Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_017220912.1 A923_RS0106780 NADP-dependent isocitrate dehydrogenase
Query= BRENDA::O53611
(745 letters)
>NCBI__GCF_000276805.1:WP_017220912.1
Length = 745
Score = 1105 bits (2858), Expect = 0.0
Identities = 547/740 (73%), Positives = 630/740 (85%)
Query: 1 MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
MS E IIYTLTDEAPLLATY+ LPIV F AGI + SDISVAARILAEFP+YL+E
Sbjct: 1 MSEENSKIIYTLTDEAPLLATYSLLPIVEKFTSAAGIDVVKSDISVAARILAEFPEYLSE 60
Query: 61 EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
EQ++PDNL+ELGRLTQ +TNIIKLPNISASVPQL AAI ELQ +G+ +P+ P +P+TD+
Sbjct: 61 EQQLPDNLSELGRLTQDSNTNIIKLPNISASVPQLQAAISELQSQGFNIPNLPENPQTDE 120
Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
KA+ +RY++ LGSAVNPVLR+GNSDRRAPKAVK +ARKHPHSMG+WS AS+THVAHMR
Sbjct: 121 GKALLQRYSKALGSAVNPVLREGNSDRRAPKAVKNFARKHPHSMGKWSQASQTHVAHMRE 180
Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
GDFY GEKS+TLDRAR VRMEL+A++G+TI+LK + L DG++IDSM+MSK ALCDFYE+
Sbjct: 181 GDFYHGEKSITLDRARTVRMELVAENGETIILKNNLALLDGEIIDSMYMSKTALCDFYEQ 240
Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
+MQDA+ETG+MFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKH ELF LGVNVNNGLS
Sbjct: 241 EMQDAYETGMMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHDELFKKLGVNVNNGLS 300
Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
+LY KI LP+SQR+EI DLH CH HRPELAMVDS +GISN H+P+DVIVDASMPAMIR
Sbjct: 301 NLYEKIADLPSSQREEIRRDLHACHAHRPELAMVDSDKGISNLHAPNDVIVDASMPAMIR 360
Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
+GGKM+GADG+ KDTKAV PESTF+RIYQEII FCKTNG FDP TMG+VPNVGLMAQ+AE
Sbjct: 361 SGGKMWGADGRPKDTKAVIPESTFARIYQEIIAFCKTNGAFDPVTMGSVPNVGLMAQKAE 420
Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
EYGSHDKTFE P G A IVD+ TGEVL+ +NVE DIWRMC VKDAPIRDWVKL+V RA
Sbjct: 421 EYGSHDKTFEAPATGEARIVDIDTGEVLMIQNVEKDDIWRMCQVKDAPIRDWVKLSVERA 480
Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
R S PV+FWLD YRPHENELI KV YLKDH+T+GLDIQIMSQVR+MRYT ER+VRGLD
Sbjct: 481 RDSDTPVVFWLDRYRPHENELITKVNEYLKDHNTDGLDIQIMSQVRAMRYTLERVVRGLD 540
Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
TI++TGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGG++ETGAGGSAPKHV+QLVEEN
Sbjct: 541 TISSTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQLVEEN 600
Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
HLRWDSLGEFLA+ E + K+G+ +AK+L TLD A LLDN KSPSR+TGELDNR
Sbjct: 601 HLRWDSLGEFLAITVSLESVAKKSGSIKAKVLATTLDQATEMLLDNGKSPSRRTGELDNR 660
Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
GS FYL+++WA+ +A QT+D +LA FA LA L +NE IV EL QG+ VDIGGY+
Sbjct: 661 GSHFYLSLFWAKCIAEQTEDTELAAKFAPLAASLAENELKIVEELNSAQGKAVDIGGYFN 720
Query: 721 PDSDMTTAVMRPSKTFNAAL 740
D A+MRPSKTFNA L
Sbjct: 721 ADPAKMEAIMRPSKTFNAVL 740
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: 1507
Number of extensions: 50
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 WP_017220912.1 A923_RS0106780 (NADP-dependent 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.2985384.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 1328.8 0.4 0 1328.5 0.4 1.0 1 NCBI__GCF_000276805.1:WP_017220912.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017220912.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1328.5 0.4 0 0 1 740 [. 1 741 [. 1 744 [. 1.00
Alignments for each domain:
== domain 1 score: 1328.5 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGe 73
ms e++kiiytltdeapllatysllpiv+ f+++aGi+v +dis+a+rilaefpeyl+eeq+++d+l+elG+
NCBI__GCF_000276805.1:WP_017220912.1 1 MSEENSKIIYTLTDEAPLLATYSLLPIVEKFTSAAGIDVVKSDISVAARILAEFPEYLSEEQQLPDNLSELGR 73
899********************************************************************** PP
TIGR00178 74 laktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsd 146
l++ ++niiklpnisasvpql+aai elq++G+++p++pe+p+tde k++++ry+k +GsavnpvlreGnsd
NCBI__GCF_000276805.1:WP_017220912.1 74 LTQDSNTNIIKLPNISASVPQLQAAISELQSQGFNIPNLPENPQTDEGKALLQRYSKALGSAVNPVLREGNSD 146
************************************************************************* PP
TIGR00178 147 rraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklkll 219
rrap+avk++arkhph+mG+ws++s++hvahm++gdfy++eks++ld+a+ v++el+a++G++++lk++l ll
NCBI__GCF_000276805.1:WP_017220912.1 147 RRAPKAVKNFARKHPHSMGKWSQASQTHVAHMREGDFYHGEKSITLDRARTVRMELVAENGETIILKNNLALL 219
************************************************************************* PP
TIGR00178 220 dgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlG 292
dge+ids+ +sk al++f+e+e++da e+g+++slh+katmmkvs+pivfGh+vr+fykd+fakh+el+++lG
NCBI__GCF_000276805.1:WP_017220912.1 220 DGEIIDSMYMSKTALCDFYEQEMQDAYETGMMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHDELFKKLG 292
************************************************************************* PP
TIGR00178 293 ldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkm 365
++v+nGl++ly ki+ lp++++eei+ dl++++++rpelamvdsdkGi+nlh+p dvivdasmpamir++Gkm
NCBI__GCF_000276805.1:WP_017220912.1 293 VNVNNGLSNLYEKIADLPSSQREEIRRDLHACHAHRPELAMVDSDKGISNLHAPNDVIVDASMPAMIRSGGKM 365
************************************************************************* PP
TIGR00178 366 ygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvr 438
+g+dg+ kdtkavip+s++a++yq++i +ck+nGafdp tmG+vpnvGlmaqkaeeyGshdktfe +a G +r
NCBI__GCF_000276805.1:WP_017220912.1 366 WGADGRPKDTKAVIPESTFARIYQEIIAFCKTNGAFDPVTMGSVPNVGLMAQKAEEYGSHDKTFEAPATGEAR 438
************************************************************************* PP
TIGR00178 439 vvd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkd 510
+vd ++Gevl+ ++ve++diwrmcqvkdapi+dwvkl+v rar s+tp+vfwld +r+h++eli+kv++ylkd
NCBI__GCF_000276805.1:WP_017220912.1 439 IVDiDTGEVLMIQNVEKDDIWRMCQVKDAPIRDWVKLSVERARDSDTPVVFWLDRYRPHENELITKVNEYLKD 511
***99******************************************************************** PP
TIGR00178 511 hdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetG 583
h+t+Gldiqi+s+v+a+r++ler++rG dtis tGn+lrdyltdlfpi+elGtsakmls+vplmaGGGlfetG
NCBI__GCF_000276805.1:WP_017220912.1 512 HNTDGLDIQIMSQVRAMRYTLERVVRGLDTISSTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETG 584
************************************************************************* PP
TIGR00178 584 aGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGel 656
aGGsapkhvqql+eenhlrwdslGefla++ sle va k+g kakvla tld+at+ lld+ kspsr++Gel
NCBI__GCF_000276805.1:WP_017220912.1 585 AGGSAPKHVQQLVEENHLRWDSLGEFLAITVSLESVAKKSGSIKAKVLATTLDQATEMLLDNGKSPSRRTGEL 657
************************************************************************* PP
TIGR00178 657 dnrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvl 729
dnrgs+fyl +wa+ +a qted+elaa+fa++a +l++ne kiv+el+++qG+avd+gGy+++d ++++++
NCBI__GCF_000276805.1:WP_017220912.1 658 DNRGSHFYLSLFWAKCIAEQTEDTELAAKFAPLAASLAENELKIVEELNSAQGKAVDIGGYFNADPAKMEAIM 730
************************************************************************* PP
TIGR00178 730 rpsatfnaile 740
rps+tfna+l+
NCBI__GCF_000276805.1:WP_017220912.1 731 RPSKTFNAVLN 741
********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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 28.80
//
[ok]
This GapMind analysis is from Sep 24 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