Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_009130708.1 HMPREF9447_RS15575 aconitate hydratase
Query= BRENDA::Q8RP87
(747 letters)
>NCBI__GCF_000315485.1:WP_009130708.1
Length = 747
Score = 1295 bits (3350), Expect = 0.0
Identities = 631/747 (84%), Positives = 684/747 (91%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
MVYD+ ML+ FYA+YKGKME VRA L+ PLTLAEKILYTHL++ ++KNY RGEDYV+FR
Sbjct: 1 MVYDVTMLRAFYAAYKGKMERVRAVLQHPLTLAEKILYTHLFDGKEVKNYTRGEDYVSFR 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDRVAMQDATAQMALLQFMNAG+E VAVPSTVHCDHLIQAYRGA DI TAT+TN EVYD
Sbjct: 61 PDRVAMQDATAQMALLQFMNAGREQVAVPSTVHCDHLIQAYRGAREDIATATKTNEEVYD 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FLRDVSSRYGIGFW+PGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD
Sbjct: 121 FLRDVSSRYGIGFWQPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
AVDVMTGMEWELKMP+LIGV L GELNGW APKDVILKLAGILTVKGGTNAIIEYFGPGT
Sbjct: 181 AVDVMTGMEWELKMPRLIGVHLKGELNGWAAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
ASLSATGKATICNMGAEVGATTS+FPYD R+A YLKATGREEVA MADSVA DLRAD ++
Sbjct: 241 ASLSATGKATICNMGAEVGATTSIFPYDNRIATYLKATGREEVAEMADSVAGDLRADTDI 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
+ P+++YDRVIEI+LS LEPYINGPFTPDAATPISEFAEKV+ NGYPRKMEVGLIGSCT
Sbjct: 301 LLAPENYYDRVIEIDLSRLEPYINGPFTPDAATPISEFAEKVLANGYPRKMEVGLIGSCT 360
Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
NSSYQD+SRAVS+ARQV +K+L VAAPLIVNPGSE+IRATAERDGM++ FEK+GATIMAN
Sbjct: 361 NSSYQDLSRAVSLARQVEKKHLKVAAPLIVNPGSERIRATAERDGMIETFEKVGATIMAN 420
Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
ACGPCIGQWKR TD+PTRKNSIVTSFNRNFAKRADGNPNT+AFVASPE+ +ALTIAGDLC
Sbjct: 421 ACGPCIGQWKRETDNPTRKNSIVTSFNRNFAKRADGNPNTYAFVASPELTMALTIAGDLC 480
Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPGGEKNEIRVAPDSQRLQLL 540
FNPL D LVN +GEKVKLSEP G+ELP GF G++GY P EK EI V P SQRLQLL
Sbjct: 481 FNPLTDALVNREGEKVKLSEPVGEELPPEGFAEGSEGYIPPRSEKTEITVNPHSQRLQLL 540
Query: 541 TPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE 600
PFPAW+G D LNMPLLIK QGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE
Sbjct: 541 QPFPAWEGTDLLNMPLLIKTQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE 600
Query: 601 TNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVILA 660
TN VWNR TNTY VSGTAK YK++GISSIVVAEENYGEGSSREHAAMEPRFL+V+VILA
Sbjct: 601 TNSVWNRSTNTYGPVSGTAKMYKSEGISSIVVAEENYGEGSSREHAAMEPRFLNVRVILA 660
Query: 661 KSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHEDGT 720
KSFARIHETNLKKQGMLA+TF DKADYD+I+EHDLISV+GL EF+PGRN +V+LHHEDGT
Sbjct: 661 KSFARIHETNLKKQGMLALTFVDKADYDKIQEHDLISVIGLTEFAPGRNFKVVLHHEDGT 720
Query: 721 EERFAVQHTYNEQQIGWFRAGSALNAK 747
+E F QHTYNE QI WFRAGSALNA+
Sbjct: 721 KESFEAQHTYNELQISWFRAGSALNAR 747
Lambda K H
0.317 0.134 0.395
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: 1699
Number of extensions: 48
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: 747
Length of database: 747
Length adjustment: 40
Effective length of query: 707
Effective length of database: 707
Effective search space: 499849
Effective search space used: 499849
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_009130708.1 HMPREF9447_RS15575 (aconitate hydratase)
to HMM TIGR01340 (aconitate hydratase, mitochondrial (EC 4.2.1.3))
# 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/TIGR01340.hmm
# target sequence database: /tmp/gapView.1533499.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01340 [M=745]
Accession: TIGR01340
Description: aconitase_mito: aconitate hydratase, mitochondrial
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 1095.4 0.0 0 1095.3 0.0 1.0 1 NCBI__GCF_000315485.1:WP_009130708.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000315485.1:WP_009130708.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1095.3 0.0 0 0 1 744 [. 12 746 .. 12 747 .] 0.97
Alignments for each domain:
== domain 1 score: 1095.3 bits; conditional E-value: 0
TIGR01340 1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqf 73
y+ + k+++vr vl+ +pltlaek+ly+hl d +e ++ + rG+ y+ ++pdrvamqda+aqmallqf
NCBI__GCF_000315485.1:WP_009130708.1 12 YAAYKGKMERVRAVLQ-HPLTLAEKILYTHLFDGKE---VKNYT--RGEDYVSFRPDRVAMQDATAQMALLQF 78
56667899*******9.*******************...45555..*************************** PP
TIGR01340 74 lsaglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyav 146
+ ag ++vavp++vhcdhli+a G+ +d+a+a+++n+ev+dfl ++ +ygi+fw+pG+Giihq+vlenya+
NCBI__GCF_000315485.1:WP_009130708.1 79 MNAGREQVAVPSTVHCDHLIQAYRGAREDIATATKTNEEVYDFLRDVSSRYGIGFWQPGAGIIHQVVLENYAF 151
************************************************************************* PP
TIGR01340 147 pGllmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklagllt 219
pG++m+GtdshtpnaGGl+++aiGvGGadavdv++g+ welk p+++Gv+l G+l+gw++pkdvilklag+lt
NCBI__GCF_000315485.1:WP_009130708.1 152 PGGMMVGTDSHTPNAGGLGMVAIGVGGADAVDVMTGMEWELKMPRLIGVHLKGELNGWAAPKDVILKLAGILT 224
************************************************************************* PP
TIGR01340 220 vkGGtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeak....vakdk 288
vkGGt ai+eyfG+G sls tG aticnmGae+Gatts+fp++++ + ylkat+r+e+ae a+ + +
NCBI__GCF_000315485.1:WP_009130708.1 225 VKGGTNAIIEYFGPGTASLSATGKATICNMGAEVGATTSIFPYDNRIATYLKATGREEVAEMADsvagDLRAD 297
***************************************************************9433212334 PP
TIGR01340 289 aellkadkdaeydelieidlsklephvnGpftpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsr 361
+++l a + yd++ieidls+lep++nGpftpd +tpis+f+ekv ++++p+k++vGliGsctnssy+d+sr
NCBI__GCF_000315485.1:WP_009130708.1 298 TDILLAP-ENYYDRVIEIDLSRLEPYINGPFTPDAATPISEFAEKVLANGYPRKMEVGLIGSCTNSSYQDLSR 369
4455444.457************************************************************** PP
TIGR01340 362 vasivkdaekaGlkskidftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgeknt 434
++s++++ ek+ lk ++++ v pGse+irat erdg++e+fek+G++++anacGpciGqw+r+ + + kn+
NCBI__GCF_000315485.1:WP_009130708.1 370 AVSLARQVEKKHLKVAAPLIVNPGSERIRATAERDGMIETFEKVGATIMANACGPCIGQWKRETD-NPTRKNS 441
**************************************************************995.56789** PP
TIGR01340 435 iltsynrnfrgrndanratmaflaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaG 507
i+ts+nrnf r d+n++t+af+aspel +al++aG+l fnpltd+l +++G + kl+ p G+elp +gf +G
NCBI__GCF_000315485.1:WP_009130708.1 442 IVTSFNRNFAKRADGNPNTYAFVASPELTMALTIAGDLCFNPLTDALVNREGEKVKLSEPVGEELPPEGFAEG 514
************************************************************************* PP
TIGR01340 508 rdtfqaesdspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldn 580
+ + ++ ++ + e++v+p+s+rlqll+pf +w+g dl ++++lik +Gkcttdhis+aGpwl+++Ghl+n
NCBI__GCF_000315485.1:WP_009130708.1 515 SEGYIPPRSE---KTEITVNPHSQRLQLLQPFPAWEGTDLLNMPLLIKTQGKCTTDHISMAGPWLRFRGHLEN 584
****988766...889********************************************************* PP
TIGR01340 581 isentligavnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgri 652
is+n+l+gavna +ge n v ++ + ++g v ++ak yk++g+ +vvaeenyGeGs+rehaa+epr+l r+
NCBI__GCF_000315485.1:WP_009130708.1 585 ISDNMLMGAVNAFNGETNSVWNRsTNTYGPVSGTAKMYKSEGISSIVVAEENYGEGSSREHAAMEPRFLNVRV 657
***********************8889999******************************************* PP
TIGR01340 653 iivksfarihetnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklk 725
i++ksfarihetnlkkqG+l ltf ++adydkiq +d +++++l+e+++ g++ ++ +++++g ++ ++
NCBI__GCF_000315485.1:WP_009130708.1 658 ILAKSFARIHETNLKKQGMLALTFVDKADYDKIQEHDLISVIGLTEFAP---GRNFKVVLHHEDGTKESFEAQ 727
************************************************9...8999999************** PP
TIGR01340 726 htlskdqieffkaGsalnl 744
ht ++ qi +f+aGsaln
NCBI__GCF_000315485.1:WP_009130708.1 728 HTYNELQISWFRAGSALNA 746
*****************95 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 37.71
//
[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