Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate GFF3859 HP15_3800 isocitrate dehydrogenase, NADP-dependent
Query= BRENDA::O53611
(745 letters)
>FitnessBrowser__Marino:GFF3859
Length = 747
Score = 1024 bits (2647), Expect = 0.0
Identities = 501/741 (67%), Positives = 599/741 (80%), Gaps = 1/741 (0%)
Query: 1 MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
M++ + I+YTLTDEAP LAT + LPI+ +A+PAGI+ E SDIS+AARILA FPDYL E
Sbjct: 1 MTSSKAKIVYTLTDEAPALATRSLLPILETYAKPAGIEFETSDISLAARILANFPDYLEE 60
Query: 61 EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
+QRVPD LAELG T+ PD NIIKLPNISAS+PQL AAIKEL ++GY VP+Y +P+ D+
Sbjct: 61 DQRVPDALAELGEYTKDPDANIIKLPNISASIPQLRAAIKELNEQGYNVPEYKENPENDE 120
Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
EK I+ RYA+ LGSAVNPVLR+GNSDRRAP AVK +ARK+PHSMGEWS ASRTHVAHMR
Sbjct: 121 EKEIQSRYAKVLGSAVNPVLREGNSDRRAPTAVKAFARKYPHSMGEWSPASRTHVAHMRG 180
Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
GDFY+ E+S+TLD+A + K GK VLK ++PL +G+V+D MFMSKKAL F+E+
Sbjct: 181 GDFYSSEQSVTLDKATKANIVFENKQGKQTVLKSDLPLQEGEVLDGMFMSKKALVKFFED 240
Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
+ D TGVMFSLHVKATMMK+SHPIVFGHAV++FYKD F K+ ELFD++GVN NNGLS
Sbjct: 241 AIADCENTGVMFSLHVKATMMKISHPIVFGHAVKVFYKDLFDKYGELFDEIGVNPNNGLS 300
Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
+ KI+ LP S++++I EDLH C+EHRPE+AMVDS +GI+N H PSDVIVDASMPAMIR
Sbjct: 301 SVVEKIKQLPESKQEQIQEDLHACYEHRPEIAMVDSVKGITNLHVPSDVIVDASMPAMIR 360
Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
GKM+ D KLKDTKAV PEST++ IYQE+INFCKT+G FDPTTMGTVPNVGLMAQ+AE
Sbjct: 361 NSGKMWARDNKLKDTKAVMPESTYATIYQEVINFCKTHGAFDPTTMGTVPNVGLMAQKAE 420
Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
EYGSHDKTFEI EDGV +V G VL NVE GDIWR C KD PIRDWVKLAV RA
Sbjct: 421 EYGSHDKTFEIKEDGVVRVV-AEDGTVLTEHNVEKGDIWRACQTKDLPIRDWVKLAVNRA 479
Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
R +GMP +FWLD R H+ +LI+KV TYLKDHDTEGLDI+IMS VR++R+T ERL+RGLD
Sbjct: 480 RATGMPAVFWLDDERAHDAQLIQKVNTYLKDHDTEGLDIRIMSPVRAIRWTMERLIRGLD 539
Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
TI+ TGN+LRDYLTDLFPILELGTSAKMLS+VPL+ GGG+YETGAGGSAPKHV+QL++EN
Sbjct: 540 TISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLLNGGGLYETGAGGSAPKHVQQLIQEN 599
Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
HLRWDSLGEFLA +++G K NERA+LLG+TLD A +LL+N++SPSR TGELDNR
Sbjct: 600 HLRWDSLGEFLATAVSLDELGEKQNNERARLLGQTLDKATERLLENNQSPSRVTGELDNR 659
Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
GS F+LA YWA+ELA Q D++L E F L+ L +N+D I+ E+T VQG P DIGGYY
Sbjct: 660 GSHFHLARYWAEELANQDSDKELKEFFTKLSAQLEENKDKILEEMTVVQGNPADIGGYYH 719
Query: 721 PDSDMTTAVMRPSKTFNAALE 741
P + VM+PS T N LE
Sbjct: 720 PPMEKVCEVMQPSATLNRILE 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: 1478
Number of extensions: 52
Number of successful extensions: 2
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: 747
Length adjustment: 40
Effective length of query: 705
Effective length of database: 707
Effective search space: 498435
Effective search space used: 498435
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 GFF3859 HP15_3800 (isocitrate dehydrogenase, NADP-dependent)
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.14741.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 1306.8 0.1 0 1306.6 0.1 1.0 1 lcl|FitnessBrowser__Marino:GFF3859 HP15_3800 isocitrate dehydrogena
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3859 HP15_3800 isocitrate dehydrogenase, NADP-dependent
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1306.6 0.1 0 0 1 741 [. 1 741 [. 1 744 [. 1.00
Alignments for each domain:
== domain 1 score: 1306.6 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGela 75
m+++kaki+ytltdeap+lat sllpi++++a++aGie et+disla+rila+fp+yl e+q+v+dalaelGe +
lcl|FitnessBrowser__Marino:GFF3859 1 MTSSKAKIVYTLTDEAPALATRSLLPILETYAKPAGIEFETSDISLAARILANFPDYLEEDQRVPDALAELGEYT 75
67889********************************************************************** PP
TIGR00178 76 ktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrrap 150
k p+aniiklpnisas+pql+aaikel+++Gy++p+y e+p++deek+i+ ryak++GsavnpvlreGnsdrrap
lcl|FitnessBrowser__Marino:GFF3859 76 KDPDANIIKLPNISASIPQLRAAIKELNEQGYNVPEYKENPENDEEKEIQSRYAKVLGSAVNPVLREGNSDRRAP 150
*************************************************************************** PP
TIGR00178 151 lavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevid 225
+avk +ark+ph+mGews +s++hvahm+ gdfy+se+sv+ld+a++ +i + k+Gk+tvlk++l+l++gev+d
lcl|FitnessBrowser__Marino:GFF3859 151 TAVKAFARKYPHSMGEWSPASRTHVAHMRGGDFYSSEQSVTLDKATKANIVFENKQGKQTVLKSDLPLQEGEVLD 225
*************************************************************************** PP
TIGR00178 226 ssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGla 300
++++skkalv+f+e+ i+d ++gv++slh+katmmk+s+pivfGh+v+vfykd f k++el++++G++ +nGl+
lcl|FitnessBrowser__Marino:GFF3859 226 GMFMSKKALVKFFEDAIADCENTGVMFSLHVKATMMKISHPIVFGHAVKVFYKDLFDKYGELFDEIGVNPNNGLS 300
*************************************************************************** PP
TIGR00178 301 dlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdt 375
+ ki++lp++k+e+i++dl+++ye+rpe+amvds kGitnlhvpsdvivdasmpamir+sGkm+++d+klkdt
lcl|FitnessBrowser__Marino:GFF3859 301 SVVEKIKQLPESKQEQIQEDLHACYEHRPEIAMVDSVKGITNLHVPSDVIVDASMPAMIRNSGKMWARDNKLKDT 375
*************************************************************************** PP
TIGR00178 376 kavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevllee 450
kav+p+s+ya +yq+vi++ck++GafdpttmGtvpnvGlmaqkaeeyGshdktfei++dGvvrvv ++G vl e+
lcl|FitnessBrowser__Marino:GFF3859 376 KAVMPESTYATIYQEVINFCKTHGAFDPTTMGTVPNVGLMAQKAEEYGSHDKTFEIKEDGVVRVVAEDGTVLTEH 450
*************************************************************************** PP
TIGR00178 451 eveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvk 525
+ve+gdiwr+cq kd pi+dwvklav+rar++g+pavfwld+erahd++li+kv++ylkdhdteGldi+i+spv+
lcl|FitnessBrowser__Marino:GFF3859 451 NVEKGDIWRACQTKDLPIRDWVKLAVNRARATGMPAVFWLDDERAHDAQLIQKVNTYLKDHDTEGLDIRIMSPVR 525
*************************************************************************** PP
TIGR00178 526 atrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenh 600
a+r+++er+ rG dtisvtGnvlrdyltdlfpilelGtsakmls+vpl++GGGl+etGaGGsapkhvqql +enh
lcl|FitnessBrowser__Marino:GFF3859 526 AIRWTMERLIRGLDTISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLLNGGGLYETGAGGSAPKHVQQLIQENH 600
*************************************************************************** PP
TIGR00178 601 lrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaa 675
lrwdslGefla a sl++++ k++ne+a++l++tld+at++ll++++spsr +Geldnrgs+f+la+ywa+ela
lcl|FitnessBrowser__Marino:GFF3859 601 LRWDSLGEFLATAVSLDELGEKQNNERARLLGQTLDKATERLLENNQSPSRVTGELDNRGSHFHLARYWAEELAN 675
*************************************************************************** PP
TIGR00178 676 qtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailea 741
q dkel++ f+ ++ l++n++ki +e++ vqG++ d+gGyy+p +++ +v++psat+n ile
lcl|FitnessBrowser__Marino:GFF3859 676 QDSDKELKEFFTKLSAQLEENKDKILEEMTVVQGNPADIGGYYHPPMEKVCEVMQPSATLNRILEE 741
***************************************************************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (747 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: 00:00:00.06
# Mc/sec: 8.06
//
[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