Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_086510825.1 BZY95_RS15600 NADP-dependent isocitrate dehydrogenase
Query= BRENDA::O53611
(745 letters)
>NCBI__GCF_002151265.1:WP_086510825.1
Length = 745
Score = 1137 bits (2940), Expect = 0.0
Identities = 553/741 (74%), Positives = 638/741 (86%)
Query: 3 AEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTEEQ 62
++ P IIYT TDEAP LATY+ LPI+ A+ + AG+++E DIS+AARIL++FPDYLT EQ
Sbjct: 2 SKTPKIIYTFTDEAPALATYSLLPIIDAYTDAAGVEVETRDISLAARILSQFPDYLTAEQ 61
Query: 63 RVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQEK 122
RV D+LAELG L + P+ NIIKLPNISAS+PQL AAIKELQ +GY +P+YP +PK D+EK
Sbjct: 62 RVEDHLAELGALAKTPEANIIKLPNISASMPQLRAAIKELQGQGYKLPEYPDEPKNDEEK 121
Query: 123 AIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRHGD 182
IK RY + GSAVNPVLR+GNSDRRAPKAVKEYARK+PHSMGEWS ASRTHV+HM GD
Sbjct: 122 EIKARYDKVKGSAVNPVLREGNSDRRAPKAVKEYARKYPHSMGEWSQASRTHVSHMHGGD 181
Query: 183 FYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEEQM 242
FY GEKSMTLDRARNV+MEL+ KSG+++VLKP+V L +G++IDSMFMSKKALC+FYE ++
Sbjct: 182 FYHGEKSMTLDRARNVKMELITKSGESLVLKPKVSLLEGEIIDSMFMSKKALCEFYEREI 241
Query: 243 QDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLSDL 302
+DA +TGVMFSLHVKATMMKVSHPIVFGH V+IFYKDAF KH LF++LGV+VNNG+ +L
Sbjct: 242 EDARKTGVMFSLHVKATMMKVSHPIVFGHCVKIFYKDAFEKHGALFEELGVDVNNGMVNL 301
Query: 303 YSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIRAG 362
Y K+++LP SQR+E+I DLH CH+ RPELAMVDSARGI+NFHSPSDVIVDASMPAMIRAG
Sbjct: 302 YDKLDTLPESQREEVIRDLHACHDQRPELAMVDSARGITNFHSPSDVIVDASMPAMIRAG 361
Query: 363 GKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAEEY 422
G+MYGADG++KD KAV PESTF+RIYQE+INFCK +G FDP TMGTVPNVGLMAQ+AEEY
Sbjct: 362 GQMYGADGRMKDVKAVIPESTFARIYQEMINFCKWHGAFDPATMGTVPNVGLMAQKAEEY 421
Query: 423 GSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRARI 482
GSHDKTFE+P DGVANI D+ TGEVLL++NVE GDIWRMC VKD PIRDWVKLAV R R
Sbjct: 422 GSHDKTFEVPADGVANITDLETGEVLLSQNVEKGDIWRMCQVKDEPIRDWVKLAVERCRD 481
Query: 483 SGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLDTI 542
SGMP +FWLDPYRPHENELIKKVKTYLKDHDT GLDIQIMSQVR+MRYT ER++RGLDTI
Sbjct: 482 SGMPAVFWLDPYRPHENELIKKVKTYLKDHDTSGLDIQIMSQVRAMRYTLERVIRGLDTI 541
Query: 543 AATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEENHL 602
+ TGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGM+ETGAGGSAPKHV+QL+EENHL
Sbjct: 542 SVTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLLEENHL 601
Query: 603 RWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNRGS 662
RWDSLGEFLAL A E + + GNERA LL LD AIG+ L+NDKSPSRK GELDNRGS
Sbjct: 602 RWDSLGEFLALTASLEHLAKRFGNERAALLADALDKAIGQFLENDKSPSRKVGELDNRGS 661
Query: 663 QFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYAPD 722
FYLA+YWA+ LAAQ +D +L FA LA+ L NE I+ EL VQG+PVDIGGYY D
Sbjct: 662 HFYLALYWARALAAQDEDAELKSLFARLAETLEANEATILDELNSVQGQPVDIGGYYHAD 721
Query: 723 SDMTTAVMRPSKTFNAALEAV 743
+ AVMRPSKT N AL V
Sbjct: 722 PALAQAVMRPSKTLNEALALV 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: 1506
Number of extensions: 37
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_086510825.1 BZY95_RS15600 (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.30427.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 1380.7 0.0 0 1380.5 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510825.1 BZY95_RS15600 NADP-dependent iso
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510825.1 BZY95_RS15600 NADP-dependent isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1380.5 0.0 0 0 4 743 .. 3 743 .. 1 744 [. 0.99
Alignments for each domain:
== domain 1 score: 1380.5 bits; conditional E-value: 0
TIGR00178 4 ekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelG 72
+++kiiyt tdeap+latysllpi+ a++++aG+evetrdisla+ril++fp+ylt eq+v+d+laelG
lcl|NCBI__GCF_002151265.1:WP_086510825.1 3 KTPKIIYTFTDEAPALATYSLLPIIDAYTDAAGVEVETRDISLAARILSQFPDYLTAEQRVEDHLAELG 71
459****************************************************************** PP
TIGR00178 73 elaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlr 141
laktpeaniiklpnisas+pql+aaikelq +Gy+lp+yp+epk+deek+ikary+k+kGsavnpvlr
lcl|NCBI__GCF_002151265.1:WP_086510825.1 72 ALAKTPEANIIKLPNISASMPQLRAAIKELQGQGYKLPEYPDEPKNDEEKEIKARYDKVKGSAVNPVLR 140
********************************************************************* PP
TIGR00178 142 eGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGket 210
eGnsdrrap+avkeyark+ph+mGews++s++hv+hm+ gdfy++eks++ld+a++vk+eli+k+G++
lcl|NCBI__GCF_002151265.1:WP_086510825.1 141 EGNSDRRAPKAVKEYARKYPHSMGEWSQASRTHVSHMHGGDFYHGEKSMTLDRARNVKMELITKSGESL 209
********************************************************************* PP
TIGR00178 211 vlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykd 279
vlk+k++ll+ge+ids+++skkal+ef+e eieda+++gv++slh+katmmkvs+pivfGh v++fykd
lcl|NCBI__GCF_002151265.1:WP_086510825.1 210 VLKPKVSLLEGEIIDSMFMSKKALCEFYEREIEDARKTGVMFSLHVKATMMKVSHPIVFGHCVKIFYKD 278
********************************************************************* PP
TIGR00178 280 vfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsd 348
+f kh++l+e+lG+dv+nG+ +ly k+++lp++++ee++ dl++++++rpelamvds++Gitn+h+psd
lcl|NCBI__GCF_002151265.1:WP_086510825.1 279 AFEKHGALFEELGVDVNNGMVNLYDKLDTLPESQREEVIRDLHACHDQRPELAMVDSARGITNFHSPSD 347
********************************************************************* PP
TIGR00178 349 vivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaq 417
vivdasmpamira+G+myg+dg+ kd kavip+s++a++yq++i++ck +Gafdp+tmGtvpnvGlmaq
lcl|NCBI__GCF_002151265.1:WP_086510825.1 348 VIVDASMPAMIRAGGQMYGADGRMKDVKAVIPESTFARIYQEMINFCKWHGAFDPATMGTVPNVGLMAQ 416
********************************************************************* PP
TIGR00178 418 kaeeyGshdktfeieadGvvrvvd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtp 485
kaeeyGshdktfe++adGv++++d ++Gevll ++ve+gdiwrmcqvkd pi+dwvklav r+r sg+p
lcl|NCBI__GCF_002151265.1:WP_086510825.1 417 KAEEYGSHDKTFEVPADGVANITDlETGEVLLSQNVEKGDIWRMCQVKDEPIRDWVKLAVERCRDSGMP 485
************************9******************************************** PP
TIGR00178 486 avfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltd 554
avfwldp+r+h++elikkv++ylkdhdt+Gldiqi+s+v+a+r++ler+ rG dtisvtGn+lrdyltd
lcl|NCBI__GCF_002151265.1:WP_086510825.1 486 AVFWLDPYRPHENELIKKVKTYLKDHDTSGLDIQIMSQVRAMRYTLERVIRGLDTISVTGNILRDYLTD 554
********************************************************************* PP
TIGR00178 555 lfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavkt 623
lfpi+elGtsakmls+vplmaGGG+fetGaGGsapkhvqql eenhlrwdslGeflal+asleh+a +
lcl|NCBI__GCF_002151265.1:WP_086510825.1 555 LFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLLEENHLRWDSLGEFLALTASLEHLAKRF 623
********************************************************************* PP
TIGR00178 624 gnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaea 692
gne+a +lad+ld+a+g++l+++kspsrkvGeldnrgs+fyla ywa++laaq ed+el++ fa +ae+
lcl|NCBI__GCF_002151265.1:WP_086510825.1 624 GNERAALLADALDKAIGQFLENDKSPSRKVGELDNRGSHFYLALYWARALAAQDEDAELKSLFARLAET 692
********************************************************************* PP
TIGR00178 693 ltkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailealk 743
l+ ne++i el++vqG++vd+gGyy++d l+++v+rps+t+n++l+ ++
lcl|NCBI__GCF_002151265.1:WP_086510825.1 693 LEANEATILDELNSVQGQPVDIGGYYHADPALAQAVMRPSKTLNEALALVA 743
**********************************************98765 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 9.64
//
[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