Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_016194830.1 ADIARSV_RS07420 aconitate hydratase
Query= BRENDA::Q8RP87
(747 letters)
>NCBI__GCF_000403135.1:WP_016194830.1
Length = 755
Score = 1021 bits (2640), Expect = 0.0
Identities = 494/747 (66%), Positives = 591/747 (79%), Gaps = 2/747 (0%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
M +D+ M++ Y++ + ++E + + +PLTL EKILY+HL+N + Y RG YV+F
Sbjct: 1 MAFDIEMIQKVYSNLESRIEAAKKVVGKPLTLTEKILYSHLWNGNAEEAYCRGTSYVDFA 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDRVAMQDATAQMALLQFM AG+ VAVPSTVHCDHLIQA GA D+E A TN+EVYD
Sbjct: 61 PDRVAMQDATAQMALLQFMQAGRPQVAVPSTVHCDHLIQAKIGATEDLEIANNTNKEVYD 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FL V ++YG+GFWKPGAGIIHQVVLENYAFPGG+M+GTDSHTPNAGGLGM+AIGVGGAD
Sbjct: 121 FLSSVCNKYGLGFWKPGAGIIHQVVLENYAFPGGLMIGTDSHTPNAGGLGMIAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
A DVM G WELK PKLIGV+LTG+L+GWT+ KDVILK+AG+LTVKGGT I+EYFG G
Sbjct: 181 ACDVMAGFAWELKFPKLIGVKLTGKLSGWTSAKDVILKVAGVLTVKGGTGCIVEYFGEGA 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
SLSATGKATICNMGAE+GATTS+F YDE+ +YL+ TGR E+A +A+ V+ L DDEV
Sbjct: 241 RSLSATGKATICNMGAEIGATTSVFGYDEKAEIYLRGTGRAEIADLANQVSVHLTGDDEV 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
A P+ ++D+VIEI+L LEP+INGPFTPD A PIS+FA V + +P K+EVGLIGSCT
Sbjct: 301 YANPELYFDQVIEIDLDTLEPHINGPFTPDLAWPISQFAAAVKEHNWPAKLEVGLIGSCT 360
Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
NSSY+DI+RA S+A+Q +KNL A V PGSE +R T ERDG +D FEK+G ++AN
Sbjct: 361 NSSYEDITRAASLAQQAVDKNLIAKAEYTVTPGSELVRYTVERDGYLDTFEKIGGVVLAN 420
Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
ACGPCIGQW RHTDDPTR+NSI+TSFNRNFAKR DGNPNT AFVASPEIV AL IAGDL
Sbjct: 421 ACGPCIGQWARHTDDPTRRNSIITSFNRNFAKRNDGNPNTHAFVASPEIVTALAIAGDLT 480
Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPG--GEKNEIRVAPDSQRLQ 538
FNPL D L+N +GE VKL EPQG E+P GF + GYQ P G E+ V S RLQ
Sbjct: 481 FNPLTDFLINENGESVKLEEPQGIEMPIKGFAVEDAGYQEPAEDGTAVEVLVDEKSSRLQ 540
Query: 539 LLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFN 598
LL PFPAW+G D + LLIKA+GKCTTDHISMAGPWL+FRGH++NIS+NML+GA+N F
Sbjct: 541 LLAPFPAWEGVDIKGLKLLIKAKGKCTTDHISMAGPWLKFRGHIDNISNNMLIGAMNYFT 600
Query: 599 GETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVI 658
+T+ V N+LT Y V T + YKA GI +IVV +ENYGEGSSREHAAMEPR L V+VI
Sbjct: 601 DQTDSVKNQLTGIYGPVPATQRAYKAAGIGTIVVGDENYGEGSSREHAAMEPRHLGVRVI 660
Query: 659 LAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHED 718
L KSFARIHETNLKKQGML VTF D DY++++E+D+I + GL F+PG+ L V+LHHED
Sbjct: 661 LVKSFARIHETNLKKQGMLGVTFDDPTDYNKVQENDIIDIEGLTSFAPGKQLHVVLHHED 720
Query: 719 GTEERFAVQHTYNEQQIGWFRAGSALN 745
G E FAV HTYN+QQI WF+AG+ALN
Sbjct: 721 GKSESFAVNHTYNQQQIEWFKAGAALN 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: 1495
Number of extensions: 50
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: 747
Length of database: 755
Length adjustment: 40
Effective length of query: 707
Effective length of database: 715
Effective search space: 505505
Effective search space used: 505505
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_016194830.1 ADIARSV_RS07420 (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.207015.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 1119.4 0.2 0 1119.2 0.2 1.0 1 NCBI__GCF_000403135.1:WP_016194830.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000403135.1:WP_016194830.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1119.2 0.2 0 0 1 745 [] 12 749 .. 12 749 .. 0.97
Alignments for each domain:
== domain 1 score: 1119.2 bits; conditional E-value: 0
TIGR01340 1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqf 73
y +l+++++ ++v++ +pltl+ek+lyshl + + ++ + rG+sy+ + pdrvamqda+aqmallqf
NCBI__GCF_000403135.1:WP_016194830.1 12 YSNLESRIEAAKKVVG-KPLTLTEKILYSHLWNGNA----EE-AYCRGTSYVDFAPDRVAMQDATAQMALLQF 78
789999*********9.***************9987....33.447*************************** PP
TIGR01340 74 lsaglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyav 146
+ ag ++vavp++vhcdhli+ak+G+++dl+ a+++nkev+dfl s+++kyg++fwkpG+Giihq+vlenya+
NCBI__GCF_000403135.1:WP_016194830.1 79 MQAGRPQVAVPSTVHCDHLIQAKIGATEDLEIANNTNKEVYDFLSSVCNKYGLGFWKPGAGIIHQVVLENYAF 151
************************************************************************* PP
TIGR01340 147 pGllmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklagllt 219
pG+lm+GtdshtpnaGGl++iaiGvGGada dv+ag welk pk++GvkltGklsgwts+kdvilk+ag+lt
NCBI__GCF_000403135.1:WP_016194830.1 152 PGGLMIGTDSHTPNAGGLGMIAIGVGGADACDVMAGFAWELKFPKLIGVKLTGKLSGWTSAKDVILKVAGVLT 224
************************************************************************* PP
TIGR01340 220 vkGGtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeak...vakdka 289
vkGGtG iveyfGeG sls tG aticnmGaeiGatts+f ++e+ + yl+ t+raeia+ a+ v
NCBI__GCF_000403135.1:WP_016194830.1 225 VKGGTGCIVEYFGEGARSLSATGKATICNMGAEIGATTSVFGYDEKAEIYLRGTGRAEIADLANqvsVHLTGD 297
*************************************************************999443333444 PP
TIGR01340 290 ellkadkdaeydelieidlsklephvnGpftpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsrv 362
+ + a+ + +d++ieidl++leph+nGpftpdl+ pis+f+ +vk+++wp kl+vGliGsctnssyed++r+
NCBI__GCF_000403135.1:WP_016194830.1 298 DEVYANPELYFDQVIEIDLDTLEPHINGPFTPDLAWPISQFAAAVKEHNWPAKLEVGLIGSCTNSSYEDITRA 370
4555777889*************************************************************** PP
TIGR01340 363 asivkdaekaGlkskidftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgeknti 435
as++++a ++ l +k+++tvtpGse +r t+erdg l++fek GgvvlanacGpciGqw r+ + +n+i
NCBI__GCF_000403135.1:WP_016194830.1 371 ASLAQQAVDKNLIAKAEYTVTPGSELVRYTVERDGYLDTFEKIGGVVLANACGPCIGQWARHTD-DPTRRNSI 442
*************************************************************984.56789*** PP
TIGR01340 436 ltsynrnfrgrndanratmaflaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaGr 508
+ts+nrnf rnd+n++t+af+aspe+vtal++aG+l+fnpltd l +++G kl+ p+G e+p kgf
NCBI__GCF_000403135.1:WP_016194830.1 443 ITSFNRNFAKRNDGNPNTHAFVASPEIVTALAIAGDLTFNPLTDFLINENGESVKLEEPQGIEMPIKGFAVED 515
************************************************************************* PP
TIGR01340 509 dtfqaesdspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldni 581
+q ++++ ++vev vd ks rlqll+pf +w+g d+kgl++lik kGkcttdhis+aGpwlk++Gh+dni
NCBI__GCF_000403135.1:WP_016194830.1 516 AGYQEPAED-GTAVEVLVDEKSSRLQLLAPFPAWEGVDIKGLKLLIKAKGKCTTDHISMAGPWLKFRGHIDNI 587
****99999.99************************************************************* PP
TIGR01340 582 sentligavnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgrii 653
s+n+liga+n+ t++ + vk++ +G +g vp++ + yka g+ +vv++enyGeGs+rehaa+epr+lG r+i
NCBI__GCF_000403135.1:WP_016194830.1 588 SNNMLIGAMNYFTDQTDSVKNQlTGIYGPVPATQRAYKAAGIGTIVVGDENYGEGSSREHAAMEPRHLGVRVI 660
**********************9************************************************** PP
TIGR01340 654 ivksfarihetnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkh 726
+vksfarihetnlkkqG+l +tf +++dy+k+q +d +++ +l+++++ gk++++ +++++gk+++ ++h
NCBI__GCF_000403135.1:WP_016194830.1 661 LVKSFARIHETNLKKQGMLGVTFDDPTDYNKVQENDIIDIEGLTSFAP---GKQLHVVLHHEDGKSESFAVNH 730
**********************************************99...9********************* PP
TIGR01340 727 tlskdqieffkaGsalnll 745
t +++qie+fkaG+aln +
NCBI__GCF_000403135.1:WP_016194830.1 731 TYNQQQIEWFKAGAALNII 749
*****************75 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 nodes)
Target sequences: 1 (755 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: 00:00:00.02
# Mc/sec: 21.52
//
[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