Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate Ac3H11_4925 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
Query= BRENDA::O53611
(745 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_4925
Length = 744
Score = 1169 bits (3025), Expect = 0.0
Identities = 579/744 (77%), Positives = 646/744 (86%)
Query: 1 MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
M+ +QPTIIYTLTDEAP LAT +FLP++R FA PAGI + SDISVAAR+L EFP++L E
Sbjct: 1 MTTQQPTIIYTLTDEAPRLATASFLPLIRTFAAPAGINVVESDISVAARVLGEFPEFLKE 60
Query: 61 EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
EQR P+ LAELG+ T PD NIIKLPNISASV QL AAI ELQ KGYA+PDYP PK D+
Sbjct: 61 EQRAPNTLAELGKKTLQPDANIIKLPNISASVSQLKAAIAELQSKGYALPDYPDQPKDDK 120
Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
EK IK RY +C+GSAVNPVLR+GNSDRRAPKAVKEYARK+PHSMGEWS ASR+HV+HM H
Sbjct: 121 EKDIKARYGKCIGSAVNPVLREGNSDRRAPKAVKEYARKNPHSMGEWSQASRSHVSHMHH 180
Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
GDFY GEKSMTLDRAR+V+MEL+ KSGKTI+LKP+V L D +VIDSMFMSKKAL +FYE+
Sbjct: 181 GDFYHGEKSMTLDRARDVKMELITKSGKTIILKPKVSLLDREVIDSMFMSKKALLEFYEK 240
Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
+++DA +TGVMFSLHVKATMMKVSHPIVFGH VRIFYKDAFAKH + FD+LGVNVNNG+
Sbjct: 241 EIEDARKTGVMFSLHVKATMMKVSHPIVFGHCVRIFYKDAFAKHAKTFDELGVNVNNGMV 300
Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
DLYSKIE+LP SQRDEI DLH CHEHRPELAMVDSA+GI+NFHSP+D+IVDASMPAMIR
Sbjct: 301 DLYSKIETLPQSQRDEIKRDLHACHEHRPELAMVDSAKGITNFHSPNDIIVDASMPAMIR 360
Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
GKM+ A+G+LKD KAV PESTF+RIYQEIINFCK +G FDP TMGTVPNVGLMAQQAE
Sbjct: 361 NSGKMWDANGRLKDVKAVMPESTFARIYQEIINFCKWHGAFDPKTMGTVPNVGLMAQQAE 420
Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
EYGSHDKTFEI EDGVANI D+ATGEVLL++NVE GDIWRMC VKDA IRDWVKLAV RA
Sbjct: 421 EYGSHDKTFEIAEDGVANITDLATGEVLLSQNVEQGDIWRMCQVKDAAIRDWVKLAVNRA 480
Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
R SGMPV+FWLD YRPHE ELI KVK YL +H+T GLDIQIMSQVR+MRYT ER++RGLD
Sbjct: 481 RNSGMPVVFWLDSYRPHEKELITKVKMYLHEHNTVGLDIQIMSQVRAMRYTLERVIRGLD 540
Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
TI+ATGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGMYETGAGGSAPKHV+QLVEEN
Sbjct: 541 TISATGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEEN 600
Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
HLRWDSLGEFLAL ED+G KTGN +AK+L +TLDAA GKLLDN+K+PS KTG+LDNR
Sbjct: 601 HLRWDSLGEFLALAVSLEDLGQKTGNAKAKILAQTLDAATGKLLDNNKNPSPKTGQLDNR 660
Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
GSQFYLAMYWAQELAAQT D LA FA LA +LT NE IV EL VQG+P DIGGYY
Sbjct: 661 GSQFYLAMYWAQELAAQTSDADLAAKFAPLAKLLTANEQKIVDELNAVQGQPTDIGGYYM 720
Query: 721 PDSDMTTAVMRPSKTFNAALEAVQ 744
PD AVMRPSKT N AL V+
Sbjct: 721 PDVAKLDAVMRPSKTLNDALNTVK 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: 1528
Number of extensions: 43
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: 744
Length adjustment: 40
Effective length of query: 705
Effective length of database: 704
Effective search space: 496320
Effective search space used: 496320
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 Ac3H11_4925 (Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42))
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.23770.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 1350.3 1.4 0 1350.2 1.4 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 Isocitrate dehydrogenase [NADP]
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1350.2 1.4 0 0 1 743 [. 1 744 [] 1 744 [] 1.00
Alignments for each domain:
== domain 1 score: 1350.2 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeq 62
m+t++++iiytltdeap lat s+lp++++faa+aGi+v +dis+a+r+l efpe+l eeq
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 1 MTTQQPTIIYTLTDEAPRLATASFLPLIRTFAAPAGINVVESDISVAARVLGEFPEFLKEEQ 62
889*********************************************************** PP
TIGR00178 63 kvddalaelGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdi 124
+ ++ laelG+ + p+aniiklpnisasv qlkaai elq+kGy+lpdyp++pk d+ekdi
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 63 RAPNTLAELGKKTLQPDANIIKLPNISASVSQLKAAIAELQSKGYALPDYPDQPKDDKEKDI 124
************************************************************** PP
TIGR00178 125 karyakikGsavnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyas 186
kary k+ GsavnpvlreGnsdrrap+avkeyark+ph+mGews++s+shv+hm++gdfy++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 125 KARYGKCIGSAVNPVLREGNSDRRAPKAVKEYARKNPHSMGEWSQASRSHVSHMHHGDFYHG 186
************************************************************** PP
TIGR00178 187 eksvlldaaeevkieliakdGketvlkaklklldgevidssvlskkalvefleeeiedakee 248
eks++ld+a++vk+eli+k+Gk+++lk+k++lld+evids+++skkal ef+e+eieda+++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 187 EKSMTLDRARDVKMELITKSGKTIILKPKVSLLDREVIDSMFMSKKALLEFYEKEIEDARKT 248
************************************************************** PP
TIGR00178 249 gvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslp 310
gv++slh+katmmkvs+pivfGh vr+fykd+fakha+++++lG++v+nG+ dly+kie+lp
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 249 GVMFSLHVKATMMKVSHPIVFGHCVRIFYKDAFAKHAKTFDELGVNVNNGMVDLYSKIETLP 310
************************************************************** PP
TIGR00178 311 aakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgkl 372
+++++ei+ dl++++e+rpelamvds+kGitn+h+p d+ivdasmpamir+sGkm++++g+l
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 311 QSQRDEIKRDLHACHEHRPELAMVDSAKGITNFHSPNDIIVDASMPAMIRNSGKMWDANGRL 372
************************************************************** PP
TIGR00178 373 kdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeiead 434
kd kav+p+s++a++yq++i++ck +Gafdp tmGtvpnvGlmaq+aeeyGshdktfei +d
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 373 KDVKAVMPESTFARIYQEIINFCKWHGAFDPKTMGTVPNVGLMAQQAEEYGSHDKTFEIAED 434
************************************************************** PP
TIGR00178 435 Gvvrvvd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldpera 495
Gv++++d ++Gevll ++ve+gdiwrmcqvkda i+dwvklav+rar sg+p+vfwld +r+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 435 GVANITDlATGEVLLSQNVEQGDIWRMCQVKDAAIRDWVKLAVNRARNSGMPVVFWLDSYRP 496
*******99***************************************************** PP
TIGR00178 496 hdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfp 557
h++eli+kv+ yl++h+t Gldiqi+s+v+a+r++ler+ rG dtis+tGn+lrdyltdlfp
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 497 HEKELITKVKMYLHEHNTVGLDIQIMSQVRAMRYTLERVIRGLDTISATGNILRDYLTDLFP 558
************************************************************** PP
TIGR00178 558 ilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehv 619
i+elGtsakmls+vplmaGGG++etGaGGsapkhvqql+eenhlrwdslGeflala sle++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 559 IMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEENHLRWDSLGEFLALAVSLEDL 620
************************************************************** PP
TIGR00178 620 avktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedke 681
++ktgn+kak+la+tldaatgklld++k ps k+G+ldnrgs+fyla+ywaqelaaqt d++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 621 GQKTGNAKAKILAQTLDAATGKLLDNNKNPSPKTGQLDNRGSQFYLAMYWAQELAAQTSDAD 682
************************************************************** PP
TIGR00178 682 laasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailealk 743
laa+fa++a+ lt ne+kiv el+avqG+++d+gGyy+pd ++++v+rps+t+n++l+++k
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4925 683 LAAKFAPLAKLLTANEQKIVDELNAVQGQPTDIGGYYMPDVAKLDAVMRPSKTLNDALNTVK 744
**********************************************************9885 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (744 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: 00:00:00.05
# Mc/sec: 10.98
//
[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