************************************************* PP
TIGR00178 208 ketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvf 276
k++vlk+k++lldge+ids+++skkal++f+ee++eda+++gv+lslh+katmmkvs+pivfGh+v++f
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 208 KTIVLKPKVSLLDGEIIDSMFMSKKALCDFYEEQMEDARKTGVMLSLHVKATMMKVSHPIVFGHAVKIF 276
********************************************************************* PP
TIGR00178 277 ykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhv 345
yk++f kh++l+++lG++v+nGl +ly k+eslp++k+eei+ d+++++e+rpelamvds+kGi+nlh+
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 277 YKEAFEKHGKLFDELGVNVNNGLVNLYDKLESLPSSKREEIIRDMHACHEHRPELAMVDSAKGISNLHA 345
********************************************************************* PP
TIGR00178 346 psdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGl 414
p dvivdasmpamir +Gkm+g+dg+ kdtkavip+s++a++yq++i++ck+nG+fdp tmGtvpnvGl
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 346 PNDVIVDASMPAMIRIGGKMWGADGRPKDTKAVIPESTFARIYQEIINFCKTNGNFDPVTMGTVPNVGL 414
********************************************************************* PP
TIGR00178 415 maqkaeeyGshdktfeieadGvvrvvd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarls 482
maq+aeeyGshdktfe++++G +r+vd ++Gevll ++ve+gdiwrmcqvkdapi+dwvklavtrar s
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 415 MAQQAEEYGSHDKTFEVPEAGEARIVDiATGEVLLVQNVEEGDIWRMCQVKDAPIRDWVKLAVTRARNS 483
***************************99**************************************** PP
TIGR00178 483 gtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdy 551
g+pa+fwldp+r+h++e+ikkve+ylkdhdt+Gldiqi+s+v+a+r++ler+ rG dtisvtGn+lrdy
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 484 GMPAIFWLDPYRPHEAEMIKKVETYLKDHDTTGLDIQIMSQVRAMRYTLERVIRGLDTISVTGNILRDY 552
********************************************************************* PP
TIGR00178 552 ltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehva 620
ltdlfpi+elGtsakmls+vplmaGGG++etGaGGsapkhv+ql+eenhlrwdslGeflala sle+++
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 553 LTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVKQLVEENHLRWDSLGEFLALAVSLEELG 621
********************************************************************* PP
TIGR00178 621 vktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasv 689
+kt nekakvla+tldaatgklld++k ps k+G+ldnrgs+fyla+ywaqelaaqt+d+ laa+fa++
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 622 IKTSNEKAKVLAKTLDAATGKLLDNNKNPSPKTGQLDNRGSQFYLAMYWAQELAAQTDDAALAAQFAPL 690
********************************************************************* PP
TIGR00178 690 aealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailealk 743
a+ lt+ne++iv+el+avqG+ d+gGyy+pd +++ v+rps+t+na+l+a+k
lcl|FitnessBrowser__Cup4G11:RR42_RS28800 691 AKQLTDNEQVIVGELSAVQGKQADIGGYYKPDFAKLDIVMRPSKTLNAALAAVK 744
***************************************************997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (745 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 11.97
//
[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