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.30626.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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.25
//
[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