Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_091525661.1 BM253_RS14290 aconitate hydratase
Query= BRENDA::Q8RP87
(747 letters)
>NCBI__GCF_900115115.1:WP_091525661.1
Length = 753
Score = 973 bits (2516), Expect = 0.0
Identities = 478/747 (63%), Positives = 573/747 (76%), Gaps = 2/747 (0%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
M +D++M+K Y + +++ R + RPLTL+EKILY HL+ + +ER +DYV+F
Sbjct: 1 MAFDIDMIKKVYDTMPARVDKARELVGRPLTLSEKILYAHLWEGMPSQKFERSKDYVDFA 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDRVAMQDATAQMALLQFM AGK AVPSTVHCDHLI A GAE+D+ A ++EV+D
Sbjct: 61 PDRVAMQDATAQMALLQFMQAGKSTTAVPSTVHCDHLILAKVGAEKDLAVANTQSKEVFD 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FL VS++YGIGFWKPG+GIIHQ++LENYAFPGGMM+GTDSHT NAGGLGM+AIGVGGAD
Sbjct: 121 FLSSVSNKYGIGFWKPGSGIIHQILLENYAFPGGMMIGTDSHTVNAGGLGMLAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
AVDVM GM WELK PKLIGV+LTG+LNGWTAPKDVILK+A ILTVKGGT AI+EYFG G
Sbjct: 181 AVDVMAGMAWELKFPKLIGVKLTGKLNGWTAPKDVILKVADILTVKGGTGAIVEYFGEGA 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
S+SATGK TICNMGAE+GATTS F YD+ M YL ATGR +V AD VA L AD EV
Sbjct: 241 KSMSATGKGTICNMGAEIGATTSTFGYDDSMRRYLNATGRADVVDAADKVADYLTADPEV 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
A P+ ++D++IEINLSELEP+INGPFTPD TP+S+ E+ N +P K+E GLIGSCT
Sbjct: 301 YANPEQYFDQLIEINLSELEPHINGPFTPDRGTPVSKMKEEAAKNDWPIKVEWGLIGSCT 360
Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
NSSY+D+SRAVS+ Q E + A +NPGSEQIR T ERDG++ FEKMG + N
Sbjct: 361 NSSYEDMSRAVSIVNQAVELGITPKAEFGINPGSEQIRYTIERDGIIAAFEKMGTKVFTN 420
Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
ACGPCIGQW R D KN+IV SFNRNF+KRADGNPNT AFV SPE+V AL I+G L
Sbjct: 421 ACGPCIGQWDREGADKGEKNTIVHSFNRNFSKRADGNPNTHAFVTSPEMVAALAISGRLD 480
Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAP--GGEKNEIRVAPDSQRLQ 538
FNP+ D+L+N +GE+V P GDELP+ GF + G+QAP G ++ V+PDS RLQ
Sbjct: 481 FNPITDKLLNDNGEEVMFKPPFGDELPTKGFDVEDPGFQAPAANGSSVQVIVSPDSSRLQ 540
Query: 539 LLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFN 598
LL PF WDG + LLIKA GKCTTDHISMAGPWLRFRGHL+NIS+NML+GA NAFN
Sbjct: 541 LLEPFQPWDGQNITGAKLLIKAFGKCTTDHISMAGPWLRFRGHLDNISNNMLIGAENAFN 600
Query: 599 GETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVI 658
+TN V N+LT Y+ V +QYKA GI SIVV + NYGEGSSREHAAMEPR L VK +
Sbjct: 601 NKTNSVKNQLTGEYQEVPAVQRQYKAAGIPSIVVGDHNYGEGSSREHAAMEPRHLGVKAV 660
Query: 659 LAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHED 718
L KSFARIHETNLKKQGML +TFA+++DYD+I+E D I+ + L EF+PGR L + H+D
Sbjct: 661 LVKSFARIHETNLKKQGMLGLTFANESDYDKIQEDDTINFLDLTEFAPGRQLTLEFVHKD 720
Query: 719 GTEERFAVQHTYNEQQIGWFRAGSALN 745
G+++ HTYN+ QI WF+AGSALN
Sbjct: 721 GSKDIIMANHTYNDSQIEWFKAGSALN 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: 1541
Number of extensions: 45
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: 753
Length adjustment: 40
Effective length of query: 707
Effective length of database: 713
Effective search space: 504091
Effective search space used: 504091
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_091525661.1 BM253_RS14290 (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.3011352.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 1149.1 0.1 0 1148.9 0.1 1.0 1 NCBI__GCF_900115115.1:WP_091525661.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900115115.1:WP_091525661.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1148.9 0.1 0 0 1 745 [] 12 749 .. 12 749 .. 0.98
Alignments for each domain:
== domain 1 score: 1148.9 bits; conditional E-value: 0
TIGR01340 1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqf 73
y+++ ++dk r+ ++ rpltl+ek+ly+hl + sq+ e r k y+ + pdrvamqda+aqmallqf
NCBI__GCF_900115115.1:WP_091525661.1 12 YDTMPARVDKARELVG-RPLTLSEKILYAHLWEGMP---SQKFE--RSKDYVDFAPDRVAMQDATAQMALLQF 78
889999*******999.**************97666...99999..*************************** PP
TIGR01340 74 lsaglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyav 146
+ ag + +avp++vhcdhli ak+G+ekdla a+ kevfdfl s+++kygi+fwkpGsGiihqi+lenya+
NCBI__GCF_900115115.1:WP_091525661.1 79 MQAGKSTTAVPSTVHCDHLILAKVGAEKDLAVANTQSKEVFDFLSSVSNKYGIGFWKPGSGIIHQILLENYAF 151
************************************************************************* PP
TIGR01340 147 pGllmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklagllt 219
pG++m+Gtdsht naGGl+++aiGvGGadavdv+ag+ welk pk++GvkltGkl+gwt+pkdvilk+a++lt
NCBI__GCF_900115115.1:WP_091525661.1 152 PGGMMIGTDSHTVNAGGLGMLAIGVGGADAVDVMAGMAWELKFPKLIGVKLTGKLNGWTAPKDVILKVADILT 224
************************************************************************* PP
TIGR01340 220 vkGGtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeak.vakdkae. 290
vkGGtGaiveyfGeG +s+s tG +ticnmGaeiGatts+f +++++++yl+at+ra++ ++a+ va + +
NCBI__GCF_900115115.1:WP_091525661.1 225 VKGGTGAIVEYFGEGAKSMSATGKGTICNMGAEIGATTSTFGYDDSMRRYLNATGRADVVDAADkVADYLTAd 297
**********************************************************999998344443321 PP
TIGR01340 291 .llkadkdaeydelieidlsklephvnGpftpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsrv 362
+ a+ + +d+liei+ls+leph+nGpftpd +tp+sk+ke++ k++wp k++ GliGsctnssyedmsr+
NCBI__GCF_900115115.1:WP_091525661.1 298 pEVYANPEQYFDQLIEINLSELEPHINGPFTPDRGTPVSKMKEEAAKNDWPIKVEWGLIGSCTNSSYEDMSRA 370
14557778889************************************************************** PP
TIGR01340 363 asivkdaekaGlkskidftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgeknti 435
+siv++a + G+ +k++f + pGseqir t+erdgi+ fek+G++v++nacGpciGqwdr+ kgeknti
NCBI__GCF_900115115.1:WP_091525661.1 371 VSIVNQAVELGITPKAEFGINPGSEQIRYTIERDGIIAAFEKMGTKVFTNACGPCIGQWDREG-ADKGEKNTI 442
**************************************************************9.99******* PP
TIGR01340 436 ltsynrnfrgrndanratmaflaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaGr 508
+ s+nrnf r d+n++t+af++spe+v+al+++G+l+fnp+td+l + +G e +k+p+Gdelp+kgf+
NCBI__GCF_900115115.1:WP_091525661.1 443 VHSFNRNFSKRADGNPNTHAFVTSPEMVAALAISGRLDFNPITDKLLNDNGEEVMFKPPFGDELPTKGFDVED 515
************************************************************************* PP
TIGR01340 509 dtfqaesdspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldni 581
fqa++ + ++v+v v+p+s rlqllepf++w+g++++g ++lik Gkcttdhis+aGpwl+++Ghldni
NCBI__GCF_900115115.1:WP_091525661.1 516 PGFQAPAAN-GSSVQVIVSPDSSRLQLLEPFQPWDGQNITGAKLLIKAFGKCTTDHISMAGPWLRFRGHLDNI 587
******999.9************************************************************** PP
TIGR01340 582 sentligavnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgrii 653
s+n+liga na +++ n vk++ +G++++vp++ ++yka g++ +vv+++nyGeGs+rehaa+epr+lG +++
NCBI__GCF_900115115.1:WP_091525661.1 588 SNNMLIGAENAFNNKTNSVKNQlTGEYQEVPAVQRQYKAAGIPSIVVGDHNYGEGSSREHAAMEPRHLGVKAV 660
**********************9************************************************** PP
TIGR01340 654 ivksfarihetnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkh 726
+vksfarihetnlkkqG+l ltfane+dydkiq +d+++ l+l+e+++ g++++l+ +k+g+ i ++h
NCBI__GCF_900115115.1:WP_091525661.1 661 LVKSFARIHETNLKKQGMLGLTFANESDYDKIQEDDTINFLDLTEFAP---GRQLTLEFVHKDGSKDIIMANH 730
**********************************************99...99******************** PP
TIGR01340 727 tlskdqieffkaGsalnll 745
t +++qie+fkaGsalnl+
NCBI__GCF_900115115.1:WP_091525661.1 731 TYNDSQIEWFKAGSALNLI 749
*****************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 nodes)
Target sequences: 1 (753 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: 35.29
//
[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